---
OA_type: closed access
_id: '18919'
abstract:
- lang: eng
text: The integration of theory and experiment makes possible tracking the slow
evolution of a photodoped Mott insulator to a distinct non-equilibrium metallic
phase under the influence of electron-lattice coupling.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
citation:
ama: Baykusheva DR. Through the slopes of a light-induced phase transition. Nature
Physics. 2024;20(5):684-685. doi:10.1038/s41567-024-02401-7
apa: Baykusheva, D. R. (2024). Through the slopes of a light-induced phase transition.
Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-024-02401-7
chicago: Baykusheva, Denitsa Rangelova. “Through the Slopes of a Light-Induced Phase
Transition.” Nature Physics. Springer Nature, 2024. https://doi.org/10.1038/s41567-024-02401-7.
ieee: D. R. Baykusheva, “Through the slopes of a light-induced phase transition,”
Nature Physics, vol. 20, no. 5. Springer Nature, pp. 684–685, 2024.
ista: Baykusheva DR. 2024. Through the slopes of a light-induced phase transition.
Nature Physics. 20(5), 684–685.
mla: Baykusheva, Denitsa Rangelova. “Through the Slopes of a Light-Induced Phase
Transition.” Nature Physics, vol. 20, no. 5, Springer Nature, 2024, pp.
684–85, doi:10.1038/s41567-024-02401-7.
short: D.R. Baykusheva, Nature Physics 20 (2024) 684–685.
corr_author: '1'
date_created: 2025-01-27T14:29:20Z
date_published: 2024-05-01T00:00:00Z
date_updated: 2025-09-09T12:08:10Z
day: '01'
department:
- _id: DeBa
doi: 10.1038/s41567-024-02401-7
external_id:
isi:
- '001162208200002'
intvolume: ' 20'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 684-685
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Through the slopes of a light-induced phase transition
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 20
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18920'
abstract:
- lang: eng
text: The globally distributed marine alga Emiliania huxleyi has cooling effect
on the Earth’s climate. The population density of E. huxleyi is restricted by
Nucleocytoviricota viruses, including E. huxleyi virus 201 (EhV-201). Despite
the impact of E. huxleyi viruses on the climate, there is limited information
about their structure and replication. Here, we show that the dsDNA genome inside
the EhV-201 virion is protected by an inner membrane, capsid, and outer membrane.
EhV-201 virions infect E. huxleyi by using fivefold vertices to bind to and fuse
the virus’ inner membrane with the cell plasma membrane. Progeny virions assemble
in the cytoplasm at the surface of endoplasmic reticulum–derived membrane segments.
Genome packaging initiates synchronously with the capsid assembly and completes
through an aperture in the forming capsid. The genome-filled capsids acquire an
outer membrane by budding into intracellular vesicles. EhV-201 infection induces
a loss of surface protective layers from E. huxleyi cells, which enables the continuous
release of virions by exocytosis.
acknowledgement: We acknowledge (i) the Cryo-Electron Microscopy and Tomography Core
Facility and Proteomics Core Facility of the Central European Institute of Technology
(CEITEC), Masaryk University, supported by the Ministry of Education, Youth, and
Sports of the Czech Republic (grant LM2018127); (ii) the Cellular Imaging Core Facility
supported by the Czech-BioImaging large RI project (LM2018129 funded by MEYS CR);
and (iii) Plant Sciences Core Facility for support with obtaining scientific data
presented here. We acknowledge support from the project National Institute of Virology
and Bacteriology (Program EXCELES, ID project no. LX22NPO5103), funded by the European
Union - Next Generation EU. This work received funding from the Czech Science Foundation
grant GX 19-259882X to P.P., from European Regional Development Fund-Project “MSCAfellow2@MUNI”
(no. CZ.02.2.69/0.0/0.0/18_070/0009846) to C.R.B., and from Brno PhD talent scholarship
funded by Brno city municipality to M.H.
article_number: 'eadk1954 '
article_processing_charge: Yes
article_type: original
author:
- first_name: Miroslav
full_name: Homola, Miroslav
last_name: Homola
- first_name: Renate Carina
full_name: Büttner, Renate Carina
id: 3b7984c9-17ff-11ed-b6fe-f943c4a5b626
last_name: Büttner
- first_name: Tibor
full_name: Füzik, Tibor
last_name: Füzik
- first_name: Pavel
full_name: Křepelka, Pavel
last_name: Křepelka
- first_name: Radka
full_name: Holbová, Radka
last_name: Holbová
- first_name: Jiří
full_name: Nováček, Jiří
last_name: Nováček
- first_name: Marten L.
full_name: Chaillet, Marten L.
last_name: Chaillet
- first_name: Jakub
full_name: Žák, Jakub
last_name: Žák
- first_name: Danyil
full_name: Grybchuk, Danyil
last_name: Grybchuk
- first_name: Friedrich
full_name: Förster, Friedrich
last_name: Förster
- first_name: William H.
full_name: Wilson, William H.
last_name: Wilson
- first_name: Declan C.
full_name: Schroeder, Declan C.
last_name: Schroeder
- first_name: Pavel
full_name: Plevka, Pavel
last_name: Plevka
citation:
ama: Homola M, Büttner RC, Füzik T, et al. Structure and replication cycle of a
virus infecting climate-modulating alga Emiliania huxleyi. Science Advances.
2024;10(15). doi:10.1126/sciadv.adk1954
apa: Homola, M., Büttner, R. C., Füzik, T., Křepelka, P., Holbová, R., Nováček,
J., … Plevka, P. (2024). Structure and replication cycle of a virus infecting
climate-modulating alga Emiliania huxleyi. Science Advances. American Association
for the Advancement of Science. https://doi.org/10.1126/sciadv.adk1954
chicago: Homola, Miroslav, Renate Carina Büttner, Tibor Füzik, Pavel Křepelka, Radka
Holbová, Jiří Nováček, Marten L. Chaillet, et al. “Structure and Replication Cycle
of a Virus Infecting Climate-Modulating Alga Emiliania Huxleyi.” Science Advances.
American Association for the Advancement of Science, 2024. https://doi.org/10.1126/sciadv.adk1954.
ieee: M. Homola et al., “Structure and replication cycle of a virus infecting
climate-modulating alga Emiliania huxleyi,” Science Advances, vol. 10,
no. 15. American Association for the Advancement of Science, 2024.
ista: Homola M, Büttner RC, Füzik T, Křepelka P, Holbová R, Nováček J, Chaillet
ML, Žák J, Grybchuk D, Förster F, Wilson WH, Schroeder DC, Plevka P. 2024. Structure
and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi.
Science Advances. 10(15), eadk1954.
mla: Homola, Miroslav, et al. “Structure and Replication Cycle of a Virus Infecting
Climate-Modulating Alga Emiliania Huxleyi.” Science Advances, vol. 10,
no. 15, eadk1954, American Association for the Advancement of Science, 2024, doi:10.1126/sciadv.adk1954.
short: M. Homola, R.C. Büttner, T. Füzik, P. Křepelka, R. Holbová, J. Nováček, M.L.
Chaillet, J. Žák, D. Grybchuk, F. Förster, W.H. Wilson, D.C. Schroeder, P. Plevka,
Science Advances 10 (2024).
date_created: 2025-01-27T14:32:34Z
date_published: 2024-04-01T00:00:00Z
date_updated: 2025-05-14T09:29:04Z
day: '01'
ddc:
- '570'
department:
- _id: EM-Fac
doi: 10.1126/sciadv.adk1954
external_id:
pmid:
- '38598627'
file:
- access_level: open_access
checksum: 291dd7ceccbe6bfd8e0a9157584f88e9
content_type: application/pdf
creator: dernst
date_created: 2025-01-27T14:40:08Z
date_updated: 2025-01-27T14:40:08Z
file_id: '18921'
file_name: 2024_ScienceAdv_Homola.pdf
file_size: 40623405
relation: main_file
success: 1
file_date_updated: 2025-01-27T14:40:08Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '15'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Science Advances
publication_identifier:
eissn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
link:
- relation: software
url: ' https://github.com/fuzikt/tomostarpy.'
scopus_import: '1'
status: public
title: Structure and replication cycle of a virus infecting climate-modulating alga
Emiliania huxleyi
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: 10
year: '2024'
...
---
OA_type: closed access
_id: '18922'
abstract:
- lang: eng
text: 'Let G be a directed graph with m edges and n vertices. We present a deterministic
linear-time algorithm for computing the 3-edge-connected components of G. This
is a significant improvement over the previous best bound by Georgiadis et al.
[SODA 2023], which is Õ(m√{m}) and randomized. Our result is based on a novel
characterization of 2-edge cuts in directed graphs and on a new technique that
exploits the concept of divergent spanning trees and 2-connectivity-light graphs,
and requires a careful modification of the minset-poset technique of Gabow [TALG
2016]. As a side result, our new technique yields also an oracle for providing
in constant time a minimum edge-cut for any two vertices that are not 3-edge-connected.
The oracle uses space O(n) and can be built in O(mlog n) time: given two query
vertices, it determines in constant time whether they are 3-edge-connected, or
provides a k-edge cut, with k≤ 2, that separates them.'
acknowledgement: "Giuseppe F. Italiano was partially supported by the Italian Ministry
of\r\nUniversity and Reseach under PRIN Project n. 2022TS4Y3N - EXPAND: scalable
algorithms for EXPloratory Analyses of heterogeneous and dynamic Networked Data.\r\n"
article_processing_charge: No
author:
- first_name: Loukas
full_name: Georgiadis, Loukas
last_name: Georgiadis
- first_name: Giuseppe F.
full_name: Italiano, Giuseppe F.
last_name: Italiano
- first_name: Evangelos
full_name: Kosinas, Evangelos
id: 4c7f9625-dbbc-11ee-9d86-bdcc2db5a949
last_name: Kosinas
citation:
ama: 'Georgiadis L, Italiano GF, Kosinas E. Computing the 3-edge-connected components
of directed graphs in linear time. In: 65th Annual Symposium on Foundations
of Computer Science. IEEE; 2024:62-85. doi:10.1109/focs61266.2024.00015'
apa: 'Georgiadis, L., Italiano, G. F., & Kosinas, E. (2024). Computing the 3-edge-connected
components of directed graphs in linear time. In 65th Annual Symposium on Foundations
of Computer Science (pp. 62–85). Chicago, IL, United States: IEEE. https://doi.org/10.1109/focs61266.2024.00015'
chicago: Georgiadis, Loukas, Giuseppe F. Italiano, and Evangelos Kosinas. “Computing
the 3-Edge-Connected Components of Directed Graphs in Linear Time.” In 65th
Annual Symposium on Foundations of Computer Science, 62–85. IEEE, 2024. https://doi.org/10.1109/focs61266.2024.00015.
ieee: L. Georgiadis, G. F. Italiano, and E. Kosinas, “Computing the 3-edge-connected
components of directed graphs in linear time,” in 65th Annual Symposium on
Foundations of Computer Science, Chicago, IL, United States, 2024, pp. 62–85.
ista: 'Georgiadis L, Italiano GF, Kosinas E. 2024. Computing the 3-edge-connected
components of directed graphs in linear time. 65th Annual Symposium on Foundations
of Computer Science. FOCS: Foundations of Computer Science, 62–85.'
mla: Georgiadis, Loukas, et al. “Computing the 3-Edge-Connected Components of Directed
Graphs in Linear Time.” 65th Annual Symposium on Foundations of Computer Science,
IEEE, 2024, pp. 62–85, doi:10.1109/focs61266.2024.00015.
short: L. Georgiadis, G.F. Italiano, E. Kosinas, in:, 65th Annual Symposium on Foundations
of Computer Science, IEEE, 2024, pp. 62–85.
conference:
end_date: 2024-10-30
location: Chicago, IL, United States
name: 'FOCS: Foundations of Computer Science'
start_date: 2024-10-27
corr_author: '1'
date_created: 2025-01-27T14:50:23Z
date_published: 2024-10-01T00:00:00Z
date_updated: 2025-09-09T12:08:47Z
day: '01'
department:
- _id: MoHe
doi: 10.1109/focs61266.2024.00015
external_id:
isi:
- '001419526400005'
isi: 1
language:
- iso: eng
month: '10'
oa_version: None
page: 62-85
publication: 65th Annual Symposium on Foundations of Computer Science
publication_identifier:
isbn:
- '9798331516741'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Computing the 3-edge-connected components of directed graphs in linear time
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18923'
abstract:
- lang: eng
text: 'Combinatorial optimization is a challenging problem applicable in a wide
range of fields from logistics to finance. Recently, quantum computing has been
used to attempt to solve these problems using a range of algorithms, including
parameterized quantum circuits, adiabatic protocols, and quantum annealing. These
solutions typically have several challenges: 1) there is little to no performance
gain over classical methods; 2) not all constraints and objectives may be efficiently
encoded in the quantum ansatz; and 3) the solution domain of the objective function
may not be the same as the bit strings of measurement outcomes. This work presents
“nonnative hybrid algorithms”: a framework to overcome these challenges by integrating
quantum and classical resources with a hybrid approach. By designing nonnative
quantum variational anosatzes that inherit some but not all problem structure,
measurement outcomes from the quantum computer can act as a resource to be used
by classical routines to indirectly compute optimal solutions, partially overcoming
the challenges of contemporary quantum optimization approaches. These methods
are demonstrated using a publicly available neutral-atom quantum computer on two
simple problems of Max k-Cut and maximum independent set. We find improvements
in solution quality when comparing the hybrid algorithm to its “no quantum” version,
a demonstration of a “comparative advantage.”'
acknowledgement: "The authors would like to thank Alexander Keesling, Maddie Cain,
Nate Gemelke, and Phillip Weinberg for helpful discussions and Danylo Lykov who
had early contributions to this work.\r\n10.13039/100000185-Defense Advanced Research
Projects Agency Noisy Intermediate-Scale Quantum Devices (Grant Number: W911NF2010021),
DARPA Small Business Technology Transfer program (Grant Number: 140D0422C0035)."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jonathan
full_name: Wurtz, Jonathan
last_name: Wurtz
- first_name: Stefan
full_name: Sack, Stefan
id: dd622248-f6e0-11ea-865d-ce382a1c81a5
last_name: Sack
orcid: 0000-0001-5400-8508
- first_name: Sheng-Tao
full_name: Wang, Sheng-Tao
last_name: Wang
citation:
ama: Wurtz J, Sack S, Wang S-T. Solving nonnative combinatorial optimization problems
using hybrid quantum–classical algorithms. IEEE Transactions on Quantum Engineering.
2024;5:1-14. doi:10.1109/tqe.2024.3443660
apa: Wurtz, J., Sack, S., & Wang, S.-T. (2024). Solving nonnative combinatorial
optimization problems using hybrid quantum–classical algorithms. IEEE Transactions
on Quantum Engineering. Institute of Electrical and Electronics Engineers
. https://doi.org/10.1109/tqe.2024.3443660
chicago: Wurtz, Jonathan, Stefan Sack, and Sheng-Tao Wang. “Solving Nonnative Combinatorial
Optimization Problems Using Hybrid Quantum–Classical Algorithms.” IEEE Transactions
on Quantum Engineering. Institute of Electrical and Electronics Engineers
, 2024. https://doi.org/10.1109/tqe.2024.3443660.
ieee: J. Wurtz, S. Sack, and S.-T. Wang, “Solving nonnative combinatorial optimization
problems using hybrid quantum–classical algorithms,” IEEE Transactions on Quantum
Engineering, vol. 5. Institute of Electrical and Electronics Engineers , pp.
1–14, 2024.
ista: Wurtz J, Sack S, Wang S-T. 2024. Solving nonnative combinatorial optimization
problems using hybrid quantum–classical algorithms. IEEE Transactions on Quantum
Engineering. 5, 1–14.
mla: Wurtz, Jonathan, et al. “Solving Nonnative Combinatorial Optimization Problems
Using Hybrid Quantum–Classical Algorithms.” IEEE Transactions on Quantum Engineering,
vol. 5, Institute of Electrical and Electronics Engineers , 2024, pp. 1–14, doi:10.1109/tqe.2024.3443660.
short: J. Wurtz, S. Sack, S.-T. Wang, IEEE Transactions on Quantum Engineering 5
(2024) 1–14.
date_created: 2025-01-27T15:00:44Z
date_published: 2024-08-14T00:00:00Z
date_updated: 2025-01-27T15:06:15Z
day: '14'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1109/tqe.2024.3443660
file:
- access_level: open_access
checksum: 19b84e35cba05bde72bfe7e0b54c3e6c
content_type: application/pdf
creator: dernst
date_created: 2025-01-27T15:03:09Z
date_updated: 2025-01-27T15:03:09Z
file_id: '18924'
file_name: 2024_IEEEQuantumComputing_Wurtz.pdf
file_size: 1753095
relation: main_file
success: 1
file_date_updated: 2025-01-27T15:03:09Z
has_accepted_license: '1'
intvolume: ' 5'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 1-14
publication: IEEE Transactions on Quantum Engineering
publication_identifier:
issn:
- 2689-1808
publication_status: published
publisher: 'Institute of Electrical and Electronics Engineers '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Solving nonnative combinatorial optimization problems using hybrid quantum–classical
algorithms
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2024'
...
---
OA_place: other
OA_type: green
_id: '18925'
abstract:
- lang: eng
text: Given the increasingly stringent requirements on the performance and efficiency
of communication networks, over the last years, great efforts have been made to
render networks more flexible and programmable. In particular, modern networks
support a flexible rerouting of flows, e.g., depending on the dynamically changing
traffic or network conditions. However, the underlying algorithmic problems are
still not well-understood today.In this paper, we revisit the k-Network Flow Update
problem that asks for a schedule to reroute k unsplittable flows from their current
paths to the given new paths, in a congestion-free manner in a capacitated network.
We show that the problem is already NP-hard for three acyclic flows on simple
directed graphs. Our main contribution is an efficient algorithm for sparse networks;
specifically the algorithm is fixed parameter tractable in the number of flows
and the treewidth of a graph that is the union of all flows. Our results also
settle the open complexity question in the literature.
acknowledgement: Research was supported by the Austrian Science Fund (FWF), project
I 5025-N (DELTA), 2020-2024. Esra Ceylan’s research was supported by FFG, FEMtech
Praktika für Studentinnen. Jakub Svoboda and Krishnendu Chatterjee were supported
by the European Research Council (ERC) CoG 863818 (ForM-SMArt).
article_processing_charge: No
author:
- first_name: Esra
full_name: Ceylan, Esra
id: cb1ca1d8-dcc0-11ef-baa5-9f1b3ef75933
last_name: Ceylan
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Stefan
full_name: Schmid, Stefan
last_name: Schmid
- first_name: Jakub
full_name: Svoboda, Jakub
id: 130759D2-D7DD-11E9-87D2-DE0DE6697425
last_name: Svoboda
orcid: 0000-0002-1419-3267
citation:
ama: 'Ceylan E, Chatterjee K, Schmid S, Svoboda J. Congestion-free rerouting of
network flows: Hardness and an FPT algorithm. In: NOMS 2024-2024 IEEE Network
Operations and Management Symposium. IEEE; 2024. doi:10.1109/noms59830.2024.10575579'
apa: 'Ceylan, E., Chatterjee, K., Schmid, S., & Svoboda, J. (2024). Congestion-free
rerouting of network flows: Hardness and an FPT algorithm. In NOMS 2024-2024
IEEE Network Operations and Management Symposium. Seoul, Republic of Korea:
IEEE. https://doi.org/10.1109/noms59830.2024.10575579'
chicago: 'Ceylan, Esra, Krishnendu Chatterjee, Stefan Schmid, and Jakub Svoboda.
“Congestion-Free Rerouting of Network Flows: Hardness and an FPT Algorithm.” In
NOMS 2024-2024 IEEE Network Operations and Management Symposium. IEEE,
2024. https://doi.org/10.1109/noms59830.2024.10575579.'
ieee: 'E. Ceylan, K. Chatterjee, S. Schmid, and J. Svoboda, “Congestion-free rerouting
of network flows: Hardness and an FPT algorithm,” in NOMS 2024-2024 IEEE Network
Operations and Management Symposium, Seoul, Republic of Korea, 2024.'
ista: 'Ceylan E, Chatterjee K, Schmid S, Svoboda J. 2024. Congestion-free rerouting
of network flows: Hardness and an FPT algorithm. NOMS 2024-2024 IEEE Network Operations
and Management Symposium. NOMS: Network Operations and Management Symposiu .'
mla: 'Ceylan, Esra, et al. “Congestion-Free Rerouting of Network Flows: Hardness
and an FPT Algorithm.” NOMS 2024-2024 IEEE Network Operations and Management
Symposium, IEEE, 2024, doi:10.1109/noms59830.2024.10575579.'
short: E. Ceylan, K. Chatterjee, S. Schmid, J. Svoboda, in:, NOMS 2024-2024 IEEE
Network Operations and Management Symposium, IEEE, 2024.
conference:
end_date: 2024-05-10
location: Seoul, Republic of Korea
name: 'NOMS: Network Operations and Management Symposiu '
start_date: 2024-05-06
corr_author: '1'
date_created: 2025-01-27T15:06:45Z
date_published: 2024-05-01T00:00:00Z
date_updated: 2025-11-05T07:34:27Z
day: '01'
department:
- _id: KrCh
doi: 10.1109/noms59830.2024.10575579
ec_funded: 1
external_id:
isi:
- '001270140300143'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://schmiste.github.io/noms24.pdf
month: '05'
oa: 1
oa_version: Submitted Version
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: bd622a5c-d553-11ed-ba76-bae280ba8aff
grant_number: '894907'
name: Graphical Games
publication: NOMS 2024-2024 IEEE Network Operations and Management Symposium
publication_identifier:
eissn:
- 2374-9709
isbn:
- '9798350327946'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Congestion-free rerouting of network flows: Hardness and an FPT algorithm'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '18926'
abstract:
- lang: eng
text: 'We study weak solutions to mean curvature flow satisfying Young’s angle condition
for general contact angles α ∈ (0, π). First, we construct BV solutions by using
the Allen-Cahn approximation with boundary contact energy as proposed by Owen
and Sternberg. Second, we prove the weak-strong uniqueness and stability for this
solution concept. The main ingredient for both results is a relative energy, which
can also be interpreted as a tilt excess. '
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Sebastian
full_name: Hensel, Sebastian
id: 4D23B7DA-F248-11E8-B48F-1D18A9856A87
last_name: Hensel
orcid: 0000-0001-7252-8072
- first_name: Tim
full_name: Laux, Tim
last_name: Laux
citation:
ama: 'Hensel S, Laux T. BV solutions for mean curvature flow with constant angle:
Allen-Cahn approximation and weak-strong uniqueness. Indiana University Mathematics
Journal. 2024;73(1):111-148. doi:10.1512/iumj.2024.73.9701'
apa: 'Hensel, S., & Laux, T. (2024). BV solutions for mean curvature flow with
constant angle: Allen-Cahn approximation and weak-strong uniqueness. Indiana
University Mathematics Journal. Indiana University Mathematics Journal. https://doi.org/10.1512/iumj.2024.73.9701'
chicago: 'Hensel, Sebastian, and Tim Laux. “BV Solutions for Mean Curvature Flow
with Constant Angle: Allen-Cahn Approximation and Weak-Strong Uniqueness.” Indiana
University Mathematics Journal. Indiana University Mathematics Journal, 2024.
https://doi.org/10.1512/iumj.2024.73.9701.'
ieee: 'S. Hensel and T. Laux, “BV solutions for mean curvature flow with constant
angle: Allen-Cahn approximation and weak-strong uniqueness,” Indiana University
Mathematics Journal, vol. 73, no. 1. Indiana University Mathematics Journal,
pp. 111–148, 2024.'
ista: 'Hensel S, Laux T. 2024. BV solutions for mean curvature flow with constant
angle: Allen-Cahn approximation and weak-strong uniqueness. Indiana University
Mathematics Journal. 73(1), 111–148.'
mla: 'Hensel, Sebastian, and Tim Laux. “BV Solutions for Mean Curvature Flow with
Constant Angle: Allen-Cahn Approximation and Weak-Strong Uniqueness.” Indiana
University Mathematics Journal, vol. 73, no. 1, Indiana University Mathematics
Journal, 2024, pp. 111–48, doi:10.1512/iumj.2024.73.9701.'
short: S. Hensel, T. Laux, Indiana University Mathematics Journal 73 (2024) 111–148.
corr_author: '1'
date_created: 2025-01-27T15:20:19Z
date_published: 2024-01-01T00:00:00Z
date_updated: 2025-01-27T15:23:57Z
day: '01'
department:
- _id: JuFi
doi: 10.1512/iumj.2024.73.9701
external_id:
arxiv:
- '2112.11150'
intvolume: ' 73'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2112.11150
month: '01'
oa: 1
oa_version: Preprint
page: 111-148
publication: Indiana University Mathematics Journal
publication_identifier:
issn:
- 0022-2518
publication_status: published
publisher: Indiana University Mathematics Journal
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'BV solutions for mean curvature flow with constant angle: Allen-Cahn approximation
and weak-strong uniqueness'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 73
year: '2024'
...
---
OA_place: publisher
OA_type: gold
_id: '18928'
abstract:
- lang: eng
text: "Algorithms with predictions is a new research direction that leverages machine
learned predictions for algorithm design. So far a plethora of recent works have
incorporated predictions to improve on worst-case bounds for online problems.
In this paper, we initiate the study of complexity of dynamic data structures
with predictions, including dynamic graph algorithms. Unlike online algorithms,
the goal in dynamic data structures is to maintain the solution efficiently with
every update.\r\nWe investigate three natural models of prediction: (1) δ-accurate
predictions where each predicted request matches the true request with probability
δ, (2) list-accurate predictions where a true request comes from a list of possible
requests, and (3) bounded delay predictions where the true requests are a permutation
of the predicted requests. We give general reductions among the prediction models,
showing that bounded delay is the strongest prediction model, followed by list-accurate,
and δ-accurate.\r\nFurther, we identify two broad problem classes based on lower
bounds due to the Online Matrix Vector (OMv) conjecture. Specifically, we show
that locally correctable dynamic problems have strong conditional lower bounds
for list-accurate predictions that are equivalent to the non-prediction setting,
unless list-accurate predictions are perfect. Moreover, we show that locally reducible
dynamic problems have time complexity that degrades gracefully with the quality
of bounded delay predictions. We categorize problems with known OMv lower bounds
accordingly and give several upper bounds in the delay model that show that our
lower bounds are almost tight.\r\nWe note that concurrent work by v.d.Brand et
al. [SODA '24] and Liu and Srinivas [arXiv:2307.08890] independently study dynamic
graph algorithms with predictions, but their work is mostly focused on showing
upper bounds."
acknowledgement: "Henzinger, Monika: This project has received funding from the European
Research Council (ERC) under the European Union’s Horizon 2020 research and innovation
programme (Grant agreement No. 101019564) and the Austrian Science Fund (FWF) project
Z 422-N, project I 5982-N, and project P 33775-N, with additional funding from the
netidee SCIENCE Stiftung, 2020-2024.\r\nSaha, Barna: This project is partially supported
by NSF grants 1652303, 1909046, 2112533, and HDR TRIPODS Phase II grant 2217058.\r\nWe
would like to thank Andrea Lincoln for many helpful discussions and insightful comments."
alternative_title:
- LIPIcs
article_processing_charge: Yes
arxiv: 1
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Barna
full_name: Saha, Barna
last_name: Saha
- first_name: Martin P.
full_name: Seybold, Martin P.
last_name: Seybold
- first_name: Christopher
full_name: Ye, Christopher
last_name: Ye
citation:
ama: 'Henzinger M, Saha B, Seybold MP, Ye C. On the complexity of algorithms with
predictions for dynamic graph problems. In: 15th Innovations in Theoretical
Computer Science Conference. Vol 287. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2024:62:1-62:25. doi:10.4230/LIPIcs.ITCS.2024.62'
apa: 'Henzinger, M., Saha, B., Seybold, M. P., & Ye, C. (2024). On the complexity
of algorithms with predictions for dynamic graph problems. In 15th Innovations
in Theoretical Computer Science Conference (Vol. 287, p. 62:1-62:25). Berkeley,
CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ITCS.2024.62'
chicago: Henzinger, Monika, Barna Saha, Martin P. Seybold, and Christopher Ye. “On
the Complexity of Algorithms with Predictions for Dynamic Graph Problems.” In
15th Innovations in Theoretical Computer Science Conference, 287:62:1-62:25.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.ITCS.2024.62.
ieee: M. Henzinger, B. Saha, M. P. Seybold, and C. Ye, “On the complexity of algorithms
with predictions for dynamic graph problems,” in 15th Innovations in Theoretical
Computer Science Conference, Berkeley, CA, United States, 2024, vol. 287,
p. 62:1-62:25.
ista: 'Henzinger M, Saha B, Seybold MP, Ye C. 2024. On the complexity of algorithms
with predictions for dynamic graph problems. 15th Innovations in Theoretical Computer
Science Conference. ITCS: Innovations in Theoretical Computer Science, LIPIcs,
vol. 287, 62:1-62:25.'
mla: Henzinger, Monika, et al. “On the Complexity of Algorithms with Predictions
for Dynamic Graph Problems.” 15th Innovations in Theoretical Computer Science
Conference, vol. 287, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024,
p. 62:1-62:25, doi:10.4230/LIPIcs.ITCS.2024.62.
short: M. Henzinger, B. Saha, M.P. Seybold, C. Ye, in:, 15th Innovations in Theoretical
Computer Science Conference, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2024, p. 62:1-62:25.
conference:
end_date: 2024-02-02
location: Berkeley, CA, United States
name: 'ITCS: Innovations in Theoretical Computer Science'
start_date: 2024-01-30
corr_author: '1'
date_created: 2025-01-27T15:33:42Z
date_published: 2024-01-24T00:00:00Z
date_updated: 2025-09-09T12:11:33Z
day: '24'
ddc:
- '000'
department:
- _id: MoHe
doi: 10.4230/LIPIcs.ITCS.2024.62
ec_funded: 1
external_id:
arxiv:
- '2307.16771'
isi:
- '001300389400062'
file:
- access_level: open_access
checksum: 15085a5b3697a408b92a4a7a27293927
content_type: application/pdf
creator: dernst
date_created: 2025-01-27T15:33:24Z
date_updated: 2025-01-27T15:33:24Z
file_id: '18929'
file_name: 2024_LIPICs_HenzingerMo.pdf
file_size: 1084372
relation: main_file
success: 1
file_date_updated: 2025-01-27T15:33:24Z
has_accepted_license: '1'
intvolume: ' 287'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 62:1-62:25
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: 34def286-11ca-11ed-8bc3-da5948e1613c
grant_number: Z00422
name: Efficient algorithms
- _id: bda196b2-d553-11ed-ba76-8e8ee6c21103
grant_number: I05982
name: Static and Dynamic Hierarchical Graph Decompositions
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: P33775
name: Fast Algorithms for a Reactive Network Layer
publication: 15th Innovations in Theoretical Computer Science Conference
publication_identifier:
eissn:
- 1868-8969
isbn:
- '9783959773096'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the complexity of algorithms with predictions for dynamic graph 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: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 287
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '18930'
abstract:
- lang: eng
text: "We study sumsets \U0001D49C + ℬ in the set of squares \U0001D4AE (and, more
generally, in the set of kth powers \U0001D4AEk, where k ≥2 is an integer). It
is known by a result of Gyarmati that \U0001D49C + ℬ ⊂ \U0001D4AEk ∩[1,N] implies
that min(|\U0001D49C|,|ℬ|) =Ok(logN). Here, we study how the upper bound on |ℬ|
decreases, when the size of |\U0001D49C| increases (or vice versa). In particular,
if |\U0001D49C| ≥ Ck1m m(logN)1m , then |ℬ| = Ok(m2logN), for sufficiently large
N, a positive integer m and an explicit constant C > 0. For example, with m ∼
loglogN this gives: If |\U0001D49C| ≥ CkloglogN,then |ℬ| = Ok(logN(loglogN)2)."
acknowledgement: This manuscript grew out of the second author’s MSc Thesis at Graz
University of Technology [34]. C. Elsholtz is supported by a joint FWF-ANR project
ArithRand, grant numbers FWF I 4945-N and ANR-20-CE91-0006. Both authors would like
to thank Igor Shparlinski for drawing our attention to related character sum estimates.
Furthermore, we would like to thank the referee for a careful reading of the paper.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Christian
full_name: Elsholtz, Christian
last_name: Elsholtz
- first_name: Lena
full_name: Wurzinger, Lena
id: 50c57d72-32a8-11ee-aeea-d652094d2ccd
last_name: Wurzinger
orcid: 0009-0004-5360-0074
citation:
ama: Elsholtz C, Wurzinger L. Sumsets in the set of squares. The Quarterly Journal
of Mathematics. 2024;75(4):1243-1254. doi:10.1093/qmath/haae044
apa: Elsholtz, C., & Wurzinger, L. (2024). Sumsets in the set of squares. The
Quarterly Journal of Mathematics. Oxford University Press. https://doi.org/10.1093/qmath/haae044
chicago: Elsholtz, Christian, and Lena Wurzinger. “Sumsets in the Set of Squares.”
The Quarterly Journal of Mathematics. Oxford University Press, 2024. https://doi.org/10.1093/qmath/haae044.
ieee: C. Elsholtz and L. Wurzinger, “Sumsets in the set of squares,” The Quarterly
Journal of Mathematics, vol. 75, no. 4. Oxford University Press, pp. 1243–1254,
2024.
ista: Elsholtz C, Wurzinger L. 2024. Sumsets in the set of squares. The Quarterly
Journal of Mathematics. 75(4), 1243–1254.
mla: Elsholtz, Christian, and Lena Wurzinger. “Sumsets in the Set of Squares.” The
Quarterly Journal of Mathematics, vol. 75, no. 4, Oxford University Press,
2024, pp. 1243–54, doi:10.1093/qmath/haae044.
short: C. Elsholtz, L. Wurzinger, The Quarterly Journal of Mathematics 75 (2024)
1243–1254.
corr_author: '1'
date_created: 2025-01-28T06:55:31Z
date_published: 2024-12-01T00:00:00Z
date_updated: 2025-12-04T14:46:28Z
day: '01'
ddc:
- '510'
department:
- _id: TiBr
doi: 10.1093/qmath/haae044
external_id:
isi:
- '001304396600001'
file:
- access_level: open_access
checksum: 1a06e052761d3f1e873463d6f529dd82
content_type: application/pdf
creator: dernst
date_created: 2025-01-28T07:03:51Z
date_updated: 2025-01-28T07:03:51Z
file_id: '18931'
file_name: 2024_QuarterlyJourMath_Elsholtz.pdf
file_size: 424645
relation: main_file
success: 1
file_date_updated: 2025-01-28T07:03:51Z
has_accepted_license: '1'
intvolume: ' 75'
isi: 1
issue: '4'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 1243-1254
publication: The Quarterly Journal of Mathematics
publication_identifier:
eissn:
- 1464-3847
issn:
- 0033-5606
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sumsets in the set of squares
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: 75
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18934'
abstract:
- lang: eng
text: The assembly of biomolecular condensate in eukaryotic cells and the accumulation
of amyloid deposits in neurons are processes involving the nucleation and growth
(NAG) of new protein phases. To therapeutically target protein phase separation,
drug candidates are tested in in vitro assays that monitor the increase in the
mass or size of the new phase. Limited mechanistic insight is, however, provided
if empirical or untestable kinetic models are fitted to these progress curves.
Here we present the web server NAGPKin that quantifies NAG rates using mass-based
or size-based progress curves as the input data. A report is generated containing
the fitted NAG parameters and elucidating the phase separation mechanisms at play.
The NAG parameters can be used to predict particle size distributions of, for
example, protein droplets formed by liquid-liquid phase separation (LLPS) or amyloid
fibrils formed by protein aggregation. Because minimal intervention is required
from the user, NAGPKin is a good platform for standardized reporting of LLPS and
protein self-assembly data. NAGPKin is useful for drug discovery as well as for
fundamental studies on protein phase separation. NAGPKin is freely available (no
login required) at https://nagpkin.i3s.up.pt .
acknowledgement: We thank Professor José Paulo Leal, Department of Computer Science
− Faculdade de Ciências da Universidade do Porto, for his invaluable help during
the Implementation of NAGPKin. This work is part of a project that has received
funding from the European Union’s Horizon 2020 research and innovation programme
under grant agreement no. 952334 (PhasAGE). This research was funded by the Portuguese
Foundation for Science and Technology (FCT) in the framework of project PTDC/QUI-COL/2444/2021.
article_number: mr1
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Zsuzsa
full_name: Sárkány, Zsuzsa
last_name: Sárkány
- first_name: Francisco
full_name: Figueiredo, Francisco
id: 8125cbe2-9661-11ed-a754-afe96018f37d
last_name: Figueiredo
- first_name: Sandra
full_name: Macedo-Ribeiro, Sandra
last_name: Macedo-Ribeiro
- first_name: Pedro M.
full_name: Martins, Pedro M.
last_name: Martins
citation:
ama: 'Sárkány Z, Figueiredo F, Macedo-Ribeiro S, Martins PM. NAGPKin: Nucleation-and-growth
parameters from the kinetics of protein phase separation. Molecular Biology
of the Cell. 2024;35(3). doi:10.1091/mbc.e23-07-0289'
apa: 'Sárkány, Z., Figueiredo, F., Macedo-Ribeiro, S., & Martins, P. M. (2024).
NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation.
Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/mbc.e23-07-0289'
chicago: 'Sárkány, Zsuzsa, Francisco Figueiredo, Sandra Macedo-Ribeiro, and Pedro
M. Martins. “NAGPKin: Nucleation-and-Growth Parameters from the Kinetics of Protein
Phase Separation.” Molecular Biology of the Cell. American Society for
Cell Biology, 2024. https://doi.org/10.1091/mbc.e23-07-0289.'
ieee: 'Z. Sárkány, F. Figueiredo, S. Macedo-Ribeiro, and P. M. Martins, “NAGPKin:
Nucleation-and-growth parameters from the kinetics of protein phase separation,”
Molecular Biology of the Cell, vol. 35, no. 3. American Society for Cell
Biology, 2024.'
ista: 'Sárkány Z, Figueiredo F, Macedo-Ribeiro S, Martins PM. 2024. NAGPKin: Nucleation-and-growth
parameters from the kinetics of protein phase separation. Molecular Biology of
the Cell. 35(3), mr1.'
mla: 'Sárkány, Zsuzsa, et al. “NAGPKin: Nucleation-and-Growth Parameters from the
Kinetics of Protein Phase Separation.” Molecular Biology of the Cell, vol.
35, no. 3, mr1, American Society for Cell Biology, 2024, doi:10.1091/mbc.e23-07-0289.'
short: Z. Sárkány, F. Figueiredo, S. Macedo-Ribeiro, P.M. Martins, Molecular Biology
of the Cell 35 (2024).
date_created: 2025-01-29T07:58:40Z
date_published: 2024-03-01T00:00:00Z
date_updated: 2025-01-29T08:16:20Z
day: '01'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1091/mbc.e23-07-0289
external_id:
pmid:
- '38117593'
file:
- access_level: open_access
checksum: d7deb6390f294da69321cfbe352ed611
content_type: application/pdf
creator: dernst
date_created: 2025-01-29T08:12:11Z
date_updated: 2025-01-29T08:12:11Z
file_id: '18935'
file_name: 2024_MolecularBioCell_Sarkany.pdf
file_size: 1699180
relation: main_file
success: 1
file_date_updated: 2025-01-29T08:12:11Z
has_accepted_license: '1'
intvolume: ' 35'
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Molecular Biology of the Cell
publication_identifier:
eissn:
- 1939-4586
issn:
- 1059-1524
publication_status: published
publisher: American Society for Cell Biology
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase
separation'
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2024'
...
---
OA_type: closed access
_id: '18937'
abstract:
- lang: eng
text: A detailed structural, magnetic as well as dielectric dynamics study is carried
out to investigate the influence of Bi3+ on YCrO3. All the samples crystalize
in orthorhombic structure with Pnma symmetry and the grains are mostly stretched
with Bi. A coexisting tunable fraction of both antiferromagnetic (AFM) and weak
ferromagnetic (WFM) phases is acquired by the system down to Low-T. An abnormal
negative magnetization in zero field is correlated to the competition among AFM
and WFM phases. Maximum magnetization decreases while the coercivity first increases
and then decreases with Bi is correlated to the competing effect between the local
deformation and Cr–O–Cr exchange interaction. The magnetodielectric coupling with
improved permittivity might be associated with the 6s2 lone pair electron of Bi3+.
Furthermore, ac-conductivity increases with a decrease in activation energy (0.27–0.11
eV), is explained in the framework of structural model and charge carrier hopping
between Cr3+ and Cr4+ ions.
acknowledgement: The authors would like to acknowledge MHRD, Government of India for
financial support. The author is also thankful to RRCAT, Indore for providing XPS
beamline-14 of Indus II to conduct experimental work.
article_number: '416018'
article_processing_charge: No
article_type: original
author:
- first_name: Sujata Kumari
full_name: Ray, Sujata Kumari
last_name: Ray
- first_name: Anupama
full_name: Pati, Anupama
last_name: Pati
- first_name: Payala
full_name: Sahoo, Payala
last_name: Sahoo
- first_name: A.K.
full_name: Sahoo, A.K.
last_name: Sahoo
- first_name: Saurabh
full_name: Singh, Saurabh
id: 12d625da-9cb3-11ed-9667-af09d37d3f0a
last_name: Singh
orcid: 0000-0003-2209-5269
- first_name: Tsunehiro
full_name: Takeuchi, Tsunehiro
last_name: Takeuchi
- first_name: S.
full_name: Dash, S.
last_name: Dash
citation:
ama: 'Ray SK, Pati A, Sahoo P, et al. Tunable magnetoelectronic properties in Bi3+
substituted YCrO3. Physica B: Condensed Matter. 2024;685. doi:10.1016/j.physb.2024.416018'
apa: 'Ray, S. K., Pati, A., Sahoo, P., Sahoo, A. K., Singh, S., Takeuchi, T., &
Dash, S. (2024). Tunable magnetoelectronic properties in Bi3+ substituted YCrO3.
Physica B: Condensed Matter. Elsevier. https://doi.org/10.1016/j.physb.2024.416018'
chicago: 'Ray, Sujata Kumari, Anupama Pati, Payala Sahoo, A.K. Sahoo, Saurabh Singh,
Tsunehiro Takeuchi, and S. Dash. “Tunable Magnetoelectronic Properties in Bi3+
Substituted YCrO3.” Physica B: Condensed Matter. Elsevier, 2024. https://doi.org/10.1016/j.physb.2024.416018.'
ieee: 'S. K. Ray et al., “Tunable magnetoelectronic properties in Bi3+ substituted
YCrO3,” Physica B: Condensed Matter, vol. 685. Elsevier, 2024.'
ista: 'Ray SK, Pati A, Sahoo P, Sahoo AK, Singh S, Takeuchi T, Dash S. 2024. Tunable
magnetoelectronic properties in Bi3+ substituted YCrO3. Physica B: Condensed Matter.
685, 416018.'
mla: 'Ray, Sujata Kumari, et al. “Tunable Magnetoelectronic Properties in Bi3+ Substituted
YCrO3.” Physica B: Condensed Matter, vol. 685, 416018, Elsevier, 2024,
doi:10.1016/j.physb.2024.416018.'
short: 'S.K. Ray, A. Pati, P. Sahoo, A.K. Sahoo, S. Singh, T. Takeuchi, S. Dash,
Physica B: Condensed Matter 685 (2024).'
date_created: 2025-01-29T08:33:04Z
date_published: 2024-07-15T00:00:00Z
date_updated: 2025-01-29T08:37:14Z
day: '15'
department:
- _id: MaIb
doi: 10.1016/j.physb.2024.416018
intvolume: ' 685'
language:
- iso: eng
month: '07'
oa_version: None
publication: 'Physica B: Condensed Matter'
publication_identifier:
issn:
- 0921-4526
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tunable magnetoelectronic properties in Bi3+ substituted YCrO3
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 685
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18938'
abstract:
- lang: eng
text: The synthesis of proteins as encoded in the genome depends critically on translational
fidelity. Nevertheless, errors inevitably occur, and those that result in reading
frame shifts are particularly consequential because the resulting polypeptides
are typically nonfunctional. Despite the generally maladaptive impact of such
errors, the proper decoding of certain mRNAs, including many viral mRNAs, depends
on a process known as programmed ribosomal frameshifting. The fact that these
programmed events, commonly involving a shift to the –1 frame, occur at specific
evolutionarily optimized “slippery” sites has facilitated mechanistic investigation.
By contrast, less is known about the scope and nature of error (i.e., nonprogrammed)
frameshifting. Here, we examine error frameshifting by monitoring spontaneous
frameshift events that suppress the effects of single base pair deletions affecting
two unrelated test proteins. To map the precise sites of frameshifting, we developed
a targeted mass spectrometry–based method called “translational tiling proteomics”
for interrogating the full set of possible –1 slippage events that could produce
the observed frameshift suppression. Surprisingly, such events occur at many sites
along the transcripts, involving up to one half of the available codons. Only
a subset of these resembled canonical “slippery” sites, implicating alternative
mechanisms potentially involving noncognate mispairing events. Additionally, the
aggregate frequency of these events (ranging from 1 to 10% in our test cases)
was higher than we might have anticipated. Our findings point to an unexpected
degree of mechanistic diversity among ribosomal frameshifting events and suggest
that frameshifted products may contribute more significantly to the proteome than
generally assumed.
acknowledgement: We thank S. L. Dove for valuable discussion and comments on the manuscript
and R. Hellmiss for artwork. This work was supported by NIH grants GM136247 to A.H.,
AG011085 to J.W.H., and GM132129 to J.A.P.
article_number: e2317453121
article_processing_charge: No
article_type: original
author:
- first_name: Benjamin L
full_name: Springstein, Benjamin L
id: b4eb62ef-ac72-11ed-9503-ed3b4d66c083
last_name: Springstein
orcid: 0000-0002-3461-5391
- first_name: Joao A.
full_name: Paulo, Joao A.
last_name: Paulo
- first_name: Hankum
full_name: Park, Hankum
last_name: Park
- first_name: Kemardo
full_name: Henry, Kemardo
last_name: Henry
- first_name: Eleanor
full_name: Fleming, Eleanor
last_name: Fleming
- first_name: Zoë
full_name: Feder, Zoë
last_name: Feder
- first_name: J. Wade
full_name: Harper, J. Wade
last_name: Harper
- first_name: Ann
full_name: Hochschild, Ann
last_name: Hochschild
citation:
ama: Springstein BL, Paulo JA, Park H, et al. Systematic analysis of nonprogrammed
frameshift suppression in E.coli via translational tiling proteomics. Proceedings
of the National Academy of Sciences of the United States of America. 2024;121(6).
doi:10.1073/pnas.2317453121
apa: Springstein, B. L., Paulo, J. A., Park, H., Henry, K., Fleming, E., Feder,
Z., … Hochschild, A. (2024). Systematic analysis of nonprogrammed frameshift suppression
in E.coli via translational tiling proteomics. Proceedings of the National
Academy of Sciences of the United States of America. National Academy of Sciences.
https://doi.org/10.1073/pnas.2317453121
chicago: Springstein, Benjamin L, Joao A. Paulo, Hankum Park, Kemardo Henry, Eleanor
Fleming, Zoë Feder, J. Wade Harper, and Ann Hochschild. “Systematic Analysis of
Nonprogrammed Frameshift Suppression in E.Coli via Translational Tiling Proteomics.”
Proceedings of the National Academy of Sciences of the United States of America.
National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2317453121.
ieee: B. L. Springstein et al., “Systematic analysis of nonprogrammed frameshift
suppression in E.coli via translational tiling proteomics,” Proceedings of
the National Academy of Sciences of the United States of America, vol. 121,
no. 6. National Academy of Sciences, 2024.
ista: Springstein BL, Paulo JA, Park H, Henry K, Fleming E, Feder Z, Harper JW,
Hochschild A. 2024. Systematic analysis of nonprogrammed frameshift suppression
in E.coli via translational tiling proteomics. Proceedings of the National Academy
of Sciences of the United States of America. 121(6), e2317453121.
mla: Springstein, Benjamin L., et al. “Systematic Analysis of Nonprogrammed Frameshift
Suppression in E.Coli via Translational Tiling Proteomics.” Proceedings of
the National Academy of Sciences of the United States of America, vol. 121,
no. 6, e2317453121, National Academy of Sciences, 2024, doi:10.1073/pnas.2317453121.
short: B.L. Springstein, J.A. Paulo, H. Park, K. Henry, E. Fleming, Z. Feder, J.W.
Harper, A. Hochschild, Proceedings of the National Academy of Sciences of the
United States of America 121 (2024).
date_created: 2025-01-29T08:39:27Z
date_published: 2024-02-06T00:00:00Z
date_updated: 2025-05-14T11:02:52Z
day: '06'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.1073/pnas.2317453121
external_id:
pmid:
- '38289956'
file:
- access_level: open_access
checksum: 5bd62c7cb4287e3706a1d45d6ef61fd1
content_type: application/pdf
creator: dernst
date_created: 2025-01-29T08:43:16Z
date_updated: 2025-01-29T08:43:16Z
file_id: '18939'
file_name: 2024_PNAS_Springstein.pdf
file_size: 720902
relation: main_file
success: 1
file_date_updated: 2025-01-29T08:43:16Z
has_accepted_license: '1'
intvolume: ' 121'
issue: '6'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational
tiling proteomics
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 121
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18940'
abstract:
- lang: eng
text: BMP signaling has a conserved function in patterning the dorsal-ventral body
axis in Bilateria and the directive axis in anthozoan cnidarians. So far, cnidarian
studies have focused on the role of different BMP signaling network components
in regulating pSMAD1/5 gradient formation. Much less is known about the target
genes downstream of BMP signaling. To address this, we generated a genome-wide
list of direct pSMAD1/5 target genes in the anthozoan Nematostella
vectensis, several of which were conserved in Drosophila
and Xenopus. Our ChIP-seq analysis revealed that many
of the regulatory molecules with documented bilaterally symmetric expression in
Nematostella are directly controlled by BMP signaling.
We identified several so far uncharacterized BMP-dependent transcription factors
and signaling molecules, whose bilaterally symmetric expression may be indicative
of their involvement in secondary axis patterning. One of these molecules is zswim4-6,
which encodes a novel nuclear protein that can modulate the pSMAD1/5 gradient
and potentially promote BMP-dependent gene repression.
acknowledgement: This work was funded by the Austrian Science Foundation (FWF) grants
P26962-B21 and P32705-B to GG and by the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation program (grant agreement No
637840 [QUANTPATTERN] and 863952 [ACE-OF-SPACE]) to PM. We thank Michaela Schwaiger,
Taras Kreslavsky, Hiromi Tagoh, and Patricio Ferrer Murguia for their help with
the ChIP protocol, Matthias Richter and Christian Hofer for their assistance with
in situ analyses, Emilio Gonzalez Morales for making the measurements for Figure
6—figure supplement 3, Catrin Weiler for the assistance in cloning zebrafish zswim5,
David Mörsdorf for critically reading the manuscript and help with data visualization,
and the Core Facility for Cell Imaging and Ultrastructure Research of the University
of Vienna for access to the confocal microscope.
article_processing_charge: Yes
article_type: original
author:
- first_name: Paul
full_name: Knabl, Paul
last_name: Knabl
- first_name: Alexandra
full_name: Schauer, Alexandra
id: 30A536BA-F248-11E8-B48F-1D18A9856A87
last_name: Schauer
orcid: 0000-0001-7659-9142
- first_name: Autumn P
full_name: Pomreinke, Autumn P
last_name: Pomreinke
- first_name: Bob
full_name: Zimmermann, Bob
last_name: Zimmermann
- first_name: Katherine W
full_name: Rogers, Katherine W
last_name: Rogers
- first_name: Daniel
full_name: Čapek, Daniel
last_name: Čapek
- first_name: Patrick
full_name: Müller, Patrick
last_name: Müller
- first_name: Grigory
full_name: Genikhovich, Grigory
last_name: Genikhovich
citation:
ama: Knabl P, Schauer A, Pomreinke AP, et al. Analysis of SMAD1/5 target genes in
a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator. eLife.
2024;13. doi:10.7554/elife.80803
apa: Knabl, P., Schauer, A., Pomreinke, A. P., Zimmermann, B., Rogers, K. W., Čapek,
D., … Genikhovich, G. (2024). Analysis of SMAD1/5 target genes in a sea anemone
reveals ZSWIM4-6 as a novel BMP signaling modulator. ELife. eLife Sciences
Publications. https://doi.org/10.7554/elife.80803
chicago: Knabl, Paul, Alexandra Schauer, Autumn P Pomreinke, Bob Zimmermann, Katherine
W Rogers, Daniel Čapek, Patrick Müller, and Grigory Genikhovich. “Analysis of
SMAD1/5 Target Genes in a Sea Anemone Reveals ZSWIM4-6 as a Novel BMP Signaling
Modulator.” ELife. eLife Sciences Publications, 2024. https://doi.org/10.7554/elife.80803.
ieee: P. Knabl et al., “Analysis of SMAD1/5 target genes in a sea anemone
reveals ZSWIM4-6 as a novel BMP signaling modulator,” eLife, vol. 13. eLife
Sciences Publications, 2024.
ista: Knabl P, Schauer A, Pomreinke AP, Zimmermann B, Rogers KW, Čapek D, Müller
P, Genikhovich G. 2024. Analysis of SMAD1/5 target genes in a sea anemone reveals
ZSWIM4-6 as a novel BMP signaling modulator. eLife. 13.
mla: Knabl, Paul, et al. “Analysis of SMAD1/5 Target Genes in a Sea Anemone Reveals
ZSWIM4-6 as a Novel BMP Signaling Modulator.” ELife, vol. 13, eLife Sciences
Publications, 2024, doi:10.7554/elife.80803.
short: P. Knabl, A. Schauer, A.P. Pomreinke, B. Zimmermann, K.W. Rogers, D. Čapek,
P. Müller, G. Genikhovich, ELife 13 (2024).
date_created: 2025-01-29T08:48:34Z
date_published: 2024-02-07T00:00:00Z
date_updated: 2025-01-29T08:56:21Z
day: '07'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.7554/elife.80803
file:
- access_level: open_access
checksum: 24548a184215d3f4547bba535ccfd7b1
content_type: application/pdf
creator: dernst
date_created: 2025-01-29T08:50:18Z
date_updated: 2025-01-29T08:50:18Z
file_id: '18941'
file_name: 2024_eLife_Knabl.pdf
file_size: 11855972
relation: main_file
success: 1
file_date_updated: 2025-01-29T08:50:18Z
has_accepted_license: '1'
intvolume: ' 13'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel
BMP signaling modulator
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: 13
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '18944'
abstract:
- lang: eng
text: 'Understanding connectivity patterns exhibited by endangered species living
in fragmented habitats is fundamental to improving management and conservation
actions. Such improvements can be particularly pressing at the trailing edges
of these habitats, where populations are facing the greatest challenges from climate
change, and appear even more crucial if the species is commercially harvested.
Seascape genetics have been increasingly used to meet these needs. In this study,
we examined connectivity patterns among 32 populations of the oarweed kelp Laminaria
digitata located at the species’ southern range limit. The distance
(or sampling gap) between neighboring populations ranged from a few km to a few
100s of km. By genotyping 11 microsatellite markers, we aimed to (1) refine analyses
of population structure; (2) test whether on-shelf islands are genetically more
differentiated than mainland populations; (3) evaluate the relative importance
of various abiotic conditions in shaping the genetic structure; and (4) evaluate
if the relative importance of each environmental factor varied according to sampling
schemes. Our analyses revealed a positive relationship between connectivity links
and genetic diversity: populations with high levels of connectivity were genetically
enriched while isolated populations showed signs of genetic erosion. The genetically
impoverished populations corresponded to the southernmost populations as well
as populations along the northern coast of Brittany (Locquirec, Saint-Malo Bay)
and the northernmost population in Pas-de-Calais. By performing distance-based
redundancy analysis on various sampling schemes, geographic distance appeared
as the dominant factor influencing connectivity between populations separated
by great distances, while hydrodynamic processes were the main factor when analyzing
at a final spatial resolution.'
article_processing_charge: No
article_type: original
author:
- first_name: Louise
full_name: Fouqueau, Louise
id: 1676e173-8143-11ed-8927-fe165216a93f
last_name: Fouqueau
orcid: 0000-0003-0371-9339
- first_name: L
full_name: Reynes, L
last_name: Reynes
- first_name: F
full_name: Tempera, F
last_name: Tempera
- first_name: T
full_name: Bajjouk, T
last_name: Bajjouk
- first_name: A
full_name: Blanfuné, A
last_name: Blanfuné
- first_name: C
full_name: Chevalier, C
last_name: Chevalier
- first_name: M
full_name: Laurans, M
last_name: Laurans
- first_name: S
full_name: Mauger, S
last_name: Mauger
- first_name: M
full_name: Sourisseau, M
last_name: Sourisseau
- first_name: J
full_name: Assis, J
last_name: Assis
- first_name: L
full_name: Lévêque, L
last_name: Lévêque
- first_name: M
full_name: Valero, M
last_name: Valero
citation:
ama: Fouqueau L, Reynes L, Tempera F, et al. Seascape genetic study on Laminaria
digitata underscores the critical role of sampling schemes. Marine Ecology
Progress Series. 2024;740:23-42. doi:10.3354/meps14640
apa: Fouqueau, L., Reynes, L., Tempera, F., Bajjouk, T., Blanfuné, A., Chevalier,
C., … Valero, M. (2024). Seascape genetic study on Laminaria digitata underscores
the critical role of sampling schemes. Marine Ecology Progress Series.
Inter-Research Science Center. https://doi.org/10.3354/meps14640
chicago: Fouqueau, Louise, L Reynes, F Tempera, T Bajjouk, A Blanfuné, C Chevalier,
M Laurans, et al. “Seascape Genetic Study on Laminaria Digitata Underscores the
Critical Role of Sampling Schemes.” Marine Ecology Progress Series. Inter-Research
Science Center, 2024. https://doi.org/10.3354/meps14640.
ieee: L. Fouqueau et al., “Seascape genetic study on Laminaria digitata underscores
the critical role of sampling schemes,” Marine Ecology Progress Series,
vol. 740. Inter-Research Science Center, pp. 23–42, 2024.
ista: Fouqueau L, Reynes L, Tempera F, Bajjouk T, Blanfuné A, Chevalier C, Laurans
M, Mauger S, Sourisseau M, Assis J, Lévêque L, Valero M. 2024. Seascape genetic
study on Laminaria digitata underscores the critical role of sampling schemes.
Marine Ecology Progress Series. 740, 23–42.
mla: Fouqueau, Louise, et al. “Seascape Genetic Study on Laminaria Digitata Underscores
the Critical Role of Sampling Schemes.” Marine Ecology Progress Series,
vol. 740, Inter-Research Science Center, 2024, pp. 23–42, doi:10.3354/meps14640.
short: L. Fouqueau, L. Reynes, F. Tempera, T. Bajjouk, A. Blanfuné, C. Chevalier,
M. Laurans, S. Mauger, M. Sourisseau, J. Assis, L. Lévêque, M. Valero, Marine
Ecology Progress Series 740 (2024) 23–42.
corr_author: '1'
date_created: 2025-01-29T09:09:10Z
date_published: 2024-07-25T00:00:00Z
date_updated: 2025-01-29T09:12:34Z
day: '25'
department:
- _id: NiBa
doi: 10.3354/meps14640
intvolume: ' 740'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://inria.hal.science/hal-04624490/
month: '07'
oa: 1
oa_version: Submitted Version
page: 23-42
publication: Marine Ecology Progress Series
publication_identifier:
eissn:
- 1616-1599
issn:
- 0171-8630
publication_status: published
publisher: Inter-Research Science Center
quality_controlled: '1'
scopus_import: '1'
status: public
title: Seascape genetic study on Laminaria digitata underscores the critical role
of sampling schemes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 740
year: '2024'
...
---
OA_type: closed access
_id: '18945'
abstract:
- lang: eng
text: Vaccinia-related kinase 1 (VRK1) and the δ and ε isoforms of casein kinase
1 (CK1) are linked to various disease-relevant pathways. However, the lack of
tool compounds for these kinases has significantly hampered our understanding
of their cellular functions and therapeutic potential. Here, we describe the structure-based
development of potent inhibitors of VRK1, a kinase highly expressed in various
tumor types and crucial for cell proliferation and genome integrity. Kinome-wide
profiling revealed that our compounds also inhibit CK1δ and CK1ε. We demonstrate
that dihydropteridinones 35 and 36 mimic the cellular outcomes of VRK1 depletion.
Complementary studies with existing CK1δ and CK1ε inhibitors suggest that these
kinases may play overlapping roles in cell proliferation and genome instability.
Together, our findings highlight the potential of VRK1 inhibition in treating
p53-deficient tumors and possibly enhancing the efficacy of existing cancer therapies
that target DNA stability or cell division.
acknowledgement: "R.M.C. and K.B.M. are grateful for support by FAPESP (Fundação de
Amparo à Pesquisa do Estado de São Paulo) (grants 2013/50724–5 and 2014/50897–0),
Embrapii (Empresa Brasileira de Pesquisa e Inovação Industrial), CNPq (Conselho
Nacional de Desenvolvimento Científico e Tecnológico) (grant 465651/2014–3) and
Aché Laboratórios Farmacêuticos. R.M.C. and O.G. are also grateful for support by
the Structural Genomics Consortium, a registered charity (1097737) that receives
funds from AbbVie, Bayer AG, Boehringer Ingelheim, Canada Foundation for Innovation,
Eshelman Institute for Innovation, Genentech, Genome Canada through the Ontario
Genomics Institute (OGI-196), EU/EFPIA/OICR/McGill/KTH/Diamond, Innovative Medicines
Initiative 2 Joint Undertaking (EUbOPEN Grant 875510), Janssen, Merck KGaA, Merck
& Co., Pfizer, Takeda, and Wellcome. B.L. and M.H. are grateful for support from
the Swedish Research Council, Swedish Cancer Society, Karolinska Institutet and
The Mark Foundation for Cancer Research. R.A.M.S. (2016/25320–6 and 2018/23322–7),
A.S.S. (2019/14275–8), S.N.S.V (2018/09475–5), V.M.A. (2022/00743–2) and M.R.C.
(2021/04853–4) were recipients of fellowships from the Fundação de Amparo à Pesquisa
do Estado de São Paulo, FAPESP. C.V.R. (88887.146077/2017–00), J.E.T. (88887.373547/2019–00)
and P.Z.R (88887.136432/2017–00) were the recipient of fellowships from the Coordenação
de Aperfeiçoamento de Pessoal de Nível Superior, CAPES.\r\nWe thank all members
of CQMED-UNICAMP for their help and support. We thank the staff of the Life Sciences
Core Facility (LaCTAD) at UNICAMP for the Genomics and Mass Spectrometry analysis.
We thank the NMR facility at UNICAMP Chemistry Institute for its assistance. We
thank the staff at the Northeastern Collaborative Access Team beamlines, which are
funded by the National Institute of General Medical Sciences from the National Institutes
of Health (P41 GM103403). The Pilatus 6M detector on the 24-ID-C beamline is funded
by a NIH-ORIP HEI grant (S10 RR029205). This research used resources of the Advanced
Photon Source; a U.S. Department of Energy (DOE) Office of Science User Facility
operated for the DOE Office of Science by Argonne National Laboratory under Contract
No. DE-AC02-06CH11357. We thank Diamond Light Source for access to beamline I24.
The authors thank Tammy Havener (SGC-UNC), Abid Hussain Sayyid (KI), and Yiqiu Yang
(KI) for valuable discussions and technical support."
article_processing_charge: No
article_type: original
author:
- first_name: Fernando H.
full_name: de Souza Gama, Fernando H.
last_name: de Souza Gama
- first_name: Luiz A.
full_name: Dutra, Luiz A.
last_name: Dutra
- first_name: Michael
full_name: Hawgood, Michael
last_name: Hawgood
- first_name: Caio Vinícius
full_name: dos Reis, Caio Vinícius
last_name: dos Reis
- first_name: Ricardo A. M.
full_name: Serafim, Ricardo A. M.
last_name: Serafim
- first_name: Marcos A.
full_name: Ferreira, Marcos A.
last_name: Ferreira
- first_name: Bruno V. M.
full_name: Teodoro, Bruno V. M.
last_name: Teodoro
- first_name: Jéssica Emi
full_name: Takarada, Jéssica Emi
last_name: Takarada
- first_name: André S.
full_name: Santiago, André S.
last_name: Santiago
- first_name: Dimitrios-Ilias
full_name: Balourdas, Dimitrios-Ilias
last_name: Balourdas
- first_name: Ann-Sofie
full_name: Nilsson, Ann-Sofie
last_name: Nilsson
- first_name: Bruno
full_name: Urien, Bruno
last_name: Urien
- first_name: Vitor M.
full_name: Almeida, Vitor M.
last_name: Almeida
- first_name: Carina
full_name: Gileadi, Carina
last_name: Gileadi
- first_name: Priscila Z.
full_name: Ramos, Priscila Z.
last_name: Ramos
- first_name: Anita P
full_name: Testa Salmazo, Anita P
id: 41F1F098-F248-11E8-B48F-1D18A9856A87
last_name: Testa Salmazo
- first_name: Stanley N. S.
full_name: Vasconcelos, Stanley N. S.
last_name: Vasconcelos
- first_name: Micael R.
full_name: Cunha, Micael R.
last_name: Cunha
- first_name: Susanne
full_name: Mueller, Susanne
last_name: Mueller
- first_name: Stefan
full_name: Knapp, Stefan
last_name: Knapp
- first_name: Katlin B.
full_name: Massirer, Katlin B.
last_name: Massirer
- first_name: Jonathan M.
full_name: Elkins, Jonathan M.
last_name: Elkins
- first_name: Opher
full_name: Gileadi, Opher
last_name: Gileadi
- first_name: Alessandra
full_name: Mascarello, Alessandra
last_name: Mascarello
- first_name: Bennie B. L. G.
full_name: Lemmens, Bennie B. L. G.
last_name: Lemmens
- first_name: Cristiano R. W.
full_name: Guimarães, Cristiano R. W.
last_name: Guimarães
- first_name: Hatylas
full_name: Azevedo, Hatylas
last_name: Azevedo
- first_name: Rafael M.
full_name: Couñago, Rafael M.
last_name: Couñago
citation:
ama: de Souza Gama FH, Dutra LA, Hawgood M, et al. Novel dihydropteridinone derivatives
as potent inhibitors of the understudied human kinases vaccinia-related kinase
1 and casein kinase 1δ/ε. Journal of Medicinal Chemistry. 2024;67(11):8609-8629.
doi:10.1021/acs.jmedchem.3c02250
apa: de Souza Gama, F. H., Dutra, L. A., Hawgood, M., dos Reis, C. V., Serafim,
R. A. M., Ferreira, M. A., … Couñago, R. M. (2024). Novel dihydropteridinone derivatives
as potent inhibitors of the understudied human kinases vaccinia-related kinase
1 and casein kinase 1δ/ε. Journal of Medicinal Chemistry. American Chemical
Society. https://doi.org/10.1021/acs.jmedchem.3c02250
chicago: Souza Gama, Fernando H. de, Luiz A. Dutra, Michael Hawgood, Caio Vinícius
dos Reis, Ricardo A. M. Serafim, Marcos A. Ferreira, Bruno V. M. Teodoro, et al.
“Novel Dihydropteridinone Derivatives as Potent Inhibitors of the Understudied
Human Kinases Vaccinia-Related Kinase 1 and Casein Kinase 1δ/ε.” Journal of
Medicinal Chemistry. American Chemical Society, 2024. https://doi.org/10.1021/acs.jmedchem.3c02250.
ieee: F. H. de Souza Gama et al., “Novel dihydropteridinone derivatives as
potent inhibitors of the understudied human kinases vaccinia-related kinase 1
and casein kinase 1δ/ε,” Journal of Medicinal Chemistry, vol. 67, no. 11.
American Chemical Society, pp. 8609–8629, 2024.
ista: de Souza Gama FH, Dutra LA, Hawgood M, dos Reis CV, Serafim RAM, Ferreira
MA, Teodoro BVM, Takarada JE, Santiago AS, Balourdas D-I, Nilsson A-S, Urien B,
Almeida VM, Gileadi C, Ramos PZ, Testa Salmazo AP, Vasconcelos SNS, Cunha MR,
Mueller S, Knapp S, Massirer KB, Elkins JM, Gileadi O, Mascarello A, Lemmens BBLG,
Guimarães CRW, Azevedo H, Couñago RM. 2024. Novel dihydropteridinone derivatives
as potent inhibitors of the understudied human kinases vaccinia-related kinase
1 and casein kinase 1δ/ε. Journal of Medicinal Chemistry. 67(11), 8609–8629.
mla: de Souza Gama, Fernando H., et al. “Novel Dihydropteridinone Derivatives as
Potent Inhibitors of the Understudied Human Kinases Vaccinia-Related Kinase 1
and Casein Kinase 1δ/ε.” Journal of Medicinal Chemistry, vol. 67, no. 11,
American Chemical Society, 2024, pp. 8609–29, doi:10.1021/acs.jmedchem.3c02250.
short: F.H. de Souza Gama, L.A. Dutra, M. Hawgood, C.V. dos Reis, R.A.M. Serafim,
M.A. Ferreira, B.V.M. Teodoro, J.E. Takarada, A.S. Santiago, D.-I. Balourdas,
A.-S. Nilsson, B. Urien, V.M. Almeida, C. Gileadi, P.Z. Ramos, A.P. Testa Salmazo,
S.N.S. Vasconcelos, M.R. Cunha, S. Mueller, S. Knapp, K.B. Massirer, J.M. Elkins,
O. Gileadi, A. Mascarello, B.B.L.G. Lemmens, C.R.W. Guimarães, H. Azevedo, R.M.
Couñago, Journal of Medicinal Chemistry 67 (2024) 8609–8629.
date_created: 2025-01-29T09:14:19Z
date_published: 2024-05-23T00:00:00Z
date_updated: 2025-01-29T09:19:15Z
day: '23'
department:
- _id: CaBe
doi: 10.1021/acs.jmedchem.3c02250
external_id:
pmid:
- '38780468'
intvolume: ' 67'
issue: '11'
language:
- iso: eng
month: '05'
oa_version: None
page: 8609-8629
pmid: 1
publication: Journal of Medicinal Chemistry
publication_identifier:
eissn:
- 1520-4804
issn:
- 0022-2623
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Novel dihydropteridinone derivatives as potent inhibitors of the understudied
human kinases vaccinia-related kinase 1 and casein kinase 1δ/ε
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 67
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '18948'
abstract:
- lang: eng
text: We consider a gas of N bosons with interactions in the mean-field scaling
regime. We review a recent proof of the asymptotic expansion of its spectrum and
eigenstates and two applications of this result, namely the derivation of an Edgeworth
expansion for fluctuations of one-body operators and the computation of the binding
energy of an inhomogeneous Bose gas to any order. Finally, we collect related
results for the dynamics of the weakly interacting Bose gas and for the regularized
Nelson model.
acknowledgement: It is our pleasure to thank Marco Falconi, Nataša Pavlović, Peter
Pickl, Robert Seiringer and Avy Soffer for the collaboration on the works [11, 13,
14, 21, 33, 39]. L.B. was supported by the German Research Foundation within the
Munich Center of Quantum Science and Technology (EXC 2111). N.L. acknowledges support
from the Swiss National Science Foundation through the NCCR SwissMap and funding
from the European Union’s Horizon 2020 research and innovation programme under the
Marie Skłodowska-Curie grant agreement No 101024712. S.P. acknowledges funding by
the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - project
number 512258249.
alternative_title:
- Fundamental Theories of Physics
article_processing_charge: No
arxiv: 1
author:
- first_name: Lea
full_name: Bossmann, Lea
id: A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425
last_name: Bossmann
orcid: 0000-0002-6854-1343
- first_name: Nikolai
full_name: Leopold, Nikolai
last_name: Leopold
- first_name: David Johannes
full_name: Mitrouskas, David Johannes
id: cbddacee-2b11-11eb-a02e-a2e14d04e52d
last_name: Mitrouskas
- first_name: Sören
full_name: Petrat, Sören
last_name: Petrat
citation:
ama: 'Bossmann L, Leopold N, Mitrouskas DJ, Petrat S. Asymptotic Analysis of the Weakly
Interacting Bose Gas: A Collection of Recent Results and Applications. In: Bassi
A, Goldstein S, Tumulka R, Zanghi N, eds. Physics and the Nature of Reality.
Vol 215. FTPH. Cham: Springer Nature; 2024:307-321. doi:10.1007/978-3-031-45434-9_22'
apa: 'Bossmann, L., Leopold, N., Mitrouskas, D. J., & Petrat, S. (2024). Asymptotic
Analysis of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications.
In A. Bassi, S. Goldstein, R. Tumulka, & N. Zanghi (Eds.), Physics and
the Nature of Reality (Vol. 215, pp. 307–321). Cham: Springer Nature. https://doi.org/10.1007/978-3-031-45434-9_22'
chicago: 'Bossmann, Lea, Nikolai Leopold, David Johannes Mitrouskas, and Sören Petrat.
“Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent
Results and Applications.” In Physics and the Nature of Reality, edited
by Angelo Bassi, Sheldon Goldstein, Roderich Tumulka, and Nino Zanghi, 215:307–21.
FTPH. Cham: Springer Nature, 2024. https://doi.org/10.1007/978-3-031-45434-9_22.'
ieee: 'L. Bossmann, N. Leopold, D. J. Mitrouskas, and S. Petrat, “Asymptotic Analysis
of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications,”
in Physics and the Nature of Reality, vol. 215, A. Bassi, S. Goldstein,
R. Tumulka, and N. Zanghi, Eds. Cham: Springer Nature, 2024, pp. 307–321.'
ista: 'Bossmann L, Leopold N, Mitrouskas DJ, Petrat S. 2024.Asymptotic Analysis
of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications.
In: Physics and the Nature of Reality. Fundamental Theories of Physics, vol. 215,
307–321.'
mla: 'Bossmann, Lea, et al. “Asymptotic Analysis of the Weakly Interacting Bose
Gas: A Collection of Recent Results and Applications.” Physics and the Nature
of Reality, edited by Angelo Bassi et al., vol. 215, Springer Nature, 2024,
pp. 307–21, doi:10.1007/978-3-031-45434-9_22.'
short: L. Bossmann, N. Leopold, D.J. Mitrouskas, S. Petrat, in:, A. Bassi, S. Goldstein,
R. Tumulka, N. Zanghi (Eds.), Physics and the Nature of Reality, Springer Nature,
Cham, 2024, pp. 307–321.
date_created: 2025-01-29T10:30:08Z
date_published: 2024-02-04T00:00:00Z
date_updated: 2025-01-29T10:35:10Z
day: '04'
department:
- _id: RoSe
doi: 10.1007/978-3-031-45434-9_22
editor:
- first_name: Angelo
full_name: Bassi, Angelo
last_name: Bassi
- first_name: Sheldon
full_name: Goldstein, Sheldon
last_name: Goldstein
- first_name: Roderich
full_name: Tumulka, Roderich
last_name: Tumulka
- first_name: Nino
full_name: Zanghi, Nino
last_name: Zanghi
external_id:
arxiv:
- '2304.12910'
intvolume: ' 215'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2304.12910
month: '02'
oa: 1
oa_version: Preprint
page: 307-321
place: Cham
publication: Physics and the Nature of Reality
publication_identifier:
eisbn:
- '9783031454349'
eissn:
- 2365-6425
isbn:
- '9783031454332'
issn:
- 0168-1222
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: FTPH
status: public
title: 'Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent
Results and Applications'
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 215
year: '2024'
...
---
OA_place: publisher
OA_type: gold
_id: '18949'
abstract:
- lang: eng
text: 'Speciation research—the scientific field focused on understanding the origin
and diversity of species—has a long and complex history. While relevant to one
another, the specific goals and activities of speciation researchers are highly
diverse, and scattered across a collection of different perspectives. Thus, our
understanding of speciation will benefit from efforts to bridge scientific findings
and the diverse people who do the work. In this paper, we outline two ways of
integrating speciation research: (i) scientific integration, through the bringing
together of ideas, data, and approaches; and (ii) social integration, by creating
ways for a diversity of researchers to participate in the scientific process.
We then discuss five challenges to integration: (i) the multidisciplinary nature
of speciation research, (ii) the complex language of speciation; (iii) a bias
toward certain study systems; (iv) the challenges of working across scales; and
(v) inconsistent measures and reporting standards. We provide practical steps
that individuals and groups can take to help overcome these challenges, and argue
that integration is a team effort in which we all have a role to play.'
acknowledgement: "We thank the staff of the Tvärminne Zoological Station (University
of Helsinki) for their hospitality during the workshop. We are also grateful to
everyone who applied to attend the workshop.\r\nFunding for the workshop was provided
by the European Society for Evolutionary Biology through the Special Topic Network
(STN) funding scheme."
article_number: kzae001
article_processing_charge: Yes
article_type: original
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Asher D
full_name: Cutter, Asher D
last_name: Cutter
- first_name: Ina
full_name: Satokangas, Ina
last_name: Satokangas
- first_name: Brian A
full_name: Lerch, Brian A
last_name: Lerch
- first_name: Jonathan
full_name: Rolland, Jonathan
last_name: Rolland
- first_name: Carole M
full_name: Smadja, Carole M
last_name: Smadja
- first_name: J Carolina
full_name: Segami Marzal, J Carolina
last_name: Segami Marzal
- first_name: Christopher R
full_name: Cooney, Christopher R
last_name: Cooney
- first_name: Philine G D
full_name: Feulner, Philine G D
last_name: Feulner
- first_name: Fabricius Maia Chaves Bicalho
full_name: Domingos, Fabricius Maia Chaves Bicalho
last_name: Domingos
- first_name: Henry L
full_name: North, Henry L
last_name: North
- first_name: Ryo
full_name: Yamaguchi, Ryo
last_name: Yamaguchi
- first_name: Roger K
full_name: Butlin, Roger K
last_name: Butlin
- first_name: Jochen B W
full_name: Wolf, Jochen B W
last_name: Wolf
- first_name: Jenn
full_name: Coughlan, Jenn
last_name: Coughlan
- first_name: Patrick
full_name: Heidbreder, Patrick
last_name: Heidbreder
- first_name: Rebeca
full_name: Hernández-Gutiérrez, Rebeca
last_name: Hernández-Gutiérrez
- first_name: Karen B
full_name: Barnard-Kubow, Karen B
last_name: Barnard-Kubow
- first_name: David
full_name: Peede, David
last_name: Peede
- first_name: Loïs
full_name: Rancilhac, Loïs
last_name: Rancilhac
- first_name: Rodrigo Brincalepe
full_name: Salvador, Rodrigo Brincalepe
last_name: Salvador
- first_name: Ken A
full_name: Thompson, Ken A
last_name: Thompson
- first_name: Elizabeth A
full_name: Stacy, Elizabeth A
last_name: Stacy
- first_name: Leonie C
full_name: Moyle, Leonie C
last_name: Moyle
- first_name: Martin D
full_name: Garlovsky, Martin D
last_name: Garlovsky
- first_name: Arif
full_name: Maulana, Arif
last_name: Maulana
- first_name: Annina
full_name: Kantelinen, Annina
last_name: Kantelinen
- first_name: N Ivalú
full_name: Cacho, N Ivalú
last_name: Cacho
- first_name: Hilde
full_name: Schneemann, Hilde
last_name: Schneemann
- first_name: Marisol
full_name: Domínguez, Marisol
last_name: Domínguez
- first_name: Erik B
full_name: Dopman, Erik B
last_name: Dopman
- first_name: Konrad
full_name: Lohse, Konrad
last_name: Lohse
- first_name: Sina J
full_name: Rometsch, Sina J
last_name: Rometsch
- first_name: Aaron A
full_name: Comeault, Aaron A
last_name: Comeault
- first_name: Richard M
full_name: Merrill, Richard M
last_name: Merrill
- first_name: Elizabeth S C
full_name: Scordato, Elizabeth S C
last_name: Scordato
- first_name: Sonal
full_name: Singhal, Sonal
last_name: Singhal
- first_name: Varpu
full_name: Pärssinen, Varpu
last_name: Pärssinen
- first_name: Alycia C R
full_name: Lackey, Alycia C R
last_name: Lackey
- first_name: Sanghamitra
full_name: Kumar, Sanghamitra
last_name: Kumar
- first_name: Joana I
full_name: Meier, Joana I
last_name: Meier
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Mark
full_name: Ravinet, Mark
last_name: Ravinet
- first_name: Jonna
full_name: Kulmuni, Jonna
last_name: Kulmuni
citation:
ama: Stankowski S, Cutter AD, Satokangas I, et al. Toward the integration of speciation
research. Evolutionary Journal of the Linnean Society. 2024;3(1). doi:10.1093/evolinnean/kzae001
apa: Stankowski, S., Cutter, A. D., Satokangas, I., Lerch, B. A., Rolland, J., Smadja,
C. M., … Kulmuni, J. (2024). Toward the integration of speciation research. Evolutionary
Journal of the Linnean Society. Oxford University Press. https://doi.org/10.1093/evolinnean/kzae001
chicago: Stankowski, Sean, Asher D Cutter, Ina Satokangas, Brian A Lerch, Jonathan
Rolland, Carole M Smadja, J Carolina Segami Marzal, et al. “Toward the Integration
of Speciation Research.” Evolutionary Journal of the Linnean Society. Oxford
University Press, 2024. https://doi.org/10.1093/evolinnean/kzae001.
ieee: S. Stankowski et al., “Toward the integration of speciation research,”
Evolutionary Journal of the Linnean Society, vol. 3, no. 1. Oxford University
Press, 2024.
ista: Stankowski S, Cutter AD, Satokangas I, Lerch BA, Rolland J, Smadja CM, Segami
Marzal JC, Cooney CR, Feulner PGD, Domingos FMCB, North HL, Yamaguchi R, Butlin
RK, Wolf JBW, Coughlan J, Heidbreder P, Hernández-Gutiérrez R, Barnard-Kubow KB,
Peede D, Rancilhac L, Salvador RB, Thompson KA, Stacy EA, Moyle LC, Garlovsky
MD, Maulana A, Kantelinen A, Cacho NI, Schneemann H, Domínguez M, Dopman EB, Lohse
K, Rometsch SJ, Comeault AA, Merrill RM, Scordato ESC, Singhal S, Pärssinen V,
Lackey ACR, Kumar S, Meier JI, Barton NH, Fraisse C, Ravinet M, Kulmuni J. 2024.
Toward the integration of speciation research. Evolutionary Journal of the Linnean
Society. 3(1), kzae001.
mla: Stankowski, Sean, et al. “Toward the Integration of Speciation Research.” Evolutionary
Journal of the Linnean Society, vol. 3, no. 1, kzae001, Oxford University
Press, 2024, doi:10.1093/evolinnean/kzae001.
short: S. Stankowski, A.D. Cutter, I. Satokangas, B.A. Lerch, J. Rolland, C.M. Smadja,
J.C. Segami Marzal, C.R. Cooney, P.G.D. Feulner, F.M.C.B. Domingos, H.L. North,
R. Yamaguchi, R.K. Butlin, J.B.W. Wolf, J. Coughlan, P. Heidbreder, R. Hernández-Gutiérrez,
K.B. Barnard-Kubow, D. Peede, L. Rancilhac, R.B. Salvador, K.A. Thompson, E.A.
Stacy, L.C. Moyle, M.D. Garlovsky, A. Maulana, A. Kantelinen, N.I. Cacho, H. Schneemann,
M. Domínguez, E.B. Dopman, K. Lohse, S.J. Rometsch, A.A. Comeault, R.M. Merrill,
E.S.C. Scordato, S. Singhal, V. Pärssinen, A.C.R. Lackey, S. Kumar, J.I. Meier,
N.H. Barton, C. Fraisse, M. Ravinet, J. Kulmuni, Evolutionary Journal of the Linnean
Society 3 (2024).
corr_author: '1'
date_created: 2025-01-29T10:38:17Z
date_published: 2024-02-16T00:00:00Z
date_updated: 2025-01-29T10:55:54Z
day: '16'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/evolinnean/kzae001
file:
- access_level: open_access
checksum: db08120a92527acaef476bd93f2b87f9
content_type: application/pdf
creator: dernst
date_created: 2025-01-29T10:52:40Z
date_updated: 2025-01-29T10:52:40Z
file_id: '18950'
file_name: 2024_EvolJourLinneanSoc_Stankowski.pdf
file_size: 3935454
relation: main_file
success: 1
file_date_updated: 2025-01-29T10:52:40Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '02'
oa: 1
oa_version: Published Version
publication: Evolutionary Journal of the Linnean Society
publication_identifier:
issn:
- 2752-938X
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Toward the integration of speciation research
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: repository
OA_type: gold
_id: '18951'
abstract:
- lang: eng
text: "We consider local dynamics of the dimer model (perfect matchings) on hypercubic
boxes [n] \r\nd . These consist of successively switching the dimers along alternating
cycles of prescribed (small) lengths. We study the connectivity properties of
the dimer configuration space equipped with these transitions. Answering a question
of Freire, Klivans, Milet, and Saldanha, we show that in three dimensions any
configuration admits an alternating cycle of length at most 6. We further establish
that any configuration on [n] d features order n d−2 alternating cycles of length
at most 4d−2. We also prove that the dynamics of dimer configurations on the unit
hypercube of dimension d is ergodic when switching alternating cycles of length
at most 4d−4. Finally, in the planar but non-bipartite case, we show that parallelogram-shaped
boxes in the triangular lattice are ergodic for switching alternating cycles of
lengths 4 and 6 only, thus improving a result of Kenyon and Rémila, which also
uses 8-cycles. None of our proofs make reference to height functions."
article_processing_charge: Yes
article_type: original
arxiv: 1
author:
- first_name: Ivailo
full_name: Hartarsky, Ivailo
last_name: Hartarsky
- first_name: Lyuben
full_name: Lichev, Lyuben
id: 9aa8388e-d003-11ee-8458-c4c1d7447977
last_name: Lichev
- first_name: Fabio Lucio
full_name: Toninelli, Fabio Lucio
last_name: Toninelli
citation:
ama: Hartarsky I, Lichev L, Toninelli FL. Local dimer dynamics in higher dimensions.
Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and their Interactions.
2024. doi:10.4171/aihpd/200
apa: Hartarsky, I., Lichev, L., & Toninelli, F. L. (2024). Local dimer dynamics
in higher dimensions. Annales de l’Institut Henri Poincaré D, Combinatorics,
Physics and Their Interactions. EMS Press. https://doi.org/10.4171/aihpd/200
chicago: Hartarsky, Ivailo, Lyuben Lichev, and Fabio Lucio Toninelli. “Local Dimer
Dynamics in Higher Dimensions.” Annales de l’Institut Henri Poincaré D, Combinatorics,
Physics and Their Interactions. EMS Press, 2024. https://doi.org/10.4171/aihpd/200.
ieee: I. Hartarsky, L. Lichev, and F. L. Toninelli, “Local dimer dynamics in higher
dimensions,” Annales de l’Institut Henri Poincaré D, Combinatorics, Physics
and their Interactions. EMS Press, 2024.
ista: Hartarsky I, Lichev L, Toninelli FL. 2024. Local dimer dynamics in higher
dimensions. Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and
their Interactions.
mla: Hartarsky, Ivailo, et al. “Local Dimer Dynamics in Higher Dimensions.” Annales
de l’Institut Henri Poincaré D, Combinatorics, Physics and Their Interactions,
EMS Press, 2024, doi:10.4171/aihpd/200.
short: I. Hartarsky, L. Lichev, F.L. Toninelli, Annales de l’Institut Henri Poincaré
D, Combinatorics, Physics and Their Interactions (2024).
date_created: 2025-01-29T10:57:09Z
date_published: 2024-08-26T00:00:00Z
date_updated: 2025-07-08T08:39:55Z
day: '26'
department:
- _id: MaKw
doi: 10.4171/aihpd/200
external_id:
arxiv:
- '2304.10930'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2304.10930
month: '08'
oa: 1
oa_version: Preprint
publication: Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and their
Interactions
publication_identifier:
eissn:
- 2308-5835
issn:
- 2308-5827
publication_status: epub_ahead
publisher: EMS Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Local dimer dynamics in higher dimensions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18952'
abstract:
- lang: eng
text: 'A seventh blind test of crystal structure prediction was organized by the
Cambridge Crystallographic Data Centre featuring seven target systems of varying
complexity: a silicon and iodine-containing molecule, a copper coordination complex,
a near-rigid molecule, a cocrystal, a polymorphic small agrochemical, a highly
flexible polymorphic drug candidate, and a polymorphic morpholine salt. In this
first of two parts focusing on structure generation methods, many crystal structure
prediction (CSP) methods performed well for the small but flexible agrochemical
compound, successfully reproducing the experimentally observed crystal structures,
while few groups were successful for the systems of higher complexity. A powder
X-ray diffraction (PXRD) assisted exercise demonstrated the use of CSP in successfully
determining a crystal structure from a low-quality PXRD pattern. The use of CSP
in the prediction of likely cocrystal stoichiometry was also explored, demonstrating
multiple possible approaches. Crystallographic disorder emerged as an important
theme throughout the test as both a challenge for analysis and a major achievement
where two groups blindly predicted the existence of disorder for the first time.
Additionally, large-scale comparisons of the sets of predicted crystal structures
also showed that some methods yield sets that largely contain the same crystal
structures.'
acknowledgement: "The CCDC Blind Test Team. The CCDC organizers (L. M. Hunnisett,
J. Nyman, N. Francia, I. Sugden, G. Sadiq, and J. C. Cole) gratefully acknowledge
numerous CCDC colleagues for\r\ntheir helpful feedback and suggestions on the manuscript
(P. McCabe, E. Pidcock, P. Martinez-Bulit, C. Kingsbury), providing useful python
knowledge (A. Moldovan), providing and maintaining internal compute resources (K.
Taylor, M. Burling, J. Swift, L. Wallis), monitoring and depositing structures in
the CSD (S. Ward, K. Orzechowska, V. Menon), support in organization of the blind
test meeting (E. Clarke),and improvements to the Crystal Packing Similarity tool
(M.\r\nRead). Data analysis was performed using resources provided by the Cambridge
Service for Data Driven Discovery (CSD3) operated by the University of Cambridge
Research Computing Service (www.csd3.cam.ac.uk), provided by Dell EMC and Intel
using Tier-2 funding from the Engineering and Physical Sciences Research Council
(capital grant EP/T022159/1), and DiRAC funding from the Science and Technology
Facilities Council (www.dirac.ac.uk). N. Francia thanks M. Salvalaglio for advice
on the metadynamics simulations and the University College London for providing
access to the Kathleen High Performance Computing Facility Kathleen@UCL) on which
simulations were performed. N. Francia also thanks V. Kurlin and D. E. Widdowson
for counselling on crystal structure similarity. I. Sugden and N. Francia participated
in the blind test as members of Groups 1 and 24, respectively. They were involved
in the analysis of the results.\r\nand in writing this paper only after all results
were made\r\navailable to participants."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Lily M.
full_name: Hunnisett, Lily M.
last_name: Hunnisett
- first_name: Jonas
full_name: Nyman, Jonas
last_name: Nyman
- first_name: Nicholas
full_name: Francia, Nicholas
last_name: Francia
- first_name: Nathan S.
full_name: Abraham, Nathan S.
last_name: Abraham
- first_name: Claire S.
full_name: Adjiman, Claire S.
last_name: Adjiman
- first_name: Srinivasulu
full_name: Aitipamula, Srinivasulu
last_name: Aitipamula
- first_name: Tamador
full_name: Alkhidir, Tamador
last_name: Alkhidir
- first_name: Mubarak
full_name: Almehairbi, Mubarak
last_name: Almehairbi
- first_name: Andrea
full_name: Anelli, Andrea
last_name: Anelli
- first_name: Dylan M.
full_name: Anstine, Dylan M.
last_name: Anstine
- first_name: John E.
full_name: Anthony, John E.
last_name: Anthony
- first_name: Joseph E.
full_name: Arnold, Joseph E.
last_name: Arnold
- first_name: Faezeh
full_name: Bahrami, Faezeh
last_name: Bahrami
- first_name: Michael A.
full_name: Bellucci, Michael A.
last_name: Bellucci
- first_name: Rajni M.
full_name: Bhardwaj, Rajni M.
last_name: Bhardwaj
- first_name: Imanuel
full_name: Bier, Imanuel
last_name: Bier
- first_name: Joanna A.
full_name: Bis, Joanna A.
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- first_name: A. Daniel
full_name: Boese, A. Daniel
last_name: Boese
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- first_name: Jan Gerit
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full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Sarah M.
full_name: Clarke, Sarah M.
last_name: Clarke
- first_name: Simon J.
full_name: Coles, Simon J.
last_name: Coles
- first_name: Richard I.
full_name: Cooper, Richard I.
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last_name: Sun
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full_name: Szalewicz, Krzysztof
last_name: Szalewicz
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full_name: Tan, Benjamin I.
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full_name: Tan, Lu
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last_name: Tarczynski
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full_name: Taylor, Christopher R.
last_name: Taylor
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full_name: Tuckerman, Mark E.
last_name: Tuckerman
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last_name: Utsumi
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last_name: Vogt-Maranto
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full_name: Woollam, Grahame R.
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last_name: Cole
citation:
ama: 'Hunnisett LM, Nyman J, Francia N, et al. The seventh blind test of crystal
structure prediction: Structure generation methods. Acta Crystallographica
Section B Structural Science, Crystal Engineering and Materials. 2024;80(6):517-547.
doi:10.1107/s2052520624007492'
apa: 'Hunnisett, L. M., Nyman, J., Francia, N., Abraham, N. S., Adjiman, C. S.,
Aitipamula, S., … Cole, J. C. (2024). The seventh blind test of crystal structure
prediction: Structure generation methods. Acta Crystallographica Section B
Structural Science, Crystal Engineering and Materials. International Union
of Crystallography. https://doi.org/10.1107/s2052520624007492'
chicago: 'Hunnisett, Lily M., Jonas Nyman, Nicholas Francia, Nathan S. Abraham,
Claire S. Adjiman, Srinivasulu Aitipamula, Tamador Alkhidir, et al. “The Seventh
Blind Test of Crystal Structure Prediction: Structure Generation Methods.” Acta
Crystallographica Section B Structural Science, Crystal Engineering and Materials.
International Union of Crystallography, 2024. https://doi.org/10.1107/s2052520624007492.'
ieee: 'L. M. Hunnisett et al., “The seventh blind test of crystal structure
prediction: Structure generation methods,” Acta Crystallographica Section B
Structural Science, Crystal Engineering and Materials, vol. 80, no. 6. International
Union of Crystallography, pp. 517–547, 2024.'
ista: 'Hunnisett LM et al. 2024. The seventh blind test of crystal structure prediction:
Structure generation methods. Acta Crystallographica Section B Structural Science,
Crystal Engineering and Materials. 80(6), 517–547.'
mla: 'Hunnisett, Lily M., et al. “The Seventh Blind Test of Crystal Structure Prediction:
Structure Generation Methods.” Acta Crystallographica Section B Structural
Science, Crystal Engineering and Materials, vol. 80, no. 6, International
Union of Crystallography, 2024, pp. 517–47, doi:10.1107/s2052520624007492.'
short: L.M. Hunnisett, J. Nyman, N. Francia, N.S. Abraham, C.S. Adjiman, S. Aitipamula,
T. Alkhidir, M. Almehairbi, A. Anelli, D.M. Anstine, J.E. Anthony, J.E. Arnold,
F. Bahrami, M.A. Bellucci, R.M. Bhardwaj, I. Bier, J.A. Bis, A.D. Boese, D.H.
Bowskill, J. Bramley, J.G. Brandenburg, D.E. Braun, P.W.V. Butler, J. Cadden,
S. Carino, E.J. Chan, C. Chang, B. Cheng, S.M. Clarke, S.J. Coles, R.I. Cooper,
R. Couch, R. Cuadrado, T. Darden, G.M. Day, H. Dietrich, Y. Ding, A. DiPasquale,
B. Dhokale, B.P. van Eijck, M.R.J. Elsegood, D. Firaha, W. Fu, K. Fukuzawa, J.
Glover, H. Goto, C. Greenwell, R. Guo, J. Harter, J. Helfferich, D.W.M. Hofmann,
J. Hoja, J. Hone, R. Hong, G. Hutchison, Y. Ikabata, O. Isayev, O. Ishaque, V.
Jain, Y. Jin, A. Jing, E.R. Johnson, I. Jones, K.V.J. Jose, E.A. Kabova, A. Keates,
P.F. Kelly, D. Khakimov, S. Konstantinopoulos, L.N. Kuleshova, H. Li, X. Lin,
A. List, C. Liu, Y.M. Liu, Z. Liu, Z.-P. Liu, J.W. Lubach, N. Marom, A.A. Maryewski,
H. Matsui, A. Mattei, R.A. Mayo, J.W. Melkumov, S. Mohamed, Z. Momenzadeh Abardeh,
H.S. Muddana, N. Nakayama, K.S. Nayal, M.A. Neumann, R. Nikhar, S. Obata, D. O’Connor,
A.R. Oganov, K. Okuwaki, A. Otero-de-la-Roza, C.C. Pantelides, S. Parkin, C.J.
Pickard, L. Pilia, T. Pivina, R. Podeszwa, A.J.A. Price, L.S. Price, S.L. Price,
M.R. Probert, A. Pulido, G.R. Ramteke, A.U. Rehman, S.M. Reutzel-Edens, J. Rogal,
M.J. Ross, A.F. Rumson, G. Sadiq, Z.M. Saeed, A. Salimi, M. Salvalaglio, L. Sanders
de Almada, K. Sasikumar, S. Sekharan, C. Shang, K. Shankland, K. Shinohara, B.
Shi, X. Shi, A.G. Skillman, H. Song, N. Strasser, J. van de Streek, I.J. Sugden,
G. Sun, K. Szalewicz, B.I. Tan, L. Tan, F. Tarczynski, C.R. Taylor, A. Tkatchenko,
R. Tom, M.E. Tuckerman, Y. Utsumi, L. Vogt-Maranto, J. Weatherston, L.J. Wilkinson,
R.D. Willacy, L. Wojtas, G.R. Woollam, Z. Yang, E. Yonemochi, X. Yue, Q. Zeng,
Y. Zhang, T. Zhou, Y. Zhou, R. Zubatyuk, J.C. Cole, Acta Crystallographica Section
B Structural Science, Crystal Engineering and Materials 80 (2024) 517–547.
date_created: 2025-01-29T11:07:36Z
date_published: 2024-12-01T00:00:00Z
date_updated: 2025-09-09T12:12:31Z
day: '01'
ddc:
- '540'
department:
- _id: BiCh
doi: 10.1107/s2052520624007492
external_id:
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page: 517-547
pmid: 1
publication: Acta Crystallographica Section B Structural Science, Crystal Engineering
and Materials
publication_identifier:
issn:
- 2052-5206
publication_status: published
publisher: International Union of Crystallography
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The seventh blind test of crystal structure prediction: Structure generation
methods'
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
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year: '2024'
...
---
OA_place: repository
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abstract:
- lang: eng
text: We give a simple proof that assuming the Exponential Time Hypothesis (ETH),
determining the winner of a Rabin game cannot be done in time 2o(k log k) · nO(1),
where k is the number of pairs of vertex subsets involved in the winning condition
and n is the vertex count of the game graph. While this result follows from the
lower bounds provided by Calude et al [SIAM J. Comp. 2022], our reduction is considerably
simpler and arguably provides more insight into the complexity of the problem.
In fact, the analogous lower bounds discussed by Calude et al, for solving Muller
games and multidimensional parity games, follow as simple corollaries of our approach.
Our reduction also highlights the usefulness of a certain pivot problem — Permutation
SAT — which may be of independent interest.
acknowledgement: This work is a part of projects CUTACOMBS (Ma. Pilipczuk), BOBR (Mi.
Pilipczuk), and VAMOS (K. S. Thejaswini) that have received funding from the European
Research Council (ERC) under the European Union's Horizon 2020 research and innovation
programme, grant agreements No 714704, 948057, and 101020093, respectively. Ma.
Pilipczuk is also partially supported by Polish National Science Centre SONATA BIS-12
grant number 2022/46/E/ST6/00143.
article_processing_charge: No
arxiv: 1
author:
- first_name: Antonio
full_name: Casares, Antonio
last_name: Casares
- first_name: Marcin
full_name: Pilipczuk, Marcin
last_name: Pilipczuk
- first_name: Michał
full_name: Pilipczuk, Michał
last_name: Pilipczuk
- first_name: Uéverton S.
full_name: Souza, Uéverton S.
last_name: Souza
- first_name: K. S.
full_name: Thejaswini, K. S.
id: 3807fb92-fdc1-11ee-bb4a-b4d8a431c753
last_name: Thejaswini
citation:
ama: 'Casares A, Pilipczuk M, Pilipczuk M, Souza US, Thejaswini KS. Simple and tight
complexity lower bounds for solving Rabin games. In: 2024 Symposium on Simplicity
in Algorithms. Society for Industrial and Applied Mathematics; 2024:160-167.
doi:10.1137/1.9781611977936.16'
apa: 'Casares, A., Pilipczuk, M., Pilipczuk, M., Souza, U. S., & Thejaswini,
K. S. (2024). Simple and tight complexity lower bounds for solving Rabin games.
In 2024 Symposium on Simplicity in Algorithms (pp. 160–167). Alexandria,
VA, United States: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977936.16'
chicago: Casares, Antonio, Marcin Pilipczuk, Michał Pilipczuk, Uéverton S. Souza,
and K. S. Thejaswini. “Simple and Tight Complexity Lower Bounds for Solving Rabin
Games.” In 2024 Symposium on Simplicity in Algorithms, 160–67. Society
for Industrial and Applied Mathematics, 2024. https://doi.org/10.1137/1.9781611977936.16.
ieee: A. Casares, M. Pilipczuk, M. Pilipczuk, U. S. Souza, and K. S. Thejaswini,
“Simple and tight complexity lower bounds for solving Rabin games,” in 2024
Symposium on Simplicity in Algorithms, Alexandria, VA, United States, 2024,
pp. 160–167.
ista: 'Casares A, Pilipczuk M, Pilipczuk M, Souza US, Thejaswini KS. 2024. Simple
and tight complexity lower bounds for solving Rabin games. 2024 Symposium on Simplicity
in Algorithms. SOSA: Symposium on Simplicity in Algorithms, 160–167.'
mla: Casares, Antonio, et al. “Simple and Tight Complexity Lower Bounds for Solving
Rabin Games.” 2024 Symposium on Simplicity in Algorithms, Society for Industrial
and Applied Mathematics, 2024, pp. 160–67, doi:10.1137/1.9781611977936.16.
short: A. Casares, M. Pilipczuk, M. Pilipczuk, U.S. Souza, K.S. Thejaswini, in:,
2024 Symposium on Simplicity in Algorithms, Society for Industrial and Applied
Mathematics, 2024, pp. 160–167.
conference:
end_date: 2024-01-10
location: Alexandria, VA, United States
name: 'SOSA: Symposium on Simplicity in Algorithms'
start_date: 2024-01-08
date_created: 2025-01-29T11:55:50Z
date_published: 2024-01-01T00:00:00Z
date_updated: 2025-04-14T07:55:54Z
day: '01'
department:
- _id: ToHe
doi: 10.1137/1.9781611977936.16
ec_funded: 1
external_id:
arxiv:
- '2310.20433'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2310.20433
month: '01'
oa: 1
oa_version: Preprint
page: 160-167
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 2024 Symposium on Simplicity in Algorithms
publication_identifier:
isbn:
- '9781611977936'
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Simple and tight complexity lower bounds for solving Rabin games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '18956'
abstract:
- lang: eng
text: 'Group Activity Recognition (GAR) aims to detect the activity performed by
multiple actors in a scene. Prior works model the spatio-temporal features based
on the RGB, optical flow or keypoint data types. On the contrary, our hypothesis
is that by only using the RGB data without temporality, the performance can be
maintained with a negligible loss in accuracy. To that end, we propose a novel
GAR technique for volleyball videos, DECOMPL, which consists of two complementary
branches. In the visual branch, it extracts the features using attention pooling.
In the coordinate branch, it considers the configuration of the players and extracts
the spatial information from the box coordinates. Moreover, we analyzed the Volleyball
dataset that the recent literature is mostly based on, and systematically reannotated
it to emphasize the group concept. Experimental results demonstrated the effectiveness
of the proposed model DECOMPL, which delivered the best/second best GAR performance
with the reannotations/original annotations among the comparable state-of-the-art
methods. Code and new annotations are available at GitHub: https://github.com/berkerdemirel/decompl'
article_processing_charge: No
arxiv: 1
author:
- first_name: Berker
full_name: Demirel, Berker
id: 8b4bc47f-3200-11ee-973b-8f0e7be21a9f
last_name: Demirel
- first_name: Huseyin
full_name: Ozkan, Huseyin
last_name: Ozkan
citation:
ama: 'Demirel B, Ozkan H. Decompl: Decompositional learning with attention pooling
for group activity recognition from a single volleyball image. In: 2024 IEEE
International Conference on Image Processing. IEEE; 2024:977-983. doi:10.1109/icip51287.2024.10647499'
apa: 'Demirel, B., & Ozkan, H. (2024). Decompl: Decompositional learning with
attention pooling for group activity recognition from a single volleyball image.
In 2024 IEEE International Conference on Image Processing (pp. 977–983).
Abu Dhabi, United Arab Emirates: IEEE. https://doi.org/10.1109/icip51287.2024.10647499'
chicago: 'Demirel, Berker, and Huseyin Ozkan. “Decompl: Decompositional Learning
with Attention Pooling for Group Activity Recognition from a Single Volleyball
Image.” In 2024 IEEE International Conference on Image Processing, 977–83.
IEEE, 2024. https://doi.org/10.1109/icip51287.2024.10647499.'
ieee: 'B. Demirel and H. Ozkan, “Decompl: Decompositional learning with attention
pooling for group activity recognition from a single volleyball image,” in 2024
IEEE International Conference on Image Processing, Abu Dhabi, United Arab
Emirates, 2024, pp. 977–983.'
ista: 'Demirel B, Ozkan H. 2024. Decompl: Decompositional learning with attention
pooling for group activity recognition from a single volleyball image. 2024 IEEE
International Conference on Image Processing. ICIP: International Conference on
Image Processing, 977–983.'
mla: 'Demirel, Berker, and Huseyin Ozkan. “Decompl: Decompositional Learning with
Attention Pooling for Group Activity Recognition from a Single Volleyball Image.”
2024 IEEE International Conference on Image Processing, IEEE, 2024, pp.
977–83, doi:10.1109/icip51287.2024.10647499.'
short: B. Demirel, H. Ozkan, in:, 2024 IEEE International Conference on Image Processing,
IEEE, 2024, pp. 977–983.
conference:
end_date: 2024-10-30
location: Abu Dhabi, United Arab Emirates
name: 'ICIP: International Conference on Image Processing'
start_date: 2024-10-27
corr_author: '1'
date_created: 2025-01-29T12:22:24Z
date_published: 2024-11-01T00:00:00Z
date_updated: 2025-09-09T12:13:12Z
day: '01'
department:
- _id: FrLo
doi: 10.1109/icip51287.2024.10647499
external_id:
arxiv:
- '2303.06439'
isi:
- '001442947000143'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2303.06439
month: '11'
oa: 1
oa_version: Preprint
page: 977-983
publication: 2024 IEEE International Conference on Image Processing
publication_identifier:
eisbn:
- '9798350349399'
eissn:
- 2381-8549
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/berkerdemirel/decompl
status: public
title: 'Decompl: Decompositional learning with attention pooling for group activity
recognition from a single volleyball image'
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...