---
_id: '14036'
abstract:
- lang: eng
text: Magic-angle spinning (MAS) nuclear magnetic resonance (NMR) is establishing
itself as a powerful method for the characterization of protein dynamics at the
atomic scale. We discuss here how R1ρ MAS relaxation dispersion NMR can explore
microsecond-to-millisecond motions. Progress in instrumentation, isotope labeling,
and pulse sequence design has paved the way for quantitative analyses of even
rare structural fluctuations. In addition to isotropic chemical-shift fluctuations
exploited in solution-state NMR relaxation dispersion experiments, MAS NMR has
a wider arsenal of observables, allowing to see motions even if the exchanging
states do not differ in their chemical shifts. We demonstrate the potential of
the technique for probing motions in challenging large enzymes, membrane proteins,
and protein assemblies.
acknowledgement: We thank Petra Rovó for critical reading of this manuscript. We acknowledge
the Austrian Science Foundation FWF (project AlloSpace, number I5812–B) and funding
by the Institute of Science and Technology Austria.
article_number: '102660'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Federico
full_name: Napoli, Federico
id: d42e08e7-f4fc-11eb-af0a-d71e26138f1b
last_name: Napoli
orcid: 0000-0002-9043-136X
- first_name: Lea Marie
full_name: Becker, Lea Marie
id: 36336939-eb97-11eb-a6c2-c83f1214ca79
last_name: Becker
orcid: 0000-0002-6401-5151
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Napoli F, Becker LM, Schanda P. Protein dynamics detected by magic-angle spinning
relaxation dispersion NMR. Current Opinion in Structural Biology. 2023;82(10).
doi:10.1016/j.sbi.2023.102660
apa: Napoli, F., Becker, L. M., & Schanda, P. (2023). Protein dynamics detected
by magic-angle spinning relaxation dispersion NMR. Current Opinion in Structural
Biology. Elsevier. https://doi.org/10.1016/j.sbi.2023.102660
chicago: Napoli, Federico, Lea Marie Becker, and Paul Schanda. “Protein Dynamics
Detected by Magic-Angle Spinning Relaxation Dispersion NMR.” Current Opinion
in Structural Biology. Elsevier, 2023. https://doi.org/10.1016/j.sbi.2023.102660.
ieee: F. Napoli, L. M. Becker, and P. Schanda, “Protein dynamics detected by magic-angle
spinning relaxation dispersion NMR,” Current Opinion in Structural Biology,
vol. 82, no. 10. Elsevier, 2023.
ista: Napoli F, Becker LM, Schanda P. 2023. Protein dynamics detected by magic-angle
spinning relaxation dispersion NMR. Current Opinion in Structural Biology. 82(10),
102660.
mla: Napoli, Federico, et al. “Protein Dynamics Detected by Magic-Angle Spinning
Relaxation Dispersion NMR.” Current Opinion in Structural Biology, vol.
82, no. 10, 102660, Elsevier, 2023, doi:10.1016/j.sbi.2023.102660.
short: F. Napoli, L.M. Becker, P. Schanda, Current Opinion in Structural Biology
82 (2023).
corr_author: '1'
date_created: 2023-08-13T22:01:11Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2025-04-14T09:10:17Z
day: '01'
ddc:
- '570'
department:
- _id: PaSc
doi: 10.1016/j.sbi.2023.102660
external_id:
isi:
- '001053616200001'
pmid:
- '37536064'
file:
- access_level: open_access
checksum: c850f7ac8a4234319755b672c1df69ae
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T12:36:39Z
date_updated: 2024-01-30T12:36:39Z
file_id: '14907'
file_name: 2023_CurrentOpinionStrucBio_Napoli.pdf
file_size: 1231998
relation: main_file
success: 1
file_date_updated: 2024-01-30T12:36:39Z
intvolume: ' 82'
isi: 1
issue: '10'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf
grant_number: I05812
name: AlloSpace. The emergence and mechanisms of allostery
publication: Current Opinion in Structural Biology
publication_identifier:
eissn:
- 1879-033X
issn:
- 0959-440X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Protein dynamics detected by magic-angle spinning relaxation dispersion NMR
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: 82
year: '2023'
...
---
_id: '14037'
abstract:
- lang: eng
text: 'Traditionally, nuclear spin is not considered to affect biological processes.
Recently, this has changed as isotopic fractionation that deviates from classical
mass dependence was reported both in vitro and in vivo. In these cases, the isotopic
effect correlates with the nuclear magnetic spin. Here, we show nuclear spin effects
using stable oxygen isotopes (16O, 17O, and 18O) in two separate setups: an artificial
dioxygen production system and biological aquaporin channels in cells. We observe
that oxygen dynamics in chiral environments (in particular its transport) depend
on nuclear spin, suggesting future applications for controlled isotope separation
to be used, for instance, in NMR. To demonstrate the mechanism behind our findings,
we formulate theoretical models based on a nuclear-spin-enhanced switch between
electronic spin states. Accounting for the role of nuclear spin in biology can
provide insights into the role of quantum effects in living systems and help inspire
the development of future biotechnology solutions.'
acknowledgement: N.M.-S. acknowledges the support of the Ministry of Energy, Israel,
as part of the scholarship program for graduate students in the fields of energy.
M.L. acknowledges support by the European Research Council (ERC) Starting Grant
No. 801770 (ANGULON). Y.P. acknowledges the support of the Ministry of Innovation,
Science and Technology, Israel Grant No. 1001593872. Y.P acknowledges the support
of the BSF-NSF 094 Grant No. 2022503.
article_number: e2300828120
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Ofek
full_name: Vardi, Ofek
last_name: Vardi
- first_name: Naama
full_name: Maroudas-Sklare, Naama
last_name: Maroudas-Sklare
- first_name: Yuval
full_name: Kolodny, Yuval
last_name: Kolodny
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
- first_name: Amijai
full_name: Saragovi, Amijai
last_name: Saragovi
- first_name: Nir
full_name: Galili, Nir
last_name: Galili
- first_name: Stav
full_name: Ferrera, Stav
last_name: Ferrera
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Nir
full_name: Yuran, Nir
last_name: Yuran
- first_name: Hagit P.
full_name: Affek, Hagit P.
last_name: Affek
- first_name: Boaz
full_name: Luz, Boaz
last_name: Luz
- first_name: Yonaton
full_name: Goldsmith, Yonaton
last_name: Goldsmith
- first_name: Nir
full_name: Keren, Nir
last_name: Keren
- first_name: Shira
full_name: Yochelis, Shira
last_name: Yochelis
- first_name: Itay
full_name: Halevy, Itay
last_name: Halevy
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Yossi
full_name: Paltiel, Yossi
last_name: Paltiel
citation:
ama: Vardi O, Maroudas-Sklare N, Kolodny Y, et al. Nuclear spin effects in biological
processes. Proceedings of the National Academy of Sciences of the United States
of America. 2023;120(32). doi:10.1073/pnas.2300828120
apa: Vardi, O., Maroudas-Sklare, N., Kolodny, Y., Volosniev, A., Saragovi, A., Galili,
N., … Paltiel, Y. (2023). Nuclear spin effects in biological processes. Proceedings
of the National Academy of Sciences of the United States of America. National
Academy of Sciences. https://doi.org/10.1073/pnas.2300828120
chicago: Vardi, Ofek, Naama Maroudas-Sklare, Yuval Kolodny, Artem Volosniev, Amijai
Saragovi, Nir Galili, Stav Ferrera, et al. “Nuclear Spin Effects in Biological
Processes.” Proceedings of the National Academy of Sciences of the United States
of America. National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2300828120.
ieee: O. Vardi et al., “Nuclear spin effects in biological processes,” Proceedings
of the National Academy of Sciences of the United States of America, vol.
120, no. 32. National Academy of Sciences, 2023.
ista: Vardi O, Maroudas-Sklare N, Kolodny Y, Volosniev A, Saragovi A, Galili N,
Ferrera S, Ghazaryan A, Yuran N, Affek HP, Luz B, Goldsmith Y, Keren N, Yochelis
S, Halevy I, Lemeshko M, Paltiel Y. 2023. Nuclear spin effects in biological processes.
Proceedings of the National Academy of Sciences of the United States of America.
120(32), e2300828120.
mla: Vardi, Ofek, et al. “Nuclear Spin Effects in Biological Processes.” Proceedings
of the National Academy of Sciences of the United States of America, vol.
120, no. 32, e2300828120, National Academy of Sciences, 2023, doi:10.1073/pnas.2300828120.
short: O. Vardi, N. Maroudas-Sklare, Y. Kolodny, A. Volosniev, A. Saragovi, N. Galili,
S. Ferrera, A. Ghazaryan, N. Yuran, H.P. Affek, B. Luz, Y. Goldsmith, N. Keren,
S. Yochelis, I. Halevy, M. Lemeshko, Y. Paltiel, Proceedings of the National Academy
of Sciences of the United States of America 120 (2023).
date_created: 2023-08-13T22:01:12Z
date_published: 2023-07-31T00:00:00Z
date_updated: 2025-09-09T12:47:53Z
day: '31'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1073/pnas.2300828120
ec_funded: 1
external_id:
isi:
- '001121663600001'
pmid:
- '37523549'
file:
- access_level: open_access
checksum: a5ed64788a5acef9b9a300a26fa5a177
content_type: application/pdf
creator: dernst
date_created: 2023-08-14T07:43:45Z
date_updated: 2023-08-14T07:43:45Z
file_id: '14047'
file_name: 2023_PNAS_Vardi.pdf
file_size: 1003092
relation: main_file
success: 1
file_date_updated: 2023-08-14T07:43:45Z
has_accepted_license: '1'
intvolume: ' 120'
isi: 1
issue: '32'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nuclear spin effects in biological processes
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 120
year: '2023'
...
---
_id: '14039'
abstract:
- lang: eng
text: Membranes are essential for life. They act as semi-permeable boundaries that
define cells and organelles. In addition, their surfaces actively participate
in biochemical reaction networks, where they confine proteins, align reaction
partners, and directly control enzymatic activities. Membrane-localized reactions
shape cellular membranes, define the identity of organelles, compartmentalize
biochemical processes, and can even be the source of signaling gradients that
originate at the plasma membrane and reach into the cytoplasm and nucleus. The
membrane surface is, therefore, an essential platform upon which myriad cellular
processes are scaffolded. In this review, we summarize our current understanding
of the biophysics and biochemistry of membrane-localized reactions with particular
focus on insights derived from reconstituted and cellular systems. We discuss
how the interplay of cellular factors results in their self-organization, condensation,
assembly, and activity, and the emergent properties derived from them.
acknowledgement: We acknowledge funding from the Austrian Science Fund (FWF F79, P32814-B,
and P35061-B to S.M.; P34607-B to M.L.; and P30584-B and P33066-B to T.A.L.) and
the European Research Council (ERC) under the European Union’s Horizon 2020 research
and innovation program (grant agreement no. 101045340 to M.L.). We are grateful
for comments on the manuscript by Justyna Sawa-Makarska, Verena Baumann, Marko Kojic,
Philipp Radler, Ronja Reinhardt, and Sumire Antonioli.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Thomas A.
full_name: Leonard, Thomas A.
last_name: Leonard
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Sascha
full_name: Martens, Sascha
last_name: Martens
citation:
ama: Leonard TA, Loose M, Martens S. The membrane surface as a platform that organizes
cellular and biochemical processes. Developmental Cell. 2023;58(15):1315-1332.
doi:10.1016/j.devcel.2023.06.001
apa: Leonard, T. A., Loose, M., & Martens, S. (2023). The membrane surface as
a platform that organizes cellular and biochemical processes. Developmental
Cell. Elsevier. https://doi.org/10.1016/j.devcel.2023.06.001
chicago: Leonard, Thomas A., Martin Loose, and Sascha Martens. “The Membrane Surface
as a Platform That Organizes Cellular and Biochemical Processes.” Developmental
Cell. Elsevier, 2023. https://doi.org/10.1016/j.devcel.2023.06.001.
ieee: T. A. Leonard, M. Loose, and S. Martens, “The membrane surface as a platform
that organizes cellular and biochemical processes,” Developmental Cell,
vol. 58, no. 15. Elsevier, pp. 1315–1332, 2023.
ista: Leonard TA, Loose M, Martens S. 2023. The membrane surface as a platform that
organizes cellular and biochemical processes. Developmental Cell. 58(15), 1315–1332.
mla: Leonard, Thomas A., et al. “The Membrane Surface as a Platform That Organizes
Cellular and Biochemical Processes.” Developmental Cell, vol. 58, no. 15,
Elsevier, 2023, pp. 1315–32, doi:10.1016/j.devcel.2023.06.001.
short: T.A. Leonard, M. Loose, S. Martens, Developmental Cell 58 (2023) 1315–1332.
corr_author: '1'
date_created: 2023-08-13T22:01:12Z
date_published: 2023-08-07T00:00:00Z
date_updated: 2024-10-22T11:40:18Z
day: '07'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.1016/j.devcel.2023.06.001
external_id:
isi:
- '001059110400001'
pmid:
- '37419118'
file:
- access_level: open_access
checksum: d8c5dc97cd40c26da2ec98ae723ab368
content_type: application/pdf
creator: dernst
date_created: 2023-08-14T07:57:55Z
date_updated: 2023-08-14T07:57:55Z
file_id: '14049'
file_name: 2023_DevelopmentalCell_Leonard.pdf
file_size: 3184217
relation: main_file
success: 1
file_date_updated: 2023-08-14T07:57:55Z
has_accepted_license: '1'
intvolume: ' 58'
isi: 1
issue: '15'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 1315-1332
pmid: 1
project:
- _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d
grant_number: P34607
name: In vitro reconstitution of bacterial cell division
- _id: bd6ae2ca-d553-11ed-ba76-a4aa239da5ee
grant_number: '101045340'
name: Synthetic and structural biology of Rab GTPase networks
publication: Developmental Cell
publication_identifier:
eissn:
- 1878-1551
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The membrane surface as a platform that organizes cellular and biochemical
processes
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: 58
year: '2023'
...
---
_id: '14040'
abstract:
- lang: eng
text: Robust oxygenic photosynthesis requires a suite of accessory factors to ensure
efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex.
The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction
center polypeptide and promotes the initial steps of PSII assembly, but its binding
site is unclear. Here we use cryo-electron microscopy to determine the structure
of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached.
Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that
ultimately ligate the water-oxidising Mn4CaO5 cluster, thereby preventing the
premature binding of Mn2+ and Ca2+ ions and protecting the site from damage. Interactions
with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall,
our work provides valuable insights into the early stages of PSII assembly and
the structural changes that create the binding site for the Mn4CaO5 cluster.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: ScienComp
acknowledgement: P.J.N. and J.W.M. are grateful for the support of the Biotechnology
& Biological Sciences Research Council (awards BB/L003260/1 and BB/P00931X/1). J.
Knoppová, R.S. and J. Komenda were supported by the Czech Science Foundation (project
19-29225X) and by ERC project Photoredesign (no. 854126) and L.A.S. was supported
by the Scientific Service Units (SSU) of IST Austria through resources provided
by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the
IST high-performance computing cluster.
article_number: '4681'
article_processing_charge: Yes
article_type: original
author:
- first_name: Ziyu
full_name: Zhao, Ziyu
last_name: Zhao
- first_name: Irene
full_name: Vercellino, Irene
id: 3ED6AF16-F248-11E8-B48F-1D18A9856A87
last_name: Vercellino
orcid: 0000-0001-5618-3449
- first_name: Jana
full_name: Knoppová, Jana
last_name: Knoppová
- first_name: Roman
full_name: Sobotka, Roman
last_name: Sobotka
- first_name: James W.
full_name: Murray, James W.
last_name: Murray
- first_name: Peter J.
full_name: Nixon, Peter J.
last_name: Nixon
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
- first_name: Josef
full_name: Komenda, Josef
last_name: Komenda
citation:
ama: Zhao Z, Vercellino I, Knoppová J, et al. The Ycf48 accessory factor occupies
the site of the oxygen-evolving manganese cluster during photosystem II biogenesis.
Nature Communications. 2023;14. doi:10.1038/s41467-023-40388-6
apa: Zhao, Z., Vercellino, I., Knoppová, J., Sobotka, R., Murray, J. W., Nixon,
P. J., … Komenda, J. (2023). The Ycf48 accessory factor occupies the site of the
oxygen-evolving manganese cluster during photosystem II biogenesis. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-023-40388-6
chicago: Zhao, Ziyu, Irene Vercellino, Jana Knoppová, Roman Sobotka, James W. Murray,
Peter J. Nixon, Leonid A Sazanov, and Josef Komenda. “The Ycf48 Accessory Factor
Occupies the Site of the Oxygen-Evolving Manganese Cluster during Photosystem
II Biogenesis.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-40388-6.
ieee: Z. Zhao et al., “The Ycf48 accessory factor occupies the site of the
oxygen-evolving manganese cluster during photosystem II biogenesis,” Nature
Communications, vol. 14. Springer Nature, 2023.
ista: Zhao Z, Vercellino I, Knoppová J, Sobotka R, Murray JW, Nixon PJ, Sazanov
LA, Komenda J. 2023. The Ycf48 accessory factor occupies the site of the oxygen-evolving
manganese cluster during photosystem II biogenesis. Nature Communications. 14,
4681.
mla: Zhao, Ziyu, et al. “The Ycf48 Accessory Factor Occupies the Site of the Oxygen-Evolving
Manganese Cluster during Photosystem II Biogenesis.” Nature Communications,
vol. 14, 4681, Springer Nature, 2023, doi:10.1038/s41467-023-40388-6.
short: Z. Zhao, I. Vercellino, J. Knoppová, R. Sobotka, J.W. Murray, P.J. Nixon,
L.A. Sazanov, J. Komenda, Nature Communications 14 (2023).
corr_author: '1'
date_created: 2023-08-13T22:01:13Z
date_published: 2023-08-04T00:00:00Z
date_updated: 2025-04-23T13:05:33Z
day: '04'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1038/s41467-023-40388-6
external_id:
isi:
- '001042606700004'
pmid:
- '37542031'
file:
- access_level: open_access
checksum: 3b9043df3d51c300f9be95eac3ff9d0b
content_type: application/pdf
creator: dernst
date_created: 2023-08-14T07:01:12Z
date_updated: 2023-08-14T07:01:12Z
file_id: '14044'
file_name: 2023_NatureComm_Zhao.pdf
file_size: 2315325
relation: main_file
success: 1
file_date_updated: 2023-08-14T07:01:12Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese
cluster during photosystem II biogenesis
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: 14
year: '2023'
...
---
_id: '14041'
abstract:
- lang: eng
text: Tissue morphogenesis and patterning during development involve the segregation
of cell types. Segregation is driven by differential tissue surface tensions generated
by cell types through controlling cell-cell contact formation by regulating adhesion
and actomyosin contractility-based cellular cortical tensions. We use vertebrate
tissue cell types and zebrafish germ layer progenitors as in vitro models of 3-dimensional
heterotypic segregation and developed a quantitative analysis of their dynamics
based on 3D time-lapse microscopy. We show that general inhibition of actomyosin
contractility by the Rho kinase inhibitor Y27632 delays segregation. Cell type-specific
inhibition of non-muscle myosin2 activity by overexpression of myosin assembly
inhibitor S100A4 reduces tissue surface tension, manifested in decreased compaction
during aggregation and inverted geometry observed during segregation. The same
is observed when we express a constitutively active Rho kinase isoform to ubiquitously
keep actomyosin contractility high at cell-cell and cell-medium interfaces and
thus overriding the interface-specific regulation of cortical tensions. Tissue
surface tension regulation can become an effective tool in tissue engineering.
acknowledgement: "We thank Marton Gulyas (ELTE Eötvös University) for development
of videomicroscopy experiment manager and image analysis software. Authors are grateful
to Gabor Forgacs (University of Missouri) for critical reading of earlier versions
of this manuscript as well as to Zsuzsa Akos and Andras Czirok (ELTE Eötvös University)
for fruitful discussions. This work was supported by EU FP7, ERC COLLMOT Project
No 227878 to TV, the National Research Development and Innovation Fund of Hungary,
K119359 and also Project No 2018-1.2.1-NKP-2018-00005 to LN. This project has received
funding from the European Union’s Horizon 2020 research and innovation programme
under the Marie Sklodowska-Curie grant agreement No 955576. MV was supported by
the Ja´nos Bolyai Fellowship of the Hungarian Academy of Sciences.\r\nOpen access
funding provided by Eötvös Loránd University."
article_number: '817'
article_processing_charge: Yes
article_type: original
author:
- first_name: Elod
full_name: Méhes, Elod
last_name: Méhes
- first_name: Enys
full_name: Mones, Enys
last_name: Mones
- first_name: Máté
full_name: Varga, Máté
last_name: Varga
- first_name: Áron
full_name: Zsigmond, Áron
last_name: Zsigmond
- first_name: Beáta
full_name: Biri-Kovács, Beáta
last_name: Biri-Kovács
- first_name: László
full_name: Nyitray, László
last_name: Nyitray
- first_name: Vanessa
full_name: Barone, Vanessa
id: 419EECCC-F248-11E8-B48F-1D18A9856A87
last_name: Barone
orcid: 0000-0003-2676-3367
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Tamás
full_name: Vicsek, Tamás
last_name: Vicsek
citation:
ama: Méhes E, Mones E, Varga M, et al. 3D cell segregation geometry and dynamics
are governed by tissue surface tension regulation. Communications Biology.
2023;6. doi:10.1038/s42003-023-05181-7
apa: Méhes, E., Mones, E., Varga, M., Zsigmond, Á., Biri-Kovács, B., Nyitray, L.,
… Vicsek, T. (2023). 3D cell segregation geometry and dynamics are governed by
tissue surface tension regulation. Communications Biology. Springer Nature.
https://doi.org/10.1038/s42003-023-05181-7
chicago: Méhes, Elod, Enys Mones, Máté Varga, Áron Zsigmond, Beáta Biri-Kovács,
László Nyitray, Vanessa Barone, Gabriel Krens, Carl-Philipp J Heisenberg, and
Tamás Vicsek. “3D Cell Segregation Geometry and Dynamics Are Governed by Tissue
Surface Tension Regulation.” Communications Biology. Springer Nature, 2023.
https://doi.org/10.1038/s42003-023-05181-7.
ieee: E. Méhes et al., “3D cell segregation geometry and dynamics are governed
by tissue surface tension regulation,” Communications Biology, vol. 6.
Springer Nature, 2023.
ista: Méhes E, Mones E, Varga M, Zsigmond Á, Biri-Kovács B, Nyitray L, Barone V,
Krens G, Heisenberg C-PJ, Vicsek T. 2023. 3D cell segregation geometry and dynamics
are governed by tissue surface tension regulation. Communications Biology. 6,
817.
mla: Méhes, Elod, et al. “3D Cell Segregation Geometry and Dynamics Are Governed
by Tissue Surface Tension Regulation.” Communications Biology, vol. 6,
817, Springer Nature, 2023, doi:10.1038/s42003-023-05181-7.
short: E. Méhes, E. Mones, M. Varga, Á. Zsigmond, B. Biri-Kovács, L. Nyitray, V.
Barone, G. Krens, C.-P.J. Heisenberg, T. Vicsek, Communications Biology 6 (2023).
date_created: 2023-08-13T22:01:13Z
date_published: 2023-08-04T00:00:00Z
date_updated: 2023-12-13T12:07:33Z
day: '04'
ddc:
- '570'
department:
- _id: CaHe
- _id: Bio
doi: 10.1038/s42003-023-05181-7
external_id:
isi:
- '001042544100001'
pmid:
- '37542157'
file:
- access_level: open_access
checksum: 1f9324f736bdbb76426b07736651c4cd
content_type: application/pdf
creator: dernst
date_created: 2023-08-14T07:17:36Z
date_updated: 2023-08-14T07:17:36Z
file_id: '14045'
file_name: 2023_CommBiology_Mehes.pdf
file_size: 10181997
relation: main_file
success: 1
file_date_updated: 2023-08-14T07:17:36Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Communications Biology
publication_identifier:
eissn:
- 2399-3642
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 3D cell segregation geometry and dynamics are governed by tissue surface tension
regulation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2023'
...
---
_id: '14042'
abstract:
- lang: eng
text: Long-time and large-data existence of weak solutions for initial- and boundary-value
problems concerning three-dimensional flows of incompressible fluids is nowadays
available not only for Navier–Stokes fluids but also for various fluid models
where the relation between the Cauchy stress tensor and the symmetric part of
the velocity gradient is nonlinear. The majority of such studies however concerns
models where such a dependence is explicit (the stress is a function of the velocity
gradient), which makes the class of studied models unduly restrictive. The same
concerns boundary conditions, or more precisely the slipping mechanisms on the
boundary, where the no-slip is still the most preferred condition considered in
the literature. Our main objective is to develop a robust mathematical theory
for unsteady internal flows of implicitly constituted incompressible fluids with
implicit relations between the tangential projections of the velocity and the
normal traction on the boundary. The theory covers numerous rheological models
used in chemistry, biorheology, polymer and food industry as well as in geomechanics.
It also includes, as special cases, nonlinear slip as well as stick–slip boundary
conditions. Unlike earlier studies, the conditions characterizing admissible classes
of constitutive equations are expressed by means of tools of elementary calculus.
In addition, a fully constructive proof (approximation scheme) is incorporated.
Finally, we focus on the question of uniqueness of such weak solutions.
acknowledgement: "M. Bulíček and J. Málek acknowledge the support of the project No.
20-11027X financed by the Czech Science foundation (GAČR). M. Bulíček and J. Málek
are members of the Nečas Center for Mathematical Modelling.\r\nOpen access publishing
supported by the National Technical Library in Prague."
article_number: '72'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Miroslav
full_name: Bulíček, Miroslav
last_name: Bulíček
- first_name: Josef
full_name: Málek, Josef
last_name: Málek
- first_name: Erika
full_name: Maringová, Erika
id: dbabca31-66eb-11eb-963a-fb9c22c880b4
last_name: Maringová
citation:
ama: Bulíček M, Málek J, Maringová E. On unsteady internal flows of incompressible
fluids characterized by implicit constitutive equations in the bulk and on the
boundary. Journal of Mathematical Fluid Mechanics. 2023;25(3). doi:10.1007/s00021-023-00803-w
apa: Bulíček, M., Málek, J., & Maringová, E. (2023). On unsteady internal flows
of incompressible fluids characterized by implicit constitutive equations in the
bulk and on the boundary. Journal of Mathematical Fluid Mechanics. Springer
Nature. https://doi.org/10.1007/s00021-023-00803-w
chicago: Bulíček, Miroslav, Josef Málek, and Erika Maringová. “On Unsteady Internal
Flows of Incompressible Fluids Characterized by Implicit Constitutive Equations
in the Bulk and on the Boundary.” Journal of Mathematical Fluid Mechanics.
Springer Nature, 2023. https://doi.org/10.1007/s00021-023-00803-w.
ieee: M. Bulíček, J. Málek, and E. Maringová, “On unsteady internal flows of incompressible
fluids characterized by implicit constitutive equations in the bulk and on the
boundary,” Journal of Mathematical Fluid Mechanics, vol. 25, no. 3. Springer
Nature, 2023.
ista: Bulíček M, Málek J, Maringová E. 2023. On unsteady internal flows of incompressible
fluids characterized by implicit constitutive equations in the bulk and on the
boundary. Journal of Mathematical Fluid Mechanics. 25(3), 72.
mla: Bulíček, Miroslav, et al. “On Unsteady Internal Flows of Incompressible Fluids
Characterized by Implicit Constitutive Equations in the Bulk and on the Boundary.”
Journal of Mathematical Fluid Mechanics, vol. 25, no. 3, 72, Springer Nature,
2023, doi:10.1007/s00021-023-00803-w.
short: M. Bulíček, J. Málek, E. Maringová, Journal of Mathematical Fluid Mechanics
25 (2023).
date_created: 2023-08-13T22:01:13Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2023-12-13T12:08:08Z
day: '01'
ddc:
- '510'
department:
- _id: JuFi
doi: 10.1007/s00021-023-00803-w
external_id:
arxiv:
- '2301.12834'
isi:
- '001040354900001'
file:
- access_level: open_access
checksum: c549cd8f0dd02ed60477a05ca045f481
content_type: application/pdf
creator: dernst
date_created: 2023-08-14T07:24:17Z
date_updated: 2023-08-14T07:24:17Z
file_id: '14046'
file_name: 2023_JourMathFluidMech_Bulicek.pdf
file_size: 845748
relation: main_file
success: 1
file_date_updated: 2023-08-14T07:24:17Z
has_accepted_license: '1'
intvolume: ' 25'
isi: 1
issue: '3'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication: Journal of Mathematical Fluid Mechanics
publication_identifier:
eissn:
- 1422-6952
issn:
- 1422-6928
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: On unsteady internal flows of incompressible fluids characterized by implicit
constitutive equations in the bulk and on the boundary
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: 25
year: '2023'
...
---
_id: '14043'
abstract:
- lang: eng
text: 'Over the last two decades, a significant line of work in theoretical algorithms
has made progress in solving linear systems of the form Lx=b, where L is the Laplacian
matrix of a weighted graph with weights w(i,j)>0 on the edges. The solution x
of the linear system can be interpreted as the potentials of an electrical flow
in which the resistance on edge (i, j) is 1/w(i, j). Kelner et al. (in: Proceedings
of the 45th Annual ACM Symposium on the Theory of Computing, pp 911–920, 2013.
https://doi.org/10.1145/2488608.2488724) give a combinatorial, near-linear time
algorithm that maintains the Kirchoff Current Law, and gradually enforces the
Kirchoff Potential Law by updating flows around cycles (cycle toggling). In this
paper, we consider a dual version of the algorithm that maintains the Kirchoff
Potential Law, and gradually enforces the Kirchoff Current Law by cut toggling:
each iteration updates all potentials on one side of a fundamental cut of a spanning
tree by the same amount. We prove that this dual algorithm also runs in a near-linear
number of iterations. We show, however, that if we abstract cut toggling as a
natural data structure problem, this problem can be reduced to the online vector–matrix-vector
problem, which has been conjectured to be difficult for dynamic algorithms (Henzinger
et al., in: Proceedings of the 47th Annual ACM Symposium on the Theory of Computing,
pp 21–30, 2015. https://doi.org/10.1145/2746539.2746609). The conjecture implies
that the data structure does not have an O(n1−ϵ) time algorithm for any ϵ>0, and
thus a straightforward implementation of the cut-toggling algorithm requires essentially
linear time per iteration. To circumvent the lower bound, we batch update steps,
and perform them simultaneously instead of sequentially. An appropriate choice
of batching leads to an O˜(m1.5) time cut-toggling algorithm for solving Laplacian
systems. Furthermore, we show that if we sparsify the graph and call our algorithm
recursively on the Laplacian system implied by batching and sparsifying, we can
reduce the running time to O(m1+ϵ) for any ϵ>0. Thus, the dual cut-toggling algorithm
can achieve (almost) the same running time as its primal cycle-toggling counterpart.'
acknowledgement: Monika Henzinger was supported by funding from the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
Grant agreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures
(MoDynStruct)” and from the Austrian Science Fund (FWF) project “Fast Algorithms
for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from
the netidee SCIENCE Stiftung, 2020–2024. Billy Jin was Supported in part by NSERC
fellowship PGSD3-532673-2019 and NSF grant CCF-2007009. Richard Peng was supported
in part by an NSERC Discovery Grant and NSF grant CCF-1846218. David P. Williamson
was supported in part by NSF grant CCF-2007009.
article_processing_charge: No
article_type: original
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: Billy
full_name: Jin, Billy
last_name: Jin
- first_name: Richard
full_name: Peng, Richard
last_name: Peng
- first_name: David P.
full_name: Williamson, David P.
last_name: Williamson
citation:
ama: Henzinger M, Jin B, Peng R, Williamson DP. A combinatorial cut-toggling algorithm
for solving Laplacian linear systems. Algorithmica. 2023;85:2680-3716.
doi:10.1007/s00453-023-01154-8
apa: Henzinger, M., Jin, B., Peng, R., & Williamson, D. P. (2023). A combinatorial
cut-toggling algorithm for solving Laplacian linear systems. Algorithmica.
Springer Nature. https://doi.org/10.1007/s00453-023-01154-8
chicago: Henzinger, Monika, Billy Jin, Richard Peng, and David P. Williamson. “A
Combinatorial Cut-Toggling Algorithm for Solving Laplacian Linear Systems.” Algorithmica.
Springer Nature, 2023. https://doi.org/10.1007/s00453-023-01154-8.
ieee: M. Henzinger, B. Jin, R. Peng, and D. P. Williamson, “A combinatorial cut-toggling
algorithm for solving Laplacian linear systems,” Algorithmica, vol. 85.
Springer Nature, pp. 2680–3716, 2023.
ista: Henzinger M, Jin B, Peng R, Williamson DP. 2023. A combinatorial cut-toggling
algorithm for solving Laplacian linear systems. Algorithmica. 85, 2680–3716.
mla: Henzinger, Monika, et al. “A Combinatorial Cut-Toggling Algorithm for Solving
Laplacian Linear Systems.” Algorithmica, vol. 85, Springer Nature, 2023,
pp. 2680–3716, doi:10.1007/s00453-023-01154-8.
short: M. Henzinger, B. Jin, R. Peng, D.P. Williamson, Algorithmica 85 (2023) 2680–3716.
date_created: 2023-08-13T22:01:13Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2025-04-15T06:24:05Z
day: '01'
department:
- _id: MoHe
doi: 10.1007/s00453-023-01154-8
ec_funded: 1
external_id:
arxiv:
- '2010.16316'
isi:
- '001041254900002'
intvolume: ' 85'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2010.16316
month: '12'
oa: 1
oa_version: Preprint
page: 2680-3716
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: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: P33775
name: Fast Algorithms for a Reactive Network Layer
publication: Algorithmica
publication_identifier:
eissn:
- 1432-0541
issn:
- 0178-4617
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A combinatorial cut-toggling algorithm for solving Laplacian linear systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 85
year: '2023'
...
---
_id: '14076'
abstract:
- lang: eng
text: Hyperproperties are properties that relate multiple execution traces. Previous
work on monitoring hyperproperties focused on synchronous hyperproperties, usually
specified in HyperLTL. When monitoring synchronous hyperproperties, all traces
are assumed to proceed at the same speed. We introduce (multi-trace) prefix transducers
and show how to use them for monitoring synchronous as well as, for the first
time, asynchronous hyperproperties. Prefix transducers map multiple input traces
into one or more output traces by incrementally matching prefixes of the input
traces against expressions similar to regular expressions. The prefixes of different
traces which are consumed by a single matching step of the monitor may have different
lengths. The deterministic and executable nature of prefix transducers makes them
more suitable as an intermediate formalism for runtime verification than logical
specifications, which tend to be highly non-deterministic, especially in the case
of asynchronous hyperproperties. We report on a set of experiments about monitoring
asynchronous version of observational determinism.
acknowledgement: This work was supported in part by the ERC-2020-AdG 101020093. The
authors would like to thank Ana Oliveira da Costa for commenting on a draft of the
paper.
alternative_title:
- LNCS
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Marek
full_name: Chalupa, Marek
id: 87e34708-d6c6-11ec-9f5b-9391e7be2463
last_name: Chalupa
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
citation:
ama: 'Chalupa M, Henzinger TA. Monitoring hyperproperties with prefix transducers.
In: 23nd International Conference on Runtime Verification. Vol 14245. Springer
Nature; 2023:168-190. doi:10.1007/978-3-031-44267-4_9'
apa: 'Chalupa, M., & Henzinger, T. A. (2023). Monitoring hyperproperties with
prefix transducers. In 23nd International Conference on Runtime Verification
(Vol. 14245, pp. 168–190). Thessaloniki, Greek: Springer Nature. https://doi.org/10.1007/978-3-031-44267-4_9'
chicago: Chalupa, Marek, and Thomas A Henzinger. “Monitoring Hyperproperties with
Prefix Transducers.” In 23nd International Conference on Runtime Verification,
14245:168–90. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-44267-4_9.
ieee: M. Chalupa and T. A. Henzinger, “Monitoring hyperproperties with prefix transducers,”
in 23nd International Conference on Runtime Verification, Thessaloniki,
Greek, 2023, vol. 14245, pp. 168–190.
ista: 'Chalupa M, Henzinger TA. 2023. Monitoring hyperproperties with prefix transducers.
23nd International Conference on Runtime Verification. RV: Conference on Runtime
Verification, LNCS, vol. 14245, 168–190.'
mla: Chalupa, Marek, and Thomas A. Henzinger. “Monitoring Hyperproperties with Prefix
Transducers.” 23nd International Conference on Runtime Verification, vol.
14245, Springer Nature, 2023, pp. 168–90, doi:10.1007/978-3-031-44267-4_9.
short: M. Chalupa, T.A. Henzinger, in:, 23nd International Conference on Runtime
Verification, Springer Nature, 2023, pp. 168–190.
conference:
end_date: 2023-10-07
location: Thessaloniki, Greek
name: 'RV: Conference on Runtime Verification'
start_date: 2023-10-04
corr_author: '1'
date_created: 2023-08-16T20:46:08Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2025-04-14T09:42:55Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-031-44267-4_9
ec_funded: 1
file:
- access_level: open_access
checksum: ee33bd6f1a26f4dae7a8192584869fd8
content_type: application/pdf
creator: dernst
date_created: 2023-10-16T07:15:11Z
date_updated: 2023-10-16T07:15:11Z
file_id: '14430'
file_name: 2023_LNCS_RV_Chalupa.pdf
file_size: 867256
relation: main_file
success: 1
file_date_updated: 2023-10-16T07:15:11Z
has_accepted_license: '1'
intvolume: ' 14245'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 168-190
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: 23nd International Conference on Runtime Verification
publication_identifier:
eisbn:
- 978-3-031-44267-4
isbn:
- 978-3-031-44266-7
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '15035'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Monitoring hyperproperties with prefix transducers
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14245
year: '2023'
...
---
_id: '14080'
abstract:
- lang: eng
text: Extracellular signal-regulated kinase (ERK) has been recognized as a critical
regulator in various physiological and pathological processes. Extensive research
has elucidated the signaling mechanisms governing ERK activation via biochemical
regulations with upstream molecules, particularly receptor tyrosine kinases (RTKs).
However, recent advances have highlighted the role of mechanical forces in activating
the RTK–ERK signaling pathways, thereby opening new avenues of research into mechanochemical
interplay in multicellular tissues. Here, we review the force-induced ERK activation
in cells and propose possible mechanosensing mechanisms underlying the mechanoresponsive
ERK activation. We conclude that mechanical forces are not merely passive factors
shaping cells and tissues but also active regulators of cellular signaling pathways
controlling collective cell behaviors.
acknowledgement: TH was supported by JSPS KAKENHI Grant (no. 21H05290) and the Ministry
of Education under the Research Centres of Excellence programme through the Mechanobiology
Institute at National University of Singapore and by Department of Physiology at
National University of Singapore. NH was supported by JSPS KAKENHI Grant (no. 20K22653).
KA was supported by JSPS KAKENHI Grants (no. 19H05798 and no. 22H02625). MM was
supported by JSPS KAKENHI Grants (no. 19H00993 and no. 20H05898) and JST Moonshot
R&D Grant JPMJPS2022. We appreciate Virgile Viasnoff and the lab members for their
valuable comments on the manuscript. We apologize to authors whose work could not
be highlighted due to space limitations.
article_number: '102217'
article_processing_charge: Yes (in subscription journal)
article_type: review
author:
- first_name: Tsuyoshi
full_name: Hirashima, Tsuyoshi
last_name: Hirashima
- first_name: Naoya
full_name: Hino, Naoya
id: 5299a9ce-7679-11eb-a7bc-d1e62b936307
last_name: Hino
- first_name: Kazuhiro
full_name: Aoki, Kazuhiro
last_name: Aoki
- first_name: Michiyuki
full_name: Matsuda, Michiyuki
last_name: Matsuda
citation:
ama: Hirashima T, Hino N, Aoki K, Matsuda M. Stretching the limits of extracellular
signal-related kinase (ERK) signaling — Cell mechanosensing to ERK activation.
Current Opinion in Cell Biology. 2023;84(10). doi:10.1016/j.ceb.2023.102217
apa: Hirashima, T., Hino, N., Aoki, K., & Matsuda, M. (2023). Stretching the
limits of extracellular signal-related kinase (ERK) signaling — Cell mechanosensing
to ERK activation. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2023.102217
chicago: Hirashima, Tsuyoshi, Naoya Hino, Kazuhiro Aoki, and Michiyuki Matsuda.
“Stretching the Limits of Extracellular Signal-Related Kinase (ERK) Signaling
— Cell Mechanosensing to ERK Activation.” Current Opinion in Cell Biology.
Elsevier, 2023. https://doi.org/10.1016/j.ceb.2023.102217.
ieee: T. Hirashima, N. Hino, K. Aoki, and M. Matsuda, “Stretching the limits of
extracellular signal-related kinase (ERK) signaling — Cell mechanosensing to ERK
activation,” Current Opinion in Cell Biology, vol. 84, no. 10. Elsevier,
2023.
ista: Hirashima T, Hino N, Aoki K, Matsuda M. 2023. Stretching the limits of extracellular
signal-related kinase (ERK) signaling — Cell mechanosensing to ERK activation.
Current Opinion in Cell Biology. 84(10), 102217.
mla: Hirashima, Tsuyoshi, et al. “Stretching the Limits of Extracellular Signal-Related
Kinase (ERK) Signaling — Cell Mechanosensing to ERK Activation.” Current Opinion
in Cell Biology, vol. 84, no. 10, 102217, Elsevier, 2023, doi:10.1016/j.ceb.2023.102217.
short: T. Hirashima, N. Hino, K. Aoki, M. Matsuda, Current Opinion in Cell Biology
84 (2023).
date_created: 2023-08-20T22:01:12Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2024-01-30T12:52:42Z
day: '01'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1016/j.ceb.2023.102217
external_id:
isi:
- '001054692200001'
pmid:
- '37574635'
file:
- access_level: open_access
checksum: 25923f8ae71344e8974530dd23c71bdc
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T12:52:12Z
date_updated: 2024-01-30T12:52:12Z
file_id: '14909'
file_name: 2023_CurrentOpinionCellBio_Hirashima.pdf
file_size: 1173762
relation: main_file
success: 1
file_date_updated: 2024-01-30T12:52:12Z
has_accepted_license: '1'
intvolume: ' 84'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Current Opinion in Cell Biology
publication_identifier:
eissn:
- 1879-0410
issn:
- 0955-0674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stretching the limits of extracellular signal-related kinase (ERK) signaling
— Cell mechanosensing to ERK activation
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: 84
year: '2023'
...
---
OA_place: publisher
OA_type: free access
_id: '14082'
abstract:
- lang: eng
text: Epithelial barrier function is commonly analyzed using transepithelial electrical
resistance, which measures ion flux across a monolayer, or by adding traceable
macromolecules and monitoring their passage across the monolayer. Although these
methods measure changes in global barrier function, they lack the sensitivity
needed to detect local or transient barrier breaches, and they do not reveal the
location of barrier leaks. Therefore, we previously developed a method that we
named the zinc-based ultrasensitive microscopic barrier assay (ZnUMBA), which
overcomes these limitations, allowing for detection of local tight junction leaks
with high spatiotemporal resolution. Here, we present expanded applications for
ZnUMBA. ZnUMBA can be used in Xenopus embryos to measure the dynamics of barrier
restoration and actin accumulation following laser injury. ZnUMBA can also be
effectively utilized in developing zebrafish embryos as well as cultured monolayers
of Madin–Darby canine kidney (MDCK) II epithelial cells. ZnUMBA is a powerful
and flexible method that, with minimal optimization, can be applied to multiple
systems to measure dynamic changes in barrier function with spatiotemporal precision.
acknowledged_ssus:
- _id: PreCl
- _id: Bio
acknowledgement: "The authors thank their respective lab members for feedback and
helpful discussions. We thank the bioimaging and zebrafish facilities of IST Austria
for their support.\r\nThis work was supported by the National Institutes of Health
[R01GM112794 to A.L.M.], by Grants-in-Aid for Scientific Research from the Japan
Society for the Promotion of Science [21K06156 to T.H.], by the Grant Program for
Biomedical Engineering Research from the Nakatani Foundation for Advancement of
Measuring Technologies in Biomedical Engineering [to T.H.] and by funding from the
European Research Council [advanced grant 742573 to C.-P.H.]. "
article_number: jcs260668
article_processing_charge: No
article_type: original
author:
- first_name: Tomohito
full_name: Higashi, Tomohito
last_name: Higashi
- first_name: Rachel E.
full_name: Stephenson, Rachel E.
last_name: Stephenson
- first_name: Cornelia
full_name: Schwayer, Cornelia
id: 3436488C-F248-11E8-B48F-1D18A9856A87
last_name: Schwayer
orcid: 0000-0001-5130-2226
- first_name: Karla
full_name: Huljev, Karla
id: 44C6F6A6-F248-11E8-B48F-1D18A9856A87
last_name: Huljev
- first_name: Atsuko Y.
full_name: Higashi, Atsuko Y.
last_name: Higashi
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Hideki
full_name: Chiba, Hideki
last_name: Chiba
- first_name: Ann L.
full_name: Miller, Ann L.
last_name: Miller
citation:
ama: Higashi T, Stephenson RE, Schwayer C, et al. ZnUMBA - a live imaging method
to detect local barrier breaches. Journal of Cell Science. 2023;136(15).
doi:10.1242/jcs.260668
apa: Higashi, T., Stephenson, R. E., Schwayer, C., Huljev, K., Higashi, A. Y., Heisenberg,
C.-P. J., … Miller, A. L. (2023). ZnUMBA - a live imaging method to detect local
barrier breaches. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.260668
chicago: Higashi, Tomohito, Rachel E. Stephenson, Cornelia Schwayer, Karla Huljev,
Atsuko Y. Higashi, Carl-Philipp J Heisenberg, Hideki Chiba, and Ann L. Miller.
“ZnUMBA - a Live Imaging Method to Detect Local Barrier Breaches.” Journal
of Cell Science. The Company of Biologists, 2023. https://doi.org/10.1242/jcs.260668.
ieee: T. Higashi et al., “ZnUMBA - a live imaging method to detect local
barrier breaches,” Journal of Cell Science, vol. 136, no. 15. The Company
of Biologists, 2023.
ista: Higashi T, Stephenson RE, Schwayer C, Huljev K, Higashi AY, Heisenberg C-PJ,
Chiba H, Miller AL. 2023. ZnUMBA - a live imaging method to detect local barrier
breaches. Journal of Cell Science. 136(15), jcs260668.
mla: Higashi, Tomohito, et al. “ZnUMBA - a Live Imaging Method to Detect Local Barrier
Breaches.” Journal of Cell Science, vol. 136, no. 15, jcs260668, The Company
of Biologists, 2023, doi:10.1242/jcs.260668.
short: T. Higashi, R.E. Stephenson, C. Schwayer, K. Huljev, A.Y. Higashi, C.-P.J.
Heisenberg, H. Chiba, A.L. Miller, Journal of Cell Science 136 (2023).
date_created: 2023-08-20T22:01:13Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2025-06-25T06:28:45Z
day: '01'
ddc:
- '570'
department:
- _id: CaHe
- _id: EvBe
doi: 10.1242/jcs.260668
ec_funded: 1
external_id:
isi:
- '001070149000001'
pmid:
- '37461809'
has_accepted_license: '1'
intvolume: ' 136'
isi: 1
issue: '15'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1242/jcs.260668
month: '08'
oa: 1
oa_version: None
pmid: 1
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
publication: Journal of Cell Science
publication_identifier:
eissn:
- 1477-9137
issn:
- 0021-9533
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: ZnUMBA - a live imaging method to detect local barrier breaches
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 136
year: '2023'
...
---
_id: '14083'
abstract:
- lang: eng
text: "In this work we consider the list-decodability and list-recoverability of
arbitrary q-ary codes, for all integer values of q ≥ 2. A code is called (p,L)_q-list-decodable
if every radius pn Hamming ball contains less than L codewords; (p,\U0001D4C1,L)_q-list-recoverability
is a generalization where we place radius pn Hamming balls on every point of a
combinatorial rectangle with side length \U0001D4C1 and again stipulate that there
be less than L codewords.\r\nOur main contribution is to precisely calculate the
maximum value of p for which there exist infinite families of positive rate (p,\U0001D4C1,L)_q-list-recoverable
codes, the quantity we call the zero-rate threshold. Denoting this value by p_*,
we in fact show that codes correcting a p_*+ε fraction of errors must have size
O_ε(1), i.e., independent of n. Such a result is typically referred to as a \"Plotkin
bound.\" To complement this, a standard random code with expurgation construction
shows that there exist positive rate codes correcting a p_*-ε fraction of errors.
We also follow a classical proof template (typically attributed to Elias and Bassalygo)
to derive from the zero-rate threshold other tradeoffs between rate and decoding
radius for list-decoding and list-recovery.\r\nTechnically, proving the Plotkin
bound boils down to demonstrating the Schur convexity of a certain function defined
on the q-simplex as well as the convexity of a univariate function derived from
it. We remark that an earlier argument claimed similar results for q-ary list-decoding;
however, we point out that this earlier proof is flawed."
acknowledgement: "Nicolas Resch: Research supported in part by ERC H2020 grant No.74079
(ALGSTRONGCRYPTO). Chen Yuan: Research supported in part by the National Key Research
and Development Projects under Grant 2022YFA1004900 and Grant 2021YFE0109900, the
National Natural Science Foundation of China under Grant 12101403 and Grant 12031011.\r\nAcknowledgements
YZ is grateful to Shashank Vatedka, Diyuan Wu and Fengxing Zhu for inspiring discussions."
alternative_title:
- LIPIcs
article_number: '99'
article_processing_charge: Yes
arxiv: 1
author:
- first_name: Nicolas
full_name: Resch, Nicolas
last_name: Resch
- first_name: Chen
full_name: Yuan, Chen
last_name: Yuan
- first_name: Yihan
full_name: Zhang, Yihan
id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c
last_name: Zhang
orcid: 0000-0002-6465-6258
citation:
ama: 'Resch N, Yuan C, Zhang Y. Zero-rate thresholds and new capacity bounds for
list-decoding and list-recovery. In: 50th International Colloquium on Automata,
Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.99'
apa: 'Resch, N., Yuan, C., & Zhang, Y. (2023). Zero-rate thresholds and new
capacity bounds for list-decoding and list-recovery. In 50th International
Colloquium on Automata, Languages, and Programming (Vol. 261). Paderborn,
Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.99'
chicago: Resch, Nicolas, Chen Yuan, and Yihan Zhang. “Zero-Rate Thresholds and New
Capacity Bounds for List-Decoding and List-Recovery.” In 50th International
Colloquium on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.99.
ieee: N. Resch, C. Yuan, and Y. Zhang, “Zero-rate thresholds and new capacity bounds
for list-decoding and list-recovery,” in 50th International Colloquium on Automata,
Languages, and Programming, Paderborn, Germany, 2023, vol. 261.
ista: 'Resch N, Yuan C, Zhang Y. 2023. Zero-rate thresholds and new capacity bounds
for list-decoding and list-recovery. 50th International Colloquium on Automata,
Languages, and Programming. ICALP: Automata, Languages and Programming, LIPIcs,
vol. 261, 99.'
mla: Resch, Nicolas, et al. “Zero-Rate Thresholds and New Capacity Bounds for List-Decoding
and List-Recovery.” 50th International Colloquium on Automata, Languages, and
Programming, vol. 261, 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023, doi:10.4230/LIPIcs.ICALP.2023.99.
short: N. Resch, C. Yuan, Y. Zhang, in:, 50th International Colloquium on Automata,
Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023.
conference:
end_date: 2023-07-14
location: Paderborn, Germany
name: 'ICALP: Automata, Languages and Programming'
start_date: 2023-07-10
corr_author: '1'
date_created: 2023-08-20T22:01:13Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2025-09-08T08:31:53Z
day: '01'
ddc:
- '000'
department:
- _id: MaMo
doi: 10.4230/LIPIcs.ICALP.2023.99
external_id:
arxiv:
- '2210.07754'
file:
- access_level: open_access
checksum: a449143fec3fbebb092cb8ef3b53c226
content_type: application/pdf
creator: dernst
date_created: 2023-08-21T07:23:18Z
date_updated: 2023-08-21T07:23:18Z
file_id: '14091'
file_name: 2023_LIPIcsICALP_Resch.pdf
file_size: 1141497
relation: main_file
success: 1
file_date_updated: 2023-08-21T07:23:18Z
has_accepted_license: '1'
intvolume: ' 261'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: 50th International Colloquium on Automata, Languages, and Programming
publication_identifier:
isbn:
- '9783959772785'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
record:
- id: '17330'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 261
year: '2023'
...
---
_id: '14084'
abstract:
- lang: eng
text: "A central problem in computational statistics is to convert a procedure for
sampling combinatorial objects into a procedure for counting those objects, and
vice versa. We will consider sampling problems which come from Gibbs distributions,
which are families of probability distributions over a discrete space Ω with probability
mass function of the form μ^Ω_β(ω) ∝ e^{β H(ω)} for β in an interval [β_min, β_max]
and H(ω) ∈ {0} ∪ [1, n].\r\nThe partition function is the normalization factor
Z(β) = ∑_{ω ∈ Ω} e^{β H(ω)}, and the log partition ratio is defined as q = (log
Z(β_max))/Z(β_min)\r\nWe develop a number of algorithms to estimate the counts
c_x using roughly Õ(q/ε²) samples for general Gibbs distributions and Õ(n²/ε²)
samples for integer-valued distributions (ignoring some second-order terms and
parameters), We show this is optimal up to logarithmic factors. We illustrate
with improved algorithms for counting connected subgraphs and perfect matchings
in a graph."
acknowledgement: We thank Heng Guo for helpful explanations of algorithms for sampling
connected subgraphs and matchings, Maksym Serbyn for bringing to our attention the
Wang-Landau algorithm and its use in physics.
alternative_title:
- LIPIcs
article_number: '72'
article_processing_charge: Yes
arxiv: 1
author:
- first_name: David G.
full_name: Harris, David G.
last_name: Harris
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Harris DG, Kolmogorov V. Parameter estimation for Gibbs distributions. In:
50th International Colloquium on Automata, Languages, and Programming.
Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.72'
apa: 'Harris, D. G., & Kolmogorov, V. (2023). Parameter estimation for Gibbs
distributions. In 50th International Colloquium on Automata, Languages, and
Programming (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.72'
chicago: Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs
Distributions.” In 50th International Colloquium on Automata, Languages, and
Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.72.
ieee: D. G. Harris and V. Kolmogorov, “Parameter estimation for Gibbs distributions,”
in 50th International Colloquium on Automata, Languages, and Programming,
Paderborn, Germany, 2023, vol. 261.
ista: 'Harris DG, Kolmogorov V. 2023. Parameter estimation for Gibbs distributions.
50th International Colloquium on Automata, Languages, and Programming. ICALP:
Automata, Languages and Programming, LIPIcs, vol. 261, 72.'
mla: Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs
Distributions.” 50th International Colloquium on Automata, Languages, and Programming,
vol. 261, 72, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.72.
short: D.G. Harris, V. Kolmogorov, in:, 50th International Colloquium on Automata,
Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023.
conference:
end_date: 2023-07-14
location: Paderborn, Germany
name: 'ICALP: Automata, Languages and Programming'
start_date: 2023-07-10
corr_author: '1'
date_created: 2023-08-20T22:01:14Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2025-07-10T11:50:45Z
day: '01'
ddc:
- '000'
- '510'
department:
- _id: VlKo
doi: 10.4230/LIPIcs.ICALP.2023.72
external_id:
arxiv:
- '2007.10824'
file:
- access_level: open_access
checksum: 6dee0684245bb1c524b9c955db1e933d
content_type: application/pdf
creator: dernst
date_created: 2023-08-21T06:45:16Z
date_updated: 2023-08-21T06:45:16Z
file_id: '14088'
file_name: 2023_LIPIcsICALP_Harris.pdf
file_size: 917791
relation: main_file
success: 1
file_date_updated: 2023-08-21T06:45:16Z
has_accepted_license: '1'
intvolume: ' 261'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: 50th International Colloquium on Automata, Languages, and Programming
publication_identifier:
isbn:
- '9783959772785'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
record:
- id: '18855'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Parameter estimation for Gibbs distributions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 261
year: '2023'
...
---
_id: '14085'
abstract:
- lang: eng
text: We show an (1+ϵ)-approximation algorithm for maintaining maximum s-t flow
under m edge insertions in m1/2+o(1)ϵ−1/2 amortized update time for directed,
unweighted graphs. This constitutes the first sublinear dynamic maximum flow algorithm
in general sparse graphs with arbitrarily good approximation guarantee.
acknowledgement: "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.\r\n101019564 “The Design of Modern Fully Dynamic Data Structures
(MoDynStruct)” and from the\r\nAustrian Science Fund (FWF) project “Static and Dynamic
Hierarchical Graph Decompositions”,\r\nI 5982-N, and project “Fast Algorithms for
a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the
netidee SCIENCE Stiftung, 2020–2024.\r\nThis work was done in part while Gramoz
Goranci was at Institute for Theoretical Studies, ETH Zurich, Switzerland. There,
he was supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zürich
Foundation. We also thank Richard Peng, Thatchaphol Saranurak, Sebastian Forster
and Sushant Sachdeva for helpful discussions, and the anonymous reviewers for their
insightful comments."
alternative_title:
- LIPIcs
article_number: '69'
article_processing_charge: Yes
arxiv: 1
author:
- first_name: Gramoz
full_name: Goranci, Gramoz
last_name: Goranci
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
citation:
ama: 'Goranci G, Henzinger M. Efficient data structures for incremental exact and
approximate maximum flow. In: 50th International Colloquium on Automata, Languages,
and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2023. doi:10.4230/LIPIcs.ICALP.2023.69'
apa: 'Goranci, G., & Henzinger, M. (2023). Efficient data structures for incremental
exact and approximate maximum flow. In 50th International Colloquium on Automata,
Languages, and Programming (Vol. 261). Paderborn, Germany: Schloss Dagstuhl
- Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.69'
chicago: Goranci, Gramoz, and Monika Henzinger. “Efficient Data Structures for Incremental
Exact and Approximate Maximum Flow.” In 50th International Colloquium on Automata,
Languages, and Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.69.
ieee: G. Goranci and M. Henzinger, “Efficient data structures for incremental exact
and approximate maximum flow,” in 50th International Colloquium on Automata,
Languages, and Programming, Paderborn, Germany, 2023, vol. 261.
ista: 'Goranci G, Henzinger M. 2023. Efficient data structures for incremental exact
and approximate maximum flow. 50th International Colloquium on Automata, Languages,
and Programming. ICALP: Automata, Languages and Programming, LIPIcs, vol. 261,
69.'
mla: Goranci, Gramoz, and Monika Henzinger. “Efficient Data Structures for Incremental
Exact and Approximate Maximum Flow.” 50th International Colloquium on Automata,
Languages, and Programming, vol. 261, 69, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.69.
short: G. Goranci, M. Henzinger, in:, 50th International Colloquium on Automata,
Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2023.
conference:
end_date: 2023-07-14
location: Paderborn, Germany
name: 'ICALP: Automata, Languages and Programming'
start_date: 2023-07-10
corr_author: '1'
date_created: 2023-08-20T22:01:14Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2025-06-04T07:19:37Z
day: '01'
ddc:
- '000'
department:
- _id: MoHe
doi: 10.4230/LIPIcs.ICALP.2023.69
ec_funded: 1
external_id:
arxiv:
- '2211.09606'
file:
- access_level: open_access
checksum: 074177e815a1656de5d4071c7a3dffa6
content_type: application/pdf
creator: dernst
date_created: 2023-08-21T06:59:05Z
date_updated: 2023-08-21T06:59:05Z
file_id: '14089'
file_name: 2023_LIPIcsICALP_Goranci.pdf
file_size: 875910
relation: main_file
success: 1
file_date_updated: 2023-08-21T06:59:05Z
has_accepted_license: '1'
intvolume: ' 261'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: bda196b2-d553-11ed-ba76-8e8ee6c21103
grant_number: I05982
name: Static and Dynamic Hierarchical Graph Decompositions
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: P33775
name: Fast Algorithms for a Reactive Network Layer
publication: 50th International Colloquium on Automata, Languages, and Programming
publication_identifier:
isbn:
- '9783959772785'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient data structures for incremental exact and approximate maximum flow
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 261
year: '2023'
...
---
_id: '14086'
abstract:
- lang: eng
text: "The maximization of submodular functions have found widespread application
in areas such as machine learning, combinatorial optimization, and economics,
where practitioners often wish to enforce various constraints; the matroid constraint
has been investigated extensively due to its algorithmic properties and expressive
power. Though tight approximation algorithms for general matroid constraints exist
in theory, the running times of such algorithms typically scale quadratically,
and are not practical for truly large scale settings. Recent progress has focused
on fast algorithms for important classes of matroids given in explicit form. Currently,
nearly-linear time algorithms only exist for graphic and partition matroids [Alina
Ene and Huy L. Nguyen, 2019]. In this work, we develop algorithms for monotone
submodular maximization constrained by graphic, transversal matroids, or laminar
matroids in time near-linear in the size of their representation. Our algorithms
achieve an optimal approximation of 1-1/e-ε and both generalize and accelerate
the results of Ene and Nguyen [Alina Ene and Huy L. Nguyen, 2019]. In fact, the
running time of our algorithm cannot be improved within the fast continuous greedy
framework of Badanidiyuru and Vondrák [Ashwinkumar Badanidiyuru and Jan Vondrák,
2014].\r\nTo achieve near-linear running time, we make use of dynamic data structures
that maintain bases with approximate maximum cardinality and weight under certain
element updates. These data structures need to support a weight decrease operation
and a novel Freeze operation that allows the algorithm to freeze elements (i.e.
force to be contained) in its basis regardless of future data structure operations.
For the laminar matroid, we present a new dynamic data structure using the top
tree interface of Alstrup, Holm, de Lichtenberg, and Thorup [Stephen Alstrup et
al., 2005] that maintains the maximum weight basis under insertions and deletions
of elements in O(log n) time. This data structure needs to support certain subtree
query and path update operations that are performed every insertion and deletion
that are non-trivial to handle in conjunction. For the transversal matroid the
Freeze operation corresponds to requiring the data structure to keep a certain
set S of vertices matched, a property that we call S-stability. While there is
a large body of work on dynamic matching algorithms, none are S-stable and maintain
an approximate maximum weight matching under vertex updates. We give the first
such algorithm for bipartite graphs with total running time linear (up to log
factors) in the number of edges."
acknowledgement: " Monika Henzinger: This project has received funding from the European
Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation
programme (Grant\r\nagreement No. 101019564 “The Design of Modern Fully Dynamic
Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project
“Static and Dynamic Hierarchical Graph Decompositions”, I 5982-N, and project “Fast
Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional
funding from the netidee SCIENCE Stiftung, 2020–2024. Jan Vondrák: Supported by
NSF Award 2127781."
alternative_title:
- LIPIcs
article_number: '74'
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: Paul
full_name: Liu, Paul
last_name: Liu
- first_name: Jan
full_name: Vondrák, Jan
last_name: Vondrák
- first_name: Da Wei
full_name: Zheng, Da Wei
last_name: Zheng
citation:
ama: 'Henzinger M, Liu P, Vondrák J, Zheng DW. Faster submodular maximization for
several classes of matroids. In: 50th International Colloquium on Automata,
Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.74'
apa: 'Henzinger, M., Liu, P., Vondrák, J., & Zheng, D. W. (2023). Faster submodular
maximization for several classes of matroids. In 50th International Colloquium
on Automata, Languages, and Programming (Vol. 261). Paderborn, Germany: Schloss
Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.74'
chicago: Henzinger, Monika, Paul Liu, Jan Vondrák, and Da Wei Zheng. “Faster Submodular
Maximization for Several Classes of Matroids.” In 50th International Colloquium
on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.74.
ieee: M. Henzinger, P. Liu, J. Vondrák, and D. W. Zheng, “Faster submodular maximization
for several classes of matroids,” in 50th International Colloquium on Automata,
Languages, and Programming, Paderborn, Germany, 2023, vol. 261.
ista: 'Henzinger M, Liu P, Vondrák J, Zheng DW. 2023. Faster submodular maximization
for several classes of matroids. 50th International Colloquium on Automata, Languages,
and Programming. ICALP: Automata, Languages and Programming, LIPIcs, vol. 261,
74.'
mla: Henzinger, Monika, et al. “Faster Submodular Maximization for Several Classes
of Matroids.” 50th International Colloquium on Automata, Languages, and Programming,
vol. 261, 74, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.74.
short: M. Henzinger, P. Liu, J. Vondrák, D.W. Zheng, in:, 50th International Colloquium
on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2023.
conference:
end_date: 2023-07-14
location: Paderborn, Germany
name: 'ICALP: Automata, Languages and Programming'
start_date: 2023-07-10
corr_author: '1'
date_created: 2023-08-20T22:01:14Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2025-07-10T11:50:45Z
day: '01'
ddc:
- '000'
department:
- _id: MoHe
doi: 10.4230/LIPIcs.ICALP.2023.74
ec_funded: 1
external_id:
arxiv:
- '2305.00122'
file:
- access_level: open_access
checksum: a5eef225014e003efbfbe4830fdd23cb
content_type: application/pdf
creator: dernst
date_created: 2023-08-21T07:04:36Z
date_updated: 2023-08-21T07:04:36Z
file_id: '14090'
file_name: 2023_LIPIcsICALP_HenzingerM.pdf
file_size: 930943
relation: main_file
success: 1
file_date_updated: 2023-08-21T07:04:36Z
has_accepted_license: '1'
intvolume: ' 261'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: bda196b2-d553-11ed-ba76-8e8ee6c21103
grant_number: I05982
name: Static and Dynamic Hierarchical Graph Decompositions
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: P33775
name: Fast Algorithms for a Reactive Network Layer
publication: 50th International Colloquium on Automata, Languages, and Programming
publication_identifier:
isbn:
- '9783959772785'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Faster submodular maximization for several classes of matroids
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 261
year: '2023'
...
---
_id: '14087'
abstract:
- lang: eng
text: Polar active matter of self-propelled particles sustain spontaneous flows
through the full-integer topological defects. We study theoretically the incompressible
flow profiles around ±1 defects induced by polar and dipolar active forces. We
show that dipolar forces induce vortical flows around the +1 defect, while the
flow around the −1 defect has an 8-fold rotational symmetry. The vortical flow
changes its chirality near the +1 defect core in the absence of the friction with
a substrate. We show analytically that the flow induced by polar active forces
is vortical near the +1 defect and is 4-fold symmetric near the −1 defect, while
it becomes uniform in the far-field. For a pair of oppositely charged defects,
this polar flow contributes to a mutual interaction force that depends only on
the orientation of the defect pair relative to the background polarization, and
that enhances defect pair annihilation. This is in contradiction with the effect
of dipolar active forces which decay inversely proportional with the defect separation
distance. As such, our analyses reveals a long-ranged mechanism for the pairwise
interaction between topological defects in polar active matter.
acknowledgement: J. Rø and L. A. acknowledge support from the Research Council of
Norway through the Center of Excellence funding scheme, Project No. 262644 (PoreLab).
A. D. acknowledges funding from the Novo Nordisk Foundation (grant No. NNF18SA0035142
and NERD grant No. NNF21OC0068687), Villum Fonden Grant no. 29476, and the European
Union via the ERC-Starting Grant PhysCoMeT. Views and opinions expressed are however
those of the authors only and do not necessarily reflect those of the European Union
or the European Research Council. Neither the European Union nor the granting authority
can be held responsible for them.
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Jonas
full_name: Rønning, Jonas
last_name: Rønning
- first_name: Julian B
full_name: Renaud, Julian B
id: 7af6767d-14eb-11ed-b536-a32449ae867c
last_name: Renaud
- first_name: Amin
full_name: Doostmohammadi, Amin
last_name: Doostmohammadi
- first_name: Luiza
full_name: Angheluta, Luiza
last_name: Angheluta
citation:
ama: Rønning J, Renaud JB, Doostmohammadi A, Angheluta L. Spontaneous flows and
dynamics of full-integer topological defects in polar active matter. Soft Matter.
2023;39:7513-7527. doi:10.1039/d3sm00316g
apa: Rønning, J., Renaud, J. B., Doostmohammadi, A., & Angheluta, L. (2023).
Spontaneous flows and dynamics of full-integer topological defects in polar active
matter. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/d3sm00316g
chicago: Rønning, Jonas, Julian B Renaud, Amin Doostmohammadi, and Luiza Angheluta.
“Spontaneous Flows and Dynamics of Full-Integer Topological Defects in Polar Active
Matter.” Soft Matter. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d3sm00316g.
ieee: J. Rønning, J. B. Renaud, A. Doostmohammadi, and L. Angheluta, “Spontaneous
flows and dynamics of full-integer topological defects in polar active matter,”
Soft Matter, vol. 39. Royal Society of Chemistry, pp. 7513–7527, 2023.
ista: Rønning J, Renaud JB, Doostmohammadi A, Angheluta L. 2023. Spontaneous flows
and dynamics of full-integer topological defects in polar active matter. Soft
Matter. 39, 7513–7527.
mla: Rønning, Jonas, et al. “Spontaneous Flows and Dynamics of Full-Integer Topological
Defects in Polar Active Matter.” Soft Matter, vol. 39, Royal Society of
Chemistry, 2023, pp. 7513–27, doi:10.1039/d3sm00316g.
short: J. Rønning, J.B. Renaud, A. Doostmohammadi, L. Angheluta, Soft Matter 39
(2023) 7513–7527.
date_created: 2023-08-20T22:01:15Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2025-04-23T13:03:12Z
day: '01'
ddc:
- '540'
department:
- _id: GradSch
doi: 10.1039/d3sm00316g
external_id:
arxiv:
- '2303.07063'
isi:
- '001035766100001'
pmid:
- '37493084'
file:
- access_level: open_access
checksum: b936747170d0b708172b518078c4081a
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T12:48:24Z
date_updated: 2024-01-30T12:48:24Z
file_id: '14908'
file_name: 2023_SoftMatter_Ronning.pdf
file_size: 7660662
relation: main_file
success: 1
file_date_updated: 2024-01-30T12:48:24Z
has_accepted_license: '1'
intvolume: ' 39'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 7513-7527
pmid: 1
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spontaneous flows and dynamics of full-integer topological defects in polar
active matter
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 39
year: '2023'
...
---
_id: '14103'
abstract:
- lang: eng
text: Observations of individual massive stars, super-luminous supernovae, gamma-ray
bursts, and gravitational wave events involving spectacular black hole mergers
indicate that the low-metallicity Universe is fundamentally different from our
own Galaxy. Many transient phenomena will remain enigmatic until we achieve a
firm understanding of the physics and evolution of massive stars at low metallicity
(Z). The Hubble Space Telescope has devoted 500 orbits to observing ∼250 massive
stars at low Z in the ultraviolet (UV) with the COS and STIS spectrographs under
the ULLYSES programme. The complementary X-Shooting ULLYSES (XShootU) project
provides an enhanced legacy value with high-quality optical and near-infrared
spectra obtained with the wide-wavelength coverage X-shooter spectrograph at ESO’s
Very Large Telescope. We present an overview of the XShootU project, showing that
combining ULLYSES UV and XShootU optical spectra is critical for the uniform determination
of stellar parameters such as effective temperature, surface gravity, luminosity,
and abundances, as well as wind properties such as mass-loss rates as a function
of Z. As uncertainties in stellar and wind parameters percolate into many adjacent
areas of astrophysics, the data and modelling of the XShootU project is expected
to be a game changer for our physical understanding of massive stars at low Z.
To be able to confidently interpret James Webb Space Telescope spectra of the
first stellar generations, the individual spectra of low-Z stars need to be understood,
which is exactly where XShootU can deliver.
article_number: A154
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Jorick S.
full_name: Vink, Jorick S.
last_name: Vink
- first_name: A.
full_name: Mehner, A.
last_name: Mehner
- first_name: P. A.
full_name: Crowther, P. A.
last_name: Crowther
- first_name: A.
full_name: Fullerton, A.
last_name: Fullerton
- first_name: M.
full_name: Garcia, M.
last_name: Garcia
- first_name: F.
full_name: Martins, F.
last_name: Martins
- first_name: N.
full_name: Morrell, N.
last_name: Morrell
- first_name: L. M.
full_name: Oskinova, L. M.
last_name: Oskinova
- first_name: N.
full_name: St-Louis, N.
last_name: St-Louis
- first_name: A.
full_name: ud-Doula, A.
last_name: ud-Doula
- first_name: A. A. C.
full_name: Sander, A. A. C.
last_name: Sander
- first_name: H.
full_name: Sana, H.
last_name: Sana
- first_name: J.-C.
full_name: Bouret, J.-C.
last_name: Bouret
- first_name: B.
full_name: Kubátová, B.
last_name: Kubátová
- first_name: P.
full_name: Marchant, P.
last_name: Marchant
- first_name: L. P.
full_name: Martins, L. P.
last_name: Martins
- first_name: A.
full_name: Wofford, A.
last_name: Wofford
- first_name: J. Th.
full_name: van Loon, J. Th.
last_name: van Loon
- first_name: O.
full_name: Grace Telford, O.
last_name: Grace Telford
- first_name: Ylva Louise Linsdotter
full_name: Götberg, Ylva Louise Linsdotter
id: d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d
last_name: Götberg
orcid: 0000-0002-6960-6911
- first_name: D. M.
full_name: Bowman, D. M.
last_name: Bowman
- first_name: C.
full_name: Erba, C.
last_name: Erba
- first_name: V. M.
full_name: Kalari, V. M.
last_name: Kalari
- first_name: M.
full_name: Abdul-Masih, M.
last_name: Abdul-Masih
- first_name: T.
full_name: Alkousa, T.
last_name: Alkousa
- first_name: F.
full_name: Backs, F.
last_name: Backs
- first_name: C. L.
full_name: Barbosa, C. L.
last_name: Barbosa
- first_name: S. R.
full_name: Berlanas, S. R.
last_name: Berlanas
- first_name: M.
full_name: Bernini-Peron, M.
last_name: Bernini-Peron
- first_name: J. M.
full_name: Bestenlehner, J. M.
last_name: Bestenlehner
- first_name: R.
full_name: Blomme, R.
last_name: Blomme
- first_name: J.
full_name: Bodensteiner, J.
last_name: Bodensteiner
- first_name: S. A.
full_name: Brands, S. A.
last_name: Brands
- first_name: C. J.
full_name: Evans, C. J.
last_name: Evans
- first_name: A.
full_name: David-Uraz, A.
last_name: David-Uraz
- first_name: F. A.
full_name: Driessen, F. A.
last_name: Driessen
- first_name: K.
full_name: Dsilva, K.
last_name: Dsilva
- first_name: S.
full_name: Geen, S.
last_name: Geen
- first_name: V. M. A.
full_name: Gómez-González, V. M. A.
last_name: Gómez-González
- first_name: L.
full_name: Grassitelli, L.
last_name: Grassitelli
- first_name: W.-R.
full_name: Hamann, W.-R.
last_name: Hamann
- first_name: C.
full_name: Hawcroft, C.
last_name: Hawcroft
- first_name: A.
full_name: Herrero, A.
last_name: Herrero
- first_name: E. R.
full_name: Higgins, E. R.
last_name: Higgins
- first_name: D.
full_name: John Hillier, D.
last_name: John Hillier
- first_name: R.
full_name: Ignace, R.
last_name: Ignace
- first_name: A. G.
full_name: Istrate, A. G.
last_name: Istrate
- first_name: L.
full_name: Kaper, L.
last_name: Kaper
- first_name: N. D.
full_name: Kee, N. D.
last_name: Kee
- first_name: C.
full_name: Kehrig, C.
last_name: Kehrig
- first_name: Z.
full_name: Keszthelyi, Z.
last_name: Keszthelyi
- first_name: J.
full_name: Klencki, J.
last_name: Klencki
- first_name: A.
full_name: de Koter, A.
last_name: de Koter
- first_name: R.
full_name: Kuiper, R.
last_name: Kuiper
- first_name: E.
full_name: Laplace, E.
last_name: Laplace
- first_name: C. J. K.
full_name: Larkin, C. J. K.
last_name: Larkin
- first_name: R. R.
full_name: Lefever, R. R.
last_name: Lefever
- first_name: C.
full_name: Leitherer, C.
last_name: Leitherer
- first_name: D. J.
full_name: Lennon, D. J.
last_name: Lennon
- first_name: L.
full_name: Mahy, L.
last_name: Mahy
- first_name: J.
full_name: Maíz Apellániz, J.
last_name: Maíz Apellániz
- first_name: G.
full_name: Maravelias, G.
last_name: Maravelias
- first_name: W.
full_name: Marcolino, W.
last_name: Marcolino
- first_name: A. F.
full_name: McLeod, A. F.
last_name: McLeod
- first_name: S. E.
full_name: de Mink, S. E.
last_name: de Mink
- first_name: F.
full_name: Najarro, F.
last_name: Najarro
- first_name: M. S.
full_name: Oey, M. S.
last_name: Oey
- first_name: T. N.
full_name: Parsons, T. N.
last_name: Parsons
- first_name: D.
full_name: Pauli, D.
last_name: Pauli
- first_name: M. G.
full_name: Pedersen, M. G.
last_name: Pedersen
- first_name: R. K.
full_name: Prinja, R. K.
last_name: Prinja
- first_name: V.
full_name: Ramachandran, V.
last_name: Ramachandran
- first_name: M. C.
full_name: Ramírez-Tannus, M. C.
last_name: Ramírez-Tannus
- first_name: G. N.
full_name: Sabhahit, G. N.
last_name: Sabhahit
- first_name: A.
full_name: Schootemeijer, A.
last_name: Schootemeijer
- first_name: S.
full_name: Reyero Serantes, S.
last_name: Reyero Serantes
- first_name: T.
full_name: Shenar, T.
last_name: Shenar
- first_name: G. S.
full_name: Stringfellow, G. S.
last_name: Stringfellow
- first_name: N.
full_name: Sudnik, N.
last_name: Sudnik
- first_name: F.
full_name: Tramper, F.
last_name: Tramper
- first_name: L.
full_name: Wang, L.
last_name: Wang
citation:
ama: 'Vink JS, Mehner A, Crowther PA, et al. X-shooting ULLYSES: Massive stars at
low metallicity. I. Project description. Astronomy & Astrophysics.
2023;675. doi:10.1051/0004-6361/202245650'
apa: 'Vink, J. S., Mehner, A., Crowther, P. A., Fullerton, A., Garcia, M., Martins,
F., … Wang, L. (2023). X-shooting ULLYSES: Massive stars at low metallicity. I.
Project description. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202245650'
chicago: 'Vink, Jorick S., A. Mehner, P. A. Crowther, A. Fullerton, M. Garcia, F.
Martins, N. Morrell, et al. “X-Shooting ULLYSES: Massive Stars at Low Metallicity.
I. Project Description.” Astronomy & Astrophysics. EDP Sciences, 2023.
https://doi.org/10.1051/0004-6361/202245650.'
ieee: 'J. S. Vink et al., “X-shooting ULLYSES: Massive stars at low metallicity.
I. Project description,” Astronomy & Astrophysics, vol. 675. EDP Sciences,
2023.'
ista: 'Vink JS, Mehner A, Crowther PA, Fullerton A, Garcia M, Martins F, Morrell
N, Oskinova LM, St-Louis N, ud-Doula A, Sander AAC, Sana H, Bouret J-C, Kubátová
B, Marchant P, Martins LP, Wofford A, van Loon JT, Grace Telford O, Götberg YLL,
Bowman DM, Erba C, Kalari VM, Abdul-Masih M, Alkousa T, Backs F, Barbosa CL, Berlanas
SR, Bernini-Peron M, Bestenlehner JM, Blomme R, Bodensteiner J, Brands SA, Evans
CJ, David-Uraz A, Driessen FA, Dsilva K, Geen S, Gómez-González VMA, Grassitelli
L, Hamann W-R, Hawcroft C, Herrero A, Higgins ER, John Hillier D, Ignace R, Istrate
AG, Kaper L, Kee ND, Kehrig C, Keszthelyi Z, Klencki J, de Koter A, Kuiper R,
Laplace E, Larkin CJK, Lefever RR, Leitherer C, Lennon DJ, Mahy L, Maíz Apellániz
J, Maravelias G, Marcolino W, McLeod AF, de Mink SE, Najarro F, Oey MS, Parsons
TN, Pauli D, Pedersen MG, Prinja RK, Ramachandran V, Ramírez-Tannus MC, Sabhahit
GN, Schootemeijer A, Reyero Serantes S, Shenar T, Stringfellow GS, Sudnik N, Tramper
F, Wang L. 2023. X-shooting ULLYSES: Massive stars at low metallicity. I. Project
description. Astronomy & Astrophysics. 675, A154.'
mla: 'Vink, Jorick S., et al. “X-Shooting ULLYSES: Massive Stars at Low Metallicity.
I. Project Description.” Astronomy & Astrophysics, vol. 675, A154,
EDP Sciences, 2023, doi:10.1051/0004-6361/202245650.'
short: J.S. Vink, A. Mehner, P.A. Crowther, A. Fullerton, M. Garcia, F. Martins,
N. Morrell, L.M. Oskinova, N. St-Louis, A. ud-Doula, A.A.C. Sander, H. Sana, J.-C.
Bouret, B. Kubátová, P. Marchant, L.P. Martins, A. Wofford, J.T. van Loon, O.
Grace Telford, Y.L.L. Götberg, D.M. Bowman, C. Erba, V.M. Kalari, M. Abdul-Masih,
T. Alkousa, F. Backs, C.L. Barbosa, S.R. Berlanas, M. Bernini-Peron, J.M. Bestenlehner,
R. Blomme, J. Bodensteiner, S.A. Brands, C.J. Evans, A. David-Uraz, F.A. Driessen,
K. Dsilva, S. Geen, V.M.A. Gómez-González, L. Grassitelli, W.-R. Hamann, C. Hawcroft,
A. Herrero, E.R. Higgins, D. John Hillier, R. Ignace, A.G. Istrate, L. Kaper,
N.D. Kee, C. Kehrig, Z. Keszthelyi, J. Klencki, A. de Koter, R. Kuiper, E. Laplace,
C.J.K. Larkin, R.R. Lefever, C. Leitherer, D.J. Lennon, L. Mahy, J. Maíz Apellániz,
G. Maravelias, W. Marcolino, A.F. McLeod, S.E. de Mink, F. Najarro, M.S. Oey,
T.N. Parsons, D. Pauli, M.G. Pedersen, R.K. Prinja, V. Ramachandran, M.C. Ramírez-Tannus,
G.N. Sabhahit, A. Schootemeijer, S. Reyero Serantes, T. Shenar, G.S. Stringfellow,
N. Sudnik, F. Tramper, L. Wang, Astronomy & Astrophysics 675 (2023).
date_created: 2023-08-21T10:12:35Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-08-22T11:01:07Z
day: '01'
doi: 10.1051/0004-6361/202245650
extern: '1'
external_id:
arxiv:
- '2305.06376'
intvolume: ' 675'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1051/0004-6361/202245650
month: '07'
oa: 1
oa_version: Published Version
publication: Astronomy & Astrophysics
publication_identifier:
eissn:
- 1432-0746
issn:
- 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'X-shooting ULLYSES: Massive stars at low metallicity. I. Project description'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 675
year: '2023'
...
---
_id: '14104'
abstract:
- lang: eng
text: 'Thorne–Żytkow objects (TŻO) are potential end products of the merger of a
neutron star with a non-degenerate star. In this work, we have computed the first
grid of evolutionary models of TŻOs with the MESA stellar evolution code. With
these models, we predict several observational properties of TŻOs, including their
surface temperatures and luminosities, pulsation periods, and nucleosynthetic
products. We expand the range of possible TŻO solutions to cover 3.45≲log(Teff/K)≲3.65
and 4.85≲log(L/L⊙)≲5.5. Due to the much higher densities our TŻOs reach compared
to previous models, if TŻOs form we expect them to be stable over a larger mass
range than previously predicted, without exhibiting a gap in their mass distribution.
Using the GYRE stellar pulsation code we show that TŻOs should have fundamental
pulsation periods of 1000–2000 d, and period ratios of ≈0.2–0.3. Models computed
with a large 399 isotope fully coupled nuclear network show a nucleosynthetic
signal that is different to previously predicted. We propose a new nucleosynthetic
signal to determine a star’s status as a TŻO: the isotopologues 44TiO2 and 44TiO,
which will have a shift in their spectral features as compared to stable titanium-containing
molecules. We find that in the local Universe (∼SMC metallicities and above) TŻOs
show little heavy metal enrichment, potentially explaining the difficulty in finding
TŻOs to-date.'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: R
full_name: Farmer, R
last_name: Farmer
- first_name: M
full_name: Renzo, M
last_name: Renzo
- first_name: Ylva Louise Linsdotter
full_name: Götberg, Ylva Louise Linsdotter
id: d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d
last_name: Götberg
orcid: 0000-0002-6960-6911
- first_name: E
full_name: Bellinger, E
last_name: Bellinger
- first_name: S
full_name: Justham, S
last_name: Justham
- first_name: S E
full_name: de Mink, S E
last_name: de Mink
citation:
ama: Farmer R, Renzo M, Götberg YLL, Bellinger E, Justham S, de Mink SE. Observational
predictions for Thorne–Żytkow objects. Monthly Notices of the Royal Astronomical
Society. 2023;524(2):1692-1709. doi:10.1093/mnras/stad1977
apa: Farmer, R., Renzo, M., Götberg, Y. L. L., Bellinger, E., Justham, S., &
de Mink, S. E. (2023). Observational predictions for Thorne–Żytkow objects. Monthly
Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stad1977
chicago: Farmer, R, M Renzo, Ylva Louise Linsdotter Götberg, E Bellinger, S Justham,
and S E de Mink. “Observational Predictions for Thorne–Żytkow Objects.” Monthly
Notices of the Royal Astronomical Society. Oxford University Press, 2023.
https://doi.org/10.1093/mnras/stad1977.
ieee: R. Farmer, M. Renzo, Y. L. L. Götberg, E. Bellinger, S. Justham, and S. E.
de Mink, “Observational predictions for Thorne–Żytkow objects,” Monthly Notices
of the Royal Astronomical Society, vol. 524, no. 2. Oxford University Press,
pp. 1692–1709, 2023.
ista: Farmer R, Renzo M, Götberg YLL, Bellinger E, Justham S, de Mink SE. 2023.
Observational predictions for Thorne–Żytkow objects. Monthly Notices of the Royal
Astronomical Society. 524(2), 1692–1709.
mla: Farmer, R., et al. “Observational Predictions for Thorne–Żytkow Objects.” Monthly
Notices of the Royal Astronomical Society, vol. 524, no. 2, Oxford University
Press, 2023, pp. 1692–709, doi:10.1093/mnras/stad1977.
short: R. Farmer, M. Renzo, Y.L.L. Götberg, E. Bellinger, S. Justham, S.E. de Mink,
Monthly Notices of the Royal Astronomical Society 524 (2023) 1692–1709.
date_created: 2023-08-21T10:13:56Z
date_published: 2023-09-01T00:00:00Z
date_updated: 2023-08-21T12:12:48Z
day: '01'
doi: 10.1093/mnras/stad1977
extern: '1'
external_id:
arxiv:
- '2305.07337'
intvolume: ' 524'
issue: '2'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2305.07337
month: '09'
oa: 1
oa_version: Preprint
page: 1692-1709
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
eissn:
- 1365-2966
issn:
- 0035-8711
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Observational predictions for Thorne–Żytkow objects
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 524
year: '2023'
...
---
_id: '14105'
abstract:
- lang: eng
text: "Despite their recent success, deep neural networks continue to perform poorly
when they encounter distribution shifts at test time. Many recently proposed approaches
try to counter this by aligning the model to the new distribution prior to inference.
With no labels available this requires unsupervised objectives to adapt the model
on the observed test data. In this paper, we propose Test-Time SelfTraining (TeST):
a technique that takes as input a model trained on some source data and a novel
data distribution at test time, and learns invariant and robust representations
using a student-teacher framework. We find that models adapted using TeST significantly
improve over baseline testtime adaptation algorithms. TeST achieves competitive
performance to modern domain adaptation algorithms [4, 43], while having access
to 5-10x less data at time of adaption. We thoroughly evaluate a variety of baselines
on two tasks:\r\nobject detection and image segmentation and find that models
adapted with TeST. We find that TeST sets the new stateof-the art for test-time
domain adaptation algorithms. "
article_processing_charge: No
arxiv: 1
author:
- first_name: Samarth
full_name: Sinha, Samarth
last_name: Sinha
- first_name: Peter
full_name: Gehler, Peter
last_name: Gehler
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Bernt
full_name: Schiele, Bernt
last_name: Schiele
citation:
ama: 'Sinha S, Gehler P, Locatello F, Schiele B. TeST: Test-time Self-Training under
distribution shift. In: 2023 IEEE/CVF Winter Conference on Applications of
Computer Vision. Institute of Electrical and Electronics Engineers; 2023.
doi:10.1109/wacv56688.2023.00278'
apa: 'Sinha, S., Gehler, P., Locatello, F., & Schiele, B. (2023). TeST: Test-time
Self-Training under distribution shift. In 2023 IEEE/CVF Winter Conference
on Applications of Computer Vision. Waikoloa, HI, United States: Institute
of Electrical and Electronics Engineers. https://doi.org/10.1109/wacv56688.2023.00278'
chicago: 'Sinha, Samarth, Peter Gehler, Francesco Locatello, and Bernt Schiele.
“TeST: Test-Time Self-Training under Distribution Shift.” In 2023 IEEE/CVF
Winter Conference on Applications of Computer Vision. Institute of Electrical
and Electronics Engineers, 2023. https://doi.org/10.1109/wacv56688.2023.00278.'
ieee: 'S. Sinha, P. Gehler, F. Locatello, and B. Schiele, “TeST: Test-time Self-Training
under distribution shift,” in 2023 IEEE/CVF Winter Conference on Applications
of Computer Vision, Waikoloa, HI, United States, 2023.'
ista: 'Sinha S, Gehler P, Locatello F, Schiele B. 2023. TeST: Test-time Self-Training
under distribution shift. 2023 IEEE/CVF Winter Conference on Applications of Computer
Vision. WACV: Winter Conference on Applications of Computer Vision.'
mla: 'Sinha, Samarth, et al. “TeST: Test-Time Self-Training under Distribution Shift.”
2023 IEEE/CVF Winter Conference on Applications of Computer Vision, Institute
of Electrical and Electronics Engineers, 2023, doi:10.1109/wacv56688.2023.00278.'
short: S. Sinha, P. Gehler, F. Locatello, B. Schiele, in:, 2023 IEEE/CVF Winter
Conference on Applications of Computer Vision, Institute of Electrical and Electronics
Engineers, 2023.
conference:
end_date: 2023-01-07
location: Waikoloa, HI, United States
name: 'WACV: Winter Conference on Applications of Computer Vision'
start_date: 2023-01-02
date_created: 2023-08-21T12:11:38Z
date_published: 2023-02-06T00:00:00Z
date_updated: 2023-09-06T10:26:56Z
day: '06'
department:
- _id: FrLo
doi: 10.1109/wacv56688.2023.00278
extern: '1'
external_id:
arxiv:
- '2209.11459'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2209.11459
month: '02'
oa: 1
oa_version: Preprint
publication: 2023 IEEE/CVF Winter Conference on Applications of Computer Vision
publication_identifier:
eissn:
- 2642-9381
isbn:
- '9781665493475'
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'TeST: Test-time Self-Training under distribution shift'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14192'
abstract:
- lang: eng
text: For the Fröhlich model of the large polaron, we prove that the ground state
energy as a function of the total momentum has a unique global minimum at momentum
zero. This implies the non-existence of a ground state of the translation invariant
Fröhlich Hamiltonian and thus excludes the possibility of a localization transition
at finite coupling.
acknowledgement: D.M. and K.M. thank Robert Seiringer for helpful discussions. Open
access funding provided by Institute of Science and Technology (IST Austria). Financial
support from the Agence Nationale de la Recherche (ANR) through the projects ANR-17-CE40-0016,
ANR-17-CE40-0007-01, ANR-17-EURE-0002 (J.L.) and from the European Union’s Horizon
2020 research and innovation programme under the Maria Skłodowska-Curie grant agreement
No. 665386 (K.M.) is gratefully acknowledged.
article_number: '17'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Jonas
full_name: Lampart, Jonas
last_name: Lampart
- first_name: David Johannes
full_name: Mitrouskas, David Johannes
id: cbddacee-2b11-11eb-a02e-a2e14d04e52d
last_name: Mitrouskas
- first_name: Krzysztof
full_name: Mysliwy, Krzysztof
id: 316457FC-F248-11E8-B48F-1D18A9856A87
last_name: Mysliwy
citation:
ama: Lampart J, Mitrouskas DJ, Mysliwy K. On the global minimum of the energy–momentum
relation for the polaron. Mathematical Physics, Analysis and Geometry.
2023;26(3). doi:10.1007/s11040-023-09460-x
apa: Lampart, J., Mitrouskas, D. J., & Mysliwy, K. (2023). On the global minimum
of the energy–momentum relation for the polaron. Mathematical Physics, Analysis
and Geometry. Springer Nature. https://doi.org/10.1007/s11040-023-09460-x
chicago: Lampart, Jonas, David Johannes Mitrouskas, and Krzysztof Mysliwy. “On the
Global Minimum of the Energy–Momentum Relation for the Polaron.” Mathematical
Physics, Analysis and Geometry. Springer Nature, 2023. https://doi.org/10.1007/s11040-023-09460-x.
ieee: J. Lampart, D. J. Mitrouskas, and K. Mysliwy, “On the global minimum of the
energy–momentum relation for the polaron,” Mathematical Physics, Analysis and
Geometry, vol. 26, no. 3. Springer Nature, 2023.
ista: Lampart J, Mitrouskas DJ, Mysliwy K. 2023. On the global minimum of the energy–momentum
relation for the polaron. Mathematical Physics, Analysis and Geometry. 26(3),
17.
mla: Lampart, Jonas, et al. “On the Global Minimum of the Energy–Momentum Relation
for the Polaron.” Mathematical Physics, Analysis and Geometry, vol. 26,
no. 3, 17, Springer Nature, 2023, doi:10.1007/s11040-023-09460-x.
short: J. Lampart, D.J. Mitrouskas, K. Mysliwy, Mathematical Physics, Analysis and
Geometry 26 (2023).
corr_author: '1'
date_created: 2023-08-22T14:09:47Z
date_published: 2023-07-26T00:00:00Z
date_updated: 2024-10-09T21:06:41Z
day: '26'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1007/s11040-023-09460-x
external_id:
arxiv:
- '2206.14708'
isi:
- '001032992600001'
file:
- access_level: open_access
checksum: f0941cc66cb3ed06a12ca4b7e356cfd6
content_type: application/pdf
creator: dernst
date_created: 2023-08-23T10:59:15Z
date_updated: 2023-08-23T10:59:15Z
file_id: '14225'
file_name: 2023_MathPhysics_Lampart.pdf
file_size: 317026
relation: main_file
success: 1
file_date_updated: 2023-08-23T10:59:15Z
has_accepted_license: '1'
intvolume: ' 26'
isi: 1
issue: '3'
keyword:
- Geometry and Topology
- Mathematical Physics
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Mathematical Physics, Analysis and Geometry
publication_identifier:
eissn:
- 1572-9656
issn:
- 1385-0172
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the global minimum of the energy–momentum relation for the polaron
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2023'
...
---
_id: '14207'
abstract:
- lang: eng
text: The binding problem in human cognition, concerning how the brain represents
and connects objects within a fixed network of neural connections, remains a subject
of intense debate. Most machine learning efforts addressing this issue in an unsupervised
setting have focused on slot-based methods, which may be limiting due to their
discrete nature and difficulty to express uncertainty. Recently, the Complex AutoEncoder
was proposed as an alternative that learns continuous and distributed object-centric
representations. However, it is only applicable to simple toy data. In this paper,
we present Rotating Features, a generalization of complex-valued features to higher
dimensions, and a new evaluation procedure for extracting objects from distributed
representations. Additionally, we show the applicability of our approach to pre-trained
features. Together, these advancements enable us to scale distributed object-centric
representations from simple toy to real-world data. We believe this work advances
a new paradigm for addressing the binding problem in machine learning and has
the potential to inspire further innovation in the field.
article_number: '2306.00600'
article_processing_charge: No
arxiv: 1
author:
- first_name: Sindy
full_name: Löwe, Sindy
last_name: Löwe
- first_name: Phillip
full_name: Lippe, Phillip
last_name: Lippe
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Max
full_name: Welling, Max
last_name: Welling
citation:
ama: Löwe S, Lippe P, Locatello F, Welling M. Rotating features for object discovery.
arXiv. doi:10.48550/arXiv.2306.00600
apa: Löwe, S., Lippe, P., Locatello, F., & Welling, M. (n.d.). Rotating features
for object discovery. arXiv. https://doi.org/10.48550/arXiv.2306.00600
chicago: Löwe, Sindy, Phillip Lippe, Francesco Locatello, and Max Welling. “Rotating
Features for Object Discovery.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2306.00600.
ieee: S. Löwe, P. Lippe, F. Locatello, and M. Welling, “Rotating features for object
discovery,” arXiv. .
ista: Löwe S, Lippe P, Locatello F, Welling M. Rotating features for object discovery.
arXiv, 2306.00600.
mla: Löwe, Sindy, et al. “Rotating Features for Object Discovery.” ArXiv,
2306.00600, doi:10.48550/arXiv.2306.00600.
short: S. Löwe, P. Lippe, F. Locatello, M. Welling, ArXiv (n.d.).
corr_author: '1'
date_created: 2023-08-22T14:18:00Z
date_published: 2023-06-01T00:00:00Z
date_updated: 2024-10-09T21:06:53Z
day: '01'
department:
- _id: FrLo
doi: 10.48550/arXiv.2306.00600
external_id:
arxiv:
- '2306.00600'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2306.00600
month: '06'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
status: public
title: Rotating features for object discovery
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...