---
_id: '13970'
article_processing_charge: No
article_type: original
author:
- first_name: Amiera
full_name: Madani, Amiera
last_name: Madani
- first_name: Eric T.
full_name: Sletten, Eric T.
last_name: Sletten
- first_name: Cristian
full_name: Cavedon, Cristian
last_name: Cavedon
- first_name: Peter H.
full_name: Seeberger, Peter H.
last_name: Seeberger
- first_name: Bartholomäus
full_name: Pieber, Bartholomäus
id: 93e5e5b2-0da6-11ed-8a41-af589a024726
last_name: Pieber
orcid: 0000-0001-8689-388X
citation:
ama: Madani A, Sletten ET, Cavedon C, Seeberger PH, Pieber B. Visible-light-mediated
oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose.
Organic Syntheses. 2023;100:271-286. doi:10.15227/orgsyn.100.0271
apa: Madani, A., Sletten, E. T., Cavedon, C., Seeberger, P. H., & Pieber, B.
(2023). Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose.
Organic Syntheses. Organic Syntheses. https://doi.org/10.15227/orgsyn.100.0271
chicago: Madani, Amiera, Eric T. Sletten, Cristian Cavedon, Peter H. Seeberger,
and Bartholomäus Pieber. “Visible-Light-Mediated Oxidative Debenzylation of 3-O-Benzyl-1,2:5,6-Di-O-Isopropylidene-α-D-Glucofuranose.”
Organic Syntheses. Organic Syntheses, 2023. https://doi.org/10.15227/orgsyn.100.0271.
ieee: A. Madani, E. T. Sletten, C. Cavedon, P. H. Seeberger, and B. Pieber, “Visible-light-mediated
oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose,”
Organic Syntheses, vol. 100. Organic Syntheses, pp. 271–286, 2023.
ista: Madani A, Sletten ET, Cavedon C, Seeberger PH, Pieber B. 2023. Visible-light-mediated
oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose.
Organic Syntheses. 100, 271–286.
mla: Madani, Amiera, et al. “Visible-Light-Mediated Oxidative Debenzylation of 3-O-Benzyl-1,2:5,6-Di-O-Isopropylidene-α-D-Glucofuranose.”
Organic Syntheses, vol. 100, Organic Syntheses, 2023, pp. 271–86, doi:10.15227/orgsyn.100.0271.
short: A. Madani, E.T. Sletten, C. Cavedon, P.H. Seeberger, B. Pieber, Organic Syntheses
100 (2023) 271–286.
corr_author: '1'
date_created: 2023-08-06T22:01:11Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2024-10-09T21:06:16Z
day: '01'
department:
- _id: BaPi
doi: 10.15227/orgsyn.100.0271
intvolume: ' 100'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.15227/orgsyn.100.0271
month: '07'
oa: 1
oa_version: Published Version
page: 271-286
publication: Organic Syntheses
publication_identifier:
eissn:
- 2333-3553
issn:
- 0078-6209
publication_status: published
publisher: Organic Syntheses
quality_controlled: '1'
scopus_import: '1'
status: public
title: Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 100
year: '2023'
...
---
_id: '13971'
abstract:
- lang: eng
text: When in equilibrium, thermal forces agitate molecules, which then diffuse,
collide and bind to form materials. However, the space of accessible structures
in which micron-scale particles can be organized by thermal forces is limited,
owing to the slow dynamics and metastable states. Active agents in a passive fluid
generate forces and flows, forming a bath with active fluctuations. Two unanswered
questions are whether those active agents can drive the assembly of passive components
into unconventional states and which material properties they will exhibit. Here
we show that passive, sticky beads immersed in a bath of swimming Escherichia
coli bacteria aggregate into unconventional clusters and gels that are controlled
by the activity of the bath. We observe a slow but persistent rotation of the
aggregates that originates in the chirality of the E. coli flagella and directs
aggregation into structures that are not accessible thermally. We elucidate the
aggregation mechanism with a numerical model of spinning, sticky beads and reproduce
quantitatively the experimental results. We show that internal activity controls
the phase diagram and the structure of the aggregates. Overall, our results highlight
the promising role of active baths in designing the structural and mechanical
properties of materials with unconventional phases.
acknowledgement: D.G. and J.P. thank E. Krasnopeeva, C. Guet, G. Guessous and T. Hwa
for providing the E. coli strains. This material is based upon work supported by
the US Department of Energy under award DE-SC0019769. I.P. acknowledges funding
by the European Union’s Horizon 2020 research and innovation programme under Marie
Skłodowska-Curie Grant Agreement No. 101034413. A.Š. acknowledges funding from the
European Research Council under the European Union’s Horizon 2020 research and innovation
programme (Grant No. 802960). M.C.U. acknowledges funding from the European Union’s
Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant
Agreement No. 754411.
article_processing_charge: Yes
article_type: original
author:
- first_name: Daniel
full_name: Grober, Daniel
id: abdfc56f-34fb-11ee-bd33-fd766fce5a99
last_name: Grober
- first_name: Ivan
full_name: Palaia, Ivan
id: 9c805cd2-4b75-11ec-a374-db6dd0ed57fa
last_name: Palaia
orcid: ' 0000-0002-8843-9485 '
- first_name: Mehmet C
full_name: Ucar, Mehmet C
id: 50B2A802-6007-11E9-A42B-EB23E6697425
last_name: Ucar
orcid: 0000-0003-0506-4217
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
citation:
ama: Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. Unconventional
colloidal aggregation in chiral bacterial baths. Nature Physics. 2023;19:1680-1688.
doi:10.1038/s41567-023-02136-x
apa: Grober, D., Palaia, I., Ucar, M. C., Hannezo, E. B., Šarić, A., & Palacci,
J. A. (2023). Unconventional colloidal aggregation in chiral bacterial baths.
Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02136-x
chicago: Grober, Daniel, Ivan Palaia, Mehmet C Ucar, Edouard B Hannezo, Anđela Šarić,
and Jérémie A Palacci. “Unconventional Colloidal Aggregation in Chiral Bacterial
Baths.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02136-x.
ieee: D. Grober, I. Palaia, M. C. Ucar, E. B. Hannezo, A. Šarić, and J. A. Palacci,
“Unconventional colloidal aggregation in chiral bacterial baths,” Nature Physics,
vol. 19. Springer Nature, pp. 1680–1688, 2023.
ista: Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. 2023. Unconventional
colloidal aggregation in chiral bacterial baths. Nature Physics. 19, 1680–1688.
mla: Grober, Daniel, et al. “Unconventional Colloidal Aggregation in Chiral Bacterial
Baths.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1680–88, doi:10.1038/s41567-023-02136-x.
short: D. Grober, I. Palaia, M.C. Ucar, E.B. Hannezo, A. Šarić, J.A. Palacci, Nature
Physics 19 (2023) 1680–1688.
corr_author: '1'
date_created: 2023-08-06T22:01:11Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2025-04-14T07:43:56Z
day: '01'
ddc:
- '530'
department:
- _id: EdHa
- _id: AnSa
- _id: JePa
doi: 10.1038/s41567-023-02136-x
ec_funded: 1
external_id:
isi:
- '001037346400005'
file:
- access_level: open_access
checksum: 7e282c2ebc0ac82125a04f6b4742d4c1
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T12:26:08Z
date_updated: 2024-01-30T12:26:08Z
file_id: '14906'
file_name: 2023_NaturePhysics_Grober.pdf
file_size: 6365607
relation: main_file
success: 1
file_date_updated: 2024-01-30T12:26:08Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '11'
oa: 1
oa_version: Published Version
page: 1680-1688
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unconventional colloidal aggregation in chiral bacterial baths
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2023'
...
---
_id: '13972'
abstract:
- lang: eng
text: This Special Collection is dedicated to the field of photocatalytic synthesis
and contains a diverse selection of original research contributions. It includes
studies on catalyst development, mechanistic investigations, method development
and the use of enabling technologies, illustrating the many facets of state-of-the-art
research in photocatalytic synthesis. Further, emerging topics are surveyed and
discussed in three reviews and a concept article.
article_number: e202300683
article_processing_charge: No
article_type: letter_note
author:
- first_name: Line
full_name: Næsborg, Line
last_name: Næsborg
- first_name: Bartholomäus
full_name: Pieber, Bartholomäus
id: 93e5e5b2-0da6-11ed-8a41-af589a024726
last_name: Pieber
orcid: 0000-0001-8689-388X
- first_name: Oliver S.
full_name: Wenger, Oliver S.
last_name: Wenger
citation:
ama: 'Næsborg L, Pieber B, Wenger OS. Special Collection: Photocatalytic synthesis.
ChemCatChem. 2023;15(17). doi:10.1002/cctc.202300683'
apa: 'Næsborg, L., Pieber, B., & Wenger, O. S. (2023). Special Collection: Photocatalytic
synthesis. ChemCatChem. Wiley. https://doi.org/10.1002/cctc.202300683'
chicago: 'Næsborg, Line, Bartholomäus Pieber, and Oliver S. Wenger. “Special Collection:
Photocatalytic Synthesis.” ChemCatChem. Wiley, 2023. https://doi.org/10.1002/cctc.202300683.'
ieee: 'L. Næsborg, B. Pieber, and O. S. Wenger, “Special Collection: Photocatalytic
synthesis,” ChemCatChem, vol. 15, no. 17. Wiley, 2023.'
ista: 'Næsborg L, Pieber B, Wenger OS. 2023. Special Collection: Photocatalytic
synthesis. ChemCatChem. 15(17), e202300683.'
mla: 'Næsborg, Line, et al. “Special Collection: Photocatalytic Synthesis.” ChemCatChem,
vol. 15, no. 17, e202300683, Wiley, 2023, doi:10.1002/cctc.202300683.'
short: L. Næsborg, B. Pieber, O.S. Wenger, ChemCatChem 15 (2023).
corr_author: '1'
date_created: 2023-08-06T22:01:12Z
date_published: 2023-09-08T00:00:00Z
date_updated: 2024-07-16T07:35:15Z
day: '08'
department:
- _id: BaPi
doi: 10.1002/cctc.202300683
external_id:
isi:
- '001037859900001'
intvolume: ' 15'
isi: 1
issue: '17'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/cctc.202300683
month: '09'
oa: 1
oa_version: Published Version
publication: ChemCatChem
publication_identifier:
eissn:
- 1867-3899
issn:
- 1867-3880
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Special Collection: Photocatalytic synthesis'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2023'
...
---
_id: '13973'
abstract:
- lang: eng
text: We construct families of log K3 surfaces and study the arithmetic of their
members. We use this to produce explicit surfaces with an order 5 Brauer–Manin
obstruction to the integral Hasse principle.
acknowledgement: "This paper was completed as part of a project which received funding
from the\r\nEuropean Union’s Horizon 2020 research and innovation programme under
the Marie\r\nSkłodowska-Curie grant agreement No. 754411."
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Julian
full_name: Lyczak, Julian
id: 3572849A-F248-11E8-B48F-1D18A9856A87
last_name: Lyczak
citation:
ama: Lyczak J. Order 5 Brauer–Manin obstructions to the integral Hasse principle
on log K3 surfaces. Annales de l’Institut Fourier. 2023;73(2):447-478.
doi:10.5802/aif.3529
apa: Lyczak, J. (2023). Order 5 Brauer–Manin obstructions to the integral Hasse
principle on log K3 surfaces. Annales de l’Institut Fourier. Association
des Annales de l’Institut Fourier. https://doi.org/10.5802/aif.3529
chicago: Lyczak, Julian. “Order 5 Brauer–Manin Obstructions to the Integral Hasse
Principle on Log K3 Surfaces.” Annales de l’Institut Fourier. Association
des Annales de l’Institut Fourier, 2023. https://doi.org/10.5802/aif.3529.
ieee: J. Lyczak, “Order 5 Brauer–Manin obstructions to the integral Hasse principle
on log K3 surfaces,” Annales de l’Institut Fourier, vol. 73, no. 2. Association
des Annales de l’Institut Fourier, pp. 447–478, 2023.
ista: Lyczak J. 2023. Order 5 Brauer–Manin obstructions to the integral Hasse principle
on log K3 surfaces. Annales de l’Institut Fourier. 73(2), 447–478.
mla: Lyczak, Julian. “Order 5 Brauer–Manin Obstructions to the Integral Hasse Principle
on Log K3 Surfaces.” Annales de l’Institut Fourier, vol. 73, no. 2, Association
des Annales de l’Institut Fourier, 2023, pp. 447–78, doi:10.5802/aif.3529.
short: J. Lyczak, Annales de l’Institut Fourier 73 (2023) 447–478.
corr_author: '1'
date_created: 2023-08-06T22:01:12Z
date_published: 2023-05-12T00:00:00Z
date_updated: 2025-04-14T07:43:56Z
day: '12'
ddc:
- '510'
department:
- _id: TiBr
doi: 10.5802/aif.3529
ec_funded: 1
external_id:
arxiv:
- '2005.14013'
isi:
- '001000279500001'
file:
- access_level: open_access
checksum: daf53fc614c894422e4c0fb3d2a2ae3e
content_type: application/pdf
creator: dernst
date_created: 2023-08-07T07:19:42Z
date_updated: 2023-08-07T07:19:42Z
file_id: '13977'
file_name: 2023_AnnalesFourier_Lyczak.pdf
file_size: 1529821
relation: main_file
success: 1
file_date_updated: 2023-08-07T07:19:42Z
has_accepted_license: '1'
intvolume: ' 73'
isi: 1
issue: '2'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nd/4.0/
month: '05'
oa: 1
oa_version: Published Version
page: 447-478
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Annales de l'Institut Fourier
publication_identifier:
issn:
- 0373-0956
publication_status: published
publisher: Association des Annales de l'Institut Fourier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Order 5 Brauer–Manin obstructions to the integral Hasse principle on log K3
surfaces
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 73
year: '2023'
...
---
_id: '13976'
abstract:
- lang: eng
text: Conflicts and natural disasters affect entire populations of the countries
involved and, in addition to the thousands of lives destroyed, have a substantial
negative impact on the scientific advances these countries provide. The unprovoked
invasion of Ukraine by Russia, the devastating earthquake in Turkey and Syria,
and the ongoing conflicts in the Middle East are just a few examples. Millions
of people have been killed or displaced, their futures uncertain. These events
have resulted in extensive infrastructure collapse, with loss of electricity,
transportation, and access to services. Schools, universities, and research centers
have been destroyed along with decades’ worth of data, samples, and findings.
Scholars in disaster areas face short- and long-term problems in terms of what
they can accomplish now for obtaining grants and for employment in the long run.
In our interconnected world, conflicts and disasters are no longer a local problem
but have wide-ranging impacts on the entire world, both now and in the future.
Here, we focus on the current and ongoing impact of war on the scientific community
within Ukraine and from this draw lessons that can be applied to all affected
countries where scientists at risk are facing hardship. We present and classify
examples of effective and feasible mechanisms used to support researchers in countries
facing hardship and discuss how these can be implemented with help from the international
scientific community and what more is desperately needed. Reaching out, providing
accessible training opportunities, and developing collaborations should increase
inclusion and connectivity, support scientific advancements within affected communities,
and expedite postwar and disaster recovery.
acknowledgement: "Our article is dedicated to all freedom-loving people around the
world and to the people of Ukraine who fight for our freedom. Special thanks to
Anita Bandrowski, Oleksandra V. Ivashchenko, and Sanita Reinsone for the helpful
review, valuable criticism, and useful suggestions while preparing this manuscript,
and to Tetiana Yes'kova for helping with Ukrainian translation.\r\nAll authors volunteered
their time. No funding supported work on this article."
article_number: giad045
article_processing_charge: Yes
article_type: review
author:
- first_name: Walter
full_name: Wolfsberger, Walter
last_name: Wolfsberger
- first_name: Karishma
full_name: Chhugani, Karishma
last_name: Chhugani
- first_name: Khrystyna
full_name: Shchubelka, Khrystyna
last_name: Shchubelka
- first_name: Alina
full_name: Frolova, Alina
last_name: Frolova
- first_name: Yuriy
full_name: Salyha, Yuriy
last_name: Salyha
- first_name: Oksana
full_name: Zlenko, Oksana
last_name: Zlenko
- first_name: Mykhailo
full_name: Arych, Mykhailo
last_name: Arych
- first_name: Dmytro
full_name: Dziuba, Dmytro
last_name: Dziuba
- first_name: Andrii
full_name: Parkhomenko, Andrii
last_name: Parkhomenko
- first_name: Volodymyr
full_name: Smolanka, Volodymyr
last_name: Smolanka
- first_name: Zeynep H.
full_name: Gümüş, Zeynep H.
last_name: Gümüş
- first_name: Efe
full_name: Sezgin, Efe
last_name: Sezgin
- first_name: Alondra
full_name: Diaz-Lameiro, Alondra
last_name: Diaz-Lameiro
- first_name: Viktor R.
full_name: Toth, Viktor R.
last_name: Toth
- first_name: Megi
full_name: Maci, Megi
last_name: Maci
- first_name: Eric
full_name: Bortz, Eric
last_name: Bortz
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Patricia M.
full_name: Morton, Patricia M.
last_name: Morton
- first_name: Paweł P.
full_name: Łabaj, Paweł P.
last_name: Łabaj
- first_name: Veronika
full_name: Romero, Veronika
last_name: Romero
- first_name: Jakub
full_name: Hlávka, Jakub
last_name: Hlávka
- first_name: Serghei
full_name: Mangul, Serghei
last_name: Mangul
- first_name: Taras K.
full_name: Oleksyk, Taras K.
last_name: Oleksyk
citation:
ama: 'Wolfsberger W, Chhugani K, Shchubelka K, et al. Scientists without borders:
Lessons from Ukraine. GigaScience. 2023;12. doi:10.1093/gigascience/giad045'
apa: 'Wolfsberger, W., Chhugani, K., Shchubelka, K., Frolova, A., Salyha, Y., Zlenko,
O., … Oleksyk, T. K. (2023). Scientists without borders: Lessons from Ukraine.
GigaScience. Oxford University Press. https://doi.org/10.1093/gigascience/giad045'
chicago: 'Wolfsberger, Walter, Karishma Chhugani, Khrystyna Shchubelka, Alina Frolova,
Yuriy Salyha, Oksana Zlenko, Mykhailo Arych, et al. “Scientists without Borders:
Lessons from Ukraine.” GigaScience. Oxford University Press, 2023. https://doi.org/10.1093/gigascience/giad045.'
ieee: 'W. Wolfsberger et al., “Scientists without borders: Lessons from Ukraine,”
GigaScience, vol. 12. Oxford University Press, 2023.'
ista: 'Wolfsberger W, Chhugani K, Shchubelka K, Frolova A, Salyha Y, Zlenko O, Arych
M, Dziuba D, Parkhomenko A, Smolanka V, Gümüş ZH, Sezgin E, Diaz-Lameiro A, Toth
VR, Maci M, Bortz E, Kondrashov F, Morton PM, Łabaj PP, Romero V, Hlávka J, Mangul
S, Oleksyk TK. 2023. Scientists without borders: Lessons from Ukraine. GigaScience.
12, giad045.'
mla: 'Wolfsberger, Walter, et al. “Scientists without Borders: Lessons from Ukraine.”
GigaScience, vol. 12, giad045, Oxford University Press, 2023, doi:10.1093/gigascience/giad045.'
short: W. Wolfsberger, K. Chhugani, K. Shchubelka, A. Frolova, Y. Salyha, O. Zlenko,
M. Arych, D. Dziuba, A. Parkhomenko, V. Smolanka, Z.H. Gümüş, E. Sezgin, A. Diaz-Lameiro,
V.R. Toth, M. Maci, E. Bortz, F. Kondrashov, P.M. Morton, P.P. Łabaj, V. Romero,
J. Hlávka, S. Mangul, T.K. Oleksyk, GigaScience 12 (2023).
date_created: 2023-08-06T22:01:13Z
date_published: 2023-07-27T00:00:00Z
date_updated: 2025-05-14T11:07:17Z
day: '27'
department:
- _id: FyKo
doi: 10.1093/gigascience/giad045
external_id:
isi:
- '001081086100001'
pmid:
- '37496156'
intvolume: ' 12'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/gigascience/giad045
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: GigaScience
publication_identifier:
eissn:
- 2047-217X
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1093/gigascience/giad066
scopus_import: '1'
status: public
title: 'Scientists without borders: Lessons from Ukraine'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2023'
...
---
_id: '13988'
abstract:
- lang: eng
text: Most permissionless blockchains inherently suffer from throughput limitations.
Layer-2 systems, such as side-chains or Rollups, have been proposed as a possible
strategy to overcome this limitation. Layer-2 systems interact with the main-chain
in two ways. First, users can move funds from/to the main-chain to/from the layer-2.
Second, layer-2 systems periodically synchronize with the main-chain to keep some
form of log of their activity on the main-chain - this log is key for security.
Due to this interaction with the main-chain, which is necessary and recurrent,
layer-2 systems impose some load on the main-chain. The impact of such load on
the main-chain has been, so far, poorly understood. In addition to that, layer-2
approaches typically sacrifice decentralization and security in favor of higher
throughput. This paper presents an experimental study that analyzes the current
state of Ethereum layer-2 projects. Our goal is to assess the load they impose
on Ethereum and to understand their scalability potential in the long-run. Our
analysis shows that the impact of any given layer-2 on the main-chain is the result
of both technical aspects (how state is logged on the main-chain) and user behavior
(how often users decide to transfer funds between the layer-2 and the main-chain).
Based on our observations, we infer that without efficient mechanisms that allow
users to transfer funds in a secure and fast manner directly from one layer-2
project to another, current layer-2 systems will not be able to scale Ethereum
effectively, regardless of their technical solutions. Furthermore, from our results,
we conclude that the layer-2 systems that offer similar security guarantees as
Ethereum have limited scalability potential, while approaches that offer better
performance, sacrifice security and lead to an increase in centralization which
runs against the end-goals of permissionless blockchains.
acknowledgement: This work was supported in part by the Coordenação de Aperfeiçoamento
de Pessoal de Nivel Superior (CAPES)—Brazil (CAPES), in part by the Fundação para
a Ciência e Tecnologia (FCT) under Project UIDB/50021/2020 and Grant 2020.05270.BD,
in part by the Project COSMOS (via the Orçamento de Estado (OE) with ref. PTDC/EEI-COM/29271/2017
and via the ‘‘Programa Operacional Regional de Lisboa na sua componente Fundo Europeu
de Desenvolvimento Regional (FEDER)’’ with ref. Lisboa-01-0145-FEDER-029271), and
in part by the project Angainor with reference LISBOA-01-0145-FEDER-031456 as well
as supported by Meta Platforms for the project key Transparency at Scale.
article_processing_charge: Yes
article_type: original
author:
- first_name: Ray
full_name: Neiheiser, Ray
id: f09651b9-fec0-11ec-b5d8-934aff0e52a4
last_name: Neiheiser
orcid: 0000-0001-7227-8309
- first_name: Gustavo
full_name: Inacio, Gustavo
last_name: Inacio
- first_name: Luciana
full_name: Rech, Luciana
last_name: Rech
- first_name: Carlos
full_name: Montez, Carlos
last_name: Montez
- first_name: Miguel
full_name: Matos, Miguel
last_name: Matos
- first_name: Luis
full_name: Rodrigues, Luis
last_name: Rodrigues
citation:
ama: Neiheiser R, Inacio G, Rech L, Montez C, Matos M, Rodrigues L. Practical limitations
of Ethereum’s layer-2. IEEE Access. 2023;11:8651-8662. doi:10.1109/access.2023.3237897
apa: Neiheiser, R., Inacio, G., Rech, L., Montez, C., Matos, M., & Rodrigues,
L. (2023). Practical limitations of Ethereum’s layer-2. IEEE Access. Institute
of Electrical and Electronics Engineers. https://doi.org/10.1109/access.2023.3237897
chicago: Neiheiser, Ray, Gustavo Inacio, Luciana Rech, Carlos Montez, Miguel Matos,
and Luis Rodrigues. “Practical Limitations of Ethereum’s Layer-2.” IEEE Access.
Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/access.2023.3237897.
ieee: R. Neiheiser, G. Inacio, L. Rech, C. Montez, M. Matos, and L. Rodrigues, “Practical
limitations of Ethereum’s layer-2,” IEEE Access, vol. 11. Institute of
Electrical and Electronics Engineers, pp. 8651–8662, 2023.
ista: Neiheiser R, Inacio G, Rech L, Montez C, Matos M, Rodrigues L. 2023. Practical
limitations of Ethereum’s layer-2. IEEE Access. 11, 8651–8662.
mla: Neiheiser, Ray, et al. “Practical Limitations of Ethereum’s Layer-2.” IEEE
Access, vol. 11, Institute of Electrical and Electronics Engineers, 2023,
pp. 8651–62, doi:10.1109/access.2023.3237897.
short: R. Neiheiser, G. Inacio, L. Rech, C. Montez, M. Matos, L. Rodrigues, IEEE
Access 11 (2023) 8651–8662.
corr_author: '1'
date_created: 2023-08-09T12:09:57Z
date_published: 2023-08-01T00:00:00Z
date_updated: 2024-10-09T21:06:38Z
day: '01'
ddc:
- '000'
department:
- _id: ElKo
doi: 10.1109/access.2023.3237897
external_id:
isi:
- '000927831000001'
file:
- access_level: open_access
checksum: 4b80b0ff212edf7e5842fbdd53784432
content_type: application/pdf
creator: dernst
date_created: 2023-08-22T06:37:48Z
date_updated: 2023-08-22T06:37:48Z
file_id: '14166'
file_name: 2023_IEEEAccess_Neiheiser.pdf
file_size: 1289285
relation: main_file
success: 1
file_date_updated: 2023-08-22T06:37:48Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
keyword:
- General Engineering
- General Materials Science
- General Computer Science
- Electrical and Electronic Engineering
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 8651-8662
publication: IEEE Access
publication_identifier:
issn:
- 2169-3536
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Practical limitations of Ethereum’s layer-2
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: 11
year: '2023'
...
---
_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
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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
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
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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:
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status: public
scopus_import: '1'
status: public
title: Parameter estimation for Gibbs distributions
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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
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type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 261
year: '2023'
...