---
OA_place: publisher
OA_type: hybrid
_id: '18904'
abstract:
- lang: eng
text: The Planetary Transits and Oscillations of stars mission (PLATO) will allow
us to measure surface rotation and monitor photometric activity of tens of thousands
of main sequence solar-type and subgiant stars. This paper is the first of a series
dedicated to the preparation of the analysis of stellar surface rotation and photospheric
activity with the near-future PLATO data. We describe in this work the strategy
that will be implemented in the PLATO pipeline to measure stellar surface rotation,
photometric activity, and long-term modulations. The algorithms are applied on
both noise-free and noisy simulations of solar-type stars, which include activity
cycles, latitudinal differential rotation, and spot evolution. PLATO simulated
systematics are included in the noisy light curves. We show that surface rotation
periods can be recovered with confidence for most of the stars with only six months
of observations and that the recovery rate of the analysis significantly improves
as additional observations are collected. This means that the first PLATO data
release will already provide a substantial set of measurements for this quantity,
with a significant refinement on their quality as the instrument obtains longer
light curves. Measuring the Schwabe-like magnetic activity cycle during the mission
will require that the same field be observed over a significant timescale (more
than four years). Nevertheless, PLATO will provide a vast and robust sample of
solar-type stars with constraints on the activity-cycle length. Such a sample
is lacking from previous missions dedicated to space photometry.
acknowledgement: 'This work presents results from the European Space Agency (ESA)
space mission PLATO. The PLATO payload, the PLATO Ground Segment and PLATO data
processing are joint developments of ESA and the PLATO Mission Consortium (PMC).
Funding for the PMC is provided at national levels, in particular by countries participating
in the PLATO Multilateral Agreement (Austria, Belgium, Czech Republic, Denmark,
France, Germany, Italy, Netherlands, Portugal, Spain, Sweden, Switzerland, Norway,
and United Kingdom) and institutions from Brazil. Members of the PLATO Consortium
can be found at https://platomission.com. The ESA PLATO mission website is https://www.cosmos.esa.int/plato.
The authors thank the teams working for PLATO for all their work. They acknowledge
the critical reading and the constructive comments from the anonymous referee that
significantly allowed improving the original version of this paper. They finally
thank R. Samadi for helpful advice and suggestions concerning the PSLS abilities.
S.N.B, A.F.L, S.Me, I.P and E.C acknowledge support from PLATO ASI-INAF agreement
no. 2022-28-HH.0 “PLATO Fase D”. S.N.B, L.A, A.S.B, Q.N, and A.S acknowledge financial
support by ERC Whole Sun Synergy grant #810218. S.N.B, R.A.G, L.A, A.S.B, Q.N.,
D.B.P, E.P, and A.S acknowledge the support from PLATO CNES grant. R.A.G, D.B.P,
and E.P acknowledge the support from SoHO/GOLF CNES grant. A.S.B, Q.N, and A.S acknowledge
the support from INSU/PNST grant and Solar Orbiter CNES grant. A.S acknowledges
funding from from the European Union’s Horizon-2020 research and innovation program
(grant agreement no. 776403 ExoplANETS-A) and the Programme National de Planétologie
(PNP). A.R.G.S acknowledges the support from the FCT through national funds and
FEDER through COMPETE2020 (UIDB/04434/2020, UIDP/04434/2020, 2022.03993.PTDC) and
the support from the FCT through the work contract No. 2020.02480.CEECIND/CP1631/CT0001.
S.Ma acknowledges support from the Spanish Ministry of Science and Innovation (MICINN)
with the Ramón y Cajal fellowship no. RYC-2015-17697 and through AEI under the Severo
Ochoa Centres of Excellence Programme 2020–2023 (CEX2019-000920-S). S.Ma acknowledges
support from the Spanish Ministry of Science and Innovation (MICINN) with the grant
no. PID2019-107187GB-I00. M.J.G., K.B., R.M.O, J.P, O.R., C.R. acknowledge support
from CNES. The computations were performed with the IRFU/CEA Saclay server facilities,
funded by ERC Synergy grant WholeSun No.810218, the P2IO Labex emergence project
FlarePredict, and CNES PLATO funds. Software:star-privateer (this work), pyspot
(Aigrain et al. 2015), PSLS (Samadi et al. 2019), numpy (Harris et al. 2020), matplotlib
(Hunter 2007), scipy (Virtanen et al. 2020), astropy (Astropy Collaboration 2022),
pandas (Wes McKinney 2010; The pandas development team 2020), scikit-learn (Pedregosa
et al. 2011).'
article_number: A229
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: S. N.
full_name: Breton, S. N.
last_name: Breton
- first_name: A. F.
full_name: Lanza, A. F.
last_name: Lanza
- first_name: S.
full_name: Messina, S.
last_name: Messina
- first_name: I.
full_name: Pagano, I.
last_name: Pagano
- first_name: Lisa Annabelle
full_name: Bugnet, Lisa Annabelle
id: d9edb345-f866-11ec-9b37-d119b5234501
last_name: Bugnet
orcid: 0000-0003-0142-4000
- first_name: E.
full_name: Corsaro, E.
last_name: Corsaro
- first_name: R. A.
full_name: García, R. A.
last_name: García
- first_name: S.
full_name: Mathur, S.
last_name: Mathur
- first_name: A. R. G.
full_name: Santos, A. R. G.
last_name: Santos
- first_name: S.
full_name: Aigrain, S.
last_name: Aigrain
- first_name: L.
full_name: Amard, L.
last_name: Amard
- first_name: A. S.
full_name: Brun, A. S.
last_name: Brun
- first_name: L.
full_name: Degott, L.
last_name: Degott
- first_name: Q.
full_name: Noraz, Q.
last_name: Noraz
- first_name: D. B.
full_name: Palakkatharappil, D. B.
last_name: Palakkatharappil
- first_name: E.
full_name: Panetier, E.
last_name: Panetier
- first_name: A.
full_name: Strugarek, A.
last_name: Strugarek
- first_name: K.
full_name: Belkacem, K.
last_name: Belkacem
- first_name: M.-J
full_name: Goupil, M.-J
last_name: Goupil
- first_name: R. M.
full_name: Ouazzani, R. M.
last_name: Ouazzani
- first_name: J.
full_name: Philidet, J.
last_name: Philidet
- first_name: C.
full_name: Renié, C.
last_name: Renié
- first_name: O.
full_name: Roth, O.
last_name: Roth
citation:
ama: Breton SN, Lanza AF, Messina S, et al. Measuring stellar surface rotation and
activity with the PLATO mission. I. Strategy and application to simulated light
curves. Astronomy and Astrophysics. 2024;689. doi:10.1051/0004-6361/202449893
apa: Breton, S. N., Lanza, A. F., Messina, S., Pagano, I., Bugnet, L. A., Corsaro,
E., … Roth, O. (2024). Measuring stellar surface rotation and activity with the
PLATO mission. I. Strategy and application to simulated light curves. Astronomy
and Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202449893
chicago: Breton, S. N., A. F. Lanza, S. Messina, I. Pagano, Lisa Annabelle Bugnet,
E. Corsaro, R. A. García, et al. “Measuring Stellar Surface Rotation and Activity
with the PLATO Mission. I. Strategy and Application to Simulated Light Curves.”
Astronomy and Astrophysics. EDP Sciences, 2024. https://doi.org/10.1051/0004-6361/202449893.
ieee: S. N. Breton et al., “Measuring stellar surface rotation and activity
with the PLATO mission. I. Strategy and application to simulated light curves,”
Astronomy and Astrophysics, vol. 689. EDP Sciences, 2024.
ista: Breton SN, Lanza AF, Messina S, Pagano I, Bugnet LA, Corsaro E, García RA,
Mathur S, Santos ARG, Aigrain S, Amard L, Brun AS, Degott L, Noraz Q, Palakkatharappil
DB, Panetier E, Strugarek A, Belkacem K, Goupil M-J, Ouazzani RM, Philidet J,
Renié C, Roth O. 2024. Measuring stellar surface rotation and activity with the
PLATO mission. I. Strategy and application to simulated light curves. Astronomy
and Astrophysics. 689, A229.
mla: Breton, S. N., et al. “Measuring Stellar Surface Rotation and Activity with
the PLATO Mission. I. Strategy and Application to Simulated Light Curves.” Astronomy
and Astrophysics, vol. 689, A229, EDP Sciences, 2024, doi:10.1051/0004-6361/202449893.
short: S.N. Breton, A.F. Lanza, S. Messina, I. Pagano, L.A. Bugnet, E. Corsaro,
R.A. García, S. Mathur, A.R.G. Santos, S. Aigrain, L. Amard, A.S. Brun, L. Degott,
Q. Noraz, D.B. Palakkatharappil, E. Panetier, A. Strugarek, K. Belkacem, M.-J.
Goupil, R.M. Ouazzani, J. Philidet, C. Renié, O. Roth, Astronomy and Astrophysics
689 (2024).
date_created: 2025-01-27T13:12:44Z
date_published: 2024-09-01T00:00:00Z
date_updated: 2025-09-09T12:04:24Z
day: '01'
ddc:
- '520'
department:
- _id: LiBu
doi: 10.1051/0004-6361/202449893
external_id:
arxiv:
- '2407.03709'
isi:
- '001366206400007'
file:
- access_level: open_access
checksum: 5c871ba7370a507ed6ea9fb2304d8263
content_type: application/pdf
creator: dernst
date_created: 2025-01-27T13:18:41Z
date_updated: 2025-01-27T13:18:41Z
file_id: '18905'
file_name: 2024_AstronomyAstrophysics_Breton.pdf
file_size: 6212007
relation: main_file
success: 1
file_date_updated: 2025-01-27T13:18:41Z
has_accepted_license: '1'
intvolume: ' 689'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: Astronomy and Astrophysics
publication_identifier:
eissn:
- 1432-0746
issn:
- 0004-6361
publication_status: published
publisher: EDP Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Measuring stellar surface rotation and activity with the PLATO mission. I.
Strategy and application to simulated light curves
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 689
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18906'
abstract:
- lang: eng
text: "Expander decompositions of graphs have significantly advanced the understanding
of many classical graph problems and led to numerous fundamental theoretical results.
However, their adoption in practice has been hindered due to their inherent intricacies
and large hidden factors in their asymptotic running times. Here, we introduce
the first practically efficient algorithm for computing expander decompositions
and their hierarchies and demonstrate its effectiveness and utility by incorporating
it as the core component in a novel solver for the normalized cut graph clustering
objective.\r\nOur extensive experiments on a variety of large graphs show that
our expander-based algorithm outperforms state-of-the-art solvers for normalized
cut with respect to solution quality by a large margin on a variety of graph classes
such as citation, e-mail, and social networks or web graphs while remaining competitive
in running time."
acknowledgement: "Monika Henzinger: This project has received funding from the European
Research\r\nCouncil (ERC) under the European Union’s Horizon 2020 research and innovation
programme (Grant agreement No. 101019564) and the Austrian Science Fund (FWF) grant
DOI 10.55776/Z422, grant DOI 10.55776/I5982, and grant DOI 10.55776/P33775 with
additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nHarald Räcke,
Robin Münk: This project has received funding from the Deutsche Forschungsgemeinschaft
(DFG, German Research Foundation) – 498605858 and 470029389."
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Kathrin
full_name: Hanauer, Kathrin
last_name: Hanauer
- 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: Robin
full_name: Münk, Robin
last_name: Münk
- first_name: Harald
full_name: Räcke, Harald
last_name: Räcke
- first_name: Maximilian
full_name: Vötsch, Maximilian
last_name: Vötsch
citation:
ama: 'Hanauer K, Henzinger M, Münk R, Räcke H, Vötsch M. Expander hierarchies for
normalized cuts on graphs. In: Proceedings of the 30th ACM SIGKDD Conference
on Knowledge Discovery and Data Mining. ACM; 2024:1016-1027. doi:10.1145/3637528.3671978'
apa: 'Hanauer, K., Henzinger, M., Münk, R., Räcke, H., & Vötsch, M. (2024).
Expander hierarchies for normalized cuts on graphs. In Proceedings of the 30th
ACM SIGKDD Conference on Knowledge Discovery and Data Mining (pp. 1016–1027).
Barcelona, Spain: ACM. https://doi.org/10.1145/3637528.3671978'
chicago: Hanauer, Kathrin, Monika Henzinger, Robin Münk, Harald Räcke, and Maximilian
Vötsch. “Expander Hierarchies for Normalized Cuts on Graphs.” In Proceedings
of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining,
1016–27. ACM, 2024. https://doi.org/10.1145/3637528.3671978.
ieee: K. Hanauer, M. Henzinger, R. Münk, H. Räcke, and M. Vötsch, “Expander hierarchies
for normalized cuts on graphs,” in Proceedings of the 30th ACM SIGKDD Conference
on Knowledge Discovery and Data Mining, Barcelona, Spain, 2024, pp. 1016–1027.
ista: 'Hanauer K, Henzinger M, Münk R, Räcke H, Vötsch M. 2024. Expander hierarchies
for normalized cuts on graphs. Proceedings of the 30th ACM SIGKDD Conference on
Knowledge Discovery and Data Mining. KDD: Knowledge Discovery and Data Mining,
1016–1027.'
mla: Hanauer, Kathrin, et al. “Expander Hierarchies for Normalized Cuts on Graphs.”
Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data
Mining, ACM, 2024, pp. 1016–27, doi:10.1145/3637528.3671978.
short: K. Hanauer, M. Henzinger, R. Münk, H. Räcke, M. Vötsch, in:, Proceedings
of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, ACM,
2024, pp. 1016–1027.
conference:
end_date: 2024-08-29
location: Barcelona, Spain
name: 'KDD: Knowledge Discovery and Data Mining'
start_date: 2024-08-05
date_created: 2025-01-27T13:20:26Z
date_published: 2024-09-01T00:00:00Z
date_updated: 2025-09-09T12:04:56Z
day: '01'
ddc:
- '000'
department:
- _id: MoHe
doi: 10.1145/3637528.3671978
ec_funded: 1
external_id:
isi:
- '001324524201013'
file:
- access_level: open_access
checksum: 1265d5cf6aa5f94157631651723c4a2b
content_type: application/pdf
creator: dernst
date_created: 2025-01-27T13:25:23Z
date_updated: 2025-01-27T13:25:23Z
file_id: '18907'
file_name: 2024_ACMKDD_Hanauer.pdf
file_size: 1450331
relation: main_file
success: 1
file_date_updated: 2025-01-27T13:25:23Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1016-1027
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: 34def286-11ca-11ed-8bc3-da5948e1613c
grant_number: Z00422
name: Efficient algorithms
- _id: bda196b2-d553-11ed-ba76-8e8ee6c21103
grant_number: I05982
name: Static and Dynamic Hierarchical Graph Decompositions
publication: Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery
and Data Mining
publication_identifier:
isbn:
- '9798400704901'
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: Expander hierarchies for normalized cuts on graphs
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_place: publisher
OA_type: gold
_id: '18908'
abstract:
- lang: eng
text: Chromosomal rearrangements can lead to the coupling of reproductive barriers,
but whether and how they contribute to the completion of speciation remains unclear.
Marine snails of the genus Littorina repeatedly form hybrid zones between populations
segregating for multiple inversion arrangements, providing opportunities to study
their barrier effects. Here, we analyzed 2 adjacent transects across hybrid zones
between 2 ecotypes of Littorina fabalis (“large” and “dwarf”) adapted to different
wave exposure conditions on a Swedish island. Applying whole-genome sequencing,
we found 12 putative inversions on 9 of 17 chromosomes. Nine of the putative inversions
reached near differential fixation between the 2 ecotypes, and all were in strong
linkage disequilibrium. These inversions cover 20% of the genome and carry 93%
of divergent single nucleotide polymorphisms (SNPs). Bimodal hybrid zones in both
transects indicated that the 2 ecotypes of Littorina fabalis maintain their genetic
and phenotypic integrity following contact. The bimodality reflects the strong
coupling between inversion clines and the extension of the barrier effect across
the whole genome. Demographic inference suggests that coupling arose during a
period of allopatry and has been maintained for > 1,000 generations after
secondary contact. Overall, this study shows that the coupling of multiple chromosomal
inversions contributes to strong reproductive isolation. Notably, 2 of the putative
inversions overlap with inverted genomic regions associated with ecotype differences
in a closely related species (Littorina saxatilis), suggesting the same regions,
with similar structural variants, repeatedly contribute to ecotype evolution in
distinct species.
acknowledgement: The computations and data handling were enabled by resources provided
by the Swedish National Infrastructure for Computing at UPPMAX partially funded
by the Swedish Research Council through grant agreement no. 2018-05973. We thank
all the member of the Littorina team for the stimulating discussions about the manuscripts,
James Reeves for his help the implementation of Hsplit, and Thomas Broquet for his
useful comments in the latter stage of manuscript revisions.
article_processing_charge: Yes
article_type: letter_note
author:
- first_name: Alan
full_name: Le Moan, Alan
last_name: Le Moan
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Marina
full_name: Rafajlović, Marina
last_name: Rafajlović
- first_name: Olga
full_name: Ortega-Martinez, Olga
last_name: Ortega-Martinez
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Roger K
full_name: Butlin, Roger K
last_name: Butlin
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
citation:
ama: Le Moan A, Stankowski S, Rafajlović M, et al. Coupling of twelve putative chromosomal
inversions maintains a strong barrier to gene flow between snail ecotypes. Evolution
Letters. 2024;8(4):575-586. doi:10.1093/evlett/qrae014
apa: Le Moan, A., Stankowski, S., Rafajlović, M., Ortega-Martinez, O., Faria, R.,
Butlin, R. K., & Johannesson, K. (2024). Coupling of twelve putative chromosomal
inversions maintains a strong barrier to gene flow between snail ecotypes. Evolution
Letters. Oxford University Press. https://doi.org/10.1093/evlett/qrae014
chicago: Le Moan, Alan, Sean Stankowski, Marina Rafajlović, Olga Ortega-Martinez,
Rui Faria, Roger K Butlin, and Kerstin Johannesson. “Coupling of Twelve Putative
Chromosomal Inversions Maintains a Strong Barrier to Gene Flow between Snail Ecotypes.”
Evolution Letters. Oxford University Press, 2024. https://doi.org/10.1093/evlett/qrae014.
ieee: A. Le Moan et al., “Coupling of twelve putative chromosomal inversions
maintains a strong barrier to gene flow between snail ecotypes,” Evolution
Letters, vol. 8, no. 4. Oxford University Press, pp. 575–586, 2024.
ista: Le Moan A, Stankowski S, Rafajlović M, Ortega-Martinez O, Faria R, Butlin
RK, Johannesson K. 2024. Coupling of twelve putative chromosomal inversions maintains
a strong barrier to gene flow between snail ecotypes. Evolution Letters. 8(4),
575–586.
mla: Le Moan, Alan, et al. “Coupling of Twelve Putative Chromosomal Inversions Maintains
a Strong Barrier to Gene Flow between Snail Ecotypes.” Evolution Letters,
vol. 8, no. 4, Oxford University Press, 2024, pp. 575–86, doi:10.1093/evlett/qrae014.
short: A. Le Moan, S. Stankowski, M. Rafajlović, O. Ortega-Martinez, R. Faria, R.K.
Butlin, K. Johannesson, Evolution Letters 8 (2024) 575–586.
date_created: 2025-01-27T13:30:27Z
date_published: 2024-04-23T00:00:00Z
date_updated: 2025-09-09T12:05:51Z
day: '23'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/evlett/qrae014
external_id:
isi:
- '001206532900001'
pmid:
- '39479507'
file:
- access_level: open_access
checksum: 2f7780b7b6b3489755f1815f476639c6
content_type: application/pdf
creator: dernst
date_created: 2025-01-27T13:33:14Z
date_updated: 2025-01-27T13:33:14Z
file_id: '18909'
file_name: 2024_EvolutionLetter_Moan.pdf
file_size: 24356661
relation: main_file
success: 1
file_date_updated: 2025-01-27T13:33:14Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 575-586
pmid: 1
publication: Evolution Letters
publication_identifier:
issn:
- 2056-3744
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Coupling of twelve putative chromosomal inversions maintains a strong barrier
to gene flow between snail ecotypes
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 8
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18910'
abstract:
- lang: eng
text: Proteins often undergo large-scale conformational transitions, in which secondary
and tertiary structure elements (loops, helices, and domains) change their structures
or their positions with respect to each other. Simple considerations suggest that
such dynamics should be relatively fast, but the functional cycles of many proteins
are often relatively slow. Sophisticated experimental methods are starting to
tackle this dichotomy and shed light on the contribution of large-scale conformational
dynamics to protein function. In this review, we focus on the contribution of
single-molecule Förster resonance energy transfer and nuclear magnetic resonance
(NMR) spectroscopies to the study of conformational dynamics. We briefly describe
the state of the art in each of these techniques and then point out their similarities
and differences, as well as the relative strengths and weaknesses of each. Several
case studies, in which the connection between fast conformational dynamics and
slower function has been demonstrated, are then introduced and discussed. These
examples include both enzymes and large protein machines, some of which have been
studied by both NMR and fluorescence spectroscopies.
acknowledgement: G.H. is the incumbent of the Hilda Pomeraniec Memorial Professorial
Chair. He has been partially funded by the European Research Council under the European
Union's Horizon 2020 research and innovation program (grant 742637, SMALLOSTERY),
by National Science Foundation–US-Israel Binational Science Foundation grant 2021700,
and by an Israel Science Foundation Breakthrough grant (1924/22). P.S. acknowledges
funding from the Austrian Science Fund (project “AlloSpace,” I05812) and intramural
funding from the Institute of Science and Technology Austria.
article_processing_charge: No
article_type: original
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Gilad
full_name: Haran, Gilad
last_name: Haran
citation:
ama: Schanda P, Haran G. NMR and single-molecule FRET insights into fast protein
motions and their relation to function. Annual Review of Biophysics. 2024;53:247-273.
doi:10.1146/annurev-biophys-070323-022428
apa: Schanda, P., & Haran, G. (2024). NMR and single-molecule FRET insights
into fast protein motions and their relation to function. Annual Review of
Biophysics. Annual Reviews. https://doi.org/10.1146/annurev-biophys-070323-022428
chicago: Schanda, Paul, and Gilad Haran. “NMR and Single-Molecule FRET Insights
into Fast Protein Motions and Their Relation to Function.” Annual Review of
Biophysics. Annual Reviews, 2024. https://doi.org/10.1146/annurev-biophys-070323-022428.
ieee: P. Schanda and G. Haran, “NMR and single-molecule FRET insights into fast
protein motions and their relation to function,” Annual Review of Biophysics,
vol. 53. Annual Reviews, pp. 247–273, 2024.
ista: Schanda P, Haran G. 2024. NMR and single-molecule FRET insights into fast
protein motions and their relation to function. Annual Review of Biophysics. 53,
247–273.
mla: Schanda, Paul, and Gilad Haran. “NMR and Single-Molecule FRET Insights into
Fast Protein Motions and Their Relation to Function.” Annual Review of Biophysics,
vol. 53, Annual Reviews, 2024, pp. 247–73, doi:10.1146/annurev-biophys-070323-022428.
short: P. Schanda, G. Haran, Annual Review of Biophysics 53 (2024) 247–273.
corr_author: '1'
date_created: 2025-01-27T13:40:34Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2025-09-09T12:06:24Z
day: '01'
ddc:
- '570'
department:
- _id: PaSc
doi: 10.1146/annurev-biophys-070323-022428
external_id:
isi:
- '001278237500012'
pmid:
- '38346243'
file:
- access_level: open_access
checksum: c90861542ae3f9147939030d5bafed3c
content_type: application/pdf
creator: dernst
date_created: 2025-01-27T13:44:59Z
date_updated: 2025-01-27T13:44:59Z
file_id: '18911'
file_name: 2024_AnnualReviews_Schanda.pdf
file_size: 3025589
relation: main_file
success: 1
file_date_updated: 2025-01-27T13:44:59Z
has_accepted_license: '1'
intvolume: ' 53'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 247-273
pmid: 1
project:
- _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf
grant_number: I05812
name: AlloSpace. The emergence and mechanisms of allostery
publication: Annual Review of Biophysics
publication_identifier:
eissn:
- 1936-1238
issn:
- 1936-122X
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
scopus_import: '1'
status: public
title: NMR and single-molecule FRET insights into fast protein motions and their relation
to function
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 53
year: '2024'
...
---
OA_type: closed access
_id: '18912'
abstract:
- lang: eng
text: This paper presents a computational method for automatically creating fabricable
3D wire sculptures from various input modalities, including 3D models, images,
and even text. There are several challenges to wire art creation. For example,
artists must express the desired visual as a sparse wire representation. It is
also difficult to manually bend wires in the air without guidance to fabricate
the designed 3D curves. Our workflow solves these challenges by using two core
techniques. First, we present an algorithm that automatically generates a fabricable
3D curve representation of the target based on a loss function that measures the
semantic distance between the rendered curve and the target. The loss function
can be defined using different pre-trained vision-language neural networks to
generate wire art from different input types. The loss function is then optimized
using differentiable rendering specifically targeting 3D parametric curves. Our
method can incorporate various fabrication constraints on the wire as additional
regularization terms in the optimization process. Second, we present an algorithm
to generate a 3D printable jig structure that can be used to fabricate the generated
wire path. The major challenge in the jig generation stems from the design of
an intersection-free surface mesh for 3D printing, which we address with our inflation
algorithm. The experimental results indicate that our method can handle a wider
range of input types and can produce physically fabricable wire shapes compared
to previous wire generation methods. Various wire arts have been fabricated using
our 3D-printed jig to demonstrate its effectiveness in 3D wire bending.
acknowledgement: The authors thank the anonymous reviewers for their valuable comments
and suggestions for improving the paper. This work was supported by JSPS KAKENHI
Grant Numbers JP21K11910, 23KJ0699 and JST AdCORP, Grant Number JPMJKB2302, Japan.
This work was partially supported by Israel Science Foundation Grant number 1390/19
and Joint NSFC-ISF Research Grant no. 3077/23. We thank Riku Toyota for his useful
advice on wire selection and Takeo Igarashi for his assistance in arranging the
collaboration of the authors.
article_number: '134'
article_processing_charge: No
author:
- first_name: Kenji
full_name: Tojo, Kenji
last_name: Tojo
- first_name: Ariel
full_name: Shamir, Ariel
last_name: Shamir
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Nobuyuki
full_name: Umetani, Nobuyuki
last_name: Umetani
citation:
ama: 'Tojo K, Shamir A, Bickel B, Umetani N. Fabricable 3D wire art. In: SIGGRAPH
’24: ACM SIGGRAPH 2024 Conference Papers. ACM; 2024. doi:10.1145/3641519.3657453'
apa: 'Tojo, K., Shamir, A., Bickel, B., & Umetani, N. (2024). Fabricable 3D
wire art. In SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers. Denver,
CO, United States: ACM. https://doi.org/10.1145/3641519.3657453'
chicago: 'Tojo, Kenji, Ariel Shamir, Bernd Bickel, and Nobuyuki Umetani. “Fabricable
3D Wire Art.” In SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers. ACM,
2024. https://doi.org/10.1145/3641519.3657453.'
ieee: 'K. Tojo, A. Shamir, B. Bickel, and N. Umetani, “Fabricable 3D wire art,”
in SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers, Denver, CO, United
States, 2024.'
ista: 'Tojo K, Shamir A, Bickel B, Umetani N. 2024. Fabricable 3D wire art. SIGGRAPH
’24: ACM SIGGRAPH 2024 Conference Papers. SIGGRAPH: Computer Graphics and Interactive
Techniques Conference, 134.'
mla: 'Tojo, Kenji, et al. “Fabricable 3D Wire Art.” SIGGRAPH ’24: ACM SIGGRAPH
2024 Conference Papers, 134, ACM, 2024, doi:10.1145/3641519.3657453.'
short: 'K. Tojo, A. Shamir, B. Bickel, N. Umetani, in:, SIGGRAPH ’24: ACM SIGGRAPH
2024 Conference Papers, ACM, 2024.'
conference:
end_date: 2024-08-01
location: Denver, CO, United States
name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference'
start_date: 2024-07-28
corr_author: '1'
date_created: 2025-01-27T13:47:35Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2025-09-09T12:06:57Z
day: '01'
department:
- _id: BeBi
doi: 10.1145/3641519.3657453
external_id:
isi:
- '001282218200059'
isi: 1
language:
- iso: eng
month: '07'
oa_version: None
publication: 'SIGGRAPH ''24: ACM SIGGRAPH 2024 Conference Papers'
publication_identifier:
isbn:
- '9798400705250'
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fabricable 3D wire art
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18913'
abstract:
- lang: eng
text: "With the proliferation of blockchain technology in high-value sectors, consensus
protocols are becoming critical infrastructures. The rapid innovation cycle in
Byzantine fault tolerant (BFT) consensus protocols has culminated in HotStuff,
which provides linear message complexity in the partially synchronous setting.
To achieve this, HotStuff leverages a leader that collects, aggregates, and broadcasts
the messages of other validators. This paper analyzes the security implications
of such approaches in practice, from the perspective of liveness and availability.\r\nBy
implementing attacks in a globally-distributed testbed, we show that state-of-the-art
leader-based protocols are vulnerable to denial-of-service (DoS) attacks on the
leader. Our attacks, demonstrated on committees of up to 64 validators, manage
to disrupt liveness within seconds, using only a few tens of Mbps of attack bandwidth
per validator. Crucially, the cost and effectiveness of the attacks are independent
of the committee size. Based on the outcome of these experiments, we then propose
and test effective mitigations. Our findings show that advancements in both protocol
design and network-layer defenses can greatly improve the practical resilience
of BFT consensus protocols."
acknowledgement: This work was mostly realized while Alberto Sonnino and Lefteris
Kokoris-Kogias were employed at Meta. We gratefully acknowledge support for this
project from ETH Zurich and Mysten Labs.
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Giacomo
full_name: Giuliari, Giacomo
last_name: Giuliari
- first_name: Alberto
full_name: Sonnino, Alberto
last_name: Sonnino
- first_name: Marc
full_name: Frei, Marc
last_name: Frei
- first_name: Fabio
full_name: Streun, Fabio
last_name: Streun
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Adrian
full_name: Perrig, Adrian
last_name: Perrig
citation:
ama: 'Giuliari G, Sonnino A, Frei M, Streun F, Kokoris Kogias E, Perrig A. An empirical
study of consensus protocols’ DoS resilience. In: Proceedings of the 19th ACM
Asia Conference on Computer and Communications Security. ACM; 2024:1345-1360.
doi:10.1145/3634737.3656997'
apa: 'Giuliari, G., Sonnino, A., Frei, M., Streun, F., Kokoris Kogias, E., &
Perrig, A. (2024). An empirical study of consensus protocols’ DoS resilience.
In Proceedings of the 19th ACM Asia Conference on Computer and Communications
Security (pp. 1345–1360). Singapore, Singapore: ACM. https://doi.org/10.1145/3634737.3656997'
chicago: Giuliari, Giacomo, Alberto Sonnino, Marc Frei, Fabio Streun, Eleftherios
Kokoris Kogias, and Adrian Perrig. “An Empirical Study of Consensus Protocols’
DoS Resilience.” In Proceedings of the 19th ACM Asia Conference on Computer
and Communications Security, 1345–60. ACM, 2024. https://doi.org/10.1145/3634737.3656997.
ieee: G. Giuliari, A. Sonnino, M. Frei, F. Streun, E. Kokoris Kogias, and A. Perrig,
“An empirical study of consensus protocols’ DoS resilience,” in Proceedings
of the 19th ACM Asia Conference on Computer and Communications Security, Singapore,
Singapore, 2024, pp. 1345–1360.
ista: 'Giuliari G, Sonnino A, Frei M, Streun F, Kokoris Kogias E, Perrig A. 2024.
An empirical study of consensus protocols’ DoS resilience. Proceedings of the
19th ACM Asia Conference on Computer and Communications Security. ASIACCS: Asia
Conference on Computer and Communications Security, 1345–1360.'
mla: Giuliari, Giacomo, et al. “An Empirical Study of Consensus Protocols’ DoS Resilience.”
Proceedings of the 19th ACM Asia Conference on Computer and Communications
Security, ACM, 2024, pp. 1345–60, doi:10.1145/3634737.3656997.
short: G. Giuliari, A. Sonnino, M. Frei, F. Streun, E. Kokoris Kogias, A. Perrig,
in:, Proceedings of the 19th ACM Asia Conference on Computer and Communications
Security, ACM, 2024, pp. 1345–1360.
conference:
end_date: 2024-07-05
location: Singapore, Singapore
name: 'ASIACCS: Asia Conference on Computer and Communications Security'
start_date: 2024-07-01
date_created: 2025-01-27T13:57:00Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2025-09-09T12:07:28Z
day: '01'
ddc:
- '000'
department:
- _id: ElKo
doi: 10.1145/3634737.3656997
external_id:
isi:
- '001283918100095'
file:
- access_level: open_access
checksum: 1e743ddf49d35390eb56e11eb0759150
content_type: application/pdf
creator: dernst
date_created: 2025-01-27T14:04:12Z
date_updated: 2025-01-27T14:04:12Z
file_id: '18914'
file_name: 2024_ACMAsiaCCS_Giuliari.pdf
file_size: 951940
relation: main_file
success: 1
file_date_updated: 2025-01-27T14:04:12Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1345-1360
publication: Proceedings of the 19th ACM Asia Conference on Computer and Communications
Security
publication_identifier:
isbn:
- '9798400704826'
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: An empirical study of consensus protocols’ DoS resilience
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_place: publisher
OA_type: gold
_id: '18917'
abstract:
- lang: eng
text: "An eight-partition of a finite set of points (respectively, of a continuous
mass distribution) in ℝ³ consists of three planes that divide the space into 8
octants, such that each open octant contains at most 1/8 of the points (respectively,
of the mass). In 1966, Hadwiger showed that any mass distribution in ℝ³ admits
an eight-partition; moreover, one can prescribe the normal direction of one of
the three planes. The analogous result for finite point sets follows by a standard
limit argument.\r\nWe prove the following variant of this result: Any mass distribution
(or point set) in ℝ³ admits an eight-partition for which the intersection of two
of the planes is a line with a prescribed direction.\r\nMoreover, we present an
efficient algorithm for calculating an eight-partition of a set of n points in
ℝ³ (with prescribed normal direction of one of the planes) in time O^*(n^{5/2})."
acknowledgement: "Aronov, Boris: Work has been supported by NSF grants CCF 15-40656
and CCF 20-08551, and by grant 2014/170 from the US-Israel Binational Science Foundation.
Part of this research was conducted while BA was visiting ISTA in the summers of
2022 and 2023. The visit of BA to ISTA in the summer of 2022 was supported by an
ISTA Visiting Professorship.\r\nBasit, Abdul: Work has been supported by Australian
Research Council grant DP220102212.\r\nRamesh, Indu: Work supported by a Tandon
School of Engineering Fellowship and by NSF Grant CCF-20-08551.\r\nBA and AB would
like to thank William Steiger for insightful initial discussions of the problems
addressed in this work."
article_processing_charge: Yes
arxiv: 1
author:
- first_name: Boris
full_name: Aronov, Boris
last_name: Aronov
- first_name: Abdul
full_name: Basit, Abdul
last_name: Basit
- first_name: Indu
full_name: Ramesh, Indu
last_name: Ramesh
- first_name: Gianluca
full_name: Tasinato, Gianluca
id: 0433290C-AF8F-11E9-A4C7-F729E6697425
last_name: Tasinato
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Aronov B, Basit A, Ramesh I, Tasinato G, Wagner U. Eight-partitioning points
in 3D, and efficiently too. In: 40th International Symposium on Computational
Geometry. Vol 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024:8:1-8:15.
doi:10.4230/LIPIcs.SoCG.2024.8'
apa: 'Aronov, B., Basit, A., Ramesh, I., Tasinato, G., & Wagner, U. (2024).
Eight-partitioning points in 3D, and efficiently too. In 40th International
Symposium on Computational Geometry (Vol. 293, p. 8:1-8:15). Athens, Greece:
Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2024.8'
chicago: Aronov, Boris, Abdul Basit, Indu Ramesh, Gianluca Tasinato, and Uli Wagner.
“Eight-Partitioning Points in 3D, and Efficiently Too.” In 40th International
Symposium on Computational Geometry, 293:8:1-8:15. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2024. https://doi.org/10.4230/LIPIcs.SoCG.2024.8.
ieee: B. Aronov, A. Basit, I. Ramesh, G. Tasinato, and U. Wagner, “Eight-partitioning
points in 3D, and efficiently too,” in 40th International Symposium on Computational
Geometry, Athens, Greece, 2024, vol. 293, p. 8:1-8:15.
ista: 'Aronov B, Basit A, Ramesh I, Tasinato G, Wagner U. 2024. Eight-partitioning
points in 3D, and efficiently too. 40th International Symposium on Computational
Geometry. SoCG: Symposium on Computational Geometry vol. 293, 8:1-8:15.'
mla: Aronov, Boris, et al. “Eight-Partitioning Points in 3D, and Efficiently Too.”
40th International Symposium on Computational Geometry, vol. 293, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 8:1-8:15, doi:10.4230/LIPIcs.SoCG.2024.8.
short: B. Aronov, A. Basit, I. Ramesh, G. Tasinato, U. Wagner, in:, 40th International
Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2024, p. 8:1-8:15.
conference:
end_date: 2024-06-14
location: Athens, Greece
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2024-06-11
corr_author: '1'
date_created: 2025-01-27T14:19:17Z
date_published: 2024-06-06T00:00:00Z
date_updated: 2026-02-16T12:19:08Z
day: '06'
ddc:
- '510'
department:
- _id: UlWa
- _id: GradSch
doi: 10.4230/LIPIcs.SoCG.2024.8
external_id:
arxiv:
- '2403.02627'
file:
- access_level: open_access
checksum: 443aa29ea5d948e917cfccd681dcf176
content_type: application/pdf
creator: dernst
date_created: 2025-01-27T14:17:37Z
date_updated: 2025-01-27T14:17:37Z
file_id: '18918'
file_name: 2024_LIPICs_Aronov.pdf
file_size: 880725
relation: main_file
success: 1
file_date_updated: 2025-01-27T14:17:37Z
has_accepted_license: '1'
intvolume: ' 293'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 8:1-8:15
publication: 40th International Symposium on Computational Geometry
publication_identifier:
isbn:
- '9783959773164'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
record:
- id: '19860'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Eight-partitioning points in 3D, and efficiently too
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: 293
year: '2024'
...
---
OA_type: closed access
_id: '18919'
abstract:
- lang: eng
text: The integration of theory and experiment makes possible tracking the slow
evolution of a photodoped Mott insulator to a distinct non-equilibrium metallic
phase under the influence of electron-lattice coupling.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
citation:
ama: Baykusheva DR. Through the slopes of a light-induced phase transition. Nature
Physics. 2024;20(5):684-685. doi:10.1038/s41567-024-02401-7
apa: Baykusheva, D. R. (2024). Through the slopes of a light-induced phase transition.
Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-024-02401-7
chicago: Baykusheva, Denitsa Rangelova. “Through the Slopes of a Light-Induced Phase
Transition.” Nature Physics. Springer Nature, 2024. https://doi.org/10.1038/s41567-024-02401-7.
ieee: D. R. Baykusheva, “Through the slopes of a light-induced phase transition,”
Nature Physics, vol. 20, no. 5. Springer Nature, pp. 684–685, 2024.
ista: Baykusheva DR. 2024. Through the slopes of a light-induced phase transition.
Nature Physics. 20(5), 684–685.
mla: Baykusheva, Denitsa Rangelova. “Through the Slopes of a Light-Induced Phase
Transition.” Nature Physics, vol. 20, no. 5, Springer Nature, 2024, pp.
684–85, doi:10.1038/s41567-024-02401-7.
short: D.R. Baykusheva, Nature Physics 20 (2024) 684–685.
corr_author: '1'
date_created: 2025-01-27T14:29:20Z
date_published: 2024-05-01T00:00:00Z
date_updated: 2025-09-09T12:08:10Z
day: '01'
department:
- _id: DeBa
doi: 10.1038/s41567-024-02401-7
external_id:
isi:
- '001162208200002'
intvolume: ' 20'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 684-685
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Through the slopes of a light-induced phase transition
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 20
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18920'
abstract:
- lang: eng
text: The globally distributed marine alga Emiliania huxleyi has cooling effect
on the Earth’s climate. The population density of E. huxleyi is restricted by
Nucleocytoviricota viruses, including E. huxleyi virus 201 (EhV-201). Despite
the impact of E. huxleyi viruses on the climate, there is limited information
about their structure and replication. Here, we show that the dsDNA genome inside
the EhV-201 virion is protected by an inner membrane, capsid, and outer membrane.
EhV-201 virions infect E. huxleyi by using fivefold vertices to bind to and fuse
the virus’ inner membrane with the cell plasma membrane. Progeny virions assemble
in the cytoplasm at the surface of endoplasmic reticulum–derived membrane segments.
Genome packaging initiates synchronously with the capsid assembly and completes
through an aperture in the forming capsid. The genome-filled capsids acquire an
outer membrane by budding into intracellular vesicles. EhV-201 infection induces
a loss of surface protective layers from E. huxleyi cells, which enables the continuous
release of virions by exocytosis.
acknowledgement: We acknowledge (i) the Cryo-Electron Microscopy and Tomography Core
Facility and Proteomics Core Facility of the Central European Institute of Technology
(CEITEC), Masaryk University, supported by the Ministry of Education, Youth, and
Sports of the Czech Republic (grant LM2018127); (ii) the Cellular Imaging Core Facility
supported by the Czech-BioImaging large RI project (LM2018129 funded by MEYS CR);
and (iii) Plant Sciences Core Facility for support with obtaining scientific data
presented here. We acknowledge support from the project National Institute of Virology
and Bacteriology (Program EXCELES, ID project no. LX22NPO5103), funded by the European
Union - Next Generation EU. This work received funding from the Czech Science Foundation
grant GX 19-259882X to P.P., from European Regional Development Fund-Project “MSCAfellow2@MUNI”
(no. CZ.02.2.69/0.0/0.0/18_070/0009846) to C.R.B., and from Brno PhD talent scholarship
funded by Brno city municipality to M.H.
article_number: 'eadk1954 '
article_processing_charge: Yes
article_type: original
author:
- first_name: Miroslav
full_name: Homola, Miroslav
last_name: Homola
- first_name: Renate Carina
full_name: Büttner, Renate Carina
id: 3b7984c9-17ff-11ed-b6fe-f943c4a5b626
last_name: Büttner
- first_name: Tibor
full_name: Füzik, Tibor
last_name: Füzik
- first_name: Pavel
full_name: Křepelka, Pavel
last_name: Křepelka
- first_name: Radka
full_name: Holbová, Radka
last_name: Holbová
- first_name: Jiří
full_name: Nováček, Jiří
last_name: Nováček
- first_name: Marten L.
full_name: Chaillet, Marten L.
last_name: Chaillet
- first_name: Jakub
full_name: Žák, Jakub
last_name: Žák
- first_name: Danyil
full_name: Grybchuk, Danyil
last_name: Grybchuk
- first_name: Friedrich
full_name: Förster, Friedrich
last_name: Förster
- first_name: William H.
full_name: Wilson, William H.
last_name: Wilson
- first_name: Declan C.
full_name: Schroeder, Declan C.
last_name: Schroeder
- first_name: Pavel
full_name: Plevka, Pavel
last_name: Plevka
citation:
ama: Homola M, Büttner RC, Füzik T, et al. Structure and replication cycle of a
virus infecting climate-modulating alga Emiliania huxleyi. Science Advances.
2024;10(15). doi:10.1126/sciadv.adk1954
apa: Homola, M., Büttner, R. C., Füzik, T., Křepelka, P., Holbová, R., Nováček,
J., … Plevka, P. (2024). Structure and replication cycle of a virus infecting
climate-modulating alga Emiliania huxleyi. Science Advances. American Association
for the Advancement of Science. https://doi.org/10.1126/sciadv.adk1954
chicago: Homola, Miroslav, Renate Carina Büttner, Tibor Füzik, Pavel Křepelka, Radka
Holbová, Jiří Nováček, Marten L. Chaillet, et al. “Structure and Replication Cycle
of a Virus Infecting Climate-Modulating Alga Emiliania Huxleyi.” Science Advances.
American Association for the Advancement of Science, 2024. https://doi.org/10.1126/sciadv.adk1954.
ieee: M. Homola et al., “Structure and replication cycle of a virus infecting
climate-modulating alga Emiliania huxleyi,” Science Advances, vol. 10,
no. 15. American Association for the Advancement of Science, 2024.
ista: Homola M, Büttner RC, Füzik T, Křepelka P, Holbová R, Nováček J, Chaillet
ML, Žák J, Grybchuk D, Förster F, Wilson WH, Schroeder DC, Plevka P. 2024. Structure
and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi.
Science Advances. 10(15), eadk1954.
mla: Homola, Miroslav, et al. “Structure and Replication Cycle of a Virus Infecting
Climate-Modulating Alga Emiliania Huxleyi.” Science Advances, vol. 10,
no. 15, eadk1954, American Association for the Advancement of Science, 2024, doi:10.1126/sciadv.adk1954.
short: M. Homola, R.C. Büttner, T. Füzik, P. Křepelka, R. Holbová, J. Nováček, M.L.
Chaillet, J. Žák, D. Grybchuk, F. Förster, W.H. Wilson, D.C. Schroeder, P. Plevka,
Science Advances 10 (2024).
date_created: 2025-01-27T14:32:34Z
date_published: 2024-04-01T00:00:00Z
date_updated: 2025-05-14T09:29:04Z
day: '01'
ddc:
- '570'
department:
- _id: EM-Fac
doi: 10.1126/sciadv.adk1954
external_id:
pmid:
- '38598627'
file:
- access_level: open_access
checksum: 291dd7ceccbe6bfd8e0a9157584f88e9
content_type: application/pdf
creator: dernst
date_created: 2025-01-27T14:40:08Z
date_updated: 2025-01-27T14:40:08Z
file_id: '18921'
file_name: 2024_ScienceAdv_Homola.pdf
file_size: 40623405
relation: main_file
success: 1
file_date_updated: 2025-01-27T14:40:08Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '15'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Science Advances
publication_identifier:
eissn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
link:
- relation: software
url: ' https://github.com/fuzikt/tomostarpy.'
scopus_import: '1'
status: public
title: Structure and replication cycle of a virus infecting climate-modulating alga
Emiliania huxleyi
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2024'
...
---
OA_type: closed access
_id: '18922'
abstract:
- lang: eng
text: 'Let G be a directed graph with m edges and n vertices. We present a deterministic
linear-time algorithm for computing the 3-edge-connected components of G. This
is a significant improvement over the previous best bound by Georgiadis et al.
[SODA 2023], which is Õ(m√{m}) and randomized. Our result is based on a novel
characterization of 2-edge cuts in directed graphs and on a new technique that
exploits the concept of divergent spanning trees and 2-connectivity-light graphs,
and requires a careful modification of the minset-poset technique of Gabow [TALG
2016]. As a side result, our new technique yields also an oracle for providing
in constant time a minimum edge-cut for any two vertices that are not 3-edge-connected.
The oracle uses space O(n) and can be built in O(mlog n) time: given two query
vertices, it determines in constant time whether they are 3-edge-connected, or
provides a k-edge cut, with k≤ 2, that separates them.'
acknowledgement: "Giuseppe F. Italiano was partially supported by the Italian Ministry
of\r\nUniversity and Reseach under PRIN Project n. 2022TS4Y3N - EXPAND: scalable
algorithms for EXPloratory Analyses of heterogeneous and dynamic Networked Data.\r\n"
article_processing_charge: No
author:
- first_name: Loukas
full_name: Georgiadis, Loukas
last_name: Georgiadis
- first_name: Giuseppe F.
full_name: Italiano, Giuseppe F.
last_name: Italiano
- first_name: Evangelos
full_name: Kosinas, Evangelos
id: 4c7f9625-dbbc-11ee-9d86-bdcc2db5a949
last_name: Kosinas
citation:
ama: 'Georgiadis L, Italiano GF, Kosinas E. Computing the 3-edge-connected components
of directed graphs in linear time. In: 65th Annual Symposium on Foundations
of Computer Science. IEEE; 2024:62-85. doi:10.1109/focs61266.2024.00015'
apa: 'Georgiadis, L., Italiano, G. F., & Kosinas, E. (2024). Computing the 3-edge-connected
components of directed graphs in linear time. In 65th Annual Symposium on Foundations
of Computer Science (pp. 62–85). Chicago, IL, United States: IEEE. https://doi.org/10.1109/focs61266.2024.00015'
chicago: Georgiadis, Loukas, Giuseppe F. Italiano, and Evangelos Kosinas. “Computing
the 3-Edge-Connected Components of Directed Graphs in Linear Time.” In 65th
Annual Symposium on Foundations of Computer Science, 62–85. IEEE, 2024. https://doi.org/10.1109/focs61266.2024.00015.
ieee: L. Georgiadis, G. F. Italiano, and E. Kosinas, “Computing the 3-edge-connected
components of directed graphs in linear time,” in 65th Annual Symposium on
Foundations of Computer Science, Chicago, IL, United States, 2024, pp. 62–85.
ista: 'Georgiadis L, Italiano GF, Kosinas E. 2024. Computing the 3-edge-connected
components of directed graphs in linear time. 65th Annual Symposium on Foundations
of Computer Science. FOCS: Foundations of Computer Science, 62–85.'
mla: Georgiadis, Loukas, et al. “Computing the 3-Edge-Connected Components of Directed
Graphs in Linear Time.” 65th Annual Symposium on Foundations of Computer Science,
IEEE, 2024, pp. 62–85, doi:10.1109/focs61266.2024.00015.
short: L. Georgiadis, G.F. Italiano, E. Kosinas, in:, 65th Annual Symposium on Foundations
of Computer Science, IEEE, 2024, pp. 62–85.
conference:
end_date: 2024-10-30
location: Chicago, IL, United States
name: 'FOCS: Foundations of Computer Science'
start_date: 2024-10-27
corr_author: '1'
date_created: 2025-01-27T14:50:23Z
date_published: 2024-10-01T00:00:00Z
date_updated: 2025-09-09T12:08:47Z
day: '01'
department:
- _id: MoHe
doi: 10.1109/focs61266.2024.00015
external_id:
isi:
- '001419526400005'
isi: 1
language:
- iso: eng
month: '10'
oa_version: None
page: 62-85
publication: 65th Annual Symposium on Foundations of Computer Science
publication_identifier:
isbn:
- '9798331516741'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Computing the 3-edge-connected components of directed graphs in linear time
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18923'
abstract:
- lang: eng
text: 'Combinatorial optimization is a challenging problem applicable in a wide
range of fields from logistics to finance. Recently, quantum computing has been
used to attempt to solve these problems using a range of algorithms, including
parameterized quantum circuits, adiabatic protocols, and quantum annealing. These
solutions typically have several challenges: 1) there is little to no performance
gain over classical methods; 2) not all constraints and objectives may be efficiently
encoded in the quantum ansatz; and 3) the solution domain of the objective function
may not be the same as the bit strings of measurement outcomes. This work presents
“nonnative hybrid algorithms”: a framework to overcome these challenges by integrating
quantum and classical resources with a hybrid approach. By designing nonnative
quantum variational anosatzes that inherit some but not all problem structure,
measurement outcomes from the quantum computer can act as a resource to be used
by classical routines to indirectly compute optimal solutions, partially overcoming
the challenges of contemporary quantum optimization approaches. These methods
are demonstrated using a publicly available neutral-atom quantum computer on two
simple problems of Max k-Cut and maximum independent set. We find improvements
in solution quality when comparing the hybrid algorithm to its “no quantum” version,
a demonstration of a “comparative advantage.”'
acknowledgement: "The authors would like to thank Alexander Keesling, Maddie Cain,
Nate Gemelke, and Phillip Weinberg for helpful discussions and Danylo Lykov who
had early contributions to this work.\r\n10.13039/100000185-Defense Advanced Research
Projects Agency Noisy Intermediate-Scale Quantum Devices (Grant Number: W911NF2010021),
DARPA Small Business Technology Transfer program (Grant Number: 140D0422C0035)."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jonathan
full_name: Wurtz, Jonathan
last_name: Wurtz
- first_name: Stefan
full_name: Sack, Stefan
id: dd622248-f6e0-11ea-865d-ce382a1c81a5
last_name: Sack
orcid: 0000-0001-5400-8508
- first_name: Sheng-Tao
full_name: Wang, Sheng-Tao
last_name: Wang
citation:
ama: Wurtz J, Sack S, Wang S-T. Solving nonnative combinatorial optimization problems
using hybrid quantum–classical algorithms. IEEE Transactions on Quantum Engineering.
2024;5:1-14. doi:10.1109/tqe.2024.3443660
apa: Wurtz, J., Sack, S., & Wang, S.-T. (2024). Solving nonnative combinatorial
optimization problems using hybrid quantum–classical algorithms. IEEE Transactions
on Quantum Engineering. Institute of Electrical and Electronics Engineers
. https://doi.org/10.1109/tqe.2024.3443660
chicago: Wurtz, Jonathan, Stefan Sack, and Sheng-Tao Wang. “Solving Nonnative Combinatorial
Optimization Problems Using Hybrid Quantum–Classical Algorithms.” IEEE Transactions
on Quantum Engineering. Institute of Electrical and Electronics Engineers
, 2024. https://doi.org/10.1109/tqe.2024.3443660.
ieee: J. Wurtz, S. Sack, and S.-T. Wang, “Solving nonnative combinatorial optimization
problems using hybrid quantum–classical algorithms,” IEEE Transactions on Quantum
Engineering, vol. 5. Institute of Electrical and Electronics Engineers , pp.
1–14, 2024.
ista: Wurtz J, Sack S, Wang S-T. 2024. Solving nonnative combinatorial optimization
problems using hybrid quantum–classical algorithms. IEEE Transactions on Quantum
Engineering. 5, 1–14.
mla: Wurtz, Jonathan, et al. “Solving Nonnative Combinatorial Optimization Problems
Using Hybrid Quantum–Classical Algorithms.” IEEE Transactions on Quantum Engineering,
vol. 5, Institute of Electrical and Electronics Engineers , 2024, pp. 1–14, doi:10.1109/tqe.2024.3443660.
short: J. Wurtz, S. Sack, S.-T. Wang, IEEE Transactions on Quantum Engineering 5
(2024) 1–14.
date_created: 2025-01-27T15:00:44Z
date_published: 2024-08-14T00:00:00Z
date_updated: 2025-01-27T15:06:15Z
day: '14'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1109/tqe.2024.3443660
file:
- access_level: open_access
checksum: 19b84e35cba05bde72bfe7e0b54c3e6c
content_type: application/pdf
creator: dernst
date_created: 2025-01-27T15:03:09Z
date_updated: 2025-01-27T15:03:09Z
file_id: '18924'
file_name: 2024_IEEEQuantumComputing_Wurtz.pdf
file_size: 1753095
relation: main_file
success: 1
file_date_updated: 2025-01-27T15:03:09Z
has_accepted_license: '1'
intvolume: ' 5'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 1-14
publication: IEEE Transactions on Quantum Engineering
publication_identifier:
issn:
- 2689-1808
publication_status: published
publisher: 'Institute of Electrical and Electronics Engineers '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Solving nonnative combinatorial optimization problems using hybrid quantum–classical
algorithms
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2024'
...
---
OA_place: other
OA_type: green
_id: '18925'
abstract:
- lang: eng
text: Given the increasingly stringent requirements on the performance and efficiency
of communication networks, over the last years, great efforts have been made to
render networks more flexible and programmable. In particular, modern networks
support a flexible rerouting of flows, e.g., depending on the dynamically changing
traffic or network conditions. However, the underlying algorithmic problems are
still not well-understood today.In this paper, we revisit the k-Network Flow Update
problem that asks for a schedule to reroute k unsplittable flows from their current
paths to the given new paths, in a congestion-free manner in a capacitated network.
We show that the problem is already NP-hard for three acyclic flows on simple
directed graphs. Our main contribution is an efficient algorithm for sparse networks;
specifically the algorithm is fixed parameter tractable in the number of flows
and the treewidth of a graph that is the union of all flows. Our results also
settle the open complexity question in the literature.
acknowledgement: Research was supported by the Austrian Science Fund (FWF), project
I 5025-N (DELTA), 2020-2024. Esra Ceylan’s research was supported by FFG, FEMtech
Praktika für Studentinnen. Jakub Svoboda and Krishnendu Chatterjee were supported
by the European Research Council (ERC) CoG 863818 (ForM-SMArt).
article_processing_charge: No
author:
- first_name: Esra
full_name: Ceylan, Esra
id: cb1ca1d8-dcc0-11ef-baa5-9f1b3ef75933
last_name: Ceylan
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Stefan
full_name: Schmid, Stefan
last_name: Schmid
- first_name: Jakub
full_name: Svoboda, Jakub
id: 130759D2-D7DD-11E9-87D2-DE0DE6697425
last_name: Svoboda
orcid: 0000-0002-1419-3267
citation:
ama: 'Ceylan E, Chatterjee K, Schmid S, Svoboda J. Congestion-free rerouting of
network flows: Hardness and an FPT algorithm. In: NOMS 2024-2024 IEEE Network
Operations and Management Symposium. IEEE; 2024. doi:10.1109/noms59830.2024.10575579'
apa: 'Ceylan, E., Chatterjee, K., Schmid, S., & Svoboda, J. (2024). Congestion-free
rerouting of network flows: Hardness and an FPT algorithm. In NOMS 2024-2024
IEEE Network Operations and Management Symposium. Seoul, Republic of Korea:
IEEE. https://doi.org/10.1109/noms59830.2024.10575579'
chicago: 'Ceylan, Esra, Krishnendu Chatterjee, Stefan Schmid, and Jakub Svoboda.
“Congestion-Free Rerouting of Network Flows: Hardness and an FPT Algorithm.” In
NOMS 2024-2024 IEEE Network Operations and Management Symposium. IEEE,
2024. https://doi.org/10.1109/noms59830.2024.10575579.'
ieee: 'E. Ceylan, K. Chatterjee, S. Schmid, and J. Svoboda, “Congestion-free rerouting
of network flows: Hardness and an FPT algorithm,” in NOMS 2024-2024 IEEE Network
Operations and Management Symposium, Seoul, Republic of Korea, 2024.'
ista: 'Ceylan E, Chatterjee K, Schmid S, Svoboda J. 2024. Congestion-free rerouting
of network flows: Hardness and an FPT algorithm. NOMS 2024-2024 IEEE Network Operations
and Management Symposium. NOMS: Network Operations and Management Symposiu .'
mla: 'Ceylan, Esra, et al. “Congestion-Free Rerouting of Network Flows: Hardness
and an FPT Algorithm.” NOMS 2024-2024 IEEE Network Operations and Management
Symposium, IEEE, 2024, doi:10.1109/noms59830.2024.10575579.'
short: E. Ceylan, K. Chatterjee, S. Schmid, J. Svoboda, in:, NOMS 2024-2024 IEEE
Network Operations and Management Symposium, IEEE, 2024.
conference:
end_date: 2024-05-10
location: Seoul, Republic of Korea
name: 'NOMS: Network Operations and Management Symposiu '
start_date: 2024-05-06
corr_author: '1'
date_created: 2025-01-27T15:06:45Z
date_published: 2024-05-01T00:00:00Z
date_updated: 2025-11-05T07:34:27Z
day: '01'
department:
- _id: KrCh
doi: 10.1109/noms59830.2024.10575579
ec_funded: 1
external_id:
isi:
- '001270140300143'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://schmiste.github.io/noms24.pdf
month: '05'
oa: 1
oa_version: Submitted Version
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: bd622a5c-d553-11ed-ba76-bae280ba8aff
grant_number: '894907'
name: Graphical Games
publication: NOMS 2024-2024 IEEE Network Operations and Management Symposium
publication_identifier:
eissn:
- 2374-9709
isbn:
- '9798350327946'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Congestion-free rerouting of network flows: Hardness and an FPT algorithm'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '18926'
abstract:
- lang: eng
text: 'We study weak solutions to mean curvature flow satisfying Young’s angle condition
for general contact angles α ∈ (0, π). First, we construct BV solutions by using
the Allen-Cahn approximation with boundary contact energy as proposed by Owen
and Sternberg. Second, we prove the weak-strong uniqueness and stability for this
solution concept. The main ingredient for both results is a relative energy, which
can also be interpreted as a tilt excess. '
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Sebastian
full_name: Hensel, Sebastian
id: 4D23B7DA-F248-11E8-B48F-1D18A9856A87
last_name: Hensel
orcid: 0000-0001-7252-8072
- first_name: Tim
full_name: Laux, Tim
last_name: Laux
citation:
ama: 'Hensel S, Laux T. BV solutions for mean curvature flow with constant angle:
Allen-Cahn approximation and weak-strong uniqueness. Indiana University Mathematics
Journal. 2024;73(1):111-148. doi:10.1512/iumj.2024.73.9701'
apa: 'Hensel, S., & Laux, T. (2024). BV solutions for mean curvature flow with
constant angle: Allen-Cahn approximation and weak-strong uniqueness. Indiana
University Mathematics Journal. Indiana University Mathematics Journal. https://doi.org/10.1512/iumj.2024.73.9701'
chicago: 'Hensel, Sebastian, and Tim Laux. “BV Solutions for Mean Curvature Flow
with Constant Angle: Allen-Cahn Approximation and Weak-Strong Uniqueness.” Indiana
University Mathematics Journal. Indiana University Mathematics Journal, 2024.
https://doi.org/10.1512/iumj.2024.73.9701.'
ieee: 'S. Hensel and T. Laux, “BV solutions for mean curvature flow with constant
angle: Allen-Cahn approximation and weak-strong uniqueness,” Indiana University
Mathematics Journal, vol. 73, no. 1. Indiana University Mathematics Journal,
pp. 111–148, 2024.'
ista: 'Hensel S, Laux T. 2024. BV solutions for mean curvature flow with constant
angle: Allen-Cahn approximation and weak-strong uniqueness. Indiana University
Mathematics Journal. 73(1), 111–148.'
mla: 'Hensel, Sebastian, and Tim Laux. “BV Solutions for Mean Curvature Flow with
Constant Angle: Allen-Cahn Approximation and Weak-Strong Uniqueness.” Indiana
University Mathematics Journal, vol. 73, no. 1, Indiana University Mathematics
Journal, 2024, pp. 111–48, doi:10.1512/iumj.2024.73.9701.'
short: S. Hensel, T. Laux, Indiana University Mathematics Journal 73 (2024) 111–148.
corr_author: '1'
date_created: 2025-01-27T15:20:19Z
date_published: 2024-01-01T00:00:00Z
date_updated: 2025-01-27T15:23:57Z
day: '01'
department:
- _id: JuFi
doi: 10.1512/iumj.2024.73.9701
external_id:
arxiv:
- '2112.11150'
intvolume: ' 73'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2112.11150
month: '01'
oa: 1
oa_version: Preprint
page: 111-148
publication: Indiana University Mathematics Journal
publication_identifier:
issn:
- 0022-2518
publication_status: published
publisher: Indiana University Mathematics Journal
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'BV solutions for mean curvature flow with constant angle: Allen-Cahn approximation
and weak-strong uniqueness'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 73
year: '2024'
...
---
OA_place: publisher
OA_type: gold
_id: '18928'
abstract:
- lang: eng
text: "Algorithms with predictions is a new research direction that leverages machine
learned predictions for algorithm design. So far a plethora of recent works have
incorporated predictions to improve on worst-case bounds for online problems.
In this paper, we initiate the study of complexity of dynamic data structures
with predictions, including dynamic graph algorithms. Unlike online algorithms,
the goal in dynamic data structures is to maintain the solution efficiently with
every update.\r\nWe investigate three natural models of prediction: (1) δ-accurate
predictions where each predicted request matches the true request with probability
δ, (2) list-accurate predictions where a true request comes from a list of possible
requests, and (3) bounded delay predictions where the true requests are a permutation
of the predicted requests. We give general reductions among the prediction models,
showing that bounded delay is the strongest prediction model, followed by list-accurate,
and δ-accurate.\r\nFurther, we identify two broad problem classes based on lower
bounds due to the Online Matrix Vector (OMv) conjecture. Specifically, we show
that locally correctable dynamic problems have strong conditional lower bounds
for list-accurate predictions that are equivalent to the non-prediction setting,
unless list-accurate predictions are perfect. Moreover, we show that locally reducible
dynamic problems have time complexity that degrades gracefully with the quality
of bounded delay predictions. We categorize problems with known OMv lower bounds
accordingly and give several upper bounds in the delay model that show that our
lower bounds are almost tight.\r\nWe note that concurrent work by v.d.Brand et
al. [SODA '24] and Liu and Srinivas [arXiv:2307.08890] independently study dynamic
graph algorithms with predictions, but their work is mostly focused on showing
upper bounds."
acknowledgement: "Henzinger, Monika: This project has received funding from the European
Research Council (ERC) under the European Union’s Horizon 2020 research and innovation
programme (Grant agreement No. 101019564) and the Austrian Science Fund (FWF) project
Z 422-N, project I 5982-N, and project P 33775-N, with additional funding from the
netidee SCIENCE Stiftung, 2020-2024.\r\nSaha, Barna: This project is partially supported
by NSF grants 1652303, 1909046, 2112533, and HDR TRIPODS Phase II grant 2217058.\r\nWe
would like to thank Andrea Lincoln for many helpful discussions and insightful comments."
alternative_title:
- LIPIcs
article_processing_charge: Yes
arxiv: 1
author:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Barna
full_name: Saha, Barna
last_name: Saha
- first_name: Martin P.
full_name: Seybold, Martin P.
last_name: Seybold
- first_name: Christopher
full_name: Ye, Christopher
last_name: Ye
citation:
ama: 'Henzinger M, Saha B, Seybold MP, Ye C. On the complexity of algorithms with
predictions for dynamic graph problems. In: 15th Innovations in Theoretical
Computer Science Conference. Vol 287. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2024:62:1-62:25. doi:10.4230/LIPIcs.ITCS.2024.62'
apa: 'Henzinger, M., Saha, B., Seybold, M. P., & Ye, C. (2024). On the complexity
of algorithms with predictions for dynamic graph problems. In 15th Innovations
in Theoretical Computer Science Conference (Vol. 287, p. 62:1-62:25). Berkeley,
CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ITCS.2024.62'
chicago: Henzinger, Monika, Barna Saha, Martin P. Seybold, and Christopher Ye. “On
the Complexity of Algorithms with Predictions for Dynamic Graph Problems.” In
15th Innovations in Theoretical Computer Science Conference, 287:62:1-62:25.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.ITCS.2024.62.
ieee: M. Henzinger, B. Saha, M. P. Seybold, and C. Ye, “On the complexity of algorithms
with predictions for dynamic graph problems,” in 15th Innovations in Theoretical
Computer Science Conference, Berkeley, CA, United States, 2024, vol. 287,
p. 62:1-62:25.
ista: 'Henzinger M, Saha B, Seybold MP, Ye C. 2024. On the complexity of algorithms
with predictions for dynamic graph problems. 15th Innovations in Theoretical Computer
Science Conference. ITCS: Innovations in Theoretical Computer Science, LIPIcs,
vol. 287, 62:1-62:25.'
mla: Henzinger, Monika, et al. “On the Complexity of Algorithms with Predictions
for Dynamic Graph Problems.” 15th Innovations in Theoretical Computer Science
Conference, vol. 287, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024,
p. 62:1-62:25, doi:10.4230/LIPIcs.ITCS.2024.62.
short: M. Henzinger, B. Saha, M.P. Seybold, C. Ye, in:, 15th Innovations in Theoretical
Computer Science Conference, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2024, p. 62:1-62:25.
conference:
end_date: 2024-02-02
location: Berkeley, CA, United States
name: 'ITCS: Innovations in Theoretical Computer Science'
start_date: 2024-01-30
corr_author: '1'
date_created: 2025-01-27T15:33:42Z
date_published: 2024-01-24T00:00:00Z
date_updated: 2025-09-09T12:11:33Z
day: '24'
ddc:
- '000'
department:
- _id: MoHe
doi: 10.4230/LIPIcs.ITCS.2024.62
ec_funded: 1
external_id:
arxiv:
- '2307.16771'
isi:
- '001300389400062'
file:
- access_level: open_access
checksum: 15085a5b3697a408b92a4a7a27293927
content_type: application/pdf
creator: dernst
date_created: 2025-01-27T15:33:24Z
date_updated: 2025-01-27T15:33:24Z
file_id: '18929'
file_name: 2024_LIPICs_HenzingerMo.pdf
file_size: 1084372
relation: main_file
success: 1
file_date_updated: 2025-01-27T15:33:24Z
has_accepted_license: '1'
intvolume: ' 287'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 62:1-62:25
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: 34def286-11ca-11ed-8bc3-da5948e1613c
grant_number: Z00422
name: Efficient algorithms
- _id: bda196b2-d553-11ed-ba76-8e8ee6c21103
grant_number: I05982
name: Static and Dynamic Hierarchical Graph Decompositions
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: P33775
name: Fast Algorithms for a Reactive Network Layer
publication: 15th Innovations in Theoretical Computer Science Conference
publication_identifier:
eissn:
- 1868-8969
isbn:
- '9783959773096'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the complexity of algorithms with predictions for dynamic graph problems
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 287
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '18930'
abstract:
- lang: eng
text: "We study sumsets \U0001D49C + ℬ in the set of squares \U0001D4AE (and, more
generally, in the set of kth powers \U0001D4AEk, where k ≥2 is an integer). It
is known by a result of Gyarmati that \U0001D49C + ℬ ⊂ \U0001D4AEk ∩[1,N] implies
that min(|\U0001D49C|,|ℬ|) =Ok(logN). Here, we study how the upper bound on |ℬ|
decreases, when the size of |\U0001D49C| increases (or vice versa). In particular,
if |\U0001D49C| ≥ Ck1m m(logN)1m , then |ℬ| = Ok(m2logN), for sufficiently large
N, a positive integer m and an explicit constant C > 0. For example, with m ∼
loglogN this gives: If |\U0001D49C| ≥ CkloglogN,then |ℬ| = Ok(logN(loglogN)2)."
acknowledgement: This manuscript grew out of the second author’s MSc Thesis at Graz
University of Technology [34]. C. Elsholtz is supported by a joint FWF-ANR project
ArithRand, grant numbers FWF I 4945-N and ANR-20-CE91-0006. Both authors would like
to thank Igor Shparlinski for drawing our attention to related character sum estimates.
Furthermore, we would like to thank the referee for a careful reading of the paper.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Christian
full_name: Elsholtz, Christian
last_name: Elsholtz
- first_name: Lena
full_name: Wurzinger, Lena
id: 50c57d72-32a8-11ee-aeea-d652094d2ccd
last_name: Wurzinger
orcid: 0009-0004-5360-0074
citation:
ama: Elsholtz C, Wurzinger L. Sumsets in the set of squares. The Quarterly Journal
of Mathematics. 2024;75(4):1243-1254. doi:10.1093/qmath/haae044
apa: Elsholtz, C., & Wurzinger, L. (2024). Sumsets in the set of squares. The
Quarterly Journal of Mathematics. Oxford University Press. https://doi.org/10.1093/qmath/haae044
chicago: Elsholtz, Christian, and Lena Wurzinger. “Sumsets in the Set of Squares.”
The Quarterly Journal of Mathematics. Oxford University Press, 2024. https://doi.org/10.1093/qmath/haae044.
ieee: C. Elsholtz and L. Wurzinger, “Sumsets in the set of squares,” The Quarterly
Journal of Mathematics, vol. 75, no. 4. Oxford University Press, pp. 1243–1254,
2024.
ista: Elsholtz C, Wurzinger L. 2024. Sumsets in the set of squares. The Quarterly
Journal of Mathematics. 75(4), 1243–1254.
mla: Elsholtz, Christian, and Lena Wurzinger. “Sumsets in the Set of Squares.” The
Quarterly Journal of Mathematics, vol. 75, no. 4, Oxford University Press,
2024, pp. 1243–54, doi:10.1093/qmath/haae044.
short: C. Elsholtz, L. Wurzinger, The Quarterly Journal of Mathematics 75 (2024)
1243–1254.
corr_author: '1'
date_created: 2025-01-28T06:55:31Z
date_published: 2024-12-01T00:00:00Z
date_updated: 2025-12-04T14:46:28Z
day: '01'
ddc:
- '510'
department:
- _id: TiBr
doi: 10.1093/qmath/haae044
external_id:
isi:
- '001304396600001'
file:
- access_level: open_access
checksum: 1a06e052761d3f1e873463d6f529dd82
content_type: application/pdf
creator: dernst
date_created: 2025-01-28T07:03:51Z
date_updated: 2025-01-28T07:03:51Z
file_id: '18931'
file_name: 2024_QuarterlyJourMath_Elsholtz.pdf
file_size: 424645
relation: main_file
success: 1
file_date_updated: 2025-01-28T07:03:51Z
has_accepted_license: '1'
intvolume: ' 75'
isi: 1
issue: '4'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 1243-1254
publication: The Quarterly Journal of Mathematics
publication_identifier:
eissn:
- 1464-3847
issn:
- 0033-5606
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sumsets in the set of squares
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 75
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18934'
abstract:
- lang: eng
text: The assembly of biomolecular condensate in eukaryotic cells and the accumulation
of amyloid deposits in neurons are processes involving the nucleation and growth
(NAG) of new protein phases. To therapeutically target protein phase separation,
drug candidates are tested in in vitro assays that monitor the increase in the
mass or size of the new phase. Limited mechanistic insight is, however, provided
if empirical or untestable kinetic models are fitted to these progress curves.
Here we present the web server NAGPKin that quantifies NAG rates using mass-based
or size-based progress curves as the input data. A report is generated containing
the fitted NAG parameters and elucidating the phase separation mechanisms at play.
The NAG parameters can be used to predict particle size distributions of, for
example, protein droplets formed by liquid-liquid phase separation (LLPS) or amyloid
fibrils formed by protein aggregation. Because minimal intervention is required
from the user, NAGPKin is a good platform for standardized reporting of LLPS and
protein self-assembly data. NAGPKin is useful for drug discovery as well as for
fundamental studies on protein phase separation. NAGPKin is freely available (no
login required) at https://nagpkin.i3s.up.pt .
acknowledgement: We thank Professor José Paulo Leal, Department of Computer Science
− Faculdade de Ciências da Universidade do Porto, for his invaluable help during
the Implementation of NAGPKin. This work is part of a project that has received
funding from the European Union’s Horizon 2020 research and innovation programme
under grant agreement no. 952334 (PhasAGE). This research was funded by the Portuguese
Foundation for Science and Technology (FCT) in the framework of project PTDC/QUI-COL/2444/2021.
article_number: mr1
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Zsuzsa
full_name: Sárkány, Zsuzsa
last_name: Sárkány
- first_name: Francisco
full_name: Figueiredo, Francisco
id: 8125cbe2-9661-11ed-a754-afe96018f37d
last_name: Figueiredo
- first_name: Sandra
full_name: Macedo-Ribeiro, Sandra
last_name: Macedo-Ribeiro
- first_name: Pedro M.
full_name: Martins, Pedro M.
last_name: Martins
citation:
ama: 'Sárkány Z, Figueiredo F, Macedo-Ribeiro S, Martins PM. NAGPKin: Nucleation-and-growth
parameters from the kinetics of protein phase separation. Molecular Biology
of the Cell. 2024;35(3). doi:10.1091/mbc.e23-07-0289'
apa: 'Sárkány, Z., Figueiredo, F., Macedo-Ribeiro, S., & Martins, P. M. (2024).
NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation.
Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/mbc.e23-07-0289'
chicago: 'Sárkány, Zsuzsa, Francisco Figueiredo, Sandra Macedo-Ribeiro, and Pedro
M. Martins. “NAGPKin: Nucleation-and-Growth Parameters from the Kinetics of Protein
Phase Separation.” Molecular Biology of the Cell. American Society for
Cell Biology, 2024. https://doi.org/10.1091/mbc.e23-07-0289.'
ieee: 'Z. Sárkány, F. Figueiredo, S. Macedo-Ribeiro, and P. M. Martins, “NAGPKin:
Nucleation-and-growth parameters from the kinetics of protein phase separation,”
Molecular Biology of the Cell, vol. 35, no. 3. American Society for Cell
Biology, 2024.'
ista: 'Sárkány Z, Figueiredo F, Macedo-Ribeiro S, Martins PM. 2024. NAGPKin: Nucleation-and-growth
parameters from the kinetics of protein phase separation. Molecular Biology of
the Cell. 35(3), mr1.'
mla: 'Sárkány, Zsuzsa, et al. “NAGPKin: Nucleation-and-Growth Parameters from the
Kinetics of Protein Phase Separation.” Molecular Biology of the Cell, vol.
35, no. 3, mr1, American Society for Cell Biology, 2024, doi:10.1091/mbc.e23-07-0289.'
short: Z. Sárkány, F. Figueiredo, S. Macedo-Ribeiro, P.M. Martins, Molecular Biology
of the Cell 35 (2024).
date_created: 2025-01-29T07:58:40Z
date_published: 2024-03-01T00:00:00Z
date_updated: 2025-01-29T08:16:20Z
day: '01'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1091/mbc.e23-07-0289
external_id:
pmid:
- '38117593'
file:
- access_level: open_access
checksum: d7deb6390f294da69321cfbe352ed611
content_type: application/pdf
creator: dernst
date_created: 2025-01-29T08:12:11Z
date_updated: 2025-01-29T08:12:11Z
file_id: '18935'
file_name: 2024_MolecularBioCell_Sarkany.pdf
file_size: 1699180
relation: main_file
success: 1
file_date_updated: 2025-01-29T08:12:11Z
has_accepted_license: '1'
intvolume: ' 35'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Molecular Biology of the Cell
publication_identifier:
eissn:
- 1939-4586
issn:
- 1059-1524
publication_status: published
publisher: American Society for Cell Biology
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase
separation'
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2024'
...
---
OA_type: closed access
_id: '18937'
abstract:
- lang: eng
text: A detailed structural, magnetic as well as dielectric dynamics study is carried
out to investigate the influence of Bi3+ on YCrO3. All the samples crystalize
in orthorhombic structure with Pnma symmetry and the grains are mostly stretched
with Bi. A coexisting tunable fraction of both antiferromagnetic (AFM) and weak
ferromagnetic (WFM) phases is acquired by the system down to Low-T. An abnormal
negative magnetization in zero field is correlated to the competition among AFM
and WFM phases. Maximum magnetization decreases while the coercivity first increases
and then decreases with Bi is correlated to the competing effect between the local
deformation and Cr–O–Cr exchange interaction. The magnetodielectric coupling with
improved permittivity might be associated with the 6s2 lone pair electron of Bi3+.
Furthermore, ac-conductivity increases with a decrease in activation energy (0.27–0.11
eV), is explained in the framework of structural model and charge carrier hopping
between Cr3+ and Cr4+ ions.
acknowledgement: The authors would like to acknowledge MHRD, Government of India for
financial support. The author is also thankful to RRCAT, Indore for providing XPS
beamline-14 of Indus II to conduct experimental work.
article_number: '416018'
article_processing_charge: No
article_type: original
author:
- first_name: Sujata Kumari
full_name: Ray, Sujata Kumari
last_name: Ray
- first_name: Anupama
full_name: Pati, Anupama
last_name: Pati
- first_name: Payala
full_name: Sahoo, Payala
last_name: Sahoo
- first_name: A.K.
full_name: Sahoo, A.K.
last_name: Sahoo
- first_name: Saurabh
full_name: Singh, Saurabh
id: 12d625da-9cb3-11ed-9667-af09d37d3f0a
last_name: Singh
orcid: 0000-0003-2209-5269
- first_name: Tsunehiro
full_name: Takeuchi, Tsunehiro
last_name: Takeuchi
- first_name: S.
full_name: Dash, S.
last_name: Dash
citation:
ama: 'Ray SK, Pati A, Sahoo P, et al. Tunable magnetoelectronic properties in Bi3+
substituted YCrO3. Physica B: Condensed Matter. 2024;685. doi:10.1016/j.physb.2024.416018'
apa: 'Ray, S. K., Pati, A., Sahoo, P., Sahoo, A. K., Singh, S., Takeuchi, T., &
Dash, S. (2024). Tunable magnetoelectronic properties in Bi3+ substituted YCrO3.
Physica B: Condensed Matter. Elsevier. https://doi.org/10.1016/j.physb.2024.416018'
chicago: 'Ray, Sujata Kumari, Anupama Pati, Payala Sahoo, A.K. Sahoo, Saurabh Singh,
Tsunehiro Takeuchi, and S. Dash. “Tunable Magnetoelectronic Properties in Bi3+
Substituted YCrO3.” Physica B: Condensed Matter. Elsevier, 2024. https://doi.org/10.1016/j.physb.2024.416018.'
ieee: 'S. K. Ray et al., “Tunable magnetoelectronic properties in Bi3+ substituted
YCrO3,” Physica B: Condensed Matter, vol. 685. Elsevier, 2024.'
ista: 'Ray SK, Pati A, Sahoo P, Sahoo AK, Singh S, Takeuchi T, Dash S. 2024. Tunable
magnetoelectronic properties in Bi3+ substituted YCrO3. Physica B: Condensed Matter.
685, 416018.'
mla: 'Ray, Sujata Kumari, et al. “Tunable Magnetoelectronic Properties in Bi3+ Substituted
YCrO3.” Physica B: Condensed Matter, vol. 685, 416018, Elsevier, 2024,
doi:10.1016/j.physb.2024.416018.'
short: 'S.K. Ray, A. Pati, P. Sahoo, A.K. Sahoo, S. Singh, T. Takeuchi, S. Dash,
Physica B: Condensed Matter 685 (2024).'
date_created: 2025-01-29T08:33:04Z
date_published: 2024-07-15T00:00:00Z
date_updated: 2025-01-29T08:37:14Z
day: '15'
department:
- _id: MaIb
doi: 10.1016/j.physb.2024.416018
intvolume: ' 685'
language:
- iso: eng
month: '07'
oa_version: None
publication: 'Physica B: Condensed Matter'
publication_identifier:
issn:
- 0921-4526
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tunable magnetoelectronic properties in Bi3+ substituted YCrO3
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 685
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18938'
abstract:
- lang: eng
text: The synthesis of proteins as encoded in the genome depends critically on translational
fidelity. Nevertheless, errors inevitably occur, and those that result in reading
frame shifts are particularly consequential because the resulting polypeptides
are typically nonfunctional. Despite the generally maladaptive impact of such
errors, the proper decoding of certain mRNAs, including many viral mRNAs, depends
on a process known as programmed ribosomal frameshifting. The fact that these
programmed events, commonly involving a shift to the –1 frame, occur at specific
evolutionarily optimized “slippery” sites has facilitated mechanistic investigation.
By contrast, less is known about the scope and nature of error (i.e., nonprogrammed)
frameshifting. Here, we examine error frameshifting by monitoring spontaneous
frameshift events that suppress the effects of single base pair deletions affecting
two unrelated test proteins. To map the precise sites of frameshifting, we developed
a targeted mass spectrometry–based method called “translational tiling proteomics”
for interrogating the full set of possible –1 slippage events that could produce
the observed frameshift suppression. Surprisingly, such events occur at many sites
along the transcripts, involving up to one half of the available codons. Only
a subset of these resembled canonical “slippery” sites, implicating alternative
mechanisms potentially involving noncognate mispairing events. Additionally, the
aggregate frequency of these events (ranging from 1 to 10% in our test cases)
was higher than we might have anticipated. Our findings point to an unexpected
degree of mechanistic diversity among ribosomal frameshifting events and suggest
that frameshifted products may contribute more significantly to the proteome than
generally assumed.
acknowledgement: We thank S. L. Dove for valuable discussion and comments on the manuscript
and R. Hellmiss for artwork. This work was supported by NIH grants GM136247 to A.H.,
AG011085 to J.W.H., and GM132129 to J.A.P.
article_number: e2317453121
article_processing_charge: No
article_type: original
author:
- first_name: Benjamin L
full_name: Springstein, Benjamin L
id: b4eb62ef-ac72-11ed-9503-ed3b4d66c083
last_name: Springstein
orcid: 0000-0002-3461-5391
- first_name: Joao A.
full_name: Paulo, Joao A.
last_name: Paulo
- first_name: Hankum
full_name: Park, Hankum
last_name: Park
- first_name: Kemardo
full_name: Henry, Kemardo
last_name: Henry
- first_name: Eleanor
full_name: Fleming, Eleanor
last_name: Fleming
- first_name: Zoë
full_name: Feder, Zoë
last_name: Feder
- first_name: J. Wade
full_name: Harper, J. Wade
last_name: Harper
- first_name: Ann
full_name: Hochschild, Ann
last_name: Hochschild
citation:
ama: Springstein BL, Paulo JA, Park H, et al. Systematic analysis of nonprogrammed
frameshift suppression in E.coli via translational tiling proteomics. Proceedings
of the National Academy of Sciences of the United States of America. 2024;121(6).
doi:10.1073/pnas.2317453121
apa: Springstein, B. L., Paulo, J. A., Park, H., Henry, K., Fleming, E., Feder,
Z., … Hochschild, A. (2024). Systematic analysis of nonprogrammed frameshift suppression
in E.coli via translational tiling proteomics. Proceedings of the National
Academy of Sciences of the United States of America. National Academy of Sciences.
https://doi.org/10.1073/pnas.2317453121
chicago: Springstein, Benjamin L, Joao A. Paulo, Hankum Park, Kemardo Henry, Eleanor
Fleming, Zoë Feder, J. Wade Harper, and Ann Hochschild. “Systematic Analysis of
Nonprogrammed Frameshift Suppression in E.Coli via Translational Tiling Proteomics.”
Proceedings of the National Academy of Sciences of the United States of America.
National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2317453121.
ieee: B. L. Springstein et al., “Systematic analysis of nonprogrammed frameshift
suppression in E.coli via translational tiling proteomics,” Proceedings of
the National Academy of Sciences of the United States of America, vol. 121,
no. 6. National Academy of Sciences, 2024.
ista: Springstein BL, Paulo JA, Park H, Henry K, Fleming E, Feder Z, Harper JW,
Hochschild A. 2024. Systematic analysis of nonprogrammed frameshift suppression
in E.coli via translational tiling proteomics. Proceedings of the National Academy
of Sciences of the United States of America. 121(6), e2317453121.
mla: Springstein, Benjamin L., et al. “Systematic Analysis of Nonprogrammed Frameshift
Suppression in E.Coli via Translational Tiling Proteomics.” Proceedings of
the National Academy of Sciences of the United States of America, vol. 121,
no. 6, e2317453121, National Academy of Sciences, 2024, doi:10.1073/pnas.2317453121.
short: B.L. Springstein, J.A. Paulo, H. Park, K. Henry, E. Fleming, Z. Feder, J.W.
Harper, A. Hochschild, Proceedings of the National Academy of Sciences of the
United States of America 121 (2024).
date_created: 2025-01-29T08:39:27Z
date_published: 2024-02-06T00:00:00Z
date_updated: 2025-05-14T11:02:52Z
day: '06'
ddc:
- '570'
department:
- _id: MaLo
doi: 10.1073/pnas.2317453121
external_id:
pmid:
- '38289956'
file:
- access_level: open_access
checksum: 5bd62c7cb4287e3706a1d45d6ef61fd1
content_type: application/pdf
creator: dernst
date_created: 2025-01-29T08:43:16Z
date_updated: 2025-01-29T08:43:16Z
file_id: '18939'
file_name: 2024_PNAS_Springstein.pdf
file_size: 720902
relation: main_file
success: 1
file_date_updated: 2025-01-29T08:43:16Z
has_accepted_license: '1'
intvolume: ' 121'
issue: '6'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational
tiling proteomics
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 121
year: '2024'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18940'
abstract:
- lang: eng
text: BMP signaling has a conserved function in patterning the dorsal-ventral body
axis in Bilateria and the directive axis in anthozoan cnidarians. So far, cnidarian
studies have focused on the role of different BMP signaling network components
in regulating pSMAD1/5 gradient formation. Much less is known about the target
genes downstream of BMP signaling. To address this, we generated a genome-wide
list of direct pSMAD1/5 target genes in the anthozoan Nematostella
vectensis, several of which were conserved in Drosophila
and Xenopus. Our ChIP-seq analysis revealed that many
of the regulatory molecules with documented bilaterally symmetric expression in
Nematostella are directly controlled by BMP signaling.
We identified several so far uncharacterized BMP-dependent transcription factors
and signaling molecules, whose bilaterally symmetric expression may be indicative
of their involvement in secondary axis patterning. One of these molecules is zswim4-6,
which encodes a novel nuclear protein that can modulate the pSMAD1/5 gradient
and potentially promote BMP-dependent gene repression.
acknowledgement: This work was funded by the Austrian Science Foundation (FWF) grants
P26962-B21 and P32705-B to GG and by the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation program (grant agreement No
637840 [QUANTPATTERN] and 863952 [ACE-OF-SPACE]) to PM. We thank Michaela Schwaiger,
Taras Kreslavsky, Hiromi Tagoh, and Patricio Ferrer Murguia for their help with
the ChIP protocol, Matthias Richter and Christian Hofer for their assistance with
in situ analyses, Emilio Gonzalez Morales for making the measurements for Figure
6—figure supplement 3, Catrin Weiler for the assistance in cloning zebrafish zswim5,
David Mörsdorf for critically reading the manuscript and help with data visualization,
and the Core Facility for Cell Imaging and Ultrastructure Research of the University
of Vienna for access to the confocal microscope.
article_processing_charge: Yes
article_type: original
author:
- first_name: Paul
full_name: Knabl, Paul
last_name: Knabl
- first_name: Alexandra
full_name: Schauer, Alexandra
id: 30A536BA-F248-11E8-B48F-1D18A9856A87
last_name: Schauer
orcid: 0000-0001-7659-9142
- first_name: Autumn P
full_name: Pomreinke, Autumn P
last_name: Pomreinke
- first_name: Bob
full_name: Zimmermann, Bob
last_name: Zimmermann
- first_name: Katherine W
full_name: Rogers, Katherine W
last_name: Rogers
- first_name: Daniel
full_name: Čapek, Daniel
last_name: Čapek
- first_name: Patrick
full_name: Müller, Patrick
last_name: Müller
- first_name: Grigory
full_name: Genikhovich, Grigory
last_name: Genikhovich
citation:
ama: Knabl P, Schauer A, Pomreinke AP, et al. Analysis of SMAD1/5 target genes in
a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator. eLife.
2024;13. doi:10.7554/elife.80803
apa: Knabl, P., Schauer, A., Pomreinke, A. P., Zimmermann, B., Rogers, K. W., Čapek,
D., … Genikhovich, G. (2024). Analysis of SMAD1/5 target genes in a sea anemone
reveals ZSWIM4-6 as a novel BMP signaling modulator. ELife. eLife Sciences
Publications. https://doi.org/10.7554/elife.80803
chicago: Knabl, Paul, Alexandra Schauer, Autumn P Pomreinke, Bob Zimmermann, Katherine
W Rogers, Daniel Čapek, Patrick Müller, and Grigory Genikhovich. “Analysis of
SMAD1/5 Target Genes in a Sea Anemone Reveals ZSWIM4-6 as a Novel BMP Signaling
Modulator.” ELife. eLife Sciences Publications, 2024. https://doi.org/10.7554/elife.80803.
ieee: P. Knabl et al., “Analysis of SMAD1/5 target genes in a sea anemone
reveals ZSWIM4-6 as a novel BMP signaling modulator,” eLife, vol. 13. eLife
Sciences Publications, 2024.
ista: Knabl P, Schauer A, Pomreinke AP, Zimmermann B, Rogers KW, Čapek D, Müller
P, Genikhovich G. 2024. Analysis of SMAD1/5 target genes in a sea anemone reveals
ZSWIM4-6 as a novel BMP signaling modulator. eLife. 13.
mla: Knabl, Paul, et al. “Analysis of SMAD1/5 Target Genes in a Sea Anemone Reveals
ZSWIM4-6 as a Novel BMP Signaling Modulator.” ELife, vol. 13, eLife Sciences
Publications, 2024, doi:10.7554/elife.80803.
short: P. Knabl, A. Schauer, A.P. Pomreinke, B. Zimmermann, K.W. Rogers, D. Čapek,
P. Müller, G. Genikhovich, ELife 13 (2024).
date_created: 2025-01-29T08:48:34Z
date_published: 2024-02-07T00:00:00Z
date_updated: 2025-01-29T08:56:21Z
day: '07'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.7554/elife.80803
file:
- access_level: open_access
checksum: 24548a184215d3f4547bba535ccfd7b1
content_type: application/pdf
creator: dernst
date_created: 2025-01-29T08:50:18Z
date_updated: 2025-01-29T08:50:18Z
file_id: '18941'
file_name: 2024_eLife_Knabl.pdf
file_size: 11855972
relation: main_file
success: 1
file_date_updated: 2025-01-29T08:50:18Z
has_accepted_license: '1'
intvolume: ' 13'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel
BMP signaling modulator
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '18944'
abstract:
- lang: eng
text: 'Understanding connectivity patterns exhibited by endangered species living
in fragmented habitats is fundamental to improving management and conservation
actions. Such improvements can be particularly pressing at the trailing edges
of these habitats, where populations are facing the greatest challenges from climate
change, and appear even more crucial if the species is commercially harvested.
Seascape genetics have been increasingly used to meet these needs. In this study,
we examined connectivity patterns among 32 populations of the oarweed kelp Laminaria
digitata located at the species’ southern range limit. The distance
(or sampling gap) between neighboring populations ranged from a few km to a few
100s of km. By genotyping 11 microsatellite markers, we aimed to (1) refine analyses
of population structure; (2) test whether on-shelf islands are genetically more
differentiated than mainland populations; (3) evaluate the relative importance
of various abiotic conditions in shaping the genetic structure; and (4) evaluate
if the relative importance of each environmental factor varied according to sampling
schemes. Our analyses revealed a positive relationship between connectivity links
and genetic diversity: populations with high levels of connectivity were genetically
enriched while isolated populations showed signs of genetic erosion. The genetically
impoverished populations corresponded to the southernmost populations as well
as populations along the northern coast of Brittany (Locquirec, Saint-Malo Bay)
and the northernmost population in Pas-de-Calais. By performing distance-based
redundancy analysis on various sampling schemes, geographic distance appeared
as the dominant factor influencing connectivity between populations separated
by great distances, while hydrodynamic processes were the main factor when analyzing
at a final spatial resolution.'
article_processing_charge: No
article_type: original
author:
- first_name: Louise
full_name: Fouqueau, Louise
id: 1676e173-8143-11ed-8927-fe165216a93f
last_name: Fouqueau
orcid: 0000-0003-0371-9339
- first_name: L
full_name: Reynes, L
last_name: Reynes
- first_name: F
full_name: Tempera, F
last_name: Tempera
- first_name: T
full_name: Bajjouk, T
last_name: Bajjouk
- first_name: A
full_name: Blanfuné, A
last_name: Blanfuné
- first_name: C
full_name: Chevalier, C
last_name: Chevalier
- first_name: M
full_name: Laurans, M
last_name: Laurans
- first_name: S
full_name: Mauger, S
last_name: Mauger
- first_name: M
full_name: Sourisseau, M
last_name: Sourisseau
- first_name: J
full_name: Assis, J
last_name: Assis
- first_name: L
full_name: Lévêque, L
last_name: Lévêque
- first_name: M
full_name: Valero, M
last_name: Valero
citation:
ama: Fouqueau L, Reynes L, Tempera F, et al. Seascape genetic study on Laminaria
digitata underscores the critical role of sampling schemes. Marine Ecology
Progress Series. 2024;740:23-42. doi:10.3354/meps14640
apa: Fouqueau, L., Reynes, L., Tempera, F., Bajjouk, T., Blanfuné, A., Chevalier,
C., … Valero, M. (2024). Seascape genetic study on Laminaria digitata underscores
the critical role of sampling schemes. Marine Ecology Progress Series.
Inter-Research Science Center. https://doi.org/10.3354/meps14640
chicago: Fouqueau, Louise, L Reynes, F Tempera, T Bajjouk, A Blanfuné, C Chevalier,
M Laurans, et al. “Seascape Genetic Study on Laminaria Digitata Underscores the
Critical Role of Sampling Schemes.” Marine Ecology Progress Series. Inter-Research
Science Center, 2024. https://doi.org/10.3354/meps14640.
ieee: L. Fouqueau et al., “Seascape genetic study on Laminaria digitata underscores
the critical role of sampling schemes,” Marine Ecology Progress Series,
vol. 740. Inter-Research Science Center, pp. 23–42, 2024.
ista: Fouqueau L, Reynes L, Tempera F, Bajjouk T, Blanfuné A, Chevalier C, Laurans
M, Mauger S, Sourisseau M, Assis J, Lévêque L, Valero M. 2024. Seascape genetic
study on Laminaria digitata underscores the critical role of sampling schemes.
Marine Ecology Progress Series. 740, 23–42.
mla: Fouqueau, Louise, et al. “Seascape Genetic Study on Laminaria Digitata Underscores
the Critical Role of Sampling Schemes.” Marine Ecology Progress Series,
vol. 740, Inter-Research Science Center, 2024, pp. 23–42, doi:10.3354/meps14640.
short: L. Fouqueau, L. Reynes, F. Tempera, T. Bajjouk, A. Blanfuné, C. Chevalier,
M. Laurans, S. Mauger, M. Sourisseau, J. Assis, L. Lévêque, M. Valero, Marine
Ecology Progress Series 740 (2024) 23–42.
corr_author: '1'
date_created: 2025-01-29T09:09:10Z
date_published: 2024-07-25T00:00:00Z
date_updated: 2025-01-29T09:12:34Z
day: '25'
department:
- _id: NiBa
doi: 10.3354/meps14640
intvolume: ' 740'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://inria.hal.science/hal-04624490/
month: '07'
oa: 1
oa_version: Submitted Version
page: 23-42
publication: Marine Ecology Progress Series
publication_identifier:
eissn:
- 1616-1599
issn:
- 0171-8630
publication_status: published
publisher: Inter-Research Science Center
quality_controlled: '1'
scopus_import: '1'
status: public
title: Seascape genetic study on Laminaria digitata underscores the critical role
of sampling schemes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 740
year: '2024'
...