---
OA_place: publisher
OA_type: hybrid
_id: '11182'
abstract:
- lang: eng
text: Immune cells are constantly on the move through multicellular organisms to
explore and respond to pathogens and other harmful insults. While moving, immune
cells efficiently traverse microenvironments composed of tissue cells and extracellular
fibers, which together form complex environments of various porosity, stiffness,
topography, and chemical composition. In this protocol we describe experimental
procedures to investigate immune cell migration through microenvironments of heterogeneous
porosity. In particular, we describe micro-channels, micro-pillars, and collagen
networks as cell migration paths with alternative pore size choices. Employing
micro-channels or micro-pillars that divide at junctions into alternative paths
with initially differentially sized pores allows us to precisely (1) measure the
cellular translocation time through these porous path junctions, (2) quantify
the cellular preference for individual pore sizes, and (3) image cellular components
like the nucleus and the cytoskeleton. This reductionistic experimental setup
thus can elucidate how immune cells perform decisions in complex microenvironments
of various porosity like the interstitium. The setup further allows investigation
of the underlying forces of cellular squeezing and the consequences of cellular
deformation on the integrity of the cell and its organelles. As a complementary
approach that does not require any micro-engineering expertise, we describe the
usage of three-dimensional collagen networks with different pore sizes. Whereas
we here focus on dendritic cells as a model for motile immune cells, the described
protocols are versatile as they are also applicable for other immune cell types
like neutrophils and non-immune cell types such as mesenchymal and cancer cells.
In summary, we here describe protocols to identify the mechanisms and principles
of cellular probing, decision making, and squeezing during cellular movement through
microenvironments of heterogeneous porosity.
acknowledgement: "We thank Kasia Stefanowski for excellent technical assistance, and
the Core Facility Bioimaging of the Biomedical Center (BMC) of the Ludwig-Maximilian
University for excellent support. We gratefully acknowledge financial support from
the Peter Hans Hofschneider Professorship of the Stiftung Experimentelle Biomedizin
(to J.R), from the DFG (Collaborative Research Center SFB914, project A12; and Priority
Programme SPP2332, project 492014049; both to J.R) and from the LMU Institutional
Strategy LMU-Excellent within the framework of the German Excellence Initiative
(to J.R).\r\nOpen access funding enabled and organized by Projekt DEAL."
article_number: e407
article_processing_charge: No
article_type: original
author:
- first_name: Janina
full_name: Kroll, Janina
last_name: Kroll
- first_name: Mauricio J.A.
full_name: Ruiz-Fernandez, Mauricio J.A.
last_name: Ruiz-Fernandez
- first_name: Malte B.
full_name: Braun, Malte B.
last_name: Braun
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
citation:
ama: Kroll J, Ruiz-Fernandez MJA, Braun MB, Merrin J, Renkawitz J. Quantifying the
probing and selection of microenvironmental pores by motile immune cells. Current
Protocols. 2022;2(4). doi:10.1002/cpz1.407
apa: Kroll, J., Ruiz-Fernandez, M. J. A., Braun, M. B., Merrin, J., & Renkawitz,
J. (2022). Quantifying the probing and selection of microenvironmental pores by
motile immune cells. Current Protocols. Wiley. https://doi.org/10.1002/cpz1.407
chicago: Kroll, Janina, Mauricio J.A. Ruiz-Fernandez, Malte B. Braun, Jack Merrin,
and Jörg Renkawitz. “Quantifying the Probing and Selection of Microenvironmental
Pores by Motile Immune Cells.” Current Protocols. Wiley, 2022. https://doi.org/10.1002/cpz1.407.
ieee: J. Kroll, M. J. A. Ruiz-Fernandez, M. B. Braun, J. Merrin, and J. Renkawitz,
“Quantifying the probing and selection of microenvironmental pores by motile immune
cells,” Current Protocols, vol. 2, no. 4. Wiley, 2022.
ista: Kroll J, Ruiz-Fernandez MJA, Braun MB, Merrin J, Renkawitz J. 2022. Quantifying
the probing and selection of microenvironmental pores by motile immune cells.
Current Protocols. 2(4), e407.
mla: Kroll, Janina, et al. “Quantifying the Probing and Selection of Microenvironmental
Pores by Motile Immune Cells.” Current Protocols, vol. 2, no. 4, e407,
Wiley, 2022, doi:10.1002/cpz1.407.
short: J. Kroll, M.J.A. Ruiz-Fernandez, M.B. Braun, J. Merrin, J. Renkawitz, Current
Protocols 2 (2022).
date_created: 2022-04-17T22:01:46Z
date_published: 2022-04-05T00:00:00Z
date_updated: 2024-10-14T13:16:54Z
day: '05'
ddc:
- '570'
department:
- _id: NanoFab
doi: 10.1002/cpz1.407
external_id:
pmid:
- '35384410'
file:
- access_level: open_access
checksum: 72152d005c367777f6cf2f6a477f0d52
content_type: application/pdf
creator: dernst
date_created: 2022-05-02T08:16:10Z
date_updated: 2022-05-02T08:16:10Z
file_id: '11347'
file_name: 2022_CurrentProtocols_Kroll.pdf
file_size: 2142703
relation: main_file
success: 1
file_date_updated: 2022-05-02T08:16:10Z
has_accepted_license: '1'
intvolume: ' 2'
issue: '4'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Current Protocols
publication_identifier:
eissn:
- 2691-1299
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantifying the probing and selection of microenvironmental pores by motile
immune cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 0043cee0-e5fc-11ee-9736-f83bc23afbf0
volume: 2
year: '2022'
...
---
_id: '11183'
abstract:
- lang: eng
text: "Subgraph detection has recently been one of the most studied problems in
the CONGEST model of distributed computing. In this work, we study the distributed
complexity of problems closely related to subgraph detection, mainly focusing
on induced subgraph detection. The main line of this work presents lower bounds
and parameterized algorithms w.r.t structural parameters of the input graph:\r\n-
On general graphs, we give unconditional lower bounds for induced detection of
cycles and patterns of treewidth 2 in CONGEST. Moreover, by adapting reductions
from centralized parameterized complexity, we prove lower bounds in CONGEST for
detecting patterns with a 4-clique, and for induced path detection conditional
on the hardness of triangle detection in the congested clique.\r\n- On graphs
of bounded degeneracy, we show that induced paths can be detected fast in CONGEST
using techniques from parameterized algorithms, while detecting cycles and patterns
of treewidth 2 is hard.\r\n- On graphs of bounded vertex cover number, we show
that induced subgraph detection is easy in CONGEST for any pattern graph. More
specifically, we adapt a centralized parameterized algorithm for a more general
maximum common induced subgraph detection problem to the distributed setting.
In addition to these induced subgraph detection results, we study various related
problems in the CONGEST and congested clique models, including for multicolored
versions of subgraph-detection-like problems."
acknowledgement: "Amir Nikabadi: Supported by the LABEX MILYON (ANR-10-LABX-0070)
of Université de Lyon, within the program “Investissements d’Avenir” (ANR-11-IDEX-0007)
operated by the French National Research Agency (ANR). Janne H. Korhonen: Supported
by the European Research Council (ERC) under the European Union’s Horizon 2020 research
and innovation programme (grant agreement No 805223 ScaleML).\r\nWe thank François
Le Gall and Masayuki Miyamoto for sharing their work on lower bounds for induced
subgraph detection [36]."
alternative_title:
- LIPIcs
article_number: '15'
article_processing_charge: No
author:
- first_name: Amir
full_name: Nikabadi, Amir
last_name: Nikabadi
- first_name: Janne
full_name: Korhonen, Janne
id: C5402D42-15BC-11E9-A202-CA2BE6697425
last_name: Korhonen
citation:
ama: 'Nikabadi A, Korhonen J. Beyond distributed subgraph detection: Induced subgraphs,
multicolored problems and graph parameters. In: Bramas Q, Gramoli V, Milani A,
eds. 25th International Conference on Principles of Distributed Systems.
Vol 217. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022. doi:10.4230/LIPIcs.OPODIS.2021.15'
apa: 'Nikabadi, A., & Korhonen, J. (2022). Beyond distributed subgraph detection:
Induced subgraphs, multicolored problems and graph parameters. In Q. Bramas, V.
Gramoli, & A. Milani (Eds.), 25th International Conference on Principles
of Distributed Systems (Vol. 217). Strasbourg, France: Schloss Dagstuhl -
Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.OPODIS.2021.15'
chicago: 'Nikabadi, Amir, and Janne Korhonen. “Beyond Distributed Subgraph Detection:
Induced Subgraphs, Multicolored Problems and Graph Parameters.” In 25th International
Conference on Principles of Distributed Systems, edited by Quentin Bramas,
Vincent Gramoli, and Alessia Milani, Vol. 217. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2022. https://doi.org/10.4230/LIPIcs.OPODIS.2021.15.'
ieee: 'A. Nikabadi and J. Korhonen, “Beyond distributed subgraph detection: Induced
subgraphs, multicolored problems and graph parameters,” in 25th International
Conference on Principles of Distributed Systems, Strasbourg, France, 2022,
vol. 217.'
ista: 'Nikabadi A, Korhonen J. 2022. Beyond distributed subgraph detection: Induced
subgraphs, multicolored problems and graph parameters. 25th International Conference
on Principles of Distributed Systems. OPODIS, LIPIcs, vol. 217, 15.'
mla: 'Nikabadi, Amir, and Janne Korhonen. “Beyond Distributed Subgraph Detection:
Induced Subgraphs, Multicolored Problems and Graph Parameters.” 25th International
Conference on Principles of Distributed Systems, edited by Quentin Bramas
et al., vol. 217, 15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022,
doi:10.4230/LIPIcs.OPODIS.2021.15.'
short: A. Nikabadi, J. Korhonen, in:, Q. Bramas, V. Gramoli, A. Milani (Eds.), 25th
International Conference on Principles of Distributed Systems, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2022.
conference:
end_date: 2021-12-15
location: Strasbourg, France
name: OPODIS
start_date: 2021-12-13
corr_author: '1'
date_created: 2022-04-17T22:01:47Z
date_published: 2022-02-01T00:00:00Z
date_updated: 2025-04-14T07:49:13Z
day: '01'
ddc:
- '510'
department:
- _id: DaAl
doi: 10.4230/LIPIcs.OPODIS.2021.15
ec_funded: 1
editor:
- first_name: Quentin
full_name: Bramas, Quentin
last_name: Bramas
- first_name: Vincent
full_name: Gramoli, Vincent
last_name: Gramoli
- first_name: Alessia
full_name: Milani, Alessia
last_name: Milani
file:
- access_level: open_access
checksum: 626551c14de5d4091573200ed0535752
content_type: application/pdf
creator: dernst
date_created: 2022-05-02T07:53:00Z
date_updated: 2022-05-02T07:53:00Z
file_id: '11345'
file_name: 2022_LIPICs_Nikabadi.pdf
file_size: 790396
relation: main_file
success: 1
file_date_updated: 2022-05-02T07:53:00Z
has_accepted_license: '1'
intvolume: ' 217'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: 25th International Conference on Principles of Distributed Systems
publication_identifier:
isbn:
- '9783959772198'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Beyond distributed subgraph detection: Induced subgraphs, multicolored problems
and graph parameters'
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: 217
year: '2022'
...
---
_id: '11184'
abstract:
- lang: eng
text: "Let G be a graph on n nodes. In the stochastic population protocol model,
a collection of n indistinguishable, resource-limited nodes collectively solve
tasks via pairwise interactions. In each interaction, two randomly chosen neighbors
first read each other’s states, and then update their local states. A rich line
of research has established tight upper and lower bounds on the complexity of
fundamental tasks, such as majority and leader election, in this model, when G
is a clique. Specifically, in the clique, these tasks can be solved fast, i.e.,
in n polylog n pairwise interactions, with high probability, using at most polylog
n states per node.\r\nIn this work, we consider the more general setting where
G is an arbitrary regular graph, and present a technique for simulating protocols
designed for fully-connected networks in any connected regular graph. Our main
result is a simulation that is efficient on many interesting graph families: roughly,
the simulation overhead is polylogarithmic in the number of nodes, and quadratic
in the conductance of the graph. As a sample application, we show that, in any
regular graph with conductance φ, both leader election and exact majority can
be solved in φ^{-2} ⋅ n polylog n pairwise interactions, with high probability,
using at most φ^{-2} ⋅ polylog n states per node. This shows that there are fast
and space-efficient population protocols for leader election and exact majority
on graphs with good expansion properties. We believe our results will prove generally
useful, as they allow efficient technology transfer between the well-mixed (clique)
case, and the under-explored spatial setting."
acknowledgement: "Dan Alistarh: This project has received funding from the European
Research Council (ERC)\r\nunder the European Union’s Horizon 2020 research and innovation
programme (grant agreement No.805223 ScaleML).\r\nJoel Rybicki: This project has
received from the European Union’s Horizon 2020 research and\r\ninnovation programme
under the Marie Skłodowska-Curie grant agreement No. 840605.\r\nAcknowledgements
We grateful to Giorgi Nadiradze for pointing out a generalisation of the phase clock
construction to non-regular graphs. We also thank anonymous reviewers for their
useful comments on earlier versions of this manuscript."
alternative_title:
- LIPIcs
article_number: '14'
article_processing_charge: No
arxiv: 1
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Rati
full_name: Gelashvili, Rati
last_name: Gelashvili
- first_name: Joel
full_name: Rybicki, Joel
id: 334EFD2E-F248-11E8-B48F-1D18A9856A87
last_name: Rybicki
orcid: 0000-0002-6432-6646
citation:
ama: 'Alistarh D-A, Gelashvili R, Rybicki J. Fast graphical population protocols.
In: Bramas Q, Gramoli V, Milani A, eds. 25th International Conference on Principles
of Distributed Systems. Vol 217. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2022. doi:10.4230/LIPIcs.OPODIS.2021.14'
apa: 'Alistarh, D.-A., Gelashvili, R., & Rybicki, J. (2022). Fast graphical
population protocols. In Q. Bramas, V. Gramoli, & A. Milani (Eds.), 25th
International Conference on Principles of Distributed Systems (Vol. 217).
Strasbourg, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.OPODIS.2021.14'
chicago: Alistarh, Dan-Adrian, Rati Gelashvili, and Joel Rybicki. “Fast Graphical
Population Protocols.” In 25th International Conference on Principles of Distributed
Systems, edited by Quentin Bramas, Vincent Gramoli, and Alessia Milani, Vol.
217. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. https://doi.org/10.4230/LIPIcs.OPODIS.2021.14.
ieee: D.-A. Alistarh, R. Gelashvili, and J. Rybicki, “Fast graphical population
protocols,” in 25th International Conference on Principles of Distributed Systems,
Strasbourg, France, 2022, vol. 217.
ista: Alistarh D-A, Gelashvili R, Rybicki J. 2022. Fast graphical population protocols.
25th International Conference on Principles of Distributed Systems. OPODIS, LIPIcs,
vol. 217, 14.
mla: Alistarh, Dan-Adrian, et al. “Fast Graphical Population Protocols.” 25th
International Conference on Principles of Distributed Systems, edited by Quentin
Bramas et al., vol. 217, 14, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2022, doi:10.4230/LIPIcs.OPODIS.2021.14.
short: D.-A. Alistarh, R. Gelashvili, J. Rybicki, in:, Q. Bramas, V. Gramoli, A.
Milani (Eds.), 25th International Conference on Principles of Distributed Systems,
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022.
conference:
end_date: 2021-12-15
location: Strasbourg, France
name: OPODIS
start_date: 2021-12-13
corr_author: '1'
date_created: 2022-04-17T22:01:47Z
date_published: 2022-02-01T00:00:00Z
date_updated: 2025-04-14T07:49:13Z
day: '01'
ddc:
- '510'
department:
- _id: DaAl
doi: 10.4230/LIPIcs.OPODIS.2021.14
ec_funded: 1
editor:
- first_name: Quentin
full_name: Bramas, Quentin
last_name: Bramas
- first_name: Vincent
full_name: Gramoli, Vincent
last_name: Gramoli
- first_name: Alessia
full_name: Milani, Alessia
last_name: Milani
external_id:
arxiv:
- '2102.08808'
file:
- access_level: open_access
checksum: 2c7c982174c6f98c4ca6e92539d15086
content_type: application/pdf
creator: dernst
date_created: 2022-05-02T08:06:33Z
date_updated: 2022-05-02T08:06:33Z
file_id: '11346'
file_name: 2022_LIPICs_Alistarh.pdf
file_size: 959406
relation: main_file
success: 1
file_date_updated: 2022-05-02T08:06:33Z
has_accepted_license: '1'
intvolume: ' 217'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
- _id: 26A5D39A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '840605'
name: Coordination in constrained and natural distributed systems
publication: 25th International Conference on Principles of Distributed Systems
publication_identifier:
isbn:
- '9783959772198'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fast graphical population protocols
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: 217
year: '2022'
...
---
_id: '11185'
abstract:
- lang: eng
text: Bundling crossings is a strategy which can enhance the readability of graph
drawings. In this paper we consider bundlings for families of pseudosegments,
i.e., simple curves such that any two have share at most one point at which they
cross. Our main result is that there is a polynomial-time algorithm to compute
an 8-approximation of the bundled crossing number of such instances (up to adding
a term depending on the facial structure). This 8-approximation also holds for
bundlings of good drawings of graphs. In the special case of circular drawings
the approximation factor is 8 (no extra term), this improves upon the 10-approximation
of Fink et al. [6]. We also show how to compute a 92-approximation when the intersection
graph of the pseudosegments is bipartite.
acknowledgement: This work was initiated during the Workshop on Geometric Graphs in
November 2019 in Strobl, Austria. We would like to thank Oswin Aichholzer, Fabian
Klute, Man-Kwun Chiu, Martin Balko, Pavel Valtr for their avid discussions during
the workshop. The first author has received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Sklodowska Curie grant agreement
No 754411. The second author has been supported by the German Research Foundation
DFG Project FE 340/12-1.
article_processing_charge: No
arxiv: 1
author:
- first_name: Alan M
full_name: Arroyo Guevara, Alan M
id: 3207FDC6-F248-11E8-B48F-1D18A9856A87
last_name: Arroyo Guevara
orcid: 0000-0003-2401-8670
- first_name: Stefan
full_name: Felsner, Stefan
last_name: Felsner
citation:
ama: 'Arroyo Guevara AM, Felsner S. Approximating the bundled crossing number. In:
WALCOM 2022: Algorithms and Computation. Vol 13174. LNCS. Springer Nature;
2022:383-395. doi:10.1007/978-3-030-96731-4_31'
apa: 'Arroyo Guevara, A. M., & Felsner, S. (2022). Approximating the bundled
crossing number. In WALCOM 2022: Algorithms and Computation (Vol. 13174,
pp. 383–395). Jember, Indonesia: Springer Nature. https://doi.org/10.1007/978-3-030-96731-4_31'
chicago: 'Arroyo Guevara, Alan M, and Stefan Felsner. “Approximating the Bundled
Crossing Number.” In WALCOM 2022: Algorithms and Computation, 13174:383–95.
LNCS. Springer Nature, 2022. https://doi.org/10.1007/978-3-030-96731-4_31.'
ieee: 'A. M. Arroyo Guevara and S. Felsner, “Approximating the bundled crossing
number,” in WALCOM 2022: Algorithms and Computation, Jember, Indonesia,
2022, vol. 13174, pp. 383–395.'
ista: 'Arroyo Guevara AM, Felsner S. 2022. Approximating the bundled crossing number.
WALCOM 2022: Algorithms and Computation. WALCOM: Algorithms and ComputationLNCS
vol. 13174, 383–395.'
mla: 'Arroyo Guevara, Alan M., and Stefan Felsner. “Approximating the Bundled Crossing
Number.” WALCOM 2022: Algorithms and Computation, vol. 13174, Springer
Nature, 2022, pp. 383–95, doi:10.1007/978-3-030-96731-4_31.'
short: 'A.M. Arroyo Guevara, S. Felsner, in:, WALCOM 2022: Algorithms and Computation,
Springer Nature, 2022, pp. 383–395.'
conference:
end_date: 2022-03-26
location: Jember, Indonesia
name: 'WALCOM: Algorithms and Computation'
start_date: 2022-03-24
date_created: 2022-04-17T22:01:47Z
date_published: 2022-03-16T00:00:00Z
date_updated: 2025-09-10T09:35:56Z
day: '16'
department:
- _id: UlWa
doi: 10.1007/978-3-030-96731-4_31
ec_funded: 1
external_id:
arxiv:
- '2109.14892'
isi:
- '001435074700031'
intvolume: ' 13174'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2109.14892'
month: '03'
oa: 1
oa_version: Preprint
page: 383-395
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: 'WALCOM 2022: Algorithms and Computation'
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783030967307'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '13969'
relation: later_version
status: public
scopus_import: '1'
series_title: LNCS
status: public
title: Approximating the bundled crossing number
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 13174
year: '2022'
...
---
_id: '11186'
abstract:
- lang: eng
text: "In this note, we study large deviations of the number \U0001D40D of intercalates
( 2×2 combinatorial subsquares which are themselves Latin squares) in a random
\ \U0001D45B×\U0001D45B Latin square. In particular, for constant \U0001D6FF>0
\ we prove that exp(−\U0001D442(\U0001D45B2log\U0001D45B))⩽Pr(\U0001D40D⩽(1−\U0001D6FF)\U0001D45B2/4)⩽exp(−Ω(\U0001D45B2))
\ and exp(−\U0001D442(\U0001D45B4/3(log\U0001D45B)))⩽Pr(\U0001D40D⩾(1+\U0001D6FF)\U0001D45B2/4)⩽exp(−Ω(\U0001D45B4/3(log\U0001D45B)2/3))
. As a consequence, we deduce that a typical order- \U0001D45B Latin square has
\ (1+\U0001D45C(1))\U0001D45B2/4 intercalates, matching a lower bound due to
Kwan and Sudakov and resolving an old conjecture of McKay and Wanless."
acknowledgement: "We thank Zach Hunter for pointing out some important typographical
errors. We also thank the referee for several remarks which helped improve the paper
substantially.\r\nKwan was supported by NSF grant DMS-1953990. Sah and Sawhney were
supported by NSF Graduate Research Fellowship Program DGE-1745302."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Ashwin
full_name: Sah, Ashwin
last_name: Sah
- first_name: Mehtaab
full_name: Sawhney, Mehtaab
last_name: Sawhney
citation:
ama: Kwan MA, Sah A, Sawhney M. Large deviations in random latin squares. Bulletin
of the London Mathematical Society. 2022;54(4):1420-1438. doi:10.1112/blms.12638
apa: Kwan, M. A., Sah, A., & Sawhney, M. (2022). Large deviations in random
latin squares. Bulletin of the London Mathematical Society. Wiley. https://doi.org/10.1112/blms.12638
chicago: Kwan, Matthew Alan, Ashwin Sah, and Mehtaab Sawhney. “Large Deviations
in Random Latin Squares.” Bulletin of the London Mathematical Society.
Wiley, 2022. https://doi.org/10.1112/blms.12638.
ieee: M. A. Kwan, A. Sah, and M. Sawhney, “Large deviations in random latin squares,”
Bulletin of the London Mathematical Society, vol. 54, no. 4. Wiley, pp.
1420–1438, 2022.
ista: Kwan MA, Sah A, Sawhney M. 2022. Large deviations in random latin squares.
Bulletin of the London Mathematical Society. 54(4), 1420–1438.
mla: Kwan, Matthew Alan, et al. “Large Deviations in Random Latin Squares.” Bulletin
of the London Mathematical Society, vol. 54, no. 4, Wiley, 2022, pp. 1420–38,
doi:10.1112/blms.12638.
short: M.A. Kwan, A. Sah, M. Sawhney, Bulletin of the London Mathematical Society
54 (2022) 1420–1438.
corr_author: '1'
date_created: 2022-04-17T22:01:48Z
date_published: 2022-08-01T00:00:00Z
date_updated: 2024-10-09T21:02:21Z
day: '01'
ddc:
- '510'
department:
- _id: MaKw
doi: 10.1112/blms.12638
external_id:
arxiv:
- '2106.11932'
isi:
- '000779920900001'
file:
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checksum: 02d74e7ae955ba3c808e2a8aebe6ef98
content_type: application/pdf
creator: dernst
date_created: 2023-02-03T09:43:38Z
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file_name: 2022_BulletinMathSociety_Kwan.pdf
file_size: 233758
relation: main_file
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intvolume: ' 54'
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license: https://creativecommons.org/licenses/by-nc/4.0/
month: '08'
oa: 1
oa_version: Published Version
page: 1420-1438
publication: Bulletin of the London Mathematical Society
publication_identifier:
eissn:
- 1469-2120
issn:
- 0024-6093
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Large deviations in random latin squares
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 54
year: '2022'
...
---
_id: '11321'
abstract:
- lang: eng
text: 'Here are the research data underlying the publication "Effects of fine-scale
population structure on the distribution of heterozygosity in a long-term study
of Antirrhinum majus" Further information are summed up in the README document. '
article_processing_charge: No
author:
- first_name: Parvathy
full_name: Surendranadh, Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
orcid: 0000-0001-6395-386X
- first_name: Louise S
full_name: Arathoon, Louise S
id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87
last_name: Arathoon
orcid: 0000-0003-1771-714X
- first_name: Carina
full_name: Baskett, Carina
id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87
last_name: Baskett
orcid: 0000-0002-7354-8574
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects
of fine-scale population structure on the distribution of heterozygosity in a
long-term study of Antirrhinum majus. 2022. doi:10.15479/at:ista:11321
apa: Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., &
Barton, N. H. (2022). Effects of fine-scale population structure on the distribution
of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:11321
chicago: Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field,
Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure
on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.”
Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11321.
ieee: P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H.
Barton, “Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus.” Institute of Science and Technology
Austria, 2022.
ista: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022.
Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus, Institute of Science and Technology
Austria, 10.15479/at:ista:11321.
mla: Surendranadh, Parvathy, et al. Effects of Fine-Scale Population Structure
on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.
Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11321.
short: P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton,
(2022).
contributor:
- contributor_type: project_member
first_name: Louise S
id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87
last_name: Arathoon
- contributor_type: project_member
first_name: Carina
id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87
last_name: Baskett
orcid: 0000-0002-7354-8574
- contributor_type: project_member
first_name: David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- contributor_type: project_member
first_name: Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- contributor_type: project_member
first_name: Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
corr_author: '1'
date_created: 2022-04-22T09:42:24Z
date_published: 2022-04-28T00:00:00Z
date_updated: 2025-04-15T08:20:40Z
day: '28'
ddc:
- '570'
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/at:ista:11321
file:
- access_level: open_access
checksum: 96c1b86cdf25481f2a52972fcc45ca7f
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creator: larathoo
date_created: 2022-04-22T09:39:03Z
date_updated: 2022-04-22T09:39:03Z
file_id: '11326'
file_name: Data_Code.zip
file_size: 13260571
relation: main_file
success: 1
file_date_updated: 2022-04-22T09:39:03Z
has_accepted_license: '1'
month: '04'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9192'
relation: earlier_version
status: public
- id: '8254'
relation: earlier_version
status: public
- id: '11411'
relation: used_in_publication
status: public
status: public
title: Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '11330'
abstract:
- lang: eng
text: In this article we study the noncommutative transport distance introduced
by Carlen and Maas and its entropic regularization defined by Becker and Li. We
prove a duality formula that can be understood as a quantum version of the dual
Benamou–Brenier formulation of the Wasserstein distance in terms of subsolutions
of a Hamilton–Jacobi–Bellmann equation.
acknowledgement: "The author wants to thank Jan Maas for helpful comments. He also
acknowledges financial support from the Austrian Science Fund (FWF) through Grant
Number F65 and from the European Research Council (ERC) under the European Union’s
Horizon 2020 Research and Innovation Programme (Grant Agreement No. 716117).\r\nOpen
access funding provided by Institute of Science and Technology (IST Austria)."
article_number: '19'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Melchior
full_name: Wirth, Melchior
id: 88644358-0A0E-11EA-8FA5-49A33DDC885E
last_name: Wirth
orcid: 0000-0002-0519-4241
citation:
ama: Wirth M. A dual formula for the noncommutative transport distance. Journal
of Statistical Physics. 2022;187(2). doi:10.1007/s10955-022-02911-9
apa: Wirth, M. (2022). A dual formula for the noncommutative transport distance.
Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-022-02911-9
chicago: Wirth, Melchior. “A Dual Formula for the Noncommutative Transport Distance.”
Journal of Statistical Physics. Springer Nature, 2022. https://doi.org/10.1007/s10955-022-02911-9.
ieee: M. Wirth, “A dual formula for the noncommutative transport distance,” Journal
of Statistical Physics, vol. 187, no. 2. Springer Nature, 2022.
ista: Wirth M. 2022. A dual formula for the noncommutative transport distance. Journal
of Statistical Physics. 187(2), 19.
mla: Wirth, Melchior. “A Dual Formula for the Noncommutative Transport Distance.”
Journal of Statistical Physics, vol. 187, no. 2, 19, Springer Nature, 2022,
doi:10.1007/s10955-022-02911-9.
short: M. Wirth, Journal of Statistical Physics 187 (2022).
corr_author: '1'
date_created: 2022-04-24T22:01:43Z
date_published: 2022-04-08T00:00:00Z
date_updated: 2025-06-12T06:17:37Z
day: '08'
ddc:
- '510'
- '530'
department:
- _id: JaMa
doi: 10.1007/s10955-022-02911-9
ec_funded: 1
external_id:
isi:
- '000780305000001'
pmid:
- '35509951'
file:
- access_level: open_access
checksum: f3e0b00884b7dde31347a3756788b473
content_type: application/pdf
creator: dernst
date_created: 2022-04-29T11:24:23Z
date_updated: 2022-04-29T11:24:23Z
file_id: '11338'
file_name: 2022_JourStatisticalPhysics_Wirth.pdf
file_size: 362119
relation: main_file
success: 1
file_date_updated: 2022-04-29T11:24:23Z
has_accepted_license: '1'
intvolume: ' 187'
isi: 1
issue: '2'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
publication: Journal of Statistical Physics
publication_identifier:
eissn:
- 1572-9613
issn:
- 0022-4715
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A dual formula for the noncommutative transport distance
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: 187
year: '2022'
...
---
_id: '11331'
abstract:
- lang: eng
text: "We propose separating the task of reliable transaction dissemination from
transaction ordering, to enable high-performance Byzantine fault-tolerant quorum-based
consensus. We design and evaluate a mempool protocol, Narwhal, specializing in
high-throughput reliable dissemination and storage of causal histories of transactions.
Narwhal tolerates an asynchronous network and maintains high performance despite
failures. Narwhal is designed to easily scale-out using multiple workers at each
validator, and we demonstrate that there is no foreseeable limit to the throughput
we can achieve.\r\nComposing Narwhal with a partially synchronous consensus protocol
(Narwhal-HotStuff) yields significantly better throughput even in the presence
of faults or intermittent loss of liveness due to asynchrony. However, loss of
liveness can result in higher latency. To achieve overall good performance when
faults occur we design Tusk, a zero-message overhead asynchronous consensus protocol,
to work with Narwhal. We demonstrate its high performance under a variety of configurations
and faults.\r\nAs a summary of results, on a WAN, Narwhal-Hotstuff achieves over
130,000 tx/sec at less than 2-sec latency compared with 1,800 tx/sec at 1-sec
latency for Hotstuff. Additional workers increase throughput linearly to 600,000
tx/sec without any latency increase. Tusk achieves 160,000 tx/sec with about 3
seconds latency. Under faults, both protocols maintain high throughput, but Narwhal-HotStuff
suffers from increased latency."
article_processing_charge: No
arxiv: 1
author:
- first_name: George
full_name: Danezis, George
last_name: Danezis
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Alberto
full_name: Sonnino, Alberto
last_name: Sonnino
- first_name: Alexander
full_name: Spiegelman, Alexander
last_name: Spiegelman
citation:
ama: 'Danezis G, Kokoris Kogias E, Sonnino A, Spiegelman A. Narwhal and Tusk: A
DAG-based mempool and efficient BFT consensus. In: Proceedings of the 17th
European Conference on Computer Systems. Association for Computing Machinery;
2022:34-50. doi:10.1145/3492321.3519594'
apa: 'Danezis, G., Kokoris Kogias, E., Sonnino, A., & Spiegelman, A. (2022).
Narwhal and Tusk: A DAG-based mempool and efficient BFT consensus. In Proceedings
of the 17th European Conference on Computer Systems (pp. 34–50). Rennes, France:
Association for Computing Machinery. https://doi.org/10.1145/3492321.3519594'
chicago: 'Danezis, George, Eleftherios Kokoris Kogias, Alberto Sonnino, and Alexander
Spiegelman. “Narwhal and Tusk: A DAG-Based Mempool and Efficient BFT Consensus.”
In Proceedings of the 17th European Conference on Computer Systems, 34–50.
Association for Computing Machinery, 2022. https://doi.org/10.1145/3492321.3519594.'
ieee: 'G. Danezis, E. Kokoris Kogias, A. Sonnino, and A. Spiegelman, “Narwhal and
Tusk: A DAG-based mempool and efficient BFT consensus,” in Proceedings of the
17th European Conference on Computer Systems, Rennes, France, 2022, pp. 34–50.'
ista: 'Danezis G, Kokoris Kogias E, Sonnino A, Spiegelman A. 2022. Narwhal and Tusk:
A DAG-based mempool and efficient BFT consensus. Proceedings of the 17th European
Conference on Computer Systems. EuroSys: European Conference on Computer Systems,
34–50.'
mla: 'Danezis, George, et al. “Narwhal and Tusk: A DAG-Based Mempool and Efficient
BFT Consensus.” Proceedings of the 17th European Conference on Computer Systems,
Association for Computing Machinery, 2022, pp. 34–50, doi:10.1145/3492321.3519594.'
short: G. Danezis, E. Kokoris Kogias, A. Sonnino, A. Spiegelman, in:, Proceedings
of the 17th European Conference on Computer Systems, Association for Computing
Machinery, 2022, pp. 34–50.
conference:
end_date: 2022-04-08
location: Rennes, France
name: 'EuroSys: European Conference on Computer Systems'
start_date: 2022-04-05
date_created: 2022-04-24T22:01:43Z
date_published: 2022-03-28T00:00:00Z
date_updated: 2023-08-03T06:38:40Z
day: '28'
department:
- _id: ElKo
doi: 10.1145/3492321.3519594
external_id:
arxiv:
- '2105.11827'
isi:
- '000926506800003'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2105.11827'
month: '03'
oa: 1
oa_version: Preprint
page: 34-50
publication: Proceedings of the 17th European Conference on Computer Systems
publication_identifier:
isbn:
- '9781450391627'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Narwhal and Tusk: A DAG-based mempool and efficient BFT consensus'
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2022'
...
---
_id: '11332'
abstract:
- lang: eng
text: We show that the fluctuations of the largest eigenvalue of a real symmetric
or complex Hermitian Wigner matrix of size N converge to the Tracy–Widom laws
at a rate O(N^{-1/3+\omega }), as N tends to infinity. For Wigner matrices this
improves the previous rate O(N^{-2/9+\omega }) obtained by Bourgade (J Eur Math
Soc, 2021) for generalized Wigner matrices. Our result follows from a Green function
comparison theorem, originally introduced by Erdős et al. (Adv Math 229(3):1435–1515,
2012) to prove edge universality, on a finer spectral parameter scale with improved
error estimates. The proof relies on the continuous Green function flow induced
by a matrix-valued Ornstein–Uhlenbeck process. Precise estimates on leading contributions
from the third and fourth order moments of the matrix entries are obtained using
iterative cumulant expansions and recursive comparisons for correlation functions,
along with uniform convergence estimates for correlation kernels of the Gaussian
invariant ensembles.
acknowledgement: Kevin Schnelli is supported in parts by the Swedish Research Council
Grant VR-2017-05195, and the Knut and Alice Wallenberg Foundation. Yuanyuan Xu is
supported by the Swedish Research Council Grant VR-2017-05195 and the ERC Advanced
Grant “RMTBeyond” No. 101020331.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Kevin
full_name: Schnelli, Kevin
id: 434AD0AE-F248-11E8-B48F-1D18A9856A87
last_name: Schnelli
orcid: 0000-0003-0954-3231
- first_name: Yuanyuan
full_name: Xu, Yuanyuan
id: 7902bdb1-a2a4-11eb-a164-c9216f71aea3
last_name: Xu
orcid: 0000-0003-1559-1205
citation:
ama: Schnelli K, Xu Y. Convergence rate to the Tracy–Widom laws for the largest
Eigenvalue of Wigner matrices. Communications in Mathematical Physics.
2022;393:839-907. doi:10.1007/s00220-022-04377-y
apa: Schnelli, K., & Xu, Y. (2022). Convergence rate to the Tracy–Widom laws
for the largest Eigenvalue of Wigner matrices. Communications in Mathematical
Physics. Springer Nature. https://doi.org/10.1007/s00220-022-04377-y
chicago: Schnelli, Kevin, and Yuanyuan Xu. “Convergence Rate to the Tracy–Widom
Laws for the Largest Eigenvalue of Wigner Matrices.” Communications in Mathematical
Physics. Springer Nature, 2022. https://doi.org/10.1007/s00220-022-04377-y.
ieee: K. Schnelli and Y. Xu, “Convergence rate to the Tracy–Widom laws for the largest
Eigenvalue of Wigner matrices,” Communications in Mathematical Physics,
vol. 393. Springer Nature, pp. 839–907, 2022.
ista: Schnelli K, Xu Y. 2022. Convergence rate to the Tracy–Widom laws for the largest
Eigenvalue of Wigner matrices. Communications in Mathematical Physics. 393, 839–907.
mla: Schnelli, Kevin, and Yuanyuan Xu. “Convergence Rate to the Tracy–Widom Laws
for the Largest Eigenvalue of Wigner Matrices.” Communications in Mathematical
Physics, vol. 393, Springer Nature, 2022, pp. 839–907, doi:10.1007/s00220-022-04377-y.
short: K. Schnelli, Y. Xu, Communications in Mathematical Physics 393 (2022) 839–907.
date_created: 2022-04-24T22:01:44Z
date_published: 2022-07-01T00:00:00Z
date_updated: 2025-06-11T14:01:05Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1007/s00220-022-04377-y
ec_funded: 1
external_id:
arxiv:
- '2102.04330'
isi:
- '000782737200001'
pmid:
- '35765414'
file:
- access_level: open_access
checksum: bee0278c5efa9a33d9a2dc8d354a6c51
content_type: application/pdf
creator: dernst
date_created: 2022-08-05T06:01:13Z
date_updated: 2022-08-05T06:01:13Z
file_id: '11726'
file_name: 2022_CommunMathPhys_Schnelli.pdf
file_size: 1141462
relation: main_file
success: 1
file_date_updated: 2022-08-05T06:01:13Z
has_accepted_license: '1'
intvolume: ' 393'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 839-907
pmid: 1
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: Communications in Mathematical Physics
publication_identifier:
eissn:
- 1432-0916
issn:
- 0010-3616
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Convergence rate to the Tracy–Widom laws for the largest Eigenvalue of Wigner
matrices
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: 393
year: '2022'
...
---
_id: '11334'
abstract:
- lang: eng
text: Hybridization is a common evolutionary process with multiple possible outcomes.
In vertebrates, interspecific hybridization has repeatedly generated parthenogenetic
hybrid species. However, it is unknown whether the generation of parthenogenetic
hybrids is a rare outcome of frequent hybridization between sexual species within
a genus or the typical outcome of rare hybridization events. Darevskia is a genus
of rock lizards with both hybrid parthenogenetic and sexual species. Using capture
sequencing, we estimate phylogenetic relationships and gene flow among the sexual
species, to determine how introgressive hybridization relates to the origins of
parthenogenetic hybrids. We find evidence for widespread hybridization with gene
flow, both between recently diverged species and deep branches. Surprisingly,
we find no signal of gene flow between parental species of the parthenogenetic
hybrids, suggesting that the parental pairs were either reproductively or geographically
isolated early in their divergence. The generation of parthenogenetic hybrids
in Darevskia is, then, a rare outcome of the total occurrence of hybridization
within the genus, but the typical outcome when specific species pairs hybridize.
Our results question the conventional view that parthenogenetic lineages are generated
by hybridization in a window of divergence. Instead, they suggest that some lineages
possess specific properties that underpin successful parthenogenetic reproduction.
acknowledgement: "The authors thank A. van der Meijden and F. Ahmadzadeh for providing
specimens and tissue samples, and A. Vardanyan, C. Corti, F. Jorge, and S. Drovetski
for support during field work. The authors also thank S. Qiu for assistance with
python scripting, S. Rocha for her support in BEAST analysis, and B. Wielstra for
his comments on\r\na previous version of the manuscript. SF was funded by FCT grant
SFRH/BD/81483/2011 (a PhD individual grant). AMW was funded by the European Union’s
Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant
agreement no. 797747. TS acknowledges funding from the Swiss National Science Foundation
(grants\r\nPP00P3_170627 and 31003A_182495). The work was carried out under financial
support of the projects “Preserving Armenian biodiversity: Joint Portuguese – Armenian
program for training in modern conservation biology” of Gulbenkian Foundation (Portugal)
and PTDC/BIABEC/101256/2008 of Fundação para a Ciência e a Tecnologia (FCT, Portugal)."
article_processing_charge: No
article_type: original
author:
- first_name: Susana
full_name: Freitas, Susana
last_name: Freitas
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Tanja
full_name: Schwander, Tanja
last_name: Schwander
- first_name: Marine
full_name: Arakelyan, Marine
last_name: Arakelyan
- first_name: Çetin
full_name: Ilgaz, Çetin
last_name: Ilgaz
- first_name: Yusuf
full_name: Kumlutas, Yusuf
last_name: Kumlutas
- first_name: David James
full_name: Harris, David James
last_name: Harris
- first_name: Miguel A.
full_name: Carretero, Miguel A.
last_name: Carretero
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: 'Freitas S, Westram AM, Schwander T, et al. Parthenogenesis in Darevskia lizards:
A rare outcome of common hybridization, not a common outcome of rare hybridization.
Evolution. 2022;76(5):899-914. doi:10.1111/evo.14462'
apa: 'Freitas, S., Westram, A. M., Schwander, T., Arakelyan, M., Ilgaz, Ç., Kumlutas,
Y., … Butlin, R. K. (2022). Parthenogenesis in Darevskia lizards: A rare outcome
of common hybridization, not a common outcome of rare hybridization. Evolution.
Wiley. https://doi.org/10.1111/evo.14462'
chicago: 'Freitas, Susana, Anja M Westram, Tanja Schwander, Marine Arakelyan, Çetin
Ilgaz, Yusuf Kumlutas, David James Harris, Miguel A. Carretero, and Roger K. Butlin.
“Parthenogenesis in Darevskia Lizards: A Rare Outcome of Common Hybridization,
Not a Common Outcome of Rare Hybridization.” Evolution. Wiley, 2022. https://doi.org/10.1111/evo.14462.'
ieee: 'S. Freitas et al., “Parthenogenesis in Darevskia lizards: A rare outcome
of common hybridization, not a common outcome of rare hybridization,” Evolution,
vol. 76, no. 5. Wiley, pp. 899–914, 2022.'
ista: 'Freitas S, Westram AM, Schwander T, Arakelyan M, Ilgaz Ç, Kumlutas Y, Harris
DJ, Carretero MA, Butlin RK. 2022. Parthenogenesis in Darevskia lizards: A rare
outcome of common hybridization, not a common outcome of rare hybridization. Evolution.
76(5), 899–914.'
mla: 'Freitas, Susana, et al. “Parthenogenesis in Darevskia Lizards: A Rare Outcome
of Common Hybridization, Not a Common Outcome of Rare Hybridization.” Evolution,
vol. 76, no. 5, Wiley, 2022, pp. 899–914, doi:10.1111/evo.14462.'
short: S. Freitas, A.M. Westram, T. Schwander, M. Arakelyan, Ç. Ilgaz, Y. Kumlutas,
D.J. Harris, M.A. Carretero, R.K. Butlin, Evolution 76 (2022) 899–914.
date_created: 2022-04-24T22:01:44Z
date_published: 2022-05-01T00:00:00Z
date_updated: 2025-04-14T07:48:21Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
- _id: BeVi
doi: 10.1111/evo.14462
ec_funded: 1
external_id:
isi:
- '000781632500001'
pmid:
- '35323995'
file:
- access_level: open_access
checksum: c27c025ae9afcf6c804d46a909775ee5
content_type: application/pdf
creator: dernst
date_created: 2022-08-05T06:19:28Z
date_updated: 2022-08-05T06:19:28Z
file_id: '11729'
file_name: 2022_Evolution_Freitas.pdf
file_size: 2855214
relation: main_file
success: 1
file_date_updated: 2022-08-05T06:19:28Z
has_accepted_license: '1'
intvolume: ' 76'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 899-914
pmid: 1
project:
- _id: 265B41B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '797747'
name: Theoretical and empirical approaches to understanding Parallel Adaptation
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization,
not a common outcome of rare hybridization'
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 76
year: '2022'
...
---
_id: '11336'
abstract:
- lang: eng
text: The generation of a correctly-sized cerebral cortex with all-embracing neuronal
and glial cell-type diversity critically depends on faithful radial glial progenitor
(RGP) cell proliferation/differentiation programs. Temporal RGP lineage progression
is regulated by Polycomb Repressive Complex 2 (PRC2) and loss of PRC2 activity
results in severe neurogenesis defects and microcephaly. How PRC2-dependent gene
expression instructs RGP lineage progression is unknown. Here we utilize Mosaic
Analysis with Double Markers (MADM)-based single cell technology and demonstrate
that PRC2 is not cell-autonomously required in neurogenic RGPs but rather acts
at the global tissue-wide level. Conversely, cortical astrocyte production and
maturation is cell-autonomously controlled by PRC2-dependent transcriptional regulation.
We thus reveal highly distinct and sequential PRC2 functions in RGP lineage progression
that are dependent on complex interplays between intrinsic and tissue-wide properties.
In a broader context our results imply a critical role for the genetic and cellular
niche environment in neural stem cell behavior.
acknowledged_ssus:
- _id: PreCl
- _id: Bio
- _id: LifeSc
acknowledgement: We thank A. Heger (IST Austria Preclinical Facility), A. Sommer and
C. Czepe (VBCF GmbH, NGS Unit) and S. Gharagozlou for technical support. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging & Optics
Facility (IOF), Lab Support Facility (LSF), and Preclinical Facility (PCF). N.A.
received funding from the FWF Firnberg-Programm (T 1031). The work was supported by IST institutional funds and by the European Research Council (ERC) under the European Union’s Horizon
2020 research and innovation program (grant agreement 725780 LinPro) to S.H.
article_number: abq1263
article_processing_charge: No
article_type: original
author:
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Amberg N, Pauler F, Streicher C, Hippenmeyer S. Tissue-wide genetic and cellular
landscape shapes the execution of sequential PRC2 functions in neural stem cell
lineage progression. Science Advances. 2022;8(44). doi:10.1126/sciadv.abq1263
apa: Amberg, N., Pauler, F., Streicher, C., & Hippenmeyer, S. (2022). Tissue-wide
genetic and cellular landscape shapes the execution of sequential PRC2 functions
in neural stem cell lineage progression. Science Advances. American Association
for the Advancement of Science. https://doi.org/10.1126/sciadv.abq1263
chicago: Amberg, Nicole, Florian Pauler, Carmen Streicher, and Simon Hippenmeyer.
“Tissue-Wide Genetic and Cellular Landscape Shapes the Execution of Sequential
PRC2 Functions in Neural Stem Cell Lineage Progression.” Science Advances.
American Association for the Advancement of Science, 2022. https://doi.org/10.1126/sciadv.abq1263.
ieee: N. Amberg, F. Pauler, C. Streicher, and S. Hippenmeyer, “Tissue-wide genetic
and cellular landscape shapes the execution of sequential PRC2 functions in neural
stem cell lineage progression,” Science Advances, vol. 8, no. 44. American
Association for the Advancement of Science, 2022.
ista: Amberg N, Pauler F, Streicher C, Hippenmeyer S. 2022. Tissue-wide genetic
and cellular landscape shapes the execution of sequential PRC2 functions in neural
stem cell lineage progression. Science Advances. 8(44), abq1263.
mla: Amberg, Nicole, et al. “Tissue-Wide Genetic and Cellular Landscape Shapes the
Execution of Sequential PRC2 Functions in Neural Stem Cell Lineage Progression.”
Science Advances, vol. 8, no. 44, abq1263, American Association for the
Advancement of Science, 2022, doi:10.1126/sciadv.abq1263.
short: N. Amberg, F. Pauler, C. Streicher, S. Hippenmeyer, Science Advances 8 (2022).
corr_author: '1'
date_created: 2022-04-26T15:04:50Z
date_published: 2022-11-01T00:00:00Z
date_updated: 2025-09-09T14:30:38Z
day: '01'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1126/sciadv.abq1263
ec_funded: 1
external_id:
isi:
- '000918406800019'
pmid:
- '36322669'
file:
- access_level: open_access
checksum: 0117023e188542082ca6693cf39e7f03
content_type: application/pdf
creator: patrickd
date_created: 2023-03-21T14:18:10Z
date_updated: 2023-03-21T14:18:10Z
file_id: '12742'
file_name: sciadv.abq1263.pdf
file_size: 2973998
relation: main_file
success: 1
file_date_updated: 2023-03-21T14:18:10Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '44'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
- _id: 268F8446-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: T01031
name: Role of Eed in neural stem cell lineage progression
publication: Science Advances
publication_identifier:
issn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/whole-tissue-shapes-brain-development/
scopus_import: '1'
status: public
title: Tissue-wide genetic and cellular landscape shapes the execution of sequential
PRC2 functions in neural stem cell lineage progression
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: 8
year: '2022'
...
---
_id: '11337'
abstract:
- lang: eng
text: 'Nonanalytic points in the return probability of a quantum state as a function
of time, known as dynamical quantum phase transitions (DQPTs), have received great
attention in recent years, but the understanding of their mechanism is still incomplete.
In our recent work [Phys. Rev. Lett. 126, 040602 (2021)], we demonstrated that
one-dimensional DQPTs can be produced by two distinct mechanisms, namely semiclassical
precession and entanglement generation, leading to the definition of precession
(pDQPTs) and entanglement (eDQPTs) dynamical quantum phase transitions. In this
manuscript, we extend and investigate the notion of p- and eDQPTs in two-dimensional
systems by considering semi-infinite ladders of varying width. For square lattices,
we find that pDQPTs and eDQPTs persist and are characterized by similar phenomenology
as in 1D: pDQPTs are associated with a magnetization sign change and a wide entanglement
gap, while eDQPTs correspond to suppressed local observables and avoided crossings
in the entanglement spectrum. However, DQPTs show higher sensitivity to the ladder
width and other details, challenging the extrapolation to the thermodynamic limit
especially for eDQPTs. Moving to honeycomb lattices, we also demonstrate that
lattices with an odd number of nearest neighbors give rise to phenomenologies
beyond the one-dimensional classification.'
acknowledgement: "We acknowledge support by the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation programme (Grant Agreement
No. 850899).\r\nS.D.N. also acknowledges funding from the Institute of Science and
Technology (IST) Austria, and from the European Union’s Horizon 2020 Research and
Innovation Programme under the Marie Skłodowska-Curie Grant Agreement No. 754411."
article_number: '165149'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Stefano
full_name: De Nicola, Stefano
id: 42832B76-F248-11E8-B48F-1D18A9856A87
last_name: De Nicola
orcid: 0000-0002-4842-6671
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: De Nicola S, Michailidis A, Serbyn M. Entanglement and precession in two-dimensional
dynamical quantum phase transitions. Physical Review B. 2022;105. doi:10.1103/PhysRevB.105.165149
apa: De Nicola, S., Michailidis, A., & Serbyn, M. (2022). Entanglement and precession
in two-dimensional dynamical quantum phase transitions. Physical Review B.
American Physical Society. https://doi.org/10.1103/PhysRevB.105.165149
chicago: De Nicola, Stefano, Alexios Michailidis, and Maksym Serbyn. “Entanglement
and Precession in Two-Dimensional Dynamical Quantum Phase Transitions.” Physical
Review B. American Physical Society, 2022. https://doi.org/10.1103/PhysRevB.105.165149.
ieee: S. De Nicola, A. Michailidis, and M. Serbyn, “Entanglement and precession
in two-dimensional dynamical quantum phase transitions,” Physical Review B,
vol. 105. American Physical Society, 2022.
ista: De Nicola S, Michailidis A, Serbyn M. 2022. Entanglement and precession in
two-dimensional dynamical quantum phase transitions. Physical Review B. 105, 165149.
mla: De Nicola, Stefano, et al. “Entanglement and Precession in Two-Dimensional
Dynamical Quantum Phase Transitions.” Physical Review B, vol. 105, 165149,
American Physical Society, 2022, doi:10.1103/PhysRevB.105.165149.
short: S. De Nicola, A. Michailidis, M. Serbyn, Physical Review B 105 (2022).
corr_author: '1'
date_created: 2022-04-28T08:06:10Z
date_published: 2022-04-15T00:00:00Z
date_updated: 2025-04-14T07:43:57Z
day: '15'
department:
- _id: MaSe
doi: 10.1103/PhysRevB.105.165149
ec_funded: 1
external_id:
arxiv:
- '2112.11273'
isi:
- '000806812400004'
intvolume: ' 105'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2112.11273'
month: '04'
oa: 1
oa_version: Preprint
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review B
publication_identifier:
eisbn:
- 2469-9969
issn:
- 2469-9950
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Entanglement and precession in two-dimensional dynamical quantum phase transitions
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 105
year: '2022'
...
---
_id: '11339'
abstract:
- lang: eng
text: The interaction between a cell and its environment shapes fundamental intracellular
processes such as cellular metabolism. In most cases growth rate is treated as
a proximal metric for understanding the cellular metabolic status. However, changes
in growth rate might not reflect metabolic variations in individuals responding
to environmental fluctuations. Here we use single-cell microfluidics-microscopy
combined with transcriptomics, proteomics and mathematical modelling to quantify
the accumulation of glucose within Escherichia coli cells. In contrast to the
current consensus, we reveal that environmental conditions which are comparatively
unfavourable for growth, where both nutrients and salinity are depleted, increase
glucose accumulation rates in individual bacteria and population subsets. We find
that these changes in metabolic function are underpinned by variations at the
translational and posttranslational level but not at the transcriptional level
and are not dictated by changes in cell size. The metabolic response-characteristics
identified greatly advance our fundamental understanding of the interactions between
bacteria and their environment and have important ramifications when investigating
cellular processes where salinity plays an important role.
acknowledgement: G.G. was supported by an EPSRC DTP PhD studentship (EP/M506527/1).
M.V. and K.T.A. gratefully acknowledge financial support from the EPSRC (EP/N014391/1).
U.L. was supported through a BBSRC grant (BB/V008021/1) and an MRC Proximity to
Discovery EXCITEME2 grant (MCPC17189). This work was further supported by a Royal
Society Research Grant (RG180007) awarded to S.P. and a QUEX Initiator grant awarded
to S.P. and K.T.A.. D.S.M., T.A.R. and S.P.’s work in this area is also supported
by a Marie Skłodowska-Curie project SINGEK (H2020-MSCA-ITN-2015-675752) and the
Gordon and Betty Moore Foundation Marine Microbiology Initiative (GBMF5514). B.M.I.
acknowledges support from a Wellcome Trust Institutional Strategic Support Award
to the University of Exeter (204909/Z/16/Z). This project utilised equipment funded
by the Wellcome Trust Institutional Strategic Support Fund (WT097835MF), Wellcome
Trust Multi User Equipment Award (WT101650MA) and BBSRC LOLA award (BB/K003240/1).
article_number: '385'
article_processing_charge: No
article_type: original
author:
- first_name: Georgina
full_name: Glover, Georgina
last_name: Glover
- first_name: Margaritis
full_name: Voliotis, Margaritis
last_name: Voliotis
- first_name: Urszula
full_name: Łapińska, Urszula
last_name: Łapińska
- first_name: Brandon M.
full_name: Invergo, Brandon M.
last_name: Invergo
- first_name: Darren
full_name: Soanes, Darren
last_name: Soanes
- first_name: Paul
full_name: O’Neill, Paul
last_name: O’Neill
- first_name: Karen
full_name: Moore, Karen
last_name: Moore
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
- first_name: Peter
full_name: Petrov, Peter
last_name: Petrov
- first_name: David S.
full_name: Milner, David S.
last_name: Milner
- first_name: Sumita
full_name: Roy, Sumita
last_name: Roy
- first_name: Kate
full_name: Heesom, Kate
last_name: Heesom
- first_name: Thomas A.
full_name: Richards, Thomas A.
last_name: Richards
- first_name: Krasimira
full_name: Tsaneva-Atanasova, Krasimira
last_name: Tsaneva-Atanasova
- first_name: Stefano
full_name: Pagliara, Stefano
last_name: Pagliara
citation:
ama: Glover G, Voliotis M, Łapińska U, et al. Nutrient and salt depletion synergistically
boosts glucose metabolism in individual Escherichia coli cells. Communications
Biology. 2022;5. doi:10.1038/s42003-022-03336-6
apa: Glover, G., Voliotis, M., Łapińska, U., Invergo, B. M., Soanes, D., O’Neill,
P., … Pagliara, S. (2022). Nutrient and salt depletion synergistically boosts
glucose metabolism in individual Escherichia coli cells. Communications Biology.
Springer Nature. https://doi.org/10.1038/s42003-022-03336-6
chicago: Glover, Georgina, Margaritis Voliotis, Urszula Łapińska, Brandon M. Invergo,
Darren Soanes, Paul O’Neill, Karen Moore, et al. “Nutrient and Salt Depletion
Synergistically Boosts Glucose Metabolism in Individual Escherichia Coli Cells.”
Communications Biology. Springer Nature, 2022. https://doi.org/10.1038/s42003-022-03336-6.
ieee: G. Glover et al., “Nutrient and salt depletion synergistically boosts
glucose metabolism in individual Escherichia coli cells,” Communications Biology,
vol. 5. Springer Nature, 2022.
ista: Glover G, Voliotis M, Łapińska U, Invergo BM, Soanes D, O’Neill P, Moore K,
Nikolic N, Petrov P, Milner DS, Roy S, Heesom K, Richards TA, Tsaneva-Atanasova
K, Pagliara S. 2022. Nutrient and salt depletion synergistically boosts glucose
metabolism in individual Escherichia coli cells. Communications Biology. 5, 385.
mla: Glover, Georgina, et al. “Nutrient and Salt Depletion Synergistically Boosts
Glucose Metabolism in Individual Escherichia Coli Cells.” Communications Biology,
vol. 5, 385, Springer Nature, 2022, doi:10.1038/s42003-022-03336-6.
short: G. Glover, M. Voliotis, U. Łapińska, B.M. Invergo, D. Soanes, P. O’Neill,
K. Moore, N. Nikolic, P. Petrov, D.S. Milner, S. Roy, K. Heesom, T.A. Richards,
K. Tsaneva-Atanasova, S. Pagliara, Communications Biology 5 (2022).
date_created: 2022-05-01T22:01:41Z
date_published: 2022-04-20T00:00:00Z
date_updated: 2023-08-03T06:45:26Z
day: '20'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.1038/s42003-022-03336-6
external_id:
isi:
- '000784143400001'
pmid:
- '35444215'
file:
- access_level: open_access
checksum: 7c6f76ab17393d650825cc240edc84b3
content_type: application/pdf
creator: dernst
date_created: 2022-05-02T06:26:26Z
date_updated: 2022-05-02T06:26:26Z
file_id: '11342'
file_name: 2022_CommBiology_Glover.pdf
file_size: 2827723
relation: main_file
success: 1
file_date_updated: 2022-05-02T06:26:26Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Communications Biology
publication_identifier:
eissn:
- 2399-3642
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nutrient and salt depletion synergistically boosts glucose metabolism in individual
Escherichia coli cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 5
year: '2022'
...
---
_id: '11340'
abstract:
- lang: eng
text: Like-charge attraction, driven by ionic correlations, challenges our understanding
of electrostatics both in soft and hard matter. For two charged planar surfaces
confining counterions and water, we prove that, even at relatively low correlation
strength, the relevant physics is the ground-state one, oblivious of fluctuations.
Based on this, we derive a simple and accurate interaction pressure that fulfills
known exact requirements and can be used as an effective potential. We test this
equation against implicit-solvent Monte Carlo simulations and against explicit-solvent
simulations of cement and several types of clays. We argue that water destructuring
under nanometric confinement drastically reduces dielectric screening, enhancing
ionic correlations. Our equation of state at reduced permittivity therefore explains
the exotic attractive regime reported for these materials, even in the absence
of multivalent counterions.
acknowledgement: We thank Martin Trulsson for useful discussions and for providing
us with simulation data. This work has received funding from the European Union’s
Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie
grant agreement 674979-NANOTRANS. The support received from VEGA Grant No. 2/0092/21
is acknowledged.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Ivan
full_name: Palaia, Ivan
id: 9c805cd2-4b75-11ec-a374-db6dd0ed57fa
last_name: Palaia
orcid: ' 0000-0002-8843-9485 '
- first_name: Abhay
full_name: Goyal, Abhay
last_name: Goyal
- first_name: Emanuela
full_name: Del Gado, Emanuela
last_name: Del Gado
- first_name: Ladislav
full_name: Šamaj, Ladislav
last_name: Šamaj
- first_name: Emmanuel
full_name: Trizac, Emmanuel
last_name: Trizac
citation:
ama: 'Palaia I, Goyal A, Del Gado E, Šamaj L, Trizac E. Like-charge attraction at
the nanoscale: Ground-state correlations and water destructuring. Journal of
Physical Chemistry B. 2022;126(16):3143-3149. doi:10.1021/acs.jpcb.2c00028'
apa: 'Palaia, I., Goyal, A., Del Gado, E., Šamaj, L., & Trizac, E. (2022). Like-charge
attraction at the nanoscale: Ground-state correlations and water destructuring.
Journal of Physical Chemistry B. American Chemical Society. https://doi.org/10.1021/acs.jpcb.2c00028'
chicago: 'Palaia, Ivan, Abhay Goyal, Emanuela Del Gado, Ladislav Šamaj, and Emmanuel
Trizac. “Like-Charge Attraction at the Nanoscale: Ground-State Correlations and
Water Destructuring.” Journal of Physical Chemistry B. American Chemical
Society, 2022. https://doi.org/10.1021/acs.jpcb.2c00028.'
ieee: 'I. Palaia, A. Goyal, E. Del Gado, L. Šamaj, and E. Trizac, “Like-charge attraction
at the nanoscale: Ground-state correlations and water destructuring,” Journal
of Physical Chemistry B, vol. 126, no. 16. American Chemical Society, pp.
3143–3149, 2022.'
ista: 'Palaia I, Goyal A, Del Gado E, Šamaj L, Trizac E. 2022. Like-charge attraction
at the nanoscale: Ground-state correlations and water destructuring. Journal of
Physical Chemistry B. 126(16), 3143–3149.'
mla: 'Palaia, Ivan, et al. “Like-Charge Attraction at the Nanoscale: Ground-State
Correlations and Water Destructuring.” Journal of Physical Chemistry B,
vol. 126, no. 16, American Chemical Society, 2022, pp. 3143–49, doi:10.1021/acs.jpcb.2c00028.'
short: I. Palaia, A. Goyal, E. Del Gado, L. Šamaj, E. Trizac, Journal of Physical
Chemistry B 126 (2022) 3143–3149.
date_created: 2022-05-01T22:01:42Z
date_published: 2022-04-14T00:00:00Z
date_updated: 2025-06-11T13:34:36Z
day: '14'
department:
- _id: AnSa
doi: 10.1021/acs.jpcb.2c00028
external_id:
arxiv:
- '2203.10524'
isi:
- '000796953700022'
pmid:
- '35420420'
intvolume: ' 126'
isi: 1
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2203.10524'
month: '04'
oa: 1
oa_version: Preprint
page: 3143-3149
pmid: 1
publication: Journal of Physical Chemistry B
publication_identifier:
eissn:
- 1520-5207
issn:
- 1520-6106
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Like-charge attraction at the nanoscale: Ground-state correlations and water
destructuring'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 126
year: '2022'
...
---
_id: '11341'
abstract:
- lang: eng
text: Intragenic regions that are removed during maturation of the RNA transcript—introns—are
universally present in the nuclear genomes of eukaryotes1. The budding yeast,
an otherwise intron-poor species, preserves two sets of ribosomal protein genes
that differ primarily in their introns2,3. Although studies have shed light on
the role of ribosomal protein introns under stress and starvation4,5,6, understanding
the contribution of introns to ribosome regulation remains challenging. Here,
by combining isogrowth profiling7 with single-cell protein measurements8, we show
that introns can mediate inducible phenotypic heterogeneity that confers a clear
fitness advantage. Osmotic stress leads to bimodal expression of the small ribosomal
subunit protein Rps22B, which is mediated by an intron in the 5′ untranslated
region of its transcript. The two resulting yeast subpopulations differ in their
ability to cope with starvation. Low levels of Rps22B protein result in prolonged
survival under sustained starvation, whereas high levels of Rps22B enable cells
to grow faster after transient starvation. Furthermore, yeasts growing at high
concentrations of sugar, similar to those in ripe grapes, exhibit bimodal expression
of Rps22B when approaching the stationary phase. Differential intron-mediated
regulation of ribosomal protein genes thus provides a way to diversify the population
when starvation threatens in natural environments. Our findings reveal a role
for introns in inducing phenotypic heterogeneity in changing environments, and
suggest that duplicated ribosomal protein genes in yeast contribute to resolving
the evolutionary conflict between precise expression control and environmental
responsiveness9.
acknowledged_ssus:
- _id: LifeSc
- _id: M-Shop
- _id: Bio
acknowledgement: We thank the IST Austria Life Science Facility, the Miba Machine
Shop and M. Lukačišinová for support with the liquid handling robot; the Bioimaging
Facility at IST Austria, J. Power and B. Meier at the University of Cologne, and
C. Göttlinger at the FACS Analysis Facility at the Institute for Genetics, University
of Cologne, for support with flow cytometry experiments; L. Horst for the development
of the automated experimental methods in Cologne; J. Parenteau, S. Abou Elela, G.
Stormo, M. Springer and M. Schuldiner for providing us with yeast strains; B. Fernando,
T. Fink, G. Ansmann and G. Chevreau for technical support; H. Köver, G. Tkačik,
N. Barton, A. Angermayr and B. Kavčič for support during laboratory relocation;
D. Siekhaus, M. Springer and all the members of the Bollenbach group for support
and discussions; and K. Mitosch, M. Lukačišinová, G. Liti and A. de Luna for critical
reading of our manuscript. This work was supported in part by an Austrian Science
Fund (FWF) standalone grant P 27201-B22 (to T.B.), HFSP program Grant RGP0042/2013
(to T.B.), EU Marie Curie Career Integration Grant No. 303507, and German Research
Foundation (DFG) Collaborative Research Centre (SFB) 1310 (to T.B.). A.E.-C. was
supported by a Georg Forster fellowship from the Alexander von Humboldt Foundation.
article_processing_charge: No
article_type: original
author:
- first_name: Martin
full_name: Lukacisin, Martin
id: 298FFE8C-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisin
orcid: 0000-0001-6549-4177
- first_name: Adriana
full_name: Espinosa-Cantú, Adriana
last_name: Espinosa-Cantú
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Lukacisin M, Espinosa-Cantú A, Bollenbach MT. Intron-mediated induction of
phenotypic heterogeneity. Nature. 2022;605:113-118. doi:10.1038/s41586-022-04633-0
apa: Lukacisin, M., Espinosa-Cantú, A., & Bollenbach, M. T. (2022). Intron-mediated
induction of phenotypic heterogeneity. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-04633-0
chicago: Lukacisin, Martin, Adriana Espinosa-Cantú, and Mark Tobias Bollenbach.
“Intron-Mediated Induction of Phenotypic Heterogeneity.” Nature. Springer
Nature, 2022. https://doi.org/10.1038/s41586-022-04633-0.
ieee: M. Lukacisin, A. Espinosa-Cantú, and M. T. Bollenbach, “Intron-mediated induction
of phenotypic heterogeneity,” Nature, vol. 605. Springer Nature, pp. 113–118,
2022.
ista: Lukacisin M, Espinosa-Cantú A, Bollenbach MT. 2022. Intron-mediated induction
of phenotypic heterogeneity. Nature. 605, 113–118.
mla: Lukacisin, Martin, et al. “Intron-Mediated Induction of Phenotypic Heterogeneity.”
Nature, vol. 605, Springer Nature, 2022, pp. 113–18, doi:10.1038/s41586-022-04633-0.
short: M. Lukacisin, A. Espinosa-Cantú, M.T. Bollenbach, Nature 605 (2022) 113–118.
date_created: 2022-05-01T22:01:42Z
date_published: 2022-05-05T00:00:00Z
date_updated: 2025-04-14T09:40:45Z
day: '05'
ddc:
- '570'
doi: 10.1038/s41586-022-04633-0
ec_funded: 1
external_id:
isi:
- '000784934100003'
pmid:
- '35444278'
file:
- access_level: open_access
checksum: d68cd1596bb9fd819b750fe47c8a138a
content_type: application/pdf
creator: dernst
date_created: 2022-08-05T06:08:24Z
date_updated: 2022-08-05T06:08:24Z
file_id: '11727'
file_name: 2022_Nature_Lukacisin.pdf
file_size: 25360311
relation: main_file
success: 1
file_date_updated: 2022-08-05T06:08:24Z
has_accepted_license: '1'
intvolume: ' 605'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 113-118
pmid: 1
project:
- _id: 25E83C2C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303507'
name: Optimality principles in responses to antibiotics
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Intron-mediated induction of phenotypic heterogeneity
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 605
year: '2022'
...
---
_id: '11343'
abstract:
- lang: eng
text: Multistable systems are characterized by exhibiting domain coexistence, where
each domain accounts for the different equilibrium states. In case these systems
are described by vectorial fields, domains can be connected through topological
defects. Vortices are one of the most frequent and studied topological defect
points. Optical vortices are equally relevant for their fundamental features as
beams with topological features and their applications in image processing, telecommunications,
optical tweezers, and quantum information. A natural source of optical vortices
is the interaction of light beams with matter vortices in liquid crystal cells.
The rhythms that govern the emergence of matter vortices due to fluctuations are
not established. Here, we investigate the nucleation mechanisms of the matter
vortices in liquid crystal cells and establish statistical laws that govern them.
Based on a stochastic amplitude equation, the law for the number of nucleated
vortices as a function of anisotropy, voltage, and noise level intensity is set.
Experimental observations in a nematic liquid crystal cell with homeotropic anchoring
and a negative anisotropic dielectric constant under the influence of a transversal
electric field show a qualitative agreement with the theoretical findings.
acknowledgement: "The authors thank Enrique Calisto,Michal Kowalczyk, and Michel Ferre
for fructified discussions. This work was funded by ANID—Millennium Science Initiative
Program—ICN17_012. MGC is thankful for financial support from the Fondecyt 1210353
project.\r\nOpen access funding provided by Institute of Science and Technology
(IST Austria)."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Esteban
full_name: Aguilera, Esteban
last_name: Aguilera
- first_name: Marcel G.
full_name: Clerc, Marcel G.
last_name: Clerc
- first_name: Valeska
full_name: Zambra, Valeska
id: 467ed36b-dc96-11ea-b7c8-b043a380b282
last_name: Zambra
citation:
ama: Aguilera E, Clerc MG, Zambra V. Vortices nucleation by inherent fluctuations
in nematic liquid crystal cells. Nonlinear Dynamics. 2022;108:3209-3218.
doi:10.1007/s11071-022-07396-5
apa: Aguilera, E., Clerc, M. G., & Zambra, V. (2022). Vortices nucleation by
inherent fluctuations in nematic liquid crystal cells. Nonlinear Dynamics.
Springer Nature. https://doi.org/10.1007/s11071-022-07396-5
chicago: Aguilera, Esteban, Marcel G. Clerc, and Valeska Zambra. “Vortices Nucleation
by Inherent Fluctuations in Nematic Liquid Crystal Cells.” Nonlinear Dynamics.
Springer Nature, 2022. https://doi.org/10.1007/s11071-022-07396-5.
ieee: E. Aguilera, M. G. Clerc, and V. Zambra, “Vortices nucleation by inherent
fluctuations in nematic liquid crystal cells,” Nonlinear Dynamics, vol.
108. Springer Nature, pp. 3209–3218, 2022.
ista: Aguilera E, Clerc MG, Zambra V. 2022. Vortices nucleation by inherent fluctuations
in nematic liquid crystal cells. Nonlinear Dynamics. 108, 3209–3218.
mla: Aguilera, Esteban, et al. “Vortices Nucleation by Inherent Fluctuations in
Nematic Liquid Crystal Cells.” Nonlinear Dynamics, vol. 108, Springer Nature,
2022, pp. 3209–18, doi:10.1007/s11071-022-07396-5.
short: E. Aguilera, M.G. Clerc, V. Zambra, Nonlinear Dynamics 108 (2022) 3209–3218.
corr_author: '1'
date_created: 2022-05-02T07:01:59Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2024-10-09T21:02:21Z
day: '01'
ddc:
- '530'
department:
- _id: KiMo
doi: 10.1007/s11071-022-07396-5
external_id:
isi:
- '000784871800001'
file:
- access_level: open_access
checksum: 7d80cdece4e1b1c2106e6772a9622f60
content_type: application/pdf
creator: dernst
date_created: 2022-08-05T06:13:19Z
date_updated: 2022-08-05T06:13:19Z
file_id: '11728'
file_name: 2022_NonlinearDyn_Aguilera.pdf
file_size: 1416049
relation: main_file
success: 1
file_date_updated: 2022-08-05T06:13:19Z
has_accepted_license: '1'
intvolume: ' 108'
isi: 1
keyword:
- Electrical and Electronic Engineering
- Applied Mathematics
- Mechanical Engineering
- Ocean Engineering
- Aerospace Engineering
- Control and Systems Engineering
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 3209-3218
publication: Nonlinear Dynamics
publication_identifier:
eissn:
- 1573-269X
issn:
- 0924-090X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Vortices nucleation by inherent fluctuations in nematic liquid crystal cells
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 108
year: '2022'
...
---
_id: '11351'
abstract:
- lang: eng
text: 'One hallmark of plant cells is their cell wall. They protect cells against
the environment and high turgor and mediate morphogenesis through the dynamics
of their mechanical and chemical properties. The walls are a complex polysaccharidic
structure. Although their biochemical composition is well known, how the different
components organize in the volume of the cell wall and interact with each other
is not well understood and yet is key to the wall’s mechanical properties. To
investigate the ultrastructure of the plant cell wall, we imaged the walls of
onion (Allium cepa) bulbs in a near-native state via cryo-focused ion beam milling
(cryo-FIB milling) and cryo-electron tomography (cryo-ET). This allowed the high-resolution
visualization of cellulose fibers in situ. We reveal the coexistence of dense
fiber fields bathed in a reticulated matrix we termed “meshing,” which is more
abundant at the inner surface of the cell wall. The fibers adopted a regular bimodal
angular distribution at all depths in the cell wall and bundled according to their
orientation, creating layers within the cell wall. Concomitantly, employing homogalacturonan
(HG)-specific enzymatic digestion, we observed changes in the meshing, suggesting
that it is—at least in part—composed of HG pectins. We propose the following model
for the construction of the abaxial epidermal primary cell wall: the cell deposits
successive layers of cellulose fibers at −45° and +45° relative to the cell’s
long axis and secretes the surrounding HG-rich meshing proximal to the plasma
membrane, which then migrates to more distal regions of the cell wall.'
acknowledgement: This work was supported by the Howard Hughes Medical Institute (HHMI)
and grant R35 GM122588 to G.J. and the Austrian Science Fund (FWF) P33367 to F.K.M.S.
We thank Noé Cochetel for his guidance and great help in data analysis, discovery,
and representation with the R software. We thank Hans-Ulrich Endress for graciously
providing us with the purified citrus pectin and Jozef Mravec for generating and
providing the COS488 probe. Cryo-EM work was done in the Beckman Institute Resource
Center for Transmission Electron Microscopy at Caltech. This article is subject
to HHMI’s Open Access to Publications policy. HHMI lab heads have previously granted
a nonexclusive CC BY 4.0 license to the public and a sublicensable license to HHMI
in their research articles. Pursuant to those licenses, the author accepted manuscript
of this article can be made freely available under a CC BY 4.0 license immediately
upon publication.
article_processing_charge: No
article_type: original
author:
- first_name: William J.
full_name: Nicolas, William J.
last_name: Nicolas
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Przemysław
full_name: Dutka, Przemysław
last_name: Dutka
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Grant
full_name: Jensen, Grant
last_name: Jensen
- first_name: Elliot
full_name: Meyerowitz, Elliot
last_name: Meyerowitz
citation:
ama: Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. Cryo-electron
tomography of the onion cell wall shows bimodally oriented cellulose fibers and
reticulated homogalacturonan networks. Current Biology. 2022;32(11):P2375-2389.
doi:10.1016/j.cub.2022.04.024
apa: Nicolas, W. J., Fäßler, F., Dutka, P., Schur, F. K., Jensen, G., & Meyerowitz,
E. (2022). Cryo-electron tomography of the onion cell wall shows bimodally oriented
cellulose fibers and reticulated homogalacturonan networks. Current Biology.
Elsevier. https://doi.org/10.1016/j.cub.2022.04.024
chicago: Nicolas, William J., Florian Fäßler, Przemysław Dutka, Florian KM Schur,
Grant Jensen, and Elliot Meyerowitz. “Cryo-Electron Tomography of the Onion Cell
Wall Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan
Networks.” Current Biology. Elsevier, 2022. https://doi.org/10.1016/j.cub.2022.04.024.
ieee: W. J. Nicolas, F. Fäßler, P. Dutka, F. K. Schur, G. Jensen, and E. Meyerowitz,
“Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose
fibers and reticulated homogalacturonan networks,” Current Biology, vol.
32, no. 11. Elsevier, pp. P2375-2389, 2022.
ista: Nicolas WJ, Fäßler F, Dutka P, Schur FK, Jensen G, Meyerowitz E. 2022. Cryo-electron
tomography of the onion cell wall shows bimodally oriented cellulose fibers and
reticulated homogalacturonan networks. Current Biology. 32(11), P2375-2389.
mla: Nicolas, William J., et al. “Cryo-Electron Tomography of the Onion Cell Wall
Shows Bimodally Oriented Cellulose Fibers and Reticulated Homogalacturonan Networks.”
Current Biology, vol. 32, no. 11, Elsevier, 2022, pp. P2375-2389, doi:10.1016/j.cub.2022.04.024.
short: W.J. Nicolas, F. Fäßler, P. Dutka, F.K. Schur, G. Jensen, E. Meyerowitz,
Current Biology 32 (2022) P2375-2389.
date_created: 2022-05-04T06:22:06Z
date_published: 2022-06-06T00:00:00Z
date_updated: 2025-04-15T08:25:40Z
day: '06'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1016/j.cub.2022.04.024
external_id:
isi:
- '000822399200019'
pmid:
- '35508170'
file:
- access_level: open_access
checksum: af3f24d97c016d844df237abef987639
content_type: application/pdf
creator: dernst
date_created: 2022-08-05T06:29:18Z
date_updated: 2022-08-05T06:29:18Z
file_id: '11730'
file_name: 2022_CurrentBiology_Nicolas.pdf
file_size: 12827717
relation: main_file
success: 1
file_date_updated: 2022-08-05T06:29:18Z
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
issue: '11'
keyword:
- General Agricultural and Biological Sciences
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: P2375-2389
pmid: 1
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
publication: Current Biology
publication_identifier:
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cryo-electron tomography of the onion cell wall shows bimodally oriented cellulose
fibers and reticulated homogalacturonan networks
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 32
year: '2022'
...
---
_id: '11354'
abstract:
- lang: eng
text: We construct a recurrent diffusion process with values in the space of probability
measures over an arbitrary closed Riemannian manifold of dimension d≥2. The process
is associated with the Dirichlet form defined by integration of the Wasserstein
gradient w.r.t. the Dirichlet–Ferguson measure, and is the counterpart on multidimensional
base spaces to the modified massive Arratia flow over the unit interval described
in V. Konarovskyi and M.-K. von Renesse (Comm. Pure Appl. Math. 72 (2019) 764–800).
Together with two different constructions of the process, we discuss its ergodicity,
invariant sets, finite-dimensional approximations, and Varadhan short-time asymptotics.
acknowledgement: Research supported by the Sonderforschungsbereich 1060 and the Hausdorff
Center for Mathematics. The author gratefully acknowledges funding of his current
position at IST Austria by the Austrian Science Fund (FWF) grant F65 and by the
European Research Council (ERC, Grant agreement No. 716117, awarded to Prof. Dr.
Jan Maas).
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Lorenzo
full_name: Dello Schiavo, Lorenzo
id: ECEBF480-9E4F-11EA-B557-B0823DDC885E
last_name: Dello Schiavo
orcid: 0000-0002-9881-6870
citation:
ama: Dello Schiavo L. The Dirichlet–Ferguson diffusion on the space of probability
measures over a closed Riemannian manifold. Annals of Probability. 2022;50(2):591-648.
doi:10.1214/21-AOP1541
apa: Dello Schiavo, L. (2022). The Dirichlet–Ferguson diffusion on the space of
probability measures over a closed Riemannian manifold. Annals of Probability.
Institute of Mathematical Statistics. https://doi.org/10.1214/21-AOP1541
chicago: Dello Schiavo, Lorenzo. “The Dirichlet–Ferguson Diffusion on the Space
of Probability Measures over a Closed Riemannian Manifold.” Annals of Probability.
Institute of Mathematical Statistics, 2022. https://doi.org/10.1214/21-AOP1541.
ieee: L. Dello Schiavo, “The Dirichlet–Ferguson diffusion on the space of probability
measures over a closed Riemannian manifold,” Annals of Probability, vol.
50, no. 2. Institute of Mathematical Statistics, pp. 591–648, 2022.
ista: Dello Schiavo L. 2022. The Dirichlet–Ferguson diffusion on the space of probability
measures over a closed Riemannian manifold. Annals of Probability. 50(2), 591–648.
mla: Dello Schiavo, Lorenzo. “The Dirichlet–Ferguson Diffusion on the Space of Probability
Measures over a Closed Riemannian Manifold.” Annals of Probability, vol.
50, no. 2, Institute of Mathematical Statistics, 2022, pp. 591–648, doi:10.1214/21-AOP1541.
short: L. Dello Schiavo, Annals of Probability 50 (2022) 591–648.
corr_author: '1'
date_created: 2022-05-08T22:01:44Z
date_published: 2022-03-01T00:00:00Z
date_updated: 2025-04-14T07:27:47Z
day: '01'
department:
- _id: JaMa
doi: 10.1214/21-AOP1541
ec_funded: 1
external_id:
arxiv:
- '1811.11598'
isi:
- '000773518500005'
intvolume: ' 50'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.1811.11598'
month: '03'
oa: 1
oa_version: Preprint
page: 591-648
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication: Annals of Probability
publication_identifier:
eissn:
- 2168-894X
issn:
- 0091-1798
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Dirichlet–Ferguson diffusion on the space of probability measures over
a closed Riemannian manifold
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2022'
...
---
_id: '11355'
abstract:
- lang: eng
text: "Contract-based design is a promising methodology for taming the complexity
of developing sophisticated systems. A formal contract distinguishes between assumptions,
which are constraints that the designer of a component puts on the environments
in which the component can be used safely, and guarantees, which are promises
that the designer asks from the team that implements the component. A theory of
formal contracts can be formalized as an interface theory, which supports the
composition and refinement of both assumptions and guarantees.\r\nAlthough there
is a rich landscape of contract-based design methods that address functional and
extra-functional properties, we present the first interface theory that is designed
for ensuring system-wide security properties. Our framework provides a refinement
relation and a composition operation that support both incremental design and
independent implementability. We develop our theory for both stateless and stateful
interfaces. We illustrate the applicability of our framework with an example inspired
from the automotive domain."
acknowledgement: This project has received funding from the European Union’s Horizon
2020 research and innovation programme under grant agreement No 956123 and was funded
in part by the FWF project W1255-N23 and by the ERC-2020-AdG 101020093.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
- first_name: Dejan
full_name: Nickovic, Dejan
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
- first_name: Ana Oliveira
full_name: Da Costa, Ana Oliveira
last_name: Da Costa
citation:
ama: 'Bartocci E, Ferrere T, Henzinger TA, Nickovic D, Da Costa AO. Information-flow
interfaces. In: Fundamental Approaches to Software Engineering. Vol 13241.
Springer Nature; 2022:3-22. doi:10.1007/978-3-030-99429-7_1'
apa: 'Bartocci, E., Ferrere, T., Henzinger, T. A., Nickovic, D., & Da Costa,
A. O. (2022). Information-flow interfaces. In Fundamental Approaches to Software
Engineering (Vol. 13241, pp. 3–22). Munich, Germany: Springer Nature. https://doi.org/10.1007/978-3-030-99429-7_1'
chicago: Bartocci, Ezio, Thomas Ferrere, Thomas A Henzinger, Dejan Nickovic, and
Ana Oliveira Da Costa. “Information-Flow Interfaces.” In Fundamental Approaches
to Software Engineering, 13241:3–22. Springer Nature, 2022. https://doi.org/10.1007/978-3-030-99429-7_1.
ieee: E. Bartocci, T. Ferrere, T. A. Henzinger, D. Nickovic, and A. O. Da Costa,
“Information-flow interfaces,” in Fundamental Approaches to Software Engineering,
Munich, Germany, 2022, vol. 13241, pp. 3–22.
ista: 'Bartocci E, Ferrere T, Henzinger TA, Nickovic D, Da Costa AO. 2022. Information-flow
interfaces. Fundamental Approaches to Software Engineering. FASE: Fundamental
Approaches to Software Engineering, LNCS, vol. 13241, 3–22.'
mla: Bartocci, Ezio, et al. “Information-Flow Interfaces.” Fundamental Approaches
to Software Engineering, vol. 13241, Springer Nature, 2022, pp. 3–22, doi:10.1007/978-3-030-99429-7_1.
short: E. Bartocci, T. Ferrere, T.A. Henzinger, D. Nickovic, A.O. Da Costa, in:,
Fundamental Approaches to Software Engineering, Springer Nature, 2022, pp. 3–22.
conference:
end_date: 2022-04-07
location: Munich, Germany
name: 'FASE: Fundamental Approaches to Software Engineering'
start_date: 2022-04-02
date_created: 2022-05-08T22:01:44Z
date_published: 2022-03-29T00:00:00Z
date_updated: 2025-12-30T06:50:51Z
day: '29'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-030-99429-7_1
ec_funded: 1
external_id:
isi:
- '000782393600001'
file:
- access_level: open_access
checksum: 7f6f860b20b8de2a249e9c1b4eee15cf
content_type: application/pdf
creator: dernst
date_created: 2022-05-09T06:52:44Z
date_updated: 2022-05-09T06:52:44Z
file_id: '11357'
file_name: 2022_LNCS_Bartocci.pdf
file_size: 479146
relation: main_file
success: 1
file_date_updated: 2022-05-09T06:52:44Z
has_accepted_license: '1'
intvolume: ' 13241'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 3-22
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: Fundamental Approaches to Software Engineering
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783030994280'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '17094'
relation: extended_version
status: public
scopus_import: '1'
status: public
title: Information-flow interfaces
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13241
year: '2022'
...
---
_id: '11379'
abstract:
- lang: eng
text: Bernal-stacked multilayer graphene is a versatile platform to explore quantum
transport phenomena and interaction physics due to its exceptional tunability
via electrostatic gating. For instance, upon applying a perpendicular electric
field, its band structure exhibits several off-center Dirac points (so-called
Dirac gullies) in each valley. Here, the formation of Dirac gullies and the interaction-induced
breakdown of gully coherence is explored via magnetotransport measurements in
high-quality Bernal-stacked (ABA) trilayer graphene. At zero magnetic field, multiple
Lifshitz transitions indicating the formation of Dirac gullies are identified.
In the quantum Hall regime, the emergence of Dirac gullies is evident as an increase
in Landau level degeneracy. When tuning both electric and magnetic fields, electron–electron
interactions can be controllably enhanced until, beyond critical electric and
magnetic fields, the gully degeneracy is eventually lifted. The arising correlated
ground state is consistent with a previously predicted nematic phase that spontaneously
breaks the rotational gully symmetry.
acknowledgement: "We acknowledge funding from the Center for Nanoscience (CeNS) and
by the Deutsche\r\nForschungsgemeinschaft (DFG, German Research Foundation) under
Germany’s Excellence Strategy-EXC-2111-390814868 (MCQST). K.W. and T.T. acknowledge
support from the Elemental Strategy Initiative conducted by the MEXT, Japan (Grant
Number PMXP0112101001) and JSPS KAKENHI (Grant Numbers 19H05790 and JP20H00354)."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Felix
full_name: Winterer, Felix
last_name: Winterer
- first_name: Anna M.
full_name: Seiler, Anna M.
last_name: Seiler
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Fabian R.
full_name: Geisenhof, Fabian R.
last_name: Geisenhof
- first_name: Kenji
full_name: Watanabe, Kenji
last_name: Watanabe
- first_name: Takashi
full_name: Taniguchi, Takashi
last_name: Taniguchi
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: R. Thomas
full_name: Weitz, R. Thomas
last_name: Weitz
citation:
ama: Winterer F, Seiler AM, Ghazaryan A, et al. Spontaneous gully-polarized quantum
hall states in ABA trilayer graphene. Nano Letters. 2022;22(8):3317-3322.
doi:10.1021/acs.nanolett.2c00435
apa: Winterer, F., Seiler, A. M., Ghazaryan, A., Geisenhof, F. R., Watanabe, K.,
Taniguchi, T., … Weitz, R. T. (2022). Spontaneous gully-polarized quantum hall
states in ABA trilayer graphene. Nano Letters. American Chemical Society.
https://doi.org/10.1021/acs.nanolett.2c00435
chicago: Winterer, Felix, Anna M. Seiler, Areg Ghazaryan, Fabian R. Geisenhof, Kenji
Watanabe, Takashi Taniguchi, Maksym Serbyn, and R. Thomas Weitz. “Spontaneous
Gully-Polarized Quantum Hall States in ABA Trilayer Graphene.” Nano Letters.
American Chemical Society, 2022. https://doi.org/10.1021/acs.nanolett.2c00435.
ieee: F. Winterer et al., “Spontaneous gully-polarized quantum hall states
in ABA trilayer graphene,” Nano Letters, vol. 22, no. 8. American Chemical
Society, pp. 3317–3322, 2022.
ista: Winterer F, Seiler AM, Ghazaryan A, Geisenhof FR, Watanabe K, Taniguchi T,
Serbyn M, Weitz RT. 2022. Spontaneous gully-polarized quantum hall states in ABA
trilayer graphene. Nano Letters. 22(8), 3317–3322.
mla: Winterer, Felix, et al. “Spontaneous Gully-Polarized Quantum Hall States in
ABA Trilayer Graphene.” Nano Letters, vol. 22, no. 8, American Chemical
Society, 2022, pp. 3317–22, doi:10.1021/acs.nanolett.2c00435.
short: F. Winterer, A.M. Seiler, A. Ghazaryan, F.R. Geisenhof, K. Watanabe, T. Taniguchi,
M. Serbyn, R.T. Weitz, Nano Letters 22 (2022) 3317–3322.
date_created: 2022-05-15T22:01:41Z
date_published: 2022-04-27T00:00:00Z
date_updated: 2025-06-11T13:47:08Z
day: '27'
department:
- _id: MaSe
doi: 10.1021/acs.nanolett.2c00435
external_id:
arxiv:
- '2109.00556'
isi:
- '000809056900019'
pmid:
- '35405074'
intvolume: ' 22'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2109.00556'
month: '04'
oa: 1
oa_version: Preprint
page: 3317-3322
pmid: 1
publication: Nano Letters
publication_identifier:
eissn:
- 1530-6992
issn:
- 1530-6984
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spontaneous gully-polarized quantum hall states in ABA trilayer graphene
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2022'
...