---
_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
- 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
date_created: 2022-04-22T09:42:24Z
date_published: 2022-04-28T00:00:00Z
date_updated: 2024-02-21T12:41:09Z
day: '28'
ddc:
- '570'
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/at:ista:11321
file:
- access_level: open_access
checksum: 96c1b86cdf25481f2a52972fcc45ca7f
content_type: application/x-zip-compressed
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: '11411'
relation: used_in_publication
status: public
- id: '9192'
relation: earlier_version
status: public
- id: '8254'
relation: earlier_version
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).
date_created: 2022-04-24T22:01:43Z
date_published: 2022-04-08T00:00:00Z
date_updated: 2023-08-03T06:37:49Z
day: '08'
ddc:
- '510'
- '530'
department:
- _id: JaMa
doi: 10.1007/s10955-022-02911-9
ec_funded: 1
external_id:
isi:
- '000780305000001'
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
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:
- '15729613'
issn:
- '00224715'
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
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
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: 2023-08-03T06:34:24Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1007/s00220-022-04377-y
ec_funded: 1
external_id:
arxiv:
- '2102.04330'
isi:
- '000782737200001'
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
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 393
year: '2022'
...
---
_id: '11333'
abstract:
- lang: eng
text: Adenosine triphosphate (ATP) is the energy source for various biochemical
processes and biomolecular motors in living things. Development of ATP antagonists
and their stimuli-controlled actions offer a novel approach to regulate biological
processes. Herein, we developed azobenzene-based photoswitchable ATP antagonists
for controlling the activity of motor proteins; cytoplasmic and axonemal dyneins.
The new ATP antagonists showed reversible photoswitching of cytoplasmic dynein
activity in an in vitro dynein-microtubule system due to the trans and cis photoisomerization
of their azobenzene segment. Importantly, our ATP antagonists reversibly regulated
the axonemal dynein motor activity for the force generation in a demembranated
model of Chlamydomonas reinhardtii. We found that the trans and cis isomers of
ATP antagonists significantly differ in their affinity to the ATP binding site.
article_number: e202200807
article_processing_charge: No
article_type: original
author:
- first_name: Sampreeth
full_name: Thayyil, Sampreeth
last_name: Thayyil
- first_name: Yukinori
full_name: Nishigami, Yukinori
last_name: Nishigami
- first_name: Muhammad J
full_name: Islam, Muhammad J
id: C94881D2-008F-11EA-8E08-2637E6697425
last_name: Islam
- first_name: P. K.
full_name: Hashim, P. K.
last_name: Hashim
- first_name: Ken'Ya
full_name: Furuta, Ken'Ya
last_name: Furuta
- first_name: Kazuhiro
full_name: Oiwa, Kazuhiro
last_name: Oiwa
- first_name: Jian
full_name: Yu, Jian
last_name: Yu
- first_name: Min
full_name: Yao, Min
last_name: Yao
- first_name: Toshiyuki
full_name: Nakagaki, Toshiyuki
last_name: Nakagaki
- first_name: Nobuyuki
full_name: Tamaoki, Nobuyuki
last_name: Tamaoki
citation:
ama: Thayyil S, Nishigami Y, Islam MJ, et al. Dynamic control of microbial movement
by photoswitchable ATP antagonists. Chemistry - A European Journal. 2022;28(30).
doi:10.1002/chem.202200807
apa: Thayyil, S., Nishigami, Y., Islam, M. J., Hashim, P. K., Furuta, K., Oiwa,
K., … Tamaoki, N. (2022). Dynamic control of microbial movement by photoswitchable
ATP antagonists. Chemistry - A European Journal. Wiley. https://doi.org/10.1002/chem.202200807
chicago: Thayyil, Sampreeth, Yukinori Nishigami, Muhammad J Islam, P. K. Hashim,
Ken’Ya Furuta, Kazuhiro Oiwa, Jian Yu, Min Yao, Toshiyuki Nakagaki, and Nobuyuki
Tamaoki. “Dynamic Control of Microbial Movement by Photoswitchable ATP Antagonists.”
Chemistry - A European Journal. Wiley, 2022. https://doi.org/10.1002/chem.202200807.
ieee: S. Thayyil et al., “Dynamic control of microbial movement by photoswitchable
ATP antagonists,” Chemistry - A European Journal, vol. 28, no. 30. Wiley,
2022.
ista: Thayyil S, Nishigami Y, Islam MJ, Hashim PK, Furuta K, Oiwa K, Yu J, Yao M,
Nakagaki T, Tamaoki N. 2022. Dynamic control of microbial movement by photoswitchable
ATP antagonists. Chemistry - A European Journal. 28(30), e202200807.
mla: Thayyil, Sampreeth, et al. “Dynamic Control of Microbial Movement by Photoswitchable
ATP Antagonists.” Chemistry - A European Journal, vol. 28, no. 30, e202200807,
Wiley, 2022, doi:10.1002/chem.202200807.
short: S. Thayyil, Y. Nishigami, M.J. Islam, P.K. Hashim, K. Furuta, K. Oiwa, J.
Yu, M. Yao, T. Nakagaki, N. Tamaoki, Chemistry - A European Journal 28 (2022).
date_created: 2022-04-24T22:01:44Z
date_published: 2022-05-25T00:00:00Z
date_updated: 2023-10-03T10:58:31Z
day: '25'
department:
- _id: RySh
doi: 10.1002/chem.202200807
external_id:
isi:
- '000781658800001'
pmid:
- '35332959'
intvolume: ' 28'
isi: 1
issue: '30'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/chem.202200807
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Chemistry - A European Journal
publication_identifier:
eissn:
- '15213765'
issn:
- '09476539'
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic control of microbial movement by photoswitchable ATP antagonists
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 28
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: 2023-08-03T07:00:28Z
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
license: https://creativecommons.org/licenses/by-nc/4.0/
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
- 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).
date_created: 2022-04-26T15:04:50Z
date_published: 2022-11-01T00:00:00Z
date_updated: 2023-05-31T12:24:10Z
day: '01'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.1126/sciadv.abq1263
ec_funded: 1
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'
issue: '44'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
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: T0101031
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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
- 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).
date_created: 2022-04-28T08:06:10Z
date_published: 2022-04-15T00:00:00Z
date_updated: 2023-08-03T06:33:33Z
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'
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: 2023-08-03T06:42:50Z
day: '14'
department:
- _id: AnSa
doi: 10.1021/acs.jpcb.2c00028
external_id:
arxiv:
- '2203.10524'
isi:
- '000796953700022'
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
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
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: 2023-08-03T06:44:50Z
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.
date_created: 2022-05-02T07:01:59Z
date_published: 2022-06-01T00:00:00Z
date_updated: 2023-08-03T06:46:54Z
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: '11344'
abstract:
- lang: eng
text: Until recently, Shigella and enteroinvasive Escherichia coli were thought
to be primate-restricted pathogens. The base of their pathogenicity is the type
3 secretion system (T3SS) encoded by the pINV virulence plasmid, which facilitates
host cell invasion and subsequent proliferation. A large family of T3SS effectors,
E3 ubiquitin-ligases encoded by the ipaH genes, have a key role in the Shigella
pathogenicity through the modulation of cellular ubiquitination that degrades
host proteins. However, recent genomic studies identified ipaH genes in the genomes
of Escherichia marmotae, a potential marmot pathogen, and an E. coli extracted
from fecal samples of bovine calves, suggesting that non-human hosts may also
be infected by these strains, potentially pathogenic to humans. We performed a
comparative genomic study of the functional repertoires in the ipaH gene family
in Shigella and enteroinvasive Escherichia from human and predicted non-human
hosts. We found that fewer than half of Shigella genomes had a complete set of
ipaH genes, with frequent gene losses and duplications that were not consistent
with the species tree and nomenclature. Non-human host IpaH proteins had a diverse
set of substrate-binding domains and, in contrast to the Shigella proteins, two
variants of the NEL C-terminal domain. Inconsistencies between strains phylogeny
and composition of effectors indicate horizontal gene transfer between E. coli
adapted to different hosts. These results provide a framework for understanding
of ipaH-mediated host-pathogens interactions and suggest a need for a genomic
study of fecal samples from diseased animals.
acknowledgement: 'The project was initiated with Aygul Minnegalieva and Yulia Yakovleva
at the Summer School of Molecular and Theoretical Biology (SMTB-2020), supported
by the Zimin Foundation. We thank Inna Shapovalenko, Daria Abuzova, Elizaveta Kaminskaya,
and Dmitriy Zvezdin for their contribution to the project during SMTB-2020. We also
thank Peter Vlasov for fruitful discussions.This study was supported by the Russian
Foundation for Basic Research (RFBR), Grant # 20-54-14005 and Fonds zur Förderung
der wissenschaftlichen Forschung (FWF), Grant # I5127-B. The work of OB is supported
by the European Union’s Horizon 2020 Research and Innovation Programme under the
Marie Skłodowska-Curie Grant Agreement No. 754411. '
article_number: '6868'
article_processing_charge: No
article_type: original
author:
- first_name: NO
full_name: Dranenko, NO
last_name: Dranenko
- first_name: MN
full_name: Tutukina, MN
last_name: Tutukina
- first_name: MS
full_name: Gelfand, MS
last_name: Gelfand
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
citation:
ama: Dranenko N, Tutukina M, Gelfand M, Kondrashov F, Bochkareva O. Chromosome-encoded
IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. Scientific
Reports. 2022;12. doi:10.1038/s41598-022-10827-3
apa: Dranenko, N., Tutukina, M., Gelfand, M., Kondrashov, F., & Bochkareva,
O. (2022). Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive
Escherichia. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-022-10827-3
chicago: Dranenko, NO, MN Tutukina, MS Gelfand, Fyodor Kondrashov, and Olga Bochkareva.
“Chromosome-Encoded IpaH Ubiquitin Ligases Indicate Non-Human Enteroinvasive Escherichia.”
Scientific Reports. Springer Nature, 2022. https://doi.org/10.1038/s41598-022-10827-3.
ieee: N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, and O. Bochkareva, “Chromosome-encoded
IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia,” Scientific
Reports, vol. 12. Springer Nature, 2022.
ista: Dranenko N, Tutukina M, Gelfand M, Kondrashov F, Bochkareva O. 2022. Chromosome-encoded
IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. Scientific
Reports. 12, 6868.
mla: Dranenko, NO, et al. “Chromosome-Encoded IpaH Ubiquitin Ligases Indicate Non-Human
Enteroinvasive Escherichia.” Scientific Reports, vol. 12, 6868, Springer
Nature, 2022, doi:10.1038/s41598-022-10827-3.
short: N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, O. Bochkareva, Scientific
Reports 12 (2022).
date_created: 2022-05-02T07:08:42Z
date_published: 2022-04-27T00:00:00Z
date_updated: 2023-08-03T06:59:49Z
day: '27'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1038/s41598-022-10827-3
ec_funded: 1
external_id:
isi:
- '000788639400032'
pmid:
- '35477739'
file:
- access_level: open_access
checksum: 12601b8a5c6b83bb618f92bcb963ecc9
content_type: application/pdf
creator: dernst
date_created: 2022-05-02T09:05:20Z
date_updated: 2022-05-02T09:05:20Z
file_id: '11349'
file_name: 2022_ScientificReports_Dranenko.pdf
file_size: 3564155
relation: main_file
success: 1
file_date_updated: 2022-05-02T09:05:20Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: c098eddd-5a5b-11eb-8a69-abe27170a68f
grant_number: I05127
name: Evolutionary analysis of gene regulation
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Scientific Reports
publication_identifier:
issn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive
Escherichia
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: 12
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: 2023-08-03T07:05:36Z
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: '11353'
abstract:
- lang: eng
text: Micro- and nanoscale optical or microwave cavities are used in a wide range
of classical applications and quantum science experiments, ranging from precision
measurements, laser technologies to quantum control of mechanical motion. The
dissipative photon loss via absorption, present to some extent in any optical
cavity, is known to introduce thermo-optical effects and thereby impose fundamental
limits on precision measurements. Here, we theoretically and experimentally reveal
that such dissipative photon absorption can result in quantum feedback via in-loop
field detection of the absorbed optical field, leading to the intracavity field
fluctuations to be squashed or antisquashed. A closed-loop dissipative quantum
feedback to the cavity field arises. Strikingly, this modifies the optical cavity
susceptibility in coherent response measurements (capable of both increasing or
decreasing the bare cavity linewidth) and causes excess noise and correlations
in incoherent interferometric optomechanical measurements using a cavity, that
is parametrically coupled to a mechanical oscillator. We experimentally observe
such unanticipated dissipative dynamics in optomechanical spectroscopy of sideband-cooled
optomechanical crystal cavitiess at both cryogenic temperature (approximately
8 K) and ambient conditions. The dissipative feedback introduces effective modifications
to the optical cavity linewidth and the optomechanical scattering rate and gives
rise to excess imprecision noise in the interferometric quantum measurement of
mechanical motion. Such dissipative feedback differs fundamentally from a quantum
nondemolition feedback, e.g., optical Kerr squeezing. The dissipative feedback
itself always results in an antisqueezed out-of-loop optical field, while it can
enhance the coexisting Kerr squeezing under certain conditions. Our result applies
to cavity spectroscopy in both optical and superconducting microwave cavities,
and equally applies to any dissipative feedback mechanism of different bandwidth
inside the cavity. It has wide-ranging implications for future dissipation engineering,
such as dissipation enhanced sideband cooling and Kerr squeezing, quantum frequency
conversion, and nonreciprocity in photonic systems.
acknowledgement: "L.Q. acknowledges fruitful discussions with D. Vitali, R. Schnabel,
P.K. Lam, A. Nunnenkamp, and D. Malz. This work is supported by the EUH2020 research
and innovation programme under Grant No. 732894 (FET Proactive HOT), and the European
Research Council through \r\nGrant No. 835329 (ExCOM-cCEO). This work was further
supported by Swiss National Science Foundation under Grant Agreements No. 185870
(Ambizione) and No. 204927. Samples were fabricated at the Center of MicroNanoTechnology
(CMi) at EPFL and the Binnig and Rohrer Nanotechnology Center at IBM Research-Zurich."
article_number: '020309'
article_processing_charge: No
article_type: original
author:
- first_name: Liu
full_name: Qiu, Liu
id: 45e99c0d-1eb1-11eb-9b96-ed8ab2983cac
last_name: Qiu
orcid: 0000-0003-4345-4267
- first_name: Guanhao
full_name: Huang, Guanhao
last_name: Huang
- first_name: Itay
full_name: Shomroni, Itay
last_name: Shomroni
- first_name: Jiahe
full_name: Pan, Jiahe
last_name: Pan
- first_name: Paul
full_name: Seidler, Paul
last_name: Seidler
- first_name: Tobias J.
full_name: Kippenberg, Tobias J.
last_name: Kippenberg
citation:
ama: Qiu L, Huang G, Shomroni I, Pan J, Seidler P, Kippenberg TJ. Dissipative quantum
feedback in measurements using a parametrically coupled microcavity. PRX Quantum.
2022;3(2). doi:10.1103/PRXQuantum.3.020309
apa: Qiu, L., Huang, G., Shomroni, I., Pan, J., Seidler, P., & Kippenberg, T.
J. (2022). Dissipative quantum feedback in measurements using a parametrically
coupled microcavity. PRX Quantum. American Physical Society. https://doi.org/10.1103/PRXQuantum.3.020309
chicago: Qiu, Liu, Guanhao Huang, Itay Shomroni, Jiahe Pan, Paul Seidler, and Tobias
J. Kippenberg. “Dissipative Quantum Feedback in Measurements Using a Parametrically
Coupled Microcavity.” PRX Quantum. American Physical Society, 2022. https://doi.org/10.1103/PRXQuantum.3.020309.
ieee: L. Qiu, G. Huang, I. Shomroni, J. Pan, P. Seidler, and T. J. Kippenberg, “Dissipative
quantum feedback in measurements using a parametrically coupled microcavity,”
PRX Quantum, vol. 3, no. 2. American Physical Society, 2022.
ista: Qiu L, Huang G, Shomroni I, Pan J, Seidler P, Kippenberg TJ. 2022. Dissipative
quantum feedback in measurements using a parametrically coupled microcavity. PRX
Quantum. 3(2), 020309.
mla: Qiu, Liu, et al. “Dissipative Quantum Feedback in Measurements Using a Parametrically
Coupled Microcavity.” PRX Quantum, vol. 3, no. 2, 020309, American Physical
Society, 2022, doi:10.1103/PRXQuantum.3.020309.
short: L. Qiu, G. Huang, I. Shomroni, J. Pan, P. Seidler, T.J. Kippenberg, PRX Quantum
3 (2022).
date_created: 2022-05-08T22:01:43Z
date_published: 2022-04-13T00:00:00Z
date_updated: 2023-08-03T07:05:00Z
day: '13'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.1103/PRXQuantum.3.020309
ec_funded: 1
external_id:
isi:
- '000789316700001'
file:
- access_level: open_access
checksum: 35ff9ddf1d54f64432e435b660edaeb6
content_type: application/pdf
creator: dernst
date_created: 2022-05-09T07:10:51Z
date_updated: 2022-05-09T07:10:51Z
file_id: '11358'
file_name: 2022_PRXQuantum_Qiu.pdf
file_size: 1657177
relation: main_file
success: 1
file_date_updated: 2022-05-09T07:10:51Z
has_accepted_license: '1'
intvolume: ' 3'
isi: 1
issue: '2'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 257EB838-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '732894'
name: Hybrid Optomechanical Technologies
publication: PRX Quantum
publication_identifier:
eissn:
- '26913399'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dissipative quantum feedback in measurements using a parametrically coupled
microcavity
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: 3
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.
date_created: 2022-05-08T22:01:44Z
date_published: 2022-03-01T00:00:00Z
date_updated: 2023-10-17T12:50:24Z
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: 2023-08-03T07:03:40Z
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'
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: '11356'
acknowledgement: This work was supported by the National Science Fund for Distinguished
Young Scholars (51925101), National Key Research and Development Program of China
(2018YFA0702100), 111 Project (B17002), and Lise Meitner Project (M2889-N).
article_processing_charge: No
article_type: letter_note
author:
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Bingchao
full_name: Qin, Bingchao
last_name: Qin
- first_name: Lizhong
full_name: Su, Lizhong
last_name: Su
- first_name: Li Dong
full_name: Zhao, Li Dong
last_name: Zhao
citation:
ama: Chang C, Qin B, Su L, Zhao LD. Distinct electron and hole transports in SnSe
crystals. Science Bulletin. 2022;67(11):1105-1107. doi:10.1016/j.scib.2022.04.007
apa: Chang, C., Qin, B., Su, L., & Zhao, L. D. (2022). Distinct electron and
hole transports in SnSe crystals. Science Bulletin. Elsevier. https://doi.org/10.1016/j.scib.2022.04.007
chicago: Chang, Cheng, Bingchao Qin, Lizhong Su, and Li Dong Zhao. “Distinct Electron
and Hole Transports in SnSe Crystals.” Science Bulletin. Elsevier, 2022.
https://doi.org/10.1016/j.scib.2022.04.007.
ieee: C. Chang, B. Qin, L. Su, and L. D. Zhao, “Distinct electron and hole transports
in SnSe crystals,” Science Bulletin, vol. 67, no. 11. Elsevier, pp. 1105–1107,
2022.
ista: Chang C, Qin B, Su L, Zhao LD. 2022. Distinct electron and hole transports
in SnSe crystals. Science Bulletin. 67(11), 1105–1107.
mla: Chang, Cheng, et al. “Distinct Electron and Hole Transports in SnSe Crystals.”
Science Bulletin, vol. 67, no. 11, Elsevier, 2022, pp. 1105–07, doi:10.1016/j.scib.2022.04.007.
short: C. Chang, B. Qin, L. Su, L.D. Zhao, Science Bulletin 67 (2022) 1105–1107.
date_created: 2022-05-08T22:01:44Z
date_published: 2022-06-15T00:00:00Z
date_updated: 2023-08-03T07:04:10Z
day: '15'
department:
- _id: MaIb
doi: 10.1016/j.scib.2022.04.007
external_id:
isi:
- '000835291100006'
intvolume: ' 67'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.scib.2022.04.007
month: '06'
oa: 1
oa_version: Published Version
page: 1105-1107
project:
- _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A
grant_number: M02889
name: Bottom-up Engineering for Thermoelectric Applications
publication: Science Bulletin
publication_identifier:
eissn:
- 2095-9281
issn:
- 2095-9273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distinct electron and hole transports in SnSe crystals
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 67
year: '2022'
...
---
_id: '11362'
abstract:
- lang: eng
text: "Deep learning has enabled breakthroughs in challenging computing problems
and has emerged as the standard problem-solving tool for computer vision and natural
language processing tasks.\r\nOne exception to this trend is safety-critical tasks
where robustness and resilience requirements contradict the black-box nature of
neural networks. \r\nTo deploy deep learning methods for these tasks, it is vital
to provide guarantees on neural network agents' safety and robustness criteria.
\r\nThis can be achieved by developing formal verification methods to verify the
safety and robustness properties of neural networks.\r\n\r\nOur goal is to design,
develop and assess safety verification methods for neural networks to improve
their reliability and trustworthiness in real-world applications.\r\nThis thesis
establishes techniques for the verification of compressed and adversarially trained
models as well as the design of novel neural networks for verifiably safe decision-making.\r\n\r\nFirst,
we establish the problem of verifying quantized neural networks. Quantization
is a technique that trades numerical precision for the computational efficiency
of running a neural network and is widely adopted in industry.\r\nWe show that
neglecting the reduced precision when verifying a neural network can lead to wrong
conclusions about the robustness and safety of the network, highlighting that
novel techniques for quantized network verification are necessary. We introduce
several bit-exact verification methods explicitly designed for quantized neural
networks and experimentally confirm on realistic networks that the network's robustness
and other formal properties are affected by the quantization.\r\n\r\nFurthermore,
we perform a case study providing evidence that adversarial training, a standard
technique for making neural networks more robust, has detrimental effects on the
network's performance. This robustness-accuracy tradeoff has been studied before
regarding the accuracy obtained on classification datasets where each data point
is independent of all other data points. On the other hand, we investigate the
tradeoff empirically in robot learning settings where a both, a high accuracy
and a high robustness, are desirable.\r\nOur results suggest that the negative
side-effects of adversarial training outweigh its robustness benefits in practice.\r\n\r\nFinally,
we consider the problem of verifying safety when running a Bayesian neural network
policy in a feedback loop with systems over the infinite time horizon. Bayesian
neural networks are probabilistic models for learning uncertainties in the data
and are therefore often used on robotic and healthcare applications where data
is inherently stochastic.\r\nWe introduce a method for recalibrating Bayesian
neural networks so that they yield probability distributions over safe decisions
only.\r\nOur method learns a safety certificate that guarantees safety over the
infinite time horizon to determine which decisions are safe in every possible
state of the system.\r\nWe demonstrate the effectiveness of our approach on a
series of reinforcement learning benchmarks."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
citation:
ama: Lechner M. Learning verifiable representations. 2022. doi:10.15479/at:ista:11362
apa: Lechner, M. (2022). Learning verifiable representations. Institute of
Science and Technology Austria. https://doi.org/10.15479/at:ista:11362
chicago: Lechner, Mathias. “Learning Verifiable Representations.” Institute of Science
and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11362.
ieee: M. Lechner, “Learning verifiable representations,” Institute of Science and
Technology Austria, 2022.
ista: Lechner M. 2022. Learning verifiable representations. Institute of Science
and Technology Austria.
mla: Lechner, Mathias. Learning Verifiable Representations. Institute of
Science and Technology Austria, 2022, doi:10.15479/at:ista:11362.
short: M. Lechner, Learning Verifiable Representations, Institute of Science and
Technology Austria, 2022.
date_created: 2022-05-12T07:14:01Z
date_published: 2022-05-12T00:00:00Z
date_updated: 2025-07-14T09:10:11Z
day: '12'
ddc:
- '004'
degree_awarded: PhD
department:
- _id: GradSch
- _id: ToHe
doi: 10.15479/at:ista:11362
ec_funded: 1
file:
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checksum: 8eefa9c7c10ca7e1a2ccdd731962a645
content_type: application/zip
creator: mlechner
date_created: 2022-05-13T12:33:26Z
date_updated: 2022-05-13T12:49:00Z
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content_type: application/pdf
creator: mlechner
date_created: 2022-05-16T08:02:28Z
date_updated: 2022-05-17T15:19:39Z
file_id: '11382'
file_name: thesis_main-a2.pdf
file_size: 2732536
relation: main_file
file_date_updated: 2022-05-17T15:19:39Z
has_accepted_license: '1'
keyword:
- neural networks
- verification
- machine learning
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '124'
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication_identifier:
isbn:
- 978-3-99078-017-6
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11366'
relation: part_of_dissertation
status: public
- id: '7808'
relation: part_of_dissertation
status: public
- id: '10666'
relation: part_of_dissertation
status: public
- id: '10665'
relation: part_of_dissertation
status: public
- id: '10667'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
title: Learning verifiable representations
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '11366'
abstract:
- lang: eng
text: "Adversarial training (i.e., training on adversarially perturbed input data)
is a well-studied method for making neural networks robust to potential adversarial
attacks during inference. However, the improved robustness does not\r\ncome for
free but rather is accompanied by a decrease in overall model accuracy and performance.
Recent work has shown that, in practical robot learning applications, the effects
of adversarial training do not pose a fair trade-off\r\nbut inflict a net loss
when measured in holistic robot performance. This work revisits the robustness-accuracy
trade-off in robot learning by systematically analyzing if recent advances in
robust training methods and theory in\r\nconjunction with adversarial robot learning
can make adversarial training suitable for real-world robot applications. We evaluate
a wide variety of robot learning tasks ranging from autonomous driving in a high-fidelity
environment\r\namenable to sim-to-real deployment, to mobile robot gesture recognition.
Our results demonstrate that, while these techniques make incremental improvements
on the trade-off on a relative scale, the negative side-effects caused by\r\nadversarial
training still outweigh the improvements by an order of magnitude. We conclude
that more substantial advances in robust learning methods are necessary before
they can benefit robot learning tasks in practice."
acknowledgement: "This work was supported in parts by the ERC-2020-AdG 101020093,
National Science Foundation (NSF), and JP\r\nMorgan Graduate Fellowships. We thank
Christoph Lampert for inspiring this work.\r\n"
article_number: '2204.07373'
article_processing_charge: No
arxiv: 1
author:
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Alexander
full_name: Amini, Alexander
last_name: Amini
- first_name: Daniela
full_name: Rus, Daniela
last_name: Rus
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
citation:
ama: Lechner M, Amini A, Rus D, Henzinger TA. Revisiting the adversarial robustness-accuracy
tradeoff in robot learning. arXiv. doi:10.48550/arXiv.2204.07373
apa: Lechner, M., Amini, A., Rus, D., & Henzinger, T. A. (n.d.). Revisiting
the adversarial robustness-accuracy tradeoff in robot learning. arXiv.
https://doi.org/10.48550/arXiv.2204.07373
chicago: Lechner, Mathias, Alexander Amini, Daniela Rus, and Thomas A Henzinger.
“Revisiting the Adversarial Robustness-Accuracy Tradeoff in Robot Learning.” ArXiv,
n.d. https://doi.org/10.48550/arXiv.2204.07373.
ieee: M. Lechner, A. Amini, D. Rus, and T. A. Henzinger, “Revisiting the adversarial
robustness-accuracy tradeoff in robot learning,” arXiv. .
ista: Lechner M, Amini A, Rus D, Henzinger TA. Revisiting the adversarial robustness-accuracy
tradeoff in robot learning. arXiv, 2204.07373.
mla: Lechner, Mathias, et al. “Revisiting the Adversarial Robustness-Accuracy Tradeoff
in Robot Learning.” ArXiv, 2204.07373, doi:10.48550/arXiv.2204.07373.
short: M. Lechner, A. Amini, D. Rus, T.A. Henzinger, ArXiv (n.d.).
date_created: 2022-05-12T13:20:17Z
date_published: 2022-04-15T00:00:00Z
date_updated: 2023-08-01T13:36:50Z
day: '15'
department:
- _id: ToHe
doi: 10.48550/arXiv.2204.07373
ec_funded: 1
external_id:
arxiv:
- '2204.07373'
language:
- iso: eng
main_file_link:
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url: https://doi.org/10.48550/arXiv.2204.07373
month: '04'
oa: 1
oa_version: Preprint
project:
- _id: 62781420-2b32-11ec-9570-8d9b63373d4d
call_identifier: H2020
grant_number: '101020093'
name: Vigilant Algorithmic Monitoring of Software
publication: arXiv
publication_status: submitted
related_material:
record:
- id: '11362'
relation: dissertation_contains
status: public
- id: '12704'
relation: later_version
status: public
status: public
title: Revisiting the adversarial robustness-accuracy tradeoff in robot learning
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...