---
_id: '7623'
abstract:
- lang: eng
text: A two-dimensional mathematical model for cells migrating without adhesion
capabilities is presented and analyzed. Cells are represented by their cortex,
which is modeled as an elastic curve, subject to an internal pressure force. Net
polymerization or depolymerization in the cortex is modeled via local addition
or removal of material, driving a cortical flow. The model takes the form of a
fully nonlinear degenerate parabolic system. An existence analysis is carried
out by adapting ideas from the theory of gradient flows. Numerical simulations
show that these simple rules can account for the behavior observed in experiments,
suggesting a possible mechanical mechanism for adhesion-independent motility.
acknowledgement: This work has been supported by the Vienna Science and Technology
Fund, Grant no. LS13-029. G.J. and C.S. also acknowledge support by the Austrian
Science Fund, Grants no. W1245, F 65, and W1261, as well as by the Fondation Sciences
Mathématiques de Paris, and by Paris-Sciences-et-Lettres.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Gaspard
full_name: Jankowiak, Gaspard
last_name: Jankowiak
- first_name: Diane
full_name: Peurichard, Diane
last_name: Peurichard
- first_name: Anne
full_name: Reversat, Anne
id: 35B76592-F248-11E8-B48F-1D18A9856A87
last_name: Reversat
orcid: 0000-0003-0666-8928
- first_name: Christian
full_name: Schmeiser, Christian
last_name: Schmeiser
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Jankowiak G, Peurichard D, Reversat A, Schmeiser C, Sixt MK. Modeling adhesion-independent
cell migration. Mathematical Models and Methods in Applied Sciences. 2020;30(3):513-537.
doi:10.1142/S021820252050013X
apa: Jankowiak, G., Peurichard, D., Reversat, A., Schmeiser, C., & Sixt, M.
K. (2020). Modeling adhesion-independent cell migration. Mathematical Models
and Methods in Applied Sciences. World Scientific. https://doi.org/10.1142/S021820252050013X
chicago: Jankowiak, Gaspard, Diane Peurichard, Anne Reversat, Christian Schmeiser,
and Michael K Sixt. “Modeling Adhesion-Independent Cell Migration.” Mathematical
Models and Methods in Applied Sciences. World Scientific, 2020. https://doi.org/10.1142/S021820252050013X.
ieee: G. Jankowiak, D. Peurichard, A. Reversat, C. Schmeiser, and M. K. Sixt, “Modeling
adhesion-independent cell migration,” Mathematical Models and Methods in Applied
Sciences, vol. 30, no. 3. World Scientific, pp. 513–537, 2020.
ista: Jankowiak G, Peurichard D, Reversat A, Schmeiser C, Sixt MK. 2020. Modeling
adhesion-independent cell migration. Mathematical Models and Methods in Applied
Sciences. 30(3), 513–537.
mla: Jankowiak, Gaspard, et al. “Modeling Adhesion-Independent Cell Migration.”
Mathematical Models and Methods in Applied Sciences, vol. 30, no. 3, World
Scientific, 2020, pp. 513–37, doi:10.1142/S021820252050013X.
short: G. Jankowiak, D. Peurichard, A. Reversat, C. Schmeiser, M.K. Sixt, Mathematical
Models and Methods in Applied Sciences 30 (2020) 513–537.
date_created: 2020-03-31T11:25:05Z
date_published: 2020-03-18T00:00:00Z
date_updated: 2023-08-18T10:18:56Z
day: '18'
department:
- _id: MiSi
doi: 10.1142/S021820252050013X
external_id:
arxiv:
- '1903.09426'
isi:
- '000525349900003'
intvolume: ' 30'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1903.09426
month: '03'
oa: 1
oa_version: Preprint
page: 513-537
project:
- _id: 25AD6156-B435-11E9-9278-68D0E5697425
grant_number: LS13-029
name: Modeling of Polarization and Motility of Leukocytes in Three-Dimensional Environments
publication: Mathematical Models and Methods in Applied Sciences
publication_identifier:
issn:
- '02182025'
publication_status: published
publisher: World Scientific
quality_controlled: '1'
scopus_import: '1'
status: public
title: Modeling adhesion-independent cell migration
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 30
year: '2020'
...
---
_id: '7629'
abstract:
- lang: eng
text: "This thesis is based on three main topics: In the first part, we study convergence
of discrete gradient flow structures associated with regular finite-volume discretisations
of Fokker-Planck equations. We show evolutionary I convergence of the discrete
gradient flows to the L2-Wasserstein gradient flow corresponding to the solution
of a Fokker-Planck\r\nequation in arbitrary dimension d >= 1. Along the argument,
we prove Mosco- and I-convergence results for discrete energy functionals, which
are of independent interest for convergence of equivalent gradient flow structures
in Hilbert spaces.\r\nThe second part investigates L2-Wasserstein flows on metric
graph. The starting point is a Benamou-Brenier formula for the L2-Wasserstein
distance, which is proved via a regularisation scheme for solutions of the continuity
equation, adapted to the peculiar geometric structure of metric graphs. Based
on those results, we show that the L2-Wasserstein space over a metric graph admits
a gradient flow which may be identified as a solution of a Fokker-Planck equation.\r\nIn
the third part, we focus again on the discrete gradient flows, already encountered
in the first part. We propose a variational structure which extends the gradient
flow structure to Markov chains violating the detailed-balance conditions. Using
this structure, we characterise contraction estimates for the discrete heat flow
in terms of convexity of\r\ncorresponding path-dependent energy functionals. In
addition, we use this approach to derive several functional inequalities for said
functionals."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Dominik L
full_name: Forkert, Dominik L
id: 35C79D68-F248-11E8-B48F-1D18A9856A87
last_name: Forkert
citation:
ama: Forkert DL. Gradient flows in spaces of probability measures for finite-volume
schemes, metric graphs and non-reversible Markov chains. 2020. doi:10.15479/AT:ISTA:7629
apa: Forkert, D. L. (2020). Gradient flows in spaces of probability measures
for finite-volume schemes, metric graphs and non-reversible Markov chains.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7629
chicago: Forkert, Dominik L. “Gradient Flows in Spaces of Probability Measures for
Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains.” Institute
of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7629.
ieee: D. L. Forkert, “Gradient flows in spaces of probability measures for finite-volume
schemes, metric graphs and non-reversible Markov chains,” Institute of Science
and Technology Austria, 2020.
ista: Forkert DL. 2020. Gradient flows in spaces of probability measures for finite-volume
schemes, metric graphs and non-reversible Markov chains. Institute of Science
and Technology Austria.
mla: Forkert, Dominik L. Gradient Flows in Spaces of Probability Measures for
Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains. Institute
of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7629.
short: D.L. Forkert, Gradient Flows in Spaces of Probability Measures for Finite-Volume
Schemes, Metric Graphs and Non-Reversible Markov Chains, Institute of Science
and Technology Austria, 2020.
date_created: 2020-04-02T06:40:23Z
date_published: 2020-03-31T00:00:00Z
date_updated: 2023-09-07T13:03:12Z
day: '31'
ddc:
- '510'
degree_awarded: PhD
department:
- _id: JaMa
doi: 10.15479/AT:ISTA:7629
ec_funded: 1
file:
- access_level: open_access
checksum: c814a1a6195269ca6fe48b0dca45ae8a
content_type: application/pdf
creator: dernst
date_created: 2020-04-14T10:47:59Z
date_updated: 2020-07-14T12:48:01Z
file_id: '7657'
file_name: Thesis_Forkert_PDFA.pdf
file_size: 3297129
relation: main_file
- access_level: closed
checksum: ceafb53f923d1b5bdf14b2b0f22e4a81
content_type: application/x-zip-compressed
creator: dernst
date_created: 2020-04-14T10:47:59Z
date_updated: 2020-07-14T12:48:01Z
file_id: '7658'
file_name: Thesis_Forkert_source.zip
file_size: 1063908
relation: source_file
file_date_updated: 2020-07-14T12:48:01Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '154'
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
title: Gradient flows in spaces of probability measures for finite-volume schemes,
metric graphs and non-reversible Markov chains
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '7632'
abstract:
- lang: eng
text: The posterior parietal cortex (PPC) and frontal motor areas comprise a cortical
network supporting goal-directed behaviour, with functions including sensorimotor
transformations and decision making. In primates, this network links performed
and observed actions via mirror neurons, which fire both when individuals perform
an action and when they observe the same action performed by a conspecific. Mirror
neurons are believed to be important for social learning, but it is not known
whether mirror-like neurons occur in similar networks in other social species,
such as rodents, or if they can be measured in such models using paradigms where
observers passively view a demonstrator. Therefore, we imaged Ca2+ responses in
PPC and secondary motor cortex (M2) while mice performed and observed pellet-reaching
and wheel-running tasks, and found that cell populations in both areas robustly
encoded several naturalistic behaviours. However, neural responses to the same
set of observed actions were absent, although we verified that observer mice were
attentive to performers and that PPC neurons responded reliably to visual cues.
Statistical modelling also indicated that executed actions outperformed observed
actions in predicting neural responses. These results raise the possibility that
sensorimotor action recognition in rodents could take place outside of the parieto-frontal
circuit, and underscore that detecting socially-driven neural coding depends critically
on the species and behavioural paradigm used.
article_number: '5559'
article_processing_charge: No
article_type: original
author:
- first_name: Tuce
full_name: Tombaz, Tuce
last_name: Tombaz
- first_name: Benjamin A.
full_name: Dunn, Benjamin A.
last_name: Dunn
- first_name: Karoline
full_name: Hovde, Karoline
last_name: Hovde
- first_name: Ryan J
full_name: Cubero, Ryan J
id: 850B2E12-9CD4-11E9-837F-E719E6697425
last_name: Cubero
orcid: 0000-0003-0002-1867
- first_name: Bartul
full_name: Mimica, Bartul
last_name: Mimica
- first_name: Pranav
full_name: Mamidanna, Pranav
last_name: Mamidanna
- first_name: Yasser
full_name: Roudi, Yasser
last_name: Roudi
- first_name: Jonathan R.
full_name: Whitlock, Jonathan R.
last_name: Whitlock
citation:
ama: Tombaz T, Dunn BA, Hovde K, et al. Action representation in the mouse parieto-frontal
network. Scientific reports. 2020;10(1). doi:10.1038/s41598-020-62089-6
apa: Tombaz, T., Dunn, B. A., Hovde, K., Cubero, R. J., Mimica, B., Mamidanna, P.,
… Whitlock, J. R. (2020). Action representation in the mouse parieto-frontal network.
Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-62089-6
chicago: Tombaz, Tuce, Benjamin A. Dunn, Karoline Hovde, Ryan J Cubero, Bartul Mimica,
Pranav Mamidanna, Yasser Roudi, and Jonathan R. Whitlock. “Action Representation
in the Mouse Parieto-Frontal Network.” Scientific Reports. Springer Nature,
2020. https://doi.org/10.1038/s41598-020-62089-6.
ieee: T. Tombaz et al., “Action representation in the mouse parieto-frontal
network,” Scientific reports, vol. 10, no. 1. Springer Nature, 2020.
ista: Tombaz T, Dunn BA, Hovde K, Cubero RJ, Mimica B, Mamidanna P, Roudi Y, Whitlock
JR. 2020. Action representation in the mouse parieto-frontal network. Scientific
reports. 10(1), 5559.
mla: Tombaz, Tuce, et al. “Action Representation in the Mouse Parieto-Frontal Network.”
Scientific Reports, vol. 10, no. 1, 5559, Springer Nature, 2020, doi:10.1038/s41598-020-62089-6.
short: T. Tombaz, B.A. Dunn, K. Hovde, R.J. Cubero, B. Mimica, P. Mamidanna, Y.
Roudi, J.R. Whitlock, Scientific Reports 10 (2020).
date_created: 2020-04-05T22:00:47Z
date_published: 2020-03-27T00:00:00Z
date_updated: 2023-08-18T10:25:13Z
day: '27'
ddc:
- '570'
department:
- _id: SaSi
doi: 10.1038/s41598-020-62089-6
external_id:
isi:
- '000560406800007'
file:
- access_level: open_access
checksum: e6cfaaaf7986532132934400038b824a
content_type: application/pdf
creator: dernst
date_created: 2020-04-06T10:44:23Z
date_updated: 2020-07-14T12:48:01Z
file_id: '7644'
file_name: 2020_ScientificReports_Tombaz.pdf
file_size: 2621249
relation: main_file
file_date_updated: 2020-07-14T12:48:01Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: Scientific reports
publication_identifier:
eissn:
- '20452322'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Action representation in the mouse parieto-frontal network
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: 10
year: '2020'
...
---
_id: '7634'
abstract:
- lang: eng
text: Assemblies of colloidal semiconductor nanocrystals (NCs) in the form of thin
solid films leverage the size-dependent quantum confinement properties and the
wet chemical methods vital for the development of the emerging solution-processable
electronics, photonics, and optoelectronics technologies. The ability to control
the charge carrier transport in the colloidal NC assemblies is fundamental for
altering their electronic and optical properties for the desired applications.
Here we demonstrate a strategy to render the solids of narrow-bandgap NC assemblies
exclusively electron-transporting by creating a type-II heterojunction via shelling.
Electronic transport of molecularly cross-linked PbTe@PbS core@shell NC assemblies
is measured using both a conventional solid gate transistor and an electric-double-layer
transistor, as well as compared with those of core-only PbTe NCs. In contrast
to the ambipolar characteristics demonstrated by many narrow-bandgap NCs, the
core@shell NCs exhibit exclusive n-type transport, i.e., drastically suppressed
contribution of holes to the overall transport. The PbS shell that forms a type-II
heterojunction assists the selective carrier transport by heavy doping of electrons
into the PbTe-core conduction level and simultaneously strongly localizes the
holes within the NC core valence level. This strongly enhanced n-type transport
makes these core@shell NCs suitable for applications where ambipolar characteristics
should be actively suppressed, in particular, for thermoelectric and electron-transporting
layers in photovoltaic devices.
acknowledgement: This work is partly supported by Grants-in-Aid for Scientific Research
by Young Scientist A (KAKENHI Wakate-A) No. JP17H04802, Grants-in-Aid for Scientific
Research No. JP19H05602 from the Japan Society for the Promotion of Science, and
RIKEN Incentive Research Grant (Shoreikadai) 2016. M.V.K. and M.I. acknowledge financial
support from the European Union (EU) via FP7 ERC Starting Grant 2012 (Project NANOSOLID,
GA No. 306733) and ETH Zurich via ETH career seed grant (SEED-18 16-2). Support
from Cambridge Display Technology, Ltd., and Sumitomo Chemical Company is also acknowledged.
We thank Mrs. T. Kikitsu and Dr. D. Hashizume (RIKEN-CEMS) for access to the transmission
electron microscope facility.
article_processing_charge: No
article_type: original
author:
- first_name: Retno
full_name: Miranti, Retno
last_name: Miranti
- first_name: Daiki
full_name: Shin, Daiki
last_name: Shin
- first_name: Ricky Dwi
full_name: Septianto, Ricky Dwi
last_name: Septianto
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Maksym V.
full_name: Kovalenko, Maksym V.
last_name: Kovalenko
- first_name: Nobuhiro
full_name: Matsushita, Nobuhiro
last_name: Matsushita
- first_name: Yoshihiro
full_name: Iwasa, Yoshihiro
last_name: Iwasa
- first_name: Satria Zulkarnaen
full_name: Bisri, Satria Zulkarnaen
last_name: Bisri
citation:
ama: Miranti R, Shin D, Septianto RD, et al. Exclusive electron transport in Core@Shell
PbTe@PbS colloidal semiconductor nanocrystal assemblies. ACS Nano. 2020;14(3):3242-3250.
doi:10.1021/acsnano.9b08687
apa: Miranti, R., Shin, D., Septianto, R. D., Ibáñez, M., Kovalenko, M. V., Matsushita,
N., … Bisri, S. Z. (2020). Exclusive electron transport in Core@Shell PbTe@PbS
colloidal semiconductor nanocrystal assemblies. ACS Nano. American Chemical
Society. https://doi.org/10.1021/acsnano.9b08687
chicago: Miranti, Retno, Daiki Shin, Ricky Dwi Septianto, Maria Ibáñez, Maksym V.
Kovalenko, Nobuhiro Matsushita, Yoshihiro Iwasa, and Satria Zulkarnaen Bisri.
“Exclusive Electron Transport in Core@Shell PbTe@PbS Colloidal Semiconductor Nanocrystal
Assemblies.” ACS Nano. American Chemical Society, 2020. https://doi.org/10.1021/acsnano.9b08687.
ieee: R. Miranti et al., “Exclusive electron transport in Core@Shell PbTe@PbS
colloidal semiconductor nanocrystal assemblies,” ACS Nano, vol. 14, no.
3. American Chemical Society, pp. 3242–3250, 2020.
ista: Miranti R, Shin D, Septianto RD, Ibáñez M, Kovalenko MV, Matsushita N, Iwasa
Y, Bisri SZ. 2020. Exclusive electron transport in Core@Shell PbTe@PbS colloidal
semiconductor nanocrystal assemblies. ACS Nano. 14(3), 3242–3250.
mla: Miranti, Retno, et al. “Exclusive Electron Transport in Core@Shell PbTe@PbS
Colloidal Semiconductor Nanocrystal Assemblies.” ACS Nano, vol. 14, no.
3, American Chemical Society, 2020, pp. 3242–50, doi:10.1021/acsnano.9b08687.
short: R. Miranti, D. Shin, R.D. Septianto, M. Ibáñez, M.V. Kovalenko, N. Matsushita,
Y. Iwasa, S.Z. Bisri, ACS Nano 14 (2020) 3242–3250.
date_created: 2020-04-05T22:00:48Z
date_published: 2020-03-24T00:00:00Z
date_updated: 2023-08-18T10:25:40Z
day: '24'
department:
- _id: MaIb
doi: 10.1021/acsnano.9b08687
external_id:
isi:
- '000526301400057'
pmid:
- '32073817'
intvolume: ' 14'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 3242-3250
pmid: 1
publication: ACS Nano
publication_identifier:
eissn:
- 1936-086X
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Exclusive electron transport in Core@Shell PbTe@PbS colloidal semiconductor
nanocrystal assemblies
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 14
year: '2020'
...
---
_id: '7635'
abstract:
- lang: eng
text: Concurrent programming can be notoriously complex and error-prone. Programming
bugs can arise from a variety of sources, such as operation re-reordering, or
incomplete understanding of the memory model. A variety of formal and model checking
methods have been developed to address this fundamental difficulty. While technically
interesting, existing academic methods are still hard to apply to the large codebases
typical of industrial deployments, which limits their practical impact.
article_processing_charge: No
author:
- first_name: Nikita
full_name: Koval, Nikita
id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87
last_name: Koval
- first_name: Mariia
full_name: Sokolova, Mariia
id: 26217AE4-77FF-11EA-8101-AD24D49E41F4
last_name: Sokolova
- first_name: Alexander
full_name: Fedorov, Alexander
last_name: Fedorov
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Dmitry
full_name: Tsitelov, Dmitry
last_name: Tsitelov
citation:
ama: 'Koval N, Sokolova M, Fedorov A, Alistarh D-A, Tsitelov D. Testing concurrency
on the JVM with Lincheck. In: Proceedings of the ACM SIGPLAN Symposium on Principles
and Practice of Parallel Programming, PPOPP. Association for Computing Machinery;
2020:423-424. doi:10.1145/3332466.3374503'
apa: 'Koval, N., Sokolova, M., Fedorov, A., Alistarh, D.-A., & Tsitelov, D.
(2020). Testing concurrency on the JVM with Lincheck. In Proceedings of the
ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP
(pp. 423–424). San Diego, CA, United States: Association for Computing Machinery.
https://doi.org/10.1145/3332466.3374503'
chicago: Koval, Nikita, Mariia Sokolova, Alexander Fedorov, Dan-Adrian Alistarh,
and Dmitry Tsitelov. “Testing Concurrency on the JVM with Lincheck.” In Proceedings
of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming,
PPOPP, 423–24. Association for Computing Machinery, 2020. https://doi.org/10.1145/3332466.3374503.
ieee: N. Koval, M. Sokolova, A. Fedorov, D.-A. Alistarh, and D. Tsitelov, “Testing
concurrency on the JVM with Lincheck,” in Proceedings of the ACM SIGPLAN Symposium
on Principles and Practice of Parallel Programming, PPOPP, San Diego, CA,
United States, 2020, pp. 423–424.
ista: 'Koval N, Sokolova M, Fedorov A, Alistarh D-A, Tsitelov D. 2020. Testing concurrency
on the JVM with Lincheck. Proceedings of the ACM SIGPLAN Symposium on Principles
and Practice of Parallel Programming, PPOPP. PPOPP: Principles and Practice of
Parallel Programming, 423–424.'
mla: Koval, Nikita, et al. “Testing Concurrency on the JVM with Lincheck.” Proceedings
of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming,
PPOPP, Association for Computing Machinery, 2020, pp. 423–24, doi:10.1145/3332466.3374503.
short: N. Koval, M. Sokolova, A. Fedorov, D.-A. Alistarh, D. Tsitelov, in:, Proceedings
of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming,
PPOPP, Association for Computing Machinery, 2020, pp. 423–424.
conference:
end_date: 2020-02-26
location: San Diego, CA, United States
name: 'PPOPP: Principles and Practice of Parallel Programming'
start_date: 2020-02-22
date_created: 2020-04-05T22:00:48Z
date_published: 2020-02-19T00:00:00Z
date_updated: 2024-02-28T12:53:46Z
day: '19'
department:
- _id: DaAl
doi: 10.1145/3332466.3374503
language:
- iso: eng
month: '02'
oa_version: None
page: 423-424
publication: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of
Parallel Programming, PPOPP
publication_identifier:
isbn:
- '9781450368186'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Testing concurrency on the JVM with Lincheck
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '7636'
abstract:
- lang: eng
text: "Balanced search trees typically use key comparisons to guide their operations,
and achieve logarithmic running time. By relying on numerical properties of the
keys, interpolation search achieves lower search complexity and better performance.
Although interpolation-based data structures were investigated in the past, their
non-blocking concurrent variants have received very little attention so far.\r\nIn
this paper, we propose the first non-blocking implementation of the classic interpolation
search tree (IST) data structure. For arbitrary key distributions, the data structure
ensures worst-case O(log n + p) amortized time for search, insertion and deletion
traversals. When the input key distributions are smooth, lookups run in expected
O(log log n + p) time, and insertion and deletion run in expected amortized O(log
log n + p) time, where p is a bound on the number of threads. To improve the scalability
of concurrent insertion and deletion, we propose a novel parallel rebuilding technique,
which should be of independent interest.\r\nWe evaluate whether the theoretical
improvements translate to practice by implementing the concurrent interpolation
search tree, and benchmarking it on uniform and nonuniform key distributions,
for dataset sizes in the millions to billions of keys. Relative to the state-of-the-art
concurrent data structures, the concurrent interpolation search tree achieves
performance improvements of up to 15% under high update rates, and of up to 50%
under moderate update rates. Further, ISTs exhibit up to 2X less cache-misses,
and consume 1.2 -- 2.6X less memory compared to the next best alternative on typical
dataset sizes. We find that the results are surprisingly robust to distributional
skew, which suggests that our data structure can be a promising alternative to
classic concurrent search structures."
acknowledgement: "This project has received funding from the European Research Council
(ERC) under the European Union Horizon 2020 research and innovation program, grant
agreement No 805223, ERC Starting Grant ScaleML. We acknowledge the support of the
Natural Sciences and\r\nEngineering Research Council of Canada (NSERC). "
article_processing_charge: No
author:
- first_name: Trevor A
full_name: Brown, Trevor A
id: 3569F0A0-F248-11E8-B48F-1D18A9856A87
last_name: Brown
- first_name: Aleksandar
full_name: Prokopec, Aleksandar
last_name: Prokopec
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Brown TA, Prokopec A, Alistarh D-A. Non-blocking interpolation search trees
with doubly-logarithmic running time. In: Proceedings of the ACM SIGPLAN Symposium
on Principles and Practice of Parallel Programming. Association for Computing
Machinery; 2020:276-291. doi:10.1145/3332466.3374542'
apa: 'Brown, T. A., Prokopec, A., & Alistarh, D.-A. (2020). Non-blocking interpolation
search trees with doubly-logarithmic running time. In Proceedings of the ACM
SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp.
276–291). San Diego, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3332466.3374542'
chicago: Brown, Trevor A, Aleksandar Prokopec, and Dan-Adrian Alistarh. “Non-Blocking
Interpolation Search Trees with Doubly-Logarithmic Running Time.” In Proceedings
of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming,
276–91. Association for Computing Machinery, 2020. https://doi.org/10.1145/3332466.3374542.
ieee: T. A. Brown, A. Prokopec, and D.-A. Alistarh, “Non-blocking interpolation
search trees with doubly-logarithmic running time,” in Proceedings of the ACM
SIGPLAN Symposium on Principles and Practice of Parallel Programming, San
Diego, CA, United States, 2020, pp. 276–291.
ista: 'Brown TA, Prokopec A, Alistarh D-A. 2020. Non-blocking interpolation search
trees with doubly-logarithmic running time. Proceedings of the ACM SIGPLAN Symposium
on Principles and Practice of Parallel Programming. PPOPP: Principles and Practice
of Parallel Programming, 276–291.'
mla: Brown, Trevor A., et al. “Non-Blocking Interpolation Search Trees with Doubly-Logarithmic
Running Time.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice
of Parallel Programming, Association for Computing Machinery, 2020, pp. 276–91,
doi:10.1145/3332466.3374542.
short: T.A. Brown, A. Prokopec, D.-A. Alistarh, in:, Proceedings of the ACM SIGPLAN
Symposium on Principles and Practice of Parallel Programming, Association for
Computing Machinery, 2020, pp. 276–291.
conference:
end_date: 2020-02-26
location: San Diego, CA, United States
name: 'PPOPP: Principles and Practice of Parallel Programming'
start_date: 2020-02-22
date_created: 2020-04-05T22:00:49Z
date_published: 2020-02-19T00:00:00Z
date_updated: 2024-02-28T12:55:14Z
day: '19'
department:
- _id: DaAl
doi: 10.1145/3332466.3374542
ec_funded: 1
external_id:
isi:
- '000564476500020'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1145/3332466.3374542
month: '02'
oa: 1
oa_version: Published Version
page: 276-291
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of
Parallel Programming
publication_identifier:
isbn:
- '9781450368186'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Non-blocking interpolation search trees with doubly-logarithmic running time
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '7637'
abstract:
- lang: eng
text: The evolution of finitely many particles obeying Langevin dynamics is described
by Dean–Kawasaki equations, a class of stochastic equations featuring a non-Lipschitz
multiplicative noise in divergence form. We derive a regularised Dean–Kawasaki
model based on second order Langevin dynamics by analysing a system of particles
interacting via a pairwise potential. Key tools of our analysis are the propagation
of chaos and Simon's compactness criterion. The model we obtain is a small-noise
stochastic perturbation of the undamped McKean–Vlasov equation. We also provide
a high-probability result for existence and uniqueness for our model.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Federico
full_name: Cornalba, Federico
id: 2CEB641C-A400-11E9-A717-D712E6697425
last_name: Cornalba
orcid: 0000-0002-6269-5149
- first_name: Tony
full_name: Shardlow, Tony
last_name: Shardlow
- first_name: Johannes
full_name: Zimmer, Johannes
last_name: Zimmer
citation:
ama: Cornalba F, Shardlow T, Zimmer J. From weakly interacting particles to a regularised
Dean-Kawasaki model. Nonlinearity. 2020;33(2):864-891. doi:10.1088/1361-6544/ab5174
apa: Cornalba, F., Shardlow, T., & Zimmer, J. (2020). From weakly interacting
particles to a regularised Dean-Kawasaki model. Nonlinearity. IOP Publishing.
https://doi.org/10.1088/1361-6544/ab5174
chicago: Cornalba, Federico, Tony Shardlow, and Johannes Zimmer. “From Weakly Interacting
Particles to a Regularised Dean-Kawasaki Model.” Nonlinearity. IOP Publishing,
2020. https://doi.org/10.1088/1361-6544/ab5174.
ieee: F. Cornalba, T. Shardlow, and J. Zimmer, “From weakly interacting particles
to a regularised Dean-Kawasaki model,” Nonlinearity, vol. 33, no. 2. IOP
Publishing, pp. 864–891, 2020.
ista: Cornalba F, Shardlow T, Zimmer J. 2020. From weakly interacting particles
to a regularised Dean-Kawasaki model. Nonlinearity. 33(2), 864–891.
mla: Cornalba, Federico, et al. “From Weakly Interacting Particles to a Regularised
Dean-Kawasaki Model.” Nonlinearity, vol. 33, no. 2, IOP Publishing, 2020,
pp. 864–91, doi:10.1088/1361-6544/ab5174.
short: F. Cornalba, T. Shardlow, J. Zimmer, Nonlinearity 33 (2020) 864–891.
date_created: 2020-04-05T22:00:49Z
date_published: 2020-01-10T00:00:00Z
date_updated: 2023-08-18T10:26:07Z
day: '10'
department:
- _id: JuFi
doi: 10.1088/1361-6544/ab5174
external_id:
arxiv:
- '1811.06448'
isi:
- '000508175400001'
intvolume: ' 33'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1811.06448
month: '01'
oa: 1
oa_version: Preprint
page: 864-891
publication: Nonlinearity
publication_identifier:
eissn:
- '13616544'
issn:
- '09517715'
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: From weakly interacting particles to a regularised Dean-Kawasaki model
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 33
year: '2020'
...
---
_id: '7638'
abstract:
- lang: eng
text: Following on from our recent work, we investigate a stochastic approach to
non-equilibrium quantum spin systems. We show how the method can be applied to
a variety of physical observables and for different initial conditions. We provide
exact formulae of broad applicability for the time-dependence of expectation values
and correlation functions following a quantum quench in terms of averages over
classical stochastic processes. We further explore the behavior of the classical
stochastic variables in the presence of dynamical quantum phase transitions, including
results for their distributions and correlation functions. We provide details
on the numerical solution of the associated stochastic differential equations,
and examine the growth of fluctuations in the classical description. We discuss
the strengths and limitations of the current implementation of the stochastic
approach and the potential for further development.
article_number: '013106'
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: B.
full_name: Doyon, B.
last_name: Doyon
- first_name: M. J.
full_name: Bhaseen, M. J.
last_name: Bhaseen
citation:
ama: 'De Nicola S, Doyon B, Bhaseen MJ. Non-equilibrium quantum spin dynamics from
classical stochastic processes. Journal of Statistical Mechanics: Theory and
Experiment. 2020;2020(1). doi:10.1088/1742-5468/ab6093'
apa: 'De Nicola, S., Doyon, B., & Bhaseen, M. J. (2020). Non-equilibrium quantum
spin dynamics from classical stochastic processes. Journal of Statistical Mechanics:
Theory and Experiment. IOP Publishing. https://doi.org/10.1088/1742-5468/ab6093'
chicago: 'De Nicola, Stefano, B. Doyon, and M. J. Bhaseen. “Non-Equilibrium Quantum
Spin Dynamics from Classical Stochastic Processes.” Journal of Statistical
Mechanics: Theory and Experiment. IOP Publishing, 2020. https://doi.org/10.1088/1742-5468/ab6093.'
ieee: 'S. De Nicola, B. Doyon, and M. J. Bhaseen, “Non-equilibrium quantum spin
dynamics from classical stochastic processes,” Journal of Statistical Mechanics:
Theory and Experiment, vol. 2020, no. 1. IOP Publishing, 2020.'
ista: 'De Nicola S, Doyon B, Bhaseen MJ. 2020. Non-equilibrium quantum spin dynamics
from classical stochastic processes. Journal of Statistical Mechanics: Theory
and Experiment. 2020(1), 013106.'
mla: 'De Nicola, Stefano, et al. “Non-Equilibrium Quantum Spin Dynamics from Classical
Stochastic Processes.” Journal of Statistical Mechanics: Theory and Experiment,
vol. 2020, no. 1, 013106, IOP Publishing, 2020, doi:10.1088/1742-5468/ab6093.'
short: 'S. De Nicola, B. Doyon, M.J. Bhaseen, Journal of Statistical Mechanics:
Theory and Experiment 2020 (2020).'
date_created: 2020-04-05T22:00:50Z
date_published: 2020-01-22T00:00:00Z
date_updated: 2023-08-18T10:27:15Z
day: '22'
ddc:
- '530'
department:
- _id: MaSe
doi: 10.1088/1742-5468/ab6093
ec_funded: 1
external_id:
arxiv:
- '1909.13142'
isi:
- '000520187500001'
file:
- access_level: open_access
checksum: 4030e683c15d30b7b4794ec7dc1b6537
content_type: application/pdf
creator: dernst
date_created: 2020-04-06T13:15:49Z
date_updated: 2020-07-14T12:48:01Z
file_id: '7648'
file_name: 2020_JournStatisticalMech_DeNicola.pdf
file_size: 3159026
relation: main_file
file_date_updated: 2020-07-14T12:48:01Z
has_accepted_license: '1'
intvolume: ' 2020'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: 'Journal of Statistical Mechanics: Theory and Experiment'
publication_identifier:
eissn:
- '17425468'
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Non-equilibrium quantum spin dynamics from classical stochastic processes
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 2020
year: '2020'
...
---
_id: '7643'
acknowledgement: 'This work was supported by the European Research Council under the
European Union’s Horizon 2020 research and innovation Programme (ERC grant agreement
number 742985), and the Austrian Science Fund (FWF, grant number I 3630-B25) to
JF. HH is supported by the China Scholarship Council (CSC scholarship). '
article_processing_charge: No
article_type: letter_note
author:
- first_name: Huibin
full_name: Han, Huibin
id: 31435098-F248-11E8-B48F-1D18A9856A87
last_name: Han
- first_name: Hana
full_name: Rakusova, Hana
id: 4CAAA450-78D2-11EA-8E57-B40A396E08BA
last_name: Rakusova
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Yuzhou
full_name: Zhang, Yuzhou
id: 3B6137F2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0003-2627-6956
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Han H, Rakusova H, Verstraeten I, Zhang Y, Friml J. SCF TIR1/AFB auxin signaling
for bending termination during shoot gravitropism. Plant Physiology. 2020;183(5):37-40.
doi:10.1104/pp.20.00212
apa: Han, H., Rakusova, H., Verstraeten, I., Zhang, Y., & Friml, J. (2020).
SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism.
Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.20.00212
chicago: Han, Huibin, Hana Rakusova, Inge Verstraeten, Yuzhou Zhang, and Jiří Friml.
“SCF TIR1/AFB Auxin Signaling for Bending Termination during Shoot Gravitropism.”
Plant Physiology. American Society of Plant Biologists, 2020. https://doi.org/10.1104/pp.20.00212.
ieee: H. Han, H. Rakusova, I. Verstraeten, Y. Zhang, and J. Friml, “SCF TIR1/AFB
auxin signaling for bending termination during shoot gravitropism,” Plant Physiology,
vol. 183, no. 5. American Society of Plant Biologists, pp. 37–40, 2020.
ista: Han H, Rakusova H, Verstraeten I, Zhang Y, Friml J. 2020. SCF TIR1/AFB auxin
signaling for bending termination during shoot gravitropism. Plant Physiology.
183(5), 37–40.
mla: Han, Huibin, et al. “SCF TIR1/AFB Auxin Signaling for Bending Termination during
Shoot Gravitropism.” Plant Physiology, vol. 183, no. 5, American Society
of Plant Biologists, 2020, pp. 37–40, doi:10.1104/pp.20.00212.
short: H. Han, H. Rakusova, I. Verstraeten, Y. Zhang, J. Friml, Plant Physiology
183 (2020) 37–40.
date_created: 2020-04-06T10:06:40Z
date_published: 2020-05-08T00:00:00Z
date_updated: 2023-09-07T13:13:04Z
day: '08'
department:
- _id: JiFr
doi: 10.1104/pp.20.00212
ec_funded: 1
external_id:
isi:
- '000536641800018'
pmid:
- '32107280'
intvolume: ' 183'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1104/pp.20.00212
month: '05'
oa: 1
oa_version: Published Version
page: 37-40
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: Plant Physiology
publication_identifier:
eissn:
- 1532-2548
issn:
- 0032-0889
publication_status: published
publisher: American Society of Plant Biologists
quality_controlled: '1'
related_material:
record:
- id: '8589'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: SCF TIR1/AFB auxin signaling for bending termination during shoot gravitropism
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 183
year: '2020'
...
---
_id: '7646'
abstract:
- lang: eng
text: In plant cells, environmental stressors promote changes in connectivity between
the cortical ER and the PM. Although this process is tightly regulated in space
and time, the molecular signals and structural components mediating these changes
in inter-organelle communication are only starting to be characterized. In this
report, we confirm the presence of a putative tethering complex containing the
synaptotagmins 1 and 5 (SYT1 and SYT5) and the Ca2+ and lipid binding protein
1 (CLB1/SYT7). This complex is enriched at ER-PM contact sites (EPCS), have slow
responses to changes in extracellular Ca2+, and display severe cytoskeleton-dependent
rearrangements in response to the trivalent lanthanum (La3+) and gadolinium (Gd3+)
rare earth elements (REEs). Although REEs are generally used as non-selective
cation channel blockers at the PM, here we show that the slow internalization
of REEs into the cytosol underlies the activation of the Ca2+/Calmodulin intracellular
signaling, the accumulation of phosphatidylinositol-4-phosphate (PI4P) at the
PM, and the cytoskeleton-dependent rearrangement of the SYT1/SYT5 EPCS complexes.
We propose that the observed EPCS rearrangements act as a slow adaptive response
to sustained stress conditions, and that this process involves the accumulation
of stress-specific phosphoinositides species at the PM.
article_processing_charge: No
article_type: original
author:
- first_name: E
full_name: Lee, E
last_name: Lee
- first_name: B
full_name: Vila Nova Santana, B
last_name: Vila Nova Santana
- first_name: E
full_name: Samuels, E
last_name: Samuels
- first_name: F
full_name: Benitez-Fuente, F
last_name: Benitez-Fuente
- first_name: E
full_name: Corsi, E
last_name: Corsi
- first_name: MA
full_name: Botella, MA
last_name: Botella
- first_name: J
full_name: Perez-Sancho, J
last_name: Perez-Sancho
- first_name: S
full_name: Vanneste, S
last_name: Vanneste
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: A
full_name: Macho, A
last_name: Macho
- first_name: A
full_name: Alves Azevedo, A
last_name: Alves Azevedo
- first_name: A
full_name: Rosado, A
last_name: Rosado
citation:
ama: Lee E, Vila Nova Santana B, Samuels E, et al. Rare earth elements induce cytoskeleton-dependent
and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in
Arabidopsis. Journal of Experimental Botany. 2020;71(14):3986–3998. doi:10.1093/jxb/eraa138
apa: Lee, E., Vila Nova Santana, B., Samuels, E., Benitez-Fuente, F., Corsi, E.,
Botella, M., … Rosado, A. (2020). Rare earth elements induce cytoskeleton-dependent
and PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in
Arabidopsis. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/eraa138
chicago: Lee, E, B Vila Nova Santana, E Samuels, F Benitez-Fuente, E Corsi, MA Botella,
J Perez-Sancho, et al. “Rare Earth Elements Induce Cytoskeleton-Dependent and
PI4P-Associated Rearrangement of SYT1/SYT5 ER-PM Contact Site Complexes in Arabidopsis.”
Journal of Experimental Botany. Oxford University Press, 2020. https://doi.org/10.1093/jxb/eraa138.
ieee: E. Lee et al., “Rare earth elements induce cytoskeleton-dependent and
PI4P-associated rearrangement of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis,”
Journal of Experimental Botany, vol. 71, no. 14. Oxford University Press,
pp. 3986–3998, 2020.
ista: Lee E, Vila Nova Santana B, Samuels E, Benitez-Fuente F, Corsi E, Botella
M, Perez-Sancho J, Vanneste S, Friml J, Macho A, Alves Azevedo A, Rosado A. 2020.
Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement
of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis. Journal of Experimental
Botany. 71(14), 3986–3998.
mla: Lee, E., et al. “Rare Earth Elements Induce Cytoskeleton-Dependent and PI4P-Associated
Rearrangement of SYT1/SYT5 ER-PM Contact Site Complexes in Arabidopsis.” Journal
of Experimental Botany, vol. 71, no. 14, Oxford University Press, 2020, pp.
3986–3998, doi:10.1093/jxb/eraa138.
short: E. Lee, B. Vila Nova Santana, E. Samuels, F. Benitez-Fuente, E. Corsi, M.
Botella, J. Perez-Sancho, S. Vanneste, J. Friml, A. Macho, A. Alves Azevedo, A.
Rosado, Journal of Experimental Botany 71 (2020) 3986–3998.
date_created: 2020-04-06T10:57:08Z
date_published: 2020-07-06T00:00:00Z
date_updated: 2023-08-18T10:27:52Z
day: '06'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1093/jxb/eraa138
external_id:
isi:
- '000553125400007'
pmid:
- '32179893'
file:
- access_level: open_access
checksum: b06aaaa93dc41896da805fe4b75cf3a1
content_type: application/pdf
creator: dernst
date_created: 2020-10-06T07:41:35Z
date_updated: 2020-10-06T07:41:35Z
file_id: '8613'
file_name: 2020_JourExperimBotany_Lee.pdf
file_size: 1916031
relation: main_file
success: 1
file_date_updated: 2020-10-06T07:41:35Z
has_accepted_license: '1'
intvolume: ' 71'
isi: 1
issue: '14'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 3986–3998
pmid: 1
publication: Journal of Experimental Botany
publication_identifier:
eissn:
- 1460-2431
issn:
- 0022-0957
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: Rare earth elements induce cytoskeleton-dependent and PI4P-associated rearrangement
of SYT1/SYT5 ER-PM contact site complexes in Arabidopsis
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: 71
year: '2020'
...
---
_id: '7650'
abstract:
- lang: eng
text: We consider a dilute, homogeneous Bose gas at positive temperature. The system
is investigated in the Gross–Pitaevskii limit, where the scattering length a is
so small that the interaction energy is of the same order of magnitude as the
spectral gap of the Laplacian, and for temperatures that are comparable to the
critical temperature of the ideal gas. We show that the difference between the
specific free energy of the interacting system and the one of the ideal gas is
to leading order given by 4πa(2ϱ2−ϱ20). Here ϱ denotes the density of the system
and ϱ0 is the expected condensate density of the ideal gas. Additionally, we show
that the one-particle density matrix of any approximate minimizer of the Gibbs
free energy functional is to leading order given by the one of the ideal gas.
This in particular proves Bose–Einstein condensation with critical temperature
given by the one of the ideal gas to leading order. One key ingredient of our
proof is a novel use of the Gibbs variational principle that goes hand in hand
with the c-number substitution.
acknowledgement: Open access funding provided by Institute of Science and Technology
(IST Austria). It is a pleasure to thank Jakob Yngvason for helpful discussions.
Financial support by the European Research Council (ERC) under the European Union’sHorizon
2020 research and innovation programme (Grant Agreement No. 694227) is gratefully
acknowledged. A. D. acknowledges funding from the European Union’s Horizon 2020
research and innovation programme under the Marie Sklodowska-Curie Grant Agreement
No. 836146.
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Andreas
full_name: Deuchert, Andreas
id: 4DA65CD0-F248-11E8-B48F-1D18A9856A87
last_name: Deuchert
orcid: 0000-0003-3146-6746
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Deuchert A, Seiringer R. Gross-Pitaevskii limit of a homogeneous Bose gas at
positive temperature. Archive for Rational Mechanics and Analysis. 2020;236(6):1217-1271.
doi:10.1007/s00205-020-01489-4
apa: Deuchert, A., & Seiringer, R. (2020). Gross-Pitaevskii limit of a homogeneous
Bose gas at positive temperature. Archive for Rational Mechanics and Analysis.
Springer Nature. https://doi.org/10.1007/s00205-020-01489-4
chicago: Deuchert, Andreas, and Robert Seiringer. “Gross-Pitaevskii Limit of a Homogeneous
Bose Gas at Positive Temperature.” Archive for Rational Mechanics and Analysis.
Springer Nature, 2020. https://doi.org/10.1007/s00205-020-01489-4.
ieee: A. Deuchert and R. Seiringer, “Gross-Pitaevskii limit of a homogeneous Bose
gas at positive temperature,” Archive for Rational Mechanics and Analysis,
vol. 236, no. 6. Springer Nature, pp. 1217–1271, 2020.
ista: Deuchert A, Seiringer R. 2020. Gross-Pitaevskii limit of a homogeneous Bose
gas at positive temperature. Archive for Rational Mechanics and Analysis. 236(6),
1217–1271.
mla: Deuchert, Andreas, and Robert Seiringer. “Gross-Pitaevskii Limit of a Homogeneous
Bose Gas at Positive Temperature.” Archive for Rational Mechanics and Analysis,
vol. 236, no. 6, Springer Nature, 2020, pp. 1217–71, doi:10.1007/s00205-020-01489-4.
short: A. Deuchert, R. Seiringer, Archive for Rational Mechanics and Analysis 236
(2020) 1217–1271.
date_created: 2020-04-08T15:18:03Z
date_published: 2020-03-09T00:00:00Z
date_updated: 2023-09-05T14:18:49Z
day: '09'
ddc:
- '510'
department:
- _id: RoSe
doi: 10.1007/s00205-020-01489-4
ec_funded: 1
external_id:
arxiv:
- '1901.11363'
isi:
- '000519415000001'
file:
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content_type: application/pdf
creator: dernst
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date_updated: 2020-11-20T13:17:42Z
file_id: '8785'
file_name: 2020_ArchRatMechanicsAnalysis_Deuchert.pdf
file_size: 704633
relation: main_file
success: 1
file_date_updated: 2020-11-20T13:17:42Z
has_accepted_license: '1'
intvolume: ' 236'
isi: 1
issue: '6'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 1217-1271
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Archive for Rational Mechanics and Analysis
publication_identifier:
eissn:
- 1432-0673
issn:
- 0003-9527
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Gross-Pitaevskii limit of a homogeneous Bose gas at positive temperature
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 236
year: '2020'
...
---
_id: '7651'
abstract:
- lang: eng
text: The growth of snail shells can be described by simple mathematical rules.
Variation in a few parameters can explain much of the diversity of shell shapes
seen in nature. However, empirical studies of gastropod shell shape variation
typically use geometric morphometric approaches, which do not capture this growth
pattern. We have developed a way to infer a set of developmentally descriptive
shape parameters based on three-dimensional logarithmic helicospiral growth and
using landmarks from two-dimensional shell images as input. We demonstrate the
utility of this approach, and compare it to the geometric morphometric approach,
using a large set of Littorina saxatilis shells in which locally adapted populations
differ in shape. Our method can be modified easily to make it applicable to a
wide range of shell forms, which would allow for investigations of the similarities
and differences between and within many different species of gastropods.
article_number: '20190721'
article_processing_charge: No
article_type: original
author:
- first_name: J.
full_name: Larsson, J.
last_name: Larsson
- 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: S.
full_name: Bengmark, S.
last_name: Bengmark
- first_name: T.
full_name: Lundh, T.
last_name: Lundh
- first_name: R. K.
full_name: Butlin, R. K.
last_name: Butlin
citation:
ama: Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. A developmentally descriptive
method for quantifying shape in gastropod shells. Journal of The Royal Society
Interface. 2020;17(163). doi:10.1098/rsif.2019.0721
apa: Larsson, J., Westram, A. M., Bengmark, S., Lundh, T., & Butlin, R. K. (2020).
A developmentally descriptive method for quantifying shape in gastropod shells.
Journal of The Royal Society Interface. The Royal Society. https://doi.org/10.1098/rsif.2019.0721
chicago: Larsson, J., Anja M Westram, S. Bengmark, T. Lundh, and R. K. Butlin. “A
Developmentally Descriptive Method for Quantifying Shape in Gastropod Shells.”
Journal of The Royal Society Interface. The Royal Society, 2020. https://doi.org/10.1098/rsif.2019.0721.
ieee: J. Larsson, A. M. Westram, S. Bengmark, T. Lundh, and R. K. Butlin, “A developmentally
descriptive method for quantifying shape in gastropod shells,” Journal of The
Royal Society Interface, vol. 17, no. 163. The Royal Society, 2020.
ista: Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. 2020. A developmentally
descriptive method for quantifying shape in gastropod shells. Journal of The Royal
Society Interface. 17(163), 20190721.
mla: Larsson, J., et al. “A Developmentally Descriptive Method for Quantifying Shape
in Gastropod Shells.” Journal of The Royal Society Interface, vol. 17,
no. 163, 20190721, The Royal Society, 2020, doi:10.1098/rsif.2019.0721.
short: J. Larsson, A.M. Westram, S. Bengmark, T. Lundh, R.K. Butlin, Journal of
The Royal Society Interface 17 (2020).
date_created: 2020-04-08T15:19:17Z
date_published: 2020-02-01T00:00:00Z
date_updated: 2021-01-12T08:14:41Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1098/rsif.2019.0721
file:
- access_level: open_access
checksum: 4eb102304402f5c56432516b84df86d6
content_type: application/pdf
creator: dernst
date_created: 2020-04-14T12:31:16Z
date_updated: 2020-07-14T12:48:01Z
file_id: '7660'
file_name: 2020_JournRoyalSociety_Larsson.pdf
file_size: 1556190
relation: main_file
file_date_updated: 2020-07-14T12:48:01Z
has_accepted_license: '1'
intvolume: ' 17'
issue: '163'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: Journal of The Royal Society Interface
publication_identifier:
eissn:
- 1742-5662
issn:
- 1742-5689
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
scopus_import: 1
status: public
title: A developmentally descriptive method for quantifying shape in gastropod shells
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: 17
year: '2020'
...
---
_id: '7652'
abstract:
- lang: eng
text: Organisms cope with change by taking advantage of transcriptional regulators.
However, when faced with rare environments, the evolution of transcriptional regulators
and their promoters may be too slow. Here, we investigate whether the intrinsic
instability of gene duplication and amplification provides a generic alternative
to canonical gene regulation. Using real-time monitoring of gene-copy-number mutations
in Escherichia coli, we show that gene duplications and amplifications enable
adaptation to fluctuating environments by rapidly generating copy-number and,
therefore, expression-level polymorphisms. This amplification-mediated gene expression
tuning (AMGET) occurs on timescales that are similar to canonical gene regulation
and can respond to rapid environmental changes. Mathematical modelling shows that
amplifications also tune gene expression in stochastic environments in which transcription-factor-based
schemes are hard to evolve or maintain. The fleeting nature of gene amplifications
gives rise to a generic population-level mechanism that relies on genetic heterogeneity
to rapidly tune the expression of any gene, without leaving any genomic signature.
acknowledgement: We thank L. Hurst, N. Barton, M. Pleska, M. Steinrück, B. Kavcic
and A. Staron for input on the manuscript, and To. Bergmiller and R. Chait for help
with microfluidics experiments. I.T. is a recipient the OMV fellowship. R.G. is
a recipient of a DOC (Doctoral Fellowship Programme of the Austrian Academy of Sciences)
Fellowship of the Austrian Academy of Sciences.
article_processing_charge: No
article_type: original
author:
- first_name: Isabella
full_name: Tomanek, Isabella
id: 3981F020-F248-11E8-B48F-1D18A9856A87
last_name: Tomanek
orcid: 0000-0001-6197-363X
- first_name: Rok
full_name: Grah, Rok
id: 483E70DE-F248-11E8-B48F-1D18A9856A87
last_name: Grah
orcid: 0000-0003-2539-3560
- first_name: M.
full_name: Lagator, M.
last_name: Lagator
- first_name: A. M. C.
full_name: Andersson, A. M. C.
last_name: Andersson
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Tomanek I, Grah R, Lagator M, et al. Gene amplification as a form of population-level
gene expression regulation. Nature Ecology & Evolution. 2020;4(4):612-625.
doi:10.1038/s41559-020-1132-7
apa: Tomanek, I., Grah, R., Lagator, M., Andersson, A. M. C., Bollback, J. P., Tkačik,
G., & Guet, C. C. (2020). Gene amplification as a form of population-level
gene expression regulation. Nature Ecology & Evolution. Springer Nature.
https://doi.org/10.1038/s41559-020-1132-7
chicago: Tomanek, Isabella, Rok Grah, M. Lagator, A. M. C. Andersson, Jonathan P
Bollback, Gašper Tkačik, and Calin C Guet. “Gene Amplification as a Form of Population-Level
Gene Expression Regulation.” Nature Ecology & Evolution. Springer Nature,
2020. https://doi.org/10.1038/s41559-020-1132-7.
ieee: I. Tomanek et al., “Gene amplification as a form of population-level
gene expression regulation,” Nature Ecology & Evolution, vol. 4, no.
4. Springer Nature, pp. 612–625, 2020.
ista: Tomanek I, Grah R, Lagator M, Andersson AMC, Bollback JP, Tkačik G, Guet CC.
2020. Gene amplification as a form of population-level gene expression regulation.
Nature Ecology & Evolution. 4(4), 612–625.
mla: Tomanek, Isabella, et al. “Gene Amplification as a Form of Population-Level
Gene Expression Regulation.” Nature Ecology & Evolution, vol. 4, no.
4, Springer Nature, 2020, pp. 612–25, doi:10.1038/s41559-020-1132-7.
short: I. Tomanek, R. Grah, M. Lagator, A.M.C. Andersson, J.P. Bollback, G. Tkačik,
C.C. Guet, Nature Ecology & Evolution 4 (2020) 612–625.
date_created: 2020-04-08T15:20:53Z
date_published: 2020-04-01T00:00:00Z
date_updated: 2024-03-25T23:30:20Z
day: '01'
ddc:
- '570'
department:
- _id: GaTk
- _id: CaGu
doi: 10.1038/s41559-020-1132-7
external_id:
isi:
- '000519008300005'
file:
- access_level: open_access
checksum: ef3bbf42023e30b2c24a6278025d2040
content_type: application/pdf
creator: dernst
date_created: 2020-10-09T09:56:01Z
date_updated: 2020-10-09T09:56:01Z
file_id: '8640'
file_name: 2020_NatureEcolEvo_Tomanek.pdf
file_size: 745242
relation: main_file
success: 1
file_date_updated: 2020-10-09T09:56:01Z
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isi: 1
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language:
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month: '04'
oa: 1
oa_version: Submitted Version
page: 612-625
project:
- _id: 267C84F4-B435-11E9-9278-68D0E5697425
name: Biophysically realistic genotype-phenotype maps for regulatory networks
publication: Nature Ecology & Evolution
publication_identifier:
issn:
- 2397-334X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/how-to-thrive-without-gene-regulation/
record:
- id: '8155'
relation: dissertation_contains
status: public
- id: '7383'
relation: research_data
status: public
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relation: research_data
status: public
- id: '8653'
relation: used_in_publication
status: public
scopus_import: '1'
status: public
title: Gene amplification as a form of population-level gene expression regulation
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 4
year: '2020'
...
---
_id: '7656'
abstract:
- lang: eng
text: 'We propose that correlations among neurons are generically strong enough
to organize neural activity patterns into a discrete set of clusters, which can
each be viewed as a population codeword. Our reasoning starts with the analysis
of retinal ganglion cell data using maximum entropy models, showing that the population
is robustly in a frustrated, marginally sub-critical, or glassy, state. This leads
to an argument that neural populations in many other brain areas might share this
structure. Next, we use latent variable models to show that this glassy state
possesses well-defined clusters of neural activity. Clusters have three appealing
properties: (i) clusters exhibit error correction, i.e., they are reproducibly
elicited by the same stimulus despite variability at the level of constituent
neurons; (ii) clusters encode qualitatively different visual features than their
constituent neurons; and (iii) clusters can be learned by downstream neural circuits
in an unsupervised fashion. We hypothesize that these properties give rise to
a “learnable” neural code which the cortical hierarchy uses to extract increasingly
complex features without supervision or reinforcement.'
article_number: '20'
article_processing_charge: No
article_type: original
author:
- first_name: Michael J.
full_name: Berry, Michael J.
last_name: Berry
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: 'Berry MJ, Tkačik G. Clustering of neural activity: A design principle for
population codes. Frontiers in Computational Neuroscience. 2020;14. doi:10.3389/fncom.2020.00020'
apa: 'Berry, M. J., & Tkačik, G. (2020). Clustering of neural activity: A design
principle for population codes. Frontiers in Computational Neuroscience.
Frontiers. https://doi.org/10.3389/fncom.2020.00020'
chicago: 'Berry, Michael J., and Gašper Tkačik. “Clustering of Neural Activity:
A Design Principle for Population Codes.” Frontiers in Computational Neuroscience.
Frontiers, 2020. https://doi.org/10.3389/fncom.2020.00020.'
ieee: 'M. J. Berry and G. Tkačik, “Clustering of neural activity: A design principle
for population codes,” Frontiers in Computational Neuroscience, vol. 14.
Frontiers, 2020.'
ista: 'Berry MJ, Tkačik G. 2020. Clustering of neural activity: A design principle
for population codes. Frontiers in Computational Neuroscience. 14, 20.'
mla: 'Berry, Michael J., and Gašper Tkačik. “Clustering of Neural Activity: A Design
Principle for Population Codes.” Frontiers in Computational Neuroscience,
vol. 14, 20, Frontiers, 2020, doi:10.3389/fncom.2020.00020.'
short: M.J. Berry, G. Tkačik, Frontiers in Computational Neuroscience 14 (2020).
date_created: 2020-04-12T22:00:40Z
date_published: 2020-03-13T00:00:00Z
date_updated: 2023-08-18T10:30:11Z
day: '13'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.3389/fncom.2020.00020
external_id:
isi:
- '000525543200001'
pmid:
- '32231528'
file:
- access_level: open_access
checksum: 2b1da23823eae9cedbb42d701945b61e
content_type: application/pdf
creator: dernst
date_created: 2020-04-14T12:20:39Z
date_updated: 2020-07-14T12:48:01Z
file_id: '7659'
file_name: 2020_Frontiers_Berry.pdf
file_size: 4082937
relation: main_file
file_date_updated: 2020-07-14T12:48:01Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Computational Neuroscience
publication_identifier:
eissn:
- '16625188'
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Clustering of neural activity: A design principle for population codes'
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: 14
year: '2020'
...
---
_id: '7663'
abstract:
- lang: eng
text: Wood, as the most abundant carbon dioxide storing bioresource, is currently
driven beyond its traditional use through creative innovations and nanotechnology.
For many properties the micro- and nanostructure plays a crucial role and one
key challenge is control and detection of chemical and physical processes in the
confined microstructure and nanopores of the wooden cell wall. In this study,
correlative Raman and atomic force microscopy show high potential for tracking
in situ molecular rearrangement of wood polymers during compression. More water
molecules (interpreted as wider cellulose microfibril distances) and disentangling
of hemicellulose chains are detected in the opened cell wall regions, whereas
an increase of lignin is revealed in the compressed areas. These results support
a new more “loose” cell wall model based on flexible lignin nanodomains and advance
our knowledge of the molecular reorganization during deformation of wood for optimized
processing and utilization.
article_processing_charge: No
article_type: original
author:
- first_name: Martin
full_name: Felhofer, Martin
last_name: Felhofer
- first_name: Peter
full_name: Bock, Peter
last_name: Bock
- first_name: Adya
full_name: Singh, Adya
last_name: Singh
- first_name: Batirtze
full_name: Prats Mateu, Batirtze
id: 299FE892-F248-11E8-B48F-1D18A9856A87
last_name: Prats Mateu
- first_name: Ronald
full_name: Zirbs, Ronald
last_name: Zirbs
- first_name: Notburga
full_name: Gierlinger, Notburga
last_name: Gierlinger
citation:
ama: Felhofer M, Bock P, Singh A, Prats Mateu B, Zirbs R, Gierlinger N. Wood deformation
leads to rearrangement of molecules at the nanoscale. Nano Letters. 2020;20(4):2647-2653.
doi:10.1021/acs.nanolett.0c00205
apa: Felhofer, M., Bock, P., Singh, A., Prats Mateu, B., Zirbs, R., & Gierlinger,
N. (2020). Wood deformation leads to rearrangement of molecules at the nanoscale.
Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.0c00205
chicago: Felhofer, Martin, Peter Bock, Adya Singh, Batirtze Prats Mateu, Ronald
Zirbs, and Notburga Gierlinger. “Wood Deformation Leads to Rearrangement of Molecules
at the Nanoscale.” Nano Letters. American Chemical Society, 2020. https://doi.org/10.1021/acs.nanolett.0c00205.
ieee: M. Felhofer, P. Bock, A. Singh, B. Prats Mateu, R. Zirbs, and N. Gierlinger,
“Wood deformation leads to rearrangement of molecules at the nanoscale,” Nano
Letters, vol. 20, no. 4. American Chemical Society, pp. 2647–2653, 2020.
ista: Felhofer M, Bock P, Singh A, Prats Mateu B, Zirbs R, Gierlinger N. 2020. Wood
deformation leads to rearrangement of molecules at the nanoscale. Nano Letters.
20(4), 2647–2653.
mla: Felhofer, Martin, et al. “Wood Deformation Leads to Rearrangement of Molecules
at the Nanoscale.” Nano Letters, vol. 20, no. 4, American Chemical Society,
2020, pp. 2647–53, doi:10.1021/acs.nanolett.0c00205.
short: M. Felhofer, P. Bock, A. Singh, B. Prats Mateu, R. Zirbs, N. Gierlinger,
Nano Letters 20 (2020) 2647–2653.
date_created: 2020-04-19T22:00:54Z
date_published: 2020-04-08T00:00:00Z
date_updated: 2023-08-21T06:12:09Z
day: '08'
ddc:
- '530'
department:
- _id: MaLo
doi: 10.1021/acs.nanolett.0c00205
external_id:
isi:
- '000526413400055'
pmid:
- '32196350'
file:
- access_level: open_access
checksum: fe46146a9c4c620592a1932a8599069e
content_type: application/pdf
creator: dernst
date_created: 2020-04-20T10:43:36Z
date_updated: 2020-07-14T12:48:01Z
file_id: '7667'
file_name: 2020_NanoLetters_Felhofer.pdf
file_size: 7108014
relation: main_file
file_date_updated: 2020-07-14T12:48:01Z
has_accepted_license: '1'
intvolume: ' 20'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 2647-2653
pmid: 1
publication: Nano Letters
publication_identifier:
eissn:
- '15306992'
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Wood deformation leads to rearrangement of molecules at the nanoscale
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: 20
year: '2020'
...
---
_id: '7664'
abstract:
- lang: eng
text: Metabotropic γ-aminobutyric acid (GABAB) receptors contribute to the control
of network activity and information processing in hippocampal circuits by regulating
neuronal excitability and synaptic transmission. The dysfunction in the dentate
gyrus (DG) has been implicated in Alzheimer´s disease (AD). Given the involvement
of GABAB receptors in AD, to determine their subcellular localisation and possible
alteration in granule cells of the DG in a mouse model of AD at 12 months of age,
we used high-resolution immunoelectron microscopic analysis. Immunohistochemistry
at the light microscopic level showed that the regional and cellular expression
pattern of GABAB1 was similar in an AD model mouse expressing mutated human amyloid
precursor protein and presenilin1 (APP/PS1) and in age-matched wild type mice.
High-resolution immunoelectron microscopy revealed a distance-dependent gradient
of immunolabelling for GABAB receptors, increasing from proximal to distal dendrites
in both wild type and APP/PS1 mice. However, the overall density of GABAB receptors
at the neuronal surface of these postsynaptic compartments of granule cells was
significantly reduced in APP/PS1 mice. Parallel to this reduction in surface receptors,
we found a significant increase in GABAB1 at cytoplasmic sites. GABAB receptors
were also detected at presynaptic sites in the molecular layer of the DG. We also
found a decrease in plasma membrane GABAB receptors in axon terminals contacting
dendritic spines of granule cells, which was more pronounced in the outer than
in the inner molecular layer. Altogether, our data showing post- and presynaptic
reduction in surface GABAB receptors in the DG suggest the alteration of the GABAB-mediated
modulation of excitability and synaptic transmission in granule cells, which may
contribute to the cognitive dysfunctions in the APP/PS1 model of AD
article_number: '2459'
article_processing_charge: No
article_type: original
author:
- first_name: Alejandro
full_name: Martín-Belmonte, Alejandro
last_name: Martín-Belmonte
- first_name: Carolina
full_name: Aguado, Carolina
last_name: Aguado
- first_name: Rocío
full_name: Alfaro-Ruíz, Rocío
last_name: Alfaro-Ruíz
- first_name: Ana Esther
full_name: Moreno-Martínez, Ana Esther
last_name: Moreno-Martínez
- first_name: Luis
full_name: De La Ossa, Luis
last_name: De La Ossa
- first_name: José
full_name: Martínez-Hernández, José
last_name: Martínez-Hernández
- first_name: Alain
full_name: Buisson, Alain
last_name: Buisson
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Yugo
full_name: Fukazawa, Yugo
last_name: Fukazawa
- first_name: Rafael
full_name: Luján, Rafael
last_name: Luján
citation:
ama: Martín-Belmonte A, Aguado C, Alfaro-Ruíz R, et al. Density of GABAB receptors
is reduced in granule cells of the hippocampus in a mouse model of Alzheimer’s
disease. International journal of molecular sciences. 2020;21(7). doi:10.3390/ijms21072459
apa: Martín-Belmonte, A., Aguado, C., Alfaro-Ruíz, R., Moreno-Martínez, A. E., De
La Ossa, L., Martínez-Hernández, J., … Luján, R. (2020). Density of GABAB receptors
is reduced in granule cells of the hippocampus in a mouse model of Alzheimer’s
disease. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms21072459
chicago: Martín-Belmonte, Alejandro, Carolina Aguado, Rocío Alfaro-Ruíz, Ana Esther
Moreno-Martínez, Luis De La Ossa, José Martínez-Hernández, Alain Buisson, Ryuichi
Shigemoto, Yugo Fukazawa, and Rafael Luján. “Density of GABAB Receptors Is Reduced
in Granule Cells of the Hippocampus in a Mouse Model of Alzheimer’s Disease.”
International Journal of Molecular Sciences. MDPI, 2020. https://doi.org/10.3390/ijms21072459.
ieee: A. Martín-Belmonte et al., “Density of GABAB receptors is reduced in
granule cells of the hippocampus in a mouse model of Alzheimer’s disease,” International
journal of molecular sciences, vol. 21, no. 7. MDPI, 2020.
ista: Martín-Belmonte A, Aguado C, Alfaro-Ruíz R, Moreno-Martínez AE, De La Ossa
L, Martínez-Hernández J, Buisson A, Shigemoto R, Fukazawa Y, Luján R. 2020. Density
of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model
of Alzheimer’s disease. International journal of molecular sciences. 21(7), 2459.
mla: Martín-Belmonte, Alejandro, et al. “Density of GABAB Receptors Is Reduced in
Granule Cells of the Hippocampus in a Mouse Model of Alzheimer’s Disease.” International
Journal of Molecular Sciences, vol. 21, no. 7, 2459, MDPI, 2020, doi:10.3390/ijms21072459.
short: A. Martín-Belmonte, C. Aguado, R. Alfaro-Ruíz, A.E. Moreno-Martínez, L. De
La Ossa, J. Martínez-Hernández, A. Buisson, R. Shigemoto, Y. Fukazawa, R. Luján,
International Journal of Molecular Sciences 21 (2020).
date_created: 2020-04-19T22:00:55Z
date_published: 2020-04-02T00:00:00Z
date_updated: 2023-08-21T06:13:19Z
day: '02'
ddc:
- '570'
department:
- _id: RySh
doi: 10.3390/ijms21072459
external_id:
isi:
- '000535574200201'
pmid:
- '32252271'
file:
- access_level: open_access
checksum: b9d2f1657d8c4a74b01a62b474d009b0
content_type: application/pdf
creator: dernst
date_created: 2020-04-20T11:43:18Z
date_updated: 2020-07-14T12:48:01Z
file_id: '7669'
file_name: 2020_JournMolecSciences_Martin_Belmonte.pdf
file_size: 2941197
relation: main_file
file_date_updated: 2020-07-14T12:48:01Z
has_accepted_license: '1'
intvolume: ' 21'
isi: 1
issue: '7'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: International journal of molecular sciences
publication_identifier:
eissn:
- '14220067'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Density of GABAB receptors is reduced in granule cells of the hippocampus in
a mouse model of Alzheimer's disease
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: 21
year: '2020'
...
---
_id: '7665'
abstract:
- lang: eng
text: Acute brain slice preparation is a powerful experimental model for investigating
the characteristics of synaptic function in the brain. Although brain tissue is
usually cut at ice-cold temperature (CT) to facilitate slicing and avoid neuronal
damage, exposure to CT causes molecular and architectural changes of synapses.
To address these issues, we investigated ultrastructural and electrophysiological
features of synapses in mouse acute cerebellar slices prepared at ice-cold and
physiological temperature (PT). In the slices prepared at CT, we found significant
spine loss and reconstruction, synaptic vesicle rearrangement and decrease in
synaptic proteins, all of which were not detected in slices prepared at PT. Consistent
with these structural findings, slices prepared at PT showed higher release probability.
Furthermore, preparation at PT allows electrophysiological recording immediately
after slicing resulting in higher detectability of long-term depression (LTD)
after motor learning compared with that at CT. These results indicate substantial
advantages of the slice preparation at PT for investigating synaptic functions
in different physiological conditions.
article_number: '63'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Kohgaku
full_name: Eguchi, Kohgaku
id: 2B7846DC-F248-11E8-B48F-1D18A9856A87
last_name: Eguchi
orcid: 0000-0002-6170-2546
- first_name: Philipp
full_name: Velicky, Philipp
id: 39BDC62C-F248-11E8-B48F-1D18A9856A87
last_name: Velicky
orcid: 0000-0002-2340-7431
- first_name: Elena
full_name: Hollergschwandtner, Elena
id: 3C054040-F248-11E8-B48F-1D18A9856A87
last_name: Hollergschwandtner
- first_name: Makoto
full_name: Itakura, Makoto
last_name: Itakura
- first_name: Yugo
full_name: Fukazawa, Yugo
last_name: Fukazawa
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: Eguchi K, Velicky P, Saeckl E, et al. Advantages of acute brain slices prepared
at physiological temperature in the characterization of synaptic functions. Frontiers
in Cellular Neuroscience. 2020;14. doi:10.3389/fncel.2020.00063
apa: Eguchi, K., Velicky, P., Saeckl, E., Itakura, M., Fukazawa, Y., Danzl, J. G.,
& Shigemoto, R. (2020). Advantages of acute brain slices prepared at physiological
temperature in the characterization of synaptic functions. Frontiers in Cellular
Neuroscience. Frontiers Media. https://doi.org/10.3389/fncel.2020.00063
chicago: Eguchi, Kohgaku, Philipp Velicky, Elena Saeckl, Makoto Itakura, Yugo Fukazawa,
Johann G Danzl, and Ryuichi Shigemoto. “Advantages of Acute Brain Slices Prepared
at Physiological Temperature in the Characterization of Synaptic Functions.” Frontiers
in Cellular Neuroscience. Frontiers Media, 2020. https://doi.org/10.3389/fncel.2020.00063.
ieee: K. Eguchi et al., “Advantages of acute brain slices prepared at physiological
temperature in the characterization of synaptic functions,” Frontiers in Cellular
Neuroscience, vol. 14. Frontiers Media, 2020.
ista: Eguchi K, Velicky P, Saeckl E, Itakura M, Fukazawa Y, Danzl JG, Shigemoto
R. 2020. Advantages of acute brain slices prepared at physiological temperature
in the characterization of synaptic functions. Frontiers in Cellular Neuroscience.
14, 63.
mla: Eguchi, Kohgaku, et al. “Advantages of Acute Brain Slices Prepared at Physiological
Temperature in the Characterization of Synaptic Functions.” Frontiers in Cellular
Neuroscience, vol. 14, 63, Frontiers Media, 2020, doi:10.3389/fncel.2020.00063.
short: K. Eguchi, P. Velicky, E. Saeckl, M. Itakura, Y. Fukazawa, J.G. Danzl, R.
Shigemoto, Frontiers in Cellular Neuroscience 14 (2020).
date_created: 2020-04-19T22:00:55Z
date_published: 2020-03-19T00:00:00Z
date_updated: 2023-08-21T06:12:48Z
day: '19'
ddc:
- '570'
department:
- _id: JoDa
- _id: RySh
doi: 10.3389/fncel.2020.00063
ec_funded: 1
external_id:
isi:
- '000525582200001'
file:
- access_level: open_access
checksum: 1c145123c6f8dc3e2e4bd5a66a1ad60e
content_type: application/pdf
creator: dernst
date_created: 2020-04-20T10:59:49Z
date_updated: 2020-07-14T12:48:01Z
file_id: '7668'
file_name: 2020_FrontiersCellularNeurosc_Eguchi.pdf
file_size: 9227283
relation: main_file
file_date_updated: 2020-07-14T12:48:01Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 2659CC84-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '793482'
name: 'Ultrastructural analysis of phosphoinositides in nerve terminals: distribution,
dynamics and physiological roles in synaptic transmission'
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694539'
name: 'In situ analysis of single channel subunit composition in neurons: physiological
implication in synaptic plasticity and behaviour'
- _id: 265CB4D0-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03600
name: Optical control of synaptic function via adhesion molecules
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Frontiers in Cellular Neuroscience
publication_identifier:
issn:
- '16625102'
publication_status: published
publisher: Frontiers Media
quality_controlled: '1'
scopus_import: '1'
status: public
title: Advantages of acute brain slices prepared at physiological temperature in the
characterization of synaptic functions
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: 14
year: '2020'
...
---
_id: '7666'
abstract:
- lang: eng
text: Generalizing the decomposition of a connected planar graph into a tree and
a dual tree, we prove a combinatorial analog of the classic Helmholtz–Hodge decomposition
of a smooth vector field. Specifically, we show that for every polyhedral complex,
K, and every dimension, p, there is a partition of the set of p-cells into a maximal
p-tree, a maximal p-cotree, and a collection of p-cells whose cardinality is the
p-th reduced Betti number of K. Given an ordering of the p-cells, this tri-partition
is unique, and it can be computed by a matrix reduction algorithm that also constructs
canonical bases of cycle and boundary groups.
acknowledgement: This project has received funding from the European Research Council
under the European Union’s Horizon 2020 research and innovation programme (Grant
Agreement No. 78818 Alpha). It is also partially supported by the DFG Collaborative
Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through Grant
No. I02979-N35 of the Austrian Science Fund (FWF).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Katharina
full_name: Ölsböck, Katharina
id: 4D4AA390-F248-11E8-B48F-1D18A9856A87
last_name: Ölsböck
orcid: 0000-0002-4672-8297
citation:
ama: Edelsbrunner H, Ölsböck K. Tri-partitions and bases of an ordered complex.
Discrete and Computational Geometry. 2020;64:759-775. doi:10.1007/s00454-020-00188-x
apa: Edelsbrunner, H., & Ölsböck, K. (2020). Tri-partitions and bases of an
ordered complex. Discrete and Computational Geometry. Springer Nature.
https://doi.org/10.1007/s00454-020-00188-x
chicago: Edelsbrunner, Herbert, and Katharina Ölsböck. “Tri-Partitions and Bases
of an Ordered Complex.” Discrete and Computational Geometry. Springer Nature,
2020. https://doi.org/10.1007/s00454-020-00188-x.
ieee: H. Edelsbrunner and K. Ölsböck, “Tri-partitions and bases of an ordered complex,”
Discrete and Computational Geometry, vol. 64. Springer Nature, pp. 759–775,
2020.
ista: Edelsbrunner H, Ölsböck K. 2020. Tri-partitions and bases of an ordered complex.
Discrete and Computational Geometry. 64, 759–775.
mla: Edelsbrunner, Herbert, and Katharina Ölsböck. “Tri-Partitions and Bases of
an Ordered Complex.” Discrete and Computational Geometry, vol. 64, Springer
Nature, 2020, pp. 759–75, doi:10.1007/s00454-020-00188-x.
short: H. Edelsbrunner, K. Ölsböck, Discrete and Computational Geometry 64 (2020)
759–775.
date_created: 2020-04-19T22:00:56Z
date_published: 2020-03-20T00:00:00Z
date_updated: 2023-08-21T06:13:48Z
day: '20'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1007/s00454-020-00188-x
ec_funded: 1
external_id:
isi:
- '000520918800001'
file:
- access_level: open_access
checksum: f8cc96e497f00c38340b5dafe0cb91d7
content_type: application/pdf
creator: dernst
date_created: 2020-11-20T13:22:21Z
date_updated: 2020-11-20T13:22:21Z
file_id: '8786'
file_name: 2020_DiscreteCompGeo_Edelsbrunner.pdf
file_size: 701673
relation: main_file
success: 1
file_date_updated: 2020-11-20T13:22:21Z
has_accepted_license: '1'
intvolume: ' 64'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 759-775
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: Discrete and Computational Geometry
publication_identifier:
eissn:
- '14320444'
issn:
- '01795376'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tri-partitions and bases of an ordered complex
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: 64
year: '2020'
...
---
_id: '7672'
abstract:
- lang: eng
text: Large overpotentials upon discharge and charge of Li-O2 cells have motivated
extensive research into heterogeneous solid electrocatalysts or non-carbon electrodes
with the aim to improve rate capability, round-trip efficiency and cycle life.
These features are equally governed by parasitic reactions, which are now recognized
to be caused by the highly reactive singlet oxygen (1O2). However, the link between
the presence of electrocatalysts and 1O2 formation in metal-O2 cells is unknown.
Here, we show that, compared to pristine carbon black electrodes, a representative
selection of electrocatalysts or non-carbon electrodes (noble metal, transition
metal compounds) may both slightly reduce or severely increase the 1O2 formation.
The individual reaction steps, where the surfaces impact the 1O2 yield are deciphered,
showing that 1O2 yield from superoxide disproportionation as well as the decomposition
of trace H2O2 are sensitive to catalysts. Transition metal compounds in general
are prone to increase 1O2.
acknowledgement: S.A.F. thanks the International Society of Electrochemistry for awarding
the Tajima Prize 2019 “in recognition of outstanding re- searches on Li-Air batteries
by the use of a range of in-situ elec- trochemical methods to achieve comprehensive
understanding of the reactions taking place at the oxygen electrode”. This article
is dedicated to the special issue of Electrochmica Acta associated with the awarding
conference. S.A.F. is indebted to and the Austrian Federal Ministry of Science,
Research and Economy and the Austrian Research Promotion Agency (grant No. 845364
) and the European Research Council (ERC) under the European Union’s Horizon 2020
research and innovation programme (grant agreement No 636069). The authors thank
J. Schlegl for manufacturing instrumentation, M. Winkler of Acib GmbH and G. Strohmeier
for help with HPLC measurements, S. Eder for cyclic voltammetry measurements, and
C. Slugovc for discussions and continuous support. We thank S. Borisov for access
and advice with fluorescence measurements. We thank EL-Cell GmbH, Hamburg, Germany
for providing the PAT-Cell-Press electrochemical cell.
article_number: '137175'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Aleksej
full_name: Samojlov, Aleksej
last_name: Samojlov
- first_name: David
full_name: Schuster, David
last_name: Schuster
- first_name: Jürgen
full_name: Kahr, Jürgen
last_name: Kahr
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Samojlov A, Schuster D, Kahr J, Freunberger SA. Surface and catalyst driven
singlet oxygen formation in Li-O2 cells. Electrochimica Acta. 2020;362(12).
doi:10.1016/j.electacta.2020.137175
apa: Samojlov, A., Schuster, D., Kahr, J., & Freunberger, S. A. (2020). Surface
and catalyst driven singlet oxygen formation in Li-O2 cells. Electrochimica
Acta. Elsevier. https://doi.org/10.1016/j.electacta.2020.137175
chicago: Samojlov, Aleksej, David Schuster, Jürgen Kahr, and Stefan Alexander Freunberger.
“Surface and Catalyst Driven Singlet Oxygen Formation in Li-O2 Cells.” Electrochimica
Acta. Elsevier, 2020. https://doi.org/10.1016/j.electacta.2020.137175.
ieee: A. Samojlov, D. Schuster, J. Kahr, and S. A. Freunberger, “Surface and catalyst
driven singlet oxygen formation in Li-O2 cells,” Electrochimica Acta, vol.
362, no. 12. Elsevier, 2020.
ista: Samojlov A, Schuster D, Kahr J, Freunberger SA. 2020. Surface and catalyst
driven singlet oxygen formation in Li-O2 cells. Electrochimica Acta. 362(12),
137175.
mla: Samojlov, Aleksej, et al. “Surface and Catalyst Driven Singlet Oxygen Formation
in Li-O2 Cells.” Electrochimica Acta, vol. 362, no. 12, 137175, Elsevier,
2020, doi:10.1016/j.electacta.2020.137175.
short: A. Samojlov, D. Schuster, J. Kahr, S.A. Freunberger, Electrochimica Acta
362 (2020).
date_created: 2020-04-20T19:29:31Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2023-08-21T06:14:21Z
day: '01'
ddc:
- '540'
department:
- _id: StFr
doi: 10.1016/j.electacta.2020.137175
external_id:
isi:
- '000582869700060'
file:
- access_level: open_access
checksum: 1ab1aa2024d431e2a089ea336bc08298
content_type: application/pdf
creator: dernst
date_created: 2020-10-01T13:20:45Z
date_updated: 2020-10-01T13:20:45Z
file_id: '8593'
file_name: 2020_ElectrochimicaActa_Samojlov.pdf
file_size: 1404030
relation: main_file
success: 1
file_date_updated: 2020-10-01T13:20:45Z
has_accepted_license: '1'
intvolume: ' 362'
isi: 1
issue: '12'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '12'
oa: 1
oa_version: Published Version
publication: Electrochimica Acta
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Surface and catalyst driven singlet oxygen formation in Li-O2 cells
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 362
year: '2020'
...
---
_id: '7673'
abstract:
- lang: eng
text: Combining drugs can improve the efficacy of treatments. However, predicting
the effect of drug combinations is still challenging. The combined potency of
drugs determines the drug interaction, which is classified as synergistic, additive,
antagonistic, or suppressive. While probabilistic, non-mechanistic models exist,
there is currently no biophysical model that can predict antibiotic interactions.
Here, we present a physiologically relevant model of the combined action of antibiotics
that inhibit protein synthesis by targeting the ribosome. This model captures
the kinetics of antibiotic binding and transport, and uses bacterial growth laws
to predict growth in the presence of antibiotic combinations. We find that this
biophysical model can produce all drug interaction types except suppression. We
show analytically that antibiotics which cannot bind to the ribosome simultaneously
generally act as substitutes for one another, leading to additive drug interactions.
Previously proposed null expectations for higher-order drug interactions follow
as a limiting case of our model. We further extend the model to include the effects
of direct physical or allosteric interactions between individual drugs on the
ribosome. Notably, such direct interactions profoundly change the combined drug
effect, depending on the kinetic parameters of the drugs used. The model makes
additional predictions for the effects of resistance genes on drug interactions
and for interactions between ribosome-targeting antibiotics and antibiotics with
other targets. These findings enhance our understanding of the interplay between
drug action and cell physiology and are a key step toward a general framework
for predicting drug interactions.
article_processing_charge: No
author:
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Tobias
full_name: Bollenbach, Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Kavcic B, Tkačik G, Bollenbach MT. A minimal biophysical model of combined
antibiotic action. bioRxiv. 2020. doi:10.1101/2020.04.18.047886
apa: Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2020). A minimal biophysical
model of combined antibiotic action. bioRxiv. Cold Spring Harbor Laboratory.
https://doi.org/10.1101/2020.04.18.047886
chicago: Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “A Minimal Biophysical
Model of Combined Antibiotic Action.” BioRxiv. Cold Spring Harbor Laboratory,
2020. https://doi.org/10.1101/2020.04.18.047886.
ieee: B. Kavcic, G. Tkačik, and M. T. Bollenbach, “A minimal biophysical model of
combined antibiotic action,” bioRxiv. Cold Spring Harbor Laboratory, 2020.
ista: Kavcic B, Tkačik G, Bollenbach MT. 2020. A minimal biophysical model of combined
antibiotic action. bioRxiv, 10.1101/2020.04.18.047886.
mla: Kavcic, Bor, et al. “A Minimal Biophysical Model of Combined Antibiotic Action.”
BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.04.18.047886.
short: B. Kavcic, G. Tkačik, M.T. Bollenbach, BioRxiv (2020).
date_created: 2020-04-22T08:27:56Z
date_published: 2020-04-18T00:00:00Z
date_updated: 2024-03-25T23:30:05Z
day: '18'
department:
- _id: GaTk
doi: 10.1101/2020.04.18.047886
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://doi.org/10.1101/2020.04.18.047886 '
month: '04'
oa: 1
oa_version: Preprint
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: bioRxiv
publication_status: published
publisher: Cold Spring Harbor Laboratory
related_material:
record:
- id: '8997'
relation: later_version
status: public
- id: '8657'
relation: dissertation_contains
status: public
status: public
title: A minimal biophysical model of combined antibiotic action
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...