---
_id: '9227'
abstract:
- lang: eng
text: In the multiway cut problem we are given a weighted undirected graph G=(V,E) and
a set T⊆V of k terminals. The goal is to find a minimum weight set of edges E′⊆E with
the property that by removing E′ from G all the terminals become disconnected.
In this paper we present a simple local search approximation algorithm for the
multiway cut problem with approximation ratio 2−2k . We present an experimental
evaluation of the performance of our local search algorithm and show that it greatly
outperforms the isolation heuristic of Dalhaus et al. and it has similar performance
as the much more complex algorithms of Calinescu et al., Sharma and Vondrak, and
Buchbinder et al. which have the currently best known approximation ratios for
this problem.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Andrew
full_name: Bloch-Hansen, Andrew
last_name: Bloch-Hansen
- first_name: Nasim
full_name: Samei, Nasim
id: C1531CAE-36E9-11EA-845F-33AA3DDC885E
last_name: Samei
- first_name: Roberto
full_name: Solis-Oba, Roberto
last_name: Solis-Oba
citation:
ama: 'Bloch-Hansen A, Samei N, Solis-Oba R. Experimental evaluation of a local search
approximation algorithm for the multiway cut problem. In: Conference on Algorithms
and Discrete Applied Mathematics. Vol 12601. Springer Nature; 2021:346-358.
doi:10.1007/978-3-030-67899-9_28'
apa: 'Bloch-Hansen, A., Samei, N., & Solis-Oba, R. (2021). Experimental evaluation
of a local search approximation algorithm for the multiway cut problem. In Conference
on Algorithms and Discrete Applied Mathematics (Vol. 12601, pp. 346–358).
Rupnagar, India: Springer Nature. https://doi.org/10.1007/978-3-030-67899-9_28'
chicago: Bloch-Hansen, Andrew, Nasim Samei, and Roberto Solis-Oba. “Experimental
Evaluation of a Local Search Approximation Algorithm for the Multiway Cut Problem.”
In Conference on Algorithms and Discrete Applied Mathematics, 12601:346–58.
Springer Nature, 2021. https://doi.org/10.1007/978-3-030-67899-9_28.
ieee: A. Bloch-Hansen, N. Samei, and R. Solis-Oba, “Experimental evaluation of a
local search approximation algorithm for the multiway cut problem,” in Conference
on Algorithms and Discrete Applied Mathematics, Rupnagar, India, 2021, vol.
12601, pp. 346–358.
ista: 'Bloch-Hansen A, Samei N, Solis-Oba R. 2021. Experimental evaluation of a
local search approximation algorithm for the multiway cut problem. Conference
on Algorithms and Discrete Applied Mathematics. CALDAM: Conference on Algorithms
and Discrete Applied Mathematics, LNCS, vol. 12601, 346–358.'
mla: Bloch-Hansen, Andrew, et al. “Experimental Evaluation of a Local Search Approximation
Algorithm for the Multiway Cut Problem.” Conference on Algorithms and Discrete
Applied Mathematics, vol. 12601, Springer Nature, 2021, pp. 346–58, doi:10.1007/978-3-030-67899-9_28.
short: A. Bloch-Hansen, N. Samei, R. Solis-Oba, in:, Conference on Algorithms and
Discrete Applied Mathematics, Springer Nature, 2021, pp. 346–358.
conference:
end_date: 2021-02-13
location: Rupnagar, India
name: 'CALDAM: Conference on Algorithms and Discrete Applied Mathematics'
start_date: 2021-02-11
date_created: 2021-03-07T23:01:25Z
date_published: 2021-01-28T00:00:00Z
date_updated: 2023-10-10T09:29:08Z
day: '28'
department:
- _id: VlKo
doi: 10.1007/978-3-030-67899-9_28
intvolume: ' 12601'
language:
- iso: eng
month: '01'
oa_version: None
page: 346-358
publication: Conference on Algorithms and Discrete Applied Mathematics
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783030678982'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Experimental evaluation of a local search approximation algorithm for the multiway
cut problem
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12601
year: '2021'
...
---
_id: '8817'
abstract:
- lang: eng
text: The paper introduces an inertial extragradient subgradient method with self-adaptive
step sizes for solving equilibrium problems in real Hilbert spaces. Weak convergence
of the proposed method is obtained under the condition that the bifunction is
pseudomonotone and Lipchitz continuous. Linear convergence is also given when
the bifunction is strongly pseudomonotone and Lipchitz continuous. Numerical implementations
and comparisons with other related inertial methods are given using test problems
including a real-world application to Nash–Cournot oligopolistic electricity market
equilibrium model.
acknowledgement: The authors are grateful to the two referees and the Associate Editor
for their comments and suggestions which have improved the earlier version of the
paper greatly. The project of Yekini Shehu has received funding from the European
Research Council (ERC) under the European Union’s Seventh Framework Program (FP7
- 2007-2013) (Grant agreement No. 616160).
article_processing_charge: No
article_type: original
author:
- first_name: Yekini
full_name: Shehu, Yekini
id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87
last_name: Shehu
orcid: 0000-0001-9224-7139
- first_name: Olaniyi S.
full_name: Iyiola, Olaniyi S.
last_name: Iyiola
- first_name: Duong Viet
full_name: Thong, Duong Viet
last_name: Thong
- first_name: Nguyen Thi Cam
full_name: Van, Nguyen Thi Cam
last_name: Van
citation:
ama: Shehu Y, Iyiola OS, Thong DV, Van NTC. An inertial subgradient extragradient
algorithm extended to pseudomonotone equilibrium problems. Mathematical Methods
of Operations Research. 2021;93(2):213-242. doi:10.1007/s00186-020-00730-w
apa: Shehu, Y., Iyiola, O. S., Thong, D. V., & Van, N. T. C. (2021). An inertial
subgradient extragradient algorithm extended to pseudomonotone equilibrium problems.
Mathematical Methods of Operations Research. Springer Nature. https://doi.org/10.1007/s00186-020-00730-w
chicago: Shehu, Yekini, Olaniyi S. Iyiola, Duong Viet Thong, and Nguyen Thi Cam
Van. “An Inertial Subgradient Extragradient Algorithm Extended to Pseudomonotone
Equilibrium Problems.” Mathematical Methods of Operations Research. Springer
Nature, 2021. https://doi.org/10.1007/s00186-020-00730-w.
ieee: Y. Shehu, O. S. Iyiola, D. V. Thong, and N. T. C. Van, “An inertial subgradient
extragradient algorithm extended to pseudomonotone equilibrium problems,” Mathematical
Methods of Operations Research, vol. 93, no. 2. Springer Nature, pp. 213–242,
2021.
ista: Shehu Y, Iyiola OS, Thong DV, Van NTC. 2021. An inertial subgradient extragradient
algorithm extended to pseudomonotone equilibrium problems. Mathematical Methods
of Operations Research. 93(2), 213–242.
mla: Shehu, Yekini, et al. “An Inertial Subgradient Extragradient Algorithm Extended
to Pseudomonotone Equilibrium Problems.” Mathematical Methods of Operations
Research, vol. 93, no. 2, Springer Nature, 2021, pp. 213–42, doi:10.1007/s00186-020-00730-w.
short: Y. Shehu, O.S. Iyiola, D.V. Thong, N.T.C. Van, Mathematical Methods of Operations
Research 93 (2021) 213–242.
date_created: 2020-11-29T23:01:18Z
date_published: 2021-04-01T00:00:00Z
date_updated: 2023-10-10T09:30:23Z
day: '01'
department:
- _id: VlKo
doi: 10.1007/s00186-020-00730-w
ec_funded: 1
external_id:
isi:
- '000590497300001'
intvolume: ' 93'
isi: 1
issue: '2'
language:
- iso: eng
month: '04'
oa_version: None
page: 213-242
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Mathematical Methods of Operations Research
publication_identifier:
eissn:
- 1432-5217
issn:
- 1432-2994
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: An inertial subgradient extragradient algorithm extended to pseudomonotone
equilibrium problems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 93
year: '2021'
...
---
_id: '9315'
abstract:
- lang: eng
text: We consider inertial iteration methods for Fermat–Weber location problem and
primal–dual three-operator splitting in real Hilbert spaces. To do these, we first
obtain weak convergence analysis and nonasymptotic O(1/n) convergence rate of
the inertial Krasnoselskii–Mann iteration for fixed point of nonexpansive operators
in infinite dimensional real Hilbert spaces under some seemingly easy to implement
conditions on the iterative parameters. One of our contributions is that the convergence
analysis and rate of convergence results are obtained using conditions which appear
not complicated and restrictive as assumed in other previous related results in
the literature. We then show that Fermat–Weber location problem and primal–dual
three-operator splitting are special cases of fixed point problem of nonexpansive
mapping and consequently obtain the convergence analysis of inertial iteration
methods for Fermat–Weber location problem and primal–dual three-operator splitting
in real Hilbert spaces. Some numerical implementations are drawn from primal–dual
three-operator splitting to support the theoretical analysis.
acknowledgement: The research of this author is supported by the Postdoctoral Fellowship
from Institute of Science and Technology (IST), Austria.
article_number: '75'
article_processing_charge: No
article_type: original
author:
- first_name: Olaniyi S.
full_name: Iyiola, Olaniyi S.
last_name: Iyiola
- first_name: Yekini
full_name: Shehu, Yekini
id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87
last_name: Shehu
orcid: 0000-0001-9224-7139
citation:
ama: Iyiola OS, Shehu Y. New convergence results for inertial Krasnoselskii–Mann
iterations in Hilbert spaces with applications. Results in Mathematics.
2021;76(2). doi:10.1007/s00025-021-01381-x
apa: Iyiola, O. S., & Shehu, Y. (2021). New convergence results for inertial
Krasnoselskii–Mann iterations in Hilbert spaces with applications. Results
in Mathematics. Springer Nature. https://doi.org/10.1007/s00025-021-01381-x
chicago: Iyiola, Olaniyi S., and Yekini Shehu. “New Convergence Results for Inertial
Krasnoselskii–Mann Iterations in Hilbert Spaces with Applications.” Results
in Mathematics. Springer Nature, 2021. https://doi.org/10.1007/s00025-021-01381-x.
ieee: O. S. Iyiola and Y. Shehu, “New convergence results for inertial Krasnoselskii–Mann
iterations in Hilbert spaces with applications,” Results in Mathematics,
vol. 76, no. 2. Springer Nature, 2021.
ista: Iyiola OS, Shehu Y. 2021. New convergence results for inertial Krasnoselskii–Mann
iterations in Hilbert spaces with applications. Results in Mathematics. 76(2),
75.
mla: Iyiola, Olaniyi S., and Yekini Shehu. “New Convergence Results for Inertial
Krasnoselskii–Mann Iterations in Hilbert Spaces with Applications.” Results
in Mathematics, vol. 76, no. 2, 75, Springer Nature, 2021, doi:10.1007/s00025-021-01381-x.
short: O.S. Iyiola, Y. Shehu, Results in Mathematics 76 (2021).
date_created: 2021-04-11T22:01:14Z
date_published: 2021-03-25T00:00:00Z
date_updated: 2023-10-10T09:47:33Z
day: '25'
department:
- _id: VlKo
doi: 10.1007/s00025-021-01381-x
external_id:
isi:
- '000632917700001'
intvolume: ' 76'
isi: 1
issue: '2'
language:
- iso: eng
month: '03'
oa_version: None
publication: Results in Mathematics
publication_identifier:
eissn:
- 1420-9012
issn:
- 1422-6383
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: New convergence results for inertial Krasnoselskii–Mann iterations in Hilbert
spaces with applications
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 76
year: '2021'
...
---
_id: '9365'
abstract:
- lang: eng
text: In this paper, we propose a new iterative method with alternated inertial
step for solving split common null point problem in real Hilbert spaces. We obtain
weak convergence of the proposed iterative algorithm. Furthermore, we introduce
the notion of bounded linear regularity property for the split common null point
problem and obtain the linear convergence property for the new algorithm under
some mild assumptions. Finally, we provide some numerical examples to demonstrate
the performance and efficiency of the proposed method.
acknowledgement: The second author has received funding from the European Research
Council (ERC) under the European Union's Seventh Framework Program (FP7-2007-2013)
(Grant agreement No. 616160).
article_processing_charge: No
article_type: original
author:
- first_name: Ferdinard U.
full_name: Ogbuisi, Ferdinard U.
last_name: Ogbuisi
- first_name: Yekini
full_name: Shehu, Yekini
id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87
last_name: Shehu
orcid: 0000-0001-9224-7139
- first_name: Jen Chih
full_name: Yao, Jen Chih
last_name: Yao
citation:
ama: Ogbuisi FU, Shehu Y, Yao JC. Convergence analysis of new inertial method for
the split common null point problem. Optimization. 2021. doi:10.1080/02331934.2021.1914035
apa: Ogbuisi, F. U., Shehu, Y., & Yao, J. C. (2021). Convergence analysis of
new inertial method for the split common null point problem. Optimization.
Taylor and Francis. https://doi.org/10.1080/02331934.2021.1914035
chicago: Ogbuisi, Ferdinard U., Yekini Shehu, and Jen Chih Yao. “Convergence Analysis
of New Inertial Method for the Split Common Null Point Problem.” Optimization.
Taylor and Francis, 2021. https://doi.org/10.1080/02331934.2021.1914035.
ieee: F. U. Ogbuisi, Y. Shehu, and J. C. Yao, “Convergence analysis of new inertial
method for the split common null point problem,” Optimization. Taylor and
Francis, 2021.
ista: Ogbuisi FU, Shehu Y, Yao JC. 2021. Convergence analysis of new inertial method
for the split common null point problem. Optimization.
mla: Ogbuisi, Ferdinard U., et al. “Convergence Analysis of New Inertial Method
for the Split Common Null Point Problem.” Optimization, Taylor and Francis,
2021, doi:10.1080/02331934.2021.1914035.
short: F.U. Ogbuisi, Y. Shehu, J.C. Yao, Optimization (2021).
date_created: 2021-05-02T22:01:29Z
date_published: 2021-04-14T00:00:00Z
date_updated: 2023-10-10T09:48:41Z
day: '14'
department:
- _id: VlKo
doi: 10.1080/02331934.2021.1914035
ec_funded: 1
external_id:
isi:
- '000640109300001'
isi: 1
language:
- iso: eng
month: '04'
oa_version: None
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Optimization
publication_identifier:
eissn:
- 1029-4945
issn:
- 0233-1934
publication_status: published
publisher: Taylor and Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: Convergence analysis of new inertial method for the split common null point
problem
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '10365'
abstract:
- lang: eng
text: The early development of many organisms involves the folding of cell monolayers,
but this behaviour is difficult to reproduce in vitro; therefore, both mechanistic
causes and effects of local curvature remain unclear. Here we study epithelial
cell monolayers on corrugated hydrogels engineered into wavy patterns, examining
how concave and convex curvatures affect cellular and nuclear shape. We find that
substrate curvature affects monolayer thickness, which is larger in valleys than
crests. We show that this feature generically arises in a vertex model, leading
to the hypothesis that cells may sense curvature by modifying the thickness of
the tissue. We find that local curvature also affects nuclear morphology and positioning,
which we explain by extending the vertex model to take into account membrane–nucleus
interactions, encoding thickness modulation in changes to nuclear deformation
and position. We propose that curvature governs the spatial distribution of yes-associated
proteins via nuclear shape and density changes. We show that curvature also induces
significant variations in lamins, chromatin condensation and cell proliferation
rate in folded epithelial tissues. Together, this work identifies active cell
mechanics and nuclear mechanoadaptation as the key players of the mechanistic
regulation of epithelia to substrate curvature.
acknowledgement: S.G. acknowledges funding from FEDER Prostem Research Project no.
1510614 (Wallonia DG06), F.R.S.-FNRS Epiforce Research Project no. T.0092.21 and
Interreg MAT(T)ISSE project, which is financially supported by Interreg France-Wallonie-Vlaanderen
(Fonds Européen de Développement Régional, FEDER-ERDF). This project was supported
by the European Research Council under the European Union’s Horizon 2020 Research
and Innovation Programme grant agreement 851288 (to E.H.), and by the Austrian Science
Fund (FWF) (P 31639; to E.H.). L.R.M. acknowledges funding from the Agence National
de la Recherche (ANR), as part of the ‘Investments d’Avenir’ Programme (I-SITE ULNE/ANR-16-IDEX-0004
ULNE). This work benefited from ANR-10-EQPX-04-01 and FEDER 12001407 grants to F.L.
W.D.V. is supported by the Research Foundation Flanders (FWO 1516619N, FWO GOO5819N,
FWO I003420N, FWO IRI I000321N) and is member of the Research Excellence Consortium
µNEURO at the University of Antwerp. M.L. is financially supported by FRIA (F.R.S.-FNRS).
M.S. is a Senior Research Associate of the Fund for Scientific Research (F.R.S.-FNRS)
and acknowledges EOS grant no. 30650939 (PRECISION). Sketches in Figs. 1a and 5e
and Extended Data Fig. 9 were drawn by C. Levicek.
article_processing_charge: No
article_type: original
author:
- first_name: Marine
full_name: Luciano, Marine
last_name: Luciano
- first_name: Shi-lei
full_name: Xue, Shi-lei
id: 31D2C804-F248-11E8-B48F-1D18A9856A87
last_name: Xue
- first_name: Winnok H.
full_name: De Vos, Winnok H.
last_name: De Vos
- first_name: Lorena
full_name: Redondo-Morata, Lorena
last_name: Redondo-Morata
- first_name: Mathieu
full_name: Surin, Mathieu
last_name: Surin
- first_name: Frank
full_name: Lafont, Frank
last_name: Lafont
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Sylvain
full_name: Gabriele, Sylvain
last_name: Gabriele
citation:
ama: Luciano M, Xue S, De Vos WH, et al. Cell monolayers sense curvature by exploiting
active mechanics and nuclear mechanoadaptation. Nature Physics. 2021;17(12):1382–1390.
doi:10.1038/s41567-021-01374-1
apa: Luciano, M., Xue, S., De Vos, W. H., Redondo-Morata, L., Surin, M., Lafont,
F., … Gabriele, S. (2021). Cell monolayers sense curvature by exploiting active
mechanics and nuclear mechanoadaptation. Nature Physics. Springer Nature.
https://doi.org/10.1038/s41567-021-01374-1
chicago: Luciano, Marine, Shi-lei Xue, Winnok H. De Vos, Lorena Redondo-Morata,
Mathieu Surin, Frank Lafont, Edouard B Hannezo, and Sylvain Gabriele. “Cell Monolayers
Sense Curvature by Exploiting Active Mechanics and Nuclear Mechanoadaptation.”
Nature Physics. Springer Nature, 2021. https://doi.org/10.1038/s41567-021-01374-1.
ieee: M. Luciano et al., “Cell monolayers sense curvature by exploiting active
mechanics and nuclear mechanoadaptation,” Nature Physics, vol. 17, no.
12. Springer Nature, pp. 1382–1390, 2021.
ista: Luciano M, Xue S, De Vos WH, Redondo-Morata L, Surin M, Lafont F, Hannezo
EB, Gabriele S. 2021. Cell monolayers sense curvature by exploiting active mechanics
and nuclear mechanoadaptation. Nature Physics. 17(12), 1382–1390.
mla: Luciano, Marine, et al. “Cell Monolayers Sense Curvature by Exploiting Active
Mechanics and Nuclear Mechanoadaptation.” Nature Physics, vol. 17, no.
12, Springer Nature, 2021, pp. 1382–1390, doi:10.1038/s41567-021-01374-1.
short: M. Luciano, S. Xue, W.H. De Vos, L. Redondo-Morata, M. Surin, F. Lafont,
E.B. Hannezo, S. Gabriele, Nature Physics 17 (2021) 1382–1390.
date_created: 2021-11-28T23:01:29Z
date_published: 2021-11-18T00:00:00Z
date_updated: 2023-10-16T06:31:54Z
day: '18'
ddc:
- '530'
department:
- _id: EdHa
doi: 10.1038/s41567-021-01374-1
ec_funded: 1
external_id:
isi:
- '000720204300004'
file:
- access_level: open_access
checksum: 5d6d76750a71d7cb632bb15417c38ef7
content_type: application/pdf
creator: channezo
date_created: 2023-10-11T09:31:43Z
date_updated: 2023-10-11T09:31:43Z
file_id: '14420'
file_name: 50145_4_merged_1630498627.pdf
file_size: 40285498
relation: main_file
success: 1
file_date_updated: 2023-10-11T09:31:43Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
issue: '12'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 1382–1390
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
- _id: 268294B6-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31639
name: Active mechano-chemical description of the cell cytoskeleton
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Webpage
relation: press_release
url: https://ist.ac.at/en/news/how-cells-feel-curvature/
scopus_import: '1'
status: public
title: Cell monolayers sense curvature by exploiting active mechanics and nuclear
mechanoadaptation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2021'
...
---
_id: '9298'
abstract:
- lang: eng
text: 'In 2008, we published the first set of guidelines for standardizing research
in autophagy. Since then, this topic has received increasing attention, and many
scientists have entered the field. Our knowledge base and relevant new technologies
have also been expanding. Thus, it is important to formulate on a regular basis
updated guidelines for monitoring autophagy in different organisms. Despite numerous
reviews, there continues to be confusion regarding acceptable methods to evaluate
autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines
for investigators to select and interpret methods to examine autophagy and related
processes, and for reviewers to provide realistic and reasonable critiques of
reports that are focused on these processes. These guidelines are not meant to
be a dogmatic set of rules, because the appropriateness of any assay largely depends
on the question being asked and the system being used. Moreover, no individual
assay is perfect for every situation, calling for the use of multiple techniques
to properly monitor autophagy in each experimental setting. Finally, several core
components of the autophagy machinery have been implicated in distinct autophagic
processes (canonical and noncanonical autophagy), implying that genetic approaches
to block autophagy should rely on targeting two or more autophagy-related genes
that ideally participate in distinct steps of the pathway. Along similar lines,
because multiple proteins involved in autophagy also regulate other cellular pathways
including apoptosis, not all of them can be used as a specific marker for bona
fide autophagic responses. Here, we critically discuss current methods of assessing
autophagy and the information they can, or cannot, provide. Our ultimate goal
is to encourage intellectual and technical innovation in the field. '
acknowledgement: This work was supported by the National Institute of General Medical
Sciences [GM131919]. Due to space and other limitations, it is not possible to include
all other sources of financial support.
article_processing_charge: No
article_type: review
author:
- first_name: Daniel J.
full_name: Klionsky, Daniel J.
last_name: Klionsky
- first_name: Amal Kamal
full_name: Abdel-Aziz, Amal Kamal
last_name: Abdel-Aziz
- first_name: Sara
full_name: Abdelfatah, Sara
last_name: Abdelfatah
- first_name: Mahmoud
full_name: Abdellatif, Mahmoud
last_name: Abdellatif
- first_name: Asghar
full_name: Abdoli, Asghar
last_name: Abdoli
- first_name: Steffen
full_name: Abel, Steffen
last_name: Abel
- first_name: Hagai
full_name: Abeliovich, Hagai
last_name: Abeliovich
- first_name: Marie H.
full_name: Abildgaard, Marie H.
last_name: Abildgaard
- first_name: Yakubu Princely
full_name: Abudu, Yakubu Princely
last_name: Abudu
- first_name: Abraham
full_name: Acevedo-Arozena, Abraham
last_name: Acevedo-Arozena
- first_name: Iannis E.
full_name: Adamopoulos, Iannis E.
last_name: Adamopoulos
- first_name: Khosrow
full_name: Adeli, Khosrow
last_name: Adeli
- first_name: Timon E.
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full_name: Martins, Joilson O.
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Z.Y. Zhou, Z. Zhou, B. Zhu, C. Zhu, G.Q. Zhu, H. Zhu, H. Zhu, H. Zhu, W.G. Zhu,
Y. Zhu, Y. Zhu, H. Zhuang, X. Zhuang, K. Zientara-Rytter, C.M. Zimmermann, E.
Ziviani, T. Zoladek, W.X. Zong, D.B. Zorov, A. Zorzano, W. Zou, Z. Zou, Z. Zou,
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date_created: 2021-03-28T22:01:44Z
date_published: 2021-02-08T00:00:00Z
date_updated: 2023-10-16T09:43:56Z
day: '08'
department:
- _id: JiFr
- _id: CaHe
doi: 10.1080/15548627.2020.1797280
external_id:
isi:
- '000636121800001'
pmid:
- '33634751'
intvolume: ' 17'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1080/15548627.2020.1797280
month: '02'
oa: 1
oa_version: Published Version
page: 1-382
pmid: 1
publication: Autophagy
publication_identifier:
eissn:
- 1554-8635
issn:
- 1554-8627
publication_status: published
publisher: Taylor & Francis
quality_controlled: '1'
scopus_import: '1'
status: public
title: Guidelines for the use and interpretation of assays for monitoring autophagy
(4th edition)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2021'
...
---
_id: '8742'
abstract:
- lang: eng
text: We develop a version of Ekedahl’s geometric sieve for integral quadratic forms
of rank at least five. As one ranges over the zeros of such quadratic forms, we
use the sieve to compute the density of coprime values of polynomials, and furthermore,
to address a question about local solubility in families of varieties parameterised
by the zeros.
article_processing_charge: No
article_type: original
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Roger
full_name: Heath-Brown, Roger
last_name: Heath-Brown
citation:
ama: Browning TD, Heath-Brown R. The geometric sieve for quadrics. Forum Mathematicum.
2021;33(1):147-165. doi:10.1515/forum-2020-0074
apa: Browning, T. D., & Heath-Brown, R. (2021). The geometric sieve for quadrics.
Forum Mathematicum. De Gruyter. https://doi.org/10.1515/forum-2020-0074
chicago: Browning, Timothy D, and Roger Heath-Brown. “The Geometric Sieve for Quadrics.”
Forum Mathematicum. De Gruyter, 2021. https://doi.org/10.1515/forum-2020-0074.
ieee: T. D. Browning and R. Heath-Brown, “The geometric sieve for quadrics,” Forum
Mathematicum, vol. 33, no. 1. De Gruyter, pp. 147–165, 2021.
ista: Browning TD, Heath-Brown R. 2021. The geometric sieve for quadrics. Forum
Mathematicum. 33(1), 147–165.
mla: Browning, Timothy D., and Roger Heath-Brown. “The Geometric Sieve for Quadrics.”
Forum Mathematicum, vol. 33, no. 1, De Gruyter, 2021, pp. 147–65, doi:10.1515/forum-2020-0074.
short: T.D. Browning, R. Heath-Brown, Forum Mathematicum 33 (2021) 147–165.
date_created: 2020-11-08T23:01:25Z
date_published: 2021-01-01T00:00:00Z
date_updated: 2023-10-17T07:39:01Z
day: '01'
department:
- _id: TiBr
doi: 10.1515/forum-2020-0074
external_id:
arxiv:
- '2003.09593'
isi:
- '000604750900008'
intvolume: ' 33'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
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url: https://arxiv.org/abs/2003.09593
month: '01'
oa: 1
oa_version: Preprint
page: 147-165
project:
- _id: 26AEDAB2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P32428
name: New frontiers of the Manin conjecture
publication: Forum Mathematicum
publication_identifier:
eissn:
- 1435-5337
issn:
- 0933-7741
publication_status: published
publisher: De Gruyter
quality_controlled: '1'
scopus_import: '1'
status: public
title: The geometric sieve for quadrics
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2021'
...
---
_id: '10035'
abstract:
- lang: eng
text: 'Many security definitions come in two flavors: a stronger “adaptive” flavor,
where the adversary can arbitrarily make various choices during the course of
the attack, and a weaker “selective” flavor where the adversary must commit to
some or all of their choices a-priori. For example, in the context of identity-based
encryption, selective security requires the adversary to decide on the identity
of the attacked party at the very beginning of the game whereas adaptive security
allows the attacker to first see the master public key and some secret keys before
making this choice. Often, it appears to be much easier to achieve selective security
than it is to achieve adaptive security. A series of several recent works shows
how to cleverly achieve adaptive security in several such scenarios including
generalized selective decryption [Pan07][FJP15], constrained PRFs [FKPR14], and
Yao’s garbled circuits [JW16]. Although the above works expressed vague intuition
that they share a common technique, the connection was never made precise. In
this work we present a new framework (published at Crypto ’17 [JKK+17a]) that
connects all of these works and allows us to present them in a unified and simplified
fashion. Having the framework in place, we show how to achieve adaptive security
for proxy re-encryption schemes (published at PKC ’19 [FKKP19]) and provide the
first adaptive security proofs for continuous group key agreement protocols (published
at S&P ’21 [KPW+21]). Questioning optimality of our framework, we then show that
currently used proof techniques cannot lead to significantly better security guarantees
for "graph-building" games (published at TCC ’21 [KKPW21a]). These games cover
generalized selective decryption, as well as the security of prominent constructions
for constrained PRFs, continuous group key agreement, and proxy re-encryption.
Finally, we revisit the adaptive security of Yao’s garbled circuits and extend
the analysis of Jafargholi and Wichs in two directions: While they prove adaptive
security only for a modified construction with increased online complexity, we
provide the first positive results for the original construction by Yao (published
at TCC ’21 [KKP21a]). On the negative side, we prove that the results of Jafargholi
and Wichs are essentially optimal by showing that no black-box reduction can provide
a significantly better security bound (published at Crypto ’21 [KKPW21c]).'
acknowledgement: "I want to acknowledge the funding by the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(682815 - TOCNeT).\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Karen
full_name: Klein, Karen
id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87
last_name: Klein
citation:
ama: Klein K. On the adaptive security of graph-based games. 2021. doi:10.15479/at:ista:10035
apa: Klein, K. (2021). On the adaptive security of graph-based games. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:10035
chicago: Klein, Karen. “On the Adaptive Security of Graph-Based Games.” Institute
of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10035.
ieee: K. Klein, “On the adaptive security of graph-based games,” Institute of Science
and Technology Austria, 2021.
ista: Klein K. 2021. On the adaptive security of graph-based games. Institute of
Science and Technology Austria.
mla: Klein, Karen. On the Adaptive Security of Graph-Based Games. Institute
of Science and Technology Austria, 2021, doi:10.15479/at:ista:10035.
short: K. Klein, On the Adaptive Security of Graph-Based Games, Institute of Science
and Technology Austria, 2021.
date_created: 2021-09-23T07:31:44Z
date_published: 2021-09-23T00:00:00Z
date_updated: 2023-10-17T09:24:07Z
day: '23'
ddc:
- '519'
degree_awarded: PhD
department:
- _id: GradSch
- _id: KrPi
doi: 10.15479/at:ista:10035
ec_funded: 1
file:
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creator: cchlebak
date_created: 2021-10-04T12:22:33Z
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date_created: 2021-10-05T07:04:37Z
date_updated: 2022-03-10T12:15:18Z
file_id: '10085'
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month: '09'
oa: 1
oa_version: Published Version
page: '276'
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
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relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
title: On the adaptive security of graph-based games
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10410'
abstract:
- lang: eng
text: The security of cryptographic primitives and protocols against adversaries
that are allowed to make adaptive choices (e.g., which parties to corrupt or which
queries to make) is notoriously difficult to establish. A broad theoretical framework
was introduced by Jafargholi et al. [Crypto’17] for this purpose. In this paper
we initiate the study of lower bounds on loss in adaptive security for certain
cryptographic protocols considered in the framework. We prove lower bounds that
almost match the upper bounds (proven using the framework) for proxy re-encryption,
prefix-constrained PRFs and generalized selective decryption, a security game
that captures the security of certain group messaging and broadcast encryption
schemes. Those primitives have in common that their security game involves an
underlying graph that can be adaptively built by the adversary. Some of our lower
bounds only apply to a restricted class of black-box reductions which we term
“oblivious” (the existing upper bounds are of this restricted type), some apply
to the broader but still restricted class of non-rewinding reductions, while our
lower bound for proxy re-encryption applies to all black-box reductions. The fact
that some of our lower bounds seem to crucially rely on obliviousness or at least
a non-rewinding reduction hints to the exciting possibility that the existing
upper bounds can be improved by using more sophisticated reductions. Our main
conceptual contribution is a two-player multi-stage game called the Builder-Pebbler
Game. We can translate bounds on the winning probabilities for various instantiations
of this game into cryptographic lower bounds for the above-mentioned primitives
using oracle separation techniques.
acknowledgement: C. Kamath—Supported by Azrieli International Postdoctoral Fellowship.
Most of the work was done while the author was at Northeastern University and Charles
University, funded by the IARPA grant IARPA/2019-19-020700009 and project PRIMUS/17/SCI/9,
respectively. K. Klein—Supported in part by ERC CoG grant 724307. Most of the work
was done while the author was at IST Austria funded by the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(682815 - TOCNeT). K. Pietrzak—Funded by the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Chethan
full_name: Kamath Hosdurg, Chethan
id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87
last_name: Kamath Hosdurg
- first_name: Karen
full_name: Klein, Karen
id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87
last_name: Klein
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Michael
full_name: Walter, Michael
id: 488F98B0-F248-11E8-B48F-1D18A9856A87
last_name: Walter
orcid: 0000-0003-3186-2482
citation:
ama: 'Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. The cost of adaptivity in
security games on graphs. In: 19th International Conference. Vol 13043.
Springer Nature; 2021:550-581. doi:10.1007/978-3-030-90453-1_19'
apa: 'Kamath Hosdurg, C., Klein, K., Pietrzak, K. Z., & Walter, M. (2021). The
cost of adaptivity in security games on graphs. In 19th International Conference
(Vol. 13043, pp. 550–581). Raleigh, NC, United States: Springer Nature. https://doi.org/10.1007/978-3-030-90453-1_19'
chicago: Kamath Hosdurg, Chethan, Karen Klein, Krzysztof Z Pietrzak, and Michael
Walter. “The Cost of Adaptivity in Security Games on Graphs.” In 19th International
Conference, 13043:550–81. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90453-1_19.
ieee: C. Kamath Hosdurg, K. Klein, K. Z. Pietrzak, and M. Walter, “The cost of adaptivity
in security games on graphs,” in 19th International Conference, Raleigh,
NC, United States, 2021, vol. 13043, pp. 550–581.
ista: 'Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. 2021. The cost of adaptivity
in security games on graphs. 19th International Conference. TCC: Theory of Cryptography,
LNCS, vol. 13043, 550–581.'
mla: Kamath Hosdurg, Chethan, et al. “The Cost of Adaptivity in Security Games on
Graphs.” 19th International Conference, vol. 13043, Springer Nature, 2021,
pp. 550–81, doi:10.1007/978-3-030-90453-1_19.
short: C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, M. Walter, in:, 19th International
Conference, Springer Nature, 2021, pp. 550–581.
conference:
end_date: 2021-11-11
location: Raleigh, NC, United States
name: 'TCC: Theory of Cryptography'
start_date: 2021-11-08
date_created: 2021-12-05T23:01:43Z
date_published: 2021-11-04T00:00:00Z
date_updated: 2023-10-17T09:24:07Z
day: '04'
department:
- _id: KrPi
doi: 10.1007/978-3-030-90453-1_19
ec_funded: 1
external_id:
isi:
- '000728364000019'
intvolume: ' 13043'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://ia.cr/2021/059
month: '11'
oa: 1
oa_version: Preprint
page: 550-581
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication: 19th International Conference
publication_identifier:
eissn:
- 1611-3349
isbn:
- 9-783-0309-0452-4
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '10048'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: The cost of adaptivity in security games on graphs
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 13043
year: '2021'
...
---
_id: '10048'
abstract:
- lang: eng
text: "The security of cryptographic primitives and protocols against adversaries
that are allowed to make adaptive choices (e.g., which parties to corrupt or which
queries to make) is notoriously difficult to establish. A broad theoretical\r\nframework
was introduced by Jafargholi et al. [Crypto’17] for this purpose. In this paper
we initiate the study of lower bounds on loss in adaptive security for certain
cryptographic protocols considered in the framework. We prove lower\r\nbounds
that almost match the upper bounds (proven using the framework) for proxy re-encryption,
prefix-constrained PRFs and generalized selective decryption, a security game
that captures the security of certain group messaging and\r\nbroadcast encryption
schemes. Those primitives have in common that their security game involves an
underlying graph that can be adaptively built by the adversary. Some of our lower
bounds only apply to a restricted class of black-box reductions which we term
“oblivious” (the existing upper bounds are of this restricted type), some apply
to the broader but still restricted class of non-rewinding reductions, while our
lower bound for proxy re-encryption applies to all black-box reductions. The fact
that some of our lower bounds seem to crucially rely on obliviousness or at least
a non-rewinding reduction hints to the exciting possibility that the existing
upper bounds can be improved by using more sophisticated reductions. Our main
conceptual contribution is a two-player multi-stage game called the Builder-Pebbler
Game. We can translate bounds on the winning probabilities for various instantiations
of this game into cryptographic lower bounds for the above-mentioned primitives
using oracle separation techniques.\r\n"
article_processing_charge: No
author:
- first_name: Chethan
full_name: Kamath Hosdurg, Chethan
id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87
last_name: Kamath Hosdurg
- first_name: Karen
full_name: Klein, Karen
id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87
last_name: Klein
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Michael
full_name: Walter, Michael
id: 488F98B0-F248-11E8-B48F-1D18A9856A87
last_name: Walter
orcid: 0000-0003-3186-2482
citation:
ama: 'Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. The cost of adaptivity in
security games on graphs. In: 19th Theory of Cryptography Conference 2021.
International Association for Cryptologic Research; 2021.'
apa: 'Kamath Hosdurg, C., Klein, K., Pietrzak, K. Z., & Walter, M. (2021). The
cost of adaptivity in security games on graphs. In 19th Theory of Cryptography
Conference 2021. Raleigh, NC, United States: International Association for
Cryptologic Research.'
chicago: Kamath Hosdurg, Chethan, Karen Klein, Krzysztof Z Pietrzak, and Michael
Walter. “The Cost of Adaptivity in Security Games on Graphs.” In 19th Theory
of Cryptography Conference 2021. International Association for Cryptologic
Research, 2021.
ieee: C. Kamath Hosdurg, K. Klein, K. Z. Pietrzak, and M. Walter, “The cost of adaptivity
in security games on graphs,” in 19th Theory of Cryptography Conference 2021,
Raleigh, NC, United States, 2021.
ista: 'Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. 2021. The cost of adaptivity
in security games on graphs. 19th Theory of Cryptography Conference 2021. TCC:
Theory of Cryptography Conference.'
mla: Kamath Hosdurg, Chethan, et al. “The Cost of Adaptivity in Security Games on
Graphs.” 19th Theory of Cryptography Conference 2021, International Association
for Cryptologic Research, 2021.
short: C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, M. Walter, in:, 19th Theory of
Cryptography Conference 2021, International Association for Cryptologic Research,
2021.
conference:
end_date: 2021-11-11
location: Raleigh, NC, United States
name: 'TCC: Theory of Cryptography Conference'
start_date: 2021-11-08
date_created: 2021-09-27T12:52:05Z
date_published: 2021-07-08T00:00:00Z
date_updated: 2023-10-17T09:24:08Z
day: '08'
department:
- _id: KrPi
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://ia.cr/2021/059
month: '07'
oa: 1
oa_version: Preprint
publication: 19th Theory of Cryptography Conference 2021
publication_status: published
publisher: International Association for Cryptologic Research
quality_controlled: '1'
related_material:
record:
- id: '10410'
relation: later_version
status: public
- id: '10035'
relation: dissertation_contains
status: public
status: public
title: The cost of adaptivity in security games on graphs
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '10738'
abstract:
- lang: eng
text: We prove an adiabatic theorem for the Landau–Pekar equations. This allows
us to derive new results on the accuracy of their use as effective equations for
the time evolution generated by the Fröhlich Hamiltonian with large coupling constant
α. In particular, we show that the time evolution of Pekar product states with
coherent phonon field and the electron being trapped by the phonons is well approximated
by the Landau–Pekar equations until times short compared to α2.
acknowledgement: "N. L. and R. S. gratefully acknowledge financial support by the
European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research
and innovation programme (grant\r\nagreement No 694227). B. S. acknowledges support
from the Swiss National Science Foundation (grant 200020_172623) and from the NCCR
SwissMAP. N. L. would like to thank\r\nAndreas Deuchert and David Mitrouskas for
interesting discussions. B. S. and R. S. would\r\nlike to thank Rupert Frank for
stimulating discussions about the time-evolution of a polaron.\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Nikolai K
full_name: Leopold, Nikolai K
id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87
last_name: Leopold
orcid: 0000-0002-0495-6822
- first_name: Simone Anna Elvira
full_name: Rademacher, Simone Anna Elvira
id: 856966FE-A408-11E9-977E-802DE6697425
last_name: Rademacher
orcid: 0000-0001-5059-4466
- first_name: Benjamin
full_name: Schlein, Benjamin
last_name: Schlein
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: 'Leopold NK, Rademacher SAE, Schlein B, Seiringer R. The Landau–Pekar equations:
Adiabatic theorem and accuracy. Analysis and PDE. 2021;14(7):2079-2100.
doi:10.2140/APDE.2021.14.2079'
apa: 'Leopold, N. K., Rademacher, S. A. E., Schlein, B., & Seiringer, R. (2021). The
Landau–Pekar equations: Adiabatic theorem and accuracy. Analysis and PDE.
Mathematical Sciences Publishers. https://doi.org/10.2140/APDE.2021.14.2079'
chicago: 'Leopold, Nikolai K, Simone Anna Elvira Rademacher, Benjamin Schlein, and
Robert Seiringer. “ The Landau–Pekar Equations: Adiabatic Theorem and Accuracy.”
Analysis and PDE. Mathematical Sciences Publishers, 2021. https://doi.org/10.2140/APDE.2021.14.2079.'
ieee: 'N. K. Leopold, S. A. E. Rademacher, B. Schlein, and R. Seiringer, “ The Landau–Pekar
equations: Adiabatic theorem and accuracy,” Analysis and PDE, vol. 14,
no. 7. Mathematical Sciences Publishers, pp. 2079–2100, 2021.'
ista: 'Leopold NK, Rademacher SAE, Schlein B, Seiringer R. 2021. The Landau–Pekar
equations: Adiabatic theorem and accuracy. Analysis and PDE. 14(7), 2079–2100.'
mla: 'Leopold, Nikolai K., et al. “ The Landau–Pekar Equations: Adiabatic Theorem
and Accuracy.” Analysis and PDE, vol. 14, no. 7, Mathematical Sciences
Publishers, 2021, pp. 2079–100, doi:10.2140/APDE.2021.14.2079.'
short: N.K. Leopold, S.A.E. Rademacher, B. Schlein, R. Seiringer, Analysis and PDE
14 (2021) 2079–2100.
date_created: 2022-02-06T23:01:33Z
date_published: 2021-11-10T00:00:00Z
date_updated: 2023-10-17T11:26:45Z
day: '10'
department:
- _id: RoSe
doi: 10.2140/APDE.2021.14.2079
ec_funded: 1
external_id:
arxiv:
- '1904.12532'
isi:
- '000733976600004'
intvolume: ' 14'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1904.12532
month: '11'
oa: 1
oa_version: Preprint
page: 2079-2100
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Analysis and PDE
publication_identifier:
eissn:
- 1948-206X
issn:
- 2157-5045
publication_status: published
publisher: Mathematical Sciences Publishers
quality_controlled: '1'
scopus_import: '1'
status: public
title: ' The Landau–Pekar equations: Adiabatic theorem and accuracy'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2021'
...
---
_id: '10429'
abstract:
- lang: eng
text: "The scalability of concurrent data structures and distributed algorithms
strongly depends on\r\nreducing the contention for shared resources and the costs
of synchronization and communication. We show how such cost reductions can be
attained by relaxing the strict consistency conditions required by sequential
implementations. In the first part of the thesis, we consider relaxation in the
context of concurrent data structures. Specifically, in data structures \r\nsuch
as priority queues, imposing strong semantics renders scalability impossible,
since a correct implementation of the remove operation should return only the
element with highest priority. Intuitively, attempting to invoke remove operations
concurrently creates a race condition. This bottleneck can be circumvented by
relaxing semantics of the affected data structure, thus allowing removal of the
elements which are no longer required to have the highest priority. We prove that
the randomized implementations of relaxed data structures provide provable guarantees
on the priority of the removed elements even under concurrency. Additionally,
we show that in some cases the relaxed data structures can be used to scale the
classical algorithms which are usually implemented with the exact ones. In the
second part, we study parallel variants of the stochastic gradient descent (SGD)
algorithm, which distribute computation among the multiple processors, thus reducing
the running time. Unfortunately, in order for standard parallel SGD to succeed,
each processor has to maintain a local copy of the necessary model parameter,
which is identical to the local copies of other processors; the overheads from
this perfect consistency in terms of communication and synchronization can negate
the speedup gained by distributing the computation. We show that the consistency
conditions required by SGD can be relaxed, allowing the algorithm to be more
flexible in terms of tolerating quantized communication, asynchrony, or even crash
faults, while its convergence remains asymptotically the same."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Giorgi
full_name: Nadiradze, Giorgi
id: 3279A00C-F248-11E8-B48F-1D18A9856A87
last_name: Nadiradze
orcid: 0000-0001-5634-0731
citation:
ama: Nadiradze G. On achieving scalability through relaxation. 2021. doi:10.15479/at:ista:10429
apa: Nadiradze, G. (2021). On achieving scalability through relaxation. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:10429
chicago: Nadiradze, Giorgi. “On Achieving Scalability through Relaxation.” Institute
of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10429.
ieee: G. Nadiradze, “On achieving scalability through relaxation,” Institute of
Science and Technology Austria, 2021.
ista: Nadiradze G. 2021. On achieving scalability through relaxation. Institute
of Science and Technology Austria.
mla: Nadiradze, Giorgi. On Achieving Scalability through Relaxation. Institute
of Science and Technology Austria, 2021, doi:10.15479/at:ista:10429.
short: G. Nadiradze, On Achieving Scalability through Relaxation, Institute of Science
and Technology Austria, 2021.
date_created: 2021-12-08T21:52:28Z
date_published: 2021-12-09T00:00:00Z
date_updated: 2023-10-17T11:48:55Z
day: '09'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: GradSch
- _id: DaAl
doi: 10.15479/at:ista:10429
ec_funded: 1
file:
- access_level: open_access
checksum: 6bf14e9a523387328f016c0689f5e10e
content_type: application/pdf
creator: gnadirad
date_created: 2021-12-09T17:47:49Z
date_updated: 2021-12-09T17:47:49Z
file_id: '10436'
file_name: Thesis_Final_09_12_2021.pdf
file_size: 2370859
relation: main_file
success: 1
- access_level: closed
checksum: 914d6c5ca86bd0add471971a8f4c4341
content_type: application/zip
creator: gnadirad
date_created: 2021-12-09T17:47:49Z
date_updated: 2022-03-28T12:55:12Z
file_id: '10437'
file_name: Thesis_Final_09_12_2021.zip
file_size: 2596924
relation: source_file
file_date_updated: 2022-03-28T12:55:12Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '132'
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10432'
relation: part_of_dissertation
status: public
- id: '6673'
relation: part_of_dissertation
status: public
- id: '5965'
relation: part_of_dissertation
status: public
- id: '10435'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
title: On achieving scalability through relaxation
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10435'
abstract:
- lang: eng
text: Decentralized optimization is emerging as a viable alternative for scalable
distributed machine learning, but also introduces new challenges in terms of synchronization
costs. To this end, several communication-reduction techniques, such as non-blocking
communication, quantization, and local steps, have been explored in the decentralized
setting. Due to the complexity of analyzing optimization in such a relaxed setting,
this line of work often assumes \emph{global} communication rounds, which require
additional synchronization. In this paper, we consider decentralized optimization
in the simpler, but harder to analyze, \emph{asynchronous gossip} model, in which
communication occurs in discrete, randomly chosen pairings among nodes. Perhaps
surprisingly, we show that a variant of SGD called \emph{SwarmSGD} still converges
in this setting, even if \emph{non-blocking communication}, \emph{quantization},
and \emph{local steps} are all applied \emph{in conjunction}, and even if the
node data distributions and underlying graph topology are both \emph{heterogenous}.
Our analysis is based on a new connection with multi-dimensional load-balancing
processes. We implement this algorithm and deploy it in a super-computing environment,
showing that it can outperform previous decentralized methods in terms of end-to-end
training time, and that it can even rival carefully-tuned large-batch SGD for
certain tasks.
acknowledgement: "We gratefully acknowledge funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement No 805223 ScaleML). PD partly conducted this work while at IST
Austria and was supported by the European Union’s Horizon 2020 programme under the
Marie Skłodowska-Curie grant agreement No. 754411. SL was funded in part by European
Research Council (ERC) under the European Union’s Horizon 2020 programme (grant
agreement DAPP, No. 678880, and EPiGRAM-HS, No. 801039).\r\n"
article_processing_charge: No
author:
- first_name: Giorgi
full_name: Nadiradze, Giorgi
id: 3279A00C-F248-11E8-B48F-1D18A9856A87
last_name: Nadiradze
orcid: 0000-0001-5634-0731
- first_name: Amirmojtaba
full_name: Sabour, Amirmojtaba
id: bcc145fd-e77f-11ea-ae8b-80d661dbff67
last_name: Sabour
- first_name: Peter
full_name: Davies, Peter
id: 11396234-BB50-11E9-B24C-90FCE5697425
last_name: Davies
orcid: 0000-0002-5646-9524
- first_name: Shigang
full_name: Li, Shigang
last_name: Li
- 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: 'Nadiradze G, Sabour A, Davies P, Li S, Alistarh D-A. Asynchronous decentralized
SGD with quantized and local updates. In: 35th Conference on Neural Information
Processing Systems. Neural Information Processing Systems Foundation; 2021.'
apa: 'Nadiradze, G., Sabour, A., Davies, P., Li, S., & Alistarh, D.-A. (2021).
Asynchronous decentralized SGD with quantized and local updates. In 35th Conference
on Neural Information Processing Systems. Sydney, Australia: Neural Information
Processing Systems Foundation.'
chicago: Nadiradze, Giorgi, Amirmojtaba Sabour, Peter Davies, Shigang Li, and Dan-Adrian
Alistarh. “Asynchronous Decentralized SGD with Quantized and Local Updates.” In
35th Conference on Neural Information Processing Systems. Neural Information
Processing Systems Foundation, 2021.
ieee: G. Nadiradze, A. Sabour, P. Davies, S. Li, and D.-A. Alistarh, “Asynchronous
decentralized SGD with quantized and local updates,” in 35th Conference on
Neural Information Processing Systems, Sydney, Australia, 2021.
ista: 'Nadiradze G, Sabour A, Davies P, Li S, Alistarh D-A. 2021. Asynchronous decentralized
SGD with quantized and local updates. 35th Conference on Neural Information Processing
Systems. NeurIPS: Neural Information Processing Systems.'
mla: Nadiradze, Giorgi, et al. “Asynchronous Decentralized SGD with Quantized and
Local Updates.” 35th Conference on Neural Information Processing Systems,
Neural Information Processing Systems Foundation, 2021.
short: G. Nadiradze, A. Sabour, P. Davies, S. Li, D.-A. Alistarh, in:, 35th Conference
on Neural Information Processing Systems, Neural Information Processing Systems
Foundation, 2021.
conference:
end_date: 2021-12-14
location: Sydney, Australia
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2021-12-06
date_created: 2021-12-09T10:59:12Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2023-10-17T11:48:56Z
day: '01'
department:
- _id: DaAl
ec_funded: 1
external_id:
arxiv:
- '1910.12308'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://papers.nips.cc/paper/2021/hash/362c99307cdc3f2d8b410652386a9dd1-Abstract.html
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: 35th Conference on Neural Information Processing Systems
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
related_material:
record:
- id: '10429'
relation: dissertation_contains
status: public
status: public
title: Asynchronous decentralized SGD with quantized and local updates
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '10593'
abstract:
- lang: eng
text: 'We study the problem of estimating a rank-$1$ signal in the presence of rotationally
invariant noise-a class of perturbations more general than Gaussian noise. Principal
Component Analysis (PCA) provides a natural estimator, and sharp results on its
performance have been obtained in the high-dimensional regime. Recently, an Approximate
Message Passing (AMP) algorithm has been proposed as an alternative estimator
with the potential to improve the accuracy of PCA. However, the existing analysis
of AMP requires an initialization that is both correlated with the signal and
independent of the noise, which is often unrealistic in practice. In this work,
we combine the two methods, and propose to initialize AMP with PCA. Our main result
is a rigorous asymptotic characterization of the performance of this estimator.
Both the AMP algorithm and its analysis differ from those previously derived in
the Gaussian setting: at every iteration, our AMP algorithm requires a specific
term to account for PCA initialization, while in the Gaussian case, PCA initialization
affects only the first iteration of AMP. The proof is based on a two-phase artificial
AMP that first approximates the PCA estimator and then mimics the true AMP. Our
numerical simulations show an excellent agreement between AMP results and theoretical
predictions, and suggest an interesting open direction on achieving Bayes-optimal
performance.'
acknowledgement: "M. Mondelli would like to thank László Erdős for helpful discussions.
M. Mondelli was partially supported by the 2019 Lopez-Loreta Prize. R. Venkataramanan
was partially supported by the Alan Turing Institute under the EPSRC grant EP/N510129/1.\r\n"
article_processing_charge: No
author:
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Ramji
full_name: Venkataramanan, Ramji
last_name: Venkataramanan
citation:
ama: 'Mondelli M, Venkataramanan R. PCA initialization for approximate message passing
in rotationally invariant models. In: 35th Conference on Neural Information
Processing Systems. Vol 35. Neural Information Processing Systems Foundation;
2021:29616-29629.'
apa: 'Mondelli, M., & Venkataramanan, R. (2021). PCA initialization for approximate
message passing in rotationally invariant models. In 35th Conference on Neural
Information Processing Systems (Vol. 35, pp. 29616–29629). Virtual: Neural
Information Processing Systems Foundation.'
chicago: Mondelli, Marco, and Ramji Venkataramanan. “PCA Initialization for Approximate
Message Passing in Rotationally Invariant Models.” In 35th Conference on Neural
Information Processing Systems, 35:29616–29. Neural Information Processing
Systems Foundation, 2021.
ieee: M. Mondelli and R. Venkataramanan, “PCA initialization for approximate message
passing in rotationally invariant models,” in 35th Conference on Neural Information
Processing Systems, Virtual, 2021, vol. 35, pp. 29616–29629.
ista: 'Mondelli M, Venkataramanan R. 2021. PCA initialization for approximate message
passing in rotationally invariant models. 35th Conference on Neural Information
Processing Systems. NeurIPS: Neural Information Processing Systems vol. 35, 29616–29629.'
mla: Mondelli, Marco, and Ramji Venkataramanan. “PCA Initialization for Approximate
Message Passing in Rotationally Invariant Models.” 35th Conference on Neural
Information Processing Systems, vol. 35, Neural Information Processing Systems
Foundation, 2021, pp. 29616–29.
short: M. Mondelli, R. Venkataramanan, in:, 35th Conference on Neural Information
Processing Systems, Neural Information Processing Systems Foundation, 2021, pp.
29616–29629.
conference:
end_date: 2021-12-14
location: Virtual
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2021-12-06
date_created: 2022-01-03T10:50:02Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2023-10-17T11:48:23Z
day: '01'
department:
- _id: MaMo
external_id:
arxiv:
- '2106.02356'
intvolume: ' 35'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2106.02356
month: '12'
oa: 1
oa_version: Preprint
page: 29616-29629
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: 35th Conference on Neural Information Processing Systems
publication_identifier:
isbn:
- '9781713845393'
issn:
- 1049-5258
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: PCA initialization for approximate message passing in rotationally invariant
models
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2021'
...
---
_id: '10594'
abstract:
- lang: eng
text: 'The question of how and why the phenomenon of mode connectivity occurs in
training deep neural networks has gained remarkable attention in the research
community. From a theoretical perspective, two possible explanations have been
proposed: (i) the loss function has connected sublevel sets, and (ii) the solutions
found by stochastic gradient descent are dropout stable. While these explanations
provide insights into the phenomenon, their assumptions are not always satisfied
in practice. In particular, the first approach requires the network to have one
layer with order of N neurons (N being the number of training samples), while
the second one requires the loss to be almost invariant after removing half of
the neurons at each layer (up to some rescaling of the remaining ones). In this
work, we improve both conditions by exploiting the quality of the features at
every intermediate layer together with a milder over-parameterization condition.
More specifically, we show that: (i) under generic assumptions on the features
of intermediate layers, it suffices that the last two hidden layers have order
of N−−√ neurons, and (ii) if subsets of features at each layer are linearly separable,
then no over-parameterization is needed to show the connectivity. Our experiments
confirm that the proposed condition ensures the connectivity of solutions found
by stochastic gradient descent, even in settings where the previous requirements
do not hold.'
acknowledgement: MM was partially supported by the 2019 Lopez-Loreta Prize. QN and
PB acknowledge support from the European Research Council (ERC) under the European
Union’s Horizon 2020 research and innovation programme (grant agreement no 757983).
article_processing_charge: No
author:
- first_name: Quynh
full_name: Nguyen, Quynh
last_name: Nguyen
- first_name: Pierre
full_name: Bréchet, Pierre
last_name: Bréchet
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
citation:
ama: 'Nguyen Q, Bréchet P, Mondelli M. When are solutions connected in deep networks?
In: 35th Conference on Neural Information Processing Systems. Vol 35. Neural
Information Processing Systems Foundation; 2021.'
apa: 'Nguyen, Q., Bréchet, P., & Mondelli, M. (2021). When are solutions connected
in deep networks? In 35th Conference on Neural Information Processing Systems
(Vol. 35). Virtual: Neural Information Processing Systems Foundation.'
chicago: Nguyen, Quynh, Pierre Bréchet, and Marco Mondelli. “When Are Solutions
Connected in Deep Networks?” In 35th Conference on Neural Information Processing
Systems, Vol. 35. Neural Information Processing Systems Foundation, 2021.
ieee: Q. Nguyen, P. Bréchet, and M. Mondelli, “When are solutions connected in deep
networks?,” in 35th Conference on Neural Information Processing Systems,
Virtual, 2021, vol. 35.
ista: Nguyen Q, Bréchet P, Mondelli M. 2021. When are solutions connected in deep
networks? 35th Conference on Neural Information Processing Systems. 35th Conference
on Neural Information Processing Systems vol. 35.
mla: Nguyen, Quynh, et al. “When Are Solutions Connected in Deep Networks?” 35th
Conference on Neural Information Processing Systems, vol. 35, Neural Information
Processing Systems Foundation, 2021.
short: Q. Nguyen, P. Bréchet, M. Mondelli, in:, 35th Conference on Neural Information
Processing Systems, Neural Information Processing Systems Foundation, 2021.
conference:
end_date: 2021-12-14
location: Virtual
name: 35th Conference on Neural Information Processing Systems
start_date: 2021-12-06
date_created: 2022-01-03T10:56:20Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2023-10-17T11:48:40Z
day: '01'
department:
- _id: MaMo
external_id:
arxiv:
- '2102.09671'
intvolume: ' 35'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2102.09671
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: 35th Conference on Neural Information Processing Systems
publication_identifier:
isbn:
- '9781713845393'
issn:
- 1049-5258
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
status: public
title: When are solutions connected in deep networks?
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2021'
...
---
_id: '9815'
abstract:
- lang: eng
text: The quantum bits (qubits) on which superconducting quantum computers are based
have energy scales corresponding to photons with GHz frequencies. The energy of
photons in the gigahertz domain is too low to allow transmission through the noisy
room-temperature environment, where the signal would be lost in thermal noise.
Optical photons, on the other hand, have much higher energies, and signals can
be detected using highly efficient single-photon detectors. Transduction from
microwave to optical frequencies is therefore a potential enabling technology
for quantum devices. However, in such a device the optical pump can be a source
of thermal noise and thus degrade the fidelity; the similarity of input microwave
state to the output optical state. In order to investigate the magnitude of this
effect we model the sub-Kelvin thermal behavior of an electro-optic transducer
based on a lithium niobate whispering gallery mode resonator. We find that there
is an optimum power level for a continuous pump, whilst pulsed operation of the
pump increases the fidelity of the conversion.
acknowledgement: NJL is supported by the MBIE Endeavour Fund (UOOX1805) and GL is
by the Julius von Haast Fellowship of New Zealand. SM acknowledges stimulating discussions
with T M Jensen.
article_number: '045005'
article_processing_charge: Yes
article_type: original
author:
- first_name: Sonia
full_name: Mobassem, Sonia
last_name: Mobassem
- first_name: Nicholas J.
full_name: Lambert, Nicholas J.
last_name: Lambert
- first_name: Alfredo R
full_name: Rueda Sanchez, Alfredo R
id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87
last_name: Rueda Sanchez
orcid: 0000-0001-6249-5860
- first_name: Johannes M
full_name: Fink, Johannes M
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Gerd
full_name: Leuchs, Gerd
last_name: Leuchs
- first_name: Harald G.L.
full_name: Schwefel, Harald G.L.
last_name: Schwefel
citation:
ama: Mobassem S, Lambert NJ, Rueda Sanchez AR, Fink JM, Leuchs G, Schwefel HGL.
Thermal noise in electro-optic devices at cryogenic temperatures. Quantum Science
and Technology. 2021;6(4). doi:10.1088/2058-9565/ac0f36
apa: Mobassem, S., Lambert, N. J., Rueda Sanchez, A. R., Fink, J. M., Leuchs, G.,
& Schwefel, H. G. L. (2021). Thermal noise in electro-optic devices at cryogenic
temperatures. Quantum Science and Technology. IOP Publishing. https://doi.org/10.1088/2058-9565/ac0f36
chicago: Mobassem, Sonia, Nicholas J. Lambert, Alfredo R Rueda Sanchez, Johannes
M Fink, Gerd Leuchs, and Harald G.L. Schwefel. “Thermal Noise in Electro-Optic
Devices at Cryogenic Temperatures.” Quantum Science and Technology. IOP
Publishing, 2021. https://doi.org/10.1088/2058-9565/ac0f36.
ieee: S. Mobassem, N. J. Lambert, A. R. Rueda Sanchez, J. M. Fink, G. Leuchs, and
H. G. L. Schwefel, “Thermal noise in electro-optic devices at cryogenic temperatures,”
Quantum Science and Technology, vol. 6, no. 4. IOP Publishing, 2021.
ista: Mobassem S, Lambert NJ, Rueda Sanchez AR, Fink JM, Leuchs G, Schwefel HGL.
2021. Thermal noise in electro-optic devices at cryogenic temperatures. Quantum
Science and Technology. 6(4), 045005.
mla: Mobassem, Sonia, et al. “Thermal Noise in Electro-Optic Devices at Cryogenic
Temperatures.” Quantum Science and Technology, vol. 6, no. 4, 045005, IOP
Publishing, 2021, doi:10.1088/2058-9565/ac0f36.
short: S. Mobassem, N.J. Lambert, A.R. Rueda Sanchez, J.M. Fink, G. Leuchs, H.G.L.
Schwefel, Quantum Science and Technology 6 (2021).
date_created: 2021-08-08T22:01:25Z
date_published: 2021-07-15T00:00:00Z
date_updated: 2023-10-17T12:54:54Z
day: '15'
ddc:
- '530'
department:
- _id: JoFi
doi: 10.1088/2058-9565/ac0f36
external_id:
arxiv:
- '2008.08764'
isi:
- '000673081500001'
file:
- access_level: open_access
checksum: b15c2c228487a75002c3b52d56f23d5c
content_type: application/pdf
creator: cchlebak
date_created: 2021-08-09T12:23:13Z
date_updated: 2021-08-09T12:23:13Z
file_id: '9836'
file_name: 2021_QuantumScienceTechnology_Mobassem.pdf
file_size: 2366118
relation: main_file
file_date_updated: 2021-08-09T12:23:13Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: Quantum Science and Technology
publication_identifier:
eissn:
- 2058-9565
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Thermal noise in electro-optic devices at cryogenic temperatures
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2021'
...
---
_id: '9978'
abstract:
- lang: eng
text: Redox mediators could catalyse otherwise slow and energy-inefficient cycling
of Li-S and Li-O 2 batteries by shuttling electrons/holes between the electrode
and the solid insulating storage materials. For mediators to work efficiently
they need to oxidize the solid with fast kinetics yet the lowest possible overpotential.
Here, we found that when the redox potentials of mediators are tuned via, e.g.,
Li + concentration in the electrolyte, they exhibit distinct threshold potentials,
where the kinetics accelerate several-fold within a range as small as 10 mV. This
phenomenon is independent of types of mediators and electrolyte. The acceleration
originates from the overpotentials required to activate fast Li + /e – extraction
and the following chemical step at specific abundant surface facets. Efficient
redox catalysis at insulating solids requires therefore carefully considering
the surface conditions of the storage materials and electrolyte-dependent redox
potentials, which may be tuned by salt concentrations or solvents.
acknowledgement: 'This work was financially supported by the National Natural Science
Foundation of China (51773092, 21975124, 11874254, 51802187, U2030206). S.A.F. is
indebted to IST Austria for support. '
article_processing_charge: No
author:
- first_name: Deqing
full_name: Cao, Deqing
last_name: Cao
- first_name: Xiaoxiao
full_name: Shen, Xiaoxiao
last_name: Shen
- first_name: Aiping
full_name: Wang, Aiping
last_name: Wang
- first_name: Fengjiao
full_name: Yu, Fengjiao
last_name: Yu
- first_name: Yuping
full_name: Wu, Yuping
last_name: Wu
- first_name: Siqi
full_name: Shi, Siqi
last_name: Shi
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Yuhui
full_name: Chen, Yuhui
last_name: Chen
citation:
ama: Cao D, Shen X, Wang A, et al. Sharp kinetic acceleration potentials during
mediated redox catalysis of insulators. Research Square. doi:10.21203/rs.3.rs-750965/v1
apa: Cao, D., Shen, X., Wang, A., Yu, F., Wu, Y., Shi, S., … Chen, Y. (n.d.). Sharp
kinetic acceleration potentials during mediated redox catalysis of insulators.
Research Square. Research Square. https://doi.org/10.21203/rs.3.rs-750965/v1
chicago: Cao, Deqing, Xiaoxiao Shen, Aiping Wang, Fengjiao Yu, Yuping Wu, Siqi Shi,
Stefan Alexander Freunberger, and Yuhui Chen. “Sharp Kinetic Acceleration Potentials
during Mediated Redox Catalysis of Insulators.” Research Square. Research
Square, n.d. https://doi.org/10.21203/rs.3.rs-750965/v1.
ieee: D. Cao et al., “Sharp kinetic acceleration potentials during mediated
redox catalysis of insulators,” Research Square. Research Square.
ista: Cao D, Shen X, Wang A, Yu F, Wu Y, Shi S, Freunberger SA, Chen Y. Sharp kinetic
acceleration potentials during mediated redox catalysis of insulators. Research
Square, 10.21203/rs.3.rs-750965/v1.
mla: Cao, Deqing, et al. “Sharp Kinetic Acceleration Potentials during Mediated
Redox Catalysis of Insulators.” Research Square, Research Square, doi:10.21203/rs.3.rs-750965/v1.
short: D. Cao, X. Shen, A. Wang, F. Yu, Y. Wu, S. Shi, S.A. Freunberger, Y. Chen,
Research Square (n.d.).
date_created: 2021-08-31T12:54:16Z
date_published: 2021-08-18T00:00:00Z
date_updated: 2023-10-17T13:06:29Z
day: '18'
ddc:
- '541'
department:
- _id: StFr
doi: 10.21203/rs.3.rs-750965/v1
file:
- access_level: open_access
checksum: 1878e91c29d5769ed5a827b0b7addf00
content_type: application/pdf
creator: cchlebak
date_created: 2021-08-31T14:02:19Z
date_updated: 2021-08-31T14:02:19Z
file_id: '9979'
file_name: 2021_ResearchSquare_Cao.pdf
file_size: 1019662
relation: main_file
success: 1
file_date_updated: 2021-08-31T14:02:19Z
has_accepted_license: '1'
keyword:
- Catalysis
- Energy engineering
- Materials theory and modeling
language:
- iso: eng
month: '08'
oa: 1
oa_version: Preprint
page: '21'
publication: Research Square
publication_identifier:
eissn:
- 2693-5015
publication_status: submitted
publisher: Research Square
related_material:
record:
- id: '10813'
relation: later_version
status: public
status: public
title: Sharp kinetic acceleration potentials during mediated redox catalysis of insulators
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: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '8730'
abstract:
- lang: eng
text: P-glycoprotein (ABCB1) and breast cancer resistance protein (ABCG2) restrict
at the blood–brain barrier (BBB) the brain distribution of the majority of currently
known molecularly targeted anticancer drugs. To improve brain delivery of dual
ABCB1/ABCG2 substrates, both ABCB1 and ABCG2 need to be inhibited simultaneously
at the BBB. We examined the feasibility of simultaneous ABCB1/ABCG2 inhibition
with i.v. co-infusion of erlotinib and tariquidar by studying brain distribution
of the model ABCB1/ABCG2 substrate [11C]erlotinib in mice and rhesus macaques
with PET. Tolerability of the erlotinib/tariquidar combination was assessed in
human embryonic stem cell-derived cerebral organoids. In mice and macaques, baseline
brain distribution of [11C]erlotinib was low (brain distribution volume, VT,brain < 0.3 mL/cm3).
Co-infusion of erlotinib and tariquidar increased VT,brain in mice by 3.0-fold
and in macaques by 3.4- to 5.0-fold, while infusion of erlotinib alone or tariquidar
alone led to less pronounced VT,brain increases in both species. Treatment of
cerebral organoids with erlotinib/tariquidar led to an induction of Caspase-3-dependent
apoptosis. Co-infusion of erlotinib/tariquidar may potentially allow for complete
ABCB1/ABCG2 inhibition at the BBB, while simultaneously achieving brain-targeted
EGFR inhibition. Our protocol may be applicable to enhance brain delivery of molecularly
targeted anticancer drugs for a more effective treatment of brain tumors.
article_processing_charge: No
article_type: original
author:
- first_name: N
full_name: Tournier, N
last_name: Tournier
- first_name: S
full_name: Goutal, S
last_name: Goutal
- first_name: S
full_name: Mairinger, S
last_name: Mairinger
- first_name: IH
full_name: Lozano, IH
last_name: Lozano
- first_name: T
full_name: Filip, T
last_name: Filip
- first_name: M
full_name: Sauberer, M
last_name: Sauberer
- first_name: F
full_name: Caillé, F
last_name: Caillé
- first_name: L
full_name: Breuil, L
last_name: Breuil
- first_name: J
full_name: Stanek, J
last_name: Stanek
- first_name: AF
full_name: Freeman, AF
last_name: Freeman
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: C
full_name: Truillet, C
last_name: Truillet
- first_name: T
full_name: Wanek, T
last_name: Wanek
- first_name: O
full_name: Langer, O
last_name: Langer
citation:
ama: Tournier N, Goutal S, Mairinger S, et al. Complete inhibition of ABCB1 and
ABCG2 at the blood-brain barrier by co-infusion of erlotinib and tariquidar to
improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. Journal
of Cerebral Blood Flow and Metabolism. 2021;41(7):1634-1646. doi:10.1177/0271678X20965500
apa: Tournier, N., Goutal, S., Mairinger, S., Lozano, I., Filip, T., Sauberer, M.,
… Langer, O. (2021). Complete inhibition of ABCB1 and ABCG2 at the blood-brain
barrier by co-infusion of erlotinib and tariquidar to improve brain delivery of
the model ABCB1/ABCG2 substrate [11C]erlotinib. Journal of Cerebral Blood Flow
and Metabolism. SAGE Publications. https://doi.org/10.1177/0271678X20965500
chicago: Tournier, N, S Goutal, S Mairinger, IH Lozano, T Filip, M Sauberer, F Caillé,
et al. “Complete Inhibition of ABCB1 and ABCG2 at the Blood-Brain Barrier by Co-Infusion
of Erlotinib and Tariquidar to Improve Brain Delivery of the Model ABCB1/ABCG2
Substrate [11C]Erlotinib.” Journal of Cerebral Blood Flow and Metabolism.
SAGE Publications, 2021. https://doi.org/10.1177/0271678X20965500.
ieee: N. Tournier et al., “Complete inhibition of ABCB1 and ABCG2 at the
blood-brain barrier by co-infusion of erlotinib and tariquidar to improve brain
delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib,” Journal of Cerebral
Blood Flow and Metabolism, vol. 41, no. 7. SAGE Publications, pp. 1634–1646,
2021.
ista: Tournier N, Goutal S, Mairinger S, Lozano I, Filip T, Sauberer M, Caillé F,
Breuil L, Stanek J, Freeman A, Novarino G, Truillet C, Wanek T, Langer O. 2021.
Complete inhibition of ABCB1 and ABCG2 at the blood-brain barrier by co-infusion
of erlotinib and tariquidar to improve brain delivery of the model ABCB1/ABCG2
substrate [11C]erlotinib. Journal of Cerebral Blood Flow and Metabolism. 41(7),
1634–1646.
mla: Tournier, N., et al. “Complete Inhibition of ABCB1 and ABCG2 at the Blood-Brain
Barrier by Co-Infusion of Erlotinib and Tariquidar to Improve Brain Delivery of
the Model ABCB1/ABCG2 Substrate [11C]Erlotinib.” Journal of Cerebral Blood
Flow and Metabolism, vol. 41, no. 7, SAGE Publications, 2021, pp. 1634–46,
doi:10.1177/0271678X20965500.
short: N. Tournier, S. Goutal, S. Mairinger, I. Lozano, T. Filip, M. Sauberer, F.
Caillé, L. Breuil, J. Stanek, A. Freeman, G. Novarino, C. Truillet, T. Wanek,
O. Langer, Journal of Cerebral Blood Flow and Metabolism 41 (2021) 1634–1646.
date_created: 2020-11-06T08:39:01Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-10-18T06:45:30Z
day: '01'
department:
- _id: GaNo
doi: 10.1177/0271678X20965500
external_id:
isi:
- '000664214100012'
pmid:
- '33081568'
intvolume: ' 41'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8221757/
month: '07'
oa: 1
oa_version: Published Version
page: 1634-1646
pmid: 1
publication: Journal of Cerebral Blood Flow and Metabolism
publication_identifier:
eissn:
- 1559-7016
issn:
- 0271-678x
publication_status: published
publisher: SAGE Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Complete inhibition of ABCB1 and ABCG2 at the blood-brain barrier by co-infusion
of erlotinib and tariquidar to improve brain delivery of the model ABCB1/ABCG2 substrate
[11C]erlotinib
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 41
year: '2021'
...
---
_id: '9383'
abstract:
- lang: eng
text: A primary roadblock to our understanding of speciation is that it usually
occurs over a timeframe that is too long to study from start to finish. The idea
of a speciation continuum provides something of a solution to this problem; rather
than observing the entire process, we can simply reconstruct it from the multitude
of speciation events that surround us. But what do we really mean when we talk
about the speciation continuum, and can it really help us understand speciation?
We explored these questions using a literature review and online survey of speciation
researchers. Although most researchers were familiar with the concept and thought
it was useful, our survey revealed extensive disagreement about what the speciation
continuum actually tells us. This is due partly to the lack of a clear definition.
Here, we provide an explicit definition that is compatible with the Biological
Species Concept. That is, the speciation continuum is a continuum of reproductive
isolation. After outlining the logic of the definition in light of alternatives,
we explain why attempts to reconstruct the speciation process from present‐day
populations will ultimately fail. We then outline how we think the speciation
continuum concept can continue to act as a foundation for understanding the continuum
of reproductive isolation that surrounds us.
acknowledgement: We thank M. Garlovsky, S. Martin, C. Cooney, C. Roux, J. Larson,
and J. Mallet for critical feedback and for discussion. K. Lohse, M. de la Cámara,
J. Cerca, M. A. Chase, C. Baskett, A. M. Westram, and N. H. Barton gave feedback
on a draft of the manuscript. O. Seehausen, two anonymous reviewers, and the AE
(Michael Kopp) provided comments that greatly improved the manuscript. V. Holzmann
made many corrections to the proofs. G. Bisschop and K. Lohse kindly contributed
the simulations and analyses presented in Box 3. We would also like to extend our
thanks to everyone who took part in the speciation survey, which received ethical
approval through the University of Sheffield Ethics Review Procedure (Application
029768). We are especially grateful to R. K. Butlin for stimulating discussion throughout
the writing of the manuscript and for feedback on an earlier draft.
article_processing_charge: No
article_type: original
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Mark
full_name: Ravinet, Mark
last_name: Ravinet
citation:
ama: Stankowski S, Ravinet M. Defining the speciation continuum. Evolution.
2021;75(6):1256-1273. doi:10.1111/evo.14215
apa: Stankowski, S., & Ravinet, M. (2021). Defining the speciation continuum.
Evolution. Oxford University Press. https://doi.org/10.1111/evo.14215
chicago: Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.”
Evolution. Oxford University Press, 2021. https://doi.org/10.1111/evo.14215.
ieee: S. Stankowski and M. Ravinet, “Defining the speciation continuum,” Evolution,
vol. 75, no. 6. Oxford University Press, pp. 1256–1273, 2021.
ista: Stankowski S, Ravinet M. 2021. Defining the speciation continuum. Evolution.
75(6), 1256–1273.
mla: Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” Evolution,
vol. 75, no. 6, Oxford University Press, 2021, pp. 1256–73, doi:10.1111/evo.14215.
short: S. Stankowski, M. Ravinet, Evolution 75 (2021) 1256–1273.
date_created: 2021-05-09T22:01:39Z
date_published: 2021-03-22T00:00:00Z
date_updated: 2023-10-18T08:16:01Z
day: '22'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/evo.14215
external_id:
isi:
- '000647226400001'
file:
- access_level: open_access
checksum: 96f6ccf15d95a4e9f7c0b27eee570fa6
content_type: application/pdf
creator: kschuh
date_created: 2022-03-25T12:02:04Z
date_updated: 2022-03-25T12:02:04Z
file_id: '10921'
file_name: 2021_Evolution_Stankowski.pdf
file_size: 719991
relation: main_file
success: 1
file_date_updated: 2022-03-25T12:02:04Z
has_accepted_license: '1'
intvolume: ' 75'
isi: 1
issue: '6'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 1256-1273
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Defining the speciation continuum
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 75
year: '2021'
...
---
_id: '10223'
abstract:
- lang: eng
text: Growth regulation tailors development in plants to their environment. A prominent
example of this is the response to gravity, in which shoots bend up and roots
bend down1. This paradox is based on opposite effects of the phytohormone auxin,
which promotes cell expansion in shoots while inhibiting it in roots via a yet
unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic
engineering and phosphoproteomics in Arabidopsis thaliana, we advance understanding
of how auxin inhibits root growth. We show that auxin activates two distinct,
antagonistically acting signalling pathways that converge on rapid regulation
of apoplastic pH, a causative determinant of growth. Cell surface-based TRANSMEMBRANE
KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma
membrane H+-ATPases for apoplast acidification, while intracellular canonical
auxin signalling promotes net cellular H+ influx, causing apoplast alkalinization.
Simultaneous activation of these two counteracting mechanisms poises roots for
rapid, fine-tuned growth modulation in navigating complex soil environments.
acknowledged_ssus:
- _id: LifeSc
- _id: M-Shop
- _id: Bio
acknowledgement: We thank N. Gnyliukh and L. Hörmayer for technical assistance and
N. Paris for sharing PM-Cyto seeds. We gratefully acknowledge the Life Science,
Machine Shop and Bioimaging Facilities of IST Austria. This project has received
funding from the European Research Council Advanced Grant (ETAP-742985) and the
Austrian Science Fund (FWF) under I 3630-B25 to J.F., the National Institutes of
Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research
(NWO; VIDI-864.13.001), Research Foundation-Flanders (FWO; Odysseus II G0D0515N)
and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R.,
the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research
to M.R. and D.W., the Australian Research Council and China National Distinguished
Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685)
and T.K. (20H05687 and 20H05910), the European Union’s Horizon 2020 research and
innovation programme under Marie Skłodowska-Curie grant agreement no. 665385 and
the DOC Fellowship of the Austrian Academy of Sciences to L.L., and the China Scholarship
Council to J.C.
article_processing_charge: No
article_type: original
author:
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Mark
full_name: Roosjen, Mark
last_name: Roosjen
- first_name: Koji
full_name: Takahashi, Koji
last_name: Takahashi
- first_name: Lesia
full_name: Rodriguez Solovey, Lesia
id: 3922B506-F248-11E8-B48F-1D18A9856A87
last_name: Rodriguez Solovey
orcid: 0000-0002-7244-7237
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Jian
full_name: Chen, Jian
last_name: Chen
- first_name: Lana
full_name: Shabala, Lana
last_name: Shabala
- first_name: Wouter
full_name: Smet, Wouter
last_name: Smet
- first_name: Hong
full_name: Ren, Hong
last_name: Ren
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Sergey
full_name: Shabala, Sergey
last_name: Shabala
- first_name: Bert
full_name: De Rybel, Bert
last_name: De Rybel
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Toshinori
full_name: Kinoshita, Toshinori
last_name: Kinoshita
- first_name: William M.
full_name: Gray, William M.
last_name: Gray
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin
signalling for H+ fluxes in root growth. Nature. 2021;599(7884):273-277.
doi:10.1038/s41586-021-04037-6
apa: Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L.,
Merrin, J., … Friml, J. (2021). Cell surface and intracellular auxin signalling
for H+ fluxes in root growth. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-04037-6
chicago: Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez
Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin
Signalling for H+ Fluxes in Root Growth.” Nature. Springer Nature,
2021. https://doi.org/10.1038/s41586-021-04037-6.
ieee: L. Li et al., “Cell surface and intracellular auxin signalling for
H+ fluxes in root growth,” Nature, vol. 599, no. 7884. Springer
Nature, pp. 273–277, 2021.
ista: Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J,
Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D,
Kinoshita T, Gray WM, Friml J. 2021. Cell surface and intracellular auxin signalling
for H+ fluxes in root growth. Nature. 599(7884), 273–277.
mla: Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+
Fluxes in Root Growth.” Nature, vol. 599, no. 7884, Springer Nature, 2021,
pp. 273–77, doi:10.1038/s41586-021-04037-6.
short: L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J.
Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel,
D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Nature 599 (2021) 273–277.
date_created: 2021-11-07T23:01:25Z
date_published: 2021-11-11T00:00:00Z
date_updated: 2023-10-18T08:30:53Z
day: '11'
department:
- _id: JiFr
- _id: NanoFab
doi: 10.1038/s41586-021-04037-6
ec_funded: 1
external_id:
isi:
- '000713338100006'
pmid:
- '34707283'
intvolume: ' 599'
isi: 1
issue: '7884'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.doi.org/10.21203/rs.3.rs-266395/v3
month: '11'
oa: 1
oa_version: Preprint
page: 273-277
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
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 26B4D67E-B435-11E9-9278-68D0E5697425
grant_number: '25351'
name: 'A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated
Rapid Growth Inhibition in Arabidopsis Root'
publication: Nature
publication_identifier:
eissn:
- '14764687'
issn:
- '00280836'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Webpage
relation: press_release
url: https://ist.ac.at/en/news/stop-and-grow/
record:
- id: '10095'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Cell surface and intracellular auxin signalling for H+ fluxes in
root growth
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 599
year: '2021'
...
---
_id: '9379'
abstract:
- lang: eng
text: When B cells encounter membrane-bound antigens, the formation and coalescence
of B cell antigen receptor (BCR) microclusters amplifies BCR signaling. The ability
of B cells to probe the surface of antigen-presenting cells (APCs) and respond
to APC-bound antigens requires remodeling of the actin cytoskeleton. Initial BCR
signaling stimulates actin-related protein (Arp) 2/3 complex-dependent actin polymerization,
which drives B cell spreading as well as the centripetal movement and coalescence
of BCR microclusters at the B cell-APC synapse. Sustained actin polymerization
depends on concomitant actin filament depolymerization, which enables the recycling
of actin monomers and Arp2/3 complexes. Cofilin-mediated severing of actin filaments
is a rate-limiting step in the morphological changes that occur during immune
synapse formation. Hence, regulators of cofilin activity such as WD repeat-containing
protein 1 (Wdr1), LIM domain kinase (LIMK), and coactosin-like 1 (Cotl1) may also
be essential for actin-dependent processes in B cells. Wdr1 enhances cofilin-mediated
actin disassembly. Conversely, Cotl1 competes with cofilin for binding to actin
and LIMK phosphorylates cofilin and prevents it from binding to actin filaments.
We now show that Wdr1 and LIMK have distinct roles in BCR-induced assembly of
the peripheral actin structures that drive B cell spreading, and that cofilin,
Wdr1, and LIMK all contribute to the actin-dependent amplification of BCR signaling
at the immune synapse. Depleting Cotl1 had no effect on these processes. Thus,
the Wdr1-LIMK-cofilin axis is critical for BCR-induced actin remodeling and for
B cell responses to APC-bound antigens.
acknowledgement: We thank the UBC Life Sciences Institute Imaging Facility andthe
UBC Flow Cytometry Facility.
article_number: '649433'
article_processing_charge: No
article_type: original
author:
- first_name: Madison
full_name: Bolger-Munro, Madison
id: 516F03FA-93A3-11EA-A7C5-D6BE3DDC885E
last_name: Bolger-Munro
orcid: 0000-0002-8176-4824
- first_name: Kate
full_name: Choi, Kate
last_name: Choi
- first_name: Faith
full_name: Cheung, Faith
last_name: Cheung
- first_name: Yi Tian
full_name: Liu, Yi Tian
last_name: Liu
- first_name: May
full_name: Dang-Lawson, May
last_name: Dang-Lawson
- first_name: Nikola
full_name: Deretic, Nikola
last_name: Deretic
- first_name: Connor
full_name: Keane, Connor
last_name: Keane
- first_name: Michael R.
full_name: Gold, Michael R.
last_name: Gold
citation:
ama: Bolger-Munro M, Choi K, Cheung F, et al. The Wdr1-LIMK-Cofilin axis controls
B cell antigen receptor-induced actin remodeling and signaling at the immune synapse.
Frontiers in Cell and Developmental Biology. 2021;9. doi:10.3389/fcell.2021.649433
apa: Bolger-Munro, M., Choi, K., Cheung, F., Liu, Y. T., Dang-Lawson, M., Deretic,
N., … Gold, M. R. (2021). The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced
actin remodeling and signaling at the immune synapse. Frontiers in Cell and
Developmental Biology. Frontiers Media. https://doi.org/10.3389/fcell.2021.649433
chicago: Bolger-Munro, Madison, Kate Choi, Faith Cheung, Yi Tian Liu, May Dang-Lawson,
Nikola Deretic, Connor Keane, and Michael R. Gold. “The Wdr1-LIMK-Cofilin Axis
Controls B Cell Antigen Receptor-Induced Actin Remodeling and Signaling at the
Immune Synapse.” Frontiers in Cell and Developmental Biology. Frontiers
Media, 2021. https://doi.org/10.3389/fcell.2021.649433.
ieee: M. Bolger-Munro et al., “The Wdr1-LIMK-Cofilin axis controls B cell
antigen receptor-induced actin remodeling and signaling at the immune synapse,”
Frontiers in Cell and Developmental Biology, vol. 9. Frontiers Media, 2021.
ista: Bolger-Munro M, Choi K, Cheung F, Liu YT, Dang-Lawson M, Deretic N, Keane
C, Gold MR. 2021. The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced
actin remodeling and signaling at the immune synapse. Frontiers in Cell and Developmental
Biology. 9, 649433.
mla: Bolger-Munro, Madison, et al. “The Wdr1-LIMK-Cofilin Axis Controls B Cell Antigen
Receptor-Induced Actin Remodeling and Signaling at the Immune Synapse.” Frontiers
in Cell and Developmental Biology, vol. 9, 649433, Frontiers Media, 2021,
doi:10.3389/fcell.2021.649433.
short: M. Bolger-Munro, K. Choi, F. Cheung, Y.T. Liu, M. Dang-Lawson, N. Deretic,
C. Keane, M.R. Gold, Frontiers in Cell and Developmental Biology 9 (2021).
date_created: 2021-05-09T22:01:37Z
date_published: 2021-04-13T00:00:00Z
date_updated: 2023-10-18T08:19:49Z
day: '13'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.3389/fcell.2021.649433
external_id:
isi:
- '000644419500001'
pmid:
- '33928084'
file:
- access_level: open_access
checksum: 8c8a03575d2f7583f88dc3b658b0976b
content_type: application/pdf
creator: kschuh
date_created: 2021-05-11T15:09:23Z
date_updated: 2021-05-11T15:09:23Z
file_id: '9386'
file_name: 2021_Frontiers_Cell_Bolger-Munro.pdf
file_size: 4076024
relation: main_file
success: 1
file_date_updated: 2021-05-11T15:09:23Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
keyword:
- B cell
- actin
- immune synapse
- cell spreading
- cofilin
- WDR1 (AIP1)
- LIM domain kinase
- B cell receptor (BCR)
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Cell and Developmental Biology
publication_identifier:
eissn:
- 2296-634X
publication_status: published
publisher: Frontiers Media
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling
and signaling at the immune synapse
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: 9
year: '2021'
...
---
_id: '9362'
abstract:
- lang: eng
text: A central goal in systems neuroscience is to understand the functions performed
by neural circuits. Previous top-down models addressed this question by comparing
the behaviour of an ideal model circuit, optimised to perform a given function,
with neural recordings. However, this requires guessing in advance what function
is being performed, which may not be possible for many neural systems. To address
this, we propose an inverse reinforcement learning (RL) framework for inferring
the function performed by a neural network from data. We assume that the responses
of each neuron in a network are optimised so as to drive the network towards ‘rewarded’
states, that are desirable for performing a given function. We then show how one
can use inverse RL to infer the reward function optimised by the network from
observing its responses. This inferred reward function can be used to predict
how the neural network should adapt its dynamics to perform the same function
when the external environment or network structure changes. This could lead to
theoretical predictions about how neural network dynamics adapt to deal with cell
death and/or varying sensory stimulus statistics.
acknowledgement: The authors would like to thank Ulisse Ferrari for useful discussions
and feedback.
article_number: e0248940
article_processing_charge: No
article_type: original
author:
- first_name: Matthew J
full_name: Chalk, Matthew J
id: 2BAAC544-F248-11E8-B48F-1D18A9856A87
last_name: Chalk
orcid: 0000-0001-7782-4436
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
citation:
ama: Chalk MJ, Tkačik G, Marre O. Inferring the function performed by a recurrent
neural network. PLoS ONE. 2021;16(4). doi:10.1371/journal.pone.0248940
apa: Chalk, M. J., Tkačik, G., & Marre, O. (2021). Inferring the function performed
by a recurrent neural network. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0248940
chicago: Chalk, Matthew J, Gašper Tkačik, and Olivier Marre. “Inferring the Function
Performed by a Recurrent Neural Network.” PLoS ONE. Public Library of Science,
2021. https://doi.org/10.1371/journal.pone.0248940.
ieee: M. J. Chalk, G. Tkačik, and O. Marre, “Inferring the function performed by
a recurrent neural network,” PLoS ONE, vol. 16, no. 4. Public Library of
Science, 2021.
ista: Chalk MJ, Tkačik G, Marre O. 2021. Inferring the function performed by a recurrent
neural network. PLoS ONE. 16(4), e0248940.
mla: Chalk, Matthew J., et al. “Inferring the Function Performed by a Recurrent
Neural Network.” PLoS ONE, vol. 16, no. 4, e0248940, Public Library of
Science, 2021, doi:10.1371/journal.pone.0248940.
short: M.J. Chalk, G. Tkačik, O. Marre, PLoS ONE 16 (2021).
date_created: 2021-05-02T22:01:28Z
date_published: 2021-04-15T00:00:00Z
date_updated: 2023-10-18T08:17:42Z
day: '15'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pone.0248940
external_id:
isi:
- '000641474900072'
pmid:
- '33857170'
file:
- access_level: open_access
checksum: c52da133850307d2031f552d998f00e8
content_type: application/pdf
creator: kschuh
date_created: 2021-05-04T13:22:19Z
date_updated: 2021-05-04T13:22:19Z
file_id: '9371'
file_name: 2021_pone_Chalk.pdf
file_size: 2768282
relation: main_file
success: 1
file_date_updated: 2021-05-04T13:22:19Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS ONE
publication_identifier:
eissn:
- '19326203'
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inferring the function performed by a recurrent neural 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2021'
...
---
_id: '9986'
abstract:
- lang: eng
text: Size control is a fundamental question in biology, showing incremental complexity
in plants, whose cells possess a rigid cell wall. The phytohormone auxin is a
vital growth regulator with central importance for differential growth control.
Our results indicate that auxin-reliant growth programs affect the molecular complexity
of xyloglucans, the major type of cell wall hemicellulose in eudicots. Auxin-dependent
induction and repression of growth coincide with reduced and enhanced molecular
complexity of xyloglucans, respectively. In agreement with a proposed function
in growth control, genetic interference with xyloglucan side decorations distinctly
modulates auxin-dependent differential growth rates. Our work proposes that auxin-dependent
growth programs have a spatially defined effect on xyloglucan’s molecular structure,
which in turn affects cell wall mechanics and specifies differential, gravitropic
hypocotyl growth.
acknowledgement: "We are grateful to Paul Knox, Markus Pauly, Malcom O’Neill, and
Ignacio Zarra for providing published material; the BOKU-VIBT Imaging Center for
access and M. Debreczeny for expertise; J.I. Thaker and Georg Seifert for critical
reading.\r\n"
article_number: '9222'
article_processing_charge: Yes
article_type: original
author:
- first_name: Silvia Melina
full_name: Velasquez, Silvia Melina
last_name: Velasquez
- first_name: Xiaoyuan
full_name: Guo, Xiaoyuan
last_name: Guo
- first_name: Marçal
full_name: Gallemi, Marçal
id: 460C6802-F248-11E8-B48F-1D18A9856A87
last_name: Gallemi
orcid: 0000-0003-4675-6893
- first_name: Bibek
full_name: Aryal, Bibek
last_name: Aryal
- first_name: Peter
full_name: Venhuizen, Peter
last_name: Venhuizen
- first_name: Elke
full_name: Barbez, Elke
last_name: Barbez
- first_name: Kai Alexander
full_name: Dünser, Kai Alexander
last_name: Dünser
- first_name: Martin
full_name: Darino, Martin
last_name: Darino
- first_name: Aleš
full_name: Pӗnčík, Aleš
last_name: Pӗnčík
- first_name: Ondřej
full_name: Novák, Ondřej
last_name: Novák
- first_name: Maria
full_name: Kalyna, Maria
last_name: Kalyna
- first_name: Gregory
full_name: Mouille, Gregory
last_name: Mouille
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Rishikesh P.
full_name: Bhalerao, Rishikesh P.
last_name: Bhalerao
- first_name: Jozef
full_name: Mravec, Jozef
last_name: Mravec
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine-Vehn
citation:
ama: Velasquez SM, Guo X, Gallemi M, et al. Xyloglucan remodeling defines auxin-dependent
differential tissue expansion in plants. International Journal of Molecular
Sciences. 2021;22(17). doi:10.3390/ijms22179222
apa: Velasquez, S. M., Guo, X., Gallemi, M., Aryal, B., Venhuizen, P., Barbez, E.,
… Kleine-Vehn, J. (2021). Xyloglucan remodeling defines auxin-dependent differential
tissue expansion in plants. International Journal of Molecular Sciences.
MDPI. https://doi.org/10.3390/ijms22179222
chicago: Velasquez, Silvia Melina, Xiaoyuan Guo, Marçal Gallemi, Bibek Aryal, Peter
Venhuizen, Elke Barbez, Kai Alexander Dünser, et al. “Xyloglucan Remodeling Defines
Auxin-Dependent Differential Tissue Expansion in Plants.” International Journal
of Molecular Sciences. MDPI, 2021. https://doi.org/10.3390/ijms22179222.
ieee: S. M. Velasquez et al., “Xyloglucan remodeling defines auxin-dependent
differential tissue expansion in plants,” International Journal of Molecular
Sciences, vol. 22, no. 17. MDPI, 2021.
ista: Velasquez SM, Guo X, Gallemi M, Aryal B, Venhuizen P, Barbez E, Dünser KA,
Darino M, Pӗnčík A, Novák O, Kalyna M, Mouille G, Benková E, Bhalerao RP, Mravec
J, Kleine-Vehn J. 2021. Xyloglucan remodeling defines auxin-dependent differential
tissue expansion in plants. International Journal of Molecular Sciences. 22(17),
9222.
mla: Velasquez, Silvia Melina, et al. “Xyloglucan Remodeling Defines Auxin-Dependent
Differential Tissue Expansion in Plants.” International Journal of Molecular
Sciences, vol. 22, no. 17, 9222, MDPI, 2021, doi:10.3390/ijms22179222.
short: S.M. Velasquez, X. Guo, M. Gallemi, B. Aryal, P. Venhuizen, E. Barbez, K.A.
Dünser, M. Darino, A. Pӗnčík, O. Novák, M. Kalyna, G. Mouille, E. Benková, R.P.
Bhalerao, J. Mravec, J. Kleine-Vehn, International Journal of Molecular Sciences
22 (2021).
date_created: 2021-09-05T22:01:24Z
date_published: 2021-08-26T00:00:00Z
date_updated: 2023-10-31T19:29:38Z
day: '26'
ddc:
- '575'
department:
- _id: EvBe
doi: 10.3390/ijms22179222
external_id:
isi:
- '000694347100001'
pmid:
- '34502129'
file:
- access_level: open_access
checksum: 6b7055cf89f1b7ed8594c3fdf56f000b
content_type: application/pdf
creator: cchlebak
date_created: 2021-09-06T12:50:19Z
date_updated: 2021-09-07T09:04:53Z
file_id: '9988'
file_name: 2021_IntJMolecularSciences_Velasquez.pdf
file_size: 2162247
relation: main_file
file_date_updated: 2021-09-07T09:04:53Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
issue: '17'
keyword:
- auxin
- growth
- cell wall
- xyloglucans
- hypocotyls
- gravitropism
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: International Journal of Molecular Sciences
publication_identifier:
eissn:
- 1422-0067
issn:
- 1661-6596
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Xyloglucan remodeling defines auxin-dependent differential tissue expansion
in plants
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: 22
year: '2021'
...
---
_id: '9189'
abstract:
- lang: eng
text: Transposable elements exist widely throughout plant genomes and play important
roles in plant evolution. Auxin is an important regulator that is traditionally
associated with root development and drought stress adaptation. The DEEPER ROOTING
1 (DRO1) gene is a key component of rice drought avoidance. Here, we identified
a transposon that acts as an autonomous auxin‐responsive promoter and its presence
at specific genome positions conveys physiological adaptations related to drought
avoidance. Rice varieties with high and auxin‐mediated transcription of DRO1 in
the root tip show deeper and longer root phenotypes and are thus better adapted
to drought. The INDITTO2 transposon contains an auxin response element and displays
auxin‐responsive promoter activity; it is thus able to convey auxin regulation
of transcription to genes in its proximity. In the rice Acuce, which displays
DRO1‐mediated drought adaptation, the INDITTO2 transposon was found to be inserted
at the promoter region of the DRO1 locus. Transgenesis‐based insertion of the
INDITTO2 transposon into the DRO1 promoter of the non‐adapted rice variety Nipponbare
was sufficient to promote its drought avoidance. Our data identify an example
of how transposons can act as promoters and convey hormonal regulation to nearby
loci, improving plant fitness in response to different abiotic stresses.
article_processing_charge: No
article_type: original
author:
- first_name: Y
full_name: Zhao, Y
last_name: Zhao
- first_name: L
full_name: Wu, L
last_name: Wu
- first_name: Q
full_name: Fu, Q
last_name: Fu
- first_name: D
full_name: Wang, D
last_name: Wang
- first_name: J
full_name: Li, J
last_name: Li
- first_name: B
full_name: Yao, B
last_name: Yao
- first_name: S
full_name: Yu, S
last_name: Yu
- first_name: L
full_name: Jiang, L
last_name: Jiang
- first_name: J
full_name: Qian, J
last_name: Qian
- first_name: X
full_name: Zhou, X
last_name: Zhou
- first_name: L
full_name: Han, L
last_name: Han
- first_name: S
full_name: Zhao, S
last_name: Zhao
- first_name: C
full_name: Ma, C
last_name: Ma
- first_name: Y
full_name: Zhang, Y
last_name: Zhang
- first_name: C
full_name: Luo, C
last_name: Luo
- first_name: Q
full_name: Dong, Q
last_name: Dong
- first_name: S
full_name: Li, S
last_name: Li
- first_name: L
full_name: Zhang, L
last_name: Zhang
- first_name: X
full_name: Jiang, X
last_name: Jiang
- first_name: Y
full_name: Li, Y
last_name: Li
- first_name: H
full_name: Luo, H
last_name: Luo
- first_name: K
full_name: Li, K
last_name: Li
- first_name: J
full_name: Yang, J
last_name: Yang
- first_name: Q
full_name: Luo, Q
last_name: Luo
- first_name: L
full_name: Li, L
last_name: Li
- first_name: S
full_name: Peng, S
last_name: Peng
- first_name: H
full_name: Huang, H
last_name: Huang
- first_name: Z
full_name: Zuo, Z
last_name: Zuo
- first_name: C
full_name: Liu, C
last_name: Liu
- first_name: L
full_name: Wang, L
last_name: Wang
- first_name: C
full_name: Li, C
last_name: Li
- first_name: X
full_name: He, X
last_name: He
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Y
full_name: Du, Y
last_name: Du
citation:
ama: Zhao Y, Wu L, Fu Q, et al. INDITTO2 transposon conveys auxin-mediated DRO1
transcription for rice drought avoidance. Plant, Cell & Environment.
2021;44(6):1846-1857. doi:10.1111/pce.14029
apa: Zhao, Y., Wu, L., Fu, Q., Wang, D., Li, J., Yao, B., … Du, Y. (2021). INDITTO2
transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance.
Plant, Cell & Environment. Wiley. https://doi.org/10.1111/pce.14029
chicago: Zhao, Y, L Wu, Q Fu, D Wang, J Li, B Yao, S Yu, et al. “INDITTO2 Transposon
Conveys Auxin-Mediated DRO1 Transcription for Rice Drought Avoidance.” Plant,
Cell & Environment. Wiley, 2021. https://doi.org/10.1111/pce.14029.
ieee: Y. Zhao et al., “INDITTO2 transposon conveys auxin-mediated DRO1 transcription
for rice drought avoidance,” Plant, Cell & Environment, vol. 44, no.
6. Wiley, pp. 1846–1857, 2021.
ista: Zhao Y, Wu L, Fu Q, Wang D, Li J, Yao B, Yu S, Jiang L, Qian J, Zhou X, Han
L, Zhao S, Ma C, Zhang Y, Luo C, Dong Q, Li S, Zhang L, Jiang X, Li Y, Luo H,
Li K, Yang J, Luo Q, Li L, Peng S, Huang H, Zuo Z, Liu C, Wang L, Li C, He X,
Friml J, Du Y. 2021. INDITTO2 transposon conveys auxin-mediated DRO1 transcription
for rice drought avoidance. Plant, Cell & Environment. 44(6), 1846–1857.
mla: Zhao, Y., et al. “INDITTO2 Transposon Conveys Auxin-Mediated DRO1 Transcription
for Rice Drought Avoidance.” Plant, Cell & Environment, vol. 44, no.
6, Wiley, 2021, pp. 1846–57, doi:10.1111/pce.14029.
short: Y. Zhao, L. Wu, Q. Fu, D. Wang, J. Li, B. Yao, S. Yu, L. Jiang, J. Qian,
X. Zhou, L. Han, S. Zhao, C. Ma, Y. Zhang, C. Luo, Q. Dong, S. Li, L. Zhang, X.
Jiang, Y. Li, H. Luo, K. Li, J. Yang, Q. Luo, L. Li, S. Peng, H. Huang, Z. Zuo,
C. Liu, L. Wang, C. Li, X. He, J. Friml, Y. Du, Plant, Cell & Environment
44 (2021) 1846–1857.
date_created: 2021-02-24T10:07:21Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-11-07T08:18:36Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1111/pce.14029
external_id:
isi:
- '000625398600001'
pmid:
- '33576018'
file:
- access_level: open_access
checksum: a812418fede076741c9c4dc07f317068
content_type: application/pdf
creator: amally
date_created: 2023-11-02T17:02:11Z
date_updated: 2023-11-02T17:02:11Z
file_id: '14481'
file_name: Zhao PlantCellEnv 2021_accepted.pdf
file_size: 8437528
relation: main_file
success: 1
file_date_updated: 2023-11-02T17:02:11Z
has_accepted_license: '1'
intvolume: ' 44'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 1846-1857
pmid: 1
publication: Plant, Cell & Environment
publication_identifier:
eissn:
- 1365-3040
issn:
- 0140-7791
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought
avoidance
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 44
year: '2021'
...
---
_id: '9792'
abstract:
- lang: eng
text: 'This paper establishes new connections between many-body quantum systems,
One-body Reduced Density Matrices Functional Theory (1RDMFT) and Optimal Transport
(OT), by interpreting the problem of computing the ground-state energy of a finite
dimensional composite quantum system at positive temperature as a non-commutative
entropy regularized Optimal Transport problem. We develop a new approach to fully
characterize the dual-primal solutions in such non-commutative setting. The mathematical
formalism is particularly relevant in quantum chemistry: numerical realizations
of the many-electron ground state energy can be computed via a non-commutative
version of Sinkhorn algorithm. Our approach allows to prove convergence and robustness
of this algorithm, which, to our best knowledge, were unknown even in the two
marginal case. Our methods are based on careful a priori estimates in the dual
problem, which we believe to be of independent interest. Finally, the above results
are extended in 1RDMFT setting, where bosonic or fermionic symmetry conditions
are enforced on the problem.'
acknowledgement: 'This work started when A.G. was visiting the Erwin Schrödinger Institute
and then continued when D.F. and L.P visited the Theoretical Chemistry Department
of the Vrije Universiteit Amsterdam. The authors thanks the hospitality of both
places and, especially, P. Gori-Giorgi and K. Giesbertz for fruitful discussions
and literature suggestions in the early state of the project. Finally, the authors
also thanks J. Maas and R. Seiringer for their feedback and useful comments to a
first draft of the article. L.P. acknowledges support by the Austrian Science Fund
(FWF), grants No W1245 and NoF65. D.F acknowledges support by the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreements No 716117 and No 694227). A.G. acknowledges funding by the European
Research Council under H2020/MSCA-IF “OTmeetsDFT” [grant ID: 795942].'
article_number: '2106.11217'
article_processing_charge: No
author:
- first_name: Dario
full_name: Feliciangeli, Dario
id: 41A639AA-F248-11E8-B48F-1D18A9856A87
last_name: Feliciangeli
orcid: 0000-0003-0754-8530
- first_name: Augusto
full_name: Gerolin, Augusto
last_name: Gerolin
- first_name: Lorenzo
full_name: Portinale, Lorenzo
id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87
last_name: Portinale
citation:
ama: Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal
transport approach to quantum composite systems at positive temperature. arXiv.
doi:10.48550/arXiv.2106.11217
apa: Feliciangeli, D., Gerolin, A., & Portinale, L. (n.d.). A non-commutative
entropic optimal transport approach to quantum composite systems at positive temperature.
arXiv. https://doi.org/10.48550/arXiv.2106.11217
chicago: Feliciangeli, Dario, Augusto Gerolin, and Lorenzo Portinale. “A Non-Commutative
Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.”
ArXiv, n.d. https://doi.org/10.48550/arXiv.2106.11217.
ieee: D. Feliciangeli, A. Gerolin, and L. Portinale, “A non-commutative entropic
optimal transport approach to quantum composite systems at positive temperature,”
arXiv. .
ista: Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal
transport approach to quantum composite systems at positive temperature. arXiv,
2106.11217.
mla: Feliciangeli, Dario, et al. “A Non-Commutative Entropic Optimal Transport Approach
to Quantum Composite Systems at Positive Temperature.” ArXiv, 2106.11217,
doi:10.48550/arXiv.2106.11217.
short: D. Feliciangeli, A. Gerolin, L. Portinale, ArXiv (n.d.).
date_created: 2021-08-06T09:07:12Z
date_published: 2021-07-21T00:00:00Z
date_updated: 2023-11-14T13:21:01Z
day: '21'
ddc:
- '510'
department:
- _id: RoSe
- _id: JaMa
doi: 10.48550/arXiv.2106.11217
ec_funded: 1
external_id:
arxiv:
- '2106.11217'
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2106.11217
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication: arXiv
publication_status: submitted
related_material:
record:
- id: '9733'
relation: dissertation_contains
status: public
- id: '10030'
relation: dissertation_contains
status: public
- id: '12911'
relation: later_version
status: public
status: public
title: A non-commutative entropic optimal transport approach to quantum composite
systems 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: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '10655'
abstract:
- lang: eng
text: "Adeno-associated viruses (AAVs) are widely used to deliver genetic material
in vivo to distinct cell types such as neurons or glial cells, allowing for targeted
manipulation. Transduction of microglia is mostly excluded from this strategy,
likely due to the cells’ heterogeneous state upon environmental changes, which
makes AAV design challenging. Here, we established the retina as a model system
for microglial AAV validation and optimization. First, we show that AAV2/6 transduced
microglia in both synaptic layers, where layer preference corresponds to the intravitreal
or subretinal delivery method. Surprisingly, we observed significantly enhanced
microglial transduction during photoreceptor degeneration. Thus, we modified the
AAV6 capsid to reduce heparin binding by introducing four point mutations (K531E,
R576Q, K493S, and K459S), resulting in increased microglial transduction in the
outer plexiform layer. Finally, to improve microglial-specific transduction, we
validated a Cre-dependent transgene delivery cassette for use in combination with
the Cx3cr1CreERT2 mouse line. Together, our results provide a foundation for future
studies optimizing AAV-mediated microglia transduction and highlight that environmental
conditions influence microglial transduction efficiency.\r\n"
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: PreCl
acknowledgement: This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement no. 715571). The research was supported by the Scientific Service
Units (SSU) of IST Austria through resources provided by the Bioimaging Facility,
the Life Science Facility, and the Pre-Clinical Facility, namely Sonja Haslinger
and Michael Schunn for their animal colony management and support. We would also
like to thank Chakrabarty Lab for sharing the plasmids for AAV2/6 production. Finally,
we would like to thank the Siegert team members for discussion about the manuscript.
article_processing_charge: Yes
article_type: original
author:
- first_name: Margaret E
full_name: Maes, Margaret E
id: 3838F452-F248-11E8-B48F-1D18A9856A87
last_name: Maes
orcid: 0000-0001-9642-1085
- first_name: Gabriele M.
full_name: Wögenstein, Gabriele M.
last_name: Wögenstein
- first_name: Gloria
full_name: Colombo, Gloria
id: 3483CF6C-F248-11E8-B48F-1D18A9856A87
last_name: Colombo
orcid: 0000-0001-9434-8902
- first_name: Raquel
full_name: Casado Polanco, Raquel
id: 15240fc1-dbcd-11ea-9d1d-ac5a786425fd
last_name: Casado Polanco
orcid: 0000-0001-8293-4568
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
citation:
ama: Maes ME, Wögenstein GM, Colombo G, Casado Polanco R, Siegert S. Optimizing
AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor
degenerative environment. Molecular Therapy - Methods and Clinical Development.
2021;23:210-224. doi:10.1016/j.omtm.2021.09.006
apa: Maes, M. E., Wögenstein, G. M., Colombo, G., Casado Polanco, R., & Siegert,
S. (2021). Optimizing AAV2/6 microglial targeting identified enhanced efficiency
in the photoreceptor degenerative environment. Molecular Therapy - Methods
and Clinical Development. Elsevier. https://doi.org/10.1016/j.omtm.2021.09.006
chicago: Maes, Margaret E, Gabriele M. Wögenstein, Gloria Colombo, Raquel Casado
Polanco, and Sandra Siegert. “Optimizing AAV2/6 Microglial Targeting Identified
Enhanced Efficiency in the Photoreceptor Degenerative Environment.” Molecular
Therapy - Methods and Clinical Development. Elsevier, 2021. https://doi.org/10.1016/j.omtm.2021.09.006.
ieee: M. E. Maes, G. M. Wögenstein, G. Colombo, R. Casado Polanco, and S. Siegert,
“Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the
photoreceptor degenerative environment,” Molecular Therapy - Methods and Clinical
Development, vol. 23. Elsevier, pp. 210–224, 2021.
ista: Maes ME, Wögenstein GM, Colombo G, Casado Polanco R, Siegert S. 2021. Optimizing
AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor
degenerative environment. Molecular Therapy - Methods and Clinical Development.
23, 210–224.
mla: Maes, Margaret E., et al. “Optimizing AAV2/6 Microglial Targeting Identified
Enhanced Efficiency in the Photoreceptor Degenerative Environment.” Molecular
Therapy - Methods and Clinical Development, vol. 23, Elsevier, 2021, pp. 210–24,
doi:10.1016/j.omtm.2021.09.006.
short: M.E. Maes, G.M. Wögenstein, G. Colombo, R. Casado Polanco, S. Siegert, Molecular
Therapy - Methods and Clinical Development 23 (2021) 210–224.
date_created: 2022-01-23T23:01:28Z
date_published: 2021-12-10T00:00:00Z
date_updated: 2023-11-16T13:12:03Z
day: '10'
ddc:
- '570'
department:
- _id: SaSi
- _id: SiHi
doi: 10.1016/j.omtm.2021.09.006
ec_funded: 1
external_id:
isi:
- '000748748500019'
file:
- access_level: open_access
checksum: 77dc540e8011c5475031bdf6ccef20a6
content_type: application/pdf
creator: cchlebak
date_created: 2022-01-24T07:43:09Z
date_updated: 2022-01-24T07:43:09Z
file_id: '10657'
file_name: 2021_MolTherMethodsClinDev_Maes.pdf
file_size: 4794147
relation: main_file
success: 1
file_date_updated: 2022-01-24T07:43:09Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 210-224
project:
- _id: 25D4A630-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715571'
name: Microglia action towards neuronal circuit formation and function in health
and disease
publication: Molecular Therapy - Methods and Clinical Development
publication_identifier:
eissn:
- 2329-0501
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the
photoreceptor degenerative environment
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2021'
...
---
_id: '10565'
abstract:
- lang: eng
text: 'Enzymatic digestion of the extracellular matrix with chondroitinase-ABC reinstates
juvenile-like plasticity in the adult cortex as it also disassembles the perineuronal
nets (PNNs). The disadvantage of the enzyme is that it must be applied intracerebrally
and it degrades the ECM for several weeks. Here, we provide two minimally invasive
and transient protocols for microglia-enabled PNN disassembly in mouse cortex:
repeated treatment with ketamine-xylazine-acepromazine (KXA) anesthesia and 60-Hz
light entrainment. We also discuss how to analyze PNNs within microglial endosomes-lysosomes.
For complete details on the use and execution of this protocol, please refer to
Venturino et al. (2021).'
acknowledged_ssus:
- _id: Bio
acknowledgement: This research was supported by the European Research Council (grant
715571 to S.S.). We thank Rouven Schulz, Michael Schunn, Claudia Gold, Gabriel Krens,
Sarah Gorkiewicz, Margaret Maes, Jürgen Siegert, Marco Benevento, and Sara Oakeley
for comments on the manuscript and the IST Austria Bioimaging Facility for the technical
support.
article_number: '101012'
article_processing_charge: Yes
article_type: original
author:
- first_name: Alessandro
full_name: Venturino, Alessandro
id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
last_name: Venturino
orcid: 0000-0003-2356-9403
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
citation:
ama: Venturino A, Siegert S. Minimally invasive protocols and quantification for
microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols.
2021;2(4). doi:10.1016/j.xpro.2021.101012
apa: Venturino, A., & Siegert, S. (2021). Minimally invasive protocols and quantification
for microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols.
Elsevier ; Cell Press. https://doi.org/10.1016/j.xpro.2021.101012
chicago: Venturino, Alessandro, and Sandra Siegert. “Minimally Invasive Protocols
and Quantification for Microglia-Mediated Perineuronal Net Disassembly in Mouse
Brain.” STAR Protocols. Elsevier ; Cell Press, 2021. https://doi.org/10.1016/j.xpro.2021.101012.
ieee: A. Venturino and S. Siegert, “Minimally invasive protocols and quantification
for microglia-mediated perineuronal net disassembly in mouse brain,” STAR Protocols,
vol. 2, no. 4. Elsevier ; Cell Press, 2021.
ista: Venturino A, Siegert S. 2021. Minimally invasive protocols and quantification
for microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols.
2(4), 101012.
mla: Venturino, Alessandro, and Sandra Siegert. “Minimally Invasive Protocols and
Quantification for Microglia-Mediated Perineuronal Net Disassembly in Mouse Brain.”
STAR Protocols, vol. 2, no. 4, 101012, Elsevier ; Cell Press, 2021, doi:10.1016/j.xpro.2021.101012.
short: A. Venturino, S. Siegert, STAR Protocols 2 (2021).
date_created: 2021-12-19T23:01:32Z
date_published: 2021-12-17T00:00:00Z
date_updated: 2023-11-16T13:11:04Z
day: '17'
ddc:
- '573'
department:
- _id: SaSi
doi: 10.1016/j.xpro.2021.101012
ec_funded: 1
file:
- access_level: open_access
checksum: 9ea2501056c5df99e84726b845e9b976
content_type: application/pdf
creator: cchlebak
date_created: 2021-12-20T08:58:40Z
date_updated: 2021-12-20T08:58:40Z
file_id: '10570'
file_name: 2021_STARProt_Venturino.pdf
file_size: 6207060
relation: main_file
success: 1
file_date_updated: 2021-12-20T08:58:40Z
has_accepted_license: '1'
intvolume: ' 2'
issue: '4'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25D4A630-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715571'
name: Microglia action towards neuronal circuit formation and function in health
and disease
publication: STAR Protocols
publication_identifier:
eissn:
- 2666-1667
publication_status: published
publisher: Elsevier ; Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Minimally invasive protocols and quantification for microglia-mediated perineuronal
net disassembly in mouse brain
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2021'
...
---
_id: '10321'
abstract:
- lang: eng
text: Mosaic analysis with double markers (MADM) technology enables the generation
of genetic mosaic tissue in mice. MADM enables concomitant fluorescent cell labeling
and introduction of a mutation of a gene of interest with single-cell resolution.
This protocol highlights major steps for the generation of genetic mosaic tissue
and the isolation and processing of respective tissues for downstream histological
analysis. For complete details on the use and execution of this protocol, please
refer to Contreras et al. (2021).
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: This research was supported by the Scientific Service Units (SSU)
at IST Austria through resources provided by the Bioimaging (BIF) and Preclinical
Facilities (PCF). We particularly thank Mohammad Goudarzi for assistance with photography
of mouse perfusion and dissection. N.A. received support from FWF Firnberg-Programm
(T 1031). This work was also supported by IST Austria institutional funds; FWF SFB
F78 to S.H.; and the European Research Council (ERC) under the European Union’s
Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro)
to S.H.
article_number: '100939'
article_processing_charge: Yes
article_type: original
author:
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Amberg N, Hippenmeyer S. Genetic mosaic dissection of candidate genes in mice
using mosaic analysis with double markers. STAR Protocols. 2021;2(4). doi:10.1016/j.xpro.2021.100939
apa: Amberg, N., & Hippenmeyer, S. (2021). Genetic mosaic dissection of candidate
genes in mice using mosaic analysis with double markers. STAR Protocols.
Cell Press. https://doi.org/10.1016/j.xpro.2021.100939
chicago: Amberg, Nicole, and Simon Hippenmeyer. “Genetic Mosaic Dissection of Candidate
Genes in Mice Using Mosaic Analysis with Double Markers.” STAR Protocols.
Cell Press, 2021. https://doi.org/10.1016/j.xpro.2021.100939.
ieee: N. Amberg and S. Hippenmeyer, “Genetic mosaic dissection of candidate genes
in mice using mosaic analysis with double markers,” STAR Protocols, vol.
2, no. 4. Cell Press, 2021.
ista: Amberg N, Hippenmeyer S. 2021. Genetic mosaic dissection of candidate genes
in mice using mosaic analysis with double markers. STAR Protocols. 2(4), 100939.
mla: Amberg, Nicole, and Simon Hippenmeyer. “Genetic Mosaic Dissection of Candidate
Genes in Mice Using Mosaic Analysis with Double Markers.” STAR Protocols,
vol. 2, no. 4, 100939, Cell Press, 2021, doi:10.1016/j.xpro.2021.100939.
short: N. Amberg, S. Hippenmeyer, STAR Protocols 2 (2021).
date_created: 2021-11-21T23:01:28Z
date_published: 2021-11-10T00:00:00Z
date_updated: 2023-11-16T13:08:03Z
day: '10'
ddc:
- '573'
department:
- _id: SiHi
doi: 10.1016/j.xpro.2021.100939
ec_funded: 1
file:
- access_level: open_access
checksum: 9e3f6d06bf583e7a8b6a9e9a60500a28
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-22T08:23:58Z
date_updated: 2021-11-22T08:23:58Z
file_id: '10329'
file_name: 2021_STARProtocols_Amberg.pdf
file_size: 7309464
relation: main_file
success: 1
file_date_updated: 2021-11-22T08:23:58Z
has_accepted_license: '1'
intvolume: ' 2'
issue: '4'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
- _id: 268F8446-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: T0101031
name: Role of Eed in neural stem cell lineage progression
- _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E
grant_number: F07805
name: Molecular Mechanisms of Neural Stem Cell Lineage Progression
publication: STAR Protocols
publication_identifier:
eissn:
- 2666-1667
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetic mosaic dissection of candidate genes in mice using mosaic analysis
with double markers
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2021'
...
---
_id: '10290'
abstract:
- lang: eng
text: A precise quantitative description of the ultrastructural characteristics
underlying biological mechanisms is often key to their understanding. This is
particularly true for dynamic extra- and intracellular filamentous assemblies,
playing a role in cell motility, cell integrity, cytokinesis, tissue formation
and maintenance. For example, genetic manipulation or modulation of actin regulatory
proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural
architecture of actin filament-rich cell peripheral structures, such as lamellipodia
or filopodia. However, the observed ultrastructural effects often remain subtle
and require sufficiently large datasets for appropriate quantitative analysis.
The acquisition of such large datasets has been enabled by recent advances in
high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates
the development of complementary approaches to maximize the extraction of relevant
biological information. We have developed a computational toolbox for the semi-automatic
quantification of segmented and vectorized filamentous networks from pre-processed
cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple
experimental conditions. GUI-based components simplify the processing of data
and allow users to obtain a large number of ultrastructural parameters describing
filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing
cryo-ET data of untreated and chemically perturbed branched actin filament networks
and that of parallel actin filament arrays. In principle, the computational toolbox
presented here is applicable for data analysis comprising any type of filaments
in regular (i.e. parallel) or random arrangement. We show that it can ease the
identification of key differences between experimental groups and facilitate the
in-depth analysis of ultrastructural data in a time-efficient manner.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: Bio
- _id: EM-Fac
acknowledgement: 'This research was supported by the Scientific Service Units (SSUs)
of IST Austria through resources provided by Scientific Computing (SciComp), the
Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy
Facility (EMF). We also thank Victor-Valentin Hodirnau for help with cryo-ET data
acquisition. The authors acknowledge support from IST Austria and from the Austrian
Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S.'
article_number: '107808'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Georgi A
full_name: Dimchev, Georgi A
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
orcid: 0000-0001-8370-6161
- first_name: Behnam
full_name: Amiri, Behnam
last_name: Amiri
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Martin
full_name: Falcke, Martin
last_name: Falcke
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for
ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal
of Structural Biology. 2021;213(4). doi:10.1016/j.jsb.2021.107808
apa: Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., & Schur, F. K. (2021).
Computational toolbox for ultrastructural quantitative analysis of filament networks
in cryo-ET data. Journal of Structural Biology. Elsevier . https://doi.org/10.1016/j.jsb.2021.107808
chicago: Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian
KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of
Filament Networks in Cryo-ET Data.” Journal of Structural Biology. Elsevier
, 2021. https://doi.org/10.1016/j.jsb.2021.107808.
ieee: G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational
toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET
data,” Journal of Structural Biology, vol. 213, no. 4. Elsevier , 2021.
ista: Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2021. Computational toolbox
for ultrastructural quantitative analysis of filament networks in cryo-ET data.
Journal of Structural Biology. 213(4), 107808.
mla: Dimchev, Georgi A., et al. “Computational Toolbox for Ultrastructural Quantitative
Analysis of Filament Networks in Cryo-ET Data.” Journal of Structural Biology,
vol. 213, no. 4, 107808, Elsevier , 2021, doi:10.1016/j.jsb.2021.107808.
short: G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, Journal of Structural
Biology 213 (2021).
date_created: 2021-11-15T12:21:42Z
date_published: 2021-11-03T00:00:00Z
date_updated: 2023-11-21T08:36:02Z
day: '03'
ddc:
- '572'
department:
- _id: FlSc
doi: 10.1016/j.jsb.2021.107808
external_id:
isi:
- '000720259500002'
file:
- access_level: open_access
checksum: 6b209e4d44775d4e02b50f78982c15fa
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-15T13:11:27Z
date_updated: 2021-11-15T13:11:27Z
file_id: '10291'
file_name: 2021_JournalStructBiol_Dimchev.pdf
file_size: 16818304
relation: main_file
success: 1
file_date_updated: 2021-11-15T13:11:27Z
has_accepted_license: '1'
intvolume: ' 213'
isi: 1
issue: '4'
keyword:
- Structural Biology
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
grant_number: P33367
name: Structure and isoform diversity of the Arp2/3 complex
- _id: 2674F658-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02495
name: Protein structure and function in filopodia across scales
publication: Journal of Structural Biology
publication_identifier:
issn:
- 1047-8477
publication_status: published
publisher: 'Elsevier '
quality_controlled: '1'
related_material:
record:
- id: '14502'
relation: software
status: public
scopus_import: '1'
status: public
title: Computational toolbox for ultrastructural quantitative analysis of filament
networks in cryo-ET data
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: 213
year: '2021'
...
---
_id: '9969'
abstract:
- lang: eng
text: 'Payment channel networks are a promising approach to improve the scalability
of cryptocurrencies: they allow to perform transactions in a peer-to-peer fashion,
along multihop routes in the network, without requiring consensus on the blockchain.
However, during the discovery of cost-efficient routes for the transaction, critical
information may be revealed about the transacting entities. This paper initiates
the study of privacy-preserving route discovery mechanisms for payment channel
networks. In particular, we present LightPIR, an approach which allows a client
to learn the shortest (or cheapest in terms of fees) path between two nodes without
revealing any information about the endpoints of the transaction to the servers.
The two main observations which allow for an efficient solution in LightPIR are
that: (1) surprisingly, hub labelling algorithms – which were developed to preprocess
“street network like” graphs so one can later efficiently compute shortest paths
– also perform well for the graphs underlying payment channel networks, and that
(2) hub labelling algorithms can be conveniently combined with private information
retrieval. LightPIR relies on a simple hub labeling heuristic on top of existing
hub labeling algorithms which leverages the specific topological features of cryptocurrency
networks to further minimize storage and bandwidth overheads. In a case study
considering the Lightning network, we show that our approach is an order of magnitude
more efficient compared to a privacy-preserving baseline based on using private
information retrieval on a database that stores all pairs shortest paths.'
article_processing_charge: No
author:
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Iosif
full_name: Salem, Iosif
last_name: Salem
- first_name: Stefan
full_name: Schmid, Stefan
last_name: Schmid
- first_name: Michelle X
full_name: Yeo, Michelle X
id: 2D82B818-F248-11E8-B48F-1D18A9856A87
last_name: Yeo
citation:
ama: 'Pietrzak KZ, Salem I, Schmid S, Yeo MX. LightPIR: Privacy-preserving route
discovery for payment channel networks. In: IEEE; 2021. doi:10.23919/IFIPNetworking52078.2021.9472205'
apa: 'Pietrzak, K. Z., Salem, I., Schmid, S., & Yeo, M. X. (2021). LightPIR:
Privacy-preserving route discovery for payment channel networks. Presented at
the 2021 IFIP Networking Conference (IFIP Networking), Espoo and Helsinki, Finland:
IEEE. https://doi.org/10.23919/IFIPNetworking52078.2021.9472205'
chicago: 'Pietrzak, Krzysztof Z, Iosif Salem, Stefan Schmid, and Michelle X Yeo.
“LightPIR: Privacy-Preserving Route Discovery for Payment Channel Networks.” IEEE,
2021. https://doi.org/10.23919/IFIPNetworking52078.2021.9472205.'
ieee: 'K. Z. Pietrzak, I. Salem, S. Schmid, and M. X. Yeo, “LightPIR: Privacy-preserving
route discovery for payment channel networks,” presented at the 2021 IFIP Networking
Conference (IFIP Networking), Espoo and Helsinki, Finland, 2021.'
ista: 'Pietrzak KZ, Salem I, Schmid S, Yeo MX. 2021. LightPIR: Privacy-preserving
route discovery for payment channel networks. 2021 IFIP Networking Conference
(IFIP Networking).'
mla: 'Pietrzak, Krzysztof Z., et al. LightPIR: Privacy-Preserving Route Discovery
for Payment Channel Networks. IEEE, 2021, doi:10.23919/IFIPNetworking52078.2021.9472205.'
short: K.Z. Pietrzak, I. Salem, S. Schmid, M.X. Yeo, in:, IEEE, 2021.
conference:
end_date: 2021-06-24
location: Espoo and Helsinki, Finland
name: 2021 IFIP Networking Conference (IFIP Networking)
start_date: 2021-06-21
date_created: 2021-08-29T22:01:16Z
date_published: 2021-06-21T00:00:00Z
date_updated: 2023-11-30T10:54:50Z
day: '21'
department:
- _id: KrPi
doi: 10.23919/IFIPNetworking52078.2021.9472205
ec_funded: 1
external_id:
arxiv:
- '2104.04293'
isi:
- '000853016800008'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2104.04293
month: '06'
oa: 1
oa_version: Submitted Version
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_identifier:
eisbn:
- 978-3-9031-7639-3
eissn:
- 1861-2288
isbn:
- 978-1-6654-4501-6
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '14506'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'LightPIR: Privacy-preserving route discovery for payment channel networks'
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9644'
abstract:
- lang: eng
text: 'We present a new approach to proving non-termination of non-deterministic
integer programs. Our technique is rather simple but efficient. It relies on a
purely syntactic reversal of the program''s transition system followed by a constraint-based
invariant synthesis with constraints coming from both the original and the reversed
transition system. The latter task is performed by a simple call to an off-the-shelf
SMT-solver, which allows us to leverage the latest advances in SMT-solving. Moreover,
our method offers a combination of features not present (as a whole) in previous
approaches: it handles programs with non-determinism, provides relative completeness
guarantees and supports programs with polynomial arithmetic. The experiments performed
with our prototype tool RevTerm show that our approach, despite its simplicity
and stronger theoretical guarantees, is at least on par with the state-of-the-art
tools, often achieving a non-trivial improvement under a proper configuration
of its parameters.'
acknowledgement: We thank the anonymous reviewers for their helpful comments. This
research was partially supported by the ERCCoG 863818 (ForM-SMArt) and the Czech
Science Foundation grant No. GJ19-15134Y.
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Ehsan Kafshdar
full_name: Goharshady, Ehsan Kafshdar
last_name: Goharshady
- first_name: Petr
full_name: Novotný, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotný
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: 'Chatterjee K, Goharshady EK, Novotný P, Zikelic D. Proving non-termination
by program reversal. In: Proceedings of the 42nd ACM SIGPLAN International
Conference on Programming Language Design and Implementation. Association
for Computing Machinery; 2021:1033-1048. doi:10.1145/3453483.3454093'
apa: 'Chatterjee, K., Goharshady, E. K., Novotný, P., & Zikelic, D. (2021).
Proving non-termination by program reversal. In Proceedings of the 42nd ACM
SIGPLAN International Conference on Programming Language Design and Implementation
(pp. 1033–1048). Online: Association for Computing Machinery. https://doi.org/10.1145/3453483.3454093'
chicago: Chatterjee, Krishnendu, Ehsan Kafshdar Goharshady, Petr Novotný, and Dorde
Zikelic. “Proving Non-Termination by Program Reversal.” In Proceedings of the
42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation,
1033–48. Association for Computing Machinery, 2021. https://doi.org/10.1145/3453483.3454093.
ieee: K. Chatterjee, E. K. Goharshady, P. Novotný, and D. Zikelic, “Proving non-termination
by program reversal,” in Proceedings of the 42nd ACM SIGPLAN International
Conference on Programming Language Design and Implementation, Online, 2021,
pp. 1033–1048.
ista: 'Chatterjee K, Goharshady EK, Novotný P, Zikelic D. 2021. Proving non-termination
by program reversal. Proceedings of the 42nd ACM SIGPLAN International Conference
on Programming Language Design and Implementation. PLDI: Programming Language
Design and Implementation, 1033–1048.'
mla: Chatterjee, Krishnendu, et al. “Proving Non-Termination by Program Reversal.”
Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation, Association for Computing Machinery, 2021,
pp. 1033–48, doi:10.1145/3453483.3454093.
short: K. Chatterjee, E.K. Goharshady, P. Novotný, D. Zikelic, in:, Proceedings
of the 42nd ACM SIGPLAN International Conference on Programming Language Design
and Implementation, Association for Computing Machinery, 2021, pp. 1033–1048.
conference:
end_date: 2021-06-26
location: Online
name: 'PLDI: Programming Language Design and Implementation'
start_date: 2021-06-20
date_created: 2021-07-11T22:01:17Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-11-30T10:55:37Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/3453483.3454093
ec_funded: 1
external_id:
arxiv:
- '2104.01189'
isi:
- '000723661700067'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2104.01189
month: '06'
oa: 1
oa_version: Preprint
page: 1033-1048
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming
Language Design and Implementation
publication_identifier:
isbn:
- '9781450383912'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '14539'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Proving non-termination by program reversal
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2021'
...
---
_id: '9760'
abstract:
- lang: eng
text: "The quantum approximate optimization algorithm (QAOA) is a prospective near-term
quantum algorithm due to its modest circuit depth and promising benchmarks. However,
an external parameter optimization required in the QAOA could become a performance
bottleneck. This motivates studies of the optimization landscape and search for
heuristic ways of parameter initialization. In this work we visualize the optimization
landscape of the QAOA applied to the MaxCut problem on random graphs, demonstrating
that random initialization of the QAOA is prone to converging to local minima
with suboptimal performance. We introduce the initialization of QAOA parameters
based on the Trotterized quantum annealing (TQA) protocol, parameterized by the
Trotter time step. We find that the TQA initialization allows to circumvent\r\nthe
issue of false minima for a broad range of time steps, yielding the same performance
as the best result out of an exponentially scaling number of random initializations.
Moreover, we demonstrate that the optimal value of the time step coincides with
the point of proliferation of Trotter errors in quantum annealing. Our results
suggest practical ways of initializing QAOA protocols on near-term quantum devices
and reveal new connections between QAOA and quantum annealing."
acknowledgement: We would like to thank D. Abanin and R. Medina for fruitful discussions
and A. Smith and I. Kim for valuable feedback on the manuscript. We acknowledge
support by the European Research Council (ERC) under the European Union’s Horizon
2020 research and innovation program (Grant Agreement No. 850899).
article_number: '491'
article_processing_charge: Yes
article_type: original
author:
- first_name: Stefan
full_name: Sack, Stefan
id: dd622248-f6e0-11ea-865d-ce382a1c81a5
last_name: Sack
orcid: 0000-0001-5400-8508
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
citation:
ama: Sack S, Serbyn M. Quantum annealing initialization of the quantum approximate
optimization algorithm. Quantum. 2021;5. doi:10.22331/Q-2021-07-01-491
apa: Sack, S., & Serbyn, M. (2021). Quantum annealing initialization of the
quantum approximate optimization algorithm. Quantum. Verein zur Förderung
des Open Access Publizierens in den Quantenwissenschaften. https://doi.org/10.22331/Q-2021-07-01-491
chicago: Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the
Quantum Approximate Optimization Algorithm.” Quantum. Verein zur Förderung
des Open Access Publizierens in den Quantenwissenschaften, 2021. https://doi.org/10.22331/Q-2021-07-01-491.
ieee: S. Sack and M. Serbyn, “Quantum annealing initialization of the quantum approximate
optimization algorithm,” Quantum, vol. 5. Verein zur Förderung des Open
Access Publizierens in den Quantenwissenschaften, 2021.
ista: Sack S, Serbyn M. 2021. Quantum annealing initialization of the quantum approximate
optimization algorithm. Quantum. 5, 491.
mla: Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the Quantum
Approximate Optimization Algorithm.” Quantum, vol. 5, 491, Verein zur Förderung
des Open Access Publizierens in den Quantenwissenschaften, 2021, doi:10.22331/Q-2021-07-01-491.
short: S. Sack, M. Serbyn, Quantum 5 (2021).
date_created: 2021-08-01T22:01:21Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-12-13T14:47:25Z
day: '01'
ddc:
- '530'
department:
- _id: GradSch
- _id: MaSe
doi: 10.22331/Q-2021-07-01-491
ec_funded: 1
external_id:
arxiv:
- '2101.05742'
isi:
- '000669830600001'
file:
- access_level: open_access
checksum: 9706c2bb8e748e9b5b138381995a7f6f
content_type: application/pdf
creator: cchlebak
date_created: 2021-08-06T06:44:31Z
date_updated: 2021-08-06T06:44:31Z
file_id: '9774'
file_name: 2021_Quantum_Sack.pdf
file_size: 2312482
relation: main_file
file_date_updated: 2021-08-06T06:44:31Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Quantum
publication_identifier:
eissn:
- 2521-327X
publication_status: published
publisher: Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften
quality_controlled: '1'
related_material:
record:
- id: '14622'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Quantum annealing initialization of the quantum approximate optimization algorithm
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2021'
...
---
_id: '10414'
abstract:
- lang: eng
text: 'We consider the almost-sure (a.s.) termination problem for probabilistic
programs, which are a stochastic extension of classical imperative programs. Lexicographic
ranking functions provide a sound and practical approach for termination of non-probabilistic
programs, and their extension to probabilistic programs is achieved via lexicographic
ranking supermartingales (LexRSMs). However, LexRSMs introduced in the previous
work have a limitation that impedes their automation: all of their components
have to be non-negative in all reachable states. This might result in LexRSM not
existing even for simple terminating programs. Our contributions are twofold:
First, we introduce a generalization of LexRSMs which allows for some components
to be negative. This standard feature of non-probabilistic termination proofs
was hitherto not known to be sound in the probabilistic setting, as the soundness
proof requires a careful analysis of the underlying stochastic process. Second,
we present polynomial-time algorithms using our generalized LexRSMs for proving
a.s. termination in broad classes of linear-arithmetic programs.'
acknowledgement: This research was partially supported by the ERC CoG 863818 (ForM-SMArt),
the Czech Science Foundation grant No. GJ19-15134Y, and the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement
No. 665385.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Ehsan Kafshdar
full_name: Goharshady, Ehsan Kafshdar
last_name: Goharshady
- first_name: Petr
full_name: Novotný, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotný
- first_name: Jiří
full_name: Zárevúcky, Jiří
last_name: Zárevúcky
- first_name: Dorde
full_name: Zikelic, Dorde
id: 294AA7A6-F248-11E8-B48F-1D18A9856A87
last_name: Zikelic
orcid: 0000-0002-4681-1699
citation:
ama: 'Chatterjee K, Goharshady EK, Novotný P, Zárevúcky J, Zikelic D. On lexicographic
proof rules for probabilistic termination. In: 24th International Symposium
on Formal Methods. Vol 13047. Springer Nature; 2021:619-639. doi:10.1007/978-3-030-90870-6_33'
apa: 'Chatterjee, K., Goharshady, E. K., Novotný, P., Zárevúcky, J., & Zikelic,
D. (2021). On lexicographic proof rules for probabilistic termination. In 24th
International Symposium on Formal Methods (Vol. 13047, pp. 619–639). Virtual:
Springer Nature. https://doi.org/10.1007/978-3-030-90870-6_33'
chicago: Chatterjee, Krishnendu, Ehsan Kafshdar Goharshady, Petr Novotný, Jiří Zárevúcky,
and Dorde Zikelic. “On Lexicographic Proof Rules for Probabilistic Termination.”
In 24th International Symposium on Formal Methods, 13047:619–39. Springer
Nature, 2021. https://doi.org/10.1007/978-3-030-90870-6_33.
ieee: K. Chatterjee, E. K. Goharshady, P. Novotný, J. Zárevúcky, and D. Zikelic,
“On lexicographic proof rules for probabilistic termination,” in 24th International
Symposium on Formal Methods, Virtual, 2021, vol. 13047, pp. 619–639.
ista: 'Chatterjee K, Goharshady EK, Novotný P, Zárevúcky J, Zikelic D. 2021. On
lexicographic proof rules for probabilistic termination. 24th International Symposium
on Formal Methods. FM: Formal Methods, LNCS, vol. 13047, 619–639.'
mla: Chatterjee, Krishnendu, et al. “On Lexicographic Proof Rules for Probabilistic
Termination.” 24th International Symposium on Formal Methods, vol. 13047,
Springer Nature, 2021, pp. 619–39, doi:10.1007/978-3-030-90870-6_33.
short: K. Chatterjee, E.K. Goharshady, P. Novotný, J. Zárevúcky, D. Zikelic, in:,
24th International Symposium on Formal Methods, Springer Nature, 2021, pp. 619–639.
conference:
end_date: 2021-11-26
location: Virtual
name: 'FM: Formal Methods'
start_date: 2021-11-20
date_created: 2021-12-05T23:01:45Z
date_published: 2021-11-10T00:00:00Z
date_updated: 2024-01-17T08:19:41Z
day: '10'
department:
- _id: KrCh
doi: 10.1007/978-3-030-90870-6_33
ec_funded: 1
external_id:
arxiv:
- '2108.02188'
isi:
- '000758218600033'
intvolume: ' 13047'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2108.02188
month: '11'
oa: 1
oa_version: Preprint
page: 619-639
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '863818'
name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: 24th International Symposium on Formal Methods
publication_identifier:
eisbn:
- 978-3-030-90870-6
eissn:
- 1611-3349
isbn:
- 9-783-0309-0869-0
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '14539'
relation: dissertation_contains
status: public
- id: '14778'
relation: later_version
status: public
scopus_import: '1'
status: public
title: On lexicographic proof rules for probabilistic termination
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13047
year: '2021'
...
---
_id: '14800'
abstract:
- lang: eng
text: 'Research on two-dimensional (2D) materials has been explosively increasing
in last seventeen years in varying subjects including condensed matter physics,
electronic engineering, materials science, and chemistry since the mechanical
exfoliation of graphene in 2004. Starting from graphene, 2D materials now have
become a big family with numerous members and diverse categories. The unique structural
features and physicochemical properties of 2D materials make them one class of
the most appealing candidates for a wide range of potential applications. In particular,
we have seen some major breakthroughs made in the field of 2D materials in last
five years not only in developing novel synthetic methods and exploring new structures/properties
but also in identifying innovative applications and pushing forward commercialisation.
In this review, we provide a critical summary on the recent progress made in the
field of 2D materials with a particular focus on last five years. After a brief
background introduction, we first discuss the major synthetic methods for 2D materials,
including the mechanical exfoliation, liquid exfoliation, vapor phase deposition,
and wet-chemical synthesis as well as phase engineering of 2D materials belonging
to the field of phase engineering of nanomaterials (PEN). We then introduce the
superconducting/optical/magnetic properties and chirality of 2D materials along
with newly emerging magic angle 2D superlattices. Following that, the promising
applications of 2D materials in electronics, optoelectronics, catalysis, energy
storage, solar cells, biomedicine, sensors, environments, etc. are described sequentially.
Thereafter, we present the theoretic calculations and simulations of 2D materials.
Finally, after concluding the current progress, we provide some personal discussions
on the existing challenges and future outlooks in this rapidly developing field. '
article_number: '2108017'
article_processing_charge: No
article_type: review
author:
- first_name: Cheng
full_name: Chang, Cheng
id: 9E331C2E-9F27-11E9-AE48-5033E6697425
last_name: Chang
orcid: 0000-0002-9515-4277
- first_name: Wei
full_name: Chen, Wei
last_name: Chen
- first_name: Ye
full_name: Chen, Ye
last_name: Chen
- first_name: Yonghua
full_name: Chen, Yonghua
last_name: Chen
- first_name: Yu
full_name: Chen, Yu
last_name: Chen
- first_name: Feng
full_name: Ding, Feng
last_name: Ding
- first_name: Chunhai
full_name: Fan, Chunhai
last_name: Fan
- first_name: Hong Jin
full_name: Fan, Hong Jin
last_name: Fan
- first_name: Zhanxi
full_name: Fan, Zhanxi
last_name: Fan
- first_name: Cheng
full_name: Gong, Cheng
last_name: Gong
- first_name: Yongji
full_name: Gong, Yongji
last_name: Gong
- first_name: Qiyuan
full_name: He, Qiyuan
last_name: He
- first_name: Xun
full_name: Hong, Xun
last_name: Hong
- first_name: Sheng
full_name: Hu, Sheng
last_name: Hu
- first_name: Weida
full_name: Hu, Weida
last_name: Hu
- first_name: Wei
full_name: Huang, Wei
last_name: Huang
- first_name: Yuan
full_name: Huang, Yuan
last_name: Huang
- first_name: Wei
full_name: Ji, Wei
last_name: Ji
- first_name: Dehui
full_name: Li, Dehui
last_name: Li
- first_name: Lain Jong
full_name: Li, Lain Jong
last_name: Li
- first_name: Qiang
full_name: Li, Qiang
last_name: Li
- first_name: Li
full_name: Lin, Li
last_name: Lin
- first_name: Chongyi
full_name: Ling, Chongyi
last_name: Ling
- first_name: Minghua
full_name: Liu, Minghua
last_name: Liu
- first_name: 'Nan'
full_name: Liu, Nan
last_name: Liu
- first_name: Zhuang
full_name: Liu, Zhuang
last_name: Liu
- first_name: Kian Ping
full_name: Loh, Kian Ping
last_name: Loh
- first_name: Jianmin
full_name: Ma, Jianmin
last_name: Ma
- first_name: Feng
full_name: Miao, Feng
last_name: Miao
- first_name: Hailin
full_name: Peng, Hailin
last_name: Peng
- first_name: Mingfei
full_name: Shao, Mingfei
last_name: Shao
- first_name: Li
full_name: Song, Li
last_name: Song
- first_name: Shao
full_name: Su, Shao
last_name: Su
- first_name: Shuo
full_name: Sun, Shuo
last_name: Sun
- first_name: Chaoliang
full_name: Tan, Chaoliang
last_name: Tan
- first_name: Zhiyong
full_name: Tang, Zhiyong
last_name: Tang
- first_name: Dingsheng
full_name: Wang, Dingsheng
last_name: Wang
- first_name: Huan
full_name: Wang, Huan
last_name: Wang
- first_name: Jinlan
full_name: Wang, Jinlan
last_name: Wang
- first_name: Xin
full_name: Wang, Xin
last_name: Wang
- first_name: Xinran
full_name: Wang, Xinran
last_name: Wang
- first_name: Andrew T.S.
full_name: Wee, Andrew T.S.
last_name: Wee
- first_name: Zhongming
full_name: Wei, Zhongming
last_name: Wei
- first_name: Yuen
full_name: Wu, Yuen
last_name: Wu
- first_name: Zhong Shuai
full_name: Wu, Zhong Shuai
last_name: Wu
- first_name: Jie
full_name: Xiong, Jie
last_name: Xiong
- first_name: Qihua
full_name: Xiong, Qihua
last_name: Xiong
- first_name: Weigao
full_name: Xu, Weigao
last_name: Xu
- first_name: Peng
full_name: Yin, Peng
last_name: Yin
- first_name: Haibo
full_name: Zeng, Haibo
last_name: Zeng
- first_name: Zhiyuan
full_name: Zeng, Zhiyuan
last_name: Zeng
- first_name: Tianyou
full_name: Zhai, Tianyou
last_name: Zhai
- first_name: Han
full_name: Zhang, Han
last_name: Zhang
- first_name: Hui
full_name: Zhang, Hui
last_name: Zhang
- first_name: Qichun
full_name: Zhang, Qichun
last_name: Zhang
- first_name: Tierui
full_name: Zhang, Tierui
last_name: Zhang
- first_name: Xiang
full_name: Zhang, Xiang
last_name: Zhang
- first_name: Li Dong
full_name: Zhao, Li Dong
last_name: Zhao
- first_name: Meiting
full_name: Zhao, Meiting
last_name: Zhao
- first_name: Weijie
full_name: Zhao, Weijie
last_name: Zhao
- first_name: Yunxuan
full_name: Zhao, Yunxuan
last_name: Zhao
- first_name: Kai Ge
full_name: Zhou, Kai Ge
last_name: Zhou
- first_name: Xing
full_name: Zhou, Xing
last_name: Zhou
- first_name: Yu
full_name: Zhou, Yu
last_name: Zhou
- first_name: Hongwei
full_name: Zhu, Hongwei
last_name: Zhu
- first_name: Hua
full_name: Zhang, Hua
last_name: Zhang
- first_name: Zhongfan
full_name: Liu, Zhongfan
last_name: Liu
citation:
ama: Chang C, Chen W, Chen Y, et al. Recent progress on two-dimensional materials.
Acta Physico-Chimica Sinica. 2021;37(12). doi:10.3866/PKU.WHXB202108017
apa: Chang, C., Chen, W., Chen, Y., Chen, Y., Chen, Y., Ding, F., … Liu, Z. (2021).
Recent progress on two-dimensional materials. Acta Physico-Chimica Sinica.
Peking University. https://doi.org/10.3866/PKU.WHXB202108017
chicago: Chang, Cheng, Wei Chen, Ye Chen, Yonghua Chen, Yu Chen, Feng Ding, Chunhai
Fan, et al. “Recent Progress on Two-Dimensional Materials.” Acta Physico-Chimica
Sinica. Peking University, 2021. https://doi.org/10.3866/PKU.WHXB202108017.
ieee: C. Chang et al., “Recent progress on two-dimensional materials,” Acta
Physico-Chimica Sinica, vol. 37, no. 12. Peking University, 2021.
ista: Chang C, Chen W, Chen Y, Chen Y, Chen Y, Ding F, Fan C, Fan HJ, Fan Z, Gong
C, Gong Y, He Q, Hong X, Hu S, Hu W, Huang W, Huang Y, Ji W, Li D, Li LJ, Li Q,
Lin L, Ling C, Liu M, Liu N, Liu Z, Loh KP, Ma J, Miao F, Peng H, Shao M, Song
L, Su S, Sun S, Tan C, Tang Z, Wang D, Wang H, Wang J, Wang X, Wang X, Wee ATS,
Wei Z, Wu Y, Wu ZS, Xiong J, Xiong Q, Xu W, Yin P, Zeng H, Zeng Z, Zhai T, Zhang
H, Zhang H, Zhang Q, Zhang T, Zhang X, Zhao LD, Zhao M, Zhao W, Zhao Y, Zhou KG,
Zhou X, Zhou Y, Zhu H, Zhang H, Liu Z. 2021. Recent progress on two-dimensional
materials. Acta Physico-Chimica Sinica. 37(12), 2108017.
mla: Chang, Cheng, et al. “Recent Progress on Two-Dimensional Materials.” Acta
Physico-Chimica Sinica, vol. 37, no. 12, 2108017, Peking University, 2021,
doi:10.3866/PKU.WHXB202108017.
short: C. Chang, W. Chen, Y. Chen, Y. Chen, Y. Chen, F. Ding, C. Fan, H.J. Fan,
Z. Fan, C. Gong, Y. Gong, Q. He, X. Hong, S. Hu, W. Hu, W. Huang, Y. Huang, W.
Ji, D. Li, L.J. Li, Q. Li, L. Lin, C. Ling, M. Liu, N. Liu, Z. Liu, K.P. Loh,
J. Ma, F. Miao, H. Peng, M. Shao, L. Song, S. Su, S. Sun, C. Tan, Z. Tang, D.
Wang, H. Wang, J. Wang, X. Wang, X. Wang, A.T.S. Wee, Z. Wei, Y. Wu, Z.S. Wu,
J. Xiong, Q. Xiong, W. Xu, P. Yin, H. Zeng, Z. Zeng, T. Zhai, H. Zhang, H. Zhang,
Q. Zhang, T. Zhang, X. Zhang, L.D. Zhao, M. Zhao, W. Zhao, Y. Zhao, K.G. Zhou,
X. Zhou, Y. Zhou, H. Zhu, H. Zhang, Z. Liu, Acta Physico-Chimica Sinica 37 (2021).
date_created: 2024-01-14T23:00:58Z
date_published: 2021-10-13T00:00:00Z
date_updated: 2024-01-17T11:29:33Z
day: '13'
department:
- _id: MaIb
doi: 10.3866/PKU.WHXB202108017
intvolume: ' 37'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.3866/PKU.WHXB202108017
month: '10'
oa: 1
oa_version: Submitted Version
publication: Acta Physico-Chimica Sinica
publication_identifier:
issn:
- 1001-4861
publication_status: published
publisher: Peking University
quality_controlled: '1'
scopus_import: '1'
status: public
title: Recent progress on two-dimensional materials
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2021'
...
---
_id: '10206'
abstract:
- lang: eng
text: Neural-network classifiers achieve high accuracy when predicting the class
of an input that they were trained to identify. Maintaining this accuracy in dynamic
environments, where inputs frequently fall outside the fixed set of initially
known classes, remains a challenge. The typical approach is to detect inputs from
novel classes and retrain the classifier on an augmented dataset. However, not
only the classifier but also the detection mechanism needs to adapt in order to
distinguish between newly learned and yet unknown input classes. To address this
challenge, we introduce an algorithmic framework for active monitoring of a neural
network. A monitor wrapped in our framework operates in parallel with the neural
network and interacts with a human user via a series of interpretable labeling
queries for incremental adaptation. In addition, we propose an adaptive quantitative
monitor to improve precision. An experimental evaluation on a diverse set of benchmarks
with varying numbers of classes confirms the benefits of our active monitoring
framework in dynamic scenarios.
acknowledgement: We thank Christoph Lampert and Alex Greengold for fruitful discussions.
This research was supported in part by the Simons Institute for the Theory of Computing,
the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award), and the
European Union’s Horizon 2020 research and innovation programme under the Marie
Skłodowska-Curie grant agreement No. 754411.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Anna
full_name: Lukina, Anna
id: CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425
last_name: Lukina
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
citation:
ama: 'Lukina A, Schilling C, Henzinger TA. Into the unknown: active monitoring of neural
networks. In: 21st International Conference on Runtime Verification. Vol
12974. Cham: Springer Nature; 2021:42-61. doi:10.1007/978-3-030-88494-9_3'
apa: 'Lukina, A., Schilling, C., & Henzinger, T. A. (2021). Into the unknown:
active monitoring of neural networks. In 21st International Conference on Runtime
Verification (Vol. 12974, pp. 42–61). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-88494-9_3'
chicago: 'Lukina, Anna, Christian Schilling, and Thomas A Henzinger. “Into the Unknown:
Active Monitoring of Neural Networks.” In 21st International Conference on
Runtime Verification, 12974:42–61. Cham: Springer Nature, 2021. https://doi.org/10.1007/978-3-030-88494-9_3.'
ieee: 'A. Lukina, C. Schilling, and T. A. Henzinger, “Into the unknown: active monitoring
of neural networks,” in 21st International Conference on Runtime Verification,
Virtual, 2021, vol. 12974, pp. 42–61.'
ista: 'Lukina A, Schilling C, Henzinger TA. 2021. Into the unknown: active monitoring
of neural networks. 21st International Conference on Runtime Verification. RV:
Runtime Verification, LNCS, vol. 12974, 42–61.'
mla: 'Lukina, Anna, et al. “Into the Unknown: Active Monitoring of Neural Networks.”
21st International Conference on Runtime Verification, vol. 12974, Springer
Nature, 2021, pp. 42–61, doi:10.1007/978-3-030-88494-9_3.'
short: A. Lukina, C. Schilling, T.A. Henzinger, in:, 21st International Conference
on Runtime Verification, Springer Nature, Cham, 2021, pp. 42–61.
conference:
end_date: 2021-10-14
location: Virtual
name: 'RV: Runtime Verification'
start_date: 2021-10-11
date_created: 2021-10-31T23:01:31Z
date_published: 2021-10-06T00:00:00Z
date_updated: 2024-01-30T12:06:56Z
day: '06'
department:
- _id: ToHe
doi: 10.1007/978-3-030-88494-9_3
ec_funded: 1
external_id:
arxiv:
- '2009.06429'
isi:
- '000719383800003'
isi: 1
keyword:
- monitoring
- neural networks
- novelty detection
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2009.06429
month: '10'
oa: 1
oa_version: Preprint
page: 42-61
place: Cham
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: 21st International Conference on Runtime Verification
publication_identifier:
eisbn:
- 978-3-030-88494-9
eissn:
- 1611-3349
isbn:
- 9-783-0308-8493-2
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '13234'
relation: extended_version
status: public
scopus_import: '1'
status: public
title: 'Into the unknown: active monitoring of neural networks'
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: '12974 '
year: '2021'
...
---
_id: '14889'
abstract:
- lang: eng
text: We consider the Fröhlich Hamiltonian with large coupling constant α. For initial
data of Pekar product form with coherent phonon field and with the electron minimizing
the corresponding energy, we provide a norm approximation of the evolution, valid
up to times of order α2. The approximation is given in terms of a Pekar product
state, evolved through the Landau-Pekar equations, corrected by a Bogoliubov dynamics
taking quantum fluctuations into account. This allows us to show that the Landau-Pekar
equations approximately describe the evolution of the electron- and one-phonon
reduced density matrices under the Fröhlich dynamics up to times of order α2.
acknowledgement: "Financial support by the European Union’s Horizon 2020 research
and innovation programme\r\nunder the Marie Skłodowska-Curie grant agreement No.
754411 (S.R.) and the European\r\nResearch Council under grant agreement No. 694227
(N.L. and R.S.), as well as by the SNSF\r\nEccellenza project PCEFP2 181153 (N.L.),
the NCCR SwissMAP (N.L. and B.S.) and by the\r\nDeutsche Forschungsgemeinschaft
(DFG) through the Research Training Group 1838: Spectral\r\nTheory and Dynamics
of Quantum Systems (D.M.) is gratefully acknowledged. B.S. gratefully\r\nacknowledges
financial support from the Swiss National Science Foundation through the Grant\r\n“Dynamical
and energetic properties of Bose-Einstein condensates” and from the European\r\nResearch
Council through the ERC-AdG CLaQS (grant agreement No 834782). D.M. thanks\r\nMarcel
Griesemer for helpful discussions."
article_processing_charge: No
article_type: original
author:
- first_name: Nikolai K
full_name: Leopold, Nikolai K
id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87
last_name: Leopold
orcid: 0000-0002-0495-6822
- first_name: David Johannes
full_name: Mitrouskas, David Johannes
id: cbddacee-2b11-11eb-a02e-a2e14d04e52d
last_name: Mitrouskas
- first_name: Simone Anna Elvira
full_name: Rademacher, Simone Anna Elvira
id: 856966FE-A408-11E9-977E-802DE6697425
last_name: Rademacher
orcid: 0000-0001-5059-4466
- first_name: Benjamin
full_name: Schlein, Benjamin
last_name: Schlein
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Leopold NK, Mitrouskas DJ, Rademacher SAE, Schlein B, Seiringer R. Landau–Pekar
equations and quantum fluctuations for the dynamics of a strongly coupled polaron.
Pure and Applied Analysis. 2021;3(4):653-676. doi:10.2140/paa.2021.3.653
apa: Leopold, N. K., Mitrouskas, D. J., Rademacher, S. A. E., Schlein, B., &
Seiringer, R. (2021). Landau–Pekar equations and quantum fluctuations for the
dynamics of a strongly coupled polaron. Pure and Applied Analysis. Mathematical
Sciences Publishers. https://doi.org/10.2140/paa.2021.3.653
chicago: Leopold, Nikolai K, David Johannes Mitrouskas, Simone Anna Elvira Rademacher,
Benjamin Schlein, and Robert Seiringer. “Landau–Pekar Equations and Quantum Fluctuations
for the Dynamics of a Strongly Coupled Polaron.” Pure and Applied Analysis.
Mathematical Sciences Publishers, 2021. https://doi.org/10.2140/paa.2021.3.653.
ieee: N. K. Leopold, D. J. Mitrouskas, S. A. E. Rademacher, B. Schlein, and R. Seiringer,
“Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly
coupled polaron,” Pure and Applied Analysis, vol. 3, no. 4. Mathematical
Sciences Publishers, pp. 653–676, 2021.
ista: Leopold NK, Mitrouskas DJ, Rademacher SAE, Schlein B, Seiringer R. 2021. Landau–Pekar
equations and quantum fluctuations for the dynamics of a strongly coupled polaron.
Pure and Applied Analysis. 3(4), 653–676.
mla: Leopold, Nikolai K., et al. “Landau–Pekar Equations and Quantum Fluctuations
for the Dynamics of a Strongly Coupled Polaron.” Pure and Applied Analysis,
vol. 3, no. 4, Mathematical Sciences Publishers, 2021, pp. 653–76, doi:10.2140/paa.2021.3.653.
short: N.K. Leopold, D.J. Mitrouskas, S.A.E. Rademacher, B. Schlein, R. Seiringer,
Pure and Applied Analysis 3 (2021) 653–676.
date_created: 2024-01-28T23:01:43Z
date_published: 2021-10-01T00:00:00Z
date_updated: 2024-02-05T10:02:45Z
day: '01'
department:
- _id: RoSe
doi: 10.2140/paa.2021.3.653
ec_funded: 1
external_id:
arxiv:
- '2005.02098'
intvolume: ' 3'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2005.02098
month: '10'
oa: 1
oa_version: Preprint
page: 653-676
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: Pure and Applied Analysis
publication_identifier:
eissn:
- 2578-5885
issn:
- 2578-5893
publication_status: published
publisher: Mathematical Sciences Publishers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Landau–Pekar equations and quantum fluctuations for the dynamics of a strongly
coupled polaron
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2021'
...
---
_id: '14890'
abstract:
- lang: eng
text: We consider a system of N interacting bosons in the mean-field scaling regime
and construct corrections to the Bogoliubov dynamics that approximate the true
N-body dynamics in norm to arbitrary precision. The N-independent corrections
are given in terms of the solutions of the Bogoliubov and Hartree equations and
satisfy a generalized form of Wick's theorem. We determine the n-point correlation
functions of the excitations around the condensate, as well as the reduced densities
of the N-body system, to arbitrary accuracy, given only the knowledge of the two-point
functions of a quasi-free state and the solution of the Hartree equation. In this
way, the complex problem of computing all n-point correlation functions for an
interacting N-body system is essentially reduced to the problem of solving the
Hartree equation and the PDEs for the Bogoliubov two-point functions.
acknowledgement: "We are grateful for the hospitality of Central China Normal University
(CCNU),\r\nwhere parts of this work were done, and thank Phan Th`anh Nam, Simone\r\nRademacher,
Robert Seiringer and Stefan Teufel for helpful discussions. L.B. gratefully acknowledges
the support by the German Research Foundation (DFG) within the Research\r\nTraining
Group 1838 “Spectral Theory and Dynamics of Quantum Systems”, and the funding\r\nfrom
the European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSk
lodowska-Curie Grant Agreement No. 754411."
article_processing_charge: No
article_type: original
author:
- first_name: Lea
full_name: Bossmann, Lea
id: A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425
last_name: Bossmann
orcid: 0000-0002-6854-1343
- first_name: Sören P
full_name: Petrat, Sören P
id: 40AC02DC-F248-11E8-B48F-1D18A9856A87
last_name: Petrat
orcid: 0000-0002-9166-5889
- first_name: Peter
full_name: Pickl, Peter
last_name: Pickl
- first_name: Avy
full_name: Soffer, Avy
last_name: Soffer
citation:
ama: Bossmann L, Petrat SP, Pickl P, Soffer A. Beyond Bogoliubov dynamics. Pure
and Applied Analysis. 2021;3(4):677-726. doi:10.2140/paa.2021.3.677
apa: Bossmann, L., Petrat, S. P., Pickl, P., & Soffer, A. (2021). Beyond Bogoliubov
dynamics. Pure and Applied Analysis. Mathematical Sciences Publishers.
https://doi.org/10.2140/paa.2021.3.677
chicago: Bossmann, Lea, Sören P Petrat, Peter Pickl, and Avy Soffer. “Beyond Bogoliubov
Dynamics.” Pure and Applied Analysis. Mathematical Sciences Publishers,
2021. https://doi.org/10.2140/paa.2021.3.677.
ieee: L. Bossmann, S. P. Petrat, P. Pickl, and A. Soffer, “Beyond Bogoliubov dynamics,”
Pure and Applied Analysis, vol. 3, no. 4. Mathematical Sciences Publishers,
pp. 677–726, 2021.
ista: Bossmann L, Petrat SP, Pickl P, Soffer A. 2021. Beyond Bogoliubov dynamics.
Pure and Applied Analysis. 3(4), 677–726.
mla: Bossmann, Lea, et al. “Beyond Bogoliubov Dynamics.” Pure and Applied Analysis,
vol. 3, no. 4, Mathematical Sciences Publishers, 2021, pp. 677–726, doi:10.2140/paa.2021.3.677.
short: L. Bossmann, S.P. Petrat, P. Pickl, A. Soffer, Pure and Applied Analysis
3 (2021) 677–726.
date_created: 2024-01-28T23:01:43Z
date_published: 2021-10-01T00:00:00Z
date_updated: 2024-02-05T09:26:31Z
day: '01'
department:
- _id: RoSe
doi: 10.2140/paa.2021.3.677
ec_funded: 1
external_id:
arxiv:
- '1912.11004'
intvolume: ' 3'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1912.11004
month: '10'
oa: 1
oa_version: Preprint
page: 677-726
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Pure and Applied Analysis
publication_identifier:
eissn:
- 2578-5885
issn:
- 2578-5893
publication_status: published
publisher: Mathematical Sciences Publishers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Beyond Bogoliubov dynamics
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2021'
...
---
_id: '15013'
abstract:
- lang: eng
text: We consider random n×n matrices X with independent and centered entries and
a general variance profile. We show that the spectral radius of X converges with
very high probability to the square root of the spectral radius of the variance
matrix of X when n tends to infinity. We also establish the optimal rate of convergence,
that is a new result even for general i.i.d. matrices beyond the explicitly solvable
Gaussian cases. The main ingredient is the proof of the local inhomogeneous circular
law [arXiv:1612.07776] at the spectral edge.
acknowledgement: Partially supported by ERC Starting Grant RandMat No. 715539 and
the SwissMap grant of Swiss National Science Foundation. Partially supported by
ERC Advanced Grant RanMat No. 338804. Partially supported by the Hausdorff Center
for Mathematics in Bonn.
article_processing_charge: No
article_type: original
author:
- first_name: Johannes
full_name: Alt, Johannes
id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87
last_name: Alt
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
citation:
ama: Alt J, Erdös L, Krüger TH. Spectral radius of random matrices with independent
entries. Probability and Mathematical Physics. 2021;2(2):221-280. doi:10.2140/pmp.2021.2.221
apa: Alt, J., Erdös, L., & Krüger, T. H. (2021). Spectral radius of random matrices
with independent entries. Probability and Mathematical Physics. Mathematical
Sciences Publishers. https://doi.org/10.2140/pmp.2021.2.221
chicago: Alt, Johannes, László Erdös, and Torben H Krüger. “Spectral Radius of Random
Matrices with Independent Entries.” Probability and Mathematical Physics.
Mathematical Sciences Publishers, 2021. https://doi.org/10.2140/pmp.2021.2.221.
ieee: J. Alt, L. Erdös, and T. H. Krüger, “Spectral radius of random matrices with
independent entries,” Probability and Mathematical Physics, vol. 2, no.
2. Mathematical Sciences Publishers, pp. 221–280, 2021.
ista: Alt J, Erdös L, Krüger TH. 2021. Spectral radius of random matrices with independent
entries. Probability and Mathematical Physics. 2(2), 221–280.
mla: Alt, Johannes, et al. “Spectral Radius of Random Matrices with Independent
Entries.” Probability and Mathematical Physics, vol. 2, no. 2, Mathematical
Sciences Publishers, 2021, pp. 221–80, doi:10.2140/pmp.2021.2.221.
short: J. Alt, L. Erdös, T.H. Krüger, Probability and Mathematical Physics 2 (2021)
221–280.
date_created: 2024-02-18T23:01:03Z
date_published: 2021-05-21T00:00:00Z
date_updated: 2024-02-19T08:30:00Z
day: '21'
department:
- _id: LaEr
doi: 10.2140/pmp.2021.2.221
ec_funded: 1
external_id:
arxiv:
- '1907.13631'
intvolume: ' 2'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1907.13631
month: '05'
oa: 1
oa_version: Preprint
page: 221-280
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Probability and Mathematical Physics
publication_identifier:
eissn:
- 2690-1005
issn:
- 2690-0998
publication_status: published
publisher: Mathematical Sciences Publishers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spectral radius of random matrices with independent entries
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2021'
...
---
_id: '9887'
abstract:
- lang: eng
text: Clathrin-mediated endocytosis is the major route of entry of cargos into cells
and thus underpins many physiological processes. During endocytosis, an area of
flat membrane is remodeled by proteins to create a spherical vesicle against intracellular
forces. The protein machinery which mediates this membrane bending in plants is
unknown. However, it is known that plant endocytosis is actin independent, thus
indicating that plants utilize a unique mechanism to mediate membrane bending
against high-turgor pressure compared to other model systems. Here, we investigate
the TPLATE complex, a plant-specific endocytosis protein complex. It has been
thought to function as a classical adaptor functioning underneath the clathrin
coat. However, by using biochemical and advanced live microscopy approaches, we
found that TPLATE is peripherally associated with clathrin-coated vesicles and
localizes at the rim of endocytosis events. As this localization is more fitting
to the protein machinery involved in membrane bending during endocytosis, we examined
cells in which the TPLATE complex was disrupted and found that the clathrin structures
present as flat patches. This suggests a requirement of the TPLATE complex for
membrane bending during plant clathrin–mediated endocytosis. Next, we used in
vitro biophysical assays to confirm that the TPLATE complex possesses protein
domains with intrinsic membrane remodeling activity. These results redefine the
role of the TPLATE complex and implicate it as a key component of the evolutionarily
distinct plant endocytosis mechanism, which mediates endocytic membrane bending
against the high-turgor pressure in plant cells.
acknowledged_ssus:
- _id: EM-Fac
- _id: LifeSc
- _id: Bio
acknowledgement: 'We gratefully thank Julie Neveu and Dr. Amanda Barranco of the Grégory
Vert laboratory for help preparing plants in France, Dr. Zuzana Gelova for help
and advice with protoplast generation, Dr. Stéphane Vassilopoulos and Dr. Florian
Schur for advice regarding EM tomography, Alejandro Marquiegui Alvaro for help with
material generation, and Dr. Lukasz Kowalski for generously gifting us the mWasabi
protein. This research was supported by the Scientific Service Units of Institute
of Science and Technology Austria (IST Austria) through resources provided by the
Electron Microscopy Facility, Lab Support Facility (particularly Dorota Jaworska),
and the Bioimaging Facility. We acknowledge the Advanced Microscopy Facility of
the Vienna BioCenter Core Facilities for use of the 3D SIM. For the mass spectrometry
analysis of proteins, we acknowledge the University of Natural Resources and Life
Sciences (BOKU) Core Facility Mass Spectrometry. This work was supported by the
following funds: A.J. is supported by funding from the Austrian Science Fund I3630B25
to J.F. P.M. and E.B. are supported by Agence Nationale de la Recherche ANR-11-EQPX-0029
Morphoscope2 and ANR-10-INBS-04 France BioImaging. S.Y.B. is supported by the NSF
No. 1121998 and 1614915. J.W. and D.V.D. are supported by the European Research
Council Grant 682436 (to D.V.D.), a China Scholarship Council Grant 201508440249
(to J.W.), and by a Ghent University Special Research Co-funding Grant ST01511051
(to J.W.).'
article_number: e2113046118
article_processing_charge: No
article_type: original
author:
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: Dana A
full_name: Dahhan, Dana A
last_name: Dahhan
- first_name: Nataliia
full_name: Gnyliukh, Nataliia
id: 390C1120-F248-11E8-B48F-1D18A9856A87
last_name: Gnyliukh
orcid: 0000-0002-2198-0509
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Vanessa
full_name: Zheden, Vanessa
id: 39C5A68A-F248-11E8-B48F-1D18A9856A87
last_name: Zheden
orcid: 0000-0002-9438-4783
- first_name: Tommaso
full_name: Costanzo, Tommaso
id: D93824F4-D9BA-11E9-BB12-F207E6697425
last_name: Costanzo
orcid: 0000-0001-9732-3815
- first_name: Pierre
full_name: Mahou, Pierre
last_name: Mahou
- first_name: Mónika
full_name: Hrtyan, Mónika
id: 45A71A74-F248-11E8-B48F-1D18A9856A87
last_name: Hrtyan
- first_name: Jie
full_name: Wang, Jie
last_name: Wang
- first_name: Juan L
full_name: Aguilera Servin, Juan L
id: 2A67C376-F248-11E8-B48F-1D18A9856A87
last_name: Aguilera Servin
orcid: 0000-0002-2862-8372
- first_name: Daniël
full_name: van Damme, Daniël
last_name: van Damme
- first_name: Emmanuel
full_name: Beaurepaire, Emmanuel
last_name: Beaurepaire
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Sebastian Y
full_name: Bednarek, Sebastian Y
last_name: Bednarek
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Johnson AJ, Dahhan DA, Gnyliukh N, et al. The TPLATE complex mediates membrane
bending during plant clathrin-mediated endocytosis. Proceedings of the National
Academy of Sciences. 2021;118(51). doi:10.1073/pnas.2113046118
apa: Johnson, A. J., Dahhan, D. A., Gnyliukh, N., Kaufmann, W., Zheden, V., Costanzo,
T., … Friml, J. (2021). The TPLATE complex mediates membrane bending during plant
clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences.
National Academy of Sciences. https://doi.org/10.1073/pnas.2113046118
chicago: Johnson, Alexander J, Dana A Dahhan, Nataliia Gnyliukh, Walter Kaufmann,
Vanessa Zheden, Tommaso Costanzo, Pierre Mahou, et al. “The TPLATE Complex Mediates
Membrane Bending during Plant Clathrin-Mediated Endocytosis.” Proceedings of
the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2113046118.
ieee: A. J. Johnson et al., “The TPLATE complex mediates membrane bending
during plant clathrin-mediated endocytosis,” Proceedings of the National Academy
of Sciences, vol. 118, no. 51. National Academy of Sciences, 2021.
ista: Johnson AJ, Dahhan DA, Gnyliukh N, Kaufmann W, Zheden V, Costanzo T, Mahou
P, Hrtyan M, Wang J, Aguilera Servin JL, van Damme D, Beaurepaire E, Loose M,
Bednarek SY, Friml J. 2021. The TPLATE complex mediates membrane bending during
plant clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences.
118(51), e2113046118.
mla: Johnson, Alexander J., et al. “The TPLATE Complex Mediates Membrane Bending
during Plant Clathrin-Mediated Endocytosis.” Proceedings of the National Academy
of Sciences, vol. 118, no. 51, e2113046118, National Academy of Sciences,
2021, doi:10.1073/pnas.2113046118.
short: A.J. Johnson, D.A. Dahhan, N. Gnyliukh, W. Kaufmann, V. Zheden, T. Costanzo,
P. Mahou, M. Hrtyan, J. Wang, J.L. Aguilera Servin, D. van Damme, E. Beaurepaire,
M. Loose, S.Y. Bednarek, J. Friml, Proceedings of the National Academy of Sciences
118 (2021).
date_created: 2021-08-11T14:11:43Z
date_published: 2021-12-14T00:00:00Z
date_updated: 2024-02-19T11:06:09Z
day: '14'
ddc:
- '580'
department:
- _id: JiFr
- _id: MaLo
- _id: EvBe
- _id: EM-Fac
- _id: NanoFab
doi: 10.1073/pnas.2113046118
external_id:
isi:
- '000736417600043'
pmid:
- '34907016'
file:
- access_level: open_access
checksum: 8d01e72e22c4fb1584e72d8601947069
content_type: application/pdf
creator: cchlebak
date_created: 2021-12-15T08:59:40Z
date_updated: 2021-12-15T08:59:40Z
file_id: '10546'
file_name: 2021_PNAS_Johnson.pdf
file_size: 2757340
relation: main_file
success: 1
file_date_updated: 2021-12-15T08:59:40Z
has_accepted_license: '1'
intvolume: ' 118'
isi: 1
issue: '51'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: earlier_version
url: https://doi.org/10.1101/2021.04.26.441441
record:
- id: '14510'
relation: dissertation_contains
status: public
- id: '14988'
relation: research_data
status: public
status: public
title: The TPLATE complex mediates membrane bending during plant clathrin-mediated
endocytosis
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: 118
year: '2021'
...
---
_id: '14984'
abstract:
- lang: eng
text: Hybrid zones are narrow geographic regions where different populations, races
or interbreeding species meet and mate, producing mixed ‘hybrid’ offspring. They
are relatively common and can be found in a diverse range of organisms and environments.
The study of hybrid zones has played an important role in our understanding of
the origin of species, with hybrid zones having been described as ‘natural laboratories’.
This is because they allow us to study,in situ, the conditions and evolutionary
forces that enable divergent taxa to remain distinct despite some ongoing gene
exchange between them.
article_processing_charge: No
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
- first_name: Daria
full_name: Shipilina, Daria
id: 428A94B0-F248-11E8-B48F-1D18A9856A87
last_name: Shipilina
orcid: 0000-0002-1145-9226
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
citation:
ama: 'Stankowski S, Shipilina D, Westram AM. Hybrid Zones. In: Encyclopedia of
Life Sciences. Vol 2. eLS. Wiley; 2021. doi:10.1002/9780470015902.a0029355'
apa: Stankowski, S., Shipilina, D., & Westram, A. M. (2021). Hybrid Zones. In
Encyclopedia of Life Sciences (Vol. 2). Wiley. https://doi.org/10.1002/9780470015902.a0029355
chicago: Stankowski, Sean, Daria Shipilina, and Anja M Westram. “Hybrid Zones.”
In Encyclopedia of Life Sciences, Vol. 2. ELS. Wiley, 2021. https://doi.org/10.1002/9780470015902.a0029355.
ieee: S. Stankowski, D. Shipilina, and A. M. Westram, “Hybrid Zones,” in Encyclopedia
of Life Sciences, vol. 2, Wiley, 2021.
ista: 'Stankowski S, Shipilina D, Westram AM. 2021.Hybrid Zones. In: Encyclopedia
of Life Sciences. vol. 2.'
mla: Stankowski, Sean, et al. “Hybrid Zones.” Encyclopedia of Life Sciences,
vol. 2, Wiley, 2021, doi:10.1002/9780470015902.a0029355.
short: S. Stankowski, D. Shipilina, A.M. Westram, in:, Encyclopedia of Life Sciences,
Wiley, 2021.
date_created: 2024-02-14T12:05:50Z
date_published: 2021-05-28T00:00:00Z
date_updated: 2024-02-19T09:54:18Z
day: '28'
department:
- _id: NiBa
doi: 10.1002/9780470015902.a0029355
intvolume: ' 2'
language:
- iso: eng
month: '05'
oa_version: None
publication: Encyclopedia of Life Sciences
publication_identifier:
eisbn:
- '9780470015902'
isbn:
- '9780470016176'
publication_status: published
publisher: Wiley
quality_controlled: '1'
series_title: eLS
status: public
title: Hybrid Zones
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2021'
...
---
_id: '14987'
abstract:
- lang: eng
text: "The goal of zero-shot learning is to construct a classifier that can identify
object classes for which no training examples are available. When training data
for some of the object classes is available but not for others, the name generalized
zero-shot learning is commonly used.\r\nIn a wider sense, the phrase zero-shot
is also used to describe other machine learning-based approaches that require
no training data from the problem of interest, such as zero-shot action recognition
or zero-shot machine translation."
article_processing_charge: No
author:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Lampert C. Zero-Shot Learning. In: Ikeuchi K, ed. Computer Vision.
2nd ed. Cham: Springer; 2021:1395-1397. doi:10.1007/978-3-030-63416-2_874'
apa: 'Lampert, C. (2021). Zero-Shot Learning. In K. Ikeuchi (Ed.), Computer Vision
(2nd ed., pp. 1395–1397). Cham: Springer. https://doi.org/10.1007/978-3-030-63416-2_874'
chicago: 'Lampert, Christoph. “Zero-Shot Learning.” In Computer Vision, edited
by Katsushi Ikeuchi, 2nd ed., 1395–97. Cham: Springer, 2021. https://doi.org/10.1007/978-3-030-63416-2_874.'
ieee: 'C. Lampert, “Zero-Shot Learning,” in Computer Vision, 2nd ed., K.
Ikeuchi, Ed. Cham: Springer, 2021, pp. 1395–1397.'
ista: 'Lampert C. 2021.Zero-Shot Learning. In: Computer Vision. , 1395–1397.'
mla: Lampert, Christoph. “Zero-Shot Learning.” Computer Vision, edited by
Katsushi Ikeuchi, 2nd ed., Springer, 2021, pp. 1395–97, doi:10.1007/978-3-030-63416-2_874.
short: C. Lampert, in:, K. Ikeuchi (Ed.), Computer Vision, 2nd ed., Springer, Cham,
2021, pp. 1395–1397.
date_created: 2024-02-14T14:05:32Z
date_published: 2021-10-13T00:00:00Z
date_updated: 2024-02-19T10:59:04Z
day: '13'
department:
- _id: ChLa
doi: 10.1007/978-3-030-63416-2_874
edition: '2'
editor:
- first_name: Katsushi
full_name: Ikeuchi, Katsushi
last_name: Ikeuchi
language:
- iso: eng
month: '10'
oa_version: None
page: 1395-1397
place: Cham
publication: Computer Vision
publication_identifier:
eisbn:
- '9783030634162'
isbn:
- '9783030634155'
publication_status: published
publisher: Springer
quality_controlled: '1'
status: public
title: Zero-Shot Learning
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '14988'
abstract:
- lang: eng
text: Raw data generated from the publication - The TPLATE complex mediates membrane
bending during plant clathrin-mediated endocytosis by Johnson et al., 2021 In
PNAS
article_processing_charge: No
author:
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
citation:
ama: Johnson AJ. Raw data from Johnson et al, PNAS, 2021. 2021. doi:10.5281/ZENODO.5747100
apa: Johnson, A. J. (2021). Raw data from Johnson et al, PNAS, 2021. Zenodo. https://doi.org/10.5281/ZENODO.5747100
chicago: Johnson, Alexander J. “Raw Data from Johnson et Al, PNAS, 2021.” Zenodo,
2021. https://doi.org/10.5281/ZENODO.5747100.
ieee: A. J. Johnson, “Raw data from Johnson et al, PNAS, 2021.” Zenodo, 2021.
ista: Johnson AJ. 2021. Raw data from Johnson et al, PNAS, 2021, Zenodo, 10.5281/ZENODO.5747100.
mla: Johnson, Alexander J. Raw Data from Johnson et Al, PNAS, 2021. Zenodo,
2021, doi:10.5281/ZENODO.5747100.
short: A.J. Johnson, (2021).
date_created: 2024-02-14T14:13:48Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2024-02-19T11:06:09Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.5281/ZENODO.5747100
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.5747100
month: '12'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '9887'
relation: used_in_publication
status: public
status: public
title: Raw data from Johnson et al, PNAS, 2021
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '10029'
abstract:
- lang: eng
text: Superconductor-semiconductor hybrids are platforms for realizing effective
p-wave superconductivity. Spin-orbit coupling, combined with the proximity effect,
causes the two-dimensional semiconductor to inherit p±ip intraband pairing, and
application of magnetic field can then result in transitions to the normal state,
partial Bogoliubov Fermi surfaces, or topological phases with Majorana modes.
Experimentally probing the hybrid superconductor-semiconductor interface is challenging
due to the shunting effect of the conventional superconductor. Consequently, the
nature of induced pairing remains an open question. Here, we use the circuit quantum
electrodynamics architecture to probe induced superconductivity in a two dimensional
Al-InAs hybrid system. We observe a strong suppression of superfluid density and
enhanced dissipation driven by magnetic field, which cannot be accounted for by
the depairing theory of an s-wave superconductor. These observations are explained
by a picture of independent intraband p±ip superconductors giving way to partial
Bogoliubov Fermi surfaces, and allow for the first characterization of key properties
of the hybrid superconducting system.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: This research was supported by the Scientific Service Units of IST
Austria through resources provided by the MIBA Machine Shop and the nanofabrication
facility. JS and AG were supported by funding from the European Union’s Horizon
2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement
No.754411.
article_number: '2107.03695'
article_processing_charge: No
author:
- first_name: Duc T
full_name: Phan, Duc T
id: 29C8C0B4-F248-11E8-B48F-1D18A9856A87
last_name: Phan
- first_name: Jorden L
full_name: Senior, Jorden L
id: 5479D234-2D30-11EA-89CC-40953DDC885E
last_name: Senior
orcid: 0000-0002-0672-9295
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: M.
full_name: Hatefipour, M.
last_name: Hatefipour
- first_name: W. M.
full_name: Strickland, W. M.
last_name: Strickland
- first_name: J.
full_name: Shabani, J.
last_name: Shabani
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
citation:
ama: Phan DT, Senior JL, Ghazaryan A, et al. Breakdown of induced p±ip pairing in
a superconductor-semiconductor hybrid. arXiv.
apa: Phan, D. T., Senior, J. L., Ghazaryan, A., Hatefipour, M., Strickland, W. M.,
Shabani, J., … Higginbotham, A. P. (n.d.). Breakdown of induced p±ip pairing in
a superconductor-semiconductor hybrid. arXiv.
chicago: Phan, Duc T, Jorden L Senior, Areg Ghazaryan, M. Hatefipour, W. M. Strickland,
J. Shabani, Maksym Serbyn, and Andrew P Higginbotham. “Breakdown of Induced P±ip
Pairing in a Superconductor-Semiconductor Hybrid.” ArXiv, n.d.
ieee: D. T. Phan et al., “Breakdown of induced p±ip pairing in a superconductor-semiconductor
hybrid,” arXiv. .
ista: Phan DT, Senior JL, Ghazaryan A, Hatefipour M, Strickland WM, Shabani J, Serbyn
M, Higginbotham AP. Breakdown of induced p±ip pairing in a superconductor-semiconductor
hybrid. arXiv, 2107.03695.
mla: Phan, Duc T., et al. “Breakdown of Induced P±ip Pairing in a Superconductor-Semiconductor
Hybrid.” ArXiv, 2107.03695.
short: D.T. Phan, J.L. Senior, A. Ghazaryan, M. Hatefipour, W.M. Strickland, J.
Shabani, M. Serbyn, A.P. Higginbotham, ArXiv (n.d.).
date_created: 2021-09-21T08:41:02Z
date_published: 2021-07-08T00:00:00Z
date_updated: 2024-02-21T12:36:52Z
day: '08'
department:
- _id: MaSe
- _id: AnHi
- _id: MiLe
ec_funded: 1
external_id:
arxiv:
- '2107.03695'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2107.03695
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: arXiv
publication_status: submitted
related_material:
record:
- id: '10851'
relation: later_version
status: public
- id: '9636'
relation: research_data
status: public
status: public
title: Breakdown of induced p±ip pairing in a superconductor-semiconductor hybrid
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '9291'
abstract:
- lang: eng
text: "This .zip File contains the transport data for figures presented in the main
text and supplementary material of \"Enhancement of Proximity Induced Superconductivity
in Planar Germanium\" by K. Aggarwal, et. al. \r\nThe measurements were done using
Labber Software and the data is stored in the hdf5 file format. The files can
be opened using either the Labber Log Browser (https://labber.org/overview/) or
Labber Python API (http://labber.org/online-doc/api/LogFile.html)."
article_processing_charge: No
author:
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: 'Katsaros G. Raw transport data for: Enhancement of proximity induced superconductivity
in planar germanium. 2021. doi:10.15479/AT:ISTA:9291'
apa: 'Katsaros, G. (2021). Raw transport data for: Enhancement of proximity induced
superconductivity in planar germanium. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:9291'
chicago: 'Katsaros, Georgios. “Raw Transport Data for: Enhancement of Proximity
Induced Superconductivity in Planar Germanium.” Institute of Science and Technology
Austria, 2021. https://doi.org/10.15479/AT:ISTA:9291.'
ieee: 'G. Katsaros, “Raw transport data for: Enhancement of proximity induced superconductivity
in planar germanium.” Institute of Science and Technology Austria, 2021.'
ista: 'Katsaros G. 2021. Raw transport data for: Enhancement of proximity induced
superconductivity in planar germanium, Institute of Science and Technology Austria,
10.15479/AT:ISTA:9291.'
mla: 'Katsaros, Georgios. Raw Transport Data for: Enhancement of Proximity Induced
Superconductivity in Planar Germanium. Institute of Science and Technology
Austria, 2021, doi:10.15479/AT:ISTA:9291.'
short: G. Katsaros, (2021).
date_created: 2021-03-27T13:47:49Z
date_published: 2021-03-29T00:00:00Z
date_updated: 2024-02-21T12:37:14Z
day: '29'
ddc:
- '530'
department:
- _id: GeKa
doi: 10.15479/AT:ISTA:9291
file:
- access_level: open_access
checksum: 635df3c08fc13c3dac008cd421aefbe4
content_type: application/x-zip-compressed
creator: gkatsaro
date_created: 2021-03-27T13:46:17Z
date_updated: 2021-03-27T13:46:17Z
file_id: '9292'
file_name: Raw Data- Enhancement of Superconductivity in a Planar Ge hole gas.zip
file_size: 10616071
relation: main_file
success: 1
- access_level: open_access
checksum: 12b3ca69ae7509a346711baae0b02a75
content_type: text/plain
creator: dernst
date_created: 2021-04-01T07:52:56Z
date_updated: 2021-04-01T07:52:56Z
file_id: '9302'
file_name: README.txt
file_size: 470
relation: main_file
success: 1
file_date_updated: 2021-04-01T07:52:56Z
has_accepted_license: '1'
month: '03'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
status: public
title: 'Raw transport data for: Enhancement of proximity induced superconductivity
in planar germanium'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '9636'
article_processing_charge: No
author:
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
citation:
ama: Higginbotham AP. Data for “Breakdown of induced p ± ip pairing in a superconductor-semiconductor
hybrid.” 2021.
apa: Higginbotham, A. P. (2021). Data for “Breakdown of induced p ± ip pairing in
a superconductor-semiconductor hybrid.” Institute of Science and Technology Austria.
chicago: Higginbotham, Andrew P. “Data for ‘Breakdown of Induced p ± Ip Pairing
in a Superconductor-Semiconductor Hybrid.’” Institute of Science and Technology
Austria, 2021.
ieee: A. P. Higginbotham, “Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor
hybrid.’” Institute of Science and Technology Austria, 2021.
ista: Higginbotham AP. 2021. Data for ‘Breakdown of induced p ± ip pairing in a
superconductor-semiconductor hybrid’, Institute of Science and Technology Austria.
mla: Higginbotham, Andrew P. Data for “Breakdown of Induced p ± Ip Pairing in
a Superconductor-Semiconductor Hybrid.” Institute of Science and Technology
Austria, 2021.
short: A.P. Higginbotham, (2021).
date_created: 2021-07-07T20:43:10Z
date_published: 2021-01-01T00:00:00Z
date_updated: 2024-02-21T12:36:52Z
department:
- _id: AnHi
file:
- access_level: open_access
checksum: 18e90687ec7bbd75f8bfea4d8293fb30
content_type: application/zip
creator: ahigginb
date_created: 2021-07-07T20:37:28Z
date_updated: 2021-07-07T20:37:28Z
file_id: '9637'
file_name: figures_data.zip
file_size: 3345244
relation: main_file
success: 1
file_date_updated: 2021-07-07T20:37:28Z
has_accepted_license: '1'
oa: 1
oa_version: Submitted Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10029'
relation: used_in_publication
status: public
status: public
title: Data for "Breakdown of induced p ± ip pairing in a superconductor-semiconductor
hybrid"
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '8910'
abstract:
- lang: eng
text: A semiconducting nanowire fully wrapped by a superconducting shell has been
proposed as a platform for obtaining Majorana modes at small magnetic fields.
In this study, we demonstrate that the appearance of subgap states in such structures
is actually governed by the junction region in tunneling spectroscopy measurements
and not the full-shell nanowire itself. Short tunneling regions never show subgap
states, whereas longer junctions always do. This can be understood in terms of
quantum dots forming in the junction and hosting Andreev levels in the Yu-Shiba-Rusinov
regime. The intricate magnetic field dependence of the Andreev levels, through
both the Zeeman and Little-Parks effects, may result in robust zero-bias peaks—features
that could be easily misinterpreted as originating from Majorana zero modes but
are unrelated to topological superconductivity.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: The authors thank A. Higginbotham, E. J. H. Lee and F. R. Martins
for helpful discussions. This research was supported by the Scientific Service Units
of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication
facility; the NOMIS Foundation and Microsoft; the European Union’s Horizon 2020
research and innovation program under the Marie SklodowskaCurie grant agreement
No 844511; the FETOPEN Grant Agreement No. 828948; the European Research Commission
through the grant agreement HEMs-DAM No 716655; the Spanish Ministry of Science
and Innovation through Grants PGC2018-097018-B-I00, PCI2018-093026, FIS2016-80434-P
(AEI/FEDER, EU), RYC2011-09345 (Ram´on y Cajal Programme), and the Mar´ıa de Maeztu
Programme for Units of Excellence in R&D (CEX2018-000805-M); the CSIC Research Platform
on Quantum Technologies PTI-001.
article_number: 82-88
article_processing_charge: No
article_type: original
author:
- first_name: Marco
full_name: Valentini, Marco
id: C0BB2FAC-D767-11E9-B658-BC13E6697425
last_name: Valentini
- first_name: Fernando
full_name: Peñaranda, Fernando
last_name: Peñaranda
- first_name: Andrea C
full_name: Hofmann, Andrea C
id: 340F461A-F248-11E8-B48F-1D18A9856A87
last_name: Hofmann
- first_name: Matthias
full_name: Brauns, Matthias
id: 33F94E3C-F248-11E8-B48F-1D18A9856A87
last_name: Brauns
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Peter
full_name: Krogstrup, Peter
last_name: Krogstrup
- first_name: Pablo
full_name: San-Jose, Pablo
last_name: San-Jose
- first_name: Elsa
full_name: Prada, Elsa
last_name: Prada
- first_name: Ramón
full_name: Aguado, Ramón
last_name: Aguado
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Valentini M, Peñaranda F, Hofmann AC, et al. Nontopological zero-bias peaks
in full-shell nanowires induced by flux-tunable Andreev states. Science.
2021;373(6550). doi:10.1126/science.abf1513
apa: Valentini, M., Peñaranda, F., Hofmann, A. C., Brauns, M., Hauschild, R., Krogstrup,
P., … Katsaros, G. (2021). Nontopological zero-bias peaks in full-shell nanowires
induced by flux-tunable Andreev states. Science. American Association for
the Advancement of Science. https://doi.org/10.1126/science.abf1513
chicago: Valentini, Marco, Fernando Peñaranda, Andrea C Hofmann, Matthias Brauns,
Robert Hauschild, Peter Krogstrup, Pablo San-Jose, Elsa Prada, Ramón Aguado, and
Georgios Katsaros. “Nontopological Zero-Bias Peaks in Full-Shell Nanowires Induced
by Flux-Tunable Andreev States.” Science. American Association for the
Advancement of Science, 2021. https://doi.org/10.1126/science.abf1513.
ieee: M. Valentini et al., “Nontopological zero-bias peaks in full-shell
nanowires induced by flux-tunable Andreev states,” Science, vol. 373, no.
6550. American Association for the Advancement of Science, 2021.
ista: Valentini M, Peñaranda F, Hofmann AC, Brauns M, Hauschild R, Krogstrup P,
San-Jose P, Prada E, Aguado R, Katsaros G. 2021. Nontopological zero-bias peaks
in full-shell nanowires induced by flux-tunable Andreev states. Science. 373(6550),
82–88.
mla: Valentini, Marco, et al. “Nontopological Zero-Bias Peaks in Full-Shell Nanowires
Induced by Flux-Tunable Andreev States.” Science, vol. 373, no. 6550, 82–88,
American Association for the Advancement of Science, 2021, doi:10.1126/science.abf1513.
short: M. Valentini, F. Peñaranda, A.C. Hofmann, M. Brauns, R. Hauschild, P. Krogstrup,
P. San-Jose, E. Prada, R. Aguado, G. Katsaros, Science 373 (2021).
date_created: 2020-12-02T10:51:52Z
date_published: 2021-07-02T00:00:00Z
date_updated: 2024-02-21T12:40:09Z
day: '02'
department:
- _id: GeKa
- _id: Bio
doi: 10.1126/science.abf1513
ec_funded: 1
external_id:
arxiv:
- '2008.02348'
isi:
- '000677843100034'
intvolume: ' 373'
isi: 1
issue: '6550'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2008.02348
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 262116AA-B435-11E9-9278-68D0E5697425
name: Hybrid Semiconductor - Superconductor Quantum Devices
- _id: 26A151DA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '844511'
name: Majorana bound states in Ge/SiGe heterostructures
publication: Science
publication_identifier:
eissn:
- '10959203'
issn:
- '00368075'
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/unfinding-a-split-electron/
record:
- id: '13286'
relation: dissertation_contains
status: public
- id: '9389'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable
Andreev states
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 373
year: '2021'
...
---
_id: '9323'
abstract:
- lang: eng
text: This .zip File contains the data for figures presented in the main text and
supplementary material of "A singlet triplet hole spin qubit in planar Ge" by
D. Jirovec, et. al. The measurements were done using Labber Software and the data
is stored in the hdf5 file format. The files can be opened using either the Labber
Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html).
A single file is acquired with QCodes and features the corresponding data type.
XRD data are in .dat format and a code to open the data is provided. The code
for simulations is as well provided in Python.
article_processing_charge: No
author:
- first_name: Daniel
full_name: Jirovec, Daniel
id: 4C473F58-F248-11E8-B48F-1D18A9856A87
last_name: Jirovec
orcid: 0000-0002-7197-4801
citation:
ama: Jirovec D. Research data for “A singlet-triplet hole spin qubit planar Ge.”
2021. doi:10.15479/AT:ISTA:9323
apa: Jirovec, D. (2021). Research data for “A singlet-triplet hole spin qubit planar
Ge.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9323
chicago: Jirovec, Daniel. “Research Data for ‘A Singlet-Triplet Hole Spin Qubit
Planar Ge.’” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9323.
ieee: D. Jirovec, “Research data for ‘A singlet-triplet hole spin qubit planar Ge.’”
Institute of Science and Technology Austria, 2021.
ista: Jirovec D. 2021. Research data for ‘A singlet-triplet hole spin qubit planar
Ge’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9323.
mla: Jirovec, Daniel. Research Data for “A Singlet-Triplet Hole Spin Qubit Planar
Ge.” Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9323.
short: D. Jirovec, (2021).
contributor:
- contributor_type: project_member
first_name: Daniel
id: 4C473F58-F248-11E8-B48F-1D18A9856A87
last_name: Jirovec
date_created: 2021-04-14T09:50:22Z
date_published: 2021-04-14T00:00:00Z
date_updated: 2024-02-21T12:39:15Z
day: '14'
ddc:
- '530'
department:
- _id: GradSch
- _id: GeKa
doi: 10.15479/AT:ISTA:9323
file:
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content_type: application/x-zip-compressed
creator: djirovec
date_created: 2021-04-14T09:48:47Z
date_updated: 2021-04-14T09:48:47Z
file_id: '9324'
file_name: DataRepositorySTqubit.zip
file_size: 221832287
relation: main_file
success: 1
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content_type: application/octet-stream
creator: djirovec
date_created: 2021-04-14T09:49:30Z
date_updated: 2021-04-14T09:49:30Z
file_id: '9325'
file_name: ReadMe
file_size: 4323
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success: 1
file_date_updated: 2021-04-14T09:49:30Z
has_accepted_license: '1'
month: '04'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
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- id: '8909'
relation: used_in_publication
status: public
status: public
title: Research data for "A singlet-triplet hole spin qubit planar Ge"
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '9389'
abstract:
- lang: eng
text: "This .zip File contains the transport data for \"Non-topological zero bias
peaks in full-shell nanowires induced by flux tunable Andreev states\" by M. Valentini,
et. al. \r\nThe measurements were done using Labber Software and the data is
stored in the hdf5 file format.\r\nInstructions of how to read the data are in
\"Notebook_Valentini.pdf\"."
acknowledged_ssus:
- _id: NanoFab
article_processing_charge: No
author:
- first_name: Marco
full_name: Valentini, Marco
id: C0BB2FAC-D767-11E9-B658-BC13E6697425
last_name: Valentini
citation:
ama: Valentini M. Research data for “Non-topological zero bias peaks in full-shell
nanowires induced by flux tunable Andreev states.” 2021. doi:10.15479/AT:ISTA:9389
apa: Valentini, M. (2021). Research data for “Non-topological zero bias peaks in
full-shell nanowires induced by flux tunable Andreev states.” Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:9389
chicago: Valentini, Marco. “Research Data for ‘Non-Topological Zero Bias Peaks in
Full-Shell Nanowires Induced by Flux Tunable Andreev States.’” Institute of Science
and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9389.
ieee: M. Valentini, “Research data for ‘Non-topological zero bias peaks in full-shell
nanowires induced by flux tunable Andreev states.’” Institute of Science and Technology
Austria, 2021.
ista: Valentini M. 2021. Research data for ‘Non-topological zero bias peaks in full-shell
nanowires induced by flux tunable Andreev states’, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:9389.
mla: Valentini, Marco. Research Data for “Non-Topological Zero Bias Peaks in
Full-Shell Nanowires Induced by Flux Tunable Andreev States.” Institute of
Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9389.
short: M. Valentini, (2021).
contributor:
- contributor_type: contact_person
first_name: Marco
id: C0BB2FAC-D767-11E9-B658-BC13E6697425
last_name: Valentini
date_created: 2021-05-14T12:07:53Z
date_published: 2021-01-01T00:00:00Z
date_updated: 2024-02-21T12:40:09Z
ddc:
- '530'
department:
- _id: GradSch
- _id: GeKa
doi: 10.15479/AT:ISTA:9389
file:
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content_type: application/pdf
creator: mvalenti
date_created: 2021-05-14T11:42:23Z
date_updated: 2021-05-14T11:42:23Z
file_id: '9390'
file_name: Notebook_Valentini.pdf
file_size: 10572981
relation: main_file
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checksum: 1e61a7e63949448a8db0091cdac23570
content_type: application/x-zip-compressed
creator: mvalenti
date_created: 2021-05-14T11:56:48Z
date_updated: 2021-05-14T11:56:48Z
file_id: '9391'
file_name: Experimental_data.zip
file_size: 99076111
relation: main_file
file_date_updated: 2021-05-14T11:56:48Z
has_accepted_license: '1'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8910'
relation: used_in_publication
status: public
status: public
title: Research data for "Non-topological zero bias peaks in full-shell nanowires
induced by flux tunable Andreev states"
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '10559'
abstract:
- lang: eng
text: Hole gases in planar germanium can have high mobilities in combination with
strong spin-orbit interaction and electrically tunable g factors, and are therefore
emerging as a promising platform for creating hybrid superconductor-semiconductor
devices. A key challenge towards hybrid Ge-based quantum technologies is the design
of high-quality interfaces and superconducting contacts that are robust against
magnetic fields. In this work, by combining the assets of aluminum, which provides
good contact to the Ge, and niobium, which has a significant superconducting gap,
we demonstrate highly transparent low-disordered JoFETs with relatively large
ICRN products that are capable of withstanding high magnetic fields. We furthermore
demonstrate the ability of phase-biasing individual JoFETs, opening up an avenue
to explore topological superconductivity in planar Ge. The persistence of superconductivity
in the reported hybrid devices beyond 1.8 T paves the way towards integrating
spin qubits and proximity-induced superconductivity on the same chip.
acknowledged_ssus:
- _id: NanoFab
- _id: M-Shop
acknowledgement: This research and related results were made possible with the support
of the NOMIS Foundation. This research was supported by the Scientific Service Units
of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication
facility, the European Union's Horizon 2020 research and innovation program under
the Marie Sklodowska-Curie Grant agreement No. 844511 Grant Agreement No. 862046.
ICN2 acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported
by the Severo Ochoa program from Spanish MINECO (Grant No. SEV-2017-0706) and is
funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work
has been performed in the framework of Universitat Autnoma de Barcelona Materials
Science PhD program. The HAADF-STEM microscopy was conducted in the Laboratorio
de Microscopias Avanzadas at Instituto de Nanociencia de Aragon-Universidad de Zaragoza.
Authors acknowledge the LMA-INA for offering access to their instruments and expertise.
We acknowledge support from CSIC Research Platform on Quantum Technologies PTI-001.
This project has received funding from the European Union's Horizon 2020 research
and innovation programme under Grant Agreement No. 823717 ESTEEM3. M.B. acknowledges
support from SUR Generalitat de Catalunya and the EU Social Fund; project ref. 2020
FI 00103. G.S. and M.V. acknowledge support through a projectruimte grant associated
with the Netherlands Organization of Scientific Research (NWO). J.D. acknowledges
support through FRIPRO-project 274853, which is funded by the Research Council of
Norway.
article_number: L022005
article_processing_charge: No
article_type: original
author:
- first_name: Kushagra
full_name: Aggarwal, Kushagra
id: b22ab905-3539-11eb-84c3-fc159dcd79cb
last_name: Aggarwal
orcid: 0000-0001-9985-9293
- first_name: Andrea C
full_name: Hofmann, Andrea C
id: 340F461A-F248-11E8-B48F-1D18A9856A87
last_name: Hofmann
- first_name: Daniel
full_name: Jirovec, Daniel
id: 4C473F58-F248-11E8-B48F-1D18A9856A87
last_name: Jirovec
orcid: 0000-0002-7197-4801
- first_name: Ivan
full_name: Prieto Gonzalez, Ivan
id: 2A307FE2-F248-11E8-B48F-1D18A9856A87
last_name: Prieto Gonzalez
orcid: 0000-0002-7370-5357
- first_name: Amir
full_name: Sammak, Amir
last_name: Sammak
- first_name: Marc
full_name: Botifoll, Marc
last_name: Botifoll
- first_name: Sara
full_name: Martí-Sánchez, Sara
last_name: Martí-Sánchez
- first_name: Menno
full_name: Veldhorst, Menno
last_name: Veldhorst
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Giordano
full_name: Scappucci, Giordano
last_name: Scappucci
- first_name: Jeroen
full_name: Danon, Jeroen
last_name: Danon
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Aggarwal K, Hofmann AC, Jirovec D, et al. Enhancement of proximity-induced
superconductivity in a planar Ge hole gas. Physical Review Research. 2021;3(2).
doi:10.1103/physrevresearch.3.l022005
apa: Aggarwal, K., Hofmann, A. C., Jirovec, D., Prieto Gonzalez, I., Sammak, A.,
Botifoll, M., … Katsaros, G. (2021). Enhancement of proximity-induced superconductivity
in a planar Ge hole gas. Physical Review Research. American Physical Society.
https://doi.org/10.1103/physrevresearch.3.l022005
chicago: Aggarwal, Kushagra, Andrea C Hofmann, Daniel Jirovec, Ivan Prieto Gonzalez,
Amir Sammak, Marc Botifoll, Sara Martí-Sánchez, et al. “Enhancement of Proximity-Induced
Superconductivity in a Planar Ge Hole Gas.” Physical Review Research. American
Physical Society, 2021. https://doi.org/10.1103/physrevresearch.3.l022005.
ieee: K. Aggarwal et al., “Enhancement of proximity-induced superconductivity
in a planar Ge hole gas,” Physical Review Research, vol. 3, no. 2. American
Physical Society, 2021.
ista: Aggarwal K, Hofmann AC, Jirovec D, Prieto Gonzalez I, Sammak A, Botifoll M,
Martí-Sánchez S, Veldhorst M, Arbiol J, Scappucci G, Danon J, Katsaros G. 2021.
Enhancement of proximity-induced superconductivity in a planar Ge hole gas. Physical
Review Research. 3(2), L022005.
mla: Aggarwal, Kushagra, et al. “Enhancement of Proximity-Induced Superconductivity
in a Planar Ge Hole Gas.” Physical Review Research, vol. 3, no. 2, L022005,
American Physical Society, 2021, doi:10.1103/physrevresearch.3.l022005.
short: K. Aggarwal, A.C. Hofmann, D. Jirovec, I. Prieto Gonzalez, A. Sammak, M.
Botifoll, S. Martí-Sánchez, M. Veldhorst, J. Arbiol, G. Scappucci, J. Danon, G.
Katsaros, Physical Review Research 3 (2021).
date_created: 2021-12-16T18:50:57Z
date_published: 2021-04-15T00:00:00Z
date_updated: 2024-02-21T12:41:26Z
day: '15'
ddc:
- '620'
department:
- _id: GeKa
doi: 10.1103/physrevresearch.3.l022005
ec_funded: 1
external_id:
arxiv:
- '2012.00322'
file:
- access_level: open_access
checksum: 60a1bc9c9b616b1b155044bb8cfc6484
content_type: application/pdf
creator: cchlebak
date_created: 2021-12-17T08:12:37Z
date_updated: 2021-12-17T08:12:37Z
file_id: '10561'
file_name: 2021_PhysRevResearch_Aggarwal.pdf
file_size: 1917512
relation: main_file
success: 1
file_date_updated: 2021-12-17T08:12:37Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '2'
keyword:
- general engineering
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 26A151DA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '844511'
name: Majorana bound states in Ge/SiGe heterostructures
- _id: 237E5020-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '862046'
name: TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS
publication: Physical Review Research
publication_identifier:
issn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
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relation: earlier_version
status: public
- id: '8834'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Enhancement of proximity-induced superconductivity in a planar Ge hole gas
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 3
year: '2021'
...
---
_id: '10166'
abstract:
- lang: eng
text: While sexual reproduction is widespread among many taxa, asexual lineages
have repeatedly evolved from sexual ancestors. Despite extensive research on the
evolution of sex, it is still unclear whether this switch represents a major transition
requiring major molecular reorganization, and how convergent the changes involved
are. In this study, we investigated the phylogenetic relationship and patterns
of gene expression of sexual and asexual lineages of Eurasian Artemia brine shrimp,
to assess how gene expression patterns are affected by the transition to asexuality.
We find only a few genes that are consistently associated with the evolution of
asexuality, suggesting that this shift may not require an extensive overhauling
of the meiotic machinery. While genes with sex-biased expression have high rates
of expression divergence within Eurasian Artemia, neither female- nor male-biased
genes appear to show unusual evolutionary patterns after sexuality is lost, contrary
to theoretical expectations.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: We thank the Vicoso laboratory, Thomas Lenormand and Tanja Schwander
for helpful discussions, the group of Gonzalo Gajardo, especially Cristian Gallardo-Escárate
and Margarita Parraguez Donoso, for sequencing data and advice, and the IST Scientific
Computing Group for their support. This work was supported by the European Research
Council under the European Union's Horizon 2020 research and innovation program
(grant agreement no. 715257).
article_number: '20211720'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Ariana
full_name: Macon, Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: Francisco
full_name: Hontoria, Francisco
last_name: Hontoria
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: 'Huylmans AK, Macon A, Hontoria F, Vicoso B. Transitions to asexuality and
evolution of gene expression in Artemia brine shrimp. Proceedings of the Royal
Society B: Biological Sciences. 2021;288(1959). doi:10.1098/rspb.2021.1720'
apa: 'Huylmans, A. K., Macon, A., Hontoria, F., & Vicoso, B. (2021). Transitions
to asexuality and evolution of gene expression in Artemia brine shrimp. Proceedings
of the Royal Society B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2021.1720'
chicago: 'Huylmans, Ann K, Ariana Macon, Francisco Hontoria, and Beatriz Vicoso.
“Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.”
Proceedings of the Royal Society B: Biological Sciences. The Royal Society,
2021. https://doi.org/10.1098/rspb.2021.1720.'
ieee: 'A. K. Huylmans, A. Macon, F. Hontoria, and B. Vicoso, “Transitions to asexuality
and evolution of gene expression in Artemia brine shrimp,” Proceedings of the
Royal Society B: Biological Sciences, vol. 288, no. 1959. The Royal Society,
2021.'
ista: 'Huylmans AK, Macon A, Hontoria F, Vicoso B. 2021. Transitions to asexuality
and evolution of gene expression in Artemia brine shrimp. Proceedings of the Royal
Society B: Biological Sciences. 288(1959), 20211720.'
mla: 'Huylmans, Ann K., et al. “Transitions to Asexuality and Evolution of Gene
Expression in Artemia Brine Shrimp.” Proceedings of the Royal Society B: Biological
Sciences, vol. 288, no. 1959, 20211720, The Royal Society, 2021, doi:10.1098/rspb.2021.1720.'
short: 'A.K. Huylmans, A. Macon, F. Hontoria, B. Vicoso, Proceedings of the Royal
Society B: Biological Sciences 288 (2021).'
date_created: 2021-10-21T07:46:06Z
date_published: 2021-09-22T00:00:00Z
date_updated: 2024-02-21T12:40:29Z
day: '22'
ddc:
- '595'
department:
- _id: BeVi
doi: 10.1098/rspb.2021.1720
ec_funded: 1
external_id:
isi:
- '000697643700001'
pmid:
- '34547909'
file:
- access_level: open_access
checksum: 76e7f253b7040bca2ad76f82bd7c45c0
content_type: application/pdf
creator: cchlebak
date_created: 2021-10-22T11:48:02Z
date_updated: 2021-10-22T11:48:02Z
file_id: '10172'
file_name: 2021_ProRoSocBBioSci_Huylmans.pdf
file_size: 995806
relation: main_file
success: 1
file_date_updated: 2021-10-22T11:48:02Z
has_accepted_license: '1'
intvolume: ' 288'
isi: 1
issue: '1959'
keyword:
- asexual reproduction
- parthenogenesis
- sex-biased genes
- sexual conflict
- automixis
- crustaceans
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: 'Proceedings of the Royal Society B: Biological Sciences'
publication_identifier:
eissn:
- 1471-2954
issn:
- 0962-8452
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
related_material:
link:
- relation: supplementary_material
url: https://doi.org/10.6084/m9.figshare.c.5615488.v1
record:
- id: '9949'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Transitions to asexuality and evolution of gene expression in Artemia brine
shrimp
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: 288
year: '2021'
...
---
_id: '9192'
abstract:
- lang: eng
text: Here are the research data underlying the publication " Effects of fine-scale
population structure on inbreeding in a long-term study of snapdragons (Antirrhinum
majus)." Further information are summed up in the README document.
article_processing_charge: No
author:
- first_name: Parvathy
full_name: Surendranadh, Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
- first_name: Louise S
full_name: Arathoon, Louise S
id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87
last_name: Arathoon
orcid: 0000-0003-1771-714X
- first_name: Carina
full_name: Baskett, Carina
id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87
last_name: Baskett
orcid: 0000-0002-7354-8574
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects
of fine-scale population structure on the distribution of heterozygosity in a
long-term study of Antirrhinum majus. 2021. doi:10.15479/AT:ISTA:9192
apa: Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., &
Barton, N. H. (2021). Effects of fine-scale population structure on the distribution
of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:9192
chicago: Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field,
Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure
on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.”
Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9192.
ieee: P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H.
Barton, “Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus.” Institute of Science and Technology
Austria, 2021.
ista: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2021.
Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:9192.
mla: Surendranadh, Parvathy, et al. Effects of Fine-Scale Population Structure
on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.
Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9192.
short: P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton,
(2021).
contributor:
- contributor_type: project_member
first_name: Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
- contributor_type: project_member
first_name: Louise S
id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87
last_name: Arathoon
- contributor_type: project_member
first_name: Carina
id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87
last_name: Baskett
- contributor_type: project_member
first_name: David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- contributor_type: project_member
first_name: Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- contributor_type: project_leader
first_name: Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
date_created: 2021-02-24T17:49:21Z
date_published: 2021-02-26T00:00:00Z
date_updated: 2024-02-21T12:41:09Z
day: '26'
ddc:
- '576'
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/AT:ISTA:9192
file:
- access_level: open_access
checksum: f85537815809a8a4b7da9d01163f88c0
content_type: application/x-zip-compressed
creator: larathoo
date_created: 2021-02-24T17:45:13Z
date_updated: 2021-02-24T17:45:13Z
file_id: '9193'
file_name: Data_Code.zip
file_size: 5934452
relation: main_file
success: 1
file_date_updated: 2021-02-24T17:45:13Z
has_accepted_license: '1'
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '11411'
relation: used_in_publication
status: public
- id: '11321'
relation: later_version
status: public
- id: '8254'
relation: earlier_version
status: public
status: public
title: Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '9949'
article_processing_charge: No
author:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Vicoso B. Data from Hyulmans et al 2021, “Transitions to asexuality and evolution
of gene expression in Artemia brine shrimp.” 2021. doi:10.15479/AT:ISTA:9949
apa: Vicoso, B. (2021). Data from Hyulmans et al 2021, “Transitions to asexuality
and evolution of gene expression in Artemia brine shrimp.” Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:9949
chicago: Vicoso, Beatriz. “Data from Hyulmans et Al 2021, ‘Transitions to Asexuality
and Evolution of Gene Expression in Artemia Brine Shrimp.’” Institute of Science
and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9949.
ieee: B. Vicoso, “Data from Hyulmans et al 2021, ‘Transitions to asexuality and
evolution of gene expression in Artemia brine shrimp.’” Institute of Science and
Technology Austria, 2021.
ista: Vicoso B. 2021. Data from Hyulmans et al 2021, ‘Transitions to asexuality
and evolution of gene expression in Artemia brine shrimp’, Institute of Science
and Technology Austria, 10.15479/AT:ISTA:9949.
mla: Vicoso, Beatriz. Data from Hyulmans et Al 2021, “Transitions to Asexuality
and Evolution of Gene Expression in Artemia Brine Shrimp.” Institute of Science
and Technology Austria, 2021, doi:10.15479/AT:ISTA:9949.
short: B. Vicoso, (2021).
date_created: 2021-08-21T13:44:22Z
date_published: 2021-08-24T00:00:00Z
date_updated: 2024-02-21T12:40:30Z
day: '24'
department:
- _id: BeVi
doi: 10.15479/AT:ISTA:9949
file:
- access_level: open_access
checksum: 90461837eed66beac6fa302993cf0ca9
content_type: application/zip
creator: bvicoso
date_created: 2021-08-21T13:43:59Z
date_updated: 2021-08-21T13:43:59Z
file_id: '9950'
file_name: Data.zip
file_size: 139188306
relation: main_file
success: 1
file_date_updated: 2021-08-21T13:43:59Z
has_accepted_license: '1'
month: '08'
oa: 1
oa_version: None
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10166'
relation: used_in_publication
status: public
status: public
title: Data from Hyulmans et al 2021, "Transitions to asexuality and evolution of
gene expression in Artemia brine shrimp"
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '8997'
abstract:
- lang: eng
text: Phenomenological relations such as Ohm’s or Fourier’s law have a venerable
history in physics but are still scarce in biology. This situation restrains predictive
theory. Here, we build on bacterial “growth laws,” which capture physiological
feedback between translation and cell growth, to construct a minimal biophysical
model for the combined action of ribosome-targeting antibiotics. Our model predicts
drug interactions like antagonism or synergy solely from responses to individual
drugs. We provide analytical results for limiting cases, which agree well with
numerical results. We systematically refine the model by including direct physical
interactions of different antibiotics on the ribosome. In a limiting case, our
model provides a mechanistic underpinning for recent predictions of higher-order
interactions that were derived using entropy maximization. We further refine the
model to include the effects of antibiotics that mimic starvation and the presence
of resistance genes. We describe the impact of a starvation-mimicking antibiotic
on drug interactions analytically and verify it experimentally. Our extended model
suggests a change in the type of drug interaction that depends on the strength
of resistance, which challenges established rescaling paradigms. We experimentally
show that the presence of unregulated resistance genes can lead to altered drug
interaction, which agrees with the prediction of the model. While minimal, the
model is readily adaptable and opens the door to predicting interactions of second
and higher-order in a broad range of biological systems.
acknowledgement: 'This work was supported in part by Tum stipend of Knafelj foundation
(to B.K.), Austrian Science Fund (FWF) standalone grants P 27201-B22 (to T.B.) and
P 28844(to G.T.), HFSP program Grant RGP0042/2013 (to T.B.), German Research Foundation
(DFG) individual grant BO 3502/2-1 (to T.B.), and German Research Foundation (DFG)
Collaborative Research Centre (SFB) 1310 (to T.B.). '
article_number: e1008529
article_processing_charge: Yes
article_type: original
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. Minimal biophysical model of combined antibiotic
action. PLOS Computational Biology. 2021;17. doi:10.1371/journal.pcbi.1008529
apa: Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2021). Minimal biophysical
model of combined antibiotic action. PLOS Computational Biology. Public
Library of Science. https://doi.org/10.1371/journal.pcbi.1008529
chicago: Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Minimal Biophysical
Model of Combined Antibiotic Action.” PLOS Computational Biology. Public
Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1008529.
ieee: B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Minimal biophysical model of
combined antibiotic action,” PLOS Computational Biology, vol. 17. Public
Library of Science, 2021.
ista: Kavcic B, Tkačik G, Bollenbach MT. 2021. Minimal biophysical model of combined
antibiotic action. PLOS Computational Biology. 17, e1008529.
mla: Kavcic, Bor, et al. “Minimal Biophysical Model of Combined Antibiotic Action.”
PLOS Computational Biology, vol. 17, e1008529, Public Library of Science,
2021, doi:10.1371/journal.pcbi.1008529.
short: B. Kavcic, G. Tkačik, M.T. Bollenbach, PLOS Computational Biology 17 (2021).
date_created: 2021-01-08T07:16:18Z
date_published: 2021-01-07T00:00:00Z
date_updated: 2024-02-21T12:41:41Z
day: '07'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1008529
external_id:
isi:
- '000608045000010'
file:
- access_level: open_access
checksum: e29f2b42651bef8e034781de8781ffac
content_type: application/pdf
creator: dernst
date_created: 2021-02-04T12:30:48Z
date_updated: 2021-02-04T12:30:48Z
file_id: '9092'
file_name: 2021_PlosComBio_Kavcic.pdf
file_size: 3690053
relation: main_file
success: 1
file_date_updated: 2021-02-04T12:30:48Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
keyword:
- Modelling and Simulation
- Genetics
- Molecular Biology
- Antibiotics
- Drug interactions
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
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: PLOS Computational Biology
publication_identifier:
issn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
record:
- id: '7673'
relation: earlier_version
status: public
- id: '8930'
relation: research_data
status: public
status: public
title: Minimal biophysical model of combined antibiotic action
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: 17
year: '2021'
...
---
_id: '9283'
abstract:
- lang: eng
text: Gene expression levels are influenced by multiple coexisting molecular mechanisms.
Some of these interactions such as those of transcription factors and promoters
have been studied extensively. However, predicting phenotypes of gene regulatory
networks (GRNs) remains a major challenge. Here, we use a well-defined synthetic
GRN to study in Escherichia coli how network phenotypes depend on local genetic
context, i.e. the genetic neighborhood of a transcription factor and its relative
position. We show that one GRN with fixed topology can display not only quantitatively
but also qualitatively different phenotypes, depending solely on the local genetic
context of its components. Transcriptional read-through is the main molecular
mechanism that places one transcriptional unit (TU) within two separate regulons
without the need for complex regulatory sequences. We propose that relative order
of individual TUs, with its potential for combinatorial complexity, plays an important
role in shaping phenotypes of GRNs.
acknowledgement: "We thank J Bollback, L Hurst, M Lagator, C Nizak, O Rivoire, M Savageau,
G Tkacik, and B Vicozo\r\nfor helpful discussions; A Dolinar and A Greshnova for
technical assistance; T Bollenbach for supplying the strain JW0336; C Rusnac, and
members of the Guet lab for comments. The research leading to these results has
received funding from the People Programme (Marie Curie Actions) of the European
Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n˚\r\n628377
(ANS) and an Austrian Science Fund (FWF) grant n˚ I 3901-B32 (CCG)."
article_number: e65993
article_processing_charge: Yes
article_type: original
author:
- first_name: Anna A
full_name: Nagy-Staron, Anna A
id: 3ABC5BA6-F248-11E8-B48F-1D18A9856A87
last_name: Nagy-Staron
orcid: 0000-0002-1391-8377
- first_name: Kathrin
full_name: Tomasek, Kathrin
id: 3AEC8556-F248-11E8-B48F-1D18A9856A87
last_name: Tomasek
orcid: 0000-0003-3768-877X
- first_name: Caroline
full_name: Caruso Carter, Caroline
last_name: Caruso Carter
- first_name: Elisabeth
full_name: Sonnleitner, Elisabeth
last_name: Sonnleitner
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
- first_name: Tiago
full_name: Paixão, Tiago
last_name: Paixão
- 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: Nagy-Staron AA, Tomasek K, Caruso Carter C, et al. Local genetic context shapes
the function of a gene regulatory network. eLife. 2021;10. doi:10.7554/elife.65993
apa: Nagy-Staron, A. A., Tomasek, K., Caruso Carter, C., Sonnleitner, E., Kavcic,
B., Paixão, T., & Guet, C. C. (2021). Local genetic context shapes the function
of a gene regulatory network. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.65993
chicago: Nagy-Staron, Anna A, Kathrin Tomasek, Caroline Caruso Carter, Elisabeth
Sonnleitner, Bor Kavcic, Tiago Paixão, and Calin C Guet. “Local Genetic Context
Shapes the Function of a Gene Regulatory Network.” ELife. eLife Sciences
Publications, 2021. https://doi.org/10.7554/elife.65993.
ieee: A. A. Nagy-Staron et al., “Local genetic context shapes the function
of a gene regulatory network,” eLife, vol. 10. eLife Sciences Publications,
2021.
ista: Nagy-Staron AA, Tomasek K, Caruso Carter C, Sonnleitner E, Kavcic B, Paixão
T, Guet CC. 2021. Local genetic context shapes the function of a gene regulatory
network. eLife. 10, e65993.
mla: Nagy-Staron, Anna A., et al. “Local Genetic Context Shapes the Function of
a Gene Regulatory Network.” ELife, vol. 10, e65993, eLife Sciences Publications,
2021, doi:10.7554/elife.65993.
short: A.A. Nagy-Staron, K. Tomasek, C. Caruso Carter, E. Sonnleitner, B. Kavcic,
T. Paixão, C.C. Guet, ELife 10 (2021).
date_created: 2021-03-23T10:11:46Z
date_published: 2021-03-08T00:00:00Z
date_updated: 2024-02-21T12:41:57Z
day: '08'
ddc:
- '570'
department:
- _id: GaTk
- _id: CaGu
doi: 10.7554/elife.65993
ec_funded: 1
external_id:
isi:
- '000631050900001'
file:
- access_level: open_access
checksum: 3c2f44058c2dd45a5a1027f09d263f8e
content_type: application/pdf
creator: bkavcic
date_created: 2021-03-23T10:12:58Z
date_updated: 2021-03-23T10:12:58Z
file_id: '9284'
file_name: elife-65993-v2.pdf
file_size: 1390469
relation: main_file
success: 1
file_date_updated: 2021-03-23T10:12:58Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
keyword:
- Genetics and Molecular Biology
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 2517526A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '628377'
name: 'The Systems Biology of Transcriptional Read-Through in Bacteria: from Synthetic
Networks to Genomic Studies'
- _id: 268BFA92-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03901
name: 'CyberCircuits: Cybergenetic circuits to test composability of gene networks'
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
related_material:
record:
- id: '8951'
relation: research_data
status: public
status: public
title: Local genetic context shapes the function of a gene regulatory 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: '2021'
...
---
_id: '10184'
abstract:
- lang: eng
text: "We introduce a novel technique to automatically decompose an input object’s
volume into a set of parts that can be represented by two opposite height fields.
Such decomposition enables the manufacturing of individual parts using two-piece
reusable rigid molds. Our decomposition strategy relies on a new energy formulation
that utilizes a pre-computed signal on the mesh volume representing the accessibility
for a predefined set of extraction directions. Thanks to this novel formulation,
our method allows for efficient optimization of a fabrication-aware partitioning
of volumes in a completely\r\nautomatic way. We demonstrate the efficacy of our
approach by generating valid volume partitionings for a wide range of complex
objects and physically reproducing several of them."
acknowledgement: 'The authors thank Marco Callieri for all his precious help with
the resin casts. The models used in the paper are courtesy of the Stanford 3D Scanning
Repository, the AIM@SHAPE Shape Repository, and Thingi10K Repository. The research
was partially funded by the European Research Council (ERC) MATERIALIZABLE: Intelligent
fabrication-oriented computational design and modeling (grant no. 715767).'
article_number: '272'
article_processing_charge: No
article_type: original
author:
- first_name: Thomas
full_name: Alderighi, Thomas
last_name: Alderighi
- first_name: Luigi
full_name: Malomo, Luigi
last_name: Malomo
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Paolo
full_name: Cignoni, Paolo
last_name: Cignoni
- first_name: Nico
full_name: Pietroni, Nico
last_name: Pietroni
citation:
ama: Alderighi T, Malomo L, Bickel B, Cignoni P, Pietroni N. Volume decomposition
for two-piece rigid casting. ACM Transactions on Graphics. 2021;40(6).
doi:10.1145/3478513.3480555
apa: Alderighi, T., Malomo, L., Bickel, B., Cignoni, P., & Pietroni, N. (2021).
Volume decomposition for two-piece rigid casting. ACM Transactions on Graphics.
Association for Computing Machinery. https://doi.org/10.1145/3478513.3480555
chicago: Alderighi, Thomas, Luigi Malomo, Bernd Bickel, Paolo Cignoni, and Nico
Pietroni. “Volume Decomposition for Two-Piece Rigid Casting.” ACM Transactions
on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3478513.3480555.
ieee: T. Alderighi, L. Malomo, B. Bickel, P. Cignoni, and N. Pietroni, “Volume decomposition
for two-piece rigid casting,” ACM Transactions on Graphics, vol. 40, no.
6. Association for Computing Machinery, 2021.
ista: Alderighi T, Malomo L, Bickel B, Cignoni P, Pietroni N. 2021. Volume decomposition
for two-piece rigid casting. ACM Transactions on Graphics. 40(6), 272.
mla: Alderighi, Thomas, et al. “Volume Decomposition for Two-Piece Rigid Casting.”
ACM Transactions on Graphics, vol. 40, no. 6, 272, Association for Computing
Machinery, 2021, doi:10.1145/3478513.3480555.
short: T. Alderighi, L. Malomo, B. Bickel, P. Cignoni, N. Pietroni, ACM Transactions
on Graphics 40 (2021).
date_created: 2021-10-27T07:08:19Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2024-02-28T12:52:48Z
day: '01'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.1145/3478513.3480555
ec_funded: 1
external_id:
isi:
- '000729846700077'
file:
- access_level: open_access
checksum: 384ece7a9ad1026787ba9560b04336d5
content_type: application/pdf
creator: bbickel
date_created: 2021-10-27T07:08:07Z
date_updated: 2021-10-27T07:08:07Z
file_id: '10185'
file_name: rigidmolds-authorversion.pdf
file_size: 107708317
relation: main_file
file_date_updated: 2021-10-27T07:08:07Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://vcg.isti.cnr.it/Publications/2021/AMBCP21
month: '12'
oa: 1
oa_version: Submitted Version
project:
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- '1557-7368 '
issn:
- 0730-0301
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
status: public
title: Volume decomposition for two-piece rigid casting
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 40
year: '2021'
...
---
_id: '9541'
abstract:
- lang: eng
text: The Massively Parallel Computation (MPC) model is an emerging model that distills
core aspects of distributed and parallel computation, developed as a tool to solve
combinatorial (typically graph) problems in systems of many machines with limited
space. Recent work has focused on the regime in which machines have sublinear
(in n, the number of nodes in the input graph) space, with randomized algorithms
presented for the fundamental problems of Maximal Matching and Maximal Independent
Set. However, there have been no prior corresponding deterministic algorithms.
A major challenge underlying the sublinear space setting is that the local space
of each machine might be too small to store all edges incident to a single node.
This poses a considerable obstacle compared to classical models in which each
node is assumed to know and have easy access to its incident edges. To overcome
this barrier, we introduce a new graph sparsification technique that deterministically
computes a low-degree subgraph, with the additional property that solving the
problem on this subgraph provides significant progress towards solving the problem
for the original input graph. Using this framework to derandomize the well-known
algorithm of Luby [SICOMP’86], we obtain O(log Δ + log log n)-round deterministic
MPC algorithms for solving the problems of Maximal Matching and Maximal Independent
Set with O(nɛ) space on each machine for any constant ɛ > 0. These algorithms
also run in O(log Δ) rounds in the closely related model of CONGESTED CLIQUE,
improving upon the state-of-the-art bound of O(log 2Δ) rounds by Censor-Hillel
et al. [DISC’17].
acknowledgement: "Institute of Science and Technology Austria (IST Austria). Email:
peter.davies@ist.ac.at. Work partially\r\ndone at the Department of Computer Science
and Centre for Discrete Mathematics and its Applications (DIMAP),University of Warwick.
Research partially supported by the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie grant agreement No 754411, the Centre
for Discrete Mathematics and its Applications, a Weizmann-UK Making Connections
Grant, and EPSRC award EP/N011163/1."
article_number: '16'
article_processing_charge: No
article_type: original
author:
- first_name: Artur
full_name: Czumaj, Artur
last_name: Czumaj
- first_name: Peter
full_name: Davies, Peter
id: 11396234-BB50-11E9-B24C-90FCE5697425
last_name: Davies
orcid: 0000-0002-5646-9524
- first_name: Merav
full_name: Parter, Merav
last_name: Parter
citation:
ama: Czumaj A, Davies P, Parter M. Graph sparsification for derandomizing massively
parallel computation with low space. ACM Transactions on Algorithms. 2021;17(2).
doi:10.1145/3451992
apa: Czumaj, A., Davies, P., & Parter, M. (2021). Graph sparsification for derandomizing
massively parallel computation with low space. ACM Transactions on Algorithms.
Association for Computing Machinery. https://doi.org/10.1145/3451992
chicago: Czumaj, Artur, Peter Davies, and Merav Parter. “Graph Sparsification for
Derandomizing Massively Parallel Computation with Low Space.” ACM Transactions
on Algorithms. Association for Computing Machinery, 2021. https://doi.org/10.1145/3451992.
ieee: A. Czumaj, P. Davies, and M. Parter, “Graph sparsification for derandomizing
massively parallel computation with low space,” ACM Transactions on Algorithms,
vol. 17, no. 2. Association for Computing Machinery, 2021.
ista: Czumaj A, Davies P, Parter M. 2021. Graph sparsification for derandomizing
massively parallel computation with low space. ACM Transactions on Algorithms.
17(2), 16.
mla: Czumaj, Artur, et al. “Graph Sparsification for Derandomizing Massively Parallel
Computation with Low Space.” ACM Transactions on Algorithms, vol. 17, no.
2, 16, Association for Computing Machinery, 2021, doi:10.1145/3451992.
short: A. Czumaj, P. Davies, M. Parter, ACM Transactions on Algorithms 17 (2021).
date_created: 2021-06-10T19:31:05Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2024-02-28T12:53:09Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.1145/3451992
ec_funded: 1
external_id:
arxiv:
- '1912.05390'
isi:
- '000661311300006'
file:
- access_level: open_access
checksum: a21c627683890c309a68f6389302c408
content_type: application/pdf
creator: pdavies
date_created: 2021-06-10T19:33:56Z
date_updated: 2021-06-10T19:33:56Z
file_id: '9542'
file_name: MISMM-arxiv.pdf
file_size: 587404
relation: main_file
success: 1
file_date_updated: 2021-06-10T19:33:56Z
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intvolume: ' 17'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
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month: '06'
oa: 1
oa_version: Submitted Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: ACM Transactions on Algorithms
publication_identifier:
eissn:
- 1549-6333
issn:
- 1549-6325
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '7802'
relation: earlier_version
status: public
status: public
title: Graph sparsification for derandomizing massively parallel computation with
low space
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2021'
...
---
_id: '10134'
abstract:
- lang: eng
text: We investigate the effect of coupling between translational and internal degrees
of freedom of composite quantum particles on their localization in a random potential.
We show that entanglement between the two degrees of freedom weakens localization
due to the upper bound imposed on the inverse participation ratio by purity of
a quantum state. We perform numerical calculations for a two-particle system bound
by a harmonic force in a 1D disordered lattice and a rigid rotor in a 2D disordered
lattice. We illustrate that the coupling has a dramatic effect on localization
properties, even with a small number of internal states participating in quantum
dynamics.
acknowledgement: "We acknowledge helpful discussions with W. G. Unruh and A. Rodriguez.
F. S. is supported by European Union’s\r\nHorizon 2020 research and innovation programme
under the Marie Skłodowska-Curie Grant No. 754411. M. L. acknowledges support by
the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). W. H. Z.
is\r\nsupported by Department of Energy under the Los\r\nAlamos National Laboratory
LDRD Program as well as by the U.S. Department of Energy, Office of Science, Basic\r\nEnergy
Sciences, Materials Sciences and Engineering Division, Condensed Matter Theory Program.
R. V. K. is supported by NSERC of Canada.\r\n"
article_number: '160602'
article_processing_charge: No
article_type: original
author:
- first_name: Fumika
full_name: Suzuki, Fumika
id: 650C99FC-1079-11EA-A3C0-73AE3DDC885E
last_name: Suzuki
orcid: 0000-0003-4982-5970
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
- first_name: Wojciech H.
full_name: Zurek, Wojciech H.
last_name: Zurek
- first_name: Roman V.
full_name: Krems, Roman V.
last_name: Krems
citation:
ama: Suzuki F, Lemeshko M, Zurek WH, Krems RV. Anderson localization of composite
particles. Physical Review Letters. 2021;127(16). doi:10.1103/physrevlett.127.160602
apa: Suzuki, F., Lemeshko, M., Zurek, W. H., & Krems, R. V. (2021). Anderson
localization of composite particles. Physical Review Letters. American
Physical Society . https://doi.org/10.1103/physrevlett.127.160602
chicago: Suzuki, Fumika, Mikhail Lemeshko, Wojciech H. Zurek, and Roman V. Krems.
“Anderson Localization of Composite Particles.” Physical Review Letters.
American Physical Society , 2021. https://doi.org/10.1103/physrevlett.127.160602.
ieee: F. Suzuki, M. Lemeshko, W. H. Zurek, and R. V. Krems, “Anderson localization
of composite particles,” Physical Review Letters, vol. 127, no. 16. American
Physical Society , 2021.
ista: Suzuki F, Lemeshko M, Zurek WH, Krems RV. 2021. Anderson localization of composite
particles. Physical Review Letters. 127(16), 160602.
mla: Suzuki, Fumika, et al. “Anderson Localization of Composite Particles.” Physical
Review Letters, vol. 127, no. 16, 160602, American Physical Society , 2021,
doi:10.1103/physrevlett.127.160602.
short: F. Suzuki, M. Lemeshko, W.H. Zurek, R.V. Krems, Physical Review Letters 127
(2021).
date_created: 2021-10-13T09:21:33Z
date_published: 2021-10-12T00:00:00Z
date_updated: 2024-02-29T12:34:10Z
day: '12'
department:
- _id: MiLe
doi: 10.1103/physrevlett.127.160602
ec_funded: 1
external_id:
arxiv:
- '2011.06279'
isi:
- '000707495700001'
intvolume: ' 127'
isi: 1
issue: '16'
keyword:
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2011.06279
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 2688CF98-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '801770'
name: 'Angulon: physics and applications of a new quasiparticle'
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: 'American Physical Society '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Anderson localization of composite particles
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 127
year: '2021'
...
---
_id: '9678'
abstract:
- lang: eng
text: We introduce a new graph problem, the token dropping game, and we show how
to solve it efficiently in a distributed setting. We use the token dropping game
as a tool to design an efficient distributed algorithm for stable orientations
and more generally for locally optimal semi-matchings. The prior work by Czygrinow
et al. (DISC 2012) finds a stable orientation in O(Δ^5) rounds in graphs of maximum
degree Δ, while we improve it to O(Δ^4) and also prove a lower bound of Ω(Δ).
For the more general problem of locally optimal semi-matchings, the prior upper
bound is O(S^5) and our new algorithm runs in O(C · S^4) rounds, which is an improvement
for C = o(S); here C and S are the maximum degrees of customers and servers, respectively.
acknowledgement: We thank Orr Fischer, Juho Hirvonen, and Tuomo Lempiäinen for valuable
discussions. This project has received funding from the European Union’s Horizon
2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement
No. 840605.
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Brandt, Sebastian
last_name: Brandt
- first_name: Barbara
full_name: Keller, Barbara
last_name: Keller
- first_name: Joel
full_name: Rybicki, Joel
id: 334EFD2E-F248-11E8-B48F-1D18A9856A87
last_name: Rybicki
orcid: 0000-0002-6432-6646
- first_name: Jukka
full_name: Suomela, Jukka
last_name: Suomela
- first_name: Jara
full_name: Uitto, Jara
last_name: Uitto
citation:
ama: 'Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. Efficient load-balancing
through distributed token dropping. In: Annual ACM Symposium on Parallelism
in Algorithms and Architectures. ; 2021:129-139. doi:10.1145/3409964.3461785'
apa: Brandt, S., Keller, B., Rybicki, J., Suomela, J., & Uitto, J. (2021). Efficient
load-balancing through distributed token dropping. In Annual ACM Symposium
on Parallelism in Algorithms and Architectures (pp. 129–139). Virtual Event,
United States. https://doi.org/10.1145/3409964.3461785
chicago: Brandt, Sebastian, Barbara Keller, Joel Rybicki, Jukka Suomela, and Jara
Uitto. “Efficient Load-Balancing through Distributed Token Dropping.” In Annual
ACM Symposium on Parallelism in Algorithms and Architectures, 129–39, 2021.
https://doi.org/10.1145/3409964.3461785.
ieee: S. Brandt, B. Keller, J. Rybicki, J. Suomela, and J. Uitto, “Efficient load-balancing
through distributed token dropping,” in Annual ACM Symposium on Parallelism
in Algorithms and Architectures, Virtual Event, United States, 2021, pp.
129–139.
ista: 'Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. 2021. Efficient load-balancing
through distributed token dropping. Annual ACM Symposium on Parallelism in Algorithms
and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures
, 129–139.'
mla: Brandt, Sebastian, et al. “Efficient Load-Balancing through Distributed Token
Dropping.” Annual ACM Symposium on Parallelism in Algorithms and Architectures,
2021, pp. 129–39, doi:10.1145/3409964.3461785.
short: S. Brandt, B. Keller, J. Rybicki, J. Suomela, J. Uitto, in:, Annual ACM Symposium
on Parallelism in Algorithms and Architectures, 2021, pp. 129–139.
conference:
end_date: 2021-07-08
location: ' Virtual Event, United States'
name: 'SPAA: Symposium on Parallelism in Algorithms and Architectures '
start_date: 2021-07-06
date_created: 2021-07-18T22:01:22Z
date_published: 2021-07-06T00:00:00Z
date_updated: 2024-03-05T07:13:12Z
day: '06'
department:
- _id: DaAl
doi: 10.1145/3409964.3461785
ec_funded: 1
external_id:
arxiv:
- '2005.07761'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2005.07761
month: '07'
oa: 1
oa_version: Preprint
page: 129-139
project:
- _id: 26A5D39A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '840605'
name: Coordination in constrained and natural distributed systems
publication: Annual ACM Symposium on Parallelism in Algorithms and Architectures
publication_identifier:
isbn:
- '9781450380706'
publication_status: published
quality_controlled: '1'
related_material:
record:
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relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Efficient load-balancing through distributed token dropping
type: conference
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
year: '2021'
...
---
_id: '8286'
abstract:
- lang: eng
text: "We consider the following dynamic load-balancing process: given an underlying
graph G with n nodes, in each step t≥ 0, one unit of load is created, and placed
at a randomly chosen graph node. In the same step, the chosen node picks a random
neighbor, and the two nodes balance their loads by averaging them. We are interested
in the expected gap between the minimum and maximum loads at nodes as the process
progresses, and its dependence on n and on the graph structure. Variants of the
above graphical balanced allocation process have been studied previously by Peres,
Talwar, and Wieder [Peres et al., 2015], and by Sauerwald and Sun [Sauerwald and
Sun, 2015]. These authors left as open the question of characterizing the gap
in the case of cycle graphs in the dynamic case, where weights are created during
the algorithm’s execution. For this case, the only known upper bound is of \U0001D4AA(n
log n), following from a majorization argument due to [Peres et al., 2015], which
analyzes a related graphical allocation process. In this paper, we provide an
upper bound of \U0001D4AA (√n log n) on the expected gap of the above process
for cycles of length n. We introduce a new potential analysis technique, which
enables us to bound the difference in load between k-hop neighbors on the cycle,
for any k ≤ n/2. We complement this with a \"gap covering\" argument, which bounds
the maximum value of the gap by bounding its value across all possible subsets
of a certain structure, and recursively bounding the gaps within each subset.
We provide analytical and experimental evidence that our upper bound on the gap
is tight up to a logarithmic factor. "
acknowledgement: The authors sincerely thank Thomas Sauerwald and George Giakkoupis
for insightful discussions, and Mohsen Ghaffari, Yuval Peres, and Udi Wieder for
feedback on earlier versions of this draft. We also thank the ICALP anonymous reviewers
for their very useful comments. Open access funding provided by Institute of Science
and Technology (IST Austria). Funding was provided by European Research Council
(Grant No. PR1042ERC01).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Giorgi
full_name: Nadiradze, Giorgi
id: 3279A00C-F248-11E8-B48F-1D18A9856A87
last_name: Nadiradze
orcid: 0000-0001-5634-0731
- first_name: Amirmojtaba
full_name: Sabour, Amirmojtaba
id: bcc145fd-e77f-11ea-ae8b-80d661dbff67
last_name: Sabour
citation:
ama: Alistarh D-A, Nadiradze G, Sabour A. Dynamic averaging load balancing on cycles.
Algorithmica. 2021. doi:10.1007/s00453-021-00905-9
apa: 'Alistarh, D.-A., Nadiradze, G., & Sabour, A. (2021). Dynamic averaging
load balancing on cycles. Algorithmica. Virtual, Online; Germany: Springer
Nature. https://doi.org/10.1007/s00453-021-00905-9'
chicago: Alistarh, Dan-Adrian, Giorgi Nadiradze, and Amirmojtaba Sabour. “Dynamic
Averaging Load Balancing on Cycles.” Algorithmica. Springer Nature, 2021.
https://doi.org/10.1007/s00453-021-00905-9.
ieee: D.-A. Alistarh, G. Nadiradze, and A. Sabour, “Dynamic averaging load balancing
on cycles,” Algorithmica. Springer Nature, 2021.
ista: Alistarh D-A, Nadiradze G, Sabour A. 2021. Dynamic averaging load balancing
on cycles. Algorithmica.
mla: Alistarh, Dan-Adrian, et al. “Dynamic Averaging Load Balancing on Cycles.”
Algorithmica, Springer Nature, 2021, doi:10.1007/s00453-021-00905-9.
short: D.-A. Alistarh, G. Nadiradze, A. Sabour, Algorithmica (2021).
conference:
end_date: 2020-07-11
location: Virtual, Online; Germany
name: 'ICALP: International Colloquium on Automata, Languages, and Programming '
start_date: 2020-07-08
date_created: 2020-08-24T06:24:04Z
date_published: 2021-12-24T00:00:00Z
date_updated: 2024-03-05T07:35:53Z
day: '24'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.1007/s00453-021-00905-9
ec_funded: 1
external_id:
arxiv:
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- '000734004600001'
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month: '12'
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oa_version: Published Version
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Algorithmica
publication_identifier:
eissn:
- 1432-0541
issn:
- 0178-4617
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: earlier_version
url: https://doi.org/10.4230/LIPIcs.ICALP.2020.7
record:
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status: public
title: Dynamic averaging load balancing on cycles
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
year: '2021'
...
---
_id: '9733'
abstract:
- lang: eng
text: This thesis is the result of the research carried out by the author during
his PhD at IST Austria between 2017 and 2021. It mainly focuses on the Fröhlich
polaron model, specifically to its regime of strong coupling. This model, which
is rigorously introduced and discussed in the introduction, has been of great
interest in condensed matter physics and field theory for more than eighty years.
It is used to describe an electron interacting with the atoms of a solid material
(the strength of this interaction is modeled by the presence of a coupling constant
α in the Hamiltonian of the system). The particular regime examined here, which
is mathematically described by considering the limit α →∞, displays many interesting
features related to the emergence of classical behavior, which allows for a simplified
effective description of the system under analysis. The properties, the range
of validity and a quantitative analysis of the precision of such classical approximations
are the main object of the present work. We specify our investigation to the study
of the ground state energy of the system, its dynamics and its effective mass.
For each of these problems, we provide in the introduction an overview of the
previously known results and a detailed account of the original contributions
by the author.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Dario
full_name: Feliciangeli, Dario
id: 41A639AA-F248-11E8-B48F-1D18A9856A87
last_name: Feliciangeli
orcid: 0000-0003-0754-8530
citation:
ama: Feliciangeli D. The polaron at strong coupling. 2021. doi:10.15479/at:ista:9733
apa: Feliciangeli, D. (2021). The polaron at strong coupling. Institute of
Science and Technology Austria. https://doi.org/10.15479/at:ista:9733
chicago: Feliciangeli, Dario. “The Polaron at Strong Coupling.” Institute of Science
and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9733.
ieee: D. Feliciangeli, “The polaron at strong coupling,” Institute of Science and
Technology Austria, 2021.
ista: Feliciangeli D. 2021. The polaron at strong coupling. Institute of Science
and Technology Austria.
mla: Feliciangeli, Dario. The Polaron at Strong Coupling. Institute of Science
and Technology Austria, 2021, doi:10.15479/at:ista:9733.
short: D. Feliciangeli, The Polaron at Strong Coupling, Institute of Science and
Technology Austria, 2021.
date_created: 2021-07-27T15:48:30Z
date_published: 2021-08-20T00:00:00Z
date_updated: 2024-03-06T12:30:44Z
day: '20'
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- '519'
- '539'
degree_awarded: PhD
department:
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- _id: RoSe
- _id: JaMa
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language:
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license: https://creativecommons.org/licenses/by-nd/4.0/
month: '08'
oa: 1
oa_version: Published Version
page: '180'
project:
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call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9787'
relation: part_of_dissertation
status: public
- id: '9792'
relation: part_of_dissertation
status: public
- id: '9225'
relation: part_of_dissertation
status: public
- id: '9781'
relation: part_of_dissertation
status: public
- id: '9791'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
title: The polaron at strong coupling
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '9571'
abstract:
- lang: eng
text: As the size and complexity of models and datasets grow, so does the need for
communication-efficient variants of stochastic gradient descent that can be deployed
to perform parallel model training. One popular communication-compression method
for data-parallel SGD is QSGD (Alistarh et al., 2017), which quantizes and encodes
gradients to reduce communication costs. The baseline variant of QSGD provides
strong theoretical guarantees, however, for practical purposes, the authors proposed
a heuristic variant which we call QSGDinf, which demonstrated impressive empirical
gains for distributed training of large neural networks. In this paper, we build
on this work to propose a new gradient quantization scheme, and show that it has
both stronger theoretical guarantees than QSGD, and matches and exceeds the empirical
performance of the QSGDinf heuristic and of other compression methods.
article_processing_charge: No
article_type: original
author:
- first_name: Ali
full_name: Ramezani-Kebrya, Ali
last_name: Ramezani-Kebrya
- first_name: Fartash
full_name: Faghri, Fartash
last_name: Faghri
- first_name: Ilya
full_name: Markov, Ilya
last_name: Markov
- first_name: Vitalii
full_name: Aksenov, Vitalii
id: 2980135A-F248-11E8-B48F-1D18A9856A87
last_name: Aksenov
- 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: Daniel M.
full_name: Roy, Daniel M.
last_name: Roy
citation:
ama: 'Ramezani-Kebrya A, Faghri F, Markov I, Aksenov V, Alistarh D-A, Roy DM. NUQSGD:
Provably communication-efficient data-parallel SGD via nonuniform quantization.
Journal of Machine Learning Research. 2021;22(114):1−43.'
apa: 'Ramezani-Kebrya, A., Faghri, F., Markov, I., Aksenov, V., Alistarh, D.-A.,
& Roy, D. M. (2021). NUQSGD: Provably communication-efficient data-parallel
SGD via nonuniform quantization. Journal of Machine Learning Research.
Journal of Machine Learning Research.'
chicago: 'Ramezani-Kebrya, Ali, Fartash Faghri, Ilya Markov, Vitalii Aksenov, Dan-Adrian
Alistarh, and Daniel M. Roy. “NUQSGD: Provably Communication-Efficient Data-Parallel
SGD via Nonuniform Quantization.” Journal of Machine Learning Research.
Journal of Machine Learning Research, 2021.'
ieee: 'A. Ramezani-Kebrya, F. Faghri, I. Markov, V. Aksenov, D.-A. Alistarh, and
D. M. Roy, “NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform
quantization,” Journal of Machine Learning Research, vol. 22, no. 114.
Journal of Machine Learning Research, p. 1−43, 2021.'
ista: 'Ramezani-Kebrya A, Faghri F, Markov I, Aksenov V, Alistarh D-A, Roy DM. 2021.
NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform quantization.
Journal of Machine Learning Research. 22(114), 1−43.'
mla: 'Ramezani-Kebrya, Ali, et al. “NUQSGD: Provably Communication-Efficient Data-Parallel
SGD via Nonuniform Quantization.” Journal of Machine Learning Research,
vol. 22, no. 114, Journal of Machine Learning Research, 2021, p. 1−43.'
short: A. Ramezani-Kebrya, F. Faghri, I. Markov, V. Aksenov, D.-A. Alistarh, D.M.
Roy, Journal of Machine Learning Research 22 (2021) 1−43.
date_created: 2021-06-20T22:01:33Z
date_published: 2021-04-01T00:00:00Z
date_updated: 2024-03-06T12:22:07Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
external_id:
arxiv:
- '1908.06077'
file:
- access_level: open_access
checksum: 6428aa8bcb67768b6949c99b55d5281d
content_type: application/pdf
creator: asandaue
date_created: 2021-06-23T07:09:41Z
date_updated: 2021-06-23T07:09:41Z
file_id: '9595'
file_name: 2021_JournalOfMachineLearningResearch_Ramezani-Kebrya.pdf
file_size: 11237154
relation: main_file
success: 1
file_date_updated: 2021-06-23T07:09:41Z
has_accepted_license: '1'
intvolume: ' 22'
issue: '114'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.jmlr.org/papers/v22/20-255.html
month: '04'
oa: 1
oa_version: Published Version
page: 1−43
publication: Journal of Machine Learning Research
publication_identifier:
eissn:
- '15337928'
issn:
- '15324435'
publication_status: published
publisher: Journal of Machine Learning Research
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'NUQSGD: Provably communication-efficient data-parallel SGD via nonuniform
quantization'
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: 22
year: '2021'
...
---
_id: '8544'
abstract:
- lang: eng
text: The synaptotrophic hypothesis posits that synapse formation stabilizes dendritic
branches, yet this hypothesis has not been causally tested in vivo in the mammalian
brain. Presynaptic ligand cerebellin-1 (Cbln1) and postsynaptic receptor GluD2
mediate synaptogenesis between granule cells and Purkinje cells in the molecular
layer of the cerebellar cortex. Here we show that sparse but not global knockout
of GluD2 causes under-elaboration of Purkinje cell dendrites in the deep molecular
layer and overelaboration in the superficial molecular layer. Developmental, overexpression,
structure-function, and genetic epistasis analyses indicate that dendrite morphogenesis
defects result from competitive synaptogenesis in a Cbln1/GluD2-dependent manner.
A generative model of dendritic growth based on competitive synaptogenesis largely
recapitulates GluD2 sparse and global knockout phenotypes. Our results support
the synaptotrophic hypothesis at initial stages of dendrite development, suggest
a second mode in which cumulative synapse formation inhibits further dendrite
growth, and highlight the importance of competition in dendrite morphogenesis.
acknowledgement: We thank M. Mishina for GluD2fl frozen embryos, T.C. Südhof and J.I.
Morgan for Cbln1fl mice, L. Anderson for help in generating the MADM alleles, W.
Joo for a previously unpublished construct, M. Yuzaki, K. Shen, J. Ding, and members
of the Luo lab, including J.M. Kebschull, H. Li, J. Li, T. Li, C.M. McLaughlin,
D. Pederick, J. Ren, D.C. Wang and C. Xu for discussions and critiques of the manuscript,
and M. Yuzaki for supporting Y.H.T. during the final phase of this project. Y.H.T.
was supported by a JSPS fellowship; S.A.S. was supported by a Stanford Graduate
Fellowship and an NSF Predoctoral Fellowship; L.J. is supported by a Stanford Graduate
Fellowship and an NSF Predoctoral Fellowship; M.J.W. is supported by a Burroughs
Wellcome Fund CASI Award. This work was supported by an NIH grant (R01-NS050538)
to L.L.; the European Research Council (ERC) under the European Union's Horizon
2020 research and innovations programme (No. 725780 LinPro) to S.H.; and Simons
and James S. McDonnell Foundations and an NSF CAREER award to S.G.; L.L. is an HHMI
investigator.
article_processing_charge: No
article_type: original
author:
- first_name: Yukari H.
full_name: Takeo, Yukari H.
last_name: Takeo
- first_name: S. Andrew
full_name: Shuster, S. Andrew
last_name: Shuster
- first_name: Linnie
full_name: Jiang, Linnie
last_name: Jiang
- first_name: Miley
full_name: Hu, Miley
last_name: Hu
- first_name: David J.
full_name: Luginbuhl, David J.
last_name: Luginbuhl
- first_name: Thomas
full_name: Rülicke, Thomas
last_name: Rülicke
- first_name: Ximena
full_name: Contreras, Ximena
id: 475990FE-F248-11E8-B48F-1D18A9856A87
last_name: Contreras
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Mark J.
full_name: Wagner, Mark J.
last_name: Wagner
- first_name: Surya
full_name: Ganguli, Surya
last_name: Ganguli
- first_name: Liqun
full_name: Luo, Liqun
last_name: Luo
citation:
ama: Takeo YH, Shuster SA, Jiang L, et al. GluD2- and Cbln1-mediated competitive
synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells. Neuron.
2021;109(4):P629-644.E8. doi:10.1016/j.neuron.2020.11.028
apa: Takeo, Y. H., Shuster, S. A., Jiang, L., Hu, M., Luginbuhl, D. J., Rülicke,
T., … Luo, L. (2021). GluD2- and Cbln1-mediated competitive synaptogenesis shapes
the dendritic arbors of cerebellar Purkinje cells. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.11.028
chicago: Takeo, Yukari H., S. Andrew Shuster, Linnie Jiang, Miley Hu, David J. Luginbuhl,
Thomas Rülicke, Ximena Contreras, et al. “GluD2- and Cbln1-Mediated Competitive
Synaptogenesis Shapes the Dendritic Arbors of Cerebellar Purkinje Cells.” Neuron.
Elsevier, 2021. https://doi.org/10.1016/j.neuron.2020.11.028.
ieee: Y. H. Takeo et al., “GluD2- and Cbln1-mediated competitive synaptogenesis
shapes the dendritic arbors of cerebellar Purkinje cells,” Neuron, vol.
109, no. 4. Elsevier, p. P629–644.E8, 2021.
ista: Takeo YH, Shuster SA, Jiang L, Hu M, Luginbuhl DJ, Rülicke T, Contreras X,
Hippenmeyer S, Wagner MJ, Ganguli S, Luo L. 2021. GluD2- and Cbln1-mediated competitive
synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells. Neuron.
109(4), P629–644.E8.
mla: Takeo, Yukari H., et al. “GluD2- and Cbln1-Mediated Competitive Synaptogenesis
Shapes the Dendritic Arbors of Cerebellar Purkinje Cells.” Neuron, vol.
109, no. 4, Elsevier, 2021, p. P629–644.E8, doi:10.1016/j.neuron.2020.11.028.
short: Y.H. Takeo, S.A. Shuster, L. Jiang, M. Hu, D.J. Luginbuhl, T. Rülicke, X.
Contreras, S. Hippenmeyer, M.J. Wagner, S. Ganguli, L. Luo, Neuron 109 (2021)
P629–644.E8.
date_created: 2020-09-21T11:59:47Z
date_published: 2021-02-17T00:00:00Z
date_updated: 2024-03-06T12:12:48Z
day: '17'
department:
- _id: SiHi
doi: 10.1016/j.neuron.2020.11.028
ec_funded: 1
intvolume: ' 109'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2020.06.14.151258
month: '02'
oa: 1
oa_version: Preprint
page: P629-644.E8
project:
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
publication: Neuron
publication_identifier:
eissn:
- 1097-4199
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors
of cerebellar Purkinje cells
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 109
year: '2021'
...
---
_id: '9791'
abstract:
- lang: eng
text: We provide a definition of the effective mass for the classical polaron described
by the Landau-Pekar equations. It is based on a novel variational principle, minimizing
the energy functional over states with given (initial) velocity. The resulting
formula for the polaron's effective mass agrees with the prediction by Landau
and Pekar.
acknowledgement: We thank Herbert Spohn for helpful comments. Funding from the European
Union’s Horizon 2020 research and innovation programme under the ERC grant agreement
No. 694227 (D.F. and R.S.) and under the Marie Skłodowska-Curie Grant Agreement
No. 754411 (S.R.) is gratefully acknowledged..
article_number: '2107.03720 '
article_processing_charge: No
author:
- first_name: Dario
full_name: Feliciangeli, Dario
id: 41A639AA-F248-11E8-B48F-1D18A9856A87
last_name: Feliciangeli
orcid: 0000-0003-0754-8530
- first_name: Simone Anna Elvira
full_name: Rademacher, Simone Anna Elvira
id: 856966FE-A408-11E9-977E-802DE6697425
last_name: Rademacher
orcid: 0000-0001-5059-4466
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Feliciangeli D, Rademacher SAE, Seiringer R. The effective mass problem for
the Landau-Pekar equations. arXiv.
apa: Feliciangeli, D., Rademacher, S. A. E., & Seiringer, R. (n.d.). The effective
mass problem for the Landau-Pekar equations. arXiv.
chicago: Feliciangeli, Dario, Simone Anna Elvira Rademacher, and Robert Seiringer.
“The Effective Mass Problem for the Landau-Pekar Equations.” ArXiv, n.d.
ieee: D. Feliciangeli, S. A. E. Rademacher, and R. Seiringer, “The effective mass
problem for the Landau-Pekar equations,” arXiv. .
ista: Feliciangeli D, Rademacher SAE, Seiringer R. The effective mass problem for
the Landau-Pekar equations. arXiv, 2107.03720.
mla: Feliciangeli, Dario, et al. “The Effective Mass Problem for the Landau-Pekar
Equations.” ArXiv, 2107.03720.
short: D. Feliciangeli, S.A.E. Rademacher, R. Seiringer, ArXiv (n.d.).
date_created: 2021-08-06T08:49:45Z
date_published: 2021-07-08T00:00:00Z
date_updated: 2024-03-06T12:30:45Z
day: '08'
ddc:
- '510'
department:
- _id: RoSe
ec_funded: 1
external_id:
arxiv:
- '2107.03720'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2107.03720
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694227'
name: Analysis of quantum many-body systems
publication: arXiv
publication_status: submitted
related_material:
record:
- id: '10755'
relation: later_version
status: public
- id: '9733'
relation: dissertation_contains
status: public
status: public
title: The effective mass problem for the Landau-Pekar equations
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '7553'
abstract:
- lang: eng
text: Normative theories and statistical inference provide complementary approaches
for the study of biological systems. A normative theory postulates that organisms
have adapted to efficiently solve essential tasks, and proceeds to mathematically
work out testable consequences of such optimality; parameters that maximize the
hypothesized organismal function can be derived ab initio, without reference to
experimental data. In contrast, statistical inference focuses on efficient utilization
of data to learn model parameters, without reference to any a priori notion of
biological function, utility, or fitness. Traditionally, these two approaches
were developed independently and applied separately. Here we unify them in a coherent
Bayesian framework that embeds a normative theory into a family of maximum-entropy
“optimization priors.” This family defines a smooth interpolation between a data-rich
inference regime (characteristic of “bottom-up” statistical models), and a data-limited
ab inito prediction regime (characteristic of “top-down” normative theory). We
demonstrate the applicability of our framework using data from the visual cortex,
and argue that the flexibility it affords is essential to address a number of
fundamental challenges relating to inference and prediction in complex, high-dimensional
biological problems.
acknowledgement: The authors thank Dario Ringach for providing the V1 receptive fields
and Olivier Marre for providing the retinal receptive fields. W.M. was funded by
the European Union’s Horizon 2020 research and innovation programme under the Marie
Skłodowska-Curie grant agreement no. 754411. M.H. was funded in part by Human Frontiers
Science grant no. HFSP RGP0032/2018.
article_processing_charge: No
author:
- first_name: Wiktor F
full_name: Mlynarski, Wiktor F
id: 358A453A-F248-11E8-B48F-1D18A9856A87
last_name: Mlynarski
- first_name: Michal
full_name: Hledik, Michal
id: 4171253A-F248-11E8-B48F-1D18A9856A87
last_name: Hledik
- first_name: Thomas R
full_name: Sokolowski, Thomas R
id: 3E999752-F248-11E8-B48F-1D18A9856A87
last_name: Sokolowski
orcid: 0000-0002-1287-3779
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. Statistical analysis and optimality
of neural systems. Neuron. 2021;109(7):1227-1241.e5. doi:10.1016/j.neuron.2021.01.020
apa: Mlynarski, W. F., Hledik, M., Sokolowski, T. R., & Tkačik, G. (2021). Statistical
analysis and optimality of neural systems. Neuron. Cell Press. https://doi.org/10.1016/j.neuron.2021.01.020
chicago: Mlynarski, Wiktor F, Michal Hledik, Thomas R Sokolowski, and Gašper Tkačik.
“Statistical Analysis and Optimality of Neural Systems.” Neuron. Cell Press,
2021. https://doi.org/10.1016/j.neuron.2021.01.020.
ieee: W. F. Mlynarski, M. Hledik, T. R. Sokolowski, and G. Tkačik, “Statistical
analysis and optimality of neural systems,” Neuron, vol. 109, no. 7. Cell
Press, p. 1227–1241.e5, 2021.
ista: Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. 2021. Statistical analysis
and optimality of neural systems. Neuron. 109(7), 1227–1241.e5.
mla: Mlynarski, Wiktor F., et al. “Statistical Analysis and Optimality of Neural
Systems.” Neuron, vol. 109, no. 7, Cell Press, 2021, p. 1227–1241.e5, doi:10.1016/j.neuron.2021.01.020.
short: W.F. Mlynarski, M. Hledik, T.R. Sokolowski, G. Tkačik, Neuron 109 (2021)
1227–1241.e5.
date_created: 2020-02-28T11:00:12Z
date_published: 2021-04-07T00:00:00Z
date_updated: 2024-03-06T14:22:51Z
day: '07'
department:
- _id: GaTk
doi: 10.1016/j.neuron.2021.01.020
ec_funded: 1
external_id:
isi:
- '000637809600006'
intvolume: ' 109'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/848374
month: '04'
oa: 1
oa_version: Preprint
page: 1227-1241.e5
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Neuron
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/can-evolution-be-predicted/
record:
- id: '15020'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Statistical analysis and optimality of neural systems
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 109
year: '2021'
...
---
_id: '10598'
abstract:
- lang: eng
text: ' We consider the problem of estimating a signal from measurements obtained
via a generalized linear model. We focus on estimators based on approximate message
passing (AMP), a family of iterative algorithms with many appealing features:
the performance of AMP in the high-dimensional limit can be succinctly characterized
under suitable model assumptions; AMP can also be tailored to the empirical distribution
of the signal entries, and for a wide class of estimation problems, AMP is conjectured
to be optimal among all polynomial-time algorithms. However, a major issue of
AMP is that in many models (such as phase retrieval), it requires an initialization
correlated with the ground-truth signal and independent from the measurement matrix.
Assuming that such an initialization is available is typically not realistic.
In this paper, we solve this problem by proposing an AMP algorithm initialized
with a spectral estimator. With such an initialization, the standard AMP analysis
fails since the spectral estimator depends in a complicated way on the design
matrix. Our main contribution is a rigorous characterization of the performance
of AMP with spectral initialization in the high-dimensional limit. The key technical
idea is to define and analyze a two-phase artificial AMP algorithm that first
produces the spectral estimator, and then closely approximates the iterates of
the true AMP. We also provide numerical results that demonstrate the validity
of the proposed approach. '
acknowledgement: The authors would like to thank Andrea Montanari for helpful discussions.
M. Mondelli was partially supported by the 2019 Lopez-Loreta Prize. R. Venkataramanan
was partially supported by the Alan Turing Institute under the EPSRC grant EP/N510129/1.
alternative_title:
- Proceedings of Machine Learning Research
article_processing_charge: Yes (via OA deal)
author:
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Ramji
full_name: Venkataramanan, Ramji
last_name: Venkataramanan
citation:
ama: 'Mondelli M, Venkataramanan R. Approximate message passing with spectral initialization
for generalized linear models. In: Banerjee A, Fukumizu K, eds. Proceedings
of The 24th International Conference on Artificial Intelligence and Statistics.
Vol 130. ML Research Press; 2021:397-405.'
apa: 'Mondelli, M., & Venkataramanan, R. (2021). Approximate message passing
with spectral initialization for generalized linear models. In A. Banerjee &
K. Fukumizu (Eds.), Proceedings of The 24th International Conference on Artificial
Intelligence and Statistics (Vol. 130, pp. 397–405). Virtual, San Diego, CA,
United States: ML Research Press.'
chicago: Mondelli, Marco, and Ramji Venkataramanan. “Approximate Message Passing
with Spectral Initialization for Generalized Linear Models.” In Proceedings
of The 24th International Conference on Artificial Intelligence and Statistics,
edited by Arindam Banerjee and Kenji Fukumizu, 130:397–405. ML Research Press,
2021.
ieee: M. Mondelli and R. Venkataramanan, “Approximate message passing with spectral
initialization for generalized linear models,” in Proceedings of The 24th International
Conference on Artificial Intelligence and Statistics, Virtual, San Diego,
CA, United States, 2021, vol. 130, pp. 397–405.
ista: 'Mondelli M, Venkataramanan R. 2021. Approximate message passing with spectral
initialization for generalized linear models. Proceedings of The 24th International
Conference on Artificial Intelligence and Statistics. AISTATS: Artificial Intelligence
and Statistics, Proceedings of Machine Learning Research, vol. 130, 397–405.'
mla: Mondelli, Marco, and Ramji Venkataramanan. “Approximate Message Passing with
Spectral Initialization for Generalized Linear Models.” Proceedings of The
24th International Conference on Artificial Intelligence and Statistics, edited
by Arindam Banerjee and Kenji Fukumizu, vol. 130, ML Research Press, 2021, pp.
397–405.
short: M. Mondelli, R. Venkataramanan, in:, A. Banerjee, K. Fukumizu (Eds.), Proceedings
of The 24th International Conference on Artificial Intelligence and Statistics,
ML Research Press, 2021, pp. 397–405.
conference:
end_date: 2021-04-15
location: Virtual, San Diego, CA, United States
name: 'AISTATS: Artificial Intelligence and Statistics'
start_date: 2021-04-13
date_created: 2022-01-03T11:34:22Z
date_published: 2021-04-01T00:00:00Z
date_updated: 2024-03-07T10:36:53Z
day: '01'
department:
- _id: MaMo
editor:
- first_name: Arindam
full_name: Banerjee, Arindam
last_name: Banerjee
- first_name: Kenji
full_name: Fukumizu, Kenji
last_name: Fukumizu
external_id:
arxiv:
- '2010.03460'
intvolume: ' 130'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://proceedings.mlr.press/v130/mondelli21a.html
month: '04'
oa: 1
oa_version: Preprint
page: 397-405
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: Proceedings of The 24th International Conference on Artificial Intelligence
and Statistics
publication_identifier:
issn:
- 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
related_material:
record:
- id: '12480'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Approximate message passing with spectral initialization for generalized linear
models
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 130
year: '2021'
...
---
_id: '8196'
abstract:
- lang: eng
text: This paper aims to obtain a strong convergence result for a Douglas–Rachford
splitting method with inertial extrapolation step for finding a zero of the sum
of two set-valued maximal monotone operators without any further assumption of
uniform monotonicity on any of the involved maximal monotone operators. Furthermore,
our proposed method is easy to implement and the inertial factor in our proposed
method is a natural choice. Our method of proof is of independent interest. Finally,
some numerical implementations are given to confirm the theoretical analysis.
acknowledgement: Open access funding provided by Institute of Science and Technology
(IST Austria). The project of Yekini Shehu has received funding from the European
Research Council (ERC) under the European Union’s Seventh Framework Program (FP7—2007–2013)
(Grant Agreement No. 616160). The authors are grateful to the anonymous referees
and the handling Editor for their comments and suggestions which have improved the
earlier version of the manuscript greatly.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Yekini
full_name: Shehu, Yekini
id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87
last_name: Shehu
orcid: 0000-0001-9224-7139
- first_name: Qiao-Li
full_name: Dong, Qiao-Li
last_name: Dong
- first_name: Lu-Lu
full_name: Liu, Lu-Lu
last_name: Liu
- first_name: Jen-Chih
full_name: Yao, Jen-Chih
last_name: Yao
citation:
ama: Shehu Y, Dong Q-L, Liu L-L, Yao J-C. New strong convergence method for the
sum of two maximal monotone operators. Optimization and Engineering. 2021;22:2627-2653.
doi:10.1007/s11081-020-09544-5
apa: Shehu, Y., Dong, Q.-L., Liu, L.-L., & Yao, J.-C. (2021). New strong convergence
method for the sum of two maximal monotone operators. Optimization and Engineering.
Springer Nature. https://doi.org/10.1007/s11081-020-09544-5
chicago: Shehu, Yekini, Qiao-Li Dong, Lu-Lu Liu, and Jen-Chih Yao. “New Strong Convergence
Method for the Sum of Two Maximal Monotone Operators.” Optimization and Engineering.
Springer Nature, 2021. https://doi.org/10.1007/s11081-020-09544-5.
ieee: Y. Shehu, Q.-L. Dong, L.-L. Liu, and J.-C. Yao, “New strong convergence method
for the sum of two maximal monotone operators,” Optimization and Engineering,
vol. 22. Springer Nature, pp. 2627–2653, 2021.
ista: Shehu Y, Dong Q-L, Liu L-L, Yao J-C. 2021. New strong convergence method for
the sum of two maximal monotone operators. Optimization and Engineering. 22, 2627–2653.
mla: Shehu, Yekini, et al. “New Strong Convergence Method for the Sum of Two Maximal
Monotone Operators.” Optimization and Engineering, vol. 22, Springer Nature,
2021, pp. 2627–53, doi:10.1007/s11081-020-09544-5.
short: Y. Shehu, Q.-L. Dong, L.-L. Liu, J.-C. Yao, Optimization and Engineering
22 (2021) 2627–2653.
date_created: 2020-08-03T14:29:57Z
date_published: 2021-02-25T00:00:00Z
date_updated: 2024-03-07T14:39:29Z
day: '25'
ddc:
- '510'
department:
- _id: VlKo
doi: 10.1007/s11081-020-09544-5
ec_funded: 1
external_id:
isi:
- '000559345400001'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2020-08-03T15:24:39Z
date_updated: 2020-08-03T15:24:39Z
file_id: '8197'
file_name: 2020_OptimizationEngineering_Shehu.pdf
file_size: 2137860
relation: main_file
success: 1
file_date_updated: 2020-08-03T15:24:39Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 2627-2653
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Optimization and Engineering
publication_identifier:
eissn:
- 1573-2924
issn:
- 1389-4420
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: New strong convergence method for the sum of two maximal monotone operators
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2021'
...
---
_id: '8911'
abstract:
- lang: eng
text: "In the worldwide endeavor for disruptive quantum technologies, germanium
is emerging as a versatile material to realize devices capable of encoding, processing,
or transmitting quantum information. These devices leverage special properties
of the germanium valence-band states, commonly known as holes, such as their inherently
strong spin-orbit coupling and the ability to host superconducting pairing correlations.
In this Review, we initially introduce the physics of holes in low-dimensional
germanium structures with key insights from a theoretical perspective. We then
examine the material science progress underpinning germanium-based planar heterostructures
and nanowires. We review the most significant experimental results demonstrating
key building blocks for quantum technology, such as an electrically driven universal
quantum gate set with spin qubits in quantum dots and superconductor-semiconductor
devices for hybrid quantum systems. We conclude by identifying the most promising
prospects\r\ntoward scalable quantum information processing. "
acknowledgement: "G.S., M.W.,F.A.Z acknowledge financial support from The Netherlands
Organization for Scientific Research (NWO). F.Z., D.L., G.K. acknowledge funding
from the European Union’s Horizon 2020 research and innovation programme under Grand
Agreement Nr. 862046. G.K. acknowledges funding from FP7 ERC Starting Grant 335497,
FWF Y 715-N30, FWF P-30207. S.D. acknowledges support from the European Union’s
Horizon 2020 program under Grant\r\nAgreement No. 81050 and from the Agence Nationale
de la Recherche through the TOPONANO and CMOSQSPIN projects. J.Z. acknowledges support
from the National Key R&D Program of China (Grant No. 2016YFA0301701) and Strategic
Priority Research Program of CAS (Grant No. XDB30000000). D.L. and C.K. acknowledge
the Swiss National Science Foundation and NCCR QSIT."
article_processing_charge: No
article_type: original
author:
- first_name: Giordano
full_name: Scappucci, Giordano
last_name: Scappucci
- first_name: Christoph
full_name: Kloeffel, Christoph
last_name: Kloeffel
- first_name: Floris A.
full_name: Zwanenburg, Floris A.
last_name: Zwanenburg
- first_name: Daniel
full_name: Loss, Daniel
last_name: Loss
- first_name: Maksym
full_name: Myronov, Maksym
last_name: Myronov
- first_name: Jian-Jun
full_name: Zhang, Jian-Jun
last_name: Zhang
- first_name: Silvano De
full_name: Franceschi, Silvano De
last_name: Franceschi
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
- first_name: Menno
full_name: Veldhorst, Menno
last_name: Veldhorst
citation:
ama: Scappucci G, Kloeffel C, Zwanenburg FA, et al. The germanium quantum information
route. Nature Reviews Materials. 2021;6:926–943. doi:10.1038/s41578-020-00262-z
apa: Scappucci, G., Kloeffel, C., Zwanenburg, F. A., Loss, D., Myronov, M., Zhang,
J.-J., … Veldhorst, M. (2021). The germanium quantum information route. Nature
Reviews Materials. Springer Nature. https://doi.org/10.1038/s41578-020-00262-z
chicago: Scappucci, Giordano, Christoph Kloeffel, Floris A. Zwanenburg, Daniel Loss,
Maksym Myronov, Jian-Jun Zhang, Silvano De Franceschi, Georgios Katsaros, and
Menno Veldhorst. “The Germanium Quantum Information Route.” Nature Reviews
Materials. Springer Nature, 2021. https://doi.org/10.1038/s41578-020-00262-z.
ieee: G. Scappucci et al., “The germanium quantum information route,” Nature
Reviews Materials, vol. 6. Springer Nature, pp. 926–943, 2021.
ista: Scappucci G, Kloeffel C, Zwanenburg FA, Loss D, Myronov M, Zhang J-J, Franceschi
SD, Katsaros G, Veldhorst M. 2021. The germanium quantum information route. Nature
Reviews Materials. 6, 926–943.
mla: Scappucci, Giordano, et al. “The Germanium Quantum Information Route.” Nature
Reviews Materials, vol. 6, Springer Nature, 2021, pp. 926–943, doi:10.1038/s41578-020-00262-z.
short: G. Scappucci, C. Kloeffel, F.A. Zwanenburg, D. Loss, M. Myronov, J.-J. Zhang,
S.D. Franceschi, G. Katsaros, M. Veldhorst, Nature Reviews Materials 6 (2021)
926–943.
date_created: 2020-12-02T10:52:51Z
date_published: 2021-10-01T00:00:00Z
date_updated: 2024-03-07T14:48:57Z
day: '01'
department:
- _id: GeKa
doi: 10.1038/s41578-020-00262-z
ec_funded: 1
external_id:
arxiv:
- '2004.08133'
isi:
- '000600826100003'
intvolume: ' 6'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2004.08133
month: '10'
oa: 1
oa_version: Preprint
page: '926–943 '
project:
- _id: 25517E86-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '335497'
name: Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires
- _id: 2552F888-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y00715
name: Loch Spin-Qubits und Majorana-Fermionen in Germanium
- _id: 2641CE5E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P30207
name: Hole spin orbit qubits in Ge quantum wells
publication: Nature Reviews Materials
publication_identifier:
eissn:
- 2058-8437
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The germanium quantum information route
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2021'
...
---
_id: '8338'
abstract:
- lang: eng
text: Canonical parametrisations of classical confocal coordinate systems are introduced
and exploited to construct non-planar analogues of incircular (IC) nets on individual
quadrics and systems of confocal quadrics. Intimate connections with classical
deformations of quadrics that are isometric along asymptotic lines and circular
cross-sections of quadrics are revealed. The existence of octahedral webs of surfaces
of Blaschke type generated by asymptotic and characteristic lines that are diagonally
related to lines of curvature is proved theoretically and established constructively.
Appropriate samplings (grids) of these webs lead to three-dimensional extensions
of non-planar IC nets. Three-dimensional octahedral grids composed of planes and
spatially extending (checkerboard) IC-nets are shown to arise in connection with
systems of confocal quadrics in Minkowski space. In this context, the Laguerre
geometric notion of conical octahedral grids of planes is introduced. The latter
generalise the octahedral grids derived from systems of confocal quadrics in Minkowski
space. An explicit construction of conical octahedral grids is presented. The
results are accompanied by various illustrations which are based on the explicit
formulae provided by the theory.
acknowledgement: This research was supported by the DFG Collaborative Research Center
TRR 109 “Discretization in Geometry and Dynamics”. W.K.S. was also supported by
the Australian Research Council (DP1401000851). A.V.A. was also supported by the
European Research Council (ERC) under the European Union’s Horizon 2020 research
and innovation programme (Grant Agreement No. 78818 Alpha).
article_processing_charge: No
article_type: original
author:
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Alexander I.
full_name: Bobenko, Alexander I.
last_name: Bobenko
- first_name: Wolfgang K.
full_name: Schief, Wolfgang K.
last_name: Schief
- first_name: Jan
full_name: Techter, Jan
last_name: Techter
citation:
ama: Akopyan A, Bobenko AI, Schief WK, Techter J. On mutually diagonal nets on (confocal)
quadrics and 3-dimensional webs. Discrete and Computational Geometry. 2021;66:938-976.
doi:10.1007/s00454-020-00240-w
apa: Akopyan, A., Bobenko, A. I., Schief, W. K., & Techter, J. (2021). On mutually
diagonal nets on (confocal) quadrics and 3-dimensional webs. Discrete and Computational
Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00240-w
chicago: Akopyan, Arseniy, Alexander I. Bobenko, Wolfgang K. Schief, and Jan Techter.
“On Mutually Diagonal Nets on (Confocal) Quadrics and 3-Dimensional Webs.” Discrete
and Computational Geometry. Springer Nature, 2021. https://doi.org/10.1007/s00454-020-00240-w.
ieee: A. Akopyan, A. I. Bobenko, W. K. Schief, and J. Techter, “On mutually diagonal
nets on (confocal) quadrics and 3-dimensional webs,” Discrete and Computational
Geometry, vol. 66. Springer Nature, pp. 938–976, 2021.
ista: Akopyan A, Bobenko AI, Schief WK, Techter J. 2021. On mutually diagonal nets
on (confocal) quadrics and 3-dimensional webs. Discrete and Computational Geometry.
66, 938–976.
mla: Akopyan, Arseniy, et al. “On Mutually Diagonal Nets on (Confocal) Quadrics
and 3-Dimensional Webs.” Discrete and Computational Geometry, vol. 66,
Springer Nature, 2021, pp. 938–76, doi:10.1007/s00454-020-00240-w.
short: A. Akopyan, A.I. Bobenko, W.K. Schief, J. Techter, Discrete and Computational
Geometry 66 (2021) 938–976.
date_created: 2020-09-06T22:01:13Z
date_published: 2021-10-01T00:00:00Z
date_updated: 2024-03-07T14:51:11Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/s00454-020-00240-w
ec_funded: 1
external_id:
arxiv:
- '1908.00856'
isi:
- '000564488500002'
intvolume: ' 66'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1908.00856
month: '10'
oa: 1
oa_version: Preprint
page: 938-976
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
publication: Discrete and Computational Geometry
publication_identifier:
eissn:
- 1432-0444
issn:
- 0179-5376
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 66
year: '2021'
...
---
_id: '7939'
abstract:
- lang: eng
text: "We design fast deterministic algorithms for distance computation in the Congested
Clique model. Our key contributions include:\r\n A (2+ϵ)-approximation for
all-pairs shortest paths in O(log2n/ϵ) rounds on unweighted undirected graphs.
With a small additional additive factor, this also applies for weighted graphs.
This is the first sub-polynomial constant-factor approximation for APSP in this
model.\r\n A (1+ϵ)-approximation for multi-source shortest paths from O(n−−√)
sources in O(log2n/ϵ) rounds on weighted undirected graphs. This is the first
sub-polynomial algorithm obtaining this approximation for a set of sources of
polynomial size.\r\n\r\nOur main techniques are new distance tools that are obtained
via improved algorithms for sparse matrix multiplication, which we leverage to
construct efficient hopsets and shortest paths. Furthermore, our techniques extend
to additional distance problems for which we improve upon the state-of-the-art,
including diameter approximation, and an exact single-source shortest paths algorithm
for weighted undirected graphs in O~(n1/6) rounds. "
acknowledgement: Open access funding provided by Institute of Science and Technology
(IST Austria). We thank Mohsen Ghaffari, Michael Elkin and Merav Parter for fruitful
discussions. This project has received funding from the European Union’s Horizon
2020 Research And Innovation Program under Grant Agreement No. 755839.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Keren
full_name: Censor-Hillel, Keren
last_name: Censor-Hillel
- first_name: Michal
full_name: Dory, Michal
last_name: Dory
- first_name: Janne
full_name: Korhonen, Janne
id: C5402D42-15BC-11E9-A202-CA2BE6697425
last_name: Korhonen
- first_name: Dean
full_name: Leitersdorf, Dean
last_name: Leitersdorf
citation:
ama: Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. Fast approximate shortest
paths in the congested clique. Distributed Computing. 2021;34:463-487.
doi:10.1007/s00446-020-00380-5
apa: Censor-Hillel, K., Dory, M., Korhonen, J., & Leitersdorf, D. (2021). Fast
approximate shortest paths in the congested clique. Distributed Computing.
Springer Nature. https://doi.org/10.1007/s00446-020-00380-5
chicago: Censor-Hillel, Keren, Michal Dory, Janne Korhonen, and Dean Leitersdorf.
“Fast Approximate Shortest Paths in the Congested Clique.” Distributed Computing.
Springer Nature, 2021. https://doi.org/10.1007/s00446-020-00380-5.
ieee: K. Censor-Hillel, M. Dory, J. Korhonen, and D. Leitersdorf, “Fast approximate
shortest paths in the congested clique,” Distributed Computing, vol. 34.
Springer Nature, pp. 463–487, 2021.
ista: Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. 2021. Fast approximate
shortest paths in the congested clique. Distributed Computing. 34, 463–487.
mla: Censor-Hillel, Keren, et al. “Fast Approximate Shortest Paths in the Congested
Clique.” Distributed Computing, vol. 34, Springer Nature, 2021, pp. 463–87,
doi:10.1007/s00446-020-00380-5.
short: K. Censor-Hillel, M. Dory, J. Korhonen, D. Leitersdorf, Distributed Computing
34 (2021) 463–487.
date_created: 2020-06-07T22:00:54Z
date_published: 2021-12-01T00:00:00Z
date_updated: 2024-03-07T14:43:39Z
day: '01'
department:
- _id: DaAl
doi: 10.1007/s00446-020-00380-5
external_id:
arxiv:
- '1903.05956'
isi:
- '000556444600001'
intvolume: ' 34'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s00446-020-00380-5
month: '12'
oa: 1
oa_version: Published Version
page: 463-487
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Distributed Computing
publication_identifier:
eissn:
- 1432-0452
issn:
- 0178-2770
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '6933'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Fast approximate shortest paths in the congested clique
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2021'
...
---
_id: '8248'
abstract:
- lang: eng
text: 'We consider the following setting: suppose that we are given a manifold M
in Rd with positive reach. Moreover assume that we have an embedded simplical
complex A without boundary, whose vertex set lies on the manifold, is sufficiently
dense and such that all simplices in A have sufficient quality. We prove that
if, locally, interiors of the projection of the simplices onto the tangent space
do not intersect, then A is a triangulation of the manifold, that is, they are
homeomorphic.'
acknowledgement: "Open access funding provided by the Institute of Science and Technology
(IST Austria). Arijit Ghosh is supported by the Ramanujan Fellowship (No. SB/S2/RJN-064/2015),
India.\r\nThis work has been funded by the European Research Council under the European
Union’s ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometric
Understanding in Higher Dimensions). The third author is supported by Ramanujan
Fellowship (No. SB/S2/RJN-064/2015), India. The fifth author also received funding
from the European Union’s Horizon 2020 research and innovation programme under the
Marie Skłodowska-Curie Grant Agreement No. 754411."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Jean-Daniel
full_name: Boissonnat, Jean-Daniel
last_name: Boissonnat
- first_name: Ramsay
full_name: Dyer, Ramsay
last_name: Dyer
- first_name: Arijit
full_name: Ghosh, Arijit
last_name: Ghosh
- first_name: Andre
full_name: Lieutier, Andre
last_name: Lieutier
- first_name: Mathijs
full_name: Wintraecken, Mathijs
id: 307CFBC8-F248-11E8-B48F-1D18A9856A87
last_name: Wintraecken
orcid: 0000-0002-7472-2220
citation:
ama: Boissonnat J-D, Dyer R, Ghosh A, Lieutier A, Wintraecken M. Local conditions
for triangulating submanifolds of Euclidean space. Discrete and Computational
Geometry. 2021;66:666-686. doi:10.1007/s00454-020-00233-9
apa: Boissonnat, J.-D., Dyer, R., Ghosh, A., Lieutier, A., & Wintraecken, M.
(2021). Local conditions for triangulating submanifolds of Euclidean space. Discrete
and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-020-00233-9
chicago: Boissonnat, Jean-Daniel, Ramsay Dyer, Arijit Ghosh, Andre Lieutier, and
Mathijs Wintraecken. “Local Conditions for Triangulating Submanifolds of Euclidean
Space.” Discrete and Computational Geometry. Springer Nature, 2021. https://doi.org/10.1007/s00454-020-00233-9.
ieee: J.-D. Boissonnat, R. Dyer, A. Ghosh, A. Lieutier, and M. Wintraecken, “Local
conditions for triangulating submanifolds of Euclidean space,” Discrete and
Computational Geometry, vol. 66. Springer Nature, pp. 666–686, 2021.
ista: Boissonnat J-D, Dyer R, Ghosh A, Lieutier A, Wintraecken M. 2021. Local conditions
for triangulating submanifolds of Euclidean space. Discrete and Computational
Geometry. 66, 666–686.
mla: Boissonnat, Jean-Daniel, et al. “Local Conditions for Triangulating Submanifolds
of Euclidean Space.” Discrete and Computational Geometry, vol. 66, Springer
Nature, 2021, pp. 666–86, doi:10.1007/s00454-020-00233-9.
short: J.-D. Boissonnat, R. Dyer, A. Ghosh, A. Lieutier, M. Wintraecken, Discrete
and Computational Geometry 66 (2021) 666–686.
date_created: 2020-08-11T07:11:51Z
date_published: 2021-09-01T00:00:00Z
date_updated: 2024-03-07T14:54:59Z
day: '01'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1007/s00454-020-00233-9
ec_funded: 1
external_id:
isi:
- '000558119300001'
has_accepted_license: '1'
intvolume: ' 66'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/s00454-020-00233-9
month: '09'
oa: 1
oa_version: Published Version
page: 666-686
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Discrete and Computational Geometry
publication_identifier:
eissn:
- 1432-0444
issn:
- 0179-5376
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Local conditions for triangulating submanifolds of Euclidean space
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 66
year: '2021'
...
---
_id: '9002'
abstract:
- lang: eng
text: ' We prove that, for the binary erasure channel (BEC), the polar-coding paradigm
gives rise to codes that not only approach the Shannon limit but do so under the
best possible scaling of their block length as a function of the gap to capacity.
This result exhibits the first known family of binary codes that attain both optimal
scaling and quasi-linear complexity of encoding and decoding. Our proof is based
on the construction and analysis of binary polar codes with large kernels. When
communicating reliably at rates within ε>0 of capacity, the code length n often
scales as O(1/εμ), where the constant μ is called the scaling exponent. It is
known that the optimal scaling exponent is μ=2, and it is achieved by random linear
codes. The scaling exponent of conventional polar codes (based on the 2×2 kernel)
on the BEC is μ=3.63. This falls far short of the optimal scaling guaranteed by
random codes. Our main contribution is a rigorous proof of the following result:
for the BEC, there exist ℓ×ℓ binary kernels, such that polar codes constructed
from these kernels achieve scaling exponent μ(ℓ) that tends to the optimal value
of 2 as ℓ grows. We furthermore characterize precisely how large ℓ needs to be
as a function of the gap between μ(ℓ) and 2. The resulting binary codes maintain
the recursive structure of conventional polar codes, and thereby achieve construction
complexity O(n) and encoding/decoding complexity O(nlogn).'
article_processing_charge: No
article_type: original
author:
- first_name: Arman
full_name: Fazeli, Arman
last_name: Fazeli
- first_name: Hamed
full_name: Hassani, Hamed
last_name: Hassani
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Alexander
full_name: Vardy, Alexander
last_name: Vardy
citation:
ama: 'Fazeli A, Hassani H, Mondelli M, Vardy A. Binary linear codes with optimal
scaling: Polar codes with large kernels. IEEE Transactions on Information Theory.
2021;67(9):5693-5710. doi:10.1109/TIT.2020.3038806'
apa: 'Fazeli, A., Hassani, H., Mondelli, M., & Vardy, A. (2021). Binary linear
codes with optimal scaling: Polar codes with large kernels. IEEE Transactions
on Information Theory. IEEE. https://doi.org/10.1109/TIT.2020.3038806'
chicago: 'Fazeli, Arman, Hamed Hassani, Marco Mondelli, and Alexander Vardy. “Binary
Linear Codes with Optimal Scaling: Polar Codes with Large Kernels.” IEEE Transactions
on Information Theory. IEEE, 2021. https://doi.org/10.1109/TIT.2020.3038806.'
ieee: 'A. Fazeli, H. Hassani, M. Mondelli, and A. Vardy, “Binary linear codes with
optimal scaling: Polar codes with large kernels,” IEEE Transactions on Information
Theory, vol. 67, no. 9. IEEE, pp. 5693–5710, 2021.'
ista: 'Fazeli A, Hassani H, Mondelli M, Vardy A. 2021. Binary linear codes with
optimal scaling: Polar codes with large kernels. IEEE Transactions on Information
Theory. 67(9), 5693–5710.'
mla: 'Fazeli, Arman, et al. “Binary Linear Codes with Optimal Scaling: Polar Codes
with Large Kernels.” IEEE Transactions on Information Theory, vol. 67,
no. 9, IEEE, 2021, pp. 5693–710, doi:10.1109/TIT.2020.3038806.'
short: A. Fazeli, H. Hassani, M. Mondelli, A. Vardy, IEEE Transactions on Information
Theory 67 (2021) 5693–5710.
date_created: 2021-01-10T23:01:18Z
date_published: 2021-09-01T00:00:00Z
date_updated: 2024-03-07T12:18:50Z
day: '01'
department:
- _id: MaMo
doi: 10.1109/TIT.2020.3038806
external_id:
arxiv:
- '1711.01339'
intvolume: ' 67'
issue: '9'
language:
- iso: eng
month: '09'
oa_version: Preprint
page: 5693-5710
publication: IEEE Transactions on Information Theory
publication_identifier:
eissn:
- 1557-9654
issn:
- 0018-9448
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '6665'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: 'Binary linear codes with optimal scaling: Polar codes with large kernels'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 67
year: '2021'
...
---
_id: '7883'
abstract:
- lang: eng
text: All vertebrates have a spinal cord with dimensions and shape specific to their
species. Yet how species‐specific organ size and shape are achieved is a fundamental
unresolved question in biology. The formation and sculpting of organs begins during
embryonic development. As it develops, the spinal cord extends in anterior–posterior
direction in synchrony with the overall growth of the body. The dorsoventral (DV)
and apicobasal lengths of the spinal cord neuroepithelium also change, while at
the same time a characteristic pattern of neural progenitor subtypes along the
DV axis is established and elaborated. At the basis of these changes in tissue
size and shape are biophysical determinants, such as the change in cell number,
cell size and shape, and anisotropic tissue growth. These processes are controlled
by global tissue‐scale regulators, such as morphogen signaling gradients as well
as mechanical forces. Current challenges in the field are to uncover how these
tissue‐scale regulatory mechanisms are translated to the cellular and molecular
level, and how regulation of distinct cellular processes gives rise to an overall
defined size. Addressing these questions will help not only to achieve a better
understanding of how size is controlled, but also of how tissue size is coordinated
with the specification of pattern.
acknowledgement: 'Austrian Academy of Sciences, Grant/Award Number: DOC fellowship
for Katarzyna Kuzmicz-Kowalska; Austrian Science Fund, Grant/Award Number: F78 (Stem
Cell Modulation); H2020 European Research Council, Grant/Award Number: 680037'
article_number: e383
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Katarzyna
full_name: Kuzmicz-Kowalska, Katarzyna
id: 4CED352A-F248-11E8-B48F-1D18A9856A87
last_name: Kuzmicz-Kowalska
- first_name: Anna
full_name: Kicheva, Anna
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
citation:
ama: 'Kuzmicz-Kowalska K, Kicheva A. Regulation of size and scale in vertebrate
spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology.
2021. doi:10.1002/wdev.383'
apa: 'Kuzmicz-Kowalska, K., & Kicheva, A. (2021). Regulation of size and scale
in vertebrate spinal cord development. Wiley Interdisciplinary Reviews: Developmental
Biology. Wiley. https://doi.org/10.1002/wdev.383'
chicago: 'Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and
Scale in Vertebrate Spinal Cord Development.” Wiley Interdisciplinary Reviews:
Developmental Biology. Wiley, 2021. https://doi.org/10.1002/wdev.383.'
ieee: 'K. Kuzmicz-Kowalska and A. Kicheva, “Regulation of size and scale in vertebrate
spinal cord development,” Wiley Interdisciplinary Reviews: Developmental Biology.
Wiley, 2021.'
ista: 'Kuzmicz-Kowalska K, Kicheva A. 2021. Regulation of size and scale in vertebrate
spinal cord development. Wiley Interdisciplinary Reviews: Developmental Biology.,
e383.'
mla: 'Kuzmicz-Kowalska, Katarzyna, and Anna Kicheva. “Regulation of Size and Scale
in Vertebrate Spinal Cord Development.” Wiley Interdisciplinary Reviews: Developmental
Biology, e383, Wiley, 2021, doi:10.1002/wdev.383.'
short: 'K. Kuzmicz-Kowalska, A. Kicheva, Wiley Interdisciplinary Reviews: Developmental
Biology (2021).'
date_created: 2020-05-24T22:01:00Z
date_published: 2021-04-15T00:00:00Z
date_updated: 2024-03-07T15:03:00Z
day: '15'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.1002/wdev.383
ec_funded: 1
external_id:
isi:
- '000531419400001'
pmid:
- '32391980'
file:
- access_level: open_access
checksum: f0a7745d48afa09ea7025e876a0145a8
content_type: application/pdf
creator: dernst
date_created: 2020-11-24T13:11:39Z
date_updated: 2020-11-24T13:11:39Z
file_id: '8800'
file_name: 2020_WIREs_DevBio_KuzmiczKowalska.pdf
file_size: 2527276
relation: main_file
success: 1
file_date_updated: 2020-11-24T13:11:39Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: B6FC0238-B512-11E9-945C-1524E6697425
call_identifier: H2020
grant_number: '680037'
name: Coordination of Patterning And Growth In the Spinal Cord
- _id: 267AF0E4-B435-11E9-9278-68D0E5697425
name: The role of morphogens in the regulation of neural tube growth
- _id: 059DF620-7A3F-11EA-A408-12923DDC885E
grant_number: F07802
name: Morphogen control of growth and pattern in the spinal cord
publication: 'Wiley Interdisciplinary Reviews: Developmental Biology'
publication_identifier:
eissn:
- '17597692'
issn:
- '17597684'
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '14323'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Regulation of size and scale in vertebrate spinal cord development
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '7905'
abstract:
- lang: eng
text: We investigate a sheaf-theoretic interpretation of stratification learning
from geometric and topological perspectives. Our main result is the construction
of stratification learning algorithms framed in terms of a sheaf on a partially
ordered set with the Alexandroff topology. We prove that the resulting decomposition
is the unique minimal stratification for which the strata are homogeneous and
the given sheaf is constructible. In particular, when we choose to work with the
local homology sheaf, our algorithm gives an alternative to the local homology
transfer algorithm given in Bendich et al. (Proceedings of the 23rd Annual ACM-SIAM
Symposium on Discrete Algorithms, pp. 1355–1370, ACM, New York, 2012), and the
cohomology stratification algorithm given in Nanda (Found. Comput. Math. 20(2),
195–222, 2020). Additionally, we give examples of stratifications based on the
geometric techniques of Breiding et al. (Rev. Mat. Complut. 31(3), 545–593, 2018),
illustrating how the sheaf-theoretic approach can be used to study stratifications
from both topological and geometric perspectives. This approach also points toward
future applications of sheaf theory in the study of topological data analysis
by illustrating the utility of the language of sheaf theory in generalizing existing
algorithms.
acknowledgement: Open access funding provided by Institute of Science and Technology
(IST Austria). This work was partially supported by NSF IIS-1513616 and NSF ABI-1661375.
The authors would like to thank the anonymous referees for their insightful comments.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Adam
full_name: Brown, Adam
id: 70B7FDF6-608D-11E9-9333-8535E6697425
last_name: Brown
- first_name: Bei
full_name: Wang, Bei
last_name: Wang
citation:
ama: Brown A, Wang B. Sheaf-theoretic stratification learning from geometric and
topological perspectives. Discrete and Computational Geometry. 2021;65:1166-1198.
doi:10.1007/s00454-020-00206-y
apa: Brown, A., & Wang, B. (2021). Sheaf-theoretic stratification learning from
geometric and topological perspectives. Discrete and Computational Geometry.
Springer Nature. https://doi.org/10.1007/s00454-020-00206-y
chicago: Brown, Adam, and Bei Wang. “Sheaf-Theoretic Stratification Learning from
Geometric and Topological Perspectives.” Discrete and Computational Geometry.
Springer Nature, 2021. https://doi.org/10.1007/s00454-020-00206-y.
ieee: A. Brown and B. Wang, “Sheaf-theoretic stratification learning from geometric
and topological perspectives,” Discrete and Computational Geometry, vol.
65. Springer Nature, pp. 1166–1198, 2021.
ista: Brown A, Wang B. 2021. Sheaf-theoretic stratification learning from geometric
and topological perspectives. Discrete and Computational Geometry. 65, 1166–1198.
mla: Brown, Adam, and Bei Wang. “Sheaf-Theoretic Stratification Learning from Geometric
and Topological Perspectives.” Discrete and Computational Geometry, vol.
65, Springer Nature, 2021, pp. 1166–98, doi:10.1007/s00454-020-00206-y.
short: A. Brown, B. Wang, Discrete and Computational Geometry 65 (2021) 1166–1198.
date_created: 2020-05-30T10:26:04Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2024-03-07T15:01:58Z
day: '01'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1007/s00454-020-00206-y
external_id:
arxiv:
- '1712.07734'
isi:
- '000536324700001'
file:
- access_level: open_access
checksum: 487a84ea5841b75f04f66d7ebd71b67e
content_type: application/pdf
creator: dernst
date_created: 2020-11-25T09:06:41Z
date_updated: 2020-11-25T09:06:41Z
file_id: '8803'
file_name: 2020_DiscreteCompGeometry_Brown.pdf
file_size: 1013730
relation: main_file
success: 1
file_date_updated: 2020-11-25T09:06:41Z
has_accepted_license: '1'
intvolume: ' 65'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1166-1198
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Discrete and Computational Geometry
publication_identifier:
eissn:
- 1432-0444
issn:
- 0179-5376
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sheaf-theoretic stratification learning from geometric and topological perspectives
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 65
year: '2021'
...
---
_id: '8601'
abstract:
- lang: eng
text: We consider large non-Hermitian real or complex random matrices X with independent,
identically distributed centred entries. We prove that their local eigenvalue
statistics near the spectral edge, the unit circle, coincide with those of the
Ginibre ensemble, i.e. when the matrix elements of X are Gaussian. This result
is the non-Hermitian counterpart of the universality of the Tracy–Widom distribution
at the spectral edges of the Wigner ensemble.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Giorgio
full_name: Cipolloni, Giorgio
id: 42198EFA-F248-11E8-B48F-1D18A9856A87
last_name: Cipolloni
orcid: 0000-0002-4901-7992
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: Cipolloni G, Erdös L, Schröder DJ. Edge universality for non-Hermitian random
matrices. Probability Theory and Related Fields. 2021. doi:10.1007/s00440-020-01003-7
apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2021). Edge universality for
non-Hermitian random matrices. Probability Theory and Related Fields. Springer
Nature. https://doi.org/10.1007/s00440-020-01003-7
chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Edge Universality
for Non-Hermitian Random Matrices.” Probability Theory and Related Fields.
Springer Nature, 2021. https://doi.org/10.1007/s00440-020-01003-7.
ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Edge universality for non-Hermitian
random matrices,” Probability Theory and Related Fields. Springer Nature,
2021.
ista: Cipolloni G, Erdös L, Schröder DJ. 2021. Edge universality for non-Hermitian
random matrices. Probability Theory and Related Fields.
mla: Cipolloni, Giorgio, et al. “Edge Universality for Non-Hermitian Random Matrices.”
Probability Theory and Related Fields, Springer Nature, 2021, doi:10.1007/s00440-020-01003-7.
short: G. Cipolloni, L. Erdös, D.J. Schröder, Probability Theory and Related Fields
(2021).
date_created: 2020-10-04T22:01:37Z
date_published: 2021-02-01T00:00:00Z
date_updated: 2024-03-07T15:07:53Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1007/s00440-020-01003-7
ec_funded: 1
external_id:
arxiv:
- '1908.00969'
isi:
- '000572724600002'
file:
- access_level: open_access
checksum: 611ae28d6055e1e298d53a57beb05ef4
content_type: application/pdf
creator: dernst
date_created: 2020-10-05T14:53:40Z
date_updated: 2020-10-05T14:53:40Z
file_id: '8612'
file_name: 2020_ProbTheory_Cipolloni.pdf
file_size: 497032
relation: main_file
success: 1
file_date_updated: 2020-10-05T14:53:40Z
has_accepted_license: '1'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Probability Theory and Related Fields
publication_identifier:
eissn:
- '14322064'
issn:
- '01788051'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Edge universality for non-Hermitian random matrices
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '7925'
abstract:
- lang: eng
text: In this paper, we introduce a relaxed CQ method with alternated inertial step
for solving split feasibility problems. We give convergence of the sequence generated
by our method under some suitable assumptions. Some numerical implementations
from sparse signal and image deblurring are reported to show the efficiency of
our method.
acknowledgement: Open access funding provided by Institute of Science and Technology
(IST Austria). The authors are grateful to the referees for their insightful comments
which have improved the earlier version of the manuscript greatly. The first author
has received funding from the European Research Council (ERC) under the European
Union’s Seventh Framework Program (FP7-2007-2013) (Grant agreement No. 616160).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Yekini
full_name: Shehu, Yekini
id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87
last_name: Shehu
orcid: 0000-0001-9224-7139
- first_name: Aviv
full_name: Gibali, Aviv
last_name: Gibali
citation:
ama: Shehu Y, Gibali A. New inertial relaxed method for solving split feasibilities.
Optimization Letters. 2021;15:2109-2126. doi:10.1007/s11590-020-01603-1
apa: Shehu, Y., & Gibali, A. (2021). New inertial relaxed method for solving
split feasibilities. Optimization Letters. Springer Nature. https://doi.org/10.1007/s11590-020-01603-1
chicago: Shehu, Yekini, and Aviv Gibali. “New Inertial Relaxed Method for Solving
Split Feasibilities.” Optimization Letters. Springer Nature, 2021. https://doi.org/10.1007/s11590-020-01603-1.
ieee: Y. Shehu and A. Gibali, “New inertial relaxed method for solving split feasibilities,”
Optimization Letters, vol. 15. Springer Nature, pp. 2109–2126, 2021.
ista: Shehu Y, Gibali A. 2021. New inertial relaxed method for solving split feasibilities.
Optimization Letters. 15, 2109–2126.
mla: Shehu, Yekini, and Aviv Gibali. “New Inertial Relaxed Method for Solving Split
Feasibilities.” Optimization Letters, vol. 15, Springer Nature, 2021, pp.
2109–26, doi:10.1007/s11590-020-01603-1.
short: Y. Shehu, A. Gibali, Optimization Letters 15 (2021) 2109–2126.
date_created: 2020-06-04T11:28:33Z
date_published: 2021-09-01T00:00:00Z
date_updated: 2024-03-07T15:00:43Z
day: '01'
ddc:
- '510'
department:
- _id: VlKo
doi: 10.1007/s11590-020-01603-1
ec_funded: 1
external_id:
isi:
- '000537342300001'
file:
- access_level: open_access
checksum: 63c5f31cd04626152a19f97a2476281b
content_type: application/pdf
creator: kschuh
date_created: 2024-03-07T14:58:51Z
date_updated: 2024-03-07T14:58:51Z
file_id: '15089'
file_name: 2021_OptimizationLetters_Shehu.pdf
file_size: 2148882
relation: main_file
success: 1
file_date_updated: 2024-03-07T14:58:51Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 2109-2126
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Optimization Letters
publication_identifier:
eissn:
- 1862-4480
issn:
- 1862-4472
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: New inertial relaxed method for solving split feasibilities
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2021'
...
---
_id: '9438'
abstract:
- lang: eng
text: Rigorous investigation of synaptic transmission requires analysis of unitary
synaptic events by simultaneous recording from presynaptic terminals and postsynaptic
target neurons. However, this has been achieved at only a limited number of model
synapses, including the squid giant synapse and the mammalian calyx of Held. Cortical
presynaptic terminals have been largely inaccessible to direct presynaptic recording,
due to their small size. Here, we describe a protocol for improved subcellular
patch-clamp recording in rat and mouse brain slices, with the synapse in a largely
intact environment. Slice preparation takes ~2 h, recording ~3 h and post hoc
morphological analysis 2 d. Single presynaptic hippocampal mossy fiber terminals
are stimulated minimally invasively in the bouton-attached configuration, in which
the cytoplasmic content remains unperturbed, or in the whole-bouton configuration,
in which the cytoplasmic composition can be precisely controlled. Paired pre–postsynaptic
recordings can be integrated with biocytin labeling and morphological analysis,
allowing correlative investigation of synapse structure and function. Paired recordings
can be obtained from mossy fiber terminals in slices from both rats and mice,
implying applicability to genetically modified synapses. Paired recordings can
also be performed together with axon tract stimulation or optogenetic activation,
allowing comparison of unitary and compound synaptic events in the same target
cell. Finally, paired recordings can be combined with spontaneous event analysis,
permitting collection of miniature events generated at a single identified synapse.
In conclusion, the subcellular patch-clamp techniques detailed here should facilitate
analysis of biophysics, plasticity and circuit function of cortical synapses in
the mammalian central nervous system.
acknowledged_ssus:
- _id: M-Shop
acknowledgement: This project received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement no. 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen
Forschung (Z 312-B27, Wittgenstein award to P.J., V 739-B27 to C.B.M.). We are grateful
to F. Marr and C. Altmutter for excellent technical assistance and cell reconstruction,
E. Kralli-Beller for manuscript editing, and the Scientific Service Units of IST
Austria, especially T. Asenov and Miba machine shop, for maximally efficient support.
article_processing_charge: No
article_type: original
author:
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: Yuji
full_name: Okamoto, Yuji
id: 3337E116-F248-11E8-B48F-1D18A9856A87
last_name: Okamoto
orcid: 0000-0003-0408-6094
- first_name: Carolina
full_name: Borges Merjane, Carolina
id: 4305C450-F248-11E8-B48F-1D18A9856A87
last_name: Borges Merjane
orcid: 0000-0003-0005-401X
- first_name: Victor M
full_name: Vargas Barroso, Victor M
id: 2F55A9DE-F248-11E8-B48F-1D18A9856A87
last_name: Vargas Barroso
- first_name: Benjamin
full_name: Suter, Benjamin
id: 4952F31E-F248-11E8-B48F-1D18A9856A87
last_name: Suter
orcid: 0000-0002-9885-6936
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas
PM. Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous
pre- and postsynaptic recording at cortical synapses. Nature Protocols.
2021;16(6):2947–2967. doi:10.1038/s41596-021-00526-0
apa: Vandael, D. H., Okamoto, Y., Borges Merjane, C., Vargas Barroso, V. M., Suter,
B., & Jonas, P. M. (2021). Subcellular patch-clamp techniques for single-bouton
stimulation and simultaneous pre- and postsynaptic recording at cortical synapses.
Nature Protocols. Springer Nature. https://doi.org/10.1038/s41596-021-00526-0
chicago: Vandael, David H, Yuji Okamoto, Carolina Borges Merjane, Victor M Vargas
Barroso, Benjamin Suter, and Peter M Jonas. “Subcellular Patch-Clamp Techniques
for Single-Bouton Stimulation and Simultaneous Pre- and Postsynaptic Recording
at Cortical Synapses.” Nature Protocols. Springer Nature, 2021. https://doi.org/10.1038/s41596-021-00526-0.
ieee: D. H. Vandael, Y. Okamoto, C. Borges Merjane, V. M. Vargas Barroso, B. Suter,
and P. M. Jonas, “Subcellular patch-clamp techniques for single-bouton stimulation
and simultaneous pre- and postsynaptic recording at cortical synapses,” Nature
Protocols, vol. 16, no. 6. Springer Nature, pp. 2947–2967, 2021.
ista: Vandael DH, Okamoto Y, Borges Merjane C, Vargas Barroso VM, Suter B, Jonas
PM. 2021. Subcellular patch-clamp techniques for single-bouton stimulation and
simultaneous pre- and postsynaptic recording at cortical synapses. Nature Protocols.
16(6), 2947–2967.
mla: Vandael, David H., et al. “Subcellular Patch-Clamp Techniques for Single-Bouton
Stimulation and Simultaneous Pre- and Postsynaptic Recording at Cortical Synapses.”
Nature Protocols, vol. 16, no. 6, Springer Nature, 2021, pp. 2947–2967,
doi:10.1038/s41596-021-00526-0.
short: D.H. Vandael, Y. Okamoto, C. Borges Merjane, V.M. Vargas Barroso, B. Suter,
P.M. Jonas, Nature Protocols 16 (2021) 2947–2967.
date_created: 2021-05-30T22:01:24Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-08-10T22:30:51Z
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ddc:
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department:
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ec_funded: 1
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---
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abstract:
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text: "Blood – this is what animals use to heal wounds fast and efficient. Plants
do not have blood circulation and their cells cannot move. However, plants have
evolved remarkable capacities to regenerate tissues and organs preventing further
damage. In my PhD research, I studied the wound healing in the Arabidopsis root.
I used a UV laser to ablate single cells in the root tip and observed the consequent
wound healing. Interestingly, the inner adjacent cells induced a\r\ndivision plane
switch and subsequently adopted the cell type of the killed cell to replace it.
We termed this form of wound healing “restorative divisions”. This initial observation
triggered the questions of my PhD studies: How and why do cells orient their division
planes, how do they feel the wound and why does this happen only in inner adjacent
cells.\r\nFor answering these questions, I used a quite simple experimental setup:
5 day - old seedlings were stained with propidium iodide to visualize cell walls
and dead cells; ablation was carried out using a special laser cutter and a confocal
microscope. Adaptation of the novel vertical microscope system made it possible
to observe wounds in real time. This revealed that restorative divisions occur
at increased frequency compared to normal divisions. Additionally,\r\nthe major
plant hormone auxin accumulates in wound adjacent cells and drives the expression
of the wound-stress responsive transcription factor ERF115. Using this as a marker
gene for wound responses, we found that an important part of wound signalling
is the sensing of the collapse of the ablated cell. The collapse causes a radical
pressure drop, which results in strong tissue deformations. These deformations
manifest in an invasion of the now free spot specifically by the inner adjacent
cells within seconds, probably because of higher pressure of the inner tissues.
Long-term imaging revealed that those deformed cells continuously expand towards
the wound hole and that this is crucial for the restorative division. These wound-expanding
cells exhibit an abnormal, biphasic polarity of microtubule arrays\r\nbefore the
division. Experiments inhibiting cell expansion suggest that it is the biphasic
stretching that induces those MT arrays. Adapting the micromanipulator aspiration
system from animal scientists at our institute confirmed the hypothesis that stretching
influences microtubule stability. In conclusion, this shows that microtubules
react to tissue deformation\r\nand this facilitates the observed division plane
switch. This puts mechanical cues and tensions at the most prominent position
for explaining the growth and wound healing properties of plants. Hence, it shines
light onto the importance of understanding mechanical signal transduction. "
acknowledged_ssus:
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alternative_title:
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id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
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citation:
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apa: Hörmayer, L. (2021). Wound healing in the Arabidopsis root meristem.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9992
chicago: Hörmayer, Lukas. “Wound Healing in the Arabidopsis Root Meristem.” Institute
of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9992.
ieee: L. Hörmayer, “Wound healing in the Arabidopsis root meristem,” Institute of
Science and Technology Austria, 2021.
ista: Hörmayer L. 2021. Wound healing in the Arabidopsis root meristem. Institute
of Science and Technology Austria.
mla: Hörmayer, Lukas. Wound Healing in the Arabidopsis Root Meristem. Institute
of Science and Technology Austria, 2021, doi:10.15479/at:ista:9992.
short: L. Hörmayer, Wound Healing in the Arabidopsis Root Meristem, Institute of
Science and Technology Austria, 2021.
date_created: 2021-09-09T07:37:20Z
date_published: 2021-09-13T00:00:00Z
date_updated: 2023-09-07T13:38:33Z
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full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: Wound healing in the Arabidopsis root meristem
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...
---
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abstract:
- lang: eng
text: Pattern separation is a fundamental brain computation that converts small
differences in input patterns into large differences in output patterns. Several
synaptic mechanisms of pattern separation have been proposed, including code expansion,
inhibition and plasticity; however, which of these mechanisms play a role in the
entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation
circuit, remains unclear. Here we show that a biologically realistic, full-scale
EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive
inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator.
Both external gamma-modulated inhibition and internal lateral inhibition mediated
by PV+-INs substantially contributed to pattern separation. Both local connectivity
and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness.
Similarly, mossy fiber synapses with conditional detonator properties contributed
to pattern separation. By contrast, perforant path synapses with Hebbian synaptic
plasticity and direct EC–CA3 connection shifted the network towards pattern completion.
Our results demonstrate that the specific properties of cells and synapses optimize
higher-order computations in biological networks and might be useful to improve
the deep learning capabilities of technical networks.
acknowledged_ssus:
- _id: SSU
acknowledgement: We thank A. Aertsen, N. Kopell, W. Maass, A. Roth, F. Stella and
T. Vogels for critically reading earlier versions of the manuscript. We are grateful
to F. Marr and C. Altmutter for excellent technical assistance, E. Kralli-Beller
for manuscript editing, and the Scientific Service Units of IST Austria for efficient
support. Finally, we thank T. Carnevale, L. Erdös, M. Hines, D. Nykamp and D. Schröder
for useful discussions, and R. Friedrich and S. Wiechert for sharing unpublished
data. This project received funding from the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation programme (grant agreement
no. 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z
312-B27, Wittgenstein award to P.J. and P 31815 to S.J.G.).
article_processing_charge: No
article_type: original
author:
- first_name: José
full_name: Guzmán, José
id: 30CC5506-F248-11E8-B48F-1D18A9856A87
last_name: Guzmán
orcid: 0000-0003-2209-5242
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: 'Claudia '
full_name: 'Espinoza Martinez, Claudia '
id: 31FFEE2E-F248-11E8-B48F-1D18A9856A87
last_name: Espinoza Martinez
orcid: 0000-0003-4710-2082
- first_name: Xiaomin
full_name: Zhang, Xiaomin
id: 423EC9C2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
- first_name: Benjamin
full_name: Suter, Benjamin
id: 4952F31E-F248-11E8-B48F-1D18A9856A87
last_name: Suter
orcid: 0000-0002-9885-6936
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity
rules and synaptic properties shape the efficacy of pattern separation in the
entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science.
2021;1(12):830-842. doi:10.1038/s43588-021-00157-1
apa: Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., &
Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the
efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network.
Nature Computational Science. Springer Nature. https://doi.org/10.1038/s43588-021-00157-1
chicago: Guzmán, José, Alois Schlögl, Claudia Espinoza Martinez, Xiaomin Zhang,
Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties
Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3
Network.” Nature Computational Science. Springer Nature, 2021. https://doi.org/10.1038/s43588-021-00157-1.
ieee: J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M.
Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern
separation in the entorhinal cortex–dentate gyrus–CA3 network,” Nature Computational
Science, vol. 1, no. 12. Springer Nature, pp. 830–842, 2021.
ista: Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021.
How connectivity rules and synaptic properties shape the efficacy of pattern separation
in the entorhinal cortex–dentate gyrus–CA3 network. Nature Computational Science.
1(12), 830–842.
mla: Guzmán, José, et al. “How Connectivity Rules and Synaptic Properties Shape
the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3
Network.” Nature Computational Science, vol. 1, no. 12, Springer Nature,
2021, pp. 830–42, doi:10.1038/s43588-021-00157-1.
short: J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas,
Nature Computational Science 1 (2021) 830–842.
date_created: 2022-03-04T08:32:36Z
date_published: 2021-12-16T00:00:00Z
date_updated: 2023-08-10T22:30:10Z
day: '16'
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doi: 10.1038/s43588-021-00157-1
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title: How connectivity rules and synaptic properties shape the efficacy of pattern
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...
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_id: '10110'
abstract:
- lang: eng
text: Pattern separation is a fundamental brain computation that converts small
differences in input patterns into large differences in output patterns. Several
synaptic mechanisms of pattern separation have been proposed, including code expansion,
inhibition and plasticity; however, which of these mechanisms play a role in the
entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation
circuit, remains unclear. Here we show that a biologically realistic, full-scale
EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive
inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator.
Both external gamma-modulated inhibition and internal lateral inhibition mediated
by PV+-INs substantially contributed to pattern separation. Both local connectivity
and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness.
Similarly, mossy fiber synapses with conditional detonator properties contributed
to pattern separation. By contrast, perforant path synapses with Hebbian synaptic
plasticity and direct EC–CA3 connection shifted the network towards pattern completion.
Our results demonstrate that the specific properties of cells and synapses optimize
higher-order computations in biological networks and might be useful to improve
the deep learning capabilities of technical networks.
author:
- first_name: José
full_name: Guzmán, José
id: 30CC5506-F248-11E8-B48F-1D18A9856A87
last_name: Guzmán
orcid: 0000-0003-2209-5242
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: 'Claudia '
full_name: 'Espinoza Martinez, Claudia '
id: 31FFEE2E-F248-11E8-B48F-1D18A9856A87
last_name: Espinoza Martinez
orcid: 0000-0003-4710-2082
- first_name: Xiaomin
full_name: Zhang, Xiaomin
id: 423EC9C2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
- first_name: Benjamin
full_name: Suter, Benjamin
id: 4952F31E-F248-11E8-B48F-1D18A9856A87
last_name: Suter
orcid: 0000-0002-9885-6936
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity
rules and synaptic properties shape the efficacy of pattern separation in the
entorhinal cortex–dentate gyrus–CA3 network. 2021. doi:10.15479/AT:ISTA:10110
apa: Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., &
Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the
efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network.
IST Austria. https://doi.org/10.15479/AT:ISTA:10110
chicago: Guzmán, José, Alois Schlögl, Claudia Espinoza Martinez, Xiaomin Zhang,
Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties
Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3
Network.” IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:10110.
ieee: J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M.
Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern
separation in the entorhinal cortex–dentate gyrus–CA3 network.” IST Austria, 2021.
ista: Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021.
How connectivity rules and synaptic properties shape the efficacy of pattern separation
in the entorhinal cortex–dentate gyrus–CA3 network, IST Austria, 10.15479/AT:ISTA:10110.
mla: Guzmán, José, et al. How Connectivity Rules and Synaptic Properties Shape
the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3
Network. IST Austria, 2021, doi:10.15479/AT:ISTA:10110.
short: J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas,
(2021).
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---
_id: '10077'
abstract:
- lang: eng
text: Although much is known about how single neurons in the hippocampus represent
an animal’s position, how cell-cell interactions contribute to spatial coding
remains poorly understood. Using a novel statistical estimator and theoretical
modeling, both developed in the framework of maximum entropy models, we reveal
highly structured cell-to-cell interactions whose statistics depend on familiar
vs. novel environment. In both conditions the circuit interactions optimize the
encoding of spatial information, but for regimes that differ in the signal-to-noise
ratio of their spatial inputs. Moreover, the topology of the interactions facilitates
linear decodability, making the information easy to read out by downstream circuits.
These findings suggest that the efficient coding hypothesis is not applicable
only to individual neuron properties in the sensory periphery, but also to neural
interactions in the central brain.
acknowledgement: We thank Peter Baracskay, Karola Kaefer and Hugo Malagon-Vina for
the acquisition of the data. We thank Federico Stella for comments on an earlier
version of the manuscript. MN was supported by European Union Horizon 2020 grant
665385, JC was supported by European Research Council consolidator grant 281511,
GT was supported by the Austrian Science Fund (FWF) grant P34015, CS was supported
by an IST fellow grant, National Institute of Mental Health Award 1R01MH125571-01,
by the National Science Foundation under NSF Award No. 1922658 and a Google faculty
award.
article_processing_charge: No
author:
- first_name: Michele
full_name: Nardin, Michele
id: 30BD0376-F248-11E8-B48F-1D18A9856A87
last_name: Nardin
orcid: 0000-0001-8849-6570
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Cristina
full_name: Savin, Cristina
id: 3933349E-F248-11E8-B48F-1D18A9856A87
last_name: Savin
citation:
ama: Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1
interactions optimizes spatial coding across experience. bioRxiv. doi:10.1101/2021.09.28.460602
apa: Nardin, M., Csicsvari, J. L., Tkačik, G., & Savin, C. (n.d.). The structure
of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv.
Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.09.28.460602
chicago: Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin.
“The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across
Experience.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2021.09.28.460602.
ieee: M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal
CA1 interactions optimizes spatial coding across experience,” bioRxiv.
Cold Spring Harbor Laboratory.
ista: Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1
interactions optimizes spatial coding across experience. bioRxiv, 10.1101/2021.09.28.460602.
mla: Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes
Spatial Coding across Experience.” BioRxiv, Cold Spring Harbor Laboratory,
doi:10.1101/2021.09.28.460602.
short: M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, BioRxiv (n.d.).
date_created: 2021-10-04T06:23:34Z
date_published: 2021-09-29T00:00:00Z
date_updated: 2024-03-28T23:30:16Z
day: '29'
department:
- _id: GradSch
- _id: JoCs
- _id: GaTk
doi: 10.1101/2021.09.28.460602
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2021.09.28.460602
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: 257A4776-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281511'
name: Memory-related information processing in neuronal circuits of the hippocampus
and entorhinal cortex
- _id: 626c45b5-2b32-11ec-9570-e509828c1ba6
grant_number: P34015
name: Efficient coding with biophysical realism
publication: bioRxiv
publication_status: submitted
publisher: Cold Spring Harbor Laboratory
related_material:
record:
- id: '11932'
relation: dissertation_contains
status: public
status: public
title: The structure of hippocampal CA1 interactions optimizes spatial coding across
experience
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: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2021'
...
---
_id: '9250'
abstract:
- lang: eng
text: Aprotic alkali metal–O2 batteries face two major obstacles to their chemistry
occurring efficiently, the insulating nature of the formed alkali superoxides/peroxides
and parasitic reactions that are caused by the highly reactive singlet oxygen
(1O2). Redox mediators are recognized to be key for improving rechargeability.
However, it is unclear how they affect 1O2 formation, which hinders strategies
for their improvement. Here we clarify the mechanism of mediated peroxide and
superoxide oxidation and thus explain how redox mediators either enhance or suppress
1O2 formation. We show that charging commences with peroxide oxidation to a superoxide
intermediate and that redox potentials above ~3.5 V versus Li/Li+ drive 1O2 evolution
from superoxide oxidation, while disproportionation always generates some 1O2.
We find that 1O2 suppression requires oxidation to be faster than the generation
of 1O2 from disproportionation. Oxidation rates decrease with growing driving
force following Marcus inverted-region behaviour, establishing a region of maximum
rate.
acknowledged_ssus:
- _id: M-Shop
acknowledgement: S.A.F. is indebted to the European Research Council (ERC) under the
European Union’s Horizon 2020 research and innovation programme (grant agreement
No. 636069) as well as IST Austria. O.F thanks the French National Research Agency
(STORE-EX Labex Project ANR-10-LABX-76-01). We thank EL-Cell GmbH (Hamburg, Germany)
for the pressure test cell. We thank R. Saf for help with the mass spectrometry,
J. Schlegl for manufacturing instrumentation, M. Winkler of Acib GmbH, G. Strohmeier
and R. Fürst for HPLC measurements and S. Mondal and S. Stadlbauer for kinetic measurements.
article_processing_charge: No
article_type: original
author:
- first_name: Yann K.
full_name: Petit, Yann K.
last_name: Petit
- first_name: Eléonore
full_name: Mourad, Eléonore
last_name: Mourad
- first_name: Christian
full_name: Prehal, Christian
last_name: Prehal
- first_name: Christian
full_name: Leypold, Christian
last_name: Leypold
- first_name: Andreas
full_name: Windischbacher, Andreas
last_name: Windischbacher
- first_name: Daniel
full_name: Mijailovic, Daniel
last_name: Mijailovic
- first_name: Christian
full_name: Slugovc, Christian
last_name: Slugovc
- first_name: Sergey M.
full_name: Borisov, Sergey M.
last_name: Borisov
- first_name: Egbert
full_name: Zojer, Egbert
last_name: Zojer
- first_name: Sergio
full_name: Brutti, Sergio
last_name: Brutti
- first_name: Olivier
full_name: Fontaine, Olivier
last_name: Fontaine
- 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: Petit YK, Mourad E, Prehal C, et al. Mechanism of mediated alkali peroxide
oxidation and triplet versus singlet oxygen formation. Nature Chemistry.
2021;13(5):465-471. doi:10.1038/s41557-021-00643-z
apa: Petit, Y. K., Mourad, E., Prehal, C., Leypold, C., Windischbacher, A., Mijailovic,
D., … Freunberger, S. A. (2021). Mechanism of mediated alkali peroxide oxidation
and triplet versus singlet oxygen formation. Nature Chemistry. Springer
Nature. https://doi.org/10.1038/s41557-021-00643-z
chicago: Petit, Yann K., Eléonore Mourad, Christian Prehal, Christian Leypold, Andreas
Windischbacher, Daniel Mijailovic, Christian Slugovc, et al. “Mechanism of Mediated
Alkali Peroxide Oxidation and Triplet versus Singlet Oxygen Formation.” Nature
Chemistry. Springer Nature, 2021. https://doi.org/10.1038/s41557-021-00643-z.
ieee: Y. K. Petit et al., “Mechanism of mediated alkali peroxide oxidation
and triplet versus singlet oxygen formation,” Nature Chemistry, vol. 13,
no. 5. Springer Nature, pp. 465–471, 2021.
ista: Petit YK, Mourad E, Prehal C, Leypold C, Windischbacher A, Mijailovic D, Slugovc
C, Borisov SM, Zojer E, Brutti S, Fontaine O, Freunberger SA. 2021. Mechanism
of mediated alkali peroxide oxidation and triplet versus singlet oxygen formation.
Nature Chemistry. 13(5), 465–471.
mla: Petit, Yann K., et al. “Mechanism of Mediated Alkali Peroxide Oxidation and
Triplet versus Singlet Oxygen Formation.” Nature Chemistry, vol. 13, no.
5, Springer Nature, 2021, pp. 465–71, doi:10.1038/s41557-021-00643-z.
short: Y.K. Petit, E. Mourad, C. Prehal, C. Leypold, A. Windischbacher, D. Mijailovic,
C. Slugovc, S.M. Borisov, E. Zojer, S. Brutti, O. Fontaine, S.A. Freunberger,
Nature Chemistry 13 (2021) 465–471.
date_created: 2021-03-16T11:12:20Z
date_published: 2021-03-15T00:00:00Z
date_updated: 2023-09-05T15:34:44Z
day: '15'
ddc:
- '540'
department:
- _id: StFr
doi: 10.1038/s41557-021-00643-z
external_id:
isi:
- '000629296400001'
pmid:
- '33723377'
file:
- access_level: open_access
checksum: 3ee3f8dd79ed1b7bb0929fce184c8012
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T11:46:00Z
date_updated: 2021-09-16T22:30:03Z
embargo: 2021-09-15
file_id: '9276'
file_name: 2021_NatureChem_Petit_acceptedVersion.pdf
file_size: 1811448
relation: main_file
file_date_updated: 2021-09-16T22:30:03Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '5'
keyword:
- General Chemistry
- General Chemical Engineering
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 465-471
pmid: 1
publication: Nature Chemistry
publication_identifier:
eissn:
- 1755-4349
issn:
- 1755-4330
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanism of mediated alkali peroxide oxidation and triplet versus singlet
oxygen formation
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 13
year: '2021'
...
---
_id: '9623'
abstract:
- lang: eng
text: "Cytoplasmic reorganizations are essential for morphogenesis. In large cells
like oocytes, these reorganizations become crucial in patterning the oocyte for
later stages of embryonic development. Ascidians oocytes reorganize their cytoplasm
(ooplasm) in a spectacular manner. Ooplasmic reorganization is initiated at fertilization
with the contraction of the actomyosin cortex along the animal-vegetal axis of
the oocyte, driving the accumulation of cortical endoplasmic reticulum (cER),
maternal mRNAs associated to it and a mitochondria-rich subcortical layer – the
myoplasm – in a region of the vegetal pole termed contraction pole (CP). Here
we have used the species Phallusia mammillata to investigate the changes in cell
shape that accompany these reorganizations and the mechanochemical mechanisms
underlining CP formation.\r\nWe report that the length of the animal-vegetal (AV)
axis oscillates upon fertilization: it first undergoes a cycle of fast elongation-lengthening
followed by a slow expansion of mainly the vegetal pole (VP) of the cell. We show
that the fast oscillation corresponds to a dynamic polarization of the actin cortex
as a result of a fertilization-induced increase in cortical tension in the oocyte
that triggers a rupture of the cortex at the animal pole and the establishment
of vegetal-directed cortical flows. These flows are responsible for the vegetal
accumulation of actin causing the VP to flatten. \r\nWe find that the slow expansion
of the VP, leading to CP formation, correlates with a relaxation of the vegetal
cortex and that the myoplasm plays a role in the expansion. We show that the myoplasm
is a solid-like layer that buckles under compression forces arising from the contracting
actin cortex at the VP. Straightening of the myoplasm when actin flows stops,
facilitates the expansion of the VP and the CP. Altogether, our results present
a previously unrecognized role for the myoplasm in ascidian ooplasmic segregation.
\r\n"
acknowledged_ssus:
- _id: Bio
- _id: EM-Fac
- _id: NanoFab
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Silvia
full_name: Caballero Mancebo, Silvia
id: 2F1E1758-F248-11E8-B48F-1D18A9856A87
last_name: Caballero Mancebo
orcid: 0000-0002-5223-3346
citation:
ama: Caballero Mancebo S. Fertilization-induced deformations are controlled by the
actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes. 2021.
doi:10.15479/at:ista:9623
apa: Caballero Mancebo, S. (2021). Fertilization-induced deformations are controlled
by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9623
chicago: Caballero Mancebo, Silvia. “Fertilization-Induced Deformations Are Controlled
by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes.”
Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9623.
ieee: S. Caballero Mancebo, “Fertilization-induced deformations are controlled by
the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes,”
Institute of Science and Technology Austria, 2021.
ista: Caballero Mancebo S. 2021. Fertilization-induced deformations are controlled
by the actin cortex and a mitochondria-rich subcortical layer in ascidian oocytes.
Institute of Science and Technology Austria.
mla: Caballero Mancebo, Silvia. Fertilization-Induced Deformations Are Controlled
by the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes.
Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9623.
short: S. Caballero Mancebo, Fertilization-Induced Deformations Are Controlled by
the Actin Cortex and a Mitochondria-Rich Subcortical Layer in Ascidian Oocytes,
Institute of Science and Technology Austria, 2021.
date_created: 2021-07-01T14:50:17Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-09-07T13:33:27Z
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: CaHe
doi: 10.15479/at:ista:9623
file:
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checksum: e039225a47ef32666d59bf35ddd30ecf
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: scaballe
date_created: 2021-07-01T14:48:54Z
date_updated: 2022-07-02T22:30:06Z
embargo_to: open_access
file_id: '9624'
file_name: PhDThesis_SCM.docx
file_size: 131946790
relation: source_file
- access_level: open_access
checksum: dd4d78962ea94ad95e97ca7d9af08f4b
content_type: application/pdf
creator: scaballe
date_created: 2021-07-01T14:46:25Z
date_updated: 2022-07-02T22:30:06Z
embargo: 2022-07-01
file_id: '9625'
file_name: PhDThesis_SCM.pdf
file_size: 17094958
relation: main_file
file_date_updated: 2022-07-02T22:30:06Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '111'
publication_identifier:
isbn:
- 978-3-99078-012-1
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9750'
relation: part_of_dissertation
status: public
- id: '9006'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
title: Fertilization-induced deformations are controlled by the actin cortex and a
mitochondria-rich subcortical layer in ascidian oocytes
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '9006'
abstract:
- lang: eng
text: Cytoplasm is a gel-like crowded environment composed of various macromolecules,
organelles, cytoskeletal networks, and cytosol. The structure of the cytoplasm
is highly organized and heterogeneous due to the crowding of its constituents
and their effective compartmentalization. In such an environment, the diffusive
dynamics of the molecules are restricted, an effect that is further amplified
by clustering and anchoring of molecules. Despite the crowded nature of the cytoplasm
at the microscopic scale, large-scale reorganization of the cytoplasm is essential
for important cellular functions, such as cell division and polarization. How
such mesoscale reorganization of the cytoplasm is achieved, especially for large
cells such as oocytes or syncytial tissues that can span hundreds of micrometers
in size, is only beginning to be understood. In this review, we will discuss recent
advances in elucidating the molecular, cellular, and biophysical mechanisms by
which the cytoskeleton drives cytoplasmic reorganization across different scales,
structures, and species.
acknowledgement: We would like to thank Justine Renno for illustrations and Edouard
Hannezo and members of the Heisenberg group for their comments on previous versions
of the manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Shayan
full_name: Shamipour, Shayan
id: 40B34FE2-F248-11E8-B48F-1D18A9856A87
last_name: Shamipour
- first_name: Silvia
full_name: Caballero Mancebo, Silvia
id: 2F1E1758-F248-11E8-B48F-1D18A9856A87
last_name: Caballero Mancebo
orcid: 0000-0002-5223-3346
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. Cytoplasm’s got moves. Developmental
Cell. 2021;56(2):P213-226. doi:10.1016/j.devcel.2020.12.002
apa: Shamipour, S., Caballero Mancebo, S., & Heisenberg, C.-P. J. (2021). Cytoplasm’s
got moves. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2020.12.002
chicago: Shamipour, Shayan, Silvia Caballero Mancebo, and Carl-Philipp J Heisenberg.
“Cytoplasm’s Got Moves.” Developmental Cell. Elsevier, 2021. https://doi.org/10.1016/j.devcel.2020.12.002.
ieee: S. Shamipour, S. Caballero Mancebo, and C.-P. J. Heisenberg, “Cytoplasm’s
got moves,” Developmental Cell, vol. 56, no. 2. Elsevier, pp. P213-226,
2021.
ista: Shamipour S, Caballero Mancebo S, Heisenberg C-PJ. 2021. Cytoplasm’s got moves.
Developmental Cell. 56(2), P213-226.
mla: Shamipour, Shayan, et al. “Cytoplasm’s Got Moves.” Developmental Cell,
vol. 56, no. 2, Elsevier, 2021, pp. P213-226, doi:10.1016/j.devcel.2020.12.002.
short: S. Shamipour, S. Caballero Mancebo, C.-P.J. Heisenberg, Developmental Cell
56 (2021) P213-226.
date_created: 2021-01-17T23:01:10Z
date_published: 2021-01-25T00:00:00Z
date_updated: 2024-03-28T23:30:19Z
day: '25'
department:
- _id: CaHe
doi: 10.1016/j.devcel.2020.12.002
external_id:
isi:
- '000613273900009'
pmid:
- '33321104'
intvolume: ' 56'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.devcel.2020.12.002
month: '01'
oa: 1
oa_version: Published Version
page: P213-226
pmid: 1
publication: Developmental Cell
publication_identifier:
eissn:
- '18781551'
issn:
- '15345807'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '9623'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Cytoplasm's got moves
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 56
year: '2021'
...
---
_id: '9429'
abstract:
- lang: eng
text: De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3
lead to autism spectrum disorder (ASD). In mouse, constitutive haploinsufficiency
leads to motor coordination deficits as well as ASD-relevant social and cognitive
impairments. However, induction of Cul3 haploinsufficiency later in life does
not lead to ASD-relevant behaviors, pointing to an important role of Cul3 during
a critical developmental window. Here we show that Cul3 is essential to regulate
neuronal migration and, therefore, constitutive Cul3 heterozygous mutant mice
display cortical lamination abnormalities. At the molecular level, we found that
Cul3 controls neuronal migration by tightly regulating the amount of Plastin3
(Pls3), a previously unrecognized player of neural migration. Furthermore, we
found that Pls3 cell-autonomously regulates cell migration by regulating actin
cytoskeleton organization, and its levels are inversely proportional to neural
migration speed. Finally, we provide evidence that cellular phenotypes associated
with autism-linked gene haploinsufficiency can be rescued by transcriptional activation
of the intact allele in vitro, offering a proof of concept for a potential therapeutic
approach for ASDs.
acknowledged_ssus:
- _id: PreCl
acknowledgement: We thank A. Coll Manzano, F. Freeman, M. Ladron de Guevara, and A.
Ç. Yahya for technical assistance, S. Deixler, A. Lepold, and A. Schlerka for the
management of our animal colony, as well as M. Schunn and the Preclinical Facility
team for technical assistance. We thank K. Heesom and her team at the University
of Bristol Proteomics Facility for the proteomics sample preparation, data generation,
and analysis support. We thank Y. B. Simon for kindly providing the plasmid for
lentiviral labeling. Further, we thank M. Sixt for his advice regarding cell migration
and the fruitful discussions. This work was supported by the ISTPlus postdoctoral
fellowship (Grant Agreement No. 754411) to B.B., by the European Union’s Horizon
2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM), and by
the Austrian Science Fund (FWF) to G.N. (DK W1232-B24 and SFB F7807-B) and to J.G.D
(I3600-B27).
article_number: '3058'
article_processing_charge: No
article_type: original
author:
- first_name: Jasmin
full_name: Morandell, Jasmin
id: 4739D480-F248-11E8-B48F-1D18A9856A87
last_name: Morandell
- first_name: Lena A
full_name: Schwarz, Lena A
id: 29A8453C-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- first_name: Bernadette
full_name: Basilico, Bernadette
id: 36035796-5ACA-11E9-A75E-7AF2E5697425
last_name: Basilico
orcid: 0000-0003-1843-3173
- first_name: Saren
full_name: Tasciyan, Saren
id: 4323B49C-F248-11E8-B48F-1D18A9856A87
last_name: Tasciyan
orcid: 0000-0003-1671-393X
- first_name: Georgi A
full_name: Dimchev, Georgi A
id: 38C393BE-F248-11E8-B48F-1D18A9856A87
last_name: Dimchev
orcid: 0000-0001-8370-6161
- first_name: Armel
full_name: Nicolas, Armel
id: 2A103192-F248-11E8-B48F-1D18A9856A87
last_name: Nicolas
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- first_name: Christoph
full_name: Dotter, Christoph
id: 4C66542E-F248-11E8-B48F-1D18A9856A87
last_name: Dotter
orcid: 0000-0002-9033-9096
- first_name: Lisa
full_name: Knaus, Lisa
id: 3B2ABCF4-F248-11E8-B48F-1D18A9856A87
last_name: Knaus
- first_name: Zoe
full_name: Dobler, Zoe
id: D23090A2-9057-11EA-883A-A8396FC7A38F
last_name: Dobler
- first_name: Emanuele
full_name: Cacci, Emanuele
last_name: Cacci
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Morandell J, Schwarz LA, Basilico B, et al. Cul3 regulates cytoskeleton protein
homeostasis and cell migration during a critical window of brain development.
Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23123-x
apa: Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Dimchev, G. A.,
Nicolas, A., … Novarino, G. (2021). Cul3 regulates cytoskeleton protein homeostasis
and cell migration during a critical window of brain development. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-021-23123-x
chicago: Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan,
Georgi A Dimchev, Armel Nicolas, Christoph M Sommer, et al. “Cul3 Regulates Cytoskeleton
Protein Homeostasis and Cell Migration during a Critical Window of Brain Development.”
Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23123-x.
ieee: J. Morandell et al., “Cul3 regulates cytoskeleton protein homeostasis
and cell migration during a critical window of brain development,” Nature Communications,
vol. 12, no. 1. Springer Nature, 2021.
ista: Morandell J, Schwarz LA, Basilico B, Tasciyan S, Dimchev GA, Nicolas A, Sommer
CM, Kreuzinger C, Dotter C, Knaus L, Dobler Z, Cacci E, Schur FK, Danzl JG, Novarino
G. 2021. Cul3 regulates cytoskeleton protein homeostasis and cell migration during
a critical window of brain development. Nature Communications. 12(1), 3058.
mla: Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis
and Cell Migration during a Critical Window of Brain Development.” Nature Communications,
vol. 12, no. 1, 3058, Springer Nature, 2021, doi:10.1038/s41467-021-23123-x.
short: J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, G.A. Dimchev, A. Nicolas,
C.M. Sommer, C. Kreuzinger, C. Dotter, L. Knaus, Z. Dobler, E. Cacci, F.K. Schur,
J.G. Danzl, G. Novarino, Nature Communications 12 (2021).
date_created: 2021-05-28T11:49:46Z
date_published: 2021-05-24T00:00:00Z
date_updated: 2024-03-28T23:30:23Z
day: '24'
ddc:
- '572'
department:
- _id: GaNo
- _id: JoDa
- _id: FlSc
- _id: MiSi
- _id: LifeSc
- _id: Bio
doi: 10.1038/s41467-021-23123-x
ec_funded: 1
external_id:
isi:
- '000658769900010'
file:
- access_level: open_access
checksum: 337e0f7959c35ec959984cacdcb472ba
content_type: application/pdf
creator: kschuh
date_created: 2021-05-28T12:39:43Z
date_updated: 2021-05-28T12:39:43Z
file_id: '9430'
file_name: 2021_NatureCommunications_Morandell.pdf
file_size: 9358599
relation: main_file
success: 1
file_date_updated: 2021-05-28T12:39:43Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 25444568-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715508'
name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo
and in vitro Models
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
- _id: 05A0D778-7A3F-11EA-A408-12923DDC885E
grant_number: F07807
name: Neural stem cells in autism and epilepsy
- _id: 265CB4D0-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03600
name: Optical control of synaptic function via adhesion molecules
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: press_release
url: https://ist.ac.at/en/news/defective-gene-slows-down-brain-cells/
record:
- id: '7800'
relation: earlier_version
status: public
- id: '12401'
relation: dissertation_contains
status: public
status: public
title: Cul3 regulates cytoskeleton protein homeostasis and cell migration during a
critical window of brain development
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '10058'
abstract:
- lang: eng
text: 'Quantum information and computation has become a vast field paved with opportunities
for researchers and investors. As large multinational companies and international
funds are heavily investing in quantum technologies it is still a question which
platform is best suited for the task of realizing a scalable quantum processor.
In this work we investigate hole spins in Ge quantum wells. These hold great promise
as they possess several favorable properties: a small effective mass, a strong
spin-orbit coupling, long relaxation time and an inherent immunity to hyperfine
noise. All these characteristics helped Ge hole spin qubits to evolve from a single
qubit to a fully entangled four qubit processor in only 3 years. Here, we investigated
a qubit approach leveraging the large out-of-plane g-factors of heavy hole states
in Ge quantum dots. We found this qubit to be reproducibly operable at extremely
low magnetic field and at large speeds while maintaining coherence. This was possible
because large differences of g-factors in adjacent dots can be achieved in the
out-of-plane direction. In the in-plane direction the small g-factors, on the
other hand, can be altered very effectively by the confinement potentials. Here,
we found that this can even lead to a sign change of the g-factors. The resulting
g-factor difference alters the dynamics of the system drastically and produces
effects typically attributed to a spin-orbit induced spin-flip term. The investigations
carried out in this thesis give further insights into the possibilities of holes
in Ge and reveal new physical properties that need to be considered when designing
future spin qubit experiments.'
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: The author gratefully acknowledges support by the Austrian Science
Fund (FWF), grants No P30207, and the Nomis foundation.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Daniel
full_name: Jirovec, Daniel
id: 4C473F58-F248-11E8-B48F-1D18A9856A87
last_name: Jirovec
orcid: 0000-0002-7197-4801
citation:
ama: Jirovec D. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional
Ge hole gases. 2021. doi:10.15479/at:ista:10058
apa: Jirovec, D. (2021). Singlet-Triplet qubits and spin-orbit interaction in
2-dimensional Ge hole gases. Institute of Science and Technology Austria.
https://doi.org/10.15479/at:ista:10058
chicago: Jirovec, Daniel. “Singlet-Triplet Qubits and Spin-Orbit Interaction in
2-Dimensional Ge Hole Gases.” Institute of Science and Technology Austria, 2021.
https://doi.org/10.15479/at:ista:10058.
ieee: D. Jirovec, “Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional
Ge hole gases,” Institute of Science and Technology Austria, 2021.
ista: Jirovec D. 2021. Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional
Ge hole gases. Institute of Science and Technology Austria.
mla: Jirovec, Daniel. Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional
Ge Hole Gases. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10058.
short: D. Jirovec, Singlet-Triplet Qubits and Spin-Orbit Interaction in 2-Dimensional
Ge Hole Gases, Institute of Science and Technology Austria, 2021.
date_created: 2021-09-30T07:53:49Z
date_published: 2021-10-05T00:00:00Z
date_updated: 2023-09-08T11:41:08Z
day: '05'
ddc:
- '621'
- '539'
degree_awarded: PhD
department:
- _id: GradSch
- _id: GeKa
doi: 10.15479/at:ista:10058
file:
- access_level: closed
checksum: ad6bcb24083ed7c02baaf1885c9ea3d5
content_type: application/x-zip-compressed
creator: djirovec
date_created: 2021-09-30T14:29:14Z
date_updated: 2022-12-20T23:30:07Z
embargo_to: open_access
file_id: '10061'
file_name: PHD_Thesis_Jirovec_Source.zip
file_size: 32397600
relation: source_file
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checksum: 5fbe08d4f66d1153e04c47971538fae8
content_type: application/pdf
creator: djirovec
date_created: 2021-10-05T07:56:49Z
date_updated: 2022-12-20T23:30:07Z
embargo: 2022-10-06
file_id: '10087'
file_name: PHD_Thesis_pdfa2b_1.pdf
file_size: 26910829
relation: main_file
file_date_updated: 2022-12-20T23:30:07Z
has_accepted_license: '1'
keyword:
- qubits
- quantum computing
- holes
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '151'
project:
- _id: 2641CE5E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P30207
name: Hole spin orbit qubits in Ge quantum wells
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8831'
relation: part_of_dissertation
status: public
- id: '10065'
relation: part_of_dissertation
status: public
- id: '10066'
relation: part_of_dissertation
status: public
- id: '8909'
relation: part_of_dissertation
status: public
- id: '5816'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
title: Singlet-Triplet qubits and spin-orbit interaction in 2-dimensional Ge hole
gases
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '8909'
abstract:
- lang: eng
text: Spin qubits are considered to be among the most promising candidates for building
a quantum processor. Group IV hole spin qubits have moved into the focus of interest
due to the ease of operation and compatibility with Si technology. In addition,
Ge offers the option for monolithic superconductor-semiconductor integration.
Here we demonstrate a hole spin qubit operating at fields below 10 mT, the critical
field of Al, by exploiting the large out-of-plane hole g-factors in planar Ge
and by encoding the qubit into the singlet-triplet states of a double quantum
dot. We observe electrically controlled X and Z-rotations with tunable frequencies
exceeding 100 MHz and dephasing times of 1μs which we extend beyond 15μs with
echo techniques. These results show that Ge hole singlet triplet qubits outperform
their electronic Si and GaAs based counterparts in speed and coherence, respectively.
In addition, they are on par with Ge single spin qubits, but can be operated at
much lower fields underlining their potential for on chip integration with superconducting
technologies.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: This research was supported by the Scientific Service Units of Institute
of Science and Technology (IST) Austria through resources provided by the Miba Machine
Shop and the nanofabrication facility, and was made possible with the support of
the NOMIS Foundation. This project has received funding from the European Union’s
Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant
agreements no. 844511 and no. 75441, and by the Austrian Science Fund FWF-P 30207
project. A.B. acknowledges support from the European Union Horizon 2020 FET project
microSPIRE, no. 766955. M. Botifoll and J.A. acknowledge funding from Generalitat
de Catalunya 2017 SGR 327. The Catalan Institute of Nanoscience and Nanotechnology
(ICN2) is supported by the Severo Ochoa programme from the Spanish Ministery of
Economy (MINECO) (grant no. SEV-2017-0706) and is funded by the Catalonian Research
Centre (CERCA) Programme, Generalitat de Catalunya. Part of the present work has
been performed within the framework of the Universitat Autónoma de Barcelona Materials
Science PhD programme. Part of the HAADF scanning transmission electron microscopy
was conducted in the Laboratorio de Microscopias Avanzadas at Instituto de Nanociencia
de Aragon, Universidad de Zaragoza. ICN2 acknowledge support from the Spanish Superior
Council of Scientific Research (CSIC) Research Platform on Quantum Technologies
PTI-001. M.B. acknowledges funding from the Catalan Agency for Management of University
and Research Grants (AGAUR) Generalitat de Catalunya formation of investigators
(FI) PhD grant.
article_processing_charge: No
article_type: original
author:
- first_name: Daniel
full_name: Jirovec, Daniel
id: 4C473F58-F248-11E8-B48F-1D18A9856A87
last_name: Jirovec
orcid: 0000-0002-7197-4801
- first_name: Andrea C
full_name: Hofmann, Andrea C
id: 340F461A-F248-11E8-B48F-1D18A9856A87
last_name: Hofmann
- first_name: Andrea
full_name: Ballabio, Andrea
last_name: Ballabio
- first_name: Philipp M.
full_name: Mutter, Philipp M.
last_name: Mutter
- first_name: Giulio
full_name: Tavani, Giulio
last_name: Tavani
- first_name: Marc
full_name: Botifoll, Marc
last_name: Botifoll
- first_name: Alessandro
full_name: Crippa, Alessandro
id: 1F2B21A2-F6E7-11E9-9B82-F7DBE5697425
last_name: Crippa
orcid: 0000-0002-2968-611X
- first_name: Josip
full_name: Kukucka, Josip
id: 3F5D8856-F248-11E8-B48F-1D18A9856A87
last_name: Kukucka
- first_name: Oliver
full_name: Sagi, Oliver
id: 71616374-A8E9-11E9-A7CA-09ECE5697425
last_name: Sagi
- first_name: Frederico
full_name: Martins, Frederico
id: 38F80F9A-1CB8-11EA-BC76-B49B3DDC885E
last_name: Martins
orcid: 0000-0003-2668-2401
- first_name: Jaime
full_name: Saez Mollejo, Jaime
id: e0390f72-f6e0-11ea-865d-862393336714
last_name: Saez Mollejo
- first_name: Ivan
full_name: Prieto Gonzalez, Ivan
id: 2A307FE2-F248-11E8-B48F-1D18A9856A87
last_name: Prieto Gonzalez
orcid: 0000-0002-7370-5357
- first_name: Maksim
full_name: Borovkov, Maksim
id: 2ac7a0a2-3562-11eb-9256-fbd18ea55087
last_name: Borovkov
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Daniel
full_name: Chrastina, Daniel
last_name: Chrastina
- first_name: Giovanni
full_name: Isella, Giovanni
last_name: Isella
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Jirovec D, Hofmann AC, Ballabio A, et al. A singlet triplet hole spin qubit
in planar Ge. Nature Materials. 2021;20(8):1106–1112. doi:10.1038/s41563-021-01022-2
apa: Jirovec, D., Hofmann, A. C., Ballabio, A., Mutter, P. M., Tavani, G., Botifoll,
M., … Katsaros, G. (2021). A singlet triplet hole spin qubit in planar Ge. Nature
Materials. Springer Nature. https://doi.org/10.1038/s41563-021-01022-2
chicago: Jirovec, Daniel, Andrea C Hofmann, Andrea Ballabio, Philipp M. Mutter,
Giulio Tavani, Marc Botifoll, Alessandro Crippa, et al. “A Singlet Triplet Hole
Spin Qubit in Planar Ge.” Nature Materials. Springer Nature, 2021. https://doi.org/10.1038/s41563-021-01022-2.
ieee: D. Jirovec et al., “A singlet triplet hole spin qubit in planar Ge,”
Nature Materials, vol. 20, no. 8. Springer Nature, pp. 1106–1112, 2021.
ista: Jirovec D, Hofmann AC, Ballabio A, Mutter PM, Tavani G, Botifoll M, Crippa
A, Kukucka J, Sagi O, Martins F, Saez Mollejo J, Prieto Gonzalez I, Borovkov M,
Arbiol J, Chrastina D, Isella G, Katsaros G. 2021. A singlet triplet hole spin
qubit in planar Ge. Nature Materials. 20(8), 1106–1112.
mla: Jirovec, Daniel, et al. “A Singlet Triplet Hole Spin Qubit in Planar Ge.” Nature
Materials, vol. 20, no. 8, Springer Nature, 2021, pp. 1106–1112, doi:10.1038/s41563-021-01022-2.
short: D. Jirovec, A.C. Hofmann, A. Ballabio, P.M. Mutter, G. Tavani, M. Botifoll,
A. Crippa, J. Kukucka, O. Sagi, F. Martins, J. Saez Mollejo, I. Prieto Gonzalez,
M. Borovkov, J. Arbiol, D. Chrastina, G. Isella, G. Katsaros, Nature Materials
20 (2021) 1106–1112.
date_created: 2020-12-02T10:50:47Z
date_published: 2021-08-01T00:00:00Z
date_updated: 2024-03-28T23:30:27Z
day: '01'
department:
- _id: GeKa
- _id: NanoFab
- _id: GradSch
doi: 10.1038/s41563-021-01022-2
ec_funded: 1
external_id:
arxiv:
- '2011.13755'
isi:
- '000657596400001'
intvolume: ' 20'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2011.13755
month: '08'
oa: 1
oa_version: Preprint
page: 1106–1112
project:
- _id: 26A151DA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '844511'
name: Majorana bound states in Ge/SiGe heterostructures
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 2641CE5E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P30207
name: Hole spin orbit qubits in Ge quantum wells
- _id: 262116AA-B435-11E9-9278-68D0E5697425
name: Hybrid Semiconductor - Superconductor Quantum Devices
publication: Nature Materials
publication_identifier:
eissn:
- 1476-4660
issn:
- 1476-1122
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/quantum-computing-with-holes/
record:
- id: '9323'
relation: research_data
status: public
- id: '10058'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: A singlet triplet hole spin qubit in planar Ge
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 20
year: '2021'
...
---
_id: '9397'
abstract:
- lang: eng
text: Accumulation of interstitial fluid (IF) between embryonic cells is a common
phenomenon in vertebrate embryogenesis. Unlike other model systems, where these
accumulations coalesce into a large central cavity – the blastocoel, in zebrafish,
IF is more uniformly distributed between the deep cells (DC) before the onset
of gastrulation. This is likely due to the presence of a large extraembryonic
structure – the yolk cell (YC) at the position where the blastocoel typically
forms in other model organisms. IF has long been speculated to play a role in
tissue morphogenesis during embryogenesis, but direct evidence supporting such
function is still sparse. Here we show that the relocalization of IF to the interface
between the YC and DC/epiblast is critical for axial mesendoderm (ME) cell protrusion
formation and migration along this interface, a key process in embryonic axis
formation. We further demonstrate that axial ME cell migration and IF relocalization
engage in a positive feedback loop, where axial ME migration triggers IF accumulation
ahead of the advancing axial ME tissue by mechanically compressing the overlying
epiblast cell layer. Upon compression, locally induced flow relocalizes the IF
through the porous epiblast tissue resulting in an IF accumulation ahead of the
leading axial ME. This IF accumulation, in turn, promotes cell protrusion formation
and migration of the leading axial ME cells, thereby facilitating axial ME extension.
Our findings reveal a central role of dynamic IF relocalization in orchestrating
germ layer morphogenesis during gastrulation.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Karla
full_name: Huljev, Karla
id: 44C6F6A6-F248-11E8-B48F-1D18A9856A87
last_name: Huljev
citation:
ama: Huljev K. Coordinated spatiotemporal reorganization of interstitial fluid is
required for axial mesendoderm migration in zebrafish gastrulation. 2021. doi:10.15479/at:ista:9397
apa: Huljev, K. (2021). Coordinated spatiotemporal reorganization of interstitial
fluid is required for axial mesendoderm migration in zebrafish gastrulation.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9397
chicago: Huljev, Karla. “Coordinated Spatiotemporal Reorganization of Interstitial
Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation.”
Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9397.
ieee: K. Huljev, “Coordinated spatiotemporal reorganization of interstitial fluid
is required for axial mesendoderm migration in zebrafish gastrulation,” Institute
of Science and Technology Austria, 2021.
ista: Huljev K. 2021. Coordinated spatiotemporal reorganization of interstitial
fluid is required for axial mesendoderm migration in zebrafish gastrulation. Institute
of Science and Technology Austria.
mla: Huljev, Karla. Coordinated Spatiotemporal Reorganization of Interstitial
Fluid Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation.
Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9397.
short: K. Huljev, Coordinated Spatiotemporal Reorganization of Interstitial Fluid
Is Required for Axial Mesendoderm Migration in Zebrafish Gastrulation, Institute
of Science and Technology Austria, 2021.
date_created: 2021-05-17T12:31:30Z
date_published: 2021-05-18T00:00:00Z
date_updated: 2023-09-07T13:32:32Z
day: '18'
ddc:
- '571'
degree_awarded: PhD
department:
- _id: CaHe
- _id: GradSch
doi: 10.15479/at:ista:9397
file:
- access_level: closed
checksum: 7f98532f5324a0b2f3fa8de2967baa19
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: khuljev
date_created: 2021-05-17T12:29:12Z
date_updated: 2022-05-21T22:30:04Z
embargo_to: open_access
file_id: '9398'
file_name: KHuljev_Thesis_corrections.docx
file_size: 47799741
relation: source_file
- access_level: open_access
checksum: bf512f8a1e572a543778fc4b227c01ba
content_type: application/pdf
creator: khuljev
date_created: 2021-05-18T14:50:28Z
date_updated: 2022-05-21T22:30:04Z
embargo: 2022-05-20
file_id: '9401'
file_name: new_KHuljev_Thesis_corrections.pdf
file_size: 16542131
relation: main_file
file_date_updated: 2022-05-21T22:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '101'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
title: Coordinated spatiotemporal reorganization of interstitial fluid is required
for axial mesendoderm migration in zebrafish gastrulation
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10066'
abstract:
- lang: eng
text: The potential of Si and SiGe-based devices for the scaling of quantum circuits
is tainted by device variability. Each device needs to be tuned to operation conditions.
We give a key step towards tackling this variability with an algorithm that, without
modification, is capable of tuning a 4-gate Si FinFET, a 5-gate GeSi nanowire
and a 7-gate SiGe heterostructure double quantum dot device from scratch. We achieve
tuning times of 30, 10, and 92 minutes, respectively. The algorithm also provides
insight into the parameter space landscape for each of these devices. These results
show that overarching solutions for the tuning of quantum devices are enabled
by machine learning.
acknowledged_ssus:
- _id: NanoFab
acknowledgement: "We acknowledge Ang Li, Erik P. A. M. Bakkers (University of Eindhoven)
for the fabrication of the Ge/Si nanowire. This work was supported by the Royal
Society, the EPSRC National Quantum Technology Hub in Networked Quantum Information
Technology (EP/M013243/1), Quantum Technology Capital (EP/N014995/1), EPSRC Platform
Grant\r\n(EP/R029229/1), the European Research Council (Grant agreement 948932),
the Swiss Nanoscience Institute, the\r\nNCCR SPIN, the EU H2020 European Microkelvin
Platform EMP grant No. 824109, the Scientific Service Units\r\nof IST Austria through
resources provided by the nanofabrication facility and, the FWF-P30207 project.
This publication was also made possible through support from Templeton World Charity
Foundation and John Templeton Foundation. The opinions expressed in this publication
are those of the authors and do not necessarily reflect the views of the Templeton
Foundations."
article_number: '2107.12975'
article_processing_charge: No
author:
- first_name: B.
full_name: Severin, B.
last_name: Severin
- first_name: D. T.
full_name: Lennon, D. T.
last_name: Lennon
- first_name: L. C.
full_name: Camenzind, L. C.
last_name: Camenzind
- first_name: F.
full_name: Vigneau, F.
last_name: Vigneau
- first_name: F.
full_name: Fedele, F.
last_name: Fedele
- first_name: Daniel
full_name: Jirovec, Daniel
id: 4C473F58-F248-11E8-B48F-1D18A9856A87
last_name: Jirovec
orcid: 0000-0002-7197-4801
- first_name: A.
full_name: Ballabio, A.
last_name: Ballabio
- first_name: D.
full_name: Chrastina, D.
last_name: Chrastina
- first_name: G.
full_name: Isella, G.
last_name: Isella
- first_name: M. de
full_name: Kruijf, M. de
last_name: Kruijf
- first_name: M. J.
full_name: Carballido, M. J.
last_name: Carballido
- first_name: S.
full_name: Svab, S.
last_name: Svab
- first_name: A. V.
full_name: Kuhlmann, A. V.
last_name: Kuhlmann
- first_name: F. R.
full_name: Braakman, F. R.
last_name: Braakman
- first_name: S.
full_name: Geyer, S.
last_name: Geyer
- first_name: F. N. M.
full_name: Froning, F. N. M.
last_name: Froning
- first_name: H.
full_name: Moon, H.
last_name: Moon
- first_name: M. A.
full_name: Osborne, M. A.
last_name: Osborne
- first_name: D.
full_name: Sejdinovic, D.
last_name: Sejdinovic
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
- first_name: D. M.
full_name: Zumbühl, D. M.
last_name: Zumbühl
- first_name: G. A. D.
full_name: Briggs, G. A. D.
last_name: Briggs
- first_name: N.
full_name: Ares, N.
last_name: Ares
citation:
ama: Severin B, Lennon DT, Camenzind LC, et al. Cross-architecture tuning of silicon
and SiGe-based quantum devices using machine learning. arXiv. doi:10.48550/arXiv.2107.12975
apa: Severin, B., Lennon, D. T., Camenzind, L. C., Vigneau, F., Fedele, F., Jirovec,
D., … Ares, N. (n.d.). Cross-architecture tuning of silicon and SiGe-based quantum
devices using machine learning. arXiv. https://doi.org/10.48550/arXiv.2107.12975
chicago: Severin, B., D. T. Lennon, L. C. Camenzind, F. Vigneau, F. Fedele, Daniel
Jirovec, A. Ballabio, et al. “Cross-Architecture Tuning of Silicon and SiGe-Based
Quantum Devices Using Machine Learning.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2107.12975.
ieee: B. Severin et al., “Cross-architecture tuning of silicon and SiGe-based
quantum devices using machine learning,” arXiv. .
ista: Severin B, Lennon DT, Camenzind LC, Vigneau F, Fedele F, Jirovec D, Ballabio
A, Chrastina D, Isella G, Kruijf M de, Carballido MJ, Svab S, Kuhlmann AV, Braakman
FR, Geyer S, Froning FNM, Moon H, Osborne MA, Sejdinovic D, Katsaros G, Zumbühl
DM, Briggs GAD, Ares N. Cross-architecture tuning of silicon and SiGe-based quantum
devices using machine learning. arXiv, 2107.12975.
mla: Severin, B., et al. “Cross-Architecture Tuning of Silicon and SiGe-Based Quantum
Devices Using Machine Learning.” ArXiv, 2107.12975, doi:10.48550/arXiv.2107.12975.
short: B. Severin, D.T. Lennon, L.C. Camenzind, F. Vigneau, F. Fedele, D. Jirovec,
A. Ballabio, D. Chrastina, G. Isella, M. de Kruijf, M.J. Carballido, S. Svab,
A.V. Kuhlmann, F.R. Braakman, S. Geyer, F.N.M. Froning, H. Moon, M.A. Osborne,
D. Sejdinovic, G. Katsaros, D.M. Zumbühl, G.A.D. Briggs, N. Ares, ArXiv (n.d.).
date_created: 2021-10-01T12:40:22Z
date_published: 2021-07-27T00:00:00Z
date_updated: 2024-03-28T23:30:27Z
day: '27'
department:
- _id: GeKa
doi: 10.48550/arXiv.2107.12975
external_id:
arxiv:
- '2107.12975'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2107.12975
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 2641CE5E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P30207
name: Hole spin orbit qubits in Ge quantum wells
publication: arXiv
publication_status: submitted
related_material:
record:
- id: '10058'
relation: dissertation_contains
status: public
status: public
title: Cross-architecture tuning of silicon and SiGe-based quantum devices using machine
learning
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '9437'
abstract:
- lang: eng
text: The synaptic connection from medial habenula (MHb) to interpeduncular nucleus
(IPN) is critical for emotion-related behaviors and uniquely expresses R-type
Ca2+ channels (Cav2.3) and auxiliary GABAB receptor (GBR) subunits, the K+-channel
tetramerization domain-containing proteins (KCTDs). Activation of GBRs facilitates
or inhibits transmitter release from MHb terminals depending on the IPN subnucleus,
but the role of KCTDs is unknown. We therefore examined the localization and function
of Cav2.3, GBRs, and KCTDs in this pathway in mice. We show in heterologous cells
that KCTD8 and KCTD12b directly bind to Cav2.3 and that KCTD8 potentiates Cav2.3
currents in the absence of GBRs. In the rostral IPN, KCTD8, KCTD12b, and Cav2.3
co-localize at the presynaptic active zone. Genetic deletion indicated a bidirectional
modulation of Cav2.3-mediated release by these KCTDs with a compensatory increase
of KCTD8 in the active zone in KCTD12b-deficient mice. The interaction of Cav2.3
with KCTDs therefore scales synaptic strength independent of GBR activation.
acknowledgement: We are grateful to Akari Hagiwara and Toshihisa Ohtsuka for CAST
antibody, and Masahiko Watanabe for neurexin antibody. We thank David Adams for
kindly providing the stable Cav2.3 cell line. Cav2.3 KO mice were kindly provided
by Tsutomu Tanabe. This project has received funding from the European Research
Council (ERC) and European Commission (EC), under the European Union’s Horizon 2020
research and innovation programme (ERC grant agreement no. 694539 to Ryuichi Shigemoto,
no. 692692 to Peter Jonas, and the Marie Skłodowska-Curie grant agreement no. 665385
to Cihan Önal), the Swiss National Science Foundation Grant 31003A-172881 to Bernhard
Bettler and Deutsche Forschungsgemeinschaft (For 2143) and BIOSS-2 to Akos Kulik.
article_number: e68274
article_processing_charge: No
article_type: original
author:
- first_name: Pradeep
full_name: Bhandari, Pradeep
id: 45EDD1BC-F248-11E8-B48F-1D18A9856A87
last_name: Bhandari
orcid: 0000-0003-0863-4481
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: Diego
full_name: Fernández-Fernández, Diego
last_name: Fernández-Fernández
- first_name: Thorsten
full_name: Fritzius, Thorsten
last_name: Fritzius
- first_name: David
full_name: Kleindienst, David
id: 42E121A4-F248-11E8-B48F-1D18A9856A87
last_name: Kleindienst
- first_name: Hüseyin C
full_name: Önal, Hüseyin C
id: 4659D740-F248-11E8-B48F-1D18A9856A87
last_name: Önal
orcid: 0000-0002-2771-2011
- first_name: Jacqueline-Claire
full_name: Montanaro-Punzengruber, Jacqueline-Claire
id: 3786AB44-F248-11E8-B48F-1D18A9856A87
last_name: Montanaro-Punzengruber
- first_name: Martin
full_name: Gassmann, Martin
last_name: Gassmann
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Akos
full_name: Kulik, Akos
last_name: Kulik
- first_name: Bernhard
full_name: Bettler, Bernhard
last_name: Bettler
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Peter
full_name: Koppensteiner, Peter
id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87
last_name: Koppensteiner
orcid: 0000-0002-3509-1948
citation:
ama: Bhandari P, Vandael DH, Fernández-Fernández D, et al. GABAB receptor auxiliary
subunits modulate Cav2.3-mediated release from medial habenula terminals. eLife.
2021;10. doi:10.7554/ELIFE.68274
apa: Bhandari, P., Vandael, D. H., Fernández-Fernández, D., Fritzius, T., Kleindienst,
D., Önal, H. C., … Koppensteiner, P. (2021). GABAB receptor auxiliary subunits
modulate Cav2.3-mediated release from medial habenula terminals. ELife.
eLife Sciences Publications. https://doi.org/10.7554/ELIFE.68274
chicago: Bhandari, Pradeep, David H Vandael, Diego Fernández-Fernández, Thorsten
Fritzius, David Kleindienst, Hüseyin C Önal, Jacqueline-Claire Montanaro-Punzengruber,
et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated Release from
Medial Habenula Terminals.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/ELIFE.68274.
ieee: P. Bhandari et al., “GABAB receptor auxiliary subunits modulate Cav2.3-mediated
release from medial habenula terminals,” eLife, vol. 10. eLife Sciences
Publications, 2021.
ista: Bhandari P, Vandael DH, Fernández-Fernández D, Fritzius T, Kleindienst D,
Önal HC, Montanaro-Punzengruber J-C, Gassmann M, Jonas PM, Kulik A, Bettler B,
Shigemoto R, Koppensteiner P. 2021. GABAB receptor auxiliary subunits modulate
Cav2.3-mediated release from medial habenula terminals. eLife. 10, e68274.
mla: Bhandari, Pradeep, et al. “GABAB Receptor Auxiliary Subunits Modulate Cav2.3-Mediated
Release from Medial Habenula Terminals.” ELife, vol. 10, e68274, eLife
Sciences Publications, 2021, doi:10.7554/ELIFE.68274.
short: P. Bhandari, D.H. Vandael, D. Fernández-Fernández, T. Fritzius, D. Kleindienst,
H.C. Önal, J.-C. Montanaro-Punzengruber, M. Gassmann, P.M. Jonas, A. Kulik, B.
Bettler, R. Shigemoto, P. Koppensteiner, ELife 10 (2021).
date_created: 2021-05-30T22:01:23Z
date_published: 2021-04-29T00:00:00Z
date_updated: 2024-03-28T23:30:31Z
day: '29'
ddc:
- '570'
department:
- _id: RySh
- _id: PeJo
doi: 10.7554/ELIFE.68274
ec_funded: 1
external_id:
isi:
- '000651761700001'
file:
- access_level: open_access
checksum: 6ebcb79999f889766f7cd79ee134ad28
content_type: application/pdf
creator: cziletti
date_created: 2021-05-31T09:43:09Z
date_updated: 2021-05-31T09:43:09Z
file_id: '9440'
file_name: 2021_eLife_Bhandari.pdf
file_size: 8174719
relation: main_file
success: 1
file_date_updated: 2021-05-31T09:43:09Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _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: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
related_material:
link:
- relation: earlier_version
url: https://doi.org/10.1101/2020.04.16.045112
record:
- id: '9562'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: GABAB receptor auxiliary subunits modulate Cav2.3-mediated release from medial
habenula terminals
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: '2021'
...
---
_id: '9562'
abstract:
- lang: eng
text: Left-right asymmetries can be considered a fundamental organizational principle
of the vertebrate central nervous system. The hippocampal CA3-CA1 pyramidal cell
synaptic connection shows an input-side dependent asymmetry where the hemispheric
location of the presynaptic CA3 neuron determines the synaptic properties. Left-input
synapses terminating on apical dendrites in stratum radiatum have a higher density
of NMDA receptor subunit GluN2B, a lower density of AMPA receptor subunit GluA1
and smaller areas with less often perforated PSDs. On the other hand, left-input
synapses terminating on basal dendrites in stratum oriens have lower GluN2B densities
than right-input ones. Apical and basal synapses further employ different signaling
pathways involved in LTP. SDS-digested freeze-fracture replica labeling can visualize
synaptic membrane proteins with high sensitivity and resolution, and has been
used to reveal the asymmetry at the electron microscopic level. However, it requires
time-consuming manual demarcation of the synaptic surface for quantitative measurements.
To facilitate the analysis of replica labeling, I first developed a software named
Darea, which utilizes deep-learning to automatize this demarcation. With Darea
I characterized the synaptic distribution of NMDA and AMPA receptors as well as
the voltage-gated Ca2+ channels in CA1 stratum radiatum and oriens. Second, I
explored the role of GluN2B and its carboxy-terminus in the establishment of input-side
dependent hippocampal asymmetry. In conditional knock-out mice lacking GluN2B
expression in CA1 and GluN2B-2A swap mice, where GluN2B carboxy-terminus was exchanged
to that of GluN2A, no significant asymmetries of GluN2B, GluA1 and PSD area were
detected. We further discovered a previously unknown functional asymmetry of GluN2A,
which was also lost in the swap mouse. These results demonstrate that GluN2B carboxy-terminus
plays a critical role in normal formation of input-side dependent asymmetry.
acknowledged_ssus:
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: David
full_name: Kleindienst, David
id: 42E121A4-F248-11E8-B48F-1D18A9856A87
last_name: Kleindienst
citation:
ama: 'Kleindienst D. 2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor
subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning.
2021. doi:10.15479/at:ista:9562'
apa: 'Kleindienst, D. (2021). 2B or not 2B: Hippocampal asymmetries mediated
by NMDA receptor subunit GluN2B C-terminus and high-throughput image analysis
by Deep-Learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:9562'
chicago: 'Kleindienst, David. “2B or Not 2B: Hippocampal Asymmetries Mediated by
NMDA Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by
Deep-Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:9562.'
ieee: 'D. Kleindienst, “2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor
subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning,”
Institute of Science and Technology Austria, 2021.'
ista: 'Kleindienst D. 2021. 2B or not 2B: Hippocampal asymmetries mediated by NMDA
receptor subunit GluN2B C-terminus and high-throughput image analysis by Deep-Learning.
Institute of Science and Technology Austria.'
mla: 'Kleindienst, David. 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA
Receptor Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning.
Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:9562.'
short: 'D. Kleindienst, 2B or Not 2B: Hippocampal Asymmetries Mediated by NMDA Receptor
Subunit GluN2B C-Terminus and High-Throughput Image Analysis by Deep-Learning,
Institute of Science and Technology Austria, 2021.'
date_created: 2021-06-17T14:10:47Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-09-11T12:55:53Z
day: '01'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: RySh
doi: 10.15479/at:ista:9562
file:
- access_level: open_access
checksum: 659df5518db495f679cb1df9e9bd1d94
content_type: application/pdf
creator: dkleindienst
date_created: 2021-06-17T14:03:14Z
date_updated: 2022-07-02T22:30:04Z
embargo: 2022-07-01
file_id: '9563'
file_name: Thesis.pdf
file_size: 77299142
relation: main_file
- access_level: closed
checksum: 3bcf63a2b19e5b6663be051bea332748
content_type: application/zip
creator: dkleindienst
date_created: 2021-06-17T14:04:30Z
date_updated: 2022-07-02T22:30:04Z
embargo_to: open_access
file_id: '9564'
file_name: Thesis_source.zip
file_size: 369804895
relation: source_file
file_date_updated: 2022-07-02T22:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '124'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '9756'
relation: part_of_dissertation
status: public
- id: '9437'
relation: part_of_dissertation
status: public
- id: '8532'
relation: part_of_dissertation
status: public
- id: '612'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
title: '2B or not 2B: Hippocampal asymmetries mediated by NMDA receptor subunit GluN2B
C-terminus and high-throughput image analysis by Deep-Learning'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '9756'
abstract:
- lang: eng
text: High-resolution visualization and quantification of membrane proteins contribute
to the understanding of their functions and the roles they play in physiological
and pathological conditions. Sodium dodecyl sulfate-digested freeze-fracture replica
labeling (SDS-FRL) is a powerful electron microscopy method to study quantitatively
the two-dimensional distribution of transmembrane proteins and their tightly associated
proteins. During treatment with SDS, intracellular organelles and proteins not
anchored to the replica are dissolved, whereas integral membrane proteins captured
and stabilized by carbon/platinum deposition remain on the replica. Their intra-
and extracellular domains become exposed on the surface of the replica, facilitating
the accessibility of antibodies and, therefore, providing higher labeling efficiency
than those obtained with other immunoelectron microscopy techniques. In this chapter,
we describe the protocols of SDS-FRL adapted for mammalian brain samples, and
optimization of the SDS treatment to increase the labeling efficiency for quantification
of Cav2.1, the alpha subunit of P/Q-type voltage-dependent calcium channels utilizing
deep learning algorithms.
acknowledgement: This work was supported by the European Union (European Research
Council Advanced grant no. 694539 and Human Brain Project Ref. 720270 to R. S.)
and the Austrian Academy of Sciences (DOC fellowship to D.K.).
alternative_title:
- Neuromethods
article_processing_charge: No
author:
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: David
full_name: Kleindienst, David
id: 42E121A4-F248-11E8-B48F-1D18A9856A87
last_name: Kleindienst
- first_name: Harumi
full_name: Harada, Harumi
id: 2E55CDF2-F248-11E8-B48F-1D18A9856A87
last_name: Harada
orcid: 0000-0001-7429-7896
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: 'Kaufmann W, Kleindienst D, Harada H, Shigemoto R. High-Resolution localization
and quantitation of membrane proteins by SDS-digested freeze-fracture replica
labeling (SDS-FRL). In: Receptor and Ion Channel Detection in the Brain.
Vol 169. Neuromethods. New York: Humana; 2021:267-283. doi:10.1007/978-1-0716-1522-5_19'
apa: 'Kaufmann, W., Kleindienst, D., Harada, H., & Shigemoto, R. (2021). High-Resolution
localization and quantitation of membrane proteins by SDS-digested freeze-fracture
replica labeling (SDS-FRL). In Receptor and Ion Channel Detection in the Brain
(Vol. 169, pp. 267–283). New York: Humana. https://doi.org/10.1007/978-1-0716-1522-5_19'
chicago: 'Kaufmann, Walter, David Kleindienst, Harumi Harada, and Ryuichi Shigemoto.
“High-Resolution Localization and Quantitation of Membrane Proteins by SDS-Digested
Freeze-Fracture Replica Labeling (SDS-FRL).” In Receptor and Ion Channel Detection
in the Brain, 169:267–83. Neuromethods. New York: Humana, 2021. https://doi.org/10.1007/978-1-0716-1522-5_19.'
ieee: 'W. Kaufmann, D. Kleindienst, H. Harada, and R. Shigemoto, “High-Resolution
localization and quantitation of membrane proteins by SDS-digested freeze-fracture
replica labeling (SDS-FRL),” in Receptor and Ion Channel Detection in the
Brain, vol. 169, New York: Humana, 2021, pp. 267–283.'
ista: 'Kaufmann W, Kleindienst D, Harada H, Shigemoto R. 2021.High-Resolution localization
and quantitation of membrane proteins by SDS-digested freeze-fracture replica
labeling (SDS-FRL). In: Receptor and Ion Channel Detection in the Brain. Neuromethods,
vol. 169, 267–283.'
mla: Kaufmann, Walter, et al. “High-Resolution Localization and Quantitation of
Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).”
Receptor and Ion Channel Detection in the Brain, vol. 169, Humana, 2021,
pp. 267–83, doi:10.1007/978-1-0716-1522-5_19.
short: W. Kaufmann, D. Kleindienst, H. Harada, R. Shigemoto, in:, Receptor and
Ion Channel Detection in the Brain, Humana, New York, 2021, pp. 267–283.
date_created: 2021-07-30T09:34:56Z
date_published: 2021-07-27T00:00:00Z
date_updated: 2024-03-28T23:30:31Z
day: '27'
ddc:
- '573'
department:
- _id: RySh
- _id: EM-Fac
doi: 10.1007/978-1-0716-1522-5_19
ec_funded: 1
has_accepted_license: '1'
intvolume: ' 169'
keyword:
- 'Freeze-fracture replica: Deep learning'
- Immunogold labeling
- Integral membrane protein
- Electron microscopy
language:
- iso: eng
month: '07'
oa_version: None
page: 267-283
place: New York
project:
- _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: 25CBA828-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '720270'
name: Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)
publication: ' Receptor and Ion Channel Detection in the Brain'
publication_identifier:
eisbn:
- '9781071615225'
isbn:
- '9781071615218'
publication_status: published
publisher: Humana
quality_controlled: '1'
related_material:
record:
- id: '9562'
relation: dissertation_contains
status: public
series_title: Neuromethods
status: public
title: High-Resolution localization and quantitation of membrane proteins by SDS-digested
freeze-fracture replica labeling (SDS-FRL)
type: book_chapter
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 169
year: '2021'
...
---
_id: '8934'
abstract:
- lang: eng
text: "In this thesis, we consider several of the most classical and fundamental
problems in static analysis and formal verification, including invariant generation,
reachability analysis, termination analysis of probabilistic programs, data-flow
analysis, quantitative analysis of Markov chains and Markov decision processes,
and the problem of data packing in cache management.\r\nWe use techniques from
parameterized complexity theory, polyhedral geometry, and real algebraic geometry
to significantly improve the state-of-the-art, in terms of both scalability and
completeness guarantees, for the mentioned problems. In some cases, our results
are the first theoretical improvements for the respective problems in two or three
decades."
acknowledgement: 'The research was partially supported by an IBM PhD fellowship, a
Facebook PhD fellowship, and DOC fellowship #24956 of the Austrian Academy of Sciences
(OeAW).'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
citation:
ama: Goharshady AK. Parameterized and algebro-geometric advances in static program
analysis. 2021. doi:10.15479/AT:ISTA:8934
apa: Goharshady, A. K. (2021). Parameterized and algebro-geometric advances in
static program analysis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8934
chicago: Goharshady, Amir Kafshdar. “Parameterized and Algebro-Geometric Advances
in Static Program Analysis.” Institute of Science and Technology Austria, 2021.
https://doi.org/10.15479/AT:ISTA:8934.
ieee: A. K. Goharshady, “Parameterized and algebro-geometric advances in static
program analysis,” Institute of Science and Technology Austria, 2021.
ista: Goharshady AK. 2021. Parameterized and algebro-geometric advances in static
program analysis. Institute of Science and Technology Austria.
mla: Goharshady, Amir Kafshdar. Parameterized and Algebro-Geometric Advances
in Static Program Analysis. Institute of Science and Technology Austria, 2021,
doi:10.15479/AT:ISTA:8934.
short: A.K. Goharshady, Parameterized and Algebro-Geometric Advances in Static Program
Analysis, Institute of Science and Technology Austria, 2021.
date_created: 2020-12-10T12:17:07Z
date_published: 2021-01-01T00:00:00Z
date_updated: 2023-09-22T10:03:21Z
day: '01'
ddc:
- '005'
degree_awarded: PhD
department:
- _id: KrCh
- _id: GradSch
doi: 10.15479/AT:ISTA:8934
file:
- access_level: open_access
checksum: d1b9db3725aed34dadd81274aeb9426c
content_type: application/pdf
creator: akafshda
date_created: 2020-12-22T20:08:44Z
date_updated: 2021-12-23T23:30:04Z
embargo: 2021-12-22
file_id: '8969'
file_name: Thesis-pdfa.pdf
file_size: 5251507
relation: main_file
- access_level: closed
checksum: 1661df7b393e6866d2460eba3c905130
content_type: application/zip
creator: akafshda
date_created: 2020-12-22T20:08:50Z
date_updated: 2021-03-04T23:30:04Z
embargo_to: open_access
file_id: '8970'
file_name: source.zip
file_size: 10636756
relation: source_file
file_date_updated: 2021-12-23T23:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: '278'
project:
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies
- _id: 266EEEC0-B435-11E9-9278-68D0E5697425
name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart
Contracts
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1386'
relation: part_of_dissertation
status: public
- id: '1437'
relation: part_of_dissertation
status: public
- id: '311'
relation: part_of_dissertation
status: public
- id: '6056'
relation: part_of_dissertation
status: public
- id: '6380'
relation: part_of_dissertation
status: public
- id: '639'
relation: part_of_dissertation
status: public
- id: '66'
relation: part_of_dissertation
status: public
- id: '6780'
relation: part_of_dissertation
status: public
- id: '6918'
relation: part_of_dissertation
status: public
- id: '7810'
relation: part_of_dissertation
status: public
- id: '6175'
relation: part_of_dissertation
status: public
- id: '6378'
relation: part_of_dissertation
status: public
- id: '6490'
relation: part_of_dissertation
status: public
- id: '7014'
relation: part_of_dissertation
status: public
- id: '8089'
relation: part_of_dissertation
status: public
- id: '8728'
relation: part_of_dissertation
status: public
- id: '7158'
relation: part_of_dissertation
status: public
- id: '5977'
relation: part_of_dissertation
status: public
- id: '6009'
relation: part_of_dissertation
status: public
- id: '6340'
relation: part_of_dissertation
status: public
- id: '949'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
title: Parameterized and algebro-geometric advances in static program analysis
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10307'
abstract:
- lang: eng
text: Bacteria-host interactions represent a continuous trade-off between benefit
and risk. Thus, the host immune response is faced with a non-trivial problem –
accommodate beneficial commensals and remove harmful pathogens. This is especially
difficult as molecular patterns, such as lipopolysaccharide or specific surface
organelles such as pili, are conserved in both, commensal and pathogenic bacteria.
Type 1 pili, tightly regulated by phase variation, are considered an important
virulence factor of pathogenic bacteria as they facilitate invasion into host
cells. While invasion represents a de facto passive mechanism for pathogens to
escape the host immune response, we demonstrate a fundamental role of type 1 pili
as active modulators of the innate and adaptive immune response.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
- _id: PreCl
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Kathrin
full_name: Tomasek, Kathrin
id: 3AEC8556-F248-11E8-B48F-1D18A9856A87
last_name: Tomasek
orcid: 0000-0003-3768-877X
citation:
ama: Tomasek K. Pathogenic Escherichia coli hijack the host immune response. 2021.
doi:10.15479/at:ista:10307
apa: Tomasek, K. (2021). Pathogenic Escherichia coli hijack the host immune response.
Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10307
chicago: Tomasek, Kathrin. “Pathogenic Escherichia Coli Hijack the Host Immune Response.”
Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10307.
ieee: K. Tomasek, “Pathogenic Escherichia coli hijack the host immune response,”
Institute of Science and Technology Austria, 2021.
ista: Tomasek K. 2021. Pathogenic Escherichia coli hijack the host immune response.
Institute of Science and Technology Austria.
mla: Tomasek, Kathrin. Pathogenic Escherichia Coli Hijack the Host Immune Response.
Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10307.
short: K. Tomasek, Pathogenic Escherichia Coli Hijack the Host Immune Response,
Institute of Science and Technology Austria, 2021.
date_created: 2021-11-18T15:05:06Z
date_published: 2021-11-18T00:00:00Z
date_updated: 2023-09-07T13:34:38Z
day: '18'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: MiSi
- _id: CaGu
- _id: GradSch
doi: 10.15479/at:ista:10307
file:
- access_level: open_access
checksum: b39c9e0ef18d0484d537a67551effd02
content_type: application/pdf
creator: ktomasek
date_created: 2021-11-18T15:07:31Z
date_updated: 2022-12-20T23:30:05Z
embargo: 2022-11-18
file_id: '10308'
file_name: ThesisTomasekKathrin.pdf
file_size: 13266088
relation: main_file
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checksum: c0c440ee9e5ef1102a518a4f9f023e7c
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: ktomasek
date_created: 2021-11-18T15:07:46Z
date_updated: 2022-12-20T23:30:05Z
embargo_to: open_access
file_id: '10309'
file_name: ThesisTomasekKathrin.docx
file_size: 7539509
relation: source_file
file_date_updated: 2022-12-20T23:30:05Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '73'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '10316'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-4561-241X
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
title: Pathogenic Escherichia coli hijack the host immune response
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '10316'
abstract:
- lang: eng
text: A key attribute of persistent or recurring bacterial infections is the ability
of the pathogen to evade the host’s immune response. Many Enterobacteriaceae express
type 1 pili, a pre-adapted virulence trait, to invade host epithelial cells and
establish persistent infections. However, the molecular mechanisms and strategies
by which bacteria actively circumvent the immune response of the host remain poorly
understood. Here, we identified CD14, the major co-receptor for lipopolysaccharide
detection, on dendritic cells as a previously undescribed binding partner of FimH,
the protein located at the tip of the type 1 pilus of Escherichia coli. The FimH
amino acids involved in CD14 binding are highly conserved across pathogenic and
non-pathogenic strains. Binding of pathogenic bacteria to CD14 lead to reduced
dendritic cell migration and blunted expression of co-stimulatory molecules, both
rate-limiting factors of T cell activation. While defining an active molecular
mechanism of immune evasion by pathogens, the interaction between FimH and CD14
represents a potential target to interfere with persistent and recurrent infections,
such as urinary tract infections or Crohn’s disease.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: EM-Fac
acknowledgement: We thank Ulrich Dobrindt for providing UPEC strain CFT073, Vlad Gavra
and Maximilian Götz, Bor Kavčič, Jonna Alanko and Eva Kiermaier for help with experiments
and Robert Hauschild, Julian Stopp and Saren Tasciyan for help with data analysis.
We thank the IST Austria Scientific Service Units, especially the Bioimaging facility,
the Preclinical facility and the Electron microscopy facility for technical support,
Jakob Wallner and all members of the Guet and Sixt lab for fruitful discussions
and Daria Siekhaus for critically reading the manuscript. This work was supported
by grants from the Austrian Research Promotion Agency (FEMtech 868984) to I.G.,
the European Research Council (CoG 724373) and the Austrian Science Fund (FWF P29911)
to M.S.
article_processing_charge: No
author:
- first_name: Kathrin
full_name: Tomasek, Kathrin
id: 3AEC8556-F248-11E8-B48F-1D18A9856A87
last_name: Tomasek
orcid: 0000-0003-3768-877X
- first_name: Alexander F
full_name: Leithner, Alexander F
id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87
last_name: Leithner
orcid: 0000-0002-1073-744X
- first_name: Ivana
full_name: Glatzová, Ivana
id: 727b3c7d-4939-11ec-89b3-b9b0750ab74d
last_name: Glatzová
- first_name: Michael S.
full_name: Lukesch, Michael S.
last_name: Lukesch
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-4561-241X
citation:
ama: Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated
uropathogenic Escherichia coli hijack the host immune response by binding to CD14.
bioRxiv. doi:10.1101/2021.10.18.464770
apa: Tomasek, K., Leithner, A. F., Glatzová, I., Lukesch, M. S., Guet, C. C., &
Sixt, M. K. (n.d.). Type 1 piliated uropathogenic Escherichia coli hijack the
host immune response by binding to CD14. bioRxiv. Cold Spring Harbor Laboratory.
https://doi.org/10.1101/2021.10.18.464770
chicago: Tomasek, Kathrin, Alexander F Leithner, Ivana Glatzová, Michael S. Lukesch,
Calin C Guet, and Michael K Sixt. “Type 1 Piliated Uropathogenic Escherichia Coli
Hijack the Host Immune Response by Binding to CD14.” BioRxiv. Cold Spring
Harbor Laboratory, n.d. https://doi.org/10.1101/2021.10.18.464770.
ieee: K. Tomasek, A. F. Leithner, I. Glatzová, M. S. Lukesch, C. C. Guet, and M.
K. Sixt, “Type 1 piliated uropathogenic Escherichia coli hijack the host immune
response by binding to CD14,” bioRxiv. Cold Spring Harbor Laboratory.
ista: Tomasek K, Leithner AF, Glatzová I, Lukesch MS, Guet CC, Sixt MK. Type 1 piliated
uropathogenic Escherichia coli hijack the host immune response by binding to CD14.
bioRxiv, 10.1101/2021.10.18.464770.
mla: Tomasek, Kathrin, et al. “Type 1 Piliated Uropathogenic Escherichia Coli Hijack
the Host Immune Response by Binding to CD14.” BioRxiv, Cold Spring Harbor
Laboratory, doi:10.1101/2021.10.18.464770.
short: K. Tomasek, A.F. Leithner, I. Glatzová, M.S. Lukesch, C.C. Guet, M.K. Sixt,
BioRxiv (n.d.).
date_created: 2021-11-19T12:24:16Z
date_published: 2021-10-18T00:00:00Z
date_updated: 2024-03-28T23:30:35Z
day: '18'
department:
- _id: CaGu
- _id: MiSi
doi: 10.1101/2021.10.18.464770
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/2021.10.18.464770v1
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular navigation along spatial gradients
- _id: 26018E70-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29911
name: Mechanical adaptation of lamellipodial actin
publication: bioRxiv
publication_status: submitted
publisher: Cold Spring Harbor Laboratory
related_material:
record:
- id: '11843'
relation: later_version
status: public
- id: '10307'
relation: dissertation_contains
status: public
status: public
title: Type 1 piliated uropathogenic Escherichia coli hijack the host immune response
by binding to CD14
type: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2021'
...
---
_id: '9010'
abstract:
- lang: eng
text: Availability of the essential macronutrient nitrogen in soil plays a critical
role in plant growth, development, and impacts agricultural productivity. Plants
have evolved different strategies for sensing and responding to heterogeneous
nitrogen distribution. Modulation of root system architecture, including primary
root growth and branching, is among the most essential plant adaptions to ensure
adequate nitrogen acquisition. However, the immediate molecular pathways coordinating
the adjustment of root growth in response to distinct nitrogen sources, such as
nitrate or ammonium, are poorly understood. Here, we show that growth as manifested
by cell division and elongation is synchronized by coordinated auxin flux between
two adjacent outer tissue layers of the root. This coordination is achieved by
nitrate‐dependent dephosphorylation of the PIN2 auxin efflux carrier at a previously
uncharacterized phosphorylation site, leading to subsequent PIN2 lateralization
and thereby regulating auxin flow between adjacent tissues. A dynamic computer
model based on our experimental data successfully recapitulates experimental observations.
Our study provides mechanistic insights broadening our understanding of root growth
mechanisms in dynamic environments.
acknowledged_ssus:
- _id: Bio
acknowledgement: 'We acknowledge Gergely Molnar for critical reading of the manuscript,
Alexander Johnson for language editing and Yulija Salanenka for technical assistance.
Work in the Benkova laboratory was supported by the Austrian Science Fund (FWF01_I1774S)
to KO, RA and EB. Work in the Benkova laboratory was supported by the Austrian Science
Fund (FWF01_I1774S) to KO, RA and EB and by the DOC Fellowship Programme of the
AustrianAcademy of Sciences (25008) to C.A. Work in the Wabnik laboratory was supported
by the Programa de Atraccion de Talento 2017 (Comunidad deMadrid, 2017-T1/BIO-5654
to K.W.), Severo Ochoa Programme for Centres of Excellence in R&D from the Agencia
Estatal de Investigacion of Spain (grantSEV-2016-0672 (2017-2021) to K.W. via the
CBGP) and Programa Estatal de Generacion del Conocimiento y Fortalecimiento Científico
y Tecnologico del Sistema de I+D+I 2019 (PGC2018-093387-A-I00) from MICIU (to K.W.).
M.M.was supported by a postdoctoral contract associated to SEV-2016-0672.We acknowledge
the Bioimaging Facility in IST-Austria and the Advanced Microscopy Facility of the
Vienna Bio Center Core Facilities, member of the Vienna Bio Center Austria, for
use of the OMX v43D SIM microscope. AJ was supported by the Austrian Science Fund
(FWF): I03630 to J.F'
article_number: e106862
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Krisztina
full_name: Ötvös, Krisztina
id: 29B901B0-F248-11E8-B48F-1D18A9856A87
last_name: Ötvös
orcid: 0000-0002-5503-4983
- first_name: Marco
full_name: Marconi, Marco
last_name: Marconi
- first_name: Andrea
full_name: Vega, Andrea
last_name: Vega
- first_name: Jose
full_name: O’Brien, Jose
last_name: O’Brien
- first_name: Alexander J
full_name: Johnson, Alexander J
id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
last_name: Johnson
orcid: 0000-0002-2739-8843
- first_name: Rashed
full_name: Abualia, Rashed
id: 4827E134-F248-11E8-B48F-1D18A9856A87
last_name: Abualia
orcid: 0000-0002-9357-9415
- first_name: Livio
full_name: Antonielli, Livio
last_name: Antonielli
- first_name: Juan C
full_name: Montesinos López, Juan C
id: 310A8E3E-F248-11E8-B48F-1D18A9856A87
last_name: Montesinos López
orcid: 0000-0001-9179-6099
- first_name: Yuzhou
full_name: Zhang, Yuzhou
id: 3B6137F2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0003-2627-6956
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Candela
full_name: Cuesta, Candela
id: 33A3C818-F248-11E8-B48F-1D18A9856A87
last_name: Cuesta
orcid: 0000-0003-1923-2410
- first_name: Christina
full_name: Artner, Christina
id: 45DF286A-F248-11E8-B48F-1D18A9856A87
last_name: Artner
- first_name: Eleonore
full_name: Bouguyon, Eleonore
last_name: Bouguyon
- first_name: Alain
full_name: Gojon, Alain
last_name: Gojon
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Rodrigo A.
full_name: Gutiérrez, Rodrigo A.
last_name: Gutiérrez
- first_name: Krzysztof T
full_name: Wabnik, Krzysztof T
id: 4DE369A4-F248-11E8-B48F-1D18A9856A87
last_name: Wabnik
orcid: 0000-0001-7263-0560
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Ötvös K, Marconi M, Vega A, et al. Modulation of plant root growth by nitrogen
source-defined regulation of polar auxin transport. EMBO Journal. 2021;40(3).
doi:10.15252/embj.2020106862
apa: Ötvös, K., Marconi, M., Vega, A., O’Brien, J., Johnson, A. J., Abualia, R.,
… Benková, E. (2021). Modulation of plant root growth by nitrogen source-defined
regulation of polar auxin transport. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2020106862
chicago: Ötvös, Krisztina, Marco Marconi, Andrea Vega, Jose O’Brien, Alexander J
Johnson, Rashed Abualia, Livio Antonielli, et al. “Modulation of Plant Root Growth
by Nitrogen Source-Defined Regulation of Polar Auxin Transport.” EMBO Journal.
Embo Press, 2021. https://doi.org/10.15252/embj.2020106862.
ieee: K. Ötvös et al., “Modulation of plant root growth by nitrogen source-defined
regulation of polar auxin transport,” EMBO Journal, vol. 40, no. 3. Embo
Press, 2021.
ista: Ötvös K, Marconi M, Vega A, O’Brien J, Johnson AJ, Abualia R, Antonielli L,
Montesinos López JC, Zhang Y, Tan S, Cuesta C, Artner C, Bouguyon E, Gojon A,
Friml J, Gutiérrez RA, Wabnik KT, Benková E. 2021. Modulation of plant root growth
by nitrogen source-defined regulation of polar auxin transport. EMBO Journal.
40(3), e106862.
mla: Ötvös, Krisztina, et al. “Modulation of Plant Root Growth by Nitrogen Source-Defined
Regulation of Polar Auxin Transport.” EMBO Journal, vol. 40, no. 3, e106862,
Embo Press, 2021, doi:10.15252/embj.2020106862.
short: K. Ötvös, M. Marconi, A. Vega, J. O’Brien, A.J. Johnson, R. Abualia, L. Antonielli,
J.C. Montesinos López, Y. Zhang, S. Tan, C. Cuesta, C. Artner, E. Bouguyon, A.
Gojon, J. Friml, R.A. Gutiérrez, K.T. Wabnik, E. Benková, EMBO Journal 40 (2021).
date_created: 2021-01-17T23:01:12Z
date_published: 2021-02-01T00:00:00Z
date_updated: 2024-03-28T23:30:39Z
day: '01'
ddc:
- '580'
department:
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- _id: EvBe
doi: 10.15252/embj.2020106862
external_id:
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pmid: 1
project:
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call_identifier: FWF
grant_number: I 1774-B16
name: Hormone cross-talk drives nutrient dependent plant development
- _id: 2685A872-B435-11E9-9278-68D0E5697425
name: Hormonal regulation of plant adaptive responses to environmental signals
- _id: 26538374-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03630
name: Molecular mechanisms of endocytic cargo recognition in plants
publication: EMBO Journal
publication_identifier:
eissn:
- '14602075'
issn:
- '02614189'
publication_status: published
publisher: Embo Press
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/a-plants-way-to-its-favorite-food/
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scopus_import: '1'
status: public
title: Modulation of plant root growth by nitrogen source-defined regulation of polar
auxin transport
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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: 40
year: '2021'
...
---
_id: '9913'
abstract:
- lang: eng
text: Nitrate commands genome-wide gene expression changes that impact metabolism,
physiology, plant growth, and development. In an effort to identify new components
involved in nitrate responses in plants, we analyze the Arabidopsis thaliana root
phosphoproteome in response to nitrate treatments via liquid chromatography coupled
to tandem mass spectrometry. 176 phosphoproteins show significant changes at 5
or 20 min after nitrate treatments. Proteins identified by 5 min include signaling
components such as kinases or transcription factors. In contrast, by 20 min, proteins
identified were associated with transporter activity or hormone metabolism functions,
among others. The phosphorylation profile of NITRATE TRANSPORTER 1.1 (NRT1.1)
mutant plants was significantly altered as compared to wild-type plants, confirming
its key role in nitrate signaling pathways that involves phosphorylation changes.
Integrative bioinformatics analysis highlights auxin transport as an important
mechanism modulated by nitrate signaling at the post-translational level. We validated
a new phosphorylation site in PIN2 and provide evidence that it functions in primary
and lateral root growth responses to nitrate.
acknowledgement: This work was supported by ANID—Millennium Science Initiative Program—ICN17_022,
Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation
(15090007), ANID—Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT)
1180759 (to RAG) and 1171631 (to AV). We would like to thank Unidad de Microscopía
Avanzada UC (UMA UC).
article_number: e51813
article_processing_charge: Yes
article_type: original
author:
- first_name: Andrea
full_name: Vega, Andrea
last_name: Vega
- first_name: Isabel
full_name: Fredes, Isabel
last_name: Fredes
- first_name: José
full_name: O’Brien, José
last_name: O’Brien
- first_name: Zhouxin
full_name: Shen, Zhouxin
last_name: Shen
- first_name: Krisztina
full_name: Ötvös, Krisztina
id: 29B901B0-F248-11E8-B48F-1D18A9856A87
last_name: Ötvös
orcid: 0000-0002-5503-4983
- first_name: Rashed
full_name: Abualia, Rashed
id: 4827E134-F248-11E8-B48F-1D18A9856A87
last_name: Abualia
orcid: 0000-0002-9357-9415
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Steven P.
full_name: Briggs, Steven P.
last_name: Briggs
- first_name: Rodrigo A.
full_name: Gutiérrez, Rodrigo A.
last_name: Gutiérrez
citation:
ama: Vega A, Fredes I, O’Brien J, et al. Nitrate triggered phosphoproteome changes
and a PIN2 phosphosite modulating root system architecture. EMBO Reports.
2021;22(9). doi:10.15252/embr.202051813
apa: Vega, A., Fredes, I., O’Brien, J., Shen, Z., Ötvös, K., Abualia, R., … Gutiérrez,
R. A. (2021). Nitrate triggered phosphoproteome changes and a PIN2 phosphosite
modulating root system architecture. EMBO Reports. Wiley. https://doi.org/10.15252/embr.202051813
chicago: Vega, Andrea, Isabel Fredes, José O’Brien, Zhouxin Shen, Krisztina Ötvös,
Rashed Abualia, Eva Benková, Steven P. Briggs, and Rodrigo A. Gutiérrez. “Nitrate
Triggered Phosphoproteome Changes and a PIN2 Phosphosite Modulating Root System
Architecture.” EMBO Reports. Wiley, 2021. https://doi.org/10.15252/embr.202051813.
ieee: A. Vega et al., “Nitrate triggered phosphoproteome changes and a PIN2
phosphosite modulating root system architecture,” EMBO Reports, vol. 22,
no. 9. Wiley, 2021.
ista: Vega A, Fredes I, O’Brien J, Shen Z, Ötvös K, Abualia R, Benková E, Briggs
SP, Gutiérrez RA. 2021. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite
modulating root system architecture. EMBO Reports. 22(9), e51813.
mla: Vega, Andrea, et al. “Nitrate Triggered Phosphoproteome Changes and a PIN2
Phosphosite Modulating Root System Architecture.” EMBO Reports, vol. 22,
no. 9, e51813, Wiley, 2021, doi:10.15252/embr.202051813.
short: A. Vega, I. Fredes, J. O’Brien, Z. Shen, K. Ötvös, R. Abualia, E. Benková,
S.P. Briggs, R.A. Gutiérrez, EMBO Reports 22 (2021).
date_created: 2021-08-15T22:01:30Z
date_published: 2021-09-06T00:00:00Z
date_updated: 2024-03-28T23:30:40Z
day: '06'
ddc:
- '580'
department:
- _id: EvBe
- _id: GradSch
doi: 10.15252/embr.202051813
external_id:
isi:
- '000681754200001'
pmid:
- '34357701 '
file:
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checksum: 750de03dc3b715c37090126c1548ba13
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date_updated: 2021-10-05T13:36:42Z
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publication: EMBO Reports
publication_identifier:
eissn:
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issn:
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publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '10303'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating
root system architecture
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: 22
year: '2021'
...
---
_id: '10303'
abstract:
- lang: eng
text: 'Nitrogen is an essential macronutrient determining plant growth, development
and affecting agricultural productivity. Root, as a hub that perceives and integrates
local and systemic signals on the plant’s external and endogenous nitrogen resources,
communicates with other plant organs to consolidate their physiology and development
in accordance with actual nitrogen balance. Over the last years, numerous studies
demonstrated that these comprehensive developmental adaptations rely on the interaction
between pathways controlling nitrogen homeostasis and hormonal networks acting
globally in the plant body. However, molecular insights into how the information
about the nitrogen status is translated through hormonal pathways into specific
developmental output are lacking. In my work, I addressed so far poorly understood
mechanisms underlying root-to-shoot communication that lead to a rapid re-adjustment
of shoot growth and development after nitrate provision. Applying a combination
of molecular, cell, and developmental biology approaches, genetics and grafting
experiments as well as hormonal analytics, I identified and characterized an unknown
molecular framework orchestrating shoot development with a root nitrate sensory
system. '
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Rashed
full_name: Abualia, Rashed
id: 4827E134-F248-11E8-B48F-1D18A9856A87
last_name: Abualia
orcid: 0000-0002-9357-9415
citation:
ama: Abualia R. Role of hormones in nitrate regulated growth. 2021. doi:10.15479/at:ista:10303
apa: Abualia, R. (2021). Role of hormones in nitrate regulated growth. Institute
of Science and Technology Austria. https://doi.org/10.15479/at:ista:10303
chicago: Abualia, Rashed. “Role of Hormones in Nitrate Regulated Growth.” Institute
of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10303.
ieee: R. Abualia, “Role of hormones in nitrate regulated growth,” Institute of Science
and Technology Austria, 2021.
ista: Abualia R. 2021. Role of hormones in nitrate regulated growth. Institute of
Science and Technology Austria.
mla: Abualia, Rashed. Role of Hormones in Nitrate Regulated Growth. Institute
of Science and Technology Austria, 2021, doi:10.15479/at:ista:10303.
short: R. Abualia, Role of Hormones in Nitrate Regulated Growth, Institute of Science
and Technology Austria, 2021.
date_created: 2021-11-18T11:20:59Z
date_published: 2021-11-22T00:00:00Z
date_updated: 2023-09-19T14:42:45Z
day: '22'
ddc:
- '580'
- '581'
degree_awarded: PhD
department:
- _id: GradSch
- _id: EvBe
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language:
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publication_identifier:
issn:
- 2663-337X
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related_material:
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status: public
- id: '9913'
relation: part_of_dissertation
status: public
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status: public
supervisor:
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
title: Role of hormones in nitrate regulated growth
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '9962'
abstract:
- lang: eng
text: The brain is one of the largest and most complex organs and it is composed
of billions of neurons that communicate together enabling e.g. consciousness.
The cerebral cortex is the largest site of neural integration in the central nervous
system. Concerted radial migration of newly born cortical projection neurons,
from their birthplace to their final position, is a key step in the assembly of
the cerebral cortex. The cellular and molecular mechanisms regulating radial neuronal
migration in vivo are however still unclear. Recent evidence suggests that distinct
signaling cues act cell-autonomously but differentially at certain steps during
the overall migration process. Moreover, functional analysis of genetic mosaics
(mutant neurons present in wild-type/heterozygote environment) using the MADM
(Mosaic Analysis with Double Markers) analyses in comparison to global knockout
also indicate a significant degree of non-cell-autonomous and/or community effects
in the control of cortical neuron migration. The interactions of cell-intrinsic
(cell-autonomous) and cell-extrinsic (non-cell-autonomous) components are largely
unknown. In part of this thesis work we established a MADM-based experimental
strategy for the quantitative analysis of cell-autonomous gene function versus
non-cell-autonomous and/or community effects. The direct comparison of mutant
neurons from the genetic mosaic (cell-autonomous) to mutant neurons in the conditional
and/or global knockout (cell-autonomous + non-cell-autonomous) allows to quantitatively
analyze non-cell-autonomous effects. Such analysis enable the high-resolution
analysis of projection neuron migration dynamics in distinct environments with
concomitant isolation of genomic and proteomic profiles. Using these experimental
paradigms and in combination with computational modeling we show and characterize
the nature of non-cell-autonomous effects to coordinate radial neuron migration.
Furthermore, this thesis discusses recent developments in neurodevelopment with
focus on neuronal polarization and non-cell-autonomous mechanisms in neuronal
migration.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Andi H
full_name: Hansen, Andi H
id: 38853E16-F248-11E8-B48F-1D18A9856A87
last_name: Hansen
citation:
ama: Hansen AH. Cell-autonomous gene function and non-cell-autonomous effects in
radial projection neuron migration. 2021. doi:10.15479/at:ista:9962
apa: Hansen, A. H. (2021). Cell-autonomous gene function and non-cell-autonomous
effects in radial projection neuron migration. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:9962
chicago: Hansen, Andi H. “Cell-Autonomous Gene Function and Non-Cell-Autonomous
Effects in Radial Projection Neuron Migration.” Institute of Science and Technology
Austria, 2021. https://doi.org/10.15479/at:ista:9962.
ieee: A. H. Hansen, “Cell-autonomous gene function and non-cell-autonomous effects
in radial projection neuron migration,” Institute of Science and Technology Austria,
2021.
ista: Hansen AH. 2021. Cell-autonomous gene function and non-cell-autonomous effects
in radial projection neuron migration. Institute of Science and Technology Austria.
mla: Hansen, Andi H. Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects
in Radial Projection Neuron Migration. Institute of Science and Technology
Austria, 2021, doi:10.15479/at:ista:9962.
short: A.H. Hansen, Cell-Autonomous Gene Function and Non-Cell-Autonomous Effects
in Radial Projection Neuron Migration, Institute of Science and Technology Austria,
2021.
date_created: 2021-08-29T12:36:50Z
date_published: 2021-09-02T00:00:00Z
date_updated: 2023-09-22T09:58:30Z
day: '02'
ddc:
- '570'
degree_awarded: PhD
department:
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- _id: SiHi
doi: 10.15479/at:ista:9962
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creator: ahansen
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file_size: 13457469
relation: main_file
file_date_updated: 2022-09-03T22:30:04Z
has_accepted_license: '1'
keyword:
- Neuronal migration
- Non-cell-autonomous
- Cell-autonomous
- Neurodevelopmental disease
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '182'
project:
- _id: 2625A13E-B435-11E9-9278-68D0E5697425
grant_number: '24812'
name: Molecular Mechanisms of Radial Neuronal Migration
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8569'
relation: part_of_dissertation
status: public
- id: '960'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
title: Cell-autonomous gene function and non-cell-autonomous effects in radial projection
neuron migration
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2021'
...
---
_id: '9428'
abstract:
- lang: eng
text: Thermalization is the inevitable fate of many complex quantum systems, whose
dynamics allow them to fully explore the vast configuration space regardless of
the initial state---the behaviour known as quantum ergodicity. In a quest for
experimental realizations of coherent long-time dynamics, efforts have focused
on ergodicity-breaking mechanisms, such as integrability and localization. The
recent discovery of persistent revivals in quantum simulators based on Rydberg
atoms have pointed to the existence of a new type of behaviour where the system
rapidly relaxes for most initial conditions, while certain initial states give
rise to non-ergodic dynamics. This collective effect has been named ”quantum many-body
scarring’by analogy with a related form of weak ergodicity breaking that occurs
for a single particle inside a stadium billiard potential. In this Review, we
provide a pedagogical introduction to quantum many-body scars and highlight the
emerging connections with the semiclassical quantization of many-body systems.
We discuss the relation between scars and more general routes towards weak violations
of ergodicity due to embedded algebras and non-thermal eigenstates, and highlight
possible applications of scars in quantum technology.
acknowledgement: We thank our collaborators K. Bull, S. Choi, J.-Y. Desaules, W. W.
Ho, A. Hudomal, M. Lukin, I. Martin, H. Pichler, N. Regnault, I. Vasić and in particular
A. Michailidis and C. Turner, without whom this work would not have been possible.
We also benefited from discussions with E. Altman, B. A. Bernevig, A. Chandran,
P. Fendley, V. Khemani and L. Motrunich. M.S. was supported by the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement no. 850899). D.A.A. was supported by the Swiss National Science
Foundation and by the ERC under the European Union’s Horizon 2020 research and innovation
programme (grant agreement no. 864597). Z.P. acknowledges support by the Leverhulme
Trust Research Leadership Award RL-2019-015.
article_processing_charge: No
article_type: review
author:
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Dmitry A.
full_name: Abanin, Dmitry A.
last_name: Abanin
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
citation:
ama: Serbyn M, Abanin DA, Papić Z. Quantum many-body scars and weak breaking of
ergodicity. Nature Physics. 2021;17(6):675–685. doi:10.1038/s41567-021-01230-2
apa: Serbyn, M., Abanin, D. A., & Papić, Z. (2021). Quantum many-body scars
and weak breaking of ergodicity. Nature Physics. Nature Research. https://doi.org/10.1038/s41567-021-01230-2
chicago: Serbyn, Maksym, Dmitry A. Abanin, and Zlatko Papić. “Quantum Many-Body
Scars and Weak Breaking of Ergodicity.” Nature Physics. Nature Research,
2021. https://doi.org/10.1038/s41567-021-01230-2.
ieee: M. Serbyn, D. A. Abanin, and Z. Papić, “Quantum many-body scars and weak breaking
of ergodicity,” Nature Physics, vol. 17, no. 6. Nature Research, pp. 675–685,
2021.
ista: Serbyn M, Abanin DA, Papić Z. 2021. Quantum many-body scars and weak breaking
of ergodicity. Nature Physics. 17(6), 675–685.
mla: Serbyn, Maksym, et al. “Quantum Many-Body Scars and Weak Breaking of Ergodicity.”
Nature Physics, vol. 17, no. 6, Nature Research, 2021, pp. 675–685, doi:10.1038/s41567-021-01230-2.
short: M. Serbyn, D.A. Abanin, Z. Papić, Nature Physics 17 (2021) 675–685.
date_created: 2021-05-28T09:03:50Z
date_published: 2021-06-01T00:00:00Z
date_updated: 2023-10-18T08:20:59Z
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doi: 10.1038/s41567-021-01230-2
ec_funded: 1
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arxiv:
- '2011.09486'
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date_created: 2021-09-20T09:27:43Z
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month: '06'
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oa_version: Preprint
page: 675–685
project:
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call_identifier: H2020
grant_number: '850899'
name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
publication_status: published
publisher: Nature Research
quality_controlled: '1'
status: public
title: Quantum many-body scars and weak breaking of ergodicity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2021'
...
---
_id: '8931'
abstract:
- lang: eng
text: "Auxin is a major plant growth regulator, but current models on auxin perception
and signaling cannot explain the whole plethora of auxin effects, in particular
those associated with rapid responses. A possible candidate for a component of
additional auxin perception mechanisms is the AUXIN BINDING PROTEIN 1 (ABP1),
whose function in planta remains unclear.\r\nHere we combined expression analysis
with gain- and loss-of-function approaches to analyze the role of ABP1 in plant
development. ABP1 shows a broad expression largely overlapping with, but not regulated
by, transcriptional auxin response activity. Furthermore, ABP1 activity is not
essential for the transcriptional auxin signaling. Genetic in planta analysis
revealed that abp1 loss-of-function mutants show largely normal development with
minor defects in bolting. On the other hand, ABP1 gain-of-function alleles show
a broad range of growth and developmental defects, including root and hypocotyl
growth and bending, lateral root and leaf development, bolting, as well as response
to heat stress. At the cellular level, ABP1 gain-of-function leads to impaired
auxin effect on PIN polar distribution and affects BFA-sensitive PIN intracellular
aggregation.\r\nThe gain-of-function analysis suggests a broad, but still mechanistically
unclear involvement of ABP1 in plant development, possibly masked in abp1 loss-of-function
mutants by a functional redundancy."
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: We would like to acknowledge Bioimaging and Life Science Facilities
at IST Austria for continuous support and also the Plant Sciences Core Facility
of CEITEC Masaryk University for their support with obtaining a part of the scientific
data. We gratefully acknowledge Lindy Abas for help with ABP1::GFP-ABP1 construct
design. This project has received funding from the European Research Council (ERC)
under the European Union’s Horizon 2020 research and innovation program [grant agreement
no. 742985] and Austrian Science Fund (FWF) [I 3630-B25] to J.F.; DOC Fellowship
of the Austrian Academy of Sciences to L.L.; the European Structural and Investment
Funds, Operational Programme Research, Development and Education - Project „MSCAfellow@MUNI“
[CZ.02.2.69/0.0/0.0/17_050/0008496] to M.P.. This project was also supported by
the Czech Science Foundation [GA 20-20860Y] to M.Z and MEYS CR [project no.CZ.02.1.01/0.0/0.0/16_019/0000738]
to M. Č.
article_number: '110750'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Zuzana
full_name: Gelová, Zuzana
id: 0AE74790-0E0B-11E9-ABC7-1ACFE5697425
last_name: Gelová
orcid: 0000-0003-4783-1752
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
- first_name: Markéta
full_name: Pernisová, Markéta
last_name: Pernisová
- first_name: Géraldine
full_name: Brunoud, Géraldine
last_name: Brunoud
- first_name: Xixi
full_name: Zhang, Xixi
id: 61A66458-47E9-11EA-85BA-8AEAAF14E49A
last_name: Zhang
orcid: 0000-0001-7048-4627
- first_name: Matous
full_name: Glanc, Matous
id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2
last_name: Glanc
orcid: 0000-0003-0619-7783
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: Jaroslav
full_name: Michalko, Jaroslav
id: 483727CA-F248-11E8-B48F-1D18A9856A87
last_name: Michalko
- first_name: Zlata
full_name: Pavlovicova, Zlata
last_name: Pavlovicova
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Huibin
full_name: Han, Huibin
id: 31435098-F248-11E8-B48F-1D18A9856A87
last_name: Han
- first_name: Jakub
full_name: Hajny, Jakub
id: 4800CC20-F248-11E8-B48F-1D18A9856A87
last_name: Hajny
orcid: 0000-0003-2140-7195
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Milada
full_name: Čovanová, Milada
last_name: Čovanová
- first_name: Marta
full_name: Zwiewka, Marta
last_name: Zwiewka
- first_name: Lukas
full_name: Hörmayer, Lukas
id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
last_name: Hörmayer
orcid: 0000-0001-8295-2926
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: Tongda
full_name: Xu, Tongda
last_name: Xu
- first_name: Teva
full_name: Vernoux, Teva
last_name: Vernoux
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Gelová Z, Gallei MC, Pernisová M, et al. Developmental roles of auxin binding
protein 1 in Arabidopsis thaliana. Plant Science. 2021;303. doi:10.1016/j.plantsci.2020.110750
apa: Gelová, Z., Gallei, M. C., Pernisová, M., Brunoud, G., Zhang, X., Glanc, M.,
… Friml, J. (2021). Developmental roles of auxin binding protein 1 in Arabidopsis
thaliana. Plant Science. Elsevier. https://doi.org/10.1016/j.plantsci.2020.110750
chicago: Gelová, Zuzana, Michelle C Gallei, Markéta Pernisová, Géraldine Brunoud,
Xixi Zhang, Matous Glanc, Lanxin Li, et al. “Developmental Roles of Auxin Binding
Protein 1 in Arabidopsis Thaliana.” Plant Science. Elsevier, 2021. https://doi.org/10.1016/j.plantsci.2020.110750.
ieee: Z. Gelová et al., “Developmental roles of auxin binding protein 1 in
Arabidopsis thaliana,” Plant Science, vol. 303. Elsevier, 2021.
ista: Gelová Z, Gallei MC, Pernisová M, Brunoud G, Zhang X, Glanc M, Li L, Michalko
J, Pavlovicova Z, Verstraeten I, Han H, Hajny J, Hauschild R, Čovanová M, Zwiewka
M, Hörmayer L, Fendrych M, Xu T, Vernoux T, Friml J. 2021. Developmental roles
of auxin binding protein 1 in Arabidopsis thaliana. Plant Science. 303, 110750.
mla: Gelová, Zuzana, et al. “Developmental Roles of Auxin Binding Protein 1 in Arabidopsis
Thaliana.” Plant Science, vol. 303, 110750, Elsevier, 2021, doi:10.1016/j.plantsci.2020.110750.
short: Z. Gelová, M.C. Gallei, M. Pernisová, G. Brunoud, X. Zhang, M. Glanc, L.
Li, J. Michalko, Z. Pavlovicova, I. Verstraeten, H. Han, J. Hajny, R. Hauschild,
M. Čovanová, M. Zwiewka, L. Hörmayer, M. Fendrych, T. Xu, T. Vernoux, J. Friml,
Plant Science 303 (2021).
date_created: 2020-12-09T14:48:28Z
date_published: 2021-02-01T00:00:00Z
date_updated: 2024-03-28T23:30:44Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
- _id: Bio
doi: 10.1016/j.plantsci.2020.110750
ec_funded: 1
external_id:
isi:
- '000614154500001'
pmid:
- '33487339'
file:
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checksum: a7f2562bdca62d67dfa88e271b62a629
content_type: application/pdf
creator: dernst
date_created: 2021-02-04T07:49:25Z
date_updated: 2021-02-04T07:49:25Z
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success: 1
file_date_updated: 2021-02-04T07:49:25Z
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intvolume: ' 303'
isi: 1
keyword:
- Agronomy and Crop Science
- Plant Science
- Genetics
- General Medicine
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
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
- _id: 26B4D67E-B435-11E9-9278-68D0E5697425
grant_number: '25351'
name: 'A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated
Rapid Growth Inhibition in Arabidopsis Root'
publication: Plant Science
publication_identifier:
issn:
- 0168-9452
publication_status: published
publisher: Elsevier
quality_controlled: '1'
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title: Developmental roles of auxin binding protein 1 in Arabidopsis thaliana
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...