---
_id: '15037'
abstract:
- lang: eng
text: Protein abundance and localization at the plasma membrane (PM) shapes plant
development and mediates adaptation to changing environmental conditions. It is
regulated by ubiquitination, a post-translational modification crucial for the
proper sorting of endocytosed PM proteins to the vacuole for subsequent degradation.
To understand the significance and the variety of roles played by this reversible
modification, the function of ubiquitin receptors, which translate the ubiquitin
signature into a cellular response, needs to be elucidated. In this study, we
show that TOL (TOM1-like) proteins function in plants as multivalent ubiquitin
receptors, governing ubiquitinated cargo delivery to the vacuole via the conserved
Endosomal Sorting Complex Required for Transport (ESCRT) pathway. TOL2 and TOL6
interact with components of the ESCRT machinery and bind to K63-linked ubiquitin
via two tandemly arranged conserved ubiquitin-binding domains. Mutation of these
domains results not only in a loss of ubiquitin binding but also altered localization,
abolishing TOL6 ubiquitin receptor activity. Function and localization of TOL6
is itself regulated by ubiquitination, whereby TOL6 ubiquitination potentially
modulates degradation of PM-localized cargoes, assisting in the fine-tuning of
the delicate interplay between protein recycling and downregulation. Taken together,
our findings demonstrate the function and regulation of a ubiquitin receptor that
mediates vacuolar degradation of PM proteins in higher plants.
article_processing_charge: No
article_type: original
author:
- first_name: Jeanette
full_name: Moulinier-Anzola, Jeanette
last_name: Moulinier-Anzola
- first_name: Maximilian
full_name: Schwihla, Maximilian
last_name: Schwihla
- first_name: Lucinda
full_name: De-Araújo, Lucinda
last_name: De-Araújo
- first_name: Christina
full_name: Artner, Christina
id: 45DF286A-F248-11E8-B48F-1D18A9856A87
last_name: Artner
- first_name: Lisa
full_name: Jörg, Lisa
last_name: Jörg
- first_name: Nataliia
full_name: Konstantinova, Nataliia
last_name: Konstantinova
- first_name: Christian
full_name: Luschnig, Christian
last_name: Luschnig
- first_name: Barbara
full_name: Korbei, Barbara
last_name: Korbei
citation:
ama: Moulinier-Anzola J, Schwihla M, De-Araújo L, et al. TOLs function as ubiquitin
receptors in the early steps of the ESCRT pathway in higher plants. Molecular
Plant. 2020;13(5):717-731. doi:10.1016/j.molp.2020.02.012
apa: Moulinier-Anzola, J., Schwihla, M., De-Araújo, L., Artner, C., Jörg, L., Konstantinova,
N., … Korbei, B. (2020). TOLs function as ubiquitin receptors in the early steps
of the ESCRT pathway in higher plants. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2020.02.012
chicago: Moulinier-Anzola, Jeanette, Maximilian Schwihla, Lucinda De-Araújo, Christina
Artner, Lisa Jörg, Nataliia Konstantinova, Christian Luschnig, and Barbara Korbei.
“TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway
in Higher Plants.” Molecular Plant. Elsevier, 2020. https://doi.org/10.1016/j.molp.2020.02.012.
ieee: J. Moulinier-Anzola et al., “TOLs function as ubiquitin receptors in
the early steps of the ESCRT pathway in higher plants,” Molecular Plant,
vol. 13, no. 5. Elsevier, pp. 717–731, 2020.
ista: Moulinier-Anzola J, Schwihla M, De-Araújo L, Artner C, Jörg L, Konstantinova
N, Luschnig C, Korbei B. 2020. TOLs function as ubiquitin receptors in the early
steps of the ESCRT pathway in higher plants. Molecular Plant. 13(5), 717–731.
mla: Moulinier-Anzola, Jeanette, et al. “TOLs Function as Ubiquitin Receptors in
the Early Steps of the ESCRT Pathway in Higher Plants.” Molecular Plant,
vol. 13, no. 5, Elsevier, 2020, pp. 717–31, doi:10.1016/j.molp.2020.02.012.
short: J. Moulinier-Anzola, M. Schwihla, L. De-Araújo, C. Artner, L. Jörg, N. Konstantinova,
C. Luschnig, B. Korbei, Molecular Plant 13 (2020) 717–731.
date_created: 2024-02-28T08:55:56Z
date_published: 2020-05-04T00:00:00Z
date_updated: 2024-02-28T12:41:52Z
day: '04'
ddc:
- '580'
department:
- _id: EvBe
doi: 10.1016/j.molp.2020.02.012
external_id:
pmid:
- '32087370'
file:
- access_level: open_access
checksum: c538a5008f7827f62d17d40a3bfabe65
content_type: application/pdf
creator: dernst
date_created: 2024-02-28T12:39:56Z
date_updated: 2024-02-28T12:39:56Z
file_id: '15038'
file_name: 2020_MolecularPlant_MoulinierAnzola.pdf
file_size: 3089212
relation: main_file
success: 1
file_date_updated: 2024-02-28T12:39:56Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '5'
keyword:
- Plant Science
- Molecular Biology
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '05'
oa: 1
oa_version: Published Version
page: 717-731
pmid: 1
publication: Molecular Plant
publication_identifier:
issn:
- 1674-2052
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway
in higher 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: 13
year: '2020'
...
---
_id: '15036'
abstract:
- lang: eng
text: The assembly of a septin filament requires that homologous monomers must distinguish
between one another in establishing appropriate interfaces with their neighbors.
To understand this phenomenon at the molecular level, we present the first four
crystal structures of heterodimeric septin complexes. We describe in detail the
two distinct types of G-interface present within the octameric particles, which
must polymerize to form filaments. These are formed between SEPT2 and SEPT6 and
between SEPT7 and SEPT3, and their description permits an understanding of the
structural basis for the selectivity necessary for correct filament assembly.
By replacing SEPT6 by SEPT8 or SEPT11, it is possible to rationalize Kinoshita's
postulate, which predicts the exchangeability of septins from within a subgroup.
Switches I and II, which in classical small GTPases provide a mechanism for nucleotide-dependent
conformational change, have been repurposed in septins to play a fundamental role
in molecular recognition. Specifically, it is switch I which holds the key to
discriminating between the two different G-interfaces. Moreover, residues which
are characteristic for a given subgroup play subtle, but pivotal, roles in guaranteeing
that the correct interfaces are formed.
article_processing_charge: No
article_type: original
author:
- first_name: Higor Vinícius Dias
full_name: Rosa, Higor Vinícius Dias
last_name: Rosa
- first_name: Diego Antonio
full_name: Leonardo, Diego Antonio
last_name: Leonardo
- first_name: Gabriel
full_name: Brognara, Gabriel
id: D96FFDA0-A884-11E9-9968-DC26E6697425
last_name: Brognara
- first_name: José
full_name: Brandão-Neto, José
last_name: Brandão-Neto
- first_name: Humberto
full_name: D'Muniz Pereira, Humberto
last_name: D'Muniz Pereira
- first_name: Ana Paula Ulian
full_name: Araújo, Ana Paula Ulian
last_name: Araújo
- first_name: Richard Charles
full_name: Garratt, Richard Charles
last_name: Garratt
citation:
ama: 'Rosa HVD, Leonardo DA, Brognara G, et al. Molecular recognition at septin
interfaces: The switches hold the key. Journal of Molecular Biology. 2020;432(21):5784-5801.
doi:10.1016/j.jmb.2020.09.001'
apa: 'Rosa, H. V. D., Leonardo, D. A., Brognara, G., Brandão-Neto, J., D’Muniz Pereira,
H., Araújo, A. P. U., & Garratt, R. C. (2020). Molecular recognition at septin
interfaces: The switches hold the key. Journal of Molecular Biology. Elsevier.
https://doi.org/10.1016/j.jmb.2020.09.001'
chicago: 'Rosa, Higor Vinícius Dias, Diego Antonio Leonardo, Gabriel Brognara, José
Brandão-Neto, Humberto D’Muniz Pereira, Ana Paula Ulian Araújo, and Richard Charles
Garratt. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.”
Journal of Molecular Biology. Elsevier, 2020. https://doi.org/10.1016/j.jmb.2020.09.001.'
ieee: 'H. V. D. Rosa et al., “Molecular recognition at septin interfaces:
The switches hold the key,” Journal of Molecular Biology, vol. 432, no.
21. Elsevier, pp. 5784–5801, 2020.'
ista: 'Rosa HVD, Leonardo DA, Brognara G, Brandão-Neto J, D’Muniz Pereira H, Araújo
APU, Garratt RC. 2020. Molecular recognition at septin interfaces: The switches
hold the key. Journal of Molecular Biology. 432(21), 5784–5801.'
mla: 'Rosa, Higor Vinícius Dias, et al. “Molecular Recognition at Septin Interfaces:
The Switches Hold the Key.” Journal of Molecular Biology, vol. 432, no.
21, Elsevier, 2020, pp. 5784–801, doi:10.1016/j.jmb.2020.09.001.'
short: H.V.D. Rosa, D.A. Leonardo, G. Brognara, J. Brandão-Neto, H. D’Muniz Pereira,
A.P.U. Araújo, R.C. Garratt, Journal of Molecular Biology 432 (2020) 5784–5801.
date_created: 2024-02-28T08:50:34Z
date_published: 2020-10-02T00:00:00Z
date_updated: 2024-02-28T12:37:54Z
day: '02'
department:
- _id: MaLo
doi: 10.1016/j.jmb.2020.09.001
external_id:
pmid:
- '32910969'
intvolume: ' 432'
issue: '21'
keyword:
- Molecular Biology
- Structural Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.jmb.2020.09.001
month: '10'
oa: 1
oa_version: Published Version
page: 5784-5801
pmid: 1
publication: Journal of Molecular Biology
publication_identifier:
issn:
- 0022-2836
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Molecular recognition at septin interfaces: The switches hold the key'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 432
year: '2020'
...
---
_id: '8384'
abstract:
- lang: eng
text: Previous research on animations of soap bubbles, films, and foams largely
focuses on the motion and geometric shape of the bubble surface. These works neglect
the evolution of the bubble’s thickness, which is normally responsible for visual
phenomena like surface vortices, Newton’s interference patterns, capillary waves,
and deformation-dependent rupturing of films in a foam. In this paper, we model
these natural phenomena by introducing the film thickness as a reduced degree
of freedom in the Navier-Stokes equations and deriving their equations of motion.
We discretize the equations on a nonmanifold triangle mesh surface and couple
it to an existing bubble solver. In doing so, we also introduce an incompressible
fluid solver for 2.5D films and a novel advection algorithm for convecting fields
across non-manifold surface junctions. Our simulations enhance state-of-the-art
bubble solvers with additional effects caused by convection, rippling, draining,
and evaporation of the thin film.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "We wish to thank the anonymous reviewers and the members of the
Visual Computing Group at IST Austria for their valuable feedback, especially Camille
Schreck for her help in rendering. This research was supported by the Scientific
Service Units (SSU) of IST Austria through resources provided by Scientific Computing.
We would like to thank the authors of [Belcour and Barla 2017] for providing their
implementation, the authors of [Atkins and Elliott 2010] and [Seychelles et al.
2008] for allowing us to use their results, and Rok Grah for helpful discussions.
Finally, we thank Ryoichi Ando for many discussions from the beginning of the project
that resulted in important contents of the paper including our formulation, numerical
scheme, and initial implementation. This project has received funding from the\r\nEuropean
Research Council (ERC) under the European Union’s Horizon 2020 research and innovation
programme under grant agreement No. 638176."
article_number: '31'
article_processing_charge: No
article_type: original
author:
- first_name: Sadashige
full_name: Ishida, Sadashige
id: 6F7C4B96-A8E9-11E9-A7CA-09ECE5697425
last_name: Ishida
- first_name: Peter
full_name: Synak, Peter
id: 331776E2-F248-11E8-B48F-1D18A9856A87
last_name: Synak
- first_name: Fumiya
full_name: Narita, Fumiya
last_name: Narita
- first_name: Toshiya
full_name: Hachisuka, Toshiya
last_name: Hachisuka
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Ishida S, Synak P, Narita F, Hachisuka T, Wojtan C. A model for soap film dynamics
with evolving thickness. ACM Transactions on Graphics. 2020;39(4). doi:10.1145/3386569.3392405
apa: Ishida, S., Synak, P., Narita, F., Hachisuka, T., & Wojtan, C. (2020).
A model for soap film dynamics with evolving thickness. ACM Transactions on
Graphics. Association for Computing Machinery. https://doi.org/10.1145/3386569.3392405
chicago: Ishida, Sadashige, Peter Synak, Fumiya Narita, Toshiya Hachisuka, and Chris
Wojtan. “A Model for Soap Film Dynamics with Evolving Thickness.” ACM Transactions
on Graphics. Association for Computing Machinery, 2020. https://doi.org/10.1145/3386569.3392405.
ieee: S. Ishida, P. Synak, F. Narita, T. Hachisuka, and C. Wojtan, “A model for
soap film dynamics with evolving thickness,” ACM Transactions on Graphics,
vol. 39, no. 4. Association for Computing Machinery, 2020.
ista: Ishida S, Synak P, Narita F, Hachisuka T, Wojtan C. 2020. A model for soap
film dynamics with evolving thickness. ACM Transactions on Graphics. 39(4), 31.
mla: Ishida, Sadashige, et al. “A Model for Soap Film Dynamics with Evolving Thickness.”
ACM Transactions on Graphics, vol. 39, no. 4, 31, Association for Computing
Machinery, 2020, doi:10.1145/3386569.3392405.
short: S. Ishida, P. Synak, F. Narita, T. Hachisuka, C. Wojtan, ACM Transactions
on Graphics 39 (2020).
date_created: 2020-09-13T22:01:18Z
date_published: 2020-07-08T00:00:00Z
date_updated: 2024-02-28T12:57:31Z
day: '08'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/3386569.3392405
ec_funded: 1
external_id:
isi:
- '000583700300004'
file:
- access_level: open_access
checksum: 813831ca91319d794d9748c276b24578
content_type: application/pdf
creator: dernst
date_created: 2020-11-23T09:03:19Z
date_updated: 2020-11-23T09:03:19Z
file_id: '8795'
file_name: 2020_soapfilm_submitted.pdf
file_size: 14935529
relation: main_file
success: 1
file_date_updated: 2020-11-23T09:03:19Z
has_accepted_license: '1'
intvolume: ' 39'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1145/3386569.3392405
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- '15577368'
issn:
- '07300301'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: A model for soap film dynamics with evolving thickness
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 39
year: '2020'
...
---
_id: '7802'
abstract:
- lang: eng
text: "The Massively Parallel Computation (MPC) model is an emerging model which
distills core aspects of distributed and parallel computation. It has been developed
as a tool to solve (typically graph) problems in systems where the input is distributed
over many machines with limited space.\r\n\t\r\nRecent 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 fundamental graph problems
of Maximal Matching and Maximal Independent Set. However, there have been no prior
corresponding deterministic algorithms.\r\n\t\r\n\tA major challenge underlying
the sublinear space setting is that the local space of each machine might be too
small to store all the edges incident to a single node. This poses a considerable
obstacle compared to the 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 additional desired properties. The degree of the nodes in this subgraph
is small in the sense that the edges of each node can be now stored on a single
machine. This low-degree subgraph also has the property that solving the problem
on this subgraph provides \\emph{significant} global progress, i.e., progress
towards solving the problem for the original input graph.\r\n\t\r\nUsing this
framework to derandomize the well-known randomized algorithm of Luby [SICOMP'86],
we obtain $O(\\log \\Delta+\\log\\log n)$-round deterministic MPC algorithms for
solving the fundamental problems of Maximal Matching and Maximal Independent Set
with $O(n^{\\epsilon})$ space on each machine for any constant $\\epsilon > 0$.
Based on the recent work of Ghaffari et al. [FOCS'18], this additive $O(\\log\\log
n)$ factor is conditionally essential. These algorithms can also be shown to run
in $O(\\log \\Delta)$ rounds in the closely related model of CONGESTED CLIQUE,
improving upon the state-of-the-art bound of $O(\\log^2 \\Delta)$ rounds by Censor-Hillel
et al. [DISC'17]."
article_processing_charge: No
author:
- first_name: Artur
full_name: Czumaj, Artur
last_name: Czumaj
orcid: 0000-0002-5646-9524
- 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. In: Proceedings of the 32nd ACM Symposium
on Parallelism in Algorithms and Architectures (SPAA 2020). Association for
Computing Machinery; 2020:175-185. doi:10.1145/3350755.3400282'
apa: 'Czumaj, A., Davies, P., & Parter, M. (2020). Graph sparsification for
derandomizing massively parallel computation with low space. In Proceedings
of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA
2020) (pp. 175–185). Virtual Event, United States: Association for Computing
Machinery. https://doi.org/10.1145/3350755.3400282'
chicago: Czumaj, Artur, Peter Davies, and Merav Parter. “Graph Sparsification for
Derandomizing Massively Parallel Computation with Low Space.” In Proceedings
of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA
2020), 175–85. Association for Computing Machinery, 2020. https://doi.org/10.1145/3350755.3400282.
ieee: A. Czumaj, P. Davies, and M. Parter, “Graph sparsification for derandomizing
massively parallel computation with low space,” in Proceedings of the 32nd
ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020),
Virtual Event, United States, 2020, no. 7, pp. 175–185.
ista: 'Czumaj A, Davies P, Parter M. 2020. Graph sparsification for derandomizing
massively parallel computation with low space. Proceedings of the 32nd ACM Symposium
on Parallelism in Algorithms and Architectures (SPAA 2020). SPAA: Symposium on
Parallelism in Algorithms and Architectures, 175–185.'
mla: Czumaj, Artur, et al. “Graph Sparsification for Derandomizing Massively Parallel
Computation with Low Space.” Proceedings of the 32nd ACM Symposium on Parallelism
in Algorithms and Architectures (SPAA 2020), no. 7, Association for Computing
Machinery, 2020, pp. 175–85, doi:10.1145/3350755.3400282.
short: A. Czumaj, P. Davies, M. Parter, in:, Proceedings of the 32nd ACM Symposium
on Parallelism in Algorithms and Architectures (SPAA 2020), Association for Computing
Machinery, 2020, pp. 175–185.
conference:
end_date: 2020-07-17
location: Virtual Event, United States
name: 'SPAA: Symposium on Parallelism in Algorithms and Architectures'
start_date: 2020-07-15
date_created: 2020-05-06T08:53:34Z
date_published: 2020-07-01T00:00:00Z
date_updated: 2024-02-28T12:53:09Z
day: '01'
department:
- _id: DaAl
doi: 10.1145/3350755.3400282
ec_funded: 1
external_id:
arxiv:
- '1912.05390'
isi:
- '000744436200015'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1912.05390
month: '07'
oa: 1
oa_version: Preprint
page: 175-185
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and
Architectures (SPAA 2020)
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '9541'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Graph sparsification for derandomizing massively parallel computation with
low space
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2020'
...
---
_id: '7636'
abstract:
- lang: eng
text: "Balanced search trees typically use key comparisons to guide their operations,
and achieve logarithmic running time. By relying on numerical properties of the
keys, interpolation search achieves lower search complexity and better performance.
Although interpolation-based data structures were investigated in the past, their
non-blocking concurrent variants have received very little attention so far.\r\nIn
this paper, we propose the first non-blocking implementation of the classic interpolation
search tree (IST) data structure. For arbitrary key distributions, the data structure
ensures worst-case O(log n + p) amortized time for search, insertion and deletion
traversals. When the input key distributions are smooth, lookups run in expected
O(log log n + p) time, and insertion and deletion run in expected amortized O(log
log n + p) time, where p is a bound on the number of threads. To improve the scalability
of concurrent insertion and deletion, we propose a novel parallel rebuilding technique,
which should be of independent interest.\r\nWe evaluate whether the theoretical
improvements translate to practice by implementing the concurrent interpolation
search tree, and benchmarking it on uniform and nonuniform key distributions,
for dataset sizes in the millions to billions of keys. Relative to the state-of-the-art
concurrent data structures, the concurrent interpolation search tree achieves
performance improvements of up to 15% under high update rates, and of up to 50%
under moderate update rates. Further, ISTs exhibit up to 2X less cache-misses,
and consume 1.2 -- 2.6X less memory compared to the next best alternative on typical
dataset sizes. We find that the results are surprisingly robust to distributional
skew, which suggests that our data structure can be a promising alternative to
classic concurrent search structures."
acknowledgement: "This project has received funding from the European Research Council
(ERC) under the European Union Horizon 2020 research and innovation program, grant
agreement No 805223, ERC Starting Grant ScaleML. We acknowledge the support of the
Natural Sciences and\r\nEngineering Research Council of Canada (NSERC). "
article_processing_charge: No
author:
- first_name: Trevor A
full_name: Brown, Trevor A
id: 3569F0A0-F248-11E8-B48F-1D18A9856A87
last_name: Brown
- first_name: Aleksandar
full_name: Prokopec, Aleksandar
last_name: Prokopec
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Brown TA, Prokopec A, Alistarh D-A. Non-blocking interpolation search trees
with doubly-logarithmic running time. In: Proceedings of the ACM SIGPLAN Symposium
on Principles and Practice of Parallel Programming. Association for Computing
Machinery; 2020:276-291. doi:10.1145/3332466.3374542'
apa: 'Brown, T. A., Prokopec, A., & Alistarh, D.-A. (2020). Non-blocking interpolation
search trees with doubly-logarithmic running time. In Proceedings of the ACM
SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp.
276–291). San Diego, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3332466.3374542'
chicago: Brown, Trevor A, Aleksandar Prokopec, and Dan-Adrian Alistarh. “Non-Blocking
Interpolation Search Trees with Doubly-Logarithmic Running Time.” In Proceedings
of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming,
276–91. Association for Computing Machinery, 2020. https://doi.org/10.1145/3332466.3374542.
ieee: T. A. Brown, A. Prokopec, and D.-A. Alistarh, “Non-blocking interpolation
search trees with doubly-logarithmic running time,” in Proceedings of the ACM
SIGPLAN Symposium on Principles and Practice of Parallel Programming, San
Diego, CA, United States, 2020, pp. 276–291.
ista: 'Brown TA, Prokopec A, Alistarh D-A. 2020. Non-blocking interpolation search
trees with doubly-logarithmic running time. Proceedings of the ACM SIGPLAN Symposium
on Principles and Practice of Parallel Programming. PPOPP: Principles and Practice
of Parallel Programming, 276–291.'
mla: Brown, Trevor A., et al. “Non-Blocking Interpolation Search Trees with Doubly-Logarithmic
Running Time.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice
of Parallel Programming, Association for Computing Machinery, 2020, pp. 276–91,
doi:10.1145/3332466.3374542.
short: T.A. Brown, A. Prokopec, D.-A. Alistarh, in:, Proceedings of the ACM SIGPLAN
Symposium on Principles and Practice of Parallel Programming, Association for
Computing Machinery, 2020, pp. 276–291.
conference:
end_date: 2020-02-26
location: San Diego, CA, United States
name: 'PPOPP: Principles and Practice of Parallel Programming'
start_date: 2020-02-22
date_created: 2020-04-05T22:00:49Z
date_published: 2020-02-19T00:00:00Z
date_updated: 2024-02-28T12:55:14Z
day: '19'
department:
- _id: DaAl
doi: 10.1145/3332466.3374542
ec_funded: 1
external_id:
isi:
- '000564476500020'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1145/3332466.3374542
month: '02'
oa: 1
oa_version: Published Version
page: 276-291
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of
Parallel Programming
publication_identifier:
isbn:
- '9781450368186'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Non-blocking interpolation search trees with doubly-logarithmic running time
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8191'
abstract:
- lang: eng
text: "There has been a significant amount of research on hardware and software
support for efficient concurrent data structures; yet, the question of how to
build correct, simple, and scalable data structures has not yet been definitively
settled. In this paper, we revisit this question from a minimalist perspective,
and ask: what is the smallest amount of synchronization required for correct and
efficient concurrent search data structures, and how could this minimal synchronization
support be provided in hardware?\r\n\r\nTo address these questions, we introduce
memory tagging, a simple hardware mechanism which enables the programmer to \"tag\"
a dynamic set of memory locations, at cache-line granularity, and later validate
whether the memory has been concurrently modified, with the possibility of updating
one of the underlying locations atomically if validation succeeds. We provide
several examples showing that this mechanism can enable fast and arguably simple
concurrent data structure designs, such as lists, binary search trees, balanced
search trees, range queries, and Software Transactional Memory (STM) implementations.
We provide an implementation of memory tags in the Graphite multi-core simulator,
showing that the mechanism can be implemented entirely at the level of L1 cache,
and that it can enable non-trivial speedups versus existing implementations of
the above data structures."
article_processing_charge: No
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: Trevor A
full_name: Brown, Trevor A
id: 3569F0A0-F248-11E8-B48F-1D18A9856A87
last_name: Brown
- first_name: Nandini
full_name: Singhal, Nandini
last_name: Singhal
citation:
ama: 'Alistarh D-A, Brown TA, Singhal N. Memory tagging: Minimalist synchronization
for scalable concurrent data structures. In: Annual ACM Symposium on Parallelism
in Algorithms and Architectures. Association for Computing Machinery; 2020:37-49.
doi:10.1145/3350755.3400213'
apa: 'Alistarh, D.-A., Brown, T. A., & Singhal, N. (2020). Memory tagging: Minimalist
synchronization for scalable concurrent data structures. In Annual ACM Symposium
on Parallelism in Algorithms and Architectures (pp. 37–49). Virtual Event,
United States: Association for Computing Machinery. https://doi.org/10.1145/3350755.3400213'
chicago: 'Alistarh, Dan-Adrian, Trevor A Brown, and Nandini Singhal. “Memory Tagging:
Minimalist Synchronization for Scalable Concurrent Data Structures.” In Annual
ACM Symposium on Parallelism in Algorithms and Architectures, 37–49. Association
for Computing Machinery, 2020. https://doi.org/10.1145/3350755.3400213.'
ieee: 'D.-A. Alistarh, T. A. Brown, and N. Singhal, “Memory tagging: Minimalist
synchronization for scalable concurrent data structures,” in Annual ACM Symposium
on Parallelism in Algorithms and Architectures, Virtual Event, United States,
2020, no. 7, pp. 37–49.'
ista: 'Alistarh D-A, Brown TA, Singhal N. 2020. Memory tagging: Minimalist synchronization
for scalable concurrent data structures. Annual ACM Symposium on Parallelism in
Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and
Architectures, 37–49.'
mla: 'Alistarh, Dan-Adrian, et al. “Memory Tagging: Minimalist Synchronization for
Scalable Concurrent Data Structures.” Annual ACM Symposium on Parallelism in
Algorithms and Architectures, no. 7, Association for Computing Machinery,
2020, pp. 37–49, doi:10.1145/3350755.3400213.'
short: D.-A. Alistarh, T.A. Brown, N. Singhal, in:, Annual ACM Symposium on Parallelism
in Algorithms and Architectures, Association for Computing Machinery, 2020, pp.
37–49.
conference:
end_date: 2020-07-17
location: Virtual Event, United States
name: 'SPAA: Symposium on Parallelism in Algorithms and Architectures'
start_date: 2020-07-15
date_created: 2020-08-02T22:00:58Z
date_published: 2020-07-06T00:00:00Z
date_updated: 2024-02-28T12:56:32Z
day: '06'
department:
- _id: DaAl
doi: 10.1145/3350755.3400213
external_id:
isi:
- '000744436200004'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa_version: None
page: 37-49
publication: Annual ACM Symposium on Parallelism in Algorithms and Architectures
publication_identifier:
isbn:
- '9781450369350'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Memory tagging: Minimalist synchronization for scalable concurrent data structures'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '7635'
abstract:
- lang: eng
text: Concurrent programming can be notoriously complex and error-prone. Programming
bugs can arise from a variety of sources, such as operation re-reordering, or
incomplete understanding of the memory model. A variety of formal and model checking
methods have been developed to address this fundamental difficulty. While technically
interesting, existing academic methods are still hard to apply to the large codebases
typical of industrial deployments, which limits their practical impact.
article_processing_charge: No
author:
- first_name: Nikita
full_name: Koval, Nikita
id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87
last_name: Koval
- first_name: Mariia
full_name: Sokolova, Mariia
id: 26217AE4-77FF-11EA-8101-AD24D49E41F4
last_name: Sokolova
- first_name: Alexander
full_name: Fedorov, Alexander
last_name: Fedorov
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: Dmitry
full_name: Tsitelov, Dmitry
last_name: Tsitelov
citation:
ama: 'Koval N, Sokolova M, Fedorov A, Alistarh D-A, Tsitelov D. Testing concurrency
on the JVM with Lincheck. In: Proceedings of the ACM SIGPLAN Symposium on Principles
and Practice of Parallel Programming, PPOPP. Association for Computing Machinery;
2020:423-424. doi:10.1145/3332466.3374503'
apa: 'Koval, N., Sokolova, M., Fedorov, A., Alistarh, D.-A., & Tsitelov, D.
(2020). Testing concurrency on the JVM with Lincheck. In Proceedings of the
ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP
(pp. 423–424). San Diego, CA, United States: Association for Computing Machinery.
https://doi.org/10.1145/3332466.3374503'
chicago: Koval, Nikita, Mariia Sokolova, Alexander Fedorov, Dan-Adrian Alistarh,
and Dmitry Tsitelov. “Testing Concurrency on the JVM with Lincheck.” In Proceedings
of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming,
PPOPP, 423–24. Association for Computing Machinery, 2020. https://doi.org/10.1145/3332466.3374503.
ieee: N. Koval, M. Sokolova, A. Fedorov, D.-A. Alistarh, and D. Tsitelov, “Testing
concurrency on the JVM with Lincheck,” in Proceedings of the ACM SIGPLAN Symposium
on Principles and Practice of Parallel Programming, PPOPP, San Diego, CA,
United States, 2020, pp. 423–424.
ista: 'Koval N, Sokolova M, Fedorov A, Alistarh D-A, Tsitelov D. 2020. Testing concurrency
on the JVM with Lincheck. Proceedings of the ACM SIGPLAN Symposium on Principles
and Practice of Parallel Programming, PPOPP. PPOPP: Principles and Practice of
Parallel Programming, 423–424.'
mla: Koval, Nikita, et al. “Testing Concurrency on the JVM with Lincheck.” Proceedings
of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming,
PPOPP, Association for Computing Machinery, 2020, pp. 423–24, doi:10.1145/3332466.3374503.
short: N. Koval, M. Sokolova, A. Fedorov, D.-A. Alistarh, D. Tsitelov, in:, Proceedings
of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming,
PPOPP, Association for Computing Machinery, 2020, pp. 423–424.
conference:
end_date: 2020-02-26
location: San Diego, CA, United States
name: 'PPOPP: Principles and Practice of Parallel Programming'
start_date: 2020-02-22
date_created: 2020-04-05T22:00:48Z
date_published: 2020-02-19T00:00:00Z
date_updated: 2024-02-28T12:53:46Z
day: '19'
department:
- _id: DaAl
doi: 10.1145/3332466.3374503
language:
- iso: eng
month: '02'
oa_version: None
page: 423-424
publication: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of
Parallel Programming, PPOPP
publication_identifier:
isbn:
- '9781450368186'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: Testing concurrency on the JVM with Lincheck
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8383'
abstract:
- lang: eng
text: We introduce extension-based proofs, a class of impossibility proofs that
includes valency arguments. They are modelled as an interaction between a prover
and a protocol. Using proofs based on combinatorial topology, it has been shown
that it is impossible to deterministically solve k-set agreement among n > k ≥
2 processes in a wait-free manner. However, it was unknown whether proofs based
on simpler techniques were possible. We explain why this impossibility result
cannot be obtained by an extension-based proof and, hence, extension-based proofs
are limited in power.
article_processing_charge: No
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: James
full_name: Aspnes, James
last_name: Aspnes
- first_name: Faith
full_name: Ellen, Faith
last_name: Ellen
- first_name: Rati
full_name: Gelashvili, Rati
last_name: Gelashvili
- first_name: Leqi
full_name: Zhu, Leqi
last_name: Zhu
citation:
ama: 'Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. Brief Announcement:
Why Extension-Based Proofs Fail. In: Proceedings of the 39th Symposium on Principles
of Distributed Computing. Association for Computing Machinery; 2020:54-56.
doi:10.1145/3382734.3405743'
apa: 'Alistarh, D.-A., Aspnes, J., Ellen, F., Gelashvili, R., & Zhu, L. (2020).
Brief Announcement: Why Extension-Based Proofs Fail. In Proceedings of the
39th Symposium on Principles of Distributed Computing (pp. 54–56). Virtual,
Italy: Association for Computing Machinery. https://doi.org/10.1145/3382734.3405743'
chicago: 'Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and
Leqi Zhu. “Brief Announcement: Why Extension-Based Proofs Fail.” In Proceedings
of the 39th Symposium on Principles of Distributed Computing, 54–56. Association
for Computing Machinery, 2020. https://doi.org/10.1145/3382734.3405743.'
ieee: 'D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, and L. Zhu, “Brief Announcement:
Why Extension-Based Proofs Fail,” in Proceedings of the 39th Symposium on Principles
of Distributed Computing, Virtual, Italy, 2020, pp. 54–56.'
ista: 'Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. 2020. Brief Announcement:
Why Extension-Based Proofs Fail. Proceedings of the 39th Symposium on Principles
of Distributed Computing. PODC: Principles of Distributed Computing, 54–56.'
mla: 'Alistarh, Dan-Adrian, et al. “Brief Announcement: Why Extension-Based Proofs
Fail.” Proceedings of the 39th Symposium on Principles of Distributed Computing,
Association for Computing Machinery, 2020, pp. 54–56, doi:10.1145/3382734.3405743.'
short: D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, in:, Proceedings
of the 39th Symposium on Principles of Distributed Computing, Association for
Computing Machinery, 2020, pp. 54–56.
conference:
end_date: 2020-08-07
location: Virtual, Italy
name: 'PODC: Principles of Distributed Computing'
start_date: 2020-08-03
date_created: 2020-09-13T22:01:18Z
date_published: 2020-07-31T00:00:00Z
date_updated: 2024-02-28T12:54:19Z
day: '31'
department:
- _id: DaAl
doi: 10.1145/3382734.3405743
language:
- iso: eng
month: '07'
oa_version: None
page: 54-56
publication: Proceedings of the 39th Symposium on Principles of Distributed Computing
publication_identifier:
isbn:
- '9781450375825'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Brief Announcement: Why Extension-Based Proofs Fail'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8385'
abstract:
- lang: eng
text: 'We present a method for animating yarn-level cloth effects using a thin-shell
solver. We accomplish this through numerical homogenization: we first use a large
number of yarn-level simulations to build a model of the potential energy density
of the cloth, and then use this energy density function to compute forces in a
thin shell simulator. We model several yarn-based materials, including both woven
and knitted fabrics. Our model faithfully reproduces expected effects like the
stiffness of woven fabrics, and the highly deformable nature and anisotropy of
knitted fabrics. Our approach does not require any real-world experiments nor
measurements; because the method is based entirely on simulations, it can generate
entirely new material models quickly, without the need for testing apparatuses
or human intervention. We provide data-driven models of several woven and knitted
fabrics, which can be used for efficient simulation with an off-the-shelf cloth
solver.'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "We wish to thank the anonymous reviewers and the members of the
Visual Computing Group at IST Austria for their valuable feedback. We also thank
the creators of the Berkeley Garment Library [de Joya et al. 2012] for providing
garment meshes, [Krishnamurthy and Levoy 1996] and [Turk and Levoy 1994] for the
armadillo and bunny meshes, the creators of libWetCloth [Fei et al. 2018] for their
implementation of discrete elastic rod forces, and Tomáš Skřivan for\r\ninspiring
discussions and help with Mathematica code generation. This research was supported
by the Scientific Service Units (SSU) of IST Austria through resources provided
by Scientific Computing. This project has received funding from the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation programme
under grant agreement No. 638176. Rahul Narain is supported by a Pankaj Gupta Young
Faculty Fellowship and a gift from Adobe Inc."
article_number: '48'
article_processing_charge: No
article_type: original
author:
- first_name: Georg
full_name: Sperl, Georg
id: 4DD40360-F248-11E8-B48F-1D18A9856A87
last_name: Sperl
- first_name: Rahul
full_name: Narain, Rahul
last_name: Narain
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Sperl G, Narain R, Wojtan C. Homogenized yarn-level cloth. ACM Transactions
on Graphics. 2020;39(4). doi:10.1145/3386569.3392412
apa: Sperl, G., Narain, R., & Wojtan, C. (2020). Homogenized yarn-level cloth.
ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3386569.3392412
chicago: Sperl, Georg, Rahul Narain, and Chris Wojtan. “Homogenized Yarn-Level Cloth.”
ACM Transactions on Graphics. Association for Computing Machinery, 2020.
https://doi.org/10.1145/3386569.3392412.
ieee: G. Sperl, R. Narain, and C. Wojtan, “Homogenized yarn-level cloth,” ACM
Transactions on Graphics, vol. 39, no. 4. Association for Computing Machinery,
2020.
ista: Sperl G, Narain R, Wojtan C. 2020. Homogenized yarn-level cloth. ACM Transactions
on Graphics. 39(4), 48.
mla: Sperl, Georg, et al. “Homogenized Yarn-Level Cloth.” ACM Transactions on
Graphics, vol. 39, no. 4, 48, Association for Computing Machinery, 2020, doi:10.1145/3386569.3392412.
short: G. Sperl, R. Narain, C. Wojtan, ACM Transactions on Graphics 39 (2020).
date_created: 2020-09-13T22:01:18Z
date_published: 2020-07-08T00:00:00Z
date_updated: 2024-02-28T12:57:47Z
day: '08'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/3386569.3392412
ec_funded: 1
external_id:
isi:
- '000583700300021'
file:
- access_level: open_access
checksum: cf4c1d361c3196c4bd424520a5588205
content_type: application/pdf
creator: dernst
date_created: 2020-11-23T09:01:22Z
date_updated: 2020-11-23T09:01:22Z
file_id: '8794'
file_name: 2020_hylc_submitted.pdf
file_size: 38922662
relation: main_file
success: 1
file_date_updated: 2020-11-23T09:01:22Z
has_accepted_license: '1'
intvolume: ' 39'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1145/3386569.3392412
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- '15577368'
issn:
- '07300301'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '12358'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Homogenized yarn-level cloth
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 39
year: '2020'
...
---
_id: '7956'
abstract:
- lang: eng
text: When short-range attractions are combined with long-range repulsions in colloidal
particle systems, complex microphases can emerge. Here, we study a system of isotropic
particles, which can form lamellar structures or a disordered fluid phase when
temperature is varied. We show that, at equilibrium, the lamellar structure crystallizes,
while out of equilibrium, the system forms a variety of structures at different
shear rates and temperatures above melting. The shear-induced ordering is analyzed
by means of principal component analysis and artificial neural networks, which
are applied to data of reduced dimensionality. Our results reveal the possibility
of inducing ordering by shear, potentially providing a feasible route to the fabrication
of ordered lamellar structures from isotropic particles.
article_number: '204905'
article_processing_charge: No
article_type: original
author:
- first_name: J.
full_name: Pȩkalski, J.
last_name: Pȩkalski
- first_name: Wojciech
full_name: Rzadkowski, Wojciech
id: 48C55298-F248-11E8-B48F-1D18A9856A87
last_name: Rzadkowski
orcid: 0000-0002-1106-4419
- first_name: A. Z.
full_name: Panagiotopoulos, A. Z.
last_name: Panagiotopoulos
citation:
ama: 'Pȩkalski J, Rzadkowski W, Panagiotopoulos AZ. Shear-induced ordering in systems
with competing interactions: A machine learning study. The Journal of chemical
physics. 2020;152(20). doi:10.1063/5.0005194'
apa: 'Pȩkalski, J., Rzadkowski, W., & Panagiotopoulos, A. Z. (2020). Shear-induced
ordering in systems with competing interactions: A machine learning study. The
Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0005194'
chicago: 'Pȩkalski, J., Wojciech Rzadkowski, and A. Z. Panagiotopoulos. “Shear-Induced
Ordering in Systems with Competing Interactions: A Machine Learning Study.” The
Journal of Chemical Physics. AIP Publishing, 2020. https://doi.org/10.1063/5.0005194.'
ieee: 'J. Pȩkalski, W. Rzadkowski, and A. Z. Panagiotopoulos, “Shear-induced ordering
in systems with competing interactions: A machine learning study,” The Journal
of chemical physics, vol. 152, no. 20. AIP Publishing, 2020.'
ista: 'Pȩkalski J, Rzadkowski W, Panagiotopoulos AZ. 2020. Shear-induced ordering
in systems with competing interactions: A machine learning study. The Journal
of chemical physics. 152(20), 204905.'
mla: 'Pȩkalski, J., et al. “Shear-Induced Ordering in Systems with Competing Interactions:
A Machine Learning Study.” The Journal of Chemical Physics, vol. 152, no.
20, 204905, AIP Publishing, 2020, doi:10.1063/5.0005194.'
short: J. Pȩkalski, W. Rzadkowski, A.Z. Panagiotopoulos, The Journal of Chemical
Physics 152 (2020).
date_created: 2020-06-14T22:00:49Z
date_published: 2020-05-29T00:00:00Z
date_updated: 2024-02-28T13:00:28Z
day: '29'
department:
- _id: MiLe
doi: 10.1063/5.0005194
ec_funded: 1
external_id:
arxiv:
- '2002.07294'
isi:
- '000537900300001'
intvolume: ' 152'
isi: 1
issue: '20'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1063/5.0005194
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: The Journal of chemical physics
publication_identifier:
eissn:
- '10897690'
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
record:
- id: '10759'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Shear-induced ordering in systems with competing interactions: A machine learning
study'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 152
year: '2020'
...
---
_id: '7428'
abstract:
- lang: eng
text: In the superconducting regime of FeTe(1−x)Sex, there exist two types of vortices
which are distinguished by the presence or absence of zero-energy states in their
core. To understand their origin, we examine the interplay of Zeeman coupling
and superconducting pairings in three-dimensional metals with band inversion.
Weak Zeeman fields are found to suppress intraorbital spin-singlet pairing, known
to localize the states at the ends of the vortices on the surface. On the other
hand, an orbital-triplet pairing is shown to be stable against Zeeman interactions,
but leads to delocalized zero-energy Majorana modes which extend through the vortex.
In contrast, the finite-energy vortex modes remain localized at the vortex ends
even when the pairing is of orbital-triplet form. Phenomenologically, this manifests
as an observed disappearance of zero-bias peaks within the cores of topological
vortices upon an increase of the applied magnetic field. The presence of magnetic
impurities in FeTe(1−x)Sex, which are attracted to the vortices, would lead to
such Zeeman-induced delocalization of Majorana modes in a fraction of vortices
that capture a large enough number of magnetic impurities. Our results provide
an explanation for the dichotomy between topological and nontopological vortices
recently observed in FeTe(1−x)Sex.
article_number: '020504'
article_processing_charge: No
article_type: original
author:
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: P. L.S.
full_name: Lopes, P. L.S.
last_name: Lopes
- first_name: Pavan
full_name: Hosur, Pavan
last_name: Hosur
- first_name: Matthew J.
full_name: Gilbert, Matthew J.
last_name: Gilbert
- first_name: Pouyan
full_name: Ghaemi, Pouyan
last_name: Ghaemi
citation:
ama: Ghazaryan A, Lopes PLS, Hosur P, Gilbert MJ, Ghaemi P. Effect of Zeeman coupling
on the Majorana vortex modes in iron-based topological superconductors. Physical
Review B. 2020;101(2). doi:10.1103/PhysRevB.101.020504
apa: Ghazaryan, A., Lopes, P. L. S., Hosur, P., Gilbert, M. J., & Ghaemi, P.
(2020). Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological
superconductors. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.101.020504
chicago: Ghazaryan, Areg, P. L.S. Lopes, Pavan Hosur, Matthew J. Gilbert, and Pouyan
Ghaemi. “Effect of Zeeman Coupling on the Majorana Vortex Modes in Iron-Based
Topological Superconductors.” Physical Review B. American Physical Society,
2020. https://doi.org/10.1103/PhysRevB.101.020504.
ieee: A. Ghazaryan, P. L. S. Lopes, P. Hosur, M. J. Gilbert, and P. Ghaemi, “Effect
of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors,”
Physical Review B, vol. 101, no. 2. American Physical Society, 2020.
ista: Ghazaryan A, Lopes PLS, Hosur P, Gilbert MJ, Ghaemi P. 2020. Effect of Zeeman
coupling on the Majorana vortex modes in iron-based topological superconductors.
Physical Review B. 101(2), 020504.
mla: Ghazaryan, Areg, et al. “Effect of Zeeman Coupling on the Majorana Vortex Modes
in Iron-Based Topological Superconductors.” Physical Review B, vol. 101,
no. 2, 020504, American Physical Society, 2020, doi:10.1103/PhysRevB.101.020504.
short: A. Ghazaryan, P.L.S. Lopes, P. Hosur, M.J. Gilbert, P. Ghaemi, Physical Review
B 101 (2020).
date_created: 2020-02-02T23:01:01Z
date_published: 2020-01-13T00:00:00Z
date_updated: 2024-02-28T13:11:13Z
day: '13'
department:
- _id: MiLe
doi: 10.1103/PhysRevB.101.020504
external_id:
arxiv:
- '1907.02077'
isi:
- '000506843500001'
intvolume: ' 101'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1907.02077
month: '01'
oa: 1
oa_version: Preprint
publication: Physical Review B
publication_identifier:
eissn:
- '24699969'
issn:
- '24699950'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological
superconductors
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 101
year: '2020'
...
---
_id: '8319'
abstract:
- lang: eng
text: We demonstrate that releasing atoms into free space from an optical lattice
does not deteriorate cavity-generated spin squeezing for metrological purposes.
In this work, an ensemble of 500000 spin-squeezed atoms in a high-finesse optical
cavity with near-uniform atom-cavity coupling is prepared, released into free
space, recaptured in the cavity, and probed. Up to ∼10 dB of metrologically relevant
squeezing is retrieved for 700μs free-fall times, and decaying levels of squeezing
are realized for up to 3 ms free-fall times. The degradation of squeezing results
from loss of atom-cavity coupling homogeneity between the initial squeezed state
generation and final collective state readout. A theoretical model is developed
to quantify this degradation and this model is experimentally validated.
acknowledgement: We thank N. Engelsen for comments on the manuscript. This work was
supported by the Office of Naval Research, Vannevar Bush Faculty Fellowship, Department
of Energy, and Defense Threat Reduction Agency. R.K. was partly supported by the
AQT/INQNET program at Caltech.
article_number: '012224'
article_processing_charge: No
article_type: original
author:
- first_name: Yunfan
full_name: Wu, Yunfan
last_name: Wu
- first_name: Rajiv
full_name: Krishnakumar, Rajiv
last_name: Krishnakumar
- first_name: Julián
full_name: Martínez-Rincón, Julián
last_name: Martínez-Rincón
- first_name: Benjamin K.
full_name: Malia, Benjamin K.
last_name: Malia
- first_name: Onur
full_name: Hosten, Onur
id: 4C02D85E-F248-11E8-B48F-1D18A9856A87
last_name: Hosten
orcid: 0000-0002-2031-204X
- first_name: Mark A.
full_name: Kasevich, Mark A.
last_name: Kasevich
citation:
ama: Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA. Retrieval
of cavity-generated atomic spin squeezing after free-space release. Physical
Review A. 2020;102(1). doi:10.1103/PhysRevA.102.012224
apa: Wu, Y., Krishnakumar, R., Martínez-Rincón, J., Malia, B. K., Hosten, O., &
Kasevich, M. A. (2020). Retrieval of cavity-generated atomic spin squeezing after
free-space release. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.102.012224
chicago: Wu, Yunfan, Rajiv Krishnakumar, Julián Martínez-Rincón, Benjamin K. Malia,
Onur Hosten, and Mark A. Kasevich. “Retrieval of Cavity-Generated Atomic Spin
Squeezing after Free-Space Release.” Physical Review A. American Physical
Society, 2020. https://doi.org/10.1103/PhysRevA.102.012224.
ieee: Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B. K. Malia, O. Hosten, and M.
A. Kasevich, “Retrieval of cavity-generated atomic spin squeezing after free-space
release,” Physical Review A, vol. 102, no. 1. American Physical Society,
2020.
ista: Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA.
2020. Retrieval of cavity-generated atomic spin squeezing after free-space release.
Physical Review A. 102(1), 012224.
mla: Wu, Yunfan, et al. “Retrieval of Cavity-Generated Atomic Spin Squeezing after
Free-Space Release.” Physical Review A, vol. 102, no. 1, 012224, American
Physical Society, 2020, doi:10.1103/PhysRevA.102.012224.
short: Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B.K. Malia, O. Hosten, M.A. Kasevich,
Physical Review A 102 (2020).
date_created: 2020-08-30T22:01:10Z
date_published: 2020-07-30T00:00:00Z
date_updated: 2024-02-28T13:11:28Z
day: '30'
department:
- _id: OnHo
doi: 10.1103/PhysRevA.102.012224
external_id:
arxiv:
- '1912.08334'
isi:
- '000555104200011'
intvolume: ' 102'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1912.08334
month: '07'
oa: 1
oa_version: Preprint
publication: Physical Review A
publication_identifier:
eissn:
- '24699934'
issn:
- '24699926'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Retrieval of cavity-generated atomic spin squeezing after free-space release
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 102
year: '2020'
...
---
_id: '8766'
abstract:
- lang: eng
text: "The “procedural” approach to animating ocean waves is the dominant algorithm
for animating larger bodies of water in\r\ninteractive applications as well as
in off-line productions — it provides high visual quality with a low computational
demand. In this paper, we widen the applicability of procedural water wave animation
with an extension that guarantees the satisfaction of boundary conditions imposed
by terrain while still approximating physical wave behavior. In combination with
a particle system that models wave breaking, foam, and spray, this allows us to
naturally model waves interacting with beaches and rocks. Our system is able to
animate waves at large scales at interactive frame rates on a commodity PC."
article_processing_charge: No
article_type: original
author:
- first_name: Stefan
full_name: Jeschke, Stefan
id: 44D6411A-F248-11E8-B48F-1D18A9856A87
last_name: Jeschke
- first_name: Christian
full_name: Hafner, Christian
id: 400429CC-F248-11E8-B48F-1D18A9856A87
last_name: Hafner
- first_name: Nuttapong
full_name: Chentanez, Nuttapong
last_name: Chentanez
- first_name: Miles
full_name: Macklin, Miles
last_name: Macklin
- first_name: Matthias
full_name: Müller-Fischer, Matthias
last_name: Müller-Fischer
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Jeschke S, Hafner C, Chentanez N, Macklin M, Müller-Fischer M, Wojtan C. Making
procedural water waves boundary-aware. Computer Graphics forum. 2020;39(8):47-54.
doi:10.1111/cgf.14100
apa: 'Jeschke, S., Hafner, C., Chentanez, N., Macklin, M., Müller-Fischer, M., &
Wojtan, C. (2020). Making procedural water waves boundary-aware. Computer Graphics
Forum. Online Symposium: Wiley. https://doi.org/10.1111/cgf.14100'
chicago: Jeschke, Stefan, Christian Hafner, Nuttapong Chentanez, Miles Macklin,
Matthias Müller-Fischer, and Chris Wojtan. “Making Procedural Water Waves Boundary-Aware.”
Computer Graphics Forum. Wiley, 2020. https://doi.org/10.1111/cgf.14100.
ieee: S. Jeschke, C. Hafner, N. Chentanez, M. Macklin, M. Müller-Fischer, and C.
Wojtan, “Making procedural water waves boundary-aware,” Computer Graphics forum,
vol. 39, no. 8. Wiley, pp. 47–54, 2020.
ista: Jeschke S, Hafner C, Chentanez N, Macklin M, Müller-Fischer M, Wojtan C. 2020.
Making procedural water waves boundary-aware. Computer Graphics forum. 39(8),
47–54.
mla: Jeschke, Stefan, et al. “Making Procedural Water Waves Boundary-Aware.” Computer
Graphics Forum, vol. 39, no. 8, Wiley, 2020, pp. 47–54, doi:10.1111/cgf.14100.
short: S. Jeschke, C. Hafner, N. Chentanez, M. Macklin, M. Müller-Fischer, C. Wojtan,
Computer Graphics Forum 39 (2020) 47–54.
conference:
end_date: 2020-10-09
location: Online Symposium
name: 'SCA: Symposium on Computer Animation'
start_date: 2020-10-06
date_created: 2020-11-17T10:47:48Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2024-02-28T13:58:11Z
day: '01'
department:
- _id: ChWo
- _id: BeBi
doi: 10.1111/cgf.14100
ec_funded: 1
external_id:
isi:
- '000591780400005'
intvolume: ' 39'
isi: 1
issue: '8'
language:
- iso: eng
month: '12'
oa_version: None
page: 47-54
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
- _id: 24F9549A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715767'
name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and
Modeling'
publication: Computer Graphics forum
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Making procedural water waves boundary-aware
type: journal_article
user_id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
volume: 39
year: '2020'
...
---
_id: '15055'
abstract:
- lang: eng
text: Markov decision processes (MDPs) are the defacto framework for sequential
decision making in the presence of stochastic uncertainty. A classical optimization
criterion for MDPs is to maximize the expected discounted-sum payoff, which ignores
low probability catastrophic events with highly negative impact on the system.
On the other hand, risk-averse policies require the probability of undesirable
events to be below a given threshold, but they do not account for optimization
of the expected payoff. We consider MDPs with discounted-sum payoff with failure
states which represent catastrophic outcomes. The objective of risk-constrained
planning is to maximize the expected discounted-sum payoff among risk-averse policies
that ensure the probability to encounter a failure state is below a desired threshold.
Our main contribution is an efficient risk-constrained planning algorithm that
combines UCT-like search with a predictor learned through interaction with the
MDP (in the style of AlphaZero) and with a risk-constrained action selection via
linear programming. We demonstrate the effectiveness of our approach with experiments
on classical MDPs from the literature, including benchmarks with an order of 106
states.
acknowledgement: Krishnendu Chatterjee is supported by the Austrian Science Fund (FWF)
NFN Grant No. S11407-N23 (RiSE/SHiNE), and COST Action GAMENET. Tomas Brazdil is
supported by the Grant Agency of Masaryk University grant no. MUNI/G/0739/2017 and
by the Czech Science Foundation grant No. 18-11193S. Petr Novotny and Jirı Vahala
are supported by the Czech Science Foundation grant No. GJ19-15134Y.
article_processing_charge: No
article_type: original
author:
- first_name: Tomáš
full_name: Brázdil, Tomáš
last_name: Brázdil
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Petr
full_name: Novotný, Petr
last_name: Novotný
- first_name: Jiří
full_name: Vahala, Jiří
last_name: Vahala
citation:
ama: Brázdil T, Chatterjee K, Novotný P, Vahala J. Reinforcement learning of risk-constrained
policies in Markov decision processes. Proceedings of the 34th AAAI Conference
on Artificial Intelligence. 2020;34(06):9794-9801. doi:10.1609/aaai.v34i06.6531
apa: 'Brázdil, T., Chatterjee, K., Novotný, P., & Vahala, J. (2020). Reinforcement
learning of risk-constrained policies in Markov decision processes. Proceedings
of the 34th AAAI Conference on Artificial Intelligence. New York, NY, United
States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v34i06.6531'
chicago: Brázdil, Tomáš, Krishnendu Chatterjee, Petr Novotný, and Jiří Vahala. “Reinforcement
Learning of Risk-Constrained Policies in Markov Decision Processes.” Proceedings
of the 34th AAAI Conference on Artificial Intelligence. Association for the
Advancement of Artificial Intelligence, 2020. https://doi.org/10.1609/aaai.v34i06.6531.
ieee: T. Brázdil, K. Chatterjee, P. Novotný, and J. Vahala, “Reinforcement learning
of risk-constrained policies in Markov decision processes,” Proceedings of
the 34th AAAI Conference on Artificial Intelligence, vol. 34, no. 06. Association
for the Advancement of Artificial Intelligence, pp. 9794–9801, 2020.
ista: Brázdil T, Chatterjee K, Novotný P, Vahala J. 2020. Reinforcement learning
of risk-constrained policies in Markov decision processes. Proceedings of the
34th AAAI Conference on Artificial Intelligence. 34(06), 9794–9801.
mla: Brázdil, Tomáš, et al. “Reinforcement Learning of Risk-Constrained Policies
in Markov Decision Processes.” Proceedings of the 34th AAAI Conference on Artificial
Intelligence, vol. 34, no. 06, Association for the Advancement of Artificial
Intelligence, 2020, pp. 9794–801, doi:10.1609/aaai.v34i06.6531.
short: T. Brázdil, K. Chatterjee, P. Novotný, J. Vahala, Proceedings of the 34th
AAAI Conference on Artificial Intelligence 34 (2020) 9794–9801.
conference:
end_date: 2020-02-12
location: New York, NY, United States
name: 'AAAI: Conference on Artificial Intelligence'
start_date: 2020-02-07
date_created: 2024-03-04T08:07:22Z
date_published: 2020-04-03T00:00:00Z
date_updated: 2024-03-04T08:30:16Z
day: '03'
department:
- _id: KrCh
doi: 10.1609/aaai.v34i06.6531
external_id:
arxiv:
- '2002.12086'
intvolume: ' 34'
issue: '06'
keyword:
- General Medicine
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2002.12086
month: '04'
oa: 1
oa_version: Preprint
page: 9794-9801
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
publication: Proceedings of the 34th AAAI Conference on Artificial Intelligence
publication_identifier:
issn:
- 2374-3468
publication_status: published
publisher: Association for the Advancement of Artificial Intelligence
quality_controlled: '1'
status: public
title: Reinforcement learning of risk-constrained policies in Markov decision processes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2020'
...
---
_id: '15057'
abstract:
- lang: eng
text: Vaccinia virus–related kinase (VRK) is an evolutionarily conserved nuclear
protein kinase. VRK-1, the single Caenorhabditis elegans VRK ortholog, functions
in cell division and germline proliferation. However, the role of VRK-1 in postmitotic
cells and adult life span remains unknown. Here, we show that VRK-1 increases
organismal longevity by activating the cellular energy sensor, AMP-activated protein
kinase (AMPK), via direct phosphorylation. We found that overexpression of vrk-1
in the soma of adult C. elegans increased life span and, conversely, inhibition
of vrk-1 decreased life span. In addition, vrk-1 was required for longevity conferred
by mutations that inhibit C. elegans mitochondrial respiration, which requires
AMPK. VRK-1 directly phosphorylated and up-regulated AMPK in both C. elegans and
cultured human cells. Thus, our data show that the somatic nuclear kinase, VRK-1,
promotes longevity through AMPK activation, and this function appears to be conserved
between C. elegans and humans.
acknowledgement: 'This research was supported by grants NRF-2019R1A3B2067745 and NRF-2017R1A5A1015366
funded by the Korean Government (MSIT) through the National Research Foundation
(NRF) of Korea to S.-J.V.L. and by grant Basic Science Research Program (No. 2019R1A2C2009440)
funded by the Korean Government (MSIT) through the NRF of Korea to K.-T.K. '
article_number: aaw7824
article_processing_charge: No
article_type: original
author:
- first_name: Sangsoon
full_name: Park, Sangsoon
last_name: Park
- first_name: Murat
full_name: Artan, Murat
id: C407B586-6052-11E9-B3AE-7006E6697425
last_name: Artan
orcid: 0000-0001-8945-6992
- first_name: Seung Hyun
full_name: Han, Seung Hyun
last_name: Han
- first_name: Hae-Eun H.
full_name: Park, Hae-Eun H.
last_name: Park
- first_name: Yoonji
full_name: Jung, Yoonji
last_name: Jung
- first_name: Ara B.
full_name: Hwang, Ara B.
last_name: Hwang
- first_name: Won Sik
full_name: Shin, Won Sik
last_name: Shin
- first_name: Kyong-Tai
full_name: Kim, Kyong-Tai
last_name: Kim
- first_name: Seung-Jae V.
full_name: Lee, Seung-Jae V.
last_name: Lee
citation:
ama: Park S, Artan M, Han SH, et al. VRK-1 extends life span by activation of AMPK
via phosphorylation. Science Advances. 2020;6(27). doi:10.1126/sciadv.aaw7824
apa: Park, S., Artan, M., Han, S. H., Park, H.-E. H., Jung, Y., Hwang, A. B., …
Lee, S.-J. V. (2020). VRK-1 extends life span by activation of AMPK via phosphorylation.
Science Advances. American Association for the Advancement of Science.
https://doi.org/10.1126/sciadv.aaw7824
chicago: Park, Sangsoon, Murat Artan, Seung Hyun Han, Hae-Eun H. Park, Yoonji Jung,
Ara B. Hwang, Won Sik Shin, Kyong-Tai Kim, and Seung-Jae V. Lee. “VRK-1 Extends
Life Span by Activation of AMPK via Phosphorylation.” Science Advances.
American Association for the Advancement of Science, 2020. https://doi.org/10.1126/sciadv.aaw7824.
ieee: S. Park et al., “VRK-1 extends life span by activation of AMPK via
phosphorylation,” Science Advances, vol. 6, no. 27. American Association
for the Advancement of Science, 2020.
ista: Park S, Artan M, Han SH, Park H-EH, Jung Y, Hwang AB, Shin WS, Kim K-T, Lee
S-JV. 2020. VRK-1 extends life span by activation of AMPK via phosphorylation.
Science Advances. 6(27), aaw7824.
mla: Park, Sangsoon, et al. “VRK-1 Extends Life Span by Activation of AMPK via Phosphorylation.”
Science Advances, vol. 6, no. 27, aaw7824, American Association for the
Advancement of Science, 2020, doi:10.1126/sciadv.aaw7824.
short: S. Park, M. Artan, S.H. Han, H.-E.H. Park, Y. Jung, A.B. Hwang, W.S. Shin,
K.-T. Kim, S.-J.V. Lee, Science Advances 6 (2020).
date_created: 2024-03-04T09:41:57Z
date_published: 2020-07-01T00:00:00Z
date_updated: 2024-03-04T09:52:09Z
day: '01'
ddc:
- '570'
department:
- _id: MaDe
doi: 10.1126/sciadv.aaw7824
file:
- access_level: open_access
checksum: a37157cd0de709dce5fe03f4a31cd0b6
content_type: application/pdf
creator: dernst
date_created: 2024-03-04T09:46:41Z
date_updated: 2024-03-04T09:46:41Z
file_id: '15058'
file_name: 2020_ScienceAdvances_Park.pdf
file_size: 1864415
relation: main_file
success: 1
file_date_updated: 2024-03-04T09:46:41Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '27'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '07'
oa: 1
oa_version: Published Version
publication: Science Advances
publication_identifier:
eissn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
status: public
title: VRK-1 extends life span by activation of AMPK via phosphorylation
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: 6
year: '2020'
...
---
_id: '15061'
abstract:
- lang: eng
text: The actin cytoskeleton, a dynamic network of actin filaments and associated
F-actin–binding proteins, is fundamentally important in eukaryotes. α-Actinins
are major F-actin bundlers that are inhibited by Ca2+ in nonmuscle cells. Here
we report the mechanism of Ca2+-mediated regulation of Entamoeba histolytica α-actinin-2
(EhActn2) with features expected for the common ancestor of Entamoeba and higher
eukaryotic α-actinins. Crystal structures of Ca2+-free and Ca2+-bound EhActn2
reveal a calmodulin-like domain (CaMD) uniquely inserted within the rod domain.
Integrative studies reveal an exceptionally high affinity of the EhActn2 CaMD
for Ca2+, binding of which can only be regulated in the presence of physiological
concentrations of Mg2+. Ca2+ binding triggers an increase in protein multidomain
rigidity, reducing conformational flexibility of F-actin–binding domains via interdomain
cross-talk and consequently inhibiting F-actin bundling. In vivo studies uncover
that EhActn2 plays an important role in phagocytic cup formation and might constitute
a new drug target for amoebic dysentery.
acknowledged_ssus:
- _id: LifeSc
acknowledgement: "We thank the staff of the macromolecular crystallography (MX) and
SAXS beamlines at the European Synchrotron Radiation facility, Diamond, and Swiss
Light Source for excellent support, and the Life Sciences Facility of the Institute
of Science and Technology Austria for usage of the rheometer. We thank Life Sciences
editors for editing assistance. EM data were\r\nrecorded at the EM Facility of the
Vienna BioCenter Core Facilities (Austria). Confocal microscopy was carried out
at the Advanced Instrument Research Facility, Jawaharlal Nehru University. K.D.-C.’s
research was supported by the Initial Training Network MUZIC (ITN-MUZIC) (N°238423),
Austrian Science Fund (FWF) Projects I525, I1593, P22276, P19060, and W1221, Laura
Bassi Centre of Optimized Structural Studies (N°253275), a Wellcome Trust Collaborative
Award (201543/Z/16/Z), COST Action BM1405, Vienna Science and Technology Fund (WWTF)
Chemical Biology Project LS17-008, and Christian Doppler Laboratory for High-Content
Structural Biology and Biotechnology. K.Z., J.L.A., C.S., E.A.G., and A.S. were
supported by the University of Vienna, J.K. by a Wellcome Trust Collaborative Award
and by the Centre of Optimized Structural Studies, M.P. by FWF Project I1593, E.d.A.R.
ITN-MUZIC, and FWF Projects I525 and I1593, and T.C.M. and L.C. by FWF Project I
2408-B22. E.A.G. acknowledges the PhD program Structure and Interaction of Biological
Macromolecules. M.B. acknowledges the University Grant Commission, India, for a
senior research fellowship. A.B. acknowledges a JC Bose Fellowship from the Science
Engineering Research Council. "
article_processing_charge: No
article_type: original
author:
- first_name: Nikos
full_name: Pinotsis, Nikos
last_name: Pinotsis
- first_name: Karolina
full_name: Zielinska, Karolina
last_name: Zielinska
- first_name: Mrigya
full_name: Babuta, Mrigya
last_name: Babuta
- first_name: Joan L.
full_name: Arolas, Joan L.
last_name: Arolas
- first_name: Julius
full_name: Kostan, Julius
last_name: Kostan
- first_name: Muhammad Bashir
full_name: Khan, Muhammad Bashir
last_name: Khan
- first_name: Claudia
full_name: Schreiner, Claudia
last_name: Schreiner
- first_name: Anita P
full_name: Testa Salmazo, Anita P
id: 41F1F098-F248-11E8-B48F-1D18A9856A87
last_name: Testa Salmazo
- first_name: Luciano
full_name: Ciccarelli, Luciano
last_name: Ciccarelli
- first_name: Martin
full_name: Puchinger, Martin
last_name: Puchinger
- first_name: Eirini A.
full_name: Gkougkoulia, Eirini A.
last_name: Gkougkoulia
- first_name: Euripedes de Almeida
full_name: Ribeiro, Euripedes de Almeida
last_name: Ribeiro
- first_name: Thomas C.
full_name: Marlovits, Thomas C.
last_name: Marlovits
- first_name: Alok
full_name: Bhattacharya, Alok
last_name: Bhattacharya
- first_name: Kristina
full_name: Djinovic-Carugo, Kristina
last_name: Djinovic-Carugo
citation:
ama: Pinotsis N, Zielinska K, Babuta M, et al. Calcium modulates the domain flexibility
and function of an α-actinin similar to the ancestral α-actinin. Proceedings
of the National Academy of Sciences. 2020;117(36):22101-22112. doi:10.1073/pnas.1917269117
apa: Pinotsis, N., Zielinska, K., Babuta, M., Arolas, J. L., Kostan, J., Khan, M.
B., … Djinovic-Carugo, K. (2020). Calcium modulates the domain flexibility and
function of an α-actinin similar to the ancestral α-actinin. Proceedings of
the National Academy of Sciences. Proceedings of the National Academy of Sciences.
https://doi.org/10.1073/pnas.1917269117
chicago: Pinotsis, Nikos, Karolina Zielinska, Mrigya Babuta, Joan L. Arolas, Julius
Kostan, Muhammad Bashir Khan, Claudia Schreiner, et al. “Calcium Modulates the
Domain Flexibility and Function of an α-Actinin Similar to the Ancestral α-Actinin.”
Proceedings of the National Academy of Sciences. Proceedings of the National
Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1917269117.
ieee: N. Pinotsis et al., “Calcium modulates the domain flexibility and function
of an α-actinin similar to the ancestral α-actinin,” Proceedings of the National
Academy of Sciences, vol. 117, no. 36. Proceedings of the National Academy
of Sciences, pp. 22101–22112, 2020.
ista: Pinotsis N, Zielinska K, Babuta M, Arolas JL, Kostan J, Khan MB, Schreiner
C, Testa Salmazo AP, Ciccarelli L, Puchinger M, Gkougkoulia EA, Ribeiro E de A,
Marlovits TC, Bhattacharya A, Djinovic-Carugo K. 2020. Calcium modulates the domain
flexibility and function of an α-actinin similar to the ancestral α-actinin. Proceedings
of the National Academy of Sciences. 117(36), 22101–22112.
mla: Pinotsis, Nikos, et al. “Calcium Modulates the Domain Flexibility and Function
of an α-Actinin Similar to the Ancestral α-Actinin.” Proceedings of the National
Academy of Sciences, vol. 117, no. 36, Proceedings of the National Academy
of Sciences, 2020, pp. 22101–12, doi:10.1073/pnas.1917269117.
short: N. Pinotsis, K. Zielinska, M. Babuta, J.L. Arolas, J. Kostan, M.B. Khan,
C. Schreiner, A.P. Testa Salmazo, L. Ciccarelli, M. Puchinger, E.A. Gkougkoulia,
E. de A. Ribeiro, T.C. Marlovits, A. Bhattacharya, K. Djinovic-Carugo, Proceedings
of the National Academy of Sciences 117 (2020) 22101–22112.
date_created: 2024-03-04T10:03:52Z
date_published: 2020-09-08T00:00:00Z
date_updated: 2024-03-04T10:14:44Z
day: '08'
department:
- _id: CaBe
doi: 10.1073/pnas.1917269117
external_id:
pmid:
- '32848067'
intvolume: ' 117'
issue: '36'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.191726911
month: '09'
oa: 1
oa_version: Published Version
page: 22101-22112
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: Calcium modulates the domain flexibility and function of an α-actinin similar
to the ancestral α-actinin
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 117
year: '2020'
...
---
_id: '15064'
abstract:
- lang: eng
text: We call a continuous self-map that reveals itself through a discrete set of
point-value pairs a sampled dynamical system. Capturing the available information
with chain maps on Delaunay complexes, we use persistent homology to quantify
the evidence of recurrent behavior. We establish a sampling theorem to recover
the eigenspaces of the endomorphism on homology induced by the self-map. Using
a combinatorial gradient flow arising from the discrete Morse theory for Čech
and Delaunay complexes, we construct a chain map to transform the problem from
the natural but expensive Čech complexes to the computationally efficient Delaunay
triangulations. The fast chain map algorithm has applications beyond dynamical
systems.
acknowledgement: This research has been supported by the DFG Collaborative Research
Center SFB/TRR 109 “Discretization in Geometry and Dynamics”, by Polish MNiSzW Grant
No. 2621/7.PR/12/2013/2, by the Polish National Science Center under Maestro Grant
No. 2014/14/A/ST1/00453 and Grant No. DEC-2013/09/N/ST6/02995. Open Access funding
provided by Projekt DEAL.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: U.
full_name: Bauer, U.
last_name: Bauer
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Grzegorz
full_name: Jablonski, Grzegorz
id: 4483EF78-F248-11E8-B48F-1D18A9856A87
last_name: Jablonski
orcid: 0000-0002-3536-9866
- first_name: M.
full_name: Mrozek, M.
last_name: Mrozek
citation:
ama: Bauer U, Edelsbrunner H, Jablonski G, Mrozek M. Čech-Delaunay gradient flow
and homology inference for self-maps. Journal of Applied and Computational
Topology. 2020;4(4):455-480. doi:10.1007/s41468-020-00058-8
apa: Bauer, U., Edelsbrunner, H., Jablonski, G., & Mrozek, M. (2020). Čech-Delaunay
gradient flow and homology inference for self-maps. Journal of Applied and
Computational Topology. Springer Nature. https://doi.org/10.1007/s41468-020-00058-8
chicago: Bauer, U., Herbert Edelsbrunner, Grzegorz Jablonski, and M. Mrozek. “Čech-Delaunay
Gradient Flow and Homology Inference for Self-Maps.” Journal of Applied and
Computational Topology. Springer Nature, 2020. https://doi.org/10.1007/s41468-020-00058-8.
ieee: U. Bauer, H. Edelsbrunner, G. Jablonski, and M. Mrozek, “Čech-Delaunay gradient
flow and homology inference for self-maps,” Journal of Applied and Computational
Topology, vol. 4, no. 4. Springer Nature, pp. 455–480, 2020.
ista: Bauer U, Edelsbrunner H, Jablonski G, Mrozek M. 2020. Čech-Delaunay gradient
flow and homology inference for self-maps. Journal of Applied and Computational
Topology. 4(4), 455–480.
mla: Bauer, U., et al. “Čech-Delaunay Gradient Flow and Homology Inference for Self-Maps.”
Journal of Applied and Computational Topology, vol. 4, no. 4, Springer
Nature, 2020, pp. 455–80, doi:10.1007/s41468-020-00058-8.
short: U. Bauer, H. Edelsbrunner, G. Jablonski, M. Mrozek, Journal of Applied and
Computational Topology 4 (2020) 455–480.
date_created: 2024-03-04T10:47:49Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2024-03-04T10:54:04Z
day: '01'
ddc:
- '500'
department:
- _id: HeEd
doi: 10.1007/s41468-020-00058-8
file:
- access_level: open_access
checksum: eed1168b6e66cd55272c19bb7fca8a1c
content_type: application/pdf
creator: dernst
date_created: 2024-03-04T10:52:42Z
date_updated: 2024-03-04T10:52:42Z
file_id: '15065'
file_name: 2020_JourApplCompTopology_Bauer.pdf
file_size: 851190
relation: main_file
success: 1
file_date_updated: 2024-03-04T10:52:42Z
has_accepted_license: '1'
intvolume: ' 4'
issue: '4'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 455-480
publication: Journal of Applied and Computational Topology
publication_identifier:
eissn:
- 2367-1734
issn:
- 2367-1726
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Čech-Delaunay gradient flow and homology inference for self-maps
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: 4
year: '2020'
...
---
_id: '15063'
abstract:
- lang: eng
text: We consider the least singular value of a large random matrix with real or
complex i.i.d. Gaussian entries shifted by a constant z∈C. We prove an optimal
lower tail estimate on this singular value in the critical regime where z is around
the spectral edge, thus improving the classical bound of Sankar, Spielman and
Teng (SIAM J. Matrix Anal. Appl. 28:2 (2006), 446–476) for the particular shift-perturbation
in the edge regime. Lacking Brézin–Hikami formulas in the real case, we rely on
the superbosonization formula (Comm. Math. Phys. 283:2 (2008), 343–395).
acknowledgement: Partially supported by ERC Advanced Grant No. 338804. This project
has received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Sklodowska-Curie Grant Agreement No. 66538
article_processing_charge: No
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. Optimal lower bound on the least singular
value of the shifted Ginibre ensemble. Probability and Mathematical Physics.
2020;1(1):101-146. doi:10.2140/pmp.2020.1.101
apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2020). Optimal lower bound
on the least singular value of the shifted Ginibre ensemble. Probability and
Mathematical Physics. Mathematical Sciences Publishers. https://doi.org/10.2140/pmp.2020.1.101
chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Optimal Lower
Bound on the Least Singular Value of the Shifted Ginibre Ensemble.” Probability
and Mathematical Physics. Mathematical Sciences Publishers, 2020. https://doi.org/10.2140/pmp.2020.1.101.
ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Optimal lower bound on the least
singular value of the shifted Ginibre ensemble,” Probability and Mathematical
Physics, vol. 1, no. 1. Mathematical Sciences Publishers, pp. 101–146, 2020.
ista: Cipolloni G, Erdös L, Schröder DJ. 2020. Optimal lower bound on the least
singular value of the shifted Ginibre ensemble. Probability and Mathematical Physics.
1(1), 101–146.
mla: Cipolloni, Giorgio, et al. “Optimal Lower Bound on the Least Singular Value
of the Shifted Ginibre Ensemble.” Probability and Mathematical Physics,
vol. 1, no. 1, Mathematical Sciences Publishers, 2020, pp. 101–46, doi:10.2140/pmp.2020.1.101.
short: G. Cipolloni, L. Erdös, D.J. Schröder, Probability and Mathematical Physics
1 (2020) 101–146.
date_created: 2024-03-04T10:27:57Z
date_published: 2020-11-16T00:00:00Z
date_updated: 2024-03-04T10:33:15Z
day: '16'
department:
- _id: LaEr
doi: 10.2140/pmp.2020.1.101
ec_funded: 1
external_id:
arxiv:
- '1908.01653'
intvolume: ' 1'
issue: '1'
keyword:
- General Medicine
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1908.01653
month: '11'
oa: 1
oa_version: Preprint
page: 101-146
project:
- _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 and Mathematical Physics
publication_identifier:
issn:
- 2690-1005
- 2690-0998
publication_status: published
publisher: Mathematical Sciences Publishers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optimal lower bound on the least singular value of the shifted Ginibre ensemble
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2020'
...
---
_id: '15059'
abstract:
- lang: eng
text: "In this paper we present a room temperature radiometer that can eliminate
the need of using cryostats in satellite payload reducing its weight and improving
reliability. The proposed radiometer is based on an electro-optic upconverter
that boosts up microwave photons energy by upconverting them into an optical domain
what makes them immune to thermal noise even if operating at room temperature.
The converter uses a high-quality factor whispering gallery\r\nmode (WGM) resonator
providing naturally narrow bandwidth and therefore might be useful for applications
like microwave hyperspectral sensing. The upconversion process is explained by\r\nproviding
essential information about photon conversion efficiency and sensitivity. To prove
the concept, we describe an experiment which shows state-of-the-art photon conversion
efficiency n=10-5 per mW of pump power at the frequency of 80 GHz."
acknowledgement: This work has been financially supported by Comunidad de Madrid S2018/NMT-4333
ARTINLARA-CM projects, and “FUNDACIÓN SENER” REFTA projects.
article_processing_charge: No
author:
- first_name: Michal
full_name: Wasiak, Michal
last_name: Wasiak
- first_name: Gabriel Santamaria
full_name: Botello, Gabriel Santamaria
last_name: Botello
- first_name: Kerlos Atia
full_name: Abdalmalak, Kerlos Atia
last_name: Abdalmalak
- first_name: Florian
full_name: Sedlmeir, Florian
last_name: Sedlmeir
- 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: Daniel
full_name: Segovia-Vargas, Daniel
last_name: Segovia-Vargas
- first_name: Harald G. L.
full_name: Schwefel, Harald G. L.
last_name: Schwefel
- first_name: Luis Enrique Garcia
full_name: Munoz, Luis Enrique Garcia
last_name: Munoz
citation:
ama: 'Wasiak M, Botello GS, Abdalmalak KA, et al. Compact millimeter and submillimeter-wave
photonic radiometer for cubesats. In: 14th European Conference on Antennas
and Propagation. IEEE; 2020. doi:10.23919/eucap48036.2020.9135962'
apa: 'Wasiak, M., Botello, G. S., Abdalmalak, K. A., Sedlmeir, F., Rueda Sanchez,
A. R., Segovia-Vargas, D., … Munoz, L. E. G. (2020). Compact millimeter and submillimeter-wave
photonic radiometer for cubesats. In 14th European Conference on Antennas and
Propagation. Copenhagen, Denmark: IEEE. https://doi.org/10.23919/eucap48036.2020.9135962'
chicago: Wasiak, Michal, Gabriel Santamaria Botello, Kerlos Atia Abdalmalak, Florian
Sedlmeir, Alfredo R Rueda Sanchez, Daniel Segovia-Vargas, Harald G. L. Schwefel,
and Luis Enrique Garcia Munoz. “Compact Millimeter and Submillimeter-Wave Photonic
Radiometer for Cubesats.” In 14th European Conference on Antennas and Propagation.
IEEE, 2020. https://doi.org/10.23919/eucap48036.2020.9135962.
ieee: M. Wasiak et al., “Compact millimeter and submillimeter-wave photonic
radiometer for cubesats,” in 14th European Conference on Antennas and Propagation,
Copenhagen, Denmark, 2020.
ista: 'Wasiak M, Botello GS, Abdalmalak KA, Sedlmeir F, Rueda Sanchez AR, Segovia-Vargas
D, Schwefel HGL, Munoz LEG. 2020. Compact millimeter and submillimeter-wave photonic
radiometer for cubesats. 14th European Conference on Antennas and Propagation.
EuCAP: European Conference on Antennas and Propagation.'
mla: Wasiak, Michal, et al. “Compact Millimeter and Submillimeter-Wave Photonic
Radiometer for Cubesats.” 14th European Conference on Antennas and Propagation,
IEEE, 2020, doi:10.23919/eucap48036.2020.9135962.
short: M. Wasiak, G.S. Botello, K.A. Abdalmalak, F. Sedlmeir, A.R. Rueda Sanchez,
D. Segovia-Vargas, H.G.L. Schwefel, L.E.G. Munoz, in:, 14th European Conference
on Antennas and Propagation, IEEE, 2020.
conference:
end_date: 2020-03-20
location: Copenhagen, Denmark
name: 'EuCAP: European Conference on Antennas and Propagation'
start_date: 2020-03-15
date_created: 2024-03-04T09:57:48Z
date_published: 2020-07-08T00:00:00Z
date_updated: 2024-03-04T10:02:49Z
day: '08'
department:
- _id: JoFi
doi: 10.23919/eucap48036.2020.9135962
language:
- iso: eng
month: '07'
oa_version: None
publication: 14th European Conference on Antennas and Propagation
publication_identifier:
eisbn:
- '9788831299008'
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: Compact millimeter and submillimeter-wave photonic radiometer for cubesats
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '15074'
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 the stable orientation
problem, which is a special case of the more general locally optimal semi-matching
problem. The prior work by Czygrinow et al. (DISC 2012) finds a locally optimal
semi-matching in O(Δ⁵) rounds in graphs of maximum degree Δ, which directly implies
an algorithm with the same runtime for stable orientations. We improve the runtime
to O(Δ⁴) for stable orientations and prove a lower bound of Ω(Δ) rounds.
alternative_title:
- LIPIcs
article_number: '40'
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. Brief announcement: Efficient
load-balancing through distributed token dropping. In: 34th International Symposium
on Distributed Computing. Vol 179. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2020. doi:10.4230/LIPIcs.DISC.2020.40'
apa: 'Brandt, S., Keller, B., Rybicki, J., Suomela, J., & Uitto, J. (2020).
Brief announcement: Efficient load-balancing through distributed token dropping.
In 34th International Symposium on Distributed Computing (Vol. 179). Virtual:
Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.DISC.2020.40'
chicago: 'Brandt, Sebastian, Barbara Keller, Joel Rybicki, Jukka Suomela, and Jara
Uitto. “Brief Announcement: Efficient Load-Balancing through Distributed Token
Dropping.” In 34th International Symposium on Distributed Computing, Vol.
179. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.DISC.2020.40.'
ieee: 'S. Brandt, B. Keller, J. Rybicki, J. Suomela, and J. Uitto, “Brief announcement:
Efficient load-balancing through distributed token dropping,” in 34th International
Symposium on Distributed Computing, Virtual, 2020, vol. 179.'
ista: 'Brandt S, Keller B, Rybicki J, Suomela J, Uitto J. 2020. Brief announcement:
Efficient load-balancing through distributed token dropping. 34th International
Symposium on Distributed Computing. DISC: Symposium on Distributed Computing,
LIPIcs, vol. 179, 40.'
mla: 'Brandt, Sebastian, et al. “Brief Announcement: Efficient Load-Balancing through
Distributed Token Dropping.” 34th International Symposium on Distributed Computing,
vol. 179, 40, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.DISC.2020.40.'
short: S. Brandt, B. Keller, J. Rybicki, J. Suomela, J. Uitto, in:, 34th International
Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2020.
conference:
end_date: 2020-10-16
location: Virtual
name: 'DISC: Symposium on Distributed Computing'
start_date: 2020-10-12
date_created: 2024-03-05T07:09:12Z
date_published: 2020-10-07T00:00:00Z
date_updated: 2024-03-05T07:13:13Z
day: '07'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.4230/LIPIcs.DISC.2020.40
external_id:
arxiv:
- '2005.07761'
file:
- access_level: open_access
checksum: 23e2d9321aef53092dc1e24a8ab82d72
content_type: application/pdf
creator: dernst
date_created: 2024-03-05T07:08:27Z
date_updated: 2024-03-05T07:08:27Z
file_id: '15075'
file_name: 2020_LIPIcs_Brandt.pdf
file_size: 303529
relation: main_file
success: 1
file_date_updated: 2024-03-05T07:08:27Z
has_accepted_license: '1'
intvolume: ' 179'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '10'
oa: 1
oa_version: Published Version
publication: 34th International Symposium on Distributed Computing
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
record:
- id: '9678'
relation: later_version
status: public
scopus_import: '1'
status: public
title: 'Brief announcement: Efficient load-balancing through distributed token dropping'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 179
year: '2020'
...
---
_id: '15077'
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\r\nversions of this draft. We also thank the ICALP anonymous
reviewers for their very useful comments.\r\nFunding: European Research Council
funding award PR1042ERC01"
alternative_title:
- LIPIcs
article_number: '7'
article_processing_charge: No
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.
In: 47th International Colloquium on Automata, Languages, and Programming.
Vol 168. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.ICALP.2020.7'
apa: 'Alistarh, D.-A., Nadiradze, G., & Sabour, A. (2020). Dynamic averaging
load balancing on cycles. In 47th International Colloquium on Automata, Languages,
and Programming (Vol. 168). Saarbrücken, Germany, Virtual: Schloss Dagstuhl
- Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2020.7'
chicago: Alistarh, Dan-Adrian, Giorgi Nadiradze, and Amirmojtaba Sabour. “Dynamic
Averaging Load Balancing on Cycles.” In 47th International Colloquium on Automata,
Languages, and Programming, Vol. 168. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2020. https://doi.org/10.4230/LIPIcs.ICALP.2020.7.
ieee: D.-A. Alistarh, G. Nadiradze, and A. Sabour, “Dynamic averaging load balancing
on cycles,” in 47th International Colloquium on Automata, Languages, and Programming,
Saarbrücken, Germany, Virtual, 2020, vol. 168.
ista: 'Alistarh D-A, Nadiradze G, Sabour A. 2020. Dynamic averaging load balancing
on cycles. 47th International Colloquium on Automata, Languages, and Programming.
ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs,
vol. 168, 7.'
mla: Alistarh, Dan-Adrian, et al. “Dynamic Averaging Load Balancing on Cycles.”
47th International Colloquium on Automata, Languages, and Programming,
vol. 168, 7, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.ICALP.2020.7.
short: D.-A. Alistarh, G. Nadiradze, A. Sabour, in:, 47th International Colloquium
on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2020.
conference:
end_date: 2020-07-11
location: Saarbrücken, Germany, Virtual
name: 'ICALP: International Colloquium on Automata, Languages, and Programming'
start_date: 2020-07-08
date_created: 2024-03-05T07:25:37Z
date_published: 2020-06-29T00:00:00Z
date_updated: 2024-03-05T07:35:53Z
day: '29'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.4230/LIPIcs.ICALP.2020.7
ec_funded: 1
external_id:
arxiv:
- '2003.09297'
file:
- access_level: open_access
checksum: e5eb16199f4ccfd77a321977eb3f026f
content_type: application/pdf
creator: dernst
date_created: 2024-03-05T07:25:15Z
date_updated: 2024-03-05T07:25:15Z
file_id: '15078'
file_name: 2020_LIPIcs_Alistarh.pdf
file_size: 782987
relation: main_file
success: 1
file_date_updated: 2024-03-05T07:25:15Z
has_accepted_license: '1'
intvolume: ' 168'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: 47th International Colloquium on Automata, Languages, and Programming
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
record:
- id: '8286'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Dynamic averaging load balancing on cycles
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 168
year: '2020'
...
---
_id: '15082'
abstract:
- lang: eng
text: "Two plane drawings of geometric graphs on the same set of points are called
disjoint compatible if their union is plane and they do not have an edge in common.
For a given set S of 2n points two plane drawings of perfect matchings M1 and
M2 (which do not need to be disjoint nor compatible) are disjoint tree-compatible
if there exists a plane drawing of a spanning tree T on S which is disjoint compatible
to both M1 and M2.\r\nWe show that the graph of all disjoint tree-compatible perfect
geometric matchings on 2n points in convex position is connected if and only if
2n ≥ 10. Moreover, in that case the diameter\r\nof this graph is either 4 or 5,
independent of n."
acknowledgement: Research on this work was initiated at the 6th Austrian-Japanese-Mexican-Spanish
Workshop on Discrete Geometry and continued during the 16th European Geometric Graph-Week,
both held near Strobl, Austria. We are grateful to the participants for the inspiring
atmosphere. We especially thank Alexander Pilz for bringing this class of problems
to our attention and Birgit Vogtenhuber for inspiring discussions. D.P. is partially
supported by the FWF grant I 3340-N35 (Collaborative DACH project Arrangements and
Drawings). The research stay of P.P. at IST Austria is funded by the project CZ.02.2.69/0.0/0.0/17_050/0008466
Improvement of internationalization in the field of research and development at
Charles University, through the support of quality projects MSCA-IF. This project
has received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie grant agreement No 734922.
article_number: '56'
article_processing_charge: No
author:
- first_name: Oswin
full_name: Aichholzer, Oswin
last_name: Aichholzer
- first_name: Julia
full_name: Obmann, Julia
last_name: Obmann
- first_name: Pavel
full_name: Patak, Pavel
id: B593B804-1035-11EA-B4F1-947645A5BB83
last_name: Patak
- first_name: Daniel
full_name: Perz, Daniel
last_name: Perz
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
citation:
ama: 'Aichholzer O, Obmann J, Patak P, Perz D, Tkadlec J. Disjoint tree-compatible
plane perfect matchings. In: 36th European Workshop on Computational Geometry.
; 2020.'
apa: Aichholzer, O., Obmann, J., Patak, P., Perz, D., & Tkadlec, J. (2020).
Disjoint tree-compatible plane perfect matchings. In 36th European Workshop
on Computational Geometry. Würzburg, Germany, Virtual.
chicago: Aichholzer, Oswin, Julia Obmann, Pavel Patak, Daniel Perz, and Josef Tkadlec.
“Disjoint Tree-Compatible Plane Perfect Matchings.” In 36th European Workshop
on Computational Geometry, 2020.
ieee: O. Aichholzer, J. Obmann, P. Patak, D. Perz, and J. Tkadlec, “Disjoint tree-compatible
plane perfect matchings,” in 36th European Workshop on Computational Geometry,
Würzburg, Germany, Virtual, 2020.
ista: 'Aichholzer O, Obmann J, Patak P, Perz D, Tkadlec J. 2020. Disjoint tree-compatible
plane perfect matchings. 36th European Workshop on Computational Geometry. EuroCG:
European Workshop on Computational Geometry, 56.'
mla: Aichholzer, Oswin, et al. “Disjoint Tree-Compatible Plane Perfect Matchings.”
36th European Workshop on Computational Geometry, 56, 2020.
short: O. Aichholzer, J. Obmann, P. Patak, D. Perz, J. Tkadlec, in:, 36th European
Workshop on Computational Geometry, 2020.
conference:
end_date: 2020-03-18
location: Würzburg, Germany, Virtual
name: 'EuroCG: European Workshop on Computational Geometry'
start_date: 2020-03-16
date_created: 2024-03-05T08:57:17Z
date_published: 2020-04-01T00:00:00Z
date_updated: 2024-03-05T09:00:07Z
day: '01'
department:
- _id: KrCh
- _id: UlWa
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www1.pub.informatik.uni-wuerzburg.de/eurocg2020/data/uploads/papers/eurocg20_paper_56.pdf
month: '04'
oa: 1
oa_version: Published Version
publication: 36th European Workshop on Computational Geometry
publication_status: published
quality_controlled: '1'
status: public
title: Disjoint tree-compatible plane perfect matchings
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '6748'
abstract:
- lang: eng
text: "Fitting a function by using linear combinations of a large number N of `simple'
components is one of the most fruitful ideas in statistical learning. This idea
lies at the core of a variety of methods, from two-layer neural networks to kernel
regression, to boosting. In general, the resulting risk minimization problem is
non-convex and is solved by gradient descent or its variants. Unfortunately, little
is known about global convergence properties of these approaches.\r\nHere we consider
the problem of learning a concave function f on a compact convex domain Ω⊆ℝd,
using linear combinations of `bump-like' components (neurons). The parameters
to be fitted are the centers of N bumps, and the resulting empirical risk minimization
problem is highly non-convex. We prove that, in the limit in which the number
of neurons diverges, the evolution of gradient descent converges to a Wasserstein
gradient flow in the space of probability distributions over Ω. Further, when
the bump width δ tends to 0, this gradient flow has a limit which is a viscous
porous medium equation. Remarkably, the cost function optimized by this gradient
flow exhibits a special property known as displacement convexity, which implies
exponential convergence rates for N→∞, δ→0. Surprisingly, this asymptotic theory
appears to capture well the behavior for moderate values of δ,N. Explaining this
phenomenon, and understanding the dependence on δ,N in a quantitative manner remains
an outstanding challenge."
article_processing_charge: No
article_type: original
author:
- first_name: Adel
full_name: Javanmard, Adel
last_name: Javanmard
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Andrea
full_name: Montanari, Andrea
last_name: Montanari
citation:
ama: Javanmard A, Mondelli M, Montanari A. Analysis of a two-layer neural network
via displacement convexity. Annals of Statistics. 2020;48(6):3619-3642.
doi:10.1214/20-AOS1945
apa: Javanmard, A., Mondelli, M., & Montanari, A. (2020). Analysis of a two-layer
neural network via displacement convexity. Annals of Statistics. Institute
of Mathematical Statistics. https://doi.org/10.1214/20-AOS1945
chicago: Javanmard, Adel, Marco Mondelli, and Andrea Montanari. “Analysis of a Two-Layer
Neural Network via Displacement Convexity.” Annals of Statistics. Institute
of Mathematical Statistics, 2020. https://doi.org/10.1214/20-AOS1945.
ieee: A. Javanmard, M. Mondelli, and A. Montanari, “Analysis of a two-layer neural
network via displacement convexity,” Annals of Statistics, vol. 48, no.
6. Institute of Mathematical Statistics, pp. 3619–3642, 2020.
ista: Javanmard A, Mondelli M, Montanari A. 2020. Analysis of a two-layer neural
network via displacement convexity. Annals of Statistics. 48(6), 3619–3642.
mla: Javanmard, Adel, et al. “Analysis of a Two-Layer Neural Network via Displacement
Convexity.” Annals of Statistics, vol. 48, no. 6, Institute of Mathematical
Statistics, 2020, pp. 3619–42, doi:10.1214/20-AOS1945.
short: A. Javanmard, M. Mondelli, A. Montanari, Annals of Statistics 48 (2020) 3619–3642.
date_created: 2019-07-31T09:39:42Z
date_published: 2020-12-11T00:00:00Z
date_updated: 2024-03-06T08:28:50Z
day: '11'
department:
- _id: MaMo
doi: 10.1214/20-AOS1945
external_id:
arxiv:
- '1901.01375'
isi:
- '000598369200021'
intvolume: ' 48'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1901.01375
month: '12'
oa: 1
oa_version: Preprint
page: 3619-3642
publication: Annals of Statistics
publication_identifier:
eissn:
- 1941-7330
issn:
- 1932-6157
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
status: public
title: Analysis of a two-layer neural network via displacement convexity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 48
year: '2020'
...
---
_id: '15070'
abstract:
- lang: eng
text: This workshop focused on interactions between the various perspectives on
the moduli space of Higgs bundles over a Riemann surface. This subject draws on
algebraic geometry, geometric topology, geometric analysis and mathematical physics,
and the goal was to promote interactions between these various branches of the
subject. The main current directions of research were well represented by the
participants, and the talks included many from both senior and junior participants.
article_processing_charge: No
article_type: original
author:
- first_name: Lara
full_name: Anderson, Lara
last_name: Anderson
- first_name: Tamás
full_name: Hausel, Tamás
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
- first_name: Rafe
full_name: Mazzeo, Rafe
last_name: Mazzeo
- first_name: Laura
full_name: Schaposnik, Laura
last_name: Schaposnik
citation:
ama: Anderson L, Hausel T, Mazzeo R, Schaposnik L. Geometry and physics of Higgs
bundles. Oberwolfach Reports. 2020;16(2):1357-1417. doi:10.4171/owr/2019/23
apa: Anderson, L., Hausel, T., Mazzeo, R., & Schaposnik, L. (2020). Geometry
and physics of Higgs bundles. Oberwolfach Reports. European Mathematical
Society. https://doi.org/10.4171/owr/2019/23
chicago: Anderson, Lara, Tamás Hausel, Rafe Mazzeo, and Laura Schaposnik. “Geometry
and Physics of Higgs Bundles.” Oberwolfach Reports. European Mathematical
Society, 2020. https://doi.org/10.4171/owr/2019/23.
ieee: L. Anderson, T. Hausel, R. Mazzeo, and L. Schaposnik, “Geometry and physics
of Higgs bundles,” Oberwolfach Reports, vol. 16, no. 2. European Mathematical
Society, pp. 1357–1417, 2020.
ista: Anderson L, Hausel T, Mazzeo R, Schaposnik L. 2020. Geometry and physics of
Higgs bundles. Oberwolfach Reports. 16(2), 1357–1417.
mla: Anderson, Lara, et al. “Geometry and Physics of Higgs Bundles.” Oberwolfach
Reports, vol. 16, no. 2, European Mathematical Society, 2020, pp. 1357–417,
doi:10.4171/owr/2019/23.
short: L. Anderson, T. Hausel, R. Mazzeo, L. Schaposnik, Oberwolfach Reports 16
(2020) 1357–1417.
date_created: 2024-03-04T11:36:31Z
date_published: 2020-06-04T00:00:00Z
date_updated: 2024-03-11T09:20:34Z
day: '04'
department:
- _id: TaHa
doi: 10.4171/owr/2019/23
intvolume: ' 16'
issue: '2'
keyword:
- Organic Chemistry
- Biochemistry
language:
- iso: eng
month: '06'
oa_version: None
page: 1357-1417
publication: Oberwolfach Reports
publication_identifier:
issn:
- 1660-8933
publication_status: published
publisher: European Mathematical Society
quality_controlled: '1'
status: public
title: Geometry and physics of Higgs bundles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2020'
...
---
_id: '8741'
abstract:
- lang: eng
text: "In ecology, climate and other fields, (sub)systems have been identified that
can transition into a qualitatively different state when a critical threshold
or tipping point in a driving process is crossed. An understanding of those tipping
elements is of great interest given the increasing influence of humans on the
biophysical Earth system. Complex interactions exist between tipping elements,
e.g. physical mechanisms connect subsystems of the climate system. Based on earlier
work on such coupled nonlinear systems, we systematically assessed the qualitative
long-term behaviour of interacting tipping elements. We developed an understanding
of the consequences of interactions\r\non the tipping behaviour allowing for tipping
cascades to emerge under certain conditions. The (narrative) application of\r\nthese
qualitative results to real-world examples of interacting tipping elements indicates
that tipping cascades with profound consequences may occur: the interacting Greenland
ice sheet and thermohaline ocean circulation might tip before the tipping points
of the isolated subsystems are crossed. The eutrophication of the first lake in
a lake chain might propagate through the following lakes without a crossing of
their individual critical nutrient input levels. The possibility of emerging cascading
tipping dynamics calls for the development of a unified theory of interacting
tipping elements and the quantitative analysis of interacting real-world tipping
elements."
acknowledgement: "V.K. thanks the German National Academic Foundation (Studienstiftung
des deutschen Volkes) for financial\r\nsupport. J.F.D. is grateful for financial
support by the Stordalen Foundation via the Planetary Boundary Research\r\nNetwork
(PB.net), the Earth League’s EarthDoc program and the European Research Council
Advanced Grant\r\nproject ERA (Earth Resilience in the Anthropocene). We are thankful
for support by the Leibniz Association\r\n(project DominoES).\r\nAcknowledgements.
This work has been performed in the context of the copan collaboration and the FutureLab
on Earth\r\nResilience in the Anthropocene at the Potsdam Institute for Climate
Impact Research. Furthermore, we acknowledge\r\ndiscussions with and helpful comments
by N. Wunderling, J. Heitzig and M. Wiedermann."
article_number: '200599'
article_processing_charge: No
article_type: original
author:
- first_name: Ann Kristin
full_name: Klose, Ann Kristin
last_name: Klose
- first_name: Volker
full_name: Karle, Volker
id: D7C012AE-D7ED-11E9-95E8-1EC5E5697425
last_name: Karle
orcid: 0000-0002-6963-0129
- first_name: Ricarda
full_name: Winkelmann, Ricarda
last_name: Winkelmann
- first_name: Jonathan F.
full_name: Donges, Jonathan F.
last_name: Donges
citation:
ama: 'Klose AK, Karle V, Winkelmann R, Donges JF. Emergence of cascading dynamics
in interacting tipping elements of ecology and climate: Cascading dynamics in
tipping elements. Royal Society Open Science. 2020;7(6). doi:10.1098/rsos.200599'
apa: 'Klose, A. K., Karle, V., Winkelmann, R., & Donges, J. F. (2020). Emergence
of cascading dynamics in interacting tipping elements of ecology and climate:
Cascading dynamics in tipping elements. Royal Society Open Science. The
Royal Society. https://doi.org/10.1098/rsos.200599'
chicago: 'Klose, Ann Kristin, Volker Karle, Ricarda Winkelmann, and Jonathan F.
Donges. “Emergence of Cascading Dynamics in Interacting Tipping Elements of Ecology
and Climate: Cascading Dynamics in Tipping Elements.” Royal Society Open Science.
The Royal Society, 2020. https://doi.org/10.1098/rsos.200599.'
ieee: 'A. K. Klose, V. Karle, R. Winkelmann, and J. F. Donges, “Emergence of cascading
dynamics in interacting tipping elements of ecology and climate: Cascading dynamics
in tipping elements,” Royal Society Open Science, vol. 7, no. 6. The Royal
Society, 2020.'
ista: 'Klose AK, Karle V, Winkelmann R, Donges JF. 2020. Emergence of cascading
dynamics in interacting tipping elements of ecology and climate: Cascading dynamics
in tipping elements. Royal Society Open Science. 7(6), 200599.'
mla: 'Klose, Ann Kristin, et al. “Emergence of Cascading Dynamics in Interacting
Tipping Elements of Ecology and Climate: Cascading Dynamics in Tipping Elements.”
Royal Society Open Science, vol. 7, no. 6, 200599, The Royal Society, 2020,
doi:10.1098/rsos.200599.'
short: A.K. Klose, V. Karle, R. Winkelmann, J.F. Donges, Royal Society Open Science
7 (2020).
date_created: 2020-11-08T23:01:25Z
date_published: 2020-06-01T00:00:00Z
date_updated: 2024-03-12T12:31:30Z
day: '01'
ddc:
- '530'
- '550'
department:
- _id: MiLe
doi: 10.1098/rsos.200599
external_id:
arxiv:
- '1910.12042'
isi:
- '000545625200001'
file:
- access_level: open_access
checksum: 5505c445de373bfd836eb4d3b48b1f37
content_type: application/pdf
creator: dernst
date_created: 2020-11-09T09:07:11Z
date_updated: 2020-11-09T09:07:11Z
file_id: '8748'
file_name: 2020_RoyalSocOpenScience_Klose.pdf
file_size: 1611485
relation: main_file
success: 1
file_date_updated: 2020-11-09T09:07:11Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Royal Society Open Science
publication_identifier:
eissn:
- '20545703'
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Emergence of cascading dynamics in interacting tipping elements of ecology
and climate: Cascading dynamics in tipping elements'
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: 7
year: '2020'
...
---
_id: '15079'
abstract:
- lang: eng
text: "Large complex systems tend to develop universal patterns that often represent
their essential characteristics. For example, the cumulative effects of independent
or weakly dependent random variables often yield the Gaussian universality class
via the central limit theorem. For non-commutative random variables, e.g. matrices,
the Gaussian behavior is often replaced by another universality class, commonly
called random matrix statistics. Nearby eigenvalues are strongly correlated, and,
remarkably, their correlation structure is universal, depending only on the symmetry
type of the matrix. Even more surprisingly, this feature is not restricted to
matrices; in fact Eugene Wigner, the pioneer of the field, discovered in the 1950s
that distributions of the gaps between energy levels of complicated quantum systems
universally follow the same random matrix statistics. This claim has never been
rigorously proved for any realistic physical system but experimental data and
extensive numerics leave no doubt as to its correctness. Since then random matrices
have proved to be extremely useful phenomenological models in a wide range of
applications beyond quantum physics that include number theory, statistics, neuroscience,
population dynamics, wireless communication and mathematical finance. The ubiquity
of random matrices in natural sciences is still a mystery, but recent years have
witnessed a breakthrough in the mathematical description of the statistical structure
of their spectrum. Random matrices and closely related areas such as log-gases
have become an extremely active research area in probability theory.\r\nThis workshop
brought together outstanding researchers from a variety of mathematical backgrounds
whose areas of research are linked to random matrices. While there are strong
links between their motivations, the techniques used by these researchers span
a large swath of mathematics, ranging from purely algebraic techniques to stochastic
analysis, classical probability theory, operator algebra, supersymmetry, orthogonal
polynomials, etc."
article_processing_charge: No
article_type: original
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Friedrich
full_name: Götze, Friedrich
last_name: Götze
- first_name: Alice
full_name: Guionnet, Alice
last_name: Guionnet
citation:
ama: Erdös L, Götze F, Guionnet A. Random matrices. Oberwolfach Reports.
2020;16(4):3459-3527. doi:10.4171/owr/2019/56
apa: Erdös, L., Götze, F., & Guionnet, A. (2020). Random matrices. Oberwolfach
Reports. European Mathematical Society. https://doi.org/10.4171/owr/2019/56
chicago: Erdös, László, Friedrich Götze, and Alice Guionnet. “Random Matrices.”
Oberwolfach Reports. European Mathematical Society, 2020. https://doi.org/10.4171/owr/2019/56.
ieee: L. Erdös, F. Götze, and A. Guionnet, “Random matrices,” Oberwolfach Reports,
vol. 16, no. 4. European Mathematical Society, pp. 3459–3527, 2020.
ista: Erdös L, Götze F, Guionnet A. 2020. Random matrices. Oberwolfach Reports.
16(4), 3459–3527.
mla: Erdös, László, et al. “Random Matrices.” Oberwolfach Reports, vol. 16,
no. 4, European Mathematical Society, 2020, pp. 3459–527, doi:10.4171/owr/2019/56.
short: L. Erdös, F. Götze, A. Guionnet, Oberwolfach Reports 16 (2020) 3459–3527.
date_created: 2024-03-05T07:54:44Z
date_published: 2020-11-19T00:00:00Z
date_updated: 2024-03-12T12:25:18Z
day: '19'
department:
- _id: LaEr
doi: 10.4171/owr/2019/56
intvolume: ' 16'
issue: '4'
language:
- iso: eng
month: '11'
oa_version: None
page: 3459-3527
publication: Oberwolfach Reports
publication_identifier:
issn:
- 1660-8933
publication_status: published
publisher: European Mathematical Society
quality_controlled: '1'
status: public
title: Random matrices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2020'
...
---
_id: '15072'
abstract:
- lang: eng
text: The interaction among fundamental particles in nature leads to many interesting
effects in quantum statistical mechanics; examples include superconductivity for
charged systems and superfluidity in cold gases. It is a huge challenge for mathematical
physics to understand the collective behavior of systems containing a large number
of particles, emerging from known microscopic interactions. In this workshop we
brought together researchers working on different aspects of many-body quantum
mechanics to discuss recent developments, exchange ideas and propose new challenges
and research directions.
article_processing_charge: No
article_type: original
author:
- first_name: Christian
full_name: Hainzl, Christian
last_name: Hainzl
- 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
- first_name: Simone
full_name: Warzel, Simone
last_name: Warzel
citation:
ama: Hainzl C, Schlein B, Seiringer R, Warzel S. Many-body quantum systems. Oberwolfach
Reports. 2020;16(3):2541-2603. doi:10.4171/owr/2019/41
apa: Hainzl, C., Schlein, B., Seiringer, R., & Warzel, S. (2020). Many-body
quantum systems. Oberwolfach Reports. European Mathematical Society. https://doi.org/10.4171/owr/2019/41
chicago: Hainzl, Christian, Benjamin Schlein, Robert Seiringer, and Simone Warzel.
“Many-Body Quantum Systems.” Oberwolfach Reports. European Mathematical
Society, 2020. https://doi.org/10.4171/owr/2019/41.
ieee: C. Hainzl, B. Schlein, R. Seiringer, and S. Warzel, “Many-body quantum systems,”
Oberwolfach Reports, vol. 16, no. 3. European Mathematical Society, pp.
2541–2603, 2020.
ista: Hainzl C, Schlein B, Seiringer R, Warzel S. 2020. Many-body quantum systems.
Oberwolfach Reports. 16(3), 2541–2603.
mla: Hainzl, Christian, et al. “Many-Body Quantum Systems.” Oberwolfach Reports,
vol. 16, no. 3, European Mathematical Society, 2020, pp. 2541–603, doi:10.4171/owr/2019/41.
short: C. Hainzl, B. Schlein, R. Seiringer, S. Warzel, Oberwolfach Reports 16 (2020)
2541–2603.
date_created: 2024-03-04T11:46:12Z
date_published: 2020-09-10T00:00:00Z
date_updated: 2024-03-12T12:02:00Z
day: '10'
department:
- _id: RoSe
doi: 10.4171/owr/2019/41
intvolume: ' 16'
issue: '3'
language:
- iso: eng
month: '09'
oa_version: None
page: 2541-2603
publication: Oberwolfach Reports
publication_identifier:
issn:
- 1660-8933
publication_status: published
publisher: European Mathematical Society
quality_controlled: '1'
status: public
title: Many-body quantum systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2020'
...
---
_id: '15071'
abstract:
- lang: eng
text: "A mesophilic methanogenic culture, designated JL01, was isolated from Holocene
permafrost in the Russian Arctic [1]. After long-term extensive cultivation at
15°C it turned out to be a tied binary culture of archaeal (JL01) and bacterial
(Sphaerochaeta associata GLS2) strains.\r\nStrain JL01 was a strict anaerobe and
grew on methanol, acetate and methylamines as energy and carbon sources. Cells
were irregular coccoid, non-motile, non-spore-forming, and Gram-stainpositive.
Optimum conditions for growth were 24-28 oC, pH 6.8–7.3 and 0.075-0.1 M NaCl.\r\nPhylogenetic
tree reconstructions based on 16S rRNA and concatenated alignment of broadly\r\nconserved
protein-coding genes revealed its close relation to Methanosarcina mazei S-6\r\nT
(similarity 99.5%). The comparison of whole genomic sequences (ANI) of the isolate
and the type strain of M.mazei was 98.5%, which is higher than the values recommended
for new species. Thus strain JL01 (=VKM B-2370=JCM 31898) represents the first
M. mazei isolated from permanently subzero Arcticsediments. The long-term co-cultivation
of JL01 with S. associata GLS2T showed the methane production without any additional
carbon and energy sources. Genome analysis of S. associata GLS2T revealed putative
genes involved in methanochondroithin catabolism."
acknowledgement: "The work was supported by of Russian Foundation of Basic Research:
grant № 19-04-00831 for Viktoria Shcherbakova and Olga Troshina, grant № 18-34-00334
for Viktoriia Oshurkova and Vladimir Trubitsyn. \r\nWe thank Dr Natalia Suzina (IBPM
RAS, Federal Research Center Pushchino Center for\r\nBiological Research RAS) for
the help with the microscopic studies, respectively; Dr. Margarita Meyer (Division
of Genetics, Department of Medicine, BWH and HMS, USA) and Dr Fedor Kondrashov (IST,
Austria) for their help in obtaining the genomic sequence of strain JL01. "
article_processing_charge: Yes
author:
- first_name: Viktoriia
full_name: Oshurkova, Viktoriia
last_name: Oshurkova
- first_name: Olga
full_name: Troshina, Olga
last_name: Troshina
- first_name: Vladimir
full_name: Trubitsyn, Vladimir
last_name: Trubitsyn
- first_name: Yana
full_name: Ryzhmanova, Yana
last_name: Ryzhmanova
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Viktoria
full_name: Shcherbakova, Viktoria
last_name: Shcherbakova
citation:
ama: 'Oshurkova V, Troshina O, Trubitsyn V, Ryzhmanova Y, Bochkareva O, Shcherbakova
V. Characterization of methanosarcina mazei JL01 isolated from holocene arctic
permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta
associata GLS2T. In: Proceedings of 1st International Electronic Conference
on Microbiology. MDPI; 2020. doi:10.3390/ecm2020-07116'
apa: 'Oshurkova, V., Troshina, O., Trubitsyn, V., Ryzhmanova, Y., Bochkareva, O.,
& Shcherbakova, V. (2020). Characterization of methanosarcina mazei JL01 isolated
from holocene arctic permafrost and study of the archaeon cooperation with bacterium
Sphaerochaeta associata GLS2T. In Proceedings of 1st International Electronic
Conference on Microbiology. Virtual: MDPI. https://doi.org/10.3390/ecm2020-07116'
chicago: Oshurkova, Viktoriia, Olga Troshina, Vladimir Trubitsyn, Yana Ryzhmanova,
Olga Bochkareva, and Viktoria Shcherbakova. “Characterization of Methanosarcina
Mazei JL01 Isolated from Holocene Arctic Permafrost and Study of the Archaeon
Cooperation with Bacterium Sphaerochaeta Associata GLS2T.” In Proceedings of
1st International Electronic Conference on Microbiology. MDPI, 2020. https://doi.org/10.3390/ecm2020-07116.
ieee: V. Oshurkova, O. Troshina, V. Trubitsyn, Y. Ryzhmanova, O. Bochkareva, and
V. Shcherbakova, “Characterization of methanosarcina mazei JL01 isolated from
holocene arctic permafrost and study of the archaeon cooperation with bacterium
Sphaerochaeta associata GLS2T,” in Proceedings of 1st International Electronic
Conference on Microbiology, Virtual, 2020.
ista: 'Oshurkova V, Troshina O, Trubitsyn V, Ryzhmanova Y, Bochkareva O, Shcherbakova
V. 2020. Characterization of methanosarcina mazei JL01 isolated from holocene
arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta
associata GLS2T. Proceedings of 1st International Electronic Conference on Microbiology.
ECM: Electronic Conference on Microbiology.'
mla: Oshurkova, Viktoriia, et al. “Characterization of Methanosarcina Mazei JL01
Isolated from Holocene Arctic Permafrost and Study of the Archaeon Cooperation
with Bacterium Sphaerochaeta Associata GLS2T.” Proceedings of 1st International
Electronic Conference on Microbiology, MDPI, 2020, doi:10.3390/ecm2020-07116.
short: V. Oshurkova, O. Troshina, V. Trubitsyn, Y. Ryzhmanova, O. Bochkareva, V.
Shcherbakova, in:, Proceedings of 1st International Electronic Conference on Microbiology,
MDPI, 2020.
conference:
end_date: 2020-11-30
location: Virtual
name: 'ECM: Electronic Conference on Microbiology'
start_date: 2020-11-02
date_created: 2024-03-04T11:41:31Z
date_published: 2020-11-02T00:00:00Z
date_updated: 2024-03-20T08:06:22Z
day: '02'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.3390/ecm2020-07116
file:
- access_level: open_access
checksum: d1914af7811a21a4b2744eb51b5834e3
content_type: application/pdf
creator: dernst
date_created: 2024-03-20T08:05:46Z
date_updated: 2024-03-20T08:05:46Z
file_id: '15127'
file_name: 2020_ECM_Oshurkova.pdf
file_size: 595543
relation: main_file
success: 1
file_date_updated: 2024-03-20T08:05:46Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Proceedings of 1st International Electronic Conference on Microbiology
publication_status: published
publisher: MDPI
quality_controlled: '1'
status: public
title: Characterization of methanosarcina mazei JL01 isolated from holocene arctic
permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata
GLS2T
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '7525'
abstract:
- lang: eng
text: "The medial habenula (MHb) is an evolutionary conserved epithalamic structure
important for the modulation of emotional memory. It is involved in regulation
of anxiety, compulsive behavior, addiction (nicotinic and opioid), sexual and
feeding behavior. MHb receives inputs from septal regions and projects exclusively
to the interpeduncular nucleus (IPN). Distinct sub-regions of the septum project
to different subnuclei of MHb: the bed nucleus of anterior commissure projects
to dorsal MHb and the triangular septum projects to ventral MHb. Furthermore,
the dorsal and ventral MHb project to the lateral and rostral/central IPN, respectively.
Importantly, these projections have unique features of prominent co-release of
different neurotransmitters and requirement of a peculiar type of calcium channel
for release. In general, synaptic neurotransmission requires an activity-dependent
influx of Ca2+ into the presynaptic terminal through voltage-gated calcium channels.
The calcium channel family most commonly involved in neurotransmitter release
comprises three members, P/Q-, N- and R-type with Cav2.1, Cav2.2 and Cav2.3 subunits,
respectively. In contrast to most CNS synapses that mainly express Cav2.1 and/or
Cav2.2, MHb terminals in the IPN exclusively express Cav2.3. In other parts of
the brain, such as the hippocampus, Cav2.3 is mostly located to postsynaptic elements.
This unusual presynaptic location of Cav2.3 in the MHb-IPN pathway implies unique
mechanisms of glutamate release in this pathway. One potential example of such
uniqueness is the facilitation of release by GABAB receptor (GBR) activation.
Presynaptic GBRs usually inhibit the release of neurotransmitters by inhibiting
presynaptic calcium channels. MHb shows the highest expression levels of GBR in
the brain. GBRs comprise two subunits, GABAB1 (GB1) and GABAB2 (GB2), and are
associated with auxiliary subunits, called potassium channel tetramerization domain
containing proteins (KCTD) 8, 12, 12b and 16. Among these four subunits, KCTD12b
is exclusively expressed in ventral MHb, and KCTD8 shows the strongest expression
in the whole MHb among other brain regions, indicating that KCTD8 and KCTD12b
may be involved in the unique mechanisms of neurotransmitter release mediated
by Cav2.3 and regulated by GBRs in this pathway. \r\nIn the present study, we
first verified that neurotransmission in both dorsal and ventral MHb-IPN pathways
is mainly mediated by Cav2.3 using a selective blocker of R-type channels, SNX-482.
We next found that baclofen, a GBR agonist, has facilitatory effects on release
from ventral MHb terminal in rostral IPN, whereas it has inhibitory effects on
release from dorsal MHb terminals in lateral IPN, indicating that KCTD12b expressed
exclusively in ventral MHb may have a role in the facilitatory effects of GBR
activation. In a heterologous expression system using HEK cells, we found that
KCTD8 and KCTD12b but not KCTD12 directly bind with Cav2.3. Pre-embedding immunogold
electron microscopy data show that Cav2.3 and KCTD12b are distributed most densely
in presynaptic active zone in IPN with KCTD12b being present only in rostral/central
but not lateral IPN, whereas GABAB, KCTD8 and KCTD12 are distributed most densely
in perisynaptic sites with KCTD12 present more frequently in postsynaptic elements
and only in rostral/central IPN. In freeze-fracture replica labelling, Cav2.3,
KCTD8 and KCTD12b are co-localized with each other in the same active zone indicating
that they may form complexes regulating vesicle release in rostral IPN. \r\nOn
electrophysiological studies of wild type (WT) mice, we found that paired-pulse
ratio in rostral IPN of KCTD12b knock-out (KO) mice is lower than those of WT
and KCTD8 KO mice. Consistent with this finding, in mean variance analysis, release
probability in rostral IPN of KCTD12b KO mice is higher than that of WT and KCTD8
KO mice. Although paired-pulse ratios are not different between WT and KCTD8 KO
mice, the mean variance analysis revealed significantly lower release probability
in rostral IPN of KCTD8 KO than WT mice. These results demonstrate bidirectional
regulation of Cav2.3-mediated release by KCTD8 and KCTD12b without GBR activation
in rostral IPN. Finally, we examined the baclofen effects in rostral IPN of KCTD8
and KCTD12b KO mice, and found the facilitation of release remained in both KO
mice, indicating that the peculiar effects of the GBR activation in this pathway
do not depend on the selective expression of these KCTD subunits in ventral MHb.
However, we found that presynaptic potentiation of evoked EPSC amplitude by baclofen
falls to baseline after washout faster in KCTD12b KO mice than WT, KCTD8 KO and
KCTD8/12b double KO mice. This result indicates that KCTD12b is involved in sustained
potentiation of vesicle release by GBR activation, whereas KCTD8 is involved in
its termination in the absence of KCTD12b. Consistent with these functional findings,
replica labelling revealed an increase in density of KCTD8, but not Cav2.3 or
GBR at active zone in rostral IPN of KCTD12b KO mice compared with that of WT
mice, suggesting that increased association of KCTD8 with Cav2.3 facilitates the
release probability and termination of the GBR effect in the absence of KCTD12b.\r\nIn
summary, our study provided new insights into the physiological roles of presynaptic
Cav2.3, GBRs and their auxiliary subunits KCTDs at an evolutionary conserved neuronal
circuit. Future studies will be required to identify the exact molecular mechanism
underlying the GBR-mediated presynaptic potentiation on ventral MHb terminals.
It remains to be determined whether the prominent presence of presynaptic KCTDs
at active zone could exert similar neuromodulatory functions in different pathways
of the brain.\r\n"
acknowledged_ssus:
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Pradeep
full_name: Bhandari, Pradeep
id: 45EDD1BC-F248-11E8-B48F-1D18A9856A87
last_name: Bhandari
orcid: 0000-0003-0863-4481
citation:
ama: Bhandari P. Localization and functional role of Cav2.3 in the medial habenula
to interpeduncular nucleus pathway. 2020. doi:10.15479/AT:ISTA:7525
apa: Bhandari, P. (2020). Localization and functional role of Cav2.3 in the medial
habenula to interpeduncular nucleus pathway. Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:7525
chicago: Bhandari, Pradeep. “Localization and Functional Role of Cav2.3 in the Medial
Habenula to Interpeduncular Nucleus Pathway.” Institute of Science and Technology
Austria, 2020. https://doi.org/10.15479/AT:ISTA:7525.
ieee: P. Bhandari, “Localization and functional role of Cav2.3 in the medial habenula
to interpeduncular nucleus pathway,” Institute of Science and Technology Austria,
2020.
ista: Bhandari P. 2020. Localization and functional role of Cav2.3 in the medial
habenula to interpeduncular nucleus pathway. Institute of Science and Technology
Austria.
mla: Bhandari, Pradeep. Localization and Functional Role of Cav2.3 in the Medial
Habenula to Interpeduncular Nucleus Pathway. Institute of Science and Technology
Austria, 2020, doi:10.15479/AT:ISTA:7525.
short: P. Bhandari, Localization and Functional Role of Cav2.3 in the Medial Habenula
to Interpeduncular Nucleus Pathway, Institute of Science and Technology Austria,
2020.
date_created: 2020-02-26T10:56:37Z
date_published: 2020-02-28T00:00:00Z
date_updated: 2023-09-07T13:20:03Z
day: '28'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: RySh
doi: 10.15479/AT:ISTA:7525
file:
- access_level: open_access
checksum: 4589234fdb12b4ad72273b311723a7b4
content_type: application/pdf
creator: pbhandari
date_created: 2020-02-28T08:37:53Z
date_updated: 2021-03-01T23:30:04Z
embargo: 2021-02-28
file_id: '7538'
file_name: Pradeep Bhandari Thesis.pdf
file_size: 9646346
relation: main_file
title: Localization and functional role of Cav2.3 in the medial habenula to interpeduncular
nucleus pathway
- access_level: closed
checksum: aa79490553ca0a5c9b6fbcd152e93928
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: pbhandari
date_created: 2020-02-28T08:47:14Z
date_updated: 2021-03-01T23:30:04Z
embargo_to: open_access
file_id: '7539'
file_name: Pradeep Bhandari Thesis.docx
file_size: 35252164
relation: source_file
title: Localization and functional role of Cav2.3 in the medial habenula to interpeduncular
nucleus pathway
file_date_updated: 2021-03-01T23:30:04Z
has_accepted_license: '1'
keyword:
- Cav2.3
- medial habenula (MHb)
- interpeduncular nucleus (IPN)
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '79'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
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: Localization and functional role of Cav2.3 in the medial habenula to interpeduncular
nucleus pathway
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8586'
abstract:
- lang: eng
text: Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights
into biological processes and structures within a native context. However, a major
challenge still lies in the efficient and reproducible preparation of adherent
cells for subsequent cryo-EM analysis. This is due to the sensitivity of many
cellular specimens to the varying seeding and culturing conditions required for
EM experiments, the often limited amount of cellular material and also the fragility
of EM grids and their substrate. Here, we present low-cost and reusable 3D printed
grid holders, designed to improve specimen preparation when culturing challenging
cellular samples directly on grids. The described grid holders increase cell culture
reproducibility and throughput, and reduce the resources required for cell culturing.
We show that grid holders can be integrated into various cryo-EM workflows, including
micro-patterning approaches to control cell seeding on grids, and for generating
samples for cryo-focused ion beam milling and cryo-electron tomography experiments.
Their adaptable design allows for the generation of specialized grid holders customized
to a large variety of applications.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: Bio
- _id: EM-Fac
acknowledgement: This work was supported by the Austrian Science Fund (FWF, P33367)
to FKMS. BZ acknowledges support by the Niederösterreich Fond. This research was
also supported by the Scientific Service Units (SSU) 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 thank Georgi
Dimchev (IST Austria) and Sonja Jacob (Vienna Biocenter Core Facilities) for testing
our grid holders in different experimental setups and Daniel Gütl and the Kondrashov
group (IST Austria) for granting us repeated access to their 3D printers. We also
thank Jonna Alanko and the Sixt lab (IST Austria) for providing us HeLa cells, primary
BL6 mouse tail fibroblasts, NIH 3T3 fibroblasts and human telomerase immortalised
foreskin fibroblasts for our experiments. We are thankful to Ori Avinoam and William
Wan for helpful comments on the manuscript and also thank Dorotea Fracchiolla (Art&Science)
for illustrating the graphical abstract.
article_number: '107633'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Florian
full_name: Fäßler, Florian
id: 404F5528-F248-11E8-B48F-1D18A9856A87
last_name: Fäßler
orcid: 0000-0001-7149-769X
- first_name: Bettina
full_name: Zens, Bettina
id: 45FD126C-F248-11E8-B48F-1D18A9856A87
last_name: Zens
orcid: 0000-0002-9561-1239
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- 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: Fäßler F, Zens B, Hauschild R, Schur FK. 3D printed cell culture grid holders
for improved cellular specimen preparation in cryo-electron microscopy. Journal
of Structural Biology. 2020;212(3). doi:10.1016/j.jsb.2020.107633
apa: Fäßler, F., Zens, B., Hauschild, R., & Schur, F. K. (2020). 3D printed
cell culture grid holders for improved cellular specimen preparation in cryo-electron
microscopy. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2020.107633
chicago: Fäßler, Florian, Bettina Zens, Robert Hauschild, and Florian KM Schur.
“3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation
in Cryo-Electron Microscopy.” Journal of Structural Biology. Elsevier,
2020. https://doi.org/10.1016/j.jsb.2020.107633.
ieee: F. Fäßler, B. Zens, R. Hauschild, and F. K. Schur, “3D printed cell culture
grid holders for improved cellular specimen preparation in cryo-electron microscopy,”
Journal of Structural Biology, vol. 212, no. 3. Elsevier, 2020.
ista: Fäßler F, Zens B, Hauschild R, Schur FK. 2020. 3D printed cell culture grid
holders for improved cellular specimen preparation in cryo-electron microscopy.
Journal of Structural Biology. 212(3), 107633.
mla: Fäßler, Florian, et al. “3D Printed Cell Culture Grid Holders for Improved
Cellular Specimen Preparation in Cryo-Electron Microscopy.” Journal of Structural
Biology, vol. 212, no. 3, 107633, Elsevier, 2020, doi:10.1016/j.jsb.2020.107633.
short: F. Fäßler, B. Zens, R. Hauschild, F.K. Schur, Journal of Structural Biology
212 (2020).
date_created: 2020-09-29T13:24:06Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2024-03-28T23:30:05Z
day: '01'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1016/j.jsb.2020.107633
external_id:
isi:
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file:
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creator: dernst
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file_id: '8937'
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file_size: 7076870
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success: 1
file_date_updated: 2020-12-10T14:01:10Z
has_accepted_license: '1'
intvolume: ' 212'
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issue: '3'
keyword:
- electron microscopy
- cryo-EM
- EM sample preparation
- 3D printing
- cell culture
language:
- iso: eng
month: '12'
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: 059B463C-7A3F-11EA-A408-12923DDC885E
name: NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria
publication: Journal of Structural Biology
publication_identifier:
issn:
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publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
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status: public
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scopus_import: '1'
status: public
title: 3D printed cell culture grid holders for improved cellular specimen preparation
in cryo-electron microscopy
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: 212
year: '2020'
...
---
_id: '8657'
abstract:
- lang: eng
text: "Synthesis of proteins – translation – is a fundamental process of life. Quantitative
studies anchor translation into the context of bacterial physiology and reveal
several mathematical relationships, called “growth laws,” which capture physiological
feedbacks between protein synthesis and cell growth. Growth laws describe the
dependency of the ribosome abundance as a function of growth rate, which can change
depending on the growth conditions. Perturbations of translation reveal that bacteria
employ a compensatory strategy in which the reduced translation capability results
in increased expression of the translation machinery.\r\nPerturbations of translation
are achieved in various ways; clinically interesting is the application of translation-targeting
antibiotics – translation inhibitors. The antibiotic effects on bacterial physiology
are often poorly understood. Bacterial responses to two or more simultaneously
applied antibiotics are even more puzzling. The combined antibiotic effect determines
the type of drug interaction, which ranges from synergy (the effect is stronger
than expected) to antagonism (the effect is weaker) and suppression (one of the
drugs loses its potency).\r\nIn the first part of this work, we systematically
measure the pairwise interaction network for translation inhibitors that interfere
with different steps in translation. We find that the interactions are surprisingly
diverse and tend to be more antagonistic. To explore the underlying mechanisms,
we begin with a minimal biophysical model of combined antibiotic action. We base
this model on the kinetics of antibiotic uptake and binding together with the
physiological response described by the growth laws. The biophysical model explains
some drug interactions, but not all; it specifically fails to predict suppression.\r\nIn
the second part of this work, we hypothesize that elusive suppressive drug interactions
result from the interplay between ribosomes halted in different stages of translation.
To elucidate this putative mechanism of drug interactions between translation
inhibitors, we generate translation bottlenecks genetically using in- ducible
control of translation factors that regulate well-defined translation cycle steps.
These perturbations accurately mimic antibiotic action and drug interactions,
supporting that the interplay of different translation bottlenecks partially causes
these interactions.\r\nWe extend this approach by varying two translation bottlenecks
simultaneously. This approach reveals the suppression of translocation inhibition
by inhibited translation. We rationalize this effect by modeling dense traffic
of ribosomes that move on transcripts in a translation factor-mediated manner.
This model predicts a dissolution of traffic jams caused by inhibited translocation
when the density of ribosome traffic is reduced by lowered initiation. We base
this model on the growth laws and quantitative relationships between different
translation and growth parameters.\r\nIn the final part of this work, we describe
a set of tools aimed at quantification of physiological and translation parameters.
We further develop a simple model that directly connects the abundance of a translation
factor with the growth rate, which allows us to extract physiological parameters
describing initiation. We demonstrate the development of tools for measuring translation
rate.\r\nThis thesis showcases how a combination of high-throughput growth rate
mea- surements, genetics, and modeling can reveal mechanisms of drug interactions.
Furthermore, by a gradual transition from combinations of antibiotics to precise
genetic interventions, we demonstrated the equivalency between genetic and chemi-
cal perturbations of translation. These findings tile the path for quantitative
studies of antibiotic combinations and illustrate future approaches towards the
quantitative description of translation."
acknowledged_ssus:
- _id: LifeSc
- _id: M-Shop
acknowledgement: I thank Life Science Facilities for their continuous support with
providing top-notch laboratory materials, keeping the devices humming, and coordinating
the repairs and building of custom-designed laboratory equipment with the MIBA Machine
shop.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
citation:
ama: 'Kavcic B. Perturbations of protein synthesis: from antibiotics to genetics
and physiology. 2020. doi:10.15479/AT:ISTA:8657'
apa: 'Kavcic, B. (2020). Perturbations of protein synthesis: from antibiotics
to genetics and physiology. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8657'
chicago: 'Kavcic, Bor. “Perturbations of Protein Synthesis: From Antibiotics to
Genetics and Physiology.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8657.'
ieee: 'B. Kavcic, “Perturbations of protein synthesis: from antibiotics to genetics
and physiology,” Institute of Science and Technology Austria, 2020.'
ista: 'Kavcic B. 2020. Perturbations of protein synthesis: from antibiotics to genetics
and physiology. Institute of Science and Technology Austria.'
mla: 'Kavcic, Bor. Perturbations of Protein Synthesis: From Antibiotics to Genetics
and Physiology. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8657.'
short: 'B. Kavcic, Perturbations of Protein Synthesis: From Antibiotics to Genetics
and Physiology, Institute of Science and Technology Austria, 2020.'
date_created: 2020-10-13T16:46:14Z
date_published: 2020-10-14T00:00:00Z
date_updated: 2023-09-07T13:20:48Z
day: '14'
ddc:
- '571'
- '530'
- '570'
degree_awarded: PhD
department:
- _id: GaTk
doi: 10.15479/AT:ISTA:8657
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language:
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month: '10'
oa: 1
oa_version: Published Version
page: '271'
publication_identifier:
isbn:
- 978-3-99078-011-4
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
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status: public
- id: '8250'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
title: 'Perturbations of protein synthesis: from antibiotics to genetics and physiology'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '7473'
abstract:
- lang: eng
text: How structural and functional properties of synapses relate to each other
is a fundamental question in neuroscience. Electrophysiology has elucidated mechanisms
of synaptic transmission, and electron microscopy (EM) has provided insight into
morphological properties of synapses. Here we describe an enhanced method for
functional EM (“flash and freeze”), combining optogenetic stimulation with high-pressure
freezing. We demonstrate that the improved method can be applied to intact networks
in acute brain slices and organotypic slice cultures from mice. As a proof of
concept, we probed vesicle pool changes during synaptic transmission at the hippocampal
mossy fiber-CA3 pyramidal neuron synapse. Our findings show overlap of the docked
vesicle pool and the functionally defined readily releasable pool and provide
evidence of fast endocytosis at this synapse. Functional EM with acute slices
and slice cultures has the potential to reveal the structural and functional mechanisms
of transmission in intact, genetically perturbed, and disease-affected synapses.
acknowledgement: 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. 692692 and Marie Sklodowska-Curie
708497) and from Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27
Wittgenstein award and DK W1205-B09). We thank Johann Danzl and Ryuichi Shigemoto
for critically reading the manuscript; Walter Kaufmann, Daniel Gutl, and Vanessa
Zheden for extensive EM training, advice, and experimental assistance; Benjamin
Suter for substantial help with light stimulation, ImageJ plugins for analysis,
and manuscript editing; Florian Marr and Christina Altmutter for technical support;
Eleftheria Kralli-Beller for manuscript editing; Julia König and Paul Wurzinger
(Leica Microsystems) for helpful technical discussions; and Taija Makinen for providing
the Prox1-CreERT2 mouse line.
article_processing_charge: No
article_type: original
author:
- 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: Olena
full_name: Kim, Olena
id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87
last_name: Kim
- 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: Borges Merjane C, Kim O, Jonas PM. Functional electron microscopy (“Flash and
Freeze”) of identified cortical synapses in acute brain slices. Neuron.
2020;105:992-1006. doi:10.1016/j.neuron.2019.12.022
apa: Borges Merjane, C., Kim, O., & Jonas, P. M. (2020). Functional electron
microscopy (“Flash and Freeze”) of identified cortical synapses in acute brain
slices. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.12.022
chicago: Borges Merjane, Carolina, Olena Kim, and Peter M Jonas. “Functional Electron
Microscopy (‘Flash and Freeze’) of Identified Cortical Synapses in Acute Brain
Slices.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2019.12.022.
ieee: C. Borges Merjane, O. Kim, and P. M. Jonas, “Functional electron microscopy
(‘Flash and Freeze’) of identified cortical synapses in acute brain slices,” Neuron,
vol. 105. Elsevier, pp. 992–1006, 2020.
ista: Borges Merjane C, Kim O, Jonas PM. 2020. Functional electron microscopy (“Flash
and Freeze”) of identified cortical synapses in acute brain slices. Neuron. 105,
992–1006.
mla: Borges Merjane, Carolina, et al. “Functional Electron Microscopy (‘Flash and
Freeze’) of Identified Cortical Synapses in Acute Brain Slices.” Neuron,
vol. 105, Elsevier, 2020, pp. 992–1006, doi:10.1016/j.neuron.2019.12.022.
short: C. Borges Merjane, O. Kim, P.M. Jonas, Neuron 105 (2020) 992–1006.
date_created: 2020-02-10T15:59:45Z
date_published: 2020-03-18T00:00:00Z
date_updated: 2024-03-28T23:30:07Z
day: '18'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1016/j.neuron.2019.12.022
ec_funded: 1
external_id:
isi:
- '000520854700008'
pmid:
- '31928842'
file:
- access_level: open_access
checksum: 3582664addf26859e86ac5bec3e01416
content_type: application/pdf
creator: dernst
date_created: 2020-11-20T08:58:53Z
date_updated: 2020-11-20T08:58:53Z
file_id: '8778'
file_name: 2020_Neuron_BorgesMerjane.pdf
file_size: 9712957
relation: main_file
success: 1
file_date_updated: 2020-11-20T08:58:53Z
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intvolume: ' 105'
isi: 1
language:
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license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '03'
oa: 1
oa_version: Published Version
page: 992-1006
pmid: 1
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 25BAF7B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '708497'
name: Presynaptic calcium channels distribution and impact on coupling at the hippocampal
mossy fiber synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
- _id: 25C3DBB6-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W01205
name: Zellkommunikation in Gesundheit und Krankheit
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/flash-and-freeze-reveals-dynamics-of-nerve-connections/
record:
- id: '11196'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Functional electron microscopy (“Flash and Freeze”) of identified cortical
synapses in acute brain slices
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 105
year: '2020'
...
---
_id: '8250'
abstract:
- lang: eng
text: 'Antibiotics that interfere with translation, when combined, interact in diverse
and difficult-to-predict ways. Here, we explain these interactions by “translation
bottlenecks”: points in the translation cycle where antibiotics block ribosomal
progression. To elucidate the underlying mechanisms of drug interactions between
translation inhibitors, we generate translation bottlenecks genetically using
inducible control of translation factors that regulate well-defined translation
cycle steps. These perturbations accurately mimic antibiotic action and drug interactions,
supporting that the interplay of different translation bottlenecks causes these
interactions. We further show that growth laws, combined with drug uptake and
binding kinetics, enable the direct prediction of a large fraction of observed
interactions, yet fail to predict suppression. However, varying two translation
bottlenecks simultaneously supports that dense traffic of ribosomes and competition
for translation factors account for the previously unexplained suppression. These
results highlight the importance of “continuous epistasis” in bacterial physiology.'
acknowledgement: "We thank M. Hennessey-Wesen, I. Tomanek, K. Jain, A. Staron, K.
Tomasek, M. Scott,\r\nK.C. Huang, and Z. Gitai for reading the manuscript and constructive
comments. B.K. is\r\nindebted to C. Guet for additional guidance and generous support,
which rendered this\r\nwork possible. B.K. thanks all members of Guet group for
many helpful discussions and\r\nsharing of resources. B.K. additionally acknowledges
the tremendous support from A.\r\nAngermayr and K. Mitosch with experimental work.
We further thank E. Brown for\r\nhelpful comments regarding lamotrigine, and A.
Buskirk for valuable suggestions\r\nregarding the ribosome footprint size. This
work was supported in part by Austrian\r\nScience Fund (FWF) standalone grants P
27201-B22 (to T.B.) and P 28844 (to G.T.),\r\nHFSP program Grant RGP0042/2013 (to
T.B.), German Research Foundation (DFG)\r\nstandalone grant BO 3502/2-1 (to T.B.),
and German Research Foundation (DFG)\r\nCollaborative Research Centre (SFB) 1310
(to T.B.). Open access funding provided by\r\nProjekt DEAL."
article_number: '4013'
article_processing_charge: No
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. Mechanisms of drug interactions between
translation-inhibiting antibiotics. Nature Communications. 2020;11. doi:10.1038/s41467-020-17734-z
apa: Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2020). Mechanisms of drug
interactions between translation-inhibiting antibiotics. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-020-17734-z
chicago: Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Mechanisms of
Drug Interactions between Translation-Inhibiting Antibiotics.” Nature Communications.
Springer Nature, 2020. https://doi.org/10.1038/s41467-020-17734-z.
ieee: B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Mechanisms of drug interactions
between translation-inhibiting antibiotics,” Nature Communications, vol.
11. Springer Nature, 2020.
ista: Kavcic B, Tkačik G, Bollenbach MT. 2020. Mechanisms of drug interactions between
translation-inhibiting antibiotics. Nature Communications. 11, 4013.
mla: Kavcic, Bor, et al. “Mechanisms of Drug Interactions between Translation-Inhibiting
Antibiotics.” Nature Communications, vol. 11, 4013, Springer Nature, 2020,
doi:10.1038/s41467-020-17734-z.
short: B. Kavcic, G. Tkačik, M.T. Bollenbach, Nature Communications 11 (2020).
date_created: 2020-08-12T09:13:50Z
date_published: 2020-08-11T00:00:00Z
date_updated: 2024-03-28T23:30:08Z
day: '11'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1038/s41467-020-17734-z
external_id:
isi:
- '000562769300008'
file:
- access_level: open_access
checksum: 986bebb308850a55850028d3d2b5b664
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creator: dernst
date_created: 2020-08-17T07:36:57Z
date_updated: 2020-08-17T07:36:57Z
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file_size: 1965672
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file_date_updated: 2020-08-17T07:36:57Z
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intvolume: ' 11'
isi: 1
language:
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month: '08'
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: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '8657'
relation: dissertation_contains
status: public
status: public
title: Mechanisms of drug interactions between translation-inhibiting antibiotics
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: 11
year: '2020'
...
---
_id: '7673'
abstract:
- lang: eng
text: Combining drugs can improve the efficacy of treatments. However, predicting
the effect of drug combinations is still challenging. The combined potency of
drugs determines the drug interaction, which is classified as synergistic, additive,
antagonistic, or suppressive. While probabilistic, non-mechanistic models exist,
there is currently no biophysical model that can predict antibiotic interactions.
Here, we present a physiologically relevant model of the combined action of antibiotics
that inhibit protein synthesis by targeting the ribosome. This model captures
the kinetics of antibiotic binding and transport, and uses bacterial growth laws
to predict growth in the presence of antibiotic combinations. We find that this
biophysical model can produce all drug interaction types except suppression. We
show analytically that antibiotics which cannot bind to the ribosome simultaneously
generally act as substitutes for one another, leading to additive drug interactions.
Previously proposed null expectations for higher-order drug interactions follow
as a limiting case of our model. We further extend the model to include the effects
of direct physical or allosteric interactions between individual drugs on the
ribosome. Notably, such direct interactions profoundly change the combined drug
effect, depending on the kinetic parameters of the drugs used. The model makes
additional predictions for the effects of resistance genes on drug interactions
and for interactions between ribosome-targeting antibiotics and antibiotics with
other targets. These findings enhance our understanding of the interplay between
drug action and cell physiology and are a key step toward a general framework
for predicting drug interactions.
article_processing_charge: No
author:
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Tobias
full_name: Bollenbach, Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Kavcic B, Tkačik G, Bollenbach MT. A minimal biophysical model of combined
antibiotic action. bioRxiv. 2020. doi:10.1101/2020.04.18.047886
apa: Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2020). A minimal biophysical
model of combined antibiotic action. bioRxiv. Cold Spring Harbor Laboratory.
https://doi.org/10.1101/2020.04.18.047886
chicago: Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “A Minimal Biophysical
Model of Combined Antibiotic Action.” BioRxiv. Cold Spring Harbor Laboratory,
2020. https://doi.org/10.1101/2020.04.18.047886.
ieee: B. Kavcic, G. Tkačik, and M. T. Bollenbach, “A minimal biophysical model of
combined antibiotic action,” bioRxiv. Cold Spring Harbor Laboratory, 2020.
ista: Kavcic B, Tkačik G, Bollenbach MT. 2020. A minimal biophysical model of combined
antibiotic action. bioRxiv, 10.1101/2020.04.18.047886.
mla: Kavcic, Bor, et al. “A Minimal Biophysical Model of Combined Antibiotic Action.”
BioRxiv, Cold Spring Harbor Laboratory, 2020, doi:10.1101/2020.04.18.047886.
short: B. Kavcic, G. Tkačik, M.T. Bollenbach, BioRxiv (2020).
date_created: 2020-04-22T08:27:56Z
date_published: 2020-04-18T00:00:00Z
date_updated: 2024-03-28T23:30:08Z
day: '18'
department:
- _id: GaTk
doi: 10.1101/2020.04.18.047886
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://doi.org/10.1101/2020.04.18.047886 '
month: '04'
oa: 1
oa_version: Preprint
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: bioRxiv
publication_status: published
publisher: Cold Spring Harbor Laboratory
related_material:
record:
- id: '8997'
relation: later_version
status: public
- id: '8657'
relation: dissertation_contains
status: public
status: public
title: A minimal biophysical model of combined antibiotic action
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8002'
abstract:
- lang: eng
text: Wound healing in plant tissues, consisting of rigid cell wall-encapsulated
cells, represents a considerable challenge and occurs through largely unknown
mechanisms distinct from those in animals. Owing to their inability to migrate,
plant cells rely on targeted cell division and expansion to regenerate wounds.
Strict coordination of these wound-induced responses is essential to ensure efficient,
spatially restricted wound healing. Single-cell tracking by live imaging allowed
us to gain mechanistic insight into the wound perception and coordination of wound
responses after laser-based wounding in Arabidopsis root. We revealed a crucial
contribution of the collapse of damaged cells in wound perception and detected
an auxin increase specific to cells immediately adjacent to the wound. This localized
auxin increase balances wound-induced cell expansion and restorative division
rates in a dose-dependent manner, leading to tumorous overproliferation when the
canonical TIR1 auxin signaling is disrupted. Auxin and wound-induced turgor pressure
changes together also spatially define the activation of key components of regeneration,
such as the transcription regulator ERF115. Our observations suggest that the
wound signaling involves the sensing of collapse of damaged cells and a local
auxin signaling activation to coordinate the downstream transcriptional responses
in the immediate wound vicinity.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
article_number: '202003346'
article_processing_charge: No
article_type: original
author:
- first_name: Lukas
full_name: Hörmayer, Lukas
id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
last_name: Hörmayer
orcid: 0000-0001-8295-2926
- 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: Petra
full_name: Marhavá, Petra
id: 44E59624-F248-11E8-B48F-1D18A9856A87
last_name: Marhavá
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Saiko
full_name: Yoshida, Saiko
id: 2E46069C-F248-11E8-B48F-1D18A9856A87
last_name: Yoshida
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Hörmayer L, Montesinos López JC, Marhavá P, Benková E, Yoshida S, Friml J.
Wounding-induced changes in cellular pressure and localized auxin signalling spatially
coordinate restorative divisions in roots. Proceedings of the National Academy
of Sciences. 2020;117(26). doi:10.1073/pnas.2003346117
apa: Hörmayer, L., Montesinos López, J. C., Marhavá, P., Benková, E., Yoshida, S.,
& Friml, J. (2020). Wounding-induced changes in cellular pressure and localized
auxin signalling spatially coordinate restorative divisions in roots. Proceedings
of the National Academy of Sciences. Proceedings of the National Academy of
Sciences. https://doi.org/10.1073/pnas.2003346117
chicago: Hörmayer, Lukas, Juan C Montesinos López, Petra Marhavá, Eva Benková, Saiko
Yoshida, and Jiří Friml. “Wounding-Induced Changes in Cellular Pressure and Localized
Auxin Signalling Spatially Coordinate Restorative Divisions in Roots.” Proceedings
of the National Academy of Sciences. Proceedings of the National Academy of
Sciences, 2020. https://doi.org/10.1073/pnas.2003346117.
ieee: L. Hörmayer, J. C. Montesinos López, P. Marhavá, E. Benková, S. Yoshida, and
J. Friml, “Wounding-induced changes in cellular pressure and localized auxin signalling
spatially coordinate restorative divisions in roots,” Proceedings of the National
Academy of Sciences, vol. 117, no. 26. Proceedings of the National Academy
of Sciences, 2020.
ista: Hörmayer L, Montesinos López JC, Marhavá P, Benková E, Yoshida S, Friml J.
2020. Wounding-induced changes in cellular pressure and localized auxin signalling
spatially coordinate restorative divisions in roots. Proceedings of the National
Academy of Sciences. 117(26), 202003346.
mla: Hörmayer, Lukas, et al. “Wounding-Induced Changes in Cellular Pressure and
Localized Auxin Signalling Spatially Coordinate Restorative Divisions in Roots.”
Proceedings of the National Academy of Sciences, vol. 117, no. 26, 202003346,
Proceedings of the National Academy of Sciences, 2020, doi:10.1073/pnas.2003346117.
short: L. Hörmayer, J.C. Montesinos López, P. Marhavá, E. Benková, S. Yoshida, J.
Friml, Proceedings of the National Academy of Sciences 117 (2020).
date_created: 2020-06-22T13:33:52Z
date_published: 2020-06-30T00:00:00Z
date_updated: 2024-03-28T23:30:10Z
day: '30'
ddc:
- '580'
department:
- _id: JiFr
- _id: EvBe
doi: 10.1073/pnas.2003346117
ec_funded: 1
external_id:
isi:
- '000565729700033'
pmid:
- '32541049'
file:
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content_type: application/pdf
creator: dernst
date_created: 2020-06-23T11:30:53Z
date_updated: 2020-07-14T12:48:07Z
file_id: '8009'
file_name: 2020_PNAS_Hoermayer.pdf
file_size: 2407102
relation: main_file
file_date_updated: 2020-07-14T12:48:07Z
has_accepted_license: '1'
intvolume: ' 117'
isi: 1
issue: '26'
language:
- iso: eng
month: '06'
oa: 1
oa_version: None
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: 262EF96E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29988
name: RNA-directed DNA methylation in plant development
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/how-wounded-plants-coordinate-their-healing/
record:
- id: '9992'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Wounding-induced changes in cellular pressure and localized auxin signalling
spatially coordinate restorative divisions in roots
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 117
year: '2020'
...
---
_id: '7680'
abstract:
- lang: eng
text: "Proteins and their complex dynamic interactions regulate cellular mechanisms
from sensing and transducing extracellular signals, to mediating genetic responses,
and sustaining or changing cell morphology. To manipulate these protein-protein
interactions (PPIs) that govern the behavior and fate of cells, synthetically
constructed, genetically encoded tools provide the means to precisely target proteins
of interest (POIs), and control their subcellular localization and activity in
vitro and in vivo. Ideal synthetic tools react to an orthogonal cue, i.e. a trigger
that does not activate any other endogenous process, thereby allowing manipulation
of the POI alone.\r\nIn optogenetics, naturally occurring photosensory domain
from plants, algae and bacteria are re-purposed and genetically fused to POIs.
Illumination with light of a specific wavelength triggers a conformational change
that can mediate PPIs, such as dimerization or oligomerization. By using light
as a trigger, these tools can be activated with high spatial and temporal precision,
on subcellular and millisecond scales. Chemogenetic tools consist of protein domains
that recognize and bind small molecules. By genetic fusion to POIs, these domains
can mediate PPIs upon addition of their specific ligands, which are often synthetically
designed to provide highly specific interactions and exhibit good bioavailability.\r\nMost
optogenetic tools to mediate PPIs are based on well-studied photoreceptors responding
to red, blue or near-UV light, leaving a striking gap in the green band of the
visible light spectrum. Among both optogenetic and chemogenetic tools, there is
an abundance of methods to induce PPIs, but tools to disrupt them require UV illumination,
rely on covalent linkage and subsequent enzymatic cleavage or initially result
in protein clustering of unknown stoichiometry.\r\nThis work describes how the
recently structurally and photochemically characterized green-light responsive
cobalamin-binding domains (CBDs) from bacterial transcription factors were re-purposed
to function as a green-light responsive optogenetic tool. In contrast to previously
engineered optogenetic tools, CBDs do not induce PPI, but rather confer a PPI
already upon expression, which can be rapidly disrupted by illumination. This
was employed to mimic inhibition of constitutive activity of a growth factor receptor,
and successfully implement for cell signalling in mammalian cells and in vivo
to rescue development in zebrafish. This work further describes the development
and application of a chemically induced de-dimerizer (CDD) based on a recently
identified and structurally described bacterial oxyreductase. CDD forms a dimer
upon expression in absence of its cofactor, the flavin derivative F420. Safety
and of domain expression and ligand exposure are demonstrated in vitro and in
vivo in zebrafish. The system is further applied to inhibit cell signalling output
from a chimeric receptor upon F420 treatment.\r\nCBDs and CDD expand the repertoire
of synthetic tools by providing novel mechanisms of mediating PPIs, and by recognizing
previously not utilized cues. In the future, they can readily be combined with
existing synthetic tools to functionally manipulate PPIs in vitro and in vivo."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Stephanie
full_name: Kainrath, Stephanie
id: 32CFBA64-F248-11E8-B48F-1D18A9856A87
last_name: Kainrath
citation:
ama: Kainrath S. Synthetic tools for optogenetic and chemogenetic inhibition of
cellular signals. 2020. doi:10.15479/AT:ISTA:7680
apa: Kainrath, S. (2020). Synthetic tools for optogenetic and chemogenetic inhibition
of cellular signals. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7680
chicago: Kainrath, Stephanie. “Synthetic Tools for Optogenetic and Chemogenetic
Inhibition of Cellular Signals.” Institute of Science and Technology Austria,
2020. https://doi.org/10.15479/AT:ISTA:7680.
ieee: S. Kainrath, “Synthetic tools for optogenetic and chemogenetic inhibition
of cellular signals,” Institute of Science and Technology Austria, 2020.
ista: Kainrath S. 2020. Synthetic tools for optogenetic and chemogenetic inhibition
of cellular signals. Institute of Science and Technology Austria.
mla: Kainrath, Stephanie. Synthetic Tools for Optogenetic and Chemogenetic Inhibition
of Cellular Signals. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7680.
short: S. Kainrath, Synthetic Tools for Optogenetic and Chemogenetic Inhibition
of Cellular Signals, Institute of Science and Technology Austria, 2020.
date_created: 2020-04-24T16:00:51Z
date_published: 2020-04-24T00:00:00Z
date_updated: 2023-09-22T09:20:10Z
day: '24'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:7680
file:
- access_level: open_access
checksum: fb9a4468eb27be92690728e35c823796
content_type: application/pdf
creator: stgingl
date_created: 2020-04-28T11:19:21Z
date_updated: 2021-10-31T23:30:05Z
embargo: 2021-10-30
file_id: '7692'
file_name: Thesis_without-signatures_PDFA.pdf
file_size: 3268017
relation: main_file
- access_level: closed
checksum: f6c80ca97104a631a328cb79a2c53493
content_type: application/octet-stream
creator: stgingl
date_created: 2020-04-28T11:19:24Z
date_updated: 2021-10-31T23:30:05Z
embargo_to: open_access
file_id: '7693'
file_name: Thesis_without signatures.docx
file_size: 5167703
relation: source_file
file_date_updated: 2021-10-31T23:30:05Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: None
page: '98'
publication_identifier:
eissn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1028'
relation: dissertation_contains
status: public
status: public
supervisor:
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
title: Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8620'
abstract:
- lang: eng
text: "The development of the human brain occurs through a tightly regulated series
of dynamic and adaptive processes during prenatal and postnatal life. A disruption
of this strictly orchestrated series of events can lead to a number of neurodevelopmental
conditions, including Autism Spectrum Disorders (ASDs). ASDs are a very common,
etiologically and phenotypically heterogeneous group of disorders sharing the
core symptoms of social interaction and communication deficits and restrictive
and repetitive interests and behaviors. They are estimated to affect one in 59
individuals in the U.S. and, over the last three decades, mutations in more than
a hundred genetic loci have been convincingly linked to ASD pathogenesis. Yet,
for the vast majority of these ASD-risk genes their role during brain development
and precise molecular function still remain elusive.\r\nDe novo loss of function
mutations in the ubiquitin ligase-encoding gene Cullin 3 (CUL3) lead to ASD. In
the study described here, we used Cul3 mouse models to evaluate the consequences
of Cul3 mutations in vivo. Our results show that Cul3 heterozygous knockout mice
exhibit deficits in motor coordination as well as ASD-relevant social and cognitive
impairments. Cul3+/-, Cul3+/fl Emx1-Cre and Cul3fl/fl Emx1-Cre mutant brains display
cortical lamination abnormalities due to defective migration of post-mitotic excitatory
neurons, as well as reduced numbers of excitatory and inhibitory neurons. In line
with the observed abnormal cortical organization, Cul3 heterozygous deletion is
associated with decreased spontaneous excitatory and inhibitory activity in the
cortex. At the molecular level we show that Cul3 regulates cytoskeletal and adhesion
protein abundance in the mouse embryonic cortex. Abnormal regulation of cytoskeletal
proteins in Cul3 mutant neural cells results in atypical organization of the actin
mesh at the cell leading edge. Of note, heterozygous deletion of Cul3 in adult
mice does not induce the majority of the behavioral defects observed in constitutive
Cul3 haploinsufficient animals, pointing to a critical time-window for Cul3 deficiency.\r\nIn
conclusion, our data indicate that Cul3 plays a critical role in the regulation
of cytoskeletal proteins and neuronal migration. ASD-associated defects and behavioral
abnormalities are primarily due to dosage sensitive Cul3 functions at early brain
developmental stages."
acknowledged_ssus:
- _id: Bio
- _id: PreCl
acknowledgement: I would like to especially thank Armel Nicolas from the Proteomics
and Christoph Sommer from the Bioimaging Facilities for the data analysis, and to
thank the team of the Preclinical Facility, especially Sabina Deixler, Angela Schlerka,
Anita Lepold, Mihalea Mihai and Michael Schun for taking care of the mouse line
maintenance and their great support.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Jasmin
full_name: Morandell, Jasmin
id: 4739D480-F248-11E8-B48F-1D18A9856A87
last_name: Morandell
citation:
ama: Morandell J. Illuminating the role of Cul3 in autism spectrum disorder pathogenesis.
2020. doi:10.15479/AT:ISTA:8620
apa: Morandell, J. (2020). Illuminating the role of Cul3 in autism spectrum disorder
pathogenesis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8620
chicago: Morandell, Jasmin. “Illuminating the Role of Cul3 in Autism Spectrum Disorder
Pathogenesis.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8620.
ieee: J. Morandell, “Illuminating the role of Cul3 in autism spectrum disorder pathogenesis,”
Institute of Science and Technology Austria, 2020.
ista: Morandell J. 2020. Illuminating the role of Cul3 in autism spectrum disorder
pathogenesis. Institute of Science and Technology Austria.
mla: Morandell, Jasmin. Illuminating the Role of Cul3 in Autism Spectrum Disorder
Pathogenesis. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8620.
short: J. Morandell, Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis,
Institute of Science and Technology Austria, 2020.
date_created: 2020-10-07T14:53:13Z
date_published: 2020-10-12T00:00:00Z
date_updated: 2023-09-07T13:22:14Z
day: '12'
ddc:
- '610'
degree_awarded: PhD
department:
- _id: GaNo
doi: 10.15479/AT:ISTA:8620
file:
- access_level: open_access
checksum: 7ee83e42de3e5ce2fedb44dff472f75f
content_type: application/pdf
creator: jmorande
date_created: 2020-10-07T14:41:49Z
date_updated: 2021-10-16T22:30:04Z
embargo: 2021-10-15
file_id: '8621'
file_name: Jasmin_Morandell_Thesis-2020_final.pdf
file_size: 16155786
relation: main_file
- access_level: closed
checksum: 5e0464af453734210ce7aab7b4a92e3a
content_type: application/x-zip-compressed
creator: jmorande
date_created: 2020-10-07T14:45:07Z
date_updated: 2021-10-16T22:30:04Z
embargo_to: open_access
file_id: '8622'
file_name: Jasmin_Morandell_Thesis-2020_final.zip
file_size: 24344152
relation: source_file
file_date_updated: 2021-10-16T22:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '138'
project:
- _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
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7800'
relation: part_of_dissertation
status: public
- id: '8131'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
title: Illuminating the role of Cul3 in autism spectrum disorder pathogenesis
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8340'
abstract:
- lang: eng
text: Mitochondria are sites of oxidative phosphorylation in eukaryotic cells. Oxidative
phosphorylation operates by a chemiosmotic mechanism made possible by redox-driven
proton pumping machines which establish a proton motive force across the inner
mitochondrial membrane. This electrochemical proton gradient is used to drive
ATP synthesis, which powers the majority of cellular processes such as protein
synthesis, locomotion and signalling. In this thesis I investigate the structures
and molecular mechanisms of two inner mitochondrial proton pumping enzymes, respiratory
complex I and transhydrogenase. I present the first high-resolution structure
of the full transhydrogenase from any species, and a significantly improved structure
of complex I. Improving the resolution from 3.3 Å available previously to up to
2.3 Å in this thesis allowed us to model bound water molecules, crucial in the
proton pumping mechanism. For both enzymes, up to five cryo-EM datasets with different
substrates and inhibitors bound were solved to delineate the catalytic cycle and
understand the proton pumping mechanism. In transhydrogenase, the proton channel
is gated by reversible detachment of the NADP(H)-binding domain which opens the
proton channel to the opposite sites of the membrane. In complex I, the proton
channels are gated by reversible protonation of key glutamate and lysine residues
and breaking of the water wire connecting the proton pumps with the quinone reduction
site. The tight coupling between the redox and the proton pumping reactions in
transhydrogenase is achieved by controlling the NADP(H) exchange which can only
happen when the NADP(H)-binding domain interacts with the membrane domain. In
complex I, coupling is achieved by cycling of the whole complex between the closed
state, in which quinone can get reduced, and the open state, in which NADH can
induce quinol ejection from the binding pocket. On the basis of these results
I propose detailed mechanisms for catalytic cycles of transhydrogenase and complex
I that are consistent with a large amount of previous work. In both enzymes, conformational
and electrostatic mechanisms contribute to the overall catalytic process. Results
presented here could be used for better understanding of the human pathologies
arising from deficiencies of complex I or transhydrogenase and could be used to
develop novel therapies.
acknowledged_ssus:
- _id: EM-Fac
acknowledgement: 'I acknowledge the support of IST facilities, especially the Electron
Miscroscopy facility for providing training and resources. Special thanks also go
to cryo-EM specialists who helped me to collect the data present here: Dr Valentin
Hodirnau (IST Austria), Dr Tom Heuser (IMBA, Vienna), Dr Rebecca Thompson (Uni.
of Leeds) and Dr Jirka Nováček (CEITEC). This work has been supported by iNEXT,
project number 653706, funded by the Horizon 2020 programme of the European Union.
This project has received funding from the European Union’s Horizon 2020 research
and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Domen
full_name: Kampjut, Domen
id: 37233050-F248-11E8-B48F-1D18A9856A87
last_name: Kampjut
citation:
ama: Kampjut D. Molecular mechanisms of mitochondrial redox-coupled proton pumping
enzymes. 2020. doi:10.15479/AT:ISTA:8340
apa: Kampjut, D. (2020). Molecular mechanisms of mitochondrial redox-coupled
proton pumping enzymes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8340
chicago: Kampjut, Domen. “Molecular Mechanisms of Mitochondrial Redox-Coupled Proton
Pumping Enzymes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8340.
ieee: D. Kampjut, “Molecular mechanisms of mitochondrial redox-coupled proton pumping
enzymes,” Institute of Science and Technology Austria, 2020.
ista: Kampjut D. 2020. Molecular mechanisms of mitochondrial redox-coupled proton
pumping enzymes. Institute of Science and Technology Austria.
mla: Kampjut, Domen. Molecular Mechanisms of Mitochondrial Redox-Coupled Proton
Pumping Enzymes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8340.
short: D. Kampjut, Molecular Mechanisms of Mitochondrial Redox-Coupled Proton Pumping
Enzymes, Institute of Science and Technology Austria, 2020.
date_created: 2020-09-07T18:42:23Z
date_published: 2020-09-09T00:00:00Z
date_updated: 2023-09-07T13:26:17Z
day: '09'
ddc:
- '572'
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project:
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call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication_identifier:
isbn:
- 978-3-99078-008-4
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: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
title: Molecular mechanisms of mitochondrial redox-coupled proton pumping enzymes
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '7800'
abstract:
- lang: eng
text: De novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3
(CUL3) lead to autism spectrum disorder (ASD). Here, we used Cul3 mouse models
to evaluate the consequences of Cul3 mutations in vivo. Our results show that
Cul3 haploinsufficient mice exhibit deficits in motor coordination as well as
ASD-relevant social and cognitive impairments. Cul3 mutant brain displays cortical
lamination abnormalities due to defective neuronal migration and reduced numbers
of excitatory and inhibitory neurons. In line with the observed abnormal columnar
organization, Cul3 haploinsufficiency is associated with decreased spontaneous
excitatory and inhibitory activity in the cortex. At the molecular level, employing
a quantitative proteomic approach, we show that Cul3 regulates cytoskeletal and
adhesion protein abundance in mouse embryos. Abnormal regulation of cytoskeletal
proteins in Cul3 mutant neuronal cells results in atypical organization of the
actin mesh at the cell leading edge, likely causing the observed migration deficits.
In contrast to these important functions early in development, Cul3 deficiency
appears less relevant at adult stages. In fact, induction of Cul3 haploinsufficiency
in adult mice does not result in the behavioral defects observed in constitutive
Cul3 haploinsufficient animals. Taken together, our data indicate that Cul3 has
a critical role in the regulation of cytoskeletal proteins and neuronal migration
and that ASD-associated defects and behavioral abnormalities are primarily due
to Cul3 functions at early developmental stages.
acknowledged_ssus:
- _id: PreCl
article_processing_charge: No
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: 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: 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: 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.
bioRxiv. doi:10.1101/2020.01.10.902064
apa: Morandell, J., Schwarz, L. A., Basilico, B., Tasciyan, S., Nicolas, A., Sommer,
C. M., … Novarino, G. (n.d.). Cul3 regulates cytoskeleton protein homeostasis
and cell migration during a critical window of brain development. bioRxiv.
Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.01.10.902064
chicago: Morandell, Jasmin, Lena A Schwarz, Bernadette Basilico, Saren Tasciyan,
Armel Nicolas, Christoph M Sommer, Caroline Kreuzinger, et al. “Cul3 Regulates
Cytoskeleton Protein Homeostasis and Cell Migration during a Critical Window of
Brain Development.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2020.01.10.902064 .
ieee: J. Morandell et al., “Cul3 regulates cytoskeleton protein homeostasis
and cell migration during a critical window of brain development,” bioRxiv.
Cold Spring Harbor Laboratory.
ista: Morandell J, Schwarz LA, Basilico B, Tasciyan S, Nicolas A, Sommer CM, Kreuzinger
C, Knaus L, Dobler Z, Cacci E, Danzl JG, Novarino G. Cul3 regulates cytoskeleton
protein homeostasis and cell migration during a critical window of brain development.
bioRxiv, 10.1101/2020.01.10.902064
.
mla: Morandell, Jasmin, et al. “Cul3 Regulates Cytoskeleton Protein Homeostasis
and Cell Migration during a Critical Window of Brain Development.” BioRxiv,
Cold Spring Harbor Laboratory, doi:10.1101/2020.01.10.902064 .
short: J. Morandell, L.A. Schwarz, B. Basilico, S. Tasciyan, A. Nicolas, C.M. Sommer,
C. Kreuzinger, L. Knaus, Z. Dobler, E. Cacci, J.G. Danzl, G. Novarino, BioRxiv
(n.d.).
date_created: 2020-05-05T14:31:33Z
date_published: 2020-01-11T00:00:00Z
date_updated: 2024-03-28T23:30:14Z
day: '11'
ddc:
- '570'
department:
- _id: JoDa
- _id: GaNo
- _id: LifeSc
doi: '10.1101/2020.01.10.902064 '
file:
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content_type: application/pdf
creator: rsix
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date_updated: 2020-07-14T12:48:03Z
file_id: '7801'
file_name: 2020.01.10.902064v1.full.pdf
file_size: 2931370
relation: main_file
file_date_updated: 2020-07-14T12:48:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Preprint
project:
- _id: 265CB4D0-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I03600
name: Optical control of synaptic function via adhesion molecules
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication: bioRxiv
publication_status: submitted
publisher: Cold Spring Harbor Laboratory
related_material:
record:
- id: '9429'
relation: later_version
status: public
- id: '8620'
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_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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8131'
abstract:
- lang: eng
text: The possibility to generate construct valid animal models enabled the development
and testing of therapeutic strategies targeting the core features of autism spectrum
disorders (ASDs). At the same time, these studies highlighted the necessity of
identifying sensitive developmental time windows for successful therapeutic interventions.
Animal and human studies also uncovered the possibility to stratify the variety
of ASDs in molecularly distinct subgroups, potentially facilitating effective
treatment design. Here, we focus on the molecular pathways emerging as commonly
affected by mutations in diverse ASD-risk genes, on their role during critical
windows of brain development and the potential treatments targeting these biological
processes.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Bernadette
full_name: Basilico, Bernadette
id: 36035796-5ACA-11E9-A75E-7AF2E5697425
last_name: Basilico
orcid: 0000-0003-1843-3173
- first_name: Jasmin
full_name: Morandell, Jasmin
id: 4739D480-F248-11E8-B48F-1D18A9856A87
last_name: Morandell
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Basilico B, Morandell J, Novarino G. Molecular mechanisms for targeted ASD
treatments. Current Opinion in Genetics and Development. 2020;65(12):126-137.
doi:10.1016/j.gde.2020.06.004
apa: Basilico, B., Morandell, J., & Novarino, G. (2020). Molecular mechanisms
for targeted ASD treatments. Current Opinion in Genetics and Development.
Elsevier. https://doi.org/10.1016/j.gde.2020.06.004
chicago: Basilico, Bernadette, Jasmin Morandell, and Gaia Novarino. “Molecular Mechanisms
for Targeted ASD Treatments.” Current Opinion in Genetics and Development.
Elsevier, 2020. https://doi.org/10.1016/j.gde.2020.06.004.
ieee: B. Basilico, J. Morandell, and G. Novarino, “Molecular mechanisms for targeted
ASD treatments,” Current Opinion in Genetics and Development, vol. 65,
no. 12. Elsevier, pp. 126–137, 2020.
ista: Basilico B, Morandell J, Novarino G. 2020. Molecular mechanisms for targeted
ASD treatments. Current Opinion in Genetics and Development. 65(12), 126–137.
mla: Basilico, Bernadette, et al. “Molecular Mechanisms for Targeted ASD Treatments.”
Current Opinion in Genetics and Development, vol. 65, no. 12, Elsevier,
2020, pp. 126–37, doi:10.1016/j.gde.2020.06.004.
short: B. Basilico, J. Morandell, G. Novarino, Current Opinion in Genetics and Development
65 (2020) 126–137.
date_created: 2020-07-19T22:00:58Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2024-03-28T23:30:14Z
day: '01'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.1016/j.gde.2020.06.004
ec_funded: 1
external_id:
isi:
- '000598918900019'
pmid:
- '32659636'
file:
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content_type: application/pdf
creator: dernst
date_created: 2020-07-22T06:47:45Z
date_updated: 2020-07-22T06:47:45Z
file_id: '8146'
file_name: 2020_CurrentOpGenetics_Basilico.pdf
file_size: 1381545
relation: main_file
success: 1
file_date_updated: 2020-07-22T06:47:45Z
has_accepted_license: '1'
intvolume: ' 65'
isi: 1
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 126-137
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _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
publication: Current Opinion in Genetics and Development
publication_identifier:
eissn:
- '18790380'
issn:
- 0959437X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '8620'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Molecular mechanisms for targeted ASD treatments
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 65
year: '2020'
...
---
_id: '8434'
abstract:
- lang: eng
text: 'Efficient migration on adhesive surfaces involves the protrusion of lamellipodial
actin networks and their subsequent stabilization by nascent adhesions. The actin-binding
protein lamellipodin (Lpd) is thought to play a critical role in lamellipodium
protrusion, by delivering Ena/VASP proteins onto the growing plus ends of actin
filaments and by interacting with the WAVE regulatory complex, an activator of
the Arp2/3 complex, at the leading edge. Using B16-F1 melanoma cell lines, we
demonstrate that genetic ablation of Lpd compromises protrusion efficiency and
coincident cell migration without altering essential parameters of lamellipodia,
including their maximal rate of forward advancement and actin polymerization.
We also confirmed lamellipodia and migration phenotypes with CRISPR/Cas9-mediated
Lpd knockout Rat2 fibroblasts, excluding cell type-specific effects. Moreover,
computer-aided analysis of cell-edge morphodynamics on B16-F1 cell lamellipodia
revealed that loss of Lpd correlates with reduced temporal protrusion maintenance
as a prerequisite of nascent adhesion formation. We conclude that Lpd optimizes
protrusion and nascent adhesion formation by counteracting frequent, chaotic retraction
and membrane ruffling.This article has an associated First Person interview with
the first author of the paper. '
acknowledgement: This work was supported in part by Deutsche Forschungsgemeinschaft
(DFG)[GRK2223/1, RO2414/5-1 (to K.R.), FA350/11-1 (to M.F.) and FA330/11-1 (to J.F.)],as
well as by intramural funding from the Helmholtz Association (to T.E.B.S. andK.R.).
G.D. was additionally funded by the Austrian Science Fund (FWF) LiseMeitner Program
[M-2495]. A.C.H. and M.W. are supported by the Francis CrickInstitute, which receives
its core funding from Cancer Research UK [FC001209], theMedical Research Council
[FC001209] and the Wellcome Trust [FC001209]. M.K. issupported by the Biotechnology
and Biological Sciences Research Council [BB/F011431/1, BB/J000590/1, BB/N000226/1].
Deposited in PMC for release after 6months.
article_number: jcs239020
article_processing_charge: No
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: Ashley C.
full_name: Humphries, Ashley C.
last_name: Humphries
- first_name: Matthias
full_name: Schaks, Matthias
last_name: Schaks
- first_name: Vanessa
full_name: Dimchev, Vanessa
last_name: Dimchev
- first_name: Theresia E. B.
full_name: Stradal, Theresia E. B.
last_name: Stradal
- first_name: Jan
full_name: Faix, Jan
last_name: Faix
- first_name: Matthias
full_name: Krause, Matthias
last_name: Krause
- first_name: Michael
full_name: Way, Michael
last_name: Way
- first_name: Martin
full_name: Falcke, Martin
last_name: Falcke
- first_name: Klemens
full_name: Rottner, Klemens
last_name: Rottner
citation:
ama: Dimchev GA, Amiri B, Humphries AC, et al. Lamellipodin tunes cell migration
by stabilizing protrusions and promoting adhesion formation. Journal of Cell
Science. 2020;133(7). doi:10.1242/jcs.239020
apa: Dimchev, G. A., Amiri, B., Humphries, A. C., Schaks, M., Dimchev, V., Stradal,
T. E. B., … Rottner, K. (2020). Lamellipodin tunes cell migration by stabilizing
protrusions and promoting adhesion formation. Journal of Cell Science.
The Company of Biologists. https://doi.org/10.1242/jcs.239020
chicago: Dimchev, Georgi A, Behnam Amiri, Ashley C. Humphries, Matthias Schaks,
Vanessa Dimchev, Theresia E. B. Stradal, Jan Faix, et al. “Lamellipodin Tunes
Cell Migration by Stabilizing Protrusions and Promoting Adhesion Formation.” Journal
of Cell Science. The Company of Biologists, 2020. https://doi.org/10.1242/jcs.239020.
ieee: G. A. Dimchev et al., “Lamellipodin tunes cell migration by stabilizing
protrusions and promoting adhesion formation,” Journal of Cell Science,
vol. 133, no. 7. The Company of Biologists, 2020.
ista: Dimchev GA, Amiri B, Humphries AC, Schaks M, Dimchev V, Stradal TEB, Faix
J, Krause M, Way M, Falcke M, Rottner K. 2020. Lamellipodin tunes cell migration
by stabilizing protrusions and promoting adhesion formation. Journal of Cell Science.
133(7), jcs239020.
mla: Dimchev, Georgi A., et al. “Lamellipodin Tunes Cell Migration by Stabilizing
Protrusions and Promoting Adhesion Formation.” Journal of Cell Science,
vol. 133, no. 7, jcs239020, The Company of Biologists, 2020, doi:10.1242/jcs.239020.
short: G.A. Dimchev, B. Amiri, A.C. Humphries, M. Schaks, V. Dimchev, T.E.B. Stradal,
J. Faix, M. Krause, M. Way, M. Falcke, K. Rottner, Journal of Cell Science 133
(2020).
date_created: 2020-09-17T14:00:33Z
date_published: 2020-04-09T00:00:00Z
date_updated: 2023-09-05T15:41:48Z
day: '09'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.1242/jcs.239020
external_id:
isi:
- '000534387800005'
pmid:
- ' 32094266'
file:
- access_level: open_access
checksum: ba917e551acc4ece2884b751434df9ae
content_type: application/pdf
creator: dernst
date_created: 2020-09-17T14:07:51Z
date_updated: 2020-10-11T22:30:02Z
embargo: 2020-10-10
file_id: '8435'
file_name: 2020_JournalCellScience_Dimchev.pdf
file_size: 13493302
relation: main_file
file_date_updated: 2020-10-11T22:30:02Z
has_accepted_license: '1'
intvolume: ' 133'
isi: 1
issue: '7'
keyword:
- Cell Biology
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2674F658-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02495
name: Protein structure and function in filopodia across scales
publication: Journal of Cell Science
publication_identifier:
eissn:
- 1477-9137
issn:
- 0021-9533
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
status: public
title: Lamellipodin tunes cell migration by stabilizing protrusions and promoting
adhesion formation
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 133
year: '2020'
...
---
_id: '7889'
abstract:
- lang: eng
text: Autoluminescent plants engineered to express a bacterial bioluminescence gene
cluster in plastids have not been widely adopted because of low light output.
We engineered tobacco plants with a fungal bioluminescence system that converts
caffeic acid (present in all plants) into luciferin and report self-sustained
luminescence that is visible to the naked eye. Our findings could underpin development
of a suite of imaging tools for plants.
acknowledgement: "This study was designed, performed and funded by Planta LLC. We
thank K. Wood for assisting in manuscript development. Planta acknowledges support
from the Skolkovo Innovation Centre. We thank D. Bolotin and the Milaboratory (milaboratory.com)
for access to computing and storage infrastructure. We thank S. Shakhov for providing\r\nphotography
equipment. The Synthetic Biology Group is funded by the MRC London Institute of
Medical Sciences (UKRI MC-A658-5QEA0, K.S.S.). K.S.S. is supported by an Imperial
College Research Fellowship. Experiments were partially carried out using equipment
provided by the Institute of Bioorganic Chemistry of the Russian Academy\r\nof Sciences
Сore Facility (CKP IBCH; supported by the Russian Ministry of Education and Science
Grant RFMEFI62117X0018). The F.A.K. lab is supported by ERC grant agreement 771209—CharFL.
This project received funding from the European Union’s Horizon 2020 Research and
Innovation Programme under Marie Skłodowska-Curie\r\nGrant Agreement 665385. K.S.S.
acknowledges support by President’s Grant 075-15-2019-411. Design and assembly of
some of the plasmids was supported by Russian Science Foundation grant 19-74-10102.
Imaging experiments were partially supported by Russian Science Foundation grant
17-14-01169p. LC-MS/MS analyses of extracts were\r\nsupported by Russian Science
Foundation grant 16-14-00052p. Design and assembly of plasmids was partially supported
by grant 075-15-2019-1789 from the Ministry of Science and Higher Education of the
Russian Federation allocated to the Center for Precision Genome Editing and Genetic
Technologies for Biomedicine. The authors\r\nwould like to acknowledge the work
of Genomics Core Facility of the Skolkovo Institute of Science and Technology, which
performed the sequencing and bioinformatic analysis."
article_processing_charge: No
article_type: original
author:
- first_name: Tatiana
full_name: Mitiouchkina, Tatiana
last_name: Mitiouchkina
- first_name: Alexander S.
full_name: Mishin, Alexander S.
last_name: Mishin
- first_name: Louisa
full_name: Gonzalez Somermeyer, Louisa
id: 4720D23C-F248-11E8-B48F-1D18A9856A87
last_name: Gonzalez Somermeyer
orcid: 0000-0001-9139-5383
- first_name: Nadezhda M.
full_name: Markina, Nadezhda M.
last_name: Markina
- first_name: Tatiana V.
full_name: Chepurnyh, Tatiana V.
last_name: Chepurnyh
- first_name: Elena B.
full_name: Guglya, Elena B.
last_name: Guglya
- first_name: Tatiana A.
full_name: Karataeva, Tatiana A.
last_name: Karataeva
- first_name: Kseniia A.
full_name: Palkina, Kseniia A.
last_name: Palkina
- first_name: Ekaterina S.
full_name: Shakhova, Ekaterina S.
last_name: Shakhova
- first_name: Liliia I.
full_name: Fakhranurova, Liliia I.
last_name: Fakhranurova
- first_name: Sofia V.
full_name: Chekova, Sofia V.
last_name: Chekova
- first_name: Aleksandra S.
full_name: Tsarkova, Aleksandra S.
last_name: Tsarkova
- first_name: Yaroslav V.
full_name: Golubev, Yaroslav V.
last_name: Golubev
- first_name: Vadim V.
full_name: Negrebetsky, Vadim V.
last_name: Negrebetsky
- first_name: Sergey A.
full_name: Dolgushin, Sergey A.
last_name: Dolgushin
- first_name: Pavel V.
full_name: Shalaev, Pavel V.
last_name: Shalaev
- first_name: Dmitry
full_name: Shlykov, Dmitry
last_name: Shlykov
- first_name: Olesya A.
full_name: Melnik, Olesya A.
last_name: Melnik
- first_name: Victoria O.
full_name: Shipunova, Victoria O.
last_name: Shipunova
- first_name: Sergey M.
full_name: Deyev, Sergey M.
last_name: Deyev
- first_name: Andrey I.
full_name: Bubyrev, Andrey I.
last_name: Bubyrev
- first_name: Alexander S.
full_name: Pushin, Alexander S.
last_name: Pushin
- first_name: Vladimir V.
full_name: Choob, Vladimir V.
last_name: Choob
- first_name: Sergey V.
full_name: Dolgov, Sergey V.
last_name: Dolgov
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Ilia V.
full_name: Yampolsky, Ilia V.
last_name: Yampolsky
- first_name: Karen S.
full_name: Sarkisyan, Karen S.
last_name: Sarkisyan
citation:
ama: Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, et al. Plants with genetically
encoded autoluminescence. Nature Biotechnology. 2020;38:944-946. doi:10.1038/s41587-020-0500-9
apa: Mitiouchkina, T., Mishin, A. S., Gonzalez Somermeyer, L., Markina, N. M., Chepurnyh,
T. V., Guglya, E. B., … Sarkisyan, K. S. (2020). Plants with genetically encoded
autoluminescence. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-020-0500-9
chicago: Mitiouchkina, Tatiana, Alexander S. Mishin, Louisa Gonzalez Somermeyer,
Nadezhda M. Markina, Tatiana V. Chepurnyh, Elena B. Guglya, Tatiana A. Karataeva,
et al. “Plants with Genetically Encoded Autoluminescence.” Nature Biotechnology.
Springer Nature, 2020. https://doi.org/10.1038/s41587-020-0500-9.
ieee: T. Mitiouchkina et al., “Plants with genetically encoded autoluminescence,”
Nature Biotechnology, vol. 38. Springer Nature, pp. 944–946, 2020.
ista: Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, Markina NM, Chepurnyh TV,
Guglya EB, Karataeva TA, Palkina KA, Shakhova ES, Fakhranurova LI, Chekova SV,
Tsarkova AS, Golubev YV, Negrebetsky VV, Dolgushin SA, Shalaev PV, Shlykov D,
Melnik OA, Shipunova VO, Deyev SM, Bubyrev AI, Pushin AS, Choob VV, Dolgov SV,
Kondrashov F, Yampolsky IV, Sarkisyan KS. 2020. Plants with genetically encoded
autoluminescence. Nature Biotechnology. 38, 944–946.
mla: Mitiouchkina, Tatiana, et al. “Plants with Genetically Encoded Autoluminescence.”
Nature Biotechnology, vol. 38, Springer Nature, 2020, pp. 944–46, doi:10.1038/s41587-020-0500-9.
short: T. Mitiouchkina, A.S. Mishin, L. Gonzalez Somermeyer, N.M. Markina, T.V.
Chepurnyh, E.B. Guglya, T.A. Karataeva, K.A. Palkina, E.S. Shakhova, L.I. Fakhranurova,
S.V. Chekova, A.S. Tsarkova, Y.V. Golubev, V.V. Negrebetsky, S.A. Dolgushin, P.V.
Shalaev, D. Shlykov, O.A. Melnik, V.O. Shipunova, S.M. Deyev, A.I. Bubyrev, A.S.
Pushin, V.V. Choob, S.V. Dolgov, F. Kondrashov, I.V. Yampolsky, K.S. Sarkisyan,
Nature Biotechnology 38 (2020) 944–946.
date_created: 2020-05-25T15:02:00Z
date_published: 2020-04-27T00:00:00Z
date_updated: 2023-09-05T15:30:34Z
day: '27'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1038/s41587-020-0500-9
ec_funded: 1
external_id:
isi:
- '000529298800003'
pmid:
- '32341562'
file:
- access_level: open_access
checksum: 1b30467500ec6277229a875b06e196d0
content_type: application/pdf
creator: dernst
date_created: 2020-08-28T08:57:07Z
date_updated: 2021-03-02T23:30:03Z
embargo: 2021-03-01
file_id: '8316'
file_name: 2020_NatureBiotech_Mitiouchkina.pdf
file_size: 1180086
relation: main_file
file_date_updated: 2021-03-02T23:30:03Z
has_accepted_license: '1'
intvolume: ' 38'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 944-946
pmid: 1
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
publication: Nature Biotechnology
publication_identifier:
eissn:
- 1546-1696
issn:
- 1087-0156
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41587-020-0578-0
scopus_import: '1'
status: public
title: Plants with genetically encoded autoluminescence
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 38
year: '2020'
...
---
_id: '9750'
abstract:
- lang: eng
text: Tension of the actomyosin cell cortex plays a key role in determining cell-cell
contact growth and size. The level of cortical tension outside of the cell-cell
contact, when pulling at the contact edge, scales with the total size to which
a cell-cell contact can grow1,2. Here we show in zebrafish primary germ layer
progenitor cells that this monotonic relationship only applies to a narrow range
of cortical tension increase, and that above a critical threshold, contact size
inversely scales with cortical tension. This switch from cortical tension increasing
to decreasing progenitor cell-cell contact size is caused by cortical tension
promoting E-cadherin anchoring to the actomyosin cytoskeleton, thereby increasing
clustering and stability of E-cadherin at the contact. Once tension-mediated E-cadherin
stabilization at the contact exceeds a critical threshold level, the rate by which
the contact expands in response to pulling forces from the cortex sharply drops,
leading to smaller contacts at physiologically relevant timescales of contact
formation. Thus, the activity of cortical tension in expanding cell-cell contact
size is limited by tension stabilizing E-cadherin-actin complexes at the contact.
acknowledged_ssus:
- _id: Bio
- _id: EM-Fac
- _id: SSU
acknowledgement: We would like to thank Edouard Hannezo for discussions, Shayan Shami
Pour and Daniel Capek for help with data analysis, Vanessa Barone and other members
of the Heisenberg laboratory for thoughtful discussions and comments on the manuscript.
We also thank Jack Merrin for preparing the microwells, and the Scientific Service
Units at IST Austria, specifically Bioimaging and Electron Microscopy, and the Zebrafish
Facility for continuous support. We acknowledge Hitoshi Morita for the kind gift
of VinculinB-GFP plasmid. This research was supported by an ERC Advanced Grant (MECSPEC)
to C.-P.H, EMBO Long Term grant (ALTF 187-2013) to M.S and IST Fellow Marie-Curie
COFUND No. P_IST_EU01 to J.S.
article_processing_charge: No
author:
- first_name: Jana
full_name: Slovakova, Jana
id: 30F3F2F0-F248-11E8-B48F-1D18A9856A87
last_name: Slovakova
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- 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: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Karla
full_name: Huljev, Karla
id: 44C6F6A6-F248-11E8-B48F-1D18A9856A87
last_name: Huljev
- 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: Slovakova J, Sikora MK, Caballero Mancebo S, et al. Tension-dependent stabilization
of E-cadherin limits cell-cell contact expansion. bioRxiv. 2020. doi:10.1101/2020.11.20.391284
apa: Slovakova, J., Sikora, M. K., Caballero Mancebo, S., Krens, G., Kaufmann, W.,
Huljev, K., & Heisenberg, C.-P. J. (2020). Tension-dependent stabilization
of E-cadherin limits cell-cell contact expansion. bioRxiv. Cold Spring
Harbor Laboratory. https://doi.org/10.1101/2020.11.20.391284
chicago: Slovakova, Jana, Mateusz K Sikora, Silvia Caballero Mancebo, Gabriel Krens,
Walter Kaufmann, Karla Huljev, and Carl-Philipp J Heisenberg. “Tension-Dependent
Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion.” BioRxiv.
Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/2020.11.20.391284.
ieee: J. Slovakova et al., “Tension-dependent stabilization of E-cadherin
limits cell-cell contact expansion,” bioRxiv. Cold Spring Harbor Laboratory,
2020.
ista: Slovakova J, Sikora MK, Caballero Mancebo S, Krens G, Kaufmann W, Huljev K,
Heisenberg C-PJ. 2020. Tension-dependent stabilization of E-cadherin limits cell-cell
contact expansion. bioRxiv, 10.1101/2020.11.20.391284.
mla: Slovakova, Jana, et al. “Tension-Dependent Stabilization of E-Cadherin Limits
Cell-Cell Contact Expansion.” BioRxiv, Cold Spring Harbor Laboratory, 2020,
doi:10.1101/2020.11.20.391284.
short: J. Slovakova, M.K. Sikora, S. Caballero Mancebo, G. Krens, W. Kaufmann, K.
Huljev, C.-P.J. Heisenberg, BioRxiv (2020).
date_created: 2021-07-29T11:29:50Z
date_published: 2020-11-20T00:00:00Z
date_updated: 2024-03-28T23:30:19Z
day: '20'
department:
- _id: CaHe
- _id: EM-Fac
- _id: Bio
doi: 10.1101/2020.11.20.391284
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2020.11.20.391284
month: '11'
oa: 1
oa_version: Preprint
page: '41'
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
- _id: 2521E28E-B435-11E9-9278-68D0E5697425
grant_number: 187-2013
name: Modulation of adhesion function in cell-cell contact formation by cortical
tension
publication: bioRxiv
publication_status: published
publisher: Cold Spring Harbor Laboratory
related_material:
record:
- id: '10766'
relation: later_version
status: public
- id: '9623'
relation: dissertation_contains
status: public
status: public
title: Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion
type: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2020'
...
---
_id: '7885'
abstract:
- lang: eng
text: Eukaryotic cells migrate by coupling the intracellular force of the actin
cytoskeleton to the environment. While force coupling is usually mediated by transmembrane
adhesion receptors, especially those of the integrin family, amoeboid cells such
as leukocytes can migrate extremely fast despite very low adhesive forces1. Here
we show that leukocytes cannot only migrate under low adhesion but can also transmit
forces in the complete absence of transmembrane force coupling. When confined
within three-dimensional environments, they use the topographical features of
the substrate to propel themselves. Here the retrograde flow of the actin cytoskeleton
follows the texture of the substrate, creating retrograde shear forces that are
sufficient to drive the cell body forwards. Notably, adhesion-dependent and adhesion-independent
migration are not mutually exclusive, but rather are variants of the same principle
of coupling retrograde actin flow to the environment and thus can potentially
operate interchangeably and simultaneously. As adhesion-free migration is independent
of the chemical composition of the environment, it renders cells completely autonomous
in their locomotive behaviour.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: M-Shop
acknowledgement: We thank A. Leithner and J. Renkawitz for discussion and critical
reading of the manuscript; J. Schwarz and M. Mehling for establishing the microfluidic
setups; the Bioimaging Facility of IST Austria for excellent support, as well as
the Life Science Facility and the Miba Machine Shop of IST Austria; and F. N. Arslan,
L. E. Burnett and L. Li for their work during their rotation in the IST PhD programme.
This work was supported by the European Research Council (ERC StG 281556 and CoG
724373) to M.S. and grants from the Austrian Science Fund (FWF P29911) and the WWTF
to M.S. M.H. was supported by the European Regional Development Fund Project (CZ.02.1.01/0.0/0.0/15_003/0000476).
F.G. received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie grant agreement no. 747687.
article_processing_charge: No
article_type: original
author:
- first_name: Anne
full_name: Reversat, Anne
id: 35B76592-F248-11E8-B48F-1D18A9856A87
last_name: Reversat
orcid: 0000-0003-0666-8928
- first_name: Florian R
full_name: Gärtner, Florian R
id: 397A88EE-F248-11E8-B48F-1D18A9856A87
last_name: Gärtner
orcid: 0000-0001-6120-3723
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Julian A
full_name: Stopp, Julian A
id: 489E3F00-F248-11E8-B48F-1D18A9856A87
last_name: Stopp
- first_name: Saren
full_name: Tasciyan, Saren
id: 4323B49C-F248-11E8-B48F-1D18A9856A87
last_name: Tasciyan
orcid: 0000-0003-1671-393X
- 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: Ingrid
full_name: De Vries, Ingrid
id: 4C7D837E-F248-11E8-B48F-1D18A9856A87
last_name: De Vries
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Miroslav
full_name: Hons, Miroslav
id: 4167FE56-F248-11E8-B48F-1D18A9856A87
last_name: Hons
orcid: 0000-0002-6625-3348
- first_name: Matthieu
full_name: Piel, Matthieu
last_name: Piel
- first_name: Andrew
full_name: Callan-Jones, Andrew
last_name: Callan-Jones
- first_name: Raphael
full_name: Voituriez, Raphael
last_name: Voituriez
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Reversat A, Gärtner FR, Merrin J, et al. Cellular locomotion using environmental
topography. Nature. 2020;582:582–585. doi:10.1038/s41586-020-2283-z
apa: Reversat, A., Gärtner, F. R., Merrin, J., Stopp, J. A., Tasciyan, S., Aguilera
Servin, J. L., … Sixt, M. K. (2020). Cellular locomotion using environmental topography.
Nature. Springer Nature. https://doi.org/10.1038/s41586-020-2283-z
chicago: Reversat, Anne, Florian R Gärtner, Jack Merrin, Julian A Stopp, Saren Tasciyan,
Juan L Aguilera Servin, Ingrid de Vries, et al. “Cellular Locomotion Using Environmental
Topography.” Nature. Springer Nature, 2020. https://doi.org/10.1038/s41586-020-2283-z.
ieee: A. Reversat et al., “Cellular locomotion using environmental topography,”
Nature, vol. 582. Springer Nature, pp. 582–585, 2020.
ista: Reversat A, Gärtner FR, Merrin J, Stopp JA, Tasciyan S, Aguilera Servin JL,
de Vries I, Hauschild R, Hons M, Piel M, Callan-Jones A, Voituriez R, Sixt MK.
2020. Cellular locomotion using environmental topography. Nature. 582, 582–585.
mla: Reversat, Anne, et al. “Cellular Locomotion Using Environmental Topography.”
Nature, vol. 582, Springer Nature, 2020, pp. 582–585, doi:10.1038/s41586-020-2283-z.
short: A. Reversat, F.R. Gärtner, J. Merrin, J.A. Stopp, S. Tasciyan, J.L. Aguilera
Servin, I. de Vries, R. Hauschild, M. Hons, M. Piel, A. Callan-Jones, R. Voituriez,
M.K. Sixt, Nature 582 (2020) 582–585.
date_created: 2020-05-24T22:01:01Z
date_published: 2020-06-25T00:00:00Z
date_updated: 2024-03-28T23:30:24Z
day: '25'
department:
- _id: NanoFab
- _id: Bio
- _id: MiSi
doi: 10.1038/s41586-020-2283-z
ec_funded: 1
external_id:
isi:
- '000532688300008'
intvolume: ' 582'
isi: 1
language:
- iso: eng
month: '06'
oa_version: None
page: 582–585
project:
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
- _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
- _id: 260AA4E2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '747687'
name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells
publication: Nature
publication_identifier:
eissn:
- '14764687'
issn:
- '00280836'
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/off-road-mode-enables-mobile-cells-to-move-freely/
record:
- id: '14697'
relation: dissertation_contains
status: public
- id: '12401'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Cellular locomotion using environmental topography
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 582
year: '2020'
...
---
_id: '7426'
abstract:
- lang: eng
text: This paper presents a novel abstraction technique for analyzing Lyapunov and
asymptotic stability of polyhedral switched systems. A polyhedral switched system
is a hybrid system in which the continuous dynamics is specified by polyhedral
differential inclusions, the invariants and guards are specified by polyhedral
sets and the switching between the modes do not involve reset of variables. A
finite state weighted graph abstracting the polyhedral switched system is constructed
from a finite partition of the state–space, such that the satisfaction of certain
graph conditions, such as the absence of cycles with product of weights on the
edges greater than (or equal) to 1, implies the stability of the system. However,
the graph is in general conservative and hence, the violation of the graph conditions
does not imply instability. If the analysis fails to establish stability due to
the conservativeness in the approximation, a counterexample (cycle with product
of edge weights greater than or equal to 1) indicating a potential reason for
the failure is returned. Further, a more precise approximation of the switched
system can be constructed by considering a finer partition of the state–space
in the construction of the finite weighted graph. We present experimental results
on analyzing stability of switched systems using the above method.
article_number: '100856'
article_processing_charge: No
article_type: original
author:
- first_name: Miriam
full_name: Garcia Soto, Miriam
id: 4B3207F6-F248-11E8-B48F-1D18A9856A87
last_name: Garcia Soto
orcid: 0000−0003−2936−5719
- first_name: Pavithra
full_name: Prabhakar, Pavithra
last_name: Prabhakar
citation:
ama: 'Garcia Soto M, Prabhakar P. Abstraction based verification of stability of
polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. 2020;36(5).
doi:10.1016/j.nahs.2020.100856'
apa: 'Garcia Soto, M., & Prabhakar, P. (2020). Abstraction based verification
of stability of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems.
Elsevier. https://doi.org/10.1016/j.nahs.2020.100856'
chicago: 'Garcia Soto, Miriam, and Pavithra Prabhakar. “Abstraction Based Verification
of Stability of Polyhedral Switched Systems.” Nonlinear Analysis: Hybrid Systems.
Elsevier, 2020. https://doi.org/10.1016/j.nahs.2020.100856.'
ieee: 'M. Garcia Soto and P. Prabhakar, “Abstraction based verification of stability
of polyhedral switched systems,” Nonlinear Analysis: Hybrid Systems, vol.
36, no. 5. Elsevier, 2020.'
ista: 'Garcia Soto M, Prabhakar P. 2020. Abstraction based verification of stability
of polyhedral switched systems. Nonlinear Analysis: Hybrid Systems. 36(5), 100856.'
mla: 'Garcia Soto, Miriam, and Pavithra Prabhakar. “Abstraction Based Verification
of Stability of Polyhedral Switched Systems.” Nonlinear Analysis: Hybrid Systems,
vol. 36, no. 5, 100856, Elsevier, 2020, doi:10.1016/j.nahs.2020.100856.'
short: 'M. Garcia Soto, P. Prabhakar, Nonlinear Analysis: Hybrid Systems 36 (2020).'
date_created: 2020-02-02T23:00:59Z
date_published: 2020-05-01T00:00:00Z
date_updated: 2023-08-17T14:32:54Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1016/j.nahs.2020.100856
external_id:
isi:
- '000528828600003'
file:
- access_level: open_access
checksum: 560abfddb53f9fe921b6744f59f2cfaa
content_type: application/pdf
creator: dernst
date_created: 2020-10-21T13:16:45Z
date_updated: 2022-05-16T22:30:04Z
embargo: 2022-05-15
file_id: '8688'
file_name: 2020_NAHS_GarciaSoto.pdf
file_size: 818774
relation: main_file
file_date_updated: 2022-05-16T22:30:04Z
has_accepted_license: '1'
intvolume: ' 36'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: 'Nonlinear Analysis: Hybrid Systems'
publication_identifier:
issn:
- 1751-570X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Abstraction based verification of stability of polyhedral switched systems
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 36
year: '2020'
...
---
_id: '8983'
abstract:
- lang: eng
text: Metabolic adaptation is a critical feature of migrating cells. It tunes the
metabolic programs of migrating cells to allow them to efficiently exert their
crucial roles in development, inflammatory responses and tumor metastasis. Cell
migration through physically challenging contexts requires energy. However, how
the metabolic reprogramming that underlies in vivo cell invasion is controlled
is still unanswered. In my PhD project, I identify a novel conserved metabolic
shift in Drosophila melanogaster immune cells that by modulating their bioenergetic
potential controls developmentally programmed tissue invasion. We show that this
regulation requires a novel conserved nuclear protein, named Atossa. Atossa enhances
the transcription of a set of proteins, including an RNA helicase Porthos and
two metabolic enzymes, each of which increases the tissue invasion of leading
Drosophila macrophages and can rescue the atossa mutant phenotype. Porthos selectively
regulates the translational efficiency of a subset of mRNAs containing a 5’-UTR
cis-regulatory TOP-like sequence. These 5’TOPL mRNA targets encode mitochondrial-related
proteins, including subunits of mitochondrial oxidative phosphorylation (OXPHOS)
components III and V and other metabolic-related proteins. Porthos powers up mitochondrial
OXPHOS to engender a sufficient ATP supply, which is required for tissue invasion
of leading macrophages. Atossa’s two vertebrate orthologs rescue the invasion
defect. In my PhD project, I elucidate that Atossa displays a conserved developmental
metabolic control to modulate metabolic capacities and the cellular energy state,
through altered transcription and translation, to aid the tissue infiltration
of leading cells into energy demanding barriers.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: E-Lib
- _id: CampIT
acknowledgement: Also, I would like to express my appreciation and thanks to the Bioimaging
facility, LSF, GSO, library, and IT people at IST Austria.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Shamsi
full_name: Emtenani, Shamsi
id: 49D32318-F248-11E8-B48F-1D18A9856A87
last_name: Emtenani
orcid: 0000-0001-6981-6938
citation:
ama: Emtenani S. Metabolic regulation of Drosophila macrophage tissue invasion.
2020. doi:10.15479/AT:ISTA:8983
apa: Emtenani, S. (2020). Metabolic regulation of Drosophila macrophage tissue
invasion. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8983
chicago: Emtenani, Shamsi. “Metabolic Regulation of Drosophila Macrophage Tissue
Invasion.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8983.
ieee: S. Emtenani, “Metabolic regulation of Drosophila macrophage tissue invasion,”
Institute of Science and Technology Austria, 2020.
ista: Emtenani S. 2020. Metabolic regulation of Drosophila macrophage tissue invasion.
Institute of Science and Technology Austria.
mla: Emtenani, Shamsi. Metabolic Regulation of Drosophila Macrophage Tissue Invasion.
Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8983.
short: S. Emtenani, Metabolic Regulation of Drosophila Macrophage Tissue Invasion,
Institute of Science and Technology Austria, 2020.
date_created: 2020-12-30T15:41:26Z
date_published: 2020-12-30T00:00:00Z
date_updated: 2023-09-07T13:24:17Z
day: '30'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: DaSi
doi: 10.15479/AT:ISTA:8983
file:
- access_level: open_access
checksum: ec2797ab7a6f253b35df0572b36d1b43
content_type: application/pdf
creator: semtenan
date_created: 2020-12-30T15:34:01Z
date_updated: 2021-12-31T23:30:04Z
embargo: 2021-12-30
file_id: '8984'
file_name: Thesis_Shamsi_Emtenani_pdfA.pdf
file_size: 10848175
relation: main_file
- access_level: closed
checksum: cc30e6608a9815414024cf548dff3b3a
content_type: application/pdf
creator: semtenan
date_created: 2020-12-30T15:37:36Z
date_updated: 2021-12-31T23:30:04Z
embargo_to: open_access
file_id: '8985'
file_name: Thesis_Shamsi_Emtenani_source file.pdf
file_size: 10073648
relation: source_file
file_date_updated: 2021-12-31T23:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '141'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8557'
relation: part_of_dissertation
status: public
- id: '6187'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
title: Metabolic regulation of Drosophila macrophage tissue invasion
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8557'
abstract:
- lang: eng
text: The infiltration of immune cells into tissues underlies the establishment
of tissue resident macrophages, and responses to infections and tumors. Yet the
mechanisms immune cells utilize to negotiate tissue barriers in living organisms
are not well understood, and a role for cortical actin has not been examined.
Here we find that the tissue invasion of Drosophila macrophages, also known as
plasmatocytes or hemocytes, utilizes enhanced cortical F-actin levels stimulated
by the Drosophila member of the fos proto oncogene transcription factor family
(Dfos, Kayak). RNA sequencing analysis and live imaging show that Dfos enhances
F-actin levels around the entire macrophage surface by increasing mRNA levels
of the membrane spanning molecular scaffold tetraspanin TM4SF, and the actin cross-linking
filamin Cheerio which are themselves required for invasion. Cortical F-actin levels
are critical as expressing a dominant active form of Diaphanous, a actin polymerizing
Formin, can rescue the Dfos Dominant Negative macrophage invasion defect. In vivo
imaging shows that Dfos is required to enhance the efficiency of the initial phases
of macrophage tissue entry. Genetic evidence argues that this Dfos-induced program
in macrophages counteracts the constraint produced by the tension of surrounding
tissues and buffers the mechanical properties of the macrophage nucleus from affecting
tissue entry. We thus identify tuning the cortical actin cytoskeleton through
Dfos as a key process allowing efficient forward movement of an immune cell into
surrounding tissues.
acknowledged_ssus:
- _id: LifeSc
acknowledgement: 'We thank the following for their contributions: The Drosophila Genomics
Resource Center supported by NIH grant 2P40OD010949-10A1 for plasmids, K. Brueckner.
B. Stramer, M. Uhlirova, O. Schuldiner, the Bloomington Drosophila Stock Center
supported by NIH grant P40OD018537 and the Vienna Drosophila Resource Center for
fly stocks, FlyBase (Thurmond et al., 2019) for essential genomic information, and
the BDGP in situ database for data (Tomancak et al., 2002, 2007). For antibodies,
we thank the Developmental Studies Hybridoma Bank, which was created by the Eunice
Kennedy Shriver National Institute of Child Health and Human Development of the
NIH, and is maintained at the University of Iowa, as well as J. Zeitlinger for her
generous gift of Dfos antibody. We thank the Vienna BioCenter Core Facilities for
RNA sequencing and analysis and the Life Scientific Service Units at IST Austria
for technical support and assistance with microscopy and FACS analysis. We thank
C.P. Heisenberg, P. Martin, M. Sixt and Siekhaus group members for discussions and
T.Hurd, A. Ratheesh and P. Rangan for comments on the manuscript. A.G. was supported
by the Austrian Science Fund (FWF) grant DASI_FWF01_P29638S, D.E.S. by Marie Curie
CIG 334077/IRTIM. M.S. is supported by the FWF, PhD program W1212 915 and the European
Research Council (ERC) Advanced grant (ERC-2015-AdG TNT-Tumors 694883). S.W. is
supported by an OEAW, DOC fellowship.'
article_processing_charge: No
author:
- first_name: Vera
full_name: Belyaeva, Vera
id: 47F080FE-F248-11E8-B48F-1D18A9856A87
last_name: Belyaeva
- first_name: Stephanie
full_name: Wachner, Stephanie
id: 2A95E7B0-F248-11E8-B48F-1D18A9856A87
last_name: Wachner
- first_name: Igor
full_name: Gridchyn, Igor
id: 4B60654C-F248-11E8-B48F-1D18A9856A87
last_name: Gridchyn
orcid: 0000-0002-1807-1929
- first_name: Markus
full_name: Linder, Markus
last_name: Linder
- first_name: Shamsi
full_name: Emtenani, Shamsi
id: 49D32318-F248-11E8-B48F-1D18A9856A87
last_name: Emtenani
orcid: 0000-0001-6981-6938
- first_name: Attila
full_name: György, Attila
id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87
last_name: György
orcid: 0000-0002-1819-198X
- first_name: Maria
full_name: Sibilia, Maria
last_name: Sibilia
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
citation:
ama: Belyaeva V, Wachner S, Gridchyn I, et al. Cortical actin properties controlled
by Drosophila Fos aid macrophage infiltration against surrounding tissue resistance.
bioRxiv. doi:10.1101/2020.09.18.301481
apa: Belyaeva, V., Wachner, S., Gridchyn, I., Linder, M., Emtenani, S., György,
A., … Siekhaus, D. E. (n.d.). Cortical actin properties controlled by Drosophila
Fos aid macrophage infiltration against surrounding tissue resistance. bioRxiv.
https://doi.org/10.1101/2020.09.18.301481
chicago: Belyaeva, Vera, Stephanie Wachner, Igor Gridchyn, Markus Linder, Shamsi
Emtenani, Attila György, Maria Sibilia, and Daria E Siekhaus. “Cortical Actin
Properties Controlled by Drosophila Fos Aid Macrophage Infiltration against Surrounding
Tissue Resistance.” BioRxiv, n.d. https://doi.org/10.1101/2020.09.18.301481.
ieee: V. Belyaeva et al., “Cortical actin properties controlled by Drosophila
Fos aid macrophage infiltration against surrounding tissue resistance,” bioRxiv.
.
ista: Belyaeva V, Wachner S, Gridchyn I, Linder M, Emtenani S, György A, Sibilia
M, Siekhaus DE. Cortical actin properties controlled by Drosophila Fos aid macrophage
infiltration against surrounding tissue resistance. bioRxiv, 10.1101/2020.09.18.301481.
mla: Belyaeva, Vera, et al. “Cortical Actin Properties Controlled by Drosophila
Fos Aid Macrophage Infiltration against Surrounding Tissue Resistance.” BioRxiv,
doi:10.1101/2020.09.18.301481.
short: V. Belyaeva, S. Wachner, I. Gridchyn, M. Linder, S. Emtenani, A. György,
M. Sibilia, D.E. Siekhaus, BioRxiv (n.d.).
date_created: 2020-09-23T09:36:47Z
date_published: 2020-09-18T00:00:00Z
date_updated: 2024-03-28T23:30:25Z
day: '18'
department:
- _id: DaSi
- _id: JoCs
doi: 10.1101/2020.09.18.301481
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2020.09.18.301481
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 253B6E48-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29638
name: Drosophila TNFa´s Funktion in Immunzellen
- _id: 2536F660-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '334077'
name: Investigating the role of transporters in invasive migration through junctions
- _id: 26199CA4-B435-11E9-9278-68D0E5697425
grant_number: '24800'
name: Tissue barrier penetration is crucial for immunity and metastasis
publication: bioRxiv
publication_status: submitted
related_material:
record:
- id: '10614'
relation: later_version
status: public
- id: '8983'
relation: dissertation_contains
status: public
status: public
title: Cortical actin properties controlled by Drosophila Fos aid macrophage infiltration
against surrounding tissue resistance
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8831'
abstract:
- lang: eng
text: Holes in planar Ge have high mobilities, strong spin-orbit interaction and
electrically tunable g-factors, and are therefore emerging as a promising candidate
for hybrid superconductorsemiconductor devices. This is further motivated by the
observation of supercurrent transport in planar Ge Josephson Field effect transistors
(JoFETs). A key challenge towards hybrid germanium quantum technology is the design
of high quality interfaces and superconducting contacts that are robust against
magnetic fields. By combining the assets of Al, which has a long superconducting
coherence, and Nb, which has a significant superconducting gap, we form low-disordered
JoFETs with 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: M-Shop
- _id: NanoFab
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 #844511 and the Grant Agreement #862046.
ICN2 acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported
by the Severo Ochoa\r\nprogram from Spanish MINECO (Grant No. SEV2017-0706) and
is funded by the CERCA Programme / Generalitat de Catalunya. Part of the present
work has been performed in the framework of Universitat Aut`onoma 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\r\nthe 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. GS and MV acknowledge support through a projectruimte grant associated
with the Netherlands Organization of Scientific Research (NWO)."
article_number: '2012.00322'
article_processing_charge: No
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: Marti-Sanchez, Sara
last_name: Marti-Sanchez
- 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: 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 planar Germanium. arXiv.
apa: Aggarwal, K., Hofmann, A. C., Jirovec, D., Prieto Gonzalez, I., Sammak, A.,
Botifoll, M., … Katsaros, G. (n.d.). Enhancement of proximity induced superconductivity
in planar Germanium. arXiv.
chicago: Aggarwal, Kushagra, Andrea C Hofmann, Daniel Jirovec, Ivan Prieto Gonzalez,
Amir Sammak, Marc Botifoll, Sara Marti-Sanchez, et al. “Enhancement of Proximity
Induced Superconductivity in Planar Germanium.” ArXiv, n.d.
ieee: K. Aggarwal et al., “Enhancement of proximity induced superconductivity
in planar Germanium,” arXiv. .
ista: Aggarwal K, Hofmann AC, Jirovec D, Prieto Gonzalez I, Sammak A, Botifoll M,
Marti-Sanchez S, Veldhorst M, Arbiol J, Scappucci G, Katsaros G. Enhancement of
proximity induced superconductivity in planar Germanium. arXiv, 2012.00322.
mla: Aggarwal, Kushagra, et al. “Enhancement of Proximity Induced Superconductivity
in Planar Germanium.” ArXiv, 2012.00322.
short: K. Aggarwal, A.C. Hofmann, D. Jirovec, I. Prieto Gonzalez, A. Sammak, M.
Botifoll, S. Marti-Sanchez, M. Veldhorst, J. Arbiol, G. Scappucci, G. Katsaros,
ArXiv (n.d.).
date_created: 2020-12-02T10:42:53Z
date_published: 2020-12-02T00:00:00Z
date_updated: 2024-03-28T23:30:27Z
day: '02'
ddc:
- '530'
department:
- _id: GeKa
ec_funded: 1
external_id:
arxiv:
- '2012.00322'
file:
- access_level: open_access
checksum: 22a612e206232fa94b138b2c2f957582
content_type: application/pdf
creator: gkatsaro
date_created: 2020-12-02T10:42:31Z
date_updated: 2020-12-02T10:42:31Z
file_id: '8832'
file_name: Superconducting_2D_Ge.pdf
file_size: 1697939
relation: main_file
file_date_updated: 2020-12-02T10:42:31Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
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
- _id: 237E5020-32DE-11EA-91FC-C7463DDC885E
call_identifier: H2020
grant_number: '862046'
name: TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS
publication: arXiv
publication_status: submitted
related_material:
record:
- id: '10559'
relation: later_version
status: public
- id: '8834'
relation: research_data
status: public
- id: '10058'
relation: dissertation_contains
status: public
status: public
title: Enhancement of proximity induced superconductivity in planar Germanium
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8532'
abstract:
- lang: eng
text: The molecular anatomy of synapses defines their characteristics in transmission
and plasticity. Precise measurements of the number and distribution of synaptic
proteins are important for our understanding of synapse heterogeneity within and
between brain regions. Freeze–fracture replica immunogold electron microscopy
enables us to analyze them quantitatively on a two-dimensional membrane surface.
Here, we introduce Darea software, which utilizes deep learning for analysis of
replica images and demonstrate its usefulness for quick measurements of the pre-
and postsynaptic areas, density and distribution of gold particles at synapses
in a reproducible manner. We used Darea for comparing glutamate receptor and calcium
channel distributions between hippocampal CA3-CA1 spine synapses on apical and
basal dendrites, which differ in signaling pathways involved in synaptic plasticity.
We found that apical synapses express a higher density of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic
acid (AMPA) receptors and a stronger increase of AMPA receptors with synaptic
size, while basal synapses show a larger increase in N-methyl-D-aspartate (NMDA)
receptors with size. Interestingly, AMPA and NMDA receptors are segregated within
postsynaptic sites and negatively correlated in density among both apical and
basal synapses. In the presynaptic sites, Cav2.1 voltage-gated calcium channels
show similar densities in apical and basal synapses with distributions consistent
with an exclusion zone model of calcium channel-release site topography.
acknowledgement: "This research was funded by Austrian Academy of Sciences, DOC fellowship
to D.K., European Research\r\nCouncil Advanced Grant 694539 and European Union Human
Brain Project (HBP) SGA2 785907 to R.S.\r\nWe acknowledge Elena Hollergschwandtner
for technical support."
article_number: '6737'
article_processing_charge: No
article_type: original
author:
- first_name: David
full_name: Kleindienst, David
id: 42E121A4-F248-11E8-B48F-1D18A9856A87
last_name: Kleindienst
- first_name: Jacqueline-Claire
full_name: Montanaro-Punzengruber, Jacqueline-Claire
id: 3786AB44-F248-11E8-B48F-1D18A9856A87
last_name: Montanaro-Punzengruber
- first_name: Pradeep
full_name: Bhandari, Pradeep
id: 45EDD1BC-F248-11E8-B48F-1D18A9856A87
last_name: Bhandari
orcid: 0000-0003-0863-4481
- first_name: Matthew J
full_name: Case, Matthew J
id: 44B7CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Case
- first_name: Yugo
full_name: Fukazawa, Yugo
last_name: Fukazawa
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y,
Shigemoto R. Deep learning-assisted high-throughput analysis of freeze-fracture
replica images applied to glutamate receptors and calcium channels at hippocampal
synapses. International Journal of Molecular Sciences. 2020;21(18). doi:10.3390/ijms21186737
apa: Kleindienst, D., Montanaro-Punzengruber, J.-C., Bhandari, P., Case, M. J.,
Fukazawa, Y., & Shigemoto, R. (2020). Deep learning-assisted high-throughput
analysis of freeze-fracture replica images applied to glutamate receptors and
calcium channels at hippocampal synapses. International Journal of Molecular
Sciences. MDPI. https://doi.org/10.3390/ijms21186737
chicago: Kleindienst, David, Jacqueline-Claire Montanaro-Punzengruber, Pradeep Bhandari,
Matthew J Case, Yugo Fukazawa, and Ryuichi Shigemoto. “Deep Learning-Assisted
High-Throughput Analysis of Freeze-Fracture Replica Images Applied to Glutamate
Receptors and Calcium Channels at Hippocampal Synapses.” International Journal
of Molecular Sciences. MDPI, 2020. https://doi.org/10.3390/ijms21186737.
ieee: D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M. J. Case, Y.
Fukazawa, and R. Shigemoto, “Deep learning-assisted high-throughput analysis of
freeze-fracture replica images applied to glutamate receptors and calcium channels
at hippocampal synapses,” International Journal of Molecular Sciences,
vol. 21, no. 18. MDPI, 2020.
ista: Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y,
Shigemoto R. 2020. Deep learning-assisted high-throughput analysis of freeze-fracture
replica images applied to glutamate receptors and calcium channels at hippocampal
synapses. International Journal of Molecular Sciences. 21(18), 6737.
mla: Kleindienst, David, et al. “Deep Learning-Assisted High-Throughput Analysis
of Freeze-Fracture Replica Images Applied to Glutamate Receptors and Calcium Channels
at Hippocampal Synapses.” International Journal of Molecular Sciences,
vol. 21, no. 18, 6737, MDPI, 2020, doi:10.3390/ijms21186737.
short: D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M.J. Case, Y.
Fukazawa, R. Shigemoto, International Journal of Molecular Sciences 21 (2020).
date_created: 2020-09-20T22:01:35Z
date_published: 2020-09-14T00:00:00Z
date_updated: 2024-03-28T23:30:31Z
day: '14'
ddc:
- '570'
department:
- _id: RySh
doi: 10.3390/ijms21186737
ec_funded: 1
external_id:
isi:
- '000579945300001'
file:
- access_level: open_access
checksum: 2e4f62f3cfe945b7391fc3070e5a289f
content_type: application/pdf
creator: dernst
date_created: 2020-09-21T14:08:58Z
date_updated: 2020-09-21T14:08:58Z
file_id: '8551'
file_name: 2020_JournMolecSciences_Kleindienst.pdf
file_size: 5748456
relation: main_file
success: 1
file_date_updated: 2020-09-21T14:08:58Z
has_accepted_license: '1'
intvolume: ' 21'
isi: 1
issue: '18'
language:
- iso: eng
month: '09'
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: 25D32BC0-B435-11E9-9278-68D0E5697425
name: Mechanism of formation and maintenance of input side-dependent asymmetry in
the hippocampus
- _id: 26436750-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '785907'
name: Human Brain Project Specific Grant Agreement 2 (HBP SGA 2)
publication: International Journal of Molecular Sciences
publication_identifier:
eissn:
- '14220067'
issn:
- '16616596'
publication_status: published
publisher: MDPI
quality_controlled: '1'
related_material:
record:
- id: '9562'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Deep learning-assisted high-throughput analysis of freeze-fracture replica
images applied to glutamate receptors and calcium channels at hippocampal synapses
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 21
year: '2020'
...
---
_id: '7810'
abstract:
- lang: eng
text: "Interprocedural data-flow analyses form an expressive and useful paradigm
of numerous static analysis applications, such as live variables analysis, alias
analysis and null pointers analysis. The most widely-used framework for interprocedural
data-flow analysis is IFDS, which encompasses distributive data-flow functions
over a finite domain. On-demand data-flow analyses restrict the focus of the analysis
on specific program locations and data facts. This setting provides a natural
split between (i) an offline (or preprocessing) phase, where the program is partially
analyzed and analysis summaries are created, and (ii) an online (or query) phase,
where analysis queries arrive on demand and the summaries are used to speed up
answering queries.\r\nIn this work, we consider on-demand IFDS analyses where
the queries concern program locations of the same procedure (aka same-context
queries). We exploit the fact that flow graphs of programs have low treewidth
to develop faster algorithms that are space and time optimal for many common data-flow
analyses, in both the preprocessing and the query phase. We also use treewidth
to develop query solutions that are embarrassingly parallelizable, i.e. the total
work for answering each query is split to a number of threads such that each thread
performs only a constant amount of work. Finally, we implement a static analyzer
based on our algorithms, and perform a series of on-demand analysis experiments
on standard benchmarks. Our experimental results show a drastic speed-up of the
queries after only a lightweight preprocessing phase, which significantly outperforms
existing techniques."
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: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: 'Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. Optimal and perfectly
parallel algorithms for on-demand data-flow analysis. In: European Symposium
on Programming. Vol 12075. Springer Nature; 2020:112-140. doi:10.1007/978-3-030-44914-8_5'
apa: 'Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., & Pavlogiannis, A.
(2020). Optimal and perfectly parallel algorithms for on-demand data-flow analysis.
In European Symposium on Programming (Vol. 12075, pp. 112–140). Dublin,
Ireland: Springer Nature. https://doi.org/10.1007/978-3-030-44914-8_5'
chicago: Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen,
and Andreas Pavlogiannis. “Optimal and Perfectly Parallel Algorithms for On-Demand
Data-Flow Analysis.” In European Symposium on Programming, 12075:112–40.
Springer Nature, 2020. https://doi.org/10.1007/978-3-030-44914-8_5.
ieee: K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and A. Pavlogiannis, “Optimal
and perfectly parallel algorithms for on-demand data-flow analysis,” in European
Symposium on Programming, Dublin, Ireland, 2020, vol. 12075, pp. 112–140.
ista: 'Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. 2020. Optimal
and perfectly parallel algorithms for on-demand data-flow analysis. European Symposium
on Programming. ESOP: Programming Languages and Systems, LNCS, vol. 12075, 112–140.'
mla: Chatterjee, Krishnendu, et al. “Optimal and Perfectly Parallel Algorithms for
On-Demand Data-Flow Analysis.” European Symposium on Programming, vol.
12075, Springer Nature, 2020, pp. 112–40, doi:10.1007/978-3-030-44914-8_5.
short: K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, A. Pavlogiannis, in:, European
Symposium on Programming, Springer Nature, 2020, pp. 112–140.
conference:
end_date: 2020-04-30
location: Dublin, Ireland
name: 'ESOP: Programming Languages and Systems'
start_date: 2020-04-25
date_created: 2020-05-10T22:00:50Z
date_published: 2020-04-18T00:00:00Z
date_updated: 2024-03-28T23:30:34Z
day: '18'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-030-44914-8_5
external_id:
isi:
- '000681656800005'
file:
- access_level: open_access
checksum: 8618b80f4cf7b39a60e61a6445ad9807
content_type: application/pdf
creator: dernst
date_created: 2020-05-26T13:34:48Z
date_updated: 2020-07-14T12:48:03Z
file_id: '7895'
file_name: 2020_LNCS_Chatterjee.pdf
file_size: 651250
relation: main_file
file_date_updated: 2020-07-14T12:48:03Z
has_accepted_license: '1'
intvolume: ' 12075'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 112-140
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 266EEEC0-B435-11E9-9278-68D0E5697425
name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart
Contracts
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies
publication: European Symposium on Programming
publication_identifier:
eissn:
- '16113349'
isbn:
- '9783030449131'
issn:
- '03029743'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Optimal and perfectly parallel algorithms for on-demand data-flow analysis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12075
year: '2020'
...
---
_id: '8728'
abstract:
- lang: eng
text: Discrete-time Markov Chains (MCs) and Markov Decision Processes (MDPs) are
two standard formalisms in system analysis. Their main associated quantitative
objectives are hitting probabilities, discounted sum, and mean payoff. Although
there are many techniques for computing these objectives in general MCs/MDPs,
they have not been thoroughly studied in terms of parameterized algorithms, particularly
when treewidth is used as the parameter. This is in sharp contrast to qualitative
objectives for MCs, MDPs and graph games, for which treewidth-based algorithms
yield significant complexity improvements. In this work, we show that treewidth
can also be used to obtain faster algorithms for the quantitative problems. For
an MC with n states and m transitions, we show that each of the classical quantitative
objectives can be computed in O((n+m)⋅t2) time, given a tree decomposition
of the MC with width t. Our results also imply a bound of O(κ⋅(n+m)⋅t2) for
each objective on MDPs, where κ is the number of strategy-iteration refinements
required for the given input and objective. Finally, we make an experimental evaluation
of our new algorithms on low-treewidth MCs and MDPs obtained from the DaCapo benchmark
suite. Our experiments show that on low-treewidth MCs and MDPs, our algorithms
outperform existing well-established methods by one or more orders of magnitude.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Ali
full_name: Asadi, Ali
last_name: Asadi
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Kiarash
full_name: Mohammadi, Kiarash
last_name: Mohammadi
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: 'Asadi A, Chatterjee K, Goharshady AK, Mohammadi K, Pavlogiannis A. Faster
algorithms for quantitative analysis of MCs and MDPs with small treewidth. In:
Automated Technology for Verification and Analysis. Vol 12302. Springer
Nature; 2020:253-270. doi:10.1007/978-3-030-59152-6_14'
apa: 'Asadi, A., Chatterjee, K., Goharshady, A. K., Mohammadi, K., & Pavlogiannis,
A. (2020). Faster algorithms for quantitative analysis of MCs and MDPs with small
treewidth. In Automated Technology for Verification and Analysis (Vol.
12302, pp. 253–270). Hanoi, Vietnam: Springer Nature. https://doi.org/10.1007/978-3-030-59152-6_14'
chicago: Asadi, Ali, Krishnendu Chatterjee, Amir Kafshdar Goharshady, Kiarash Mohammadi,
and Andreas Pavlogiannis. “Faster Algorithms for Quantitative Analysis of MCs
and MDPs with Small Treewidth.” In Automated Technology for Verification and
Analysis, 12302:253–70. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-59152-6_14.
ieee: A. Asadi, K. Chatterjee, A. K. Goharshady, K. Mohammadi, and A. Pavlogiannis,
“Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth,”
in Automated Technology for Verification and Analysis, Hanoi, Vietnam,
2020, vol. 12302, pp. 253–270.
ista: 'Asadi A, Chatterjee K, Goharshady AK, Mohammadi K, Pavlogiannis A. 2020.
Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth.
Automated Technology for Verification and Analysis. ATVA: Automated Technology
for Verification and Analysis, LNCS, vol. 12302, 253–270.'
mla: Asadi, Ali, et al. “Faster Algorithms for Quantitative Analysis of MCs and
MDPs with Small Treewidth.” Automated Technology for Verification and Analysis,
vol. 12302, Springer Nature, 2020, pp. 253–70, doi:10.1007/978-3-030-59152-6_14.
short: A. Asadi, K. Chatterjee, A.K. Goharshady, K. Mohammadi, A. Pavlogiannis,
in:, Automated Technology for Verification and Analysis, Springer Nature, 2020,
pp. 253–270.
conference:
end_date: 2020-10-23
location: Hanoi, Vietnam
name: 'ATVA: Automated Technology for Verification and Analysis'
start_date: 2020-10-19
date_created: 2020-11-06T07:30:05Z
date_published: 2020-10-12T00:00:00Z
date_updated: 2024-03-28T23:30:34Z
day: '12'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-030-59152-6_14
external_id:
isi:
- '000723555700014'
file:
- access_level: open_access
checksum: ae83f27e5b189d5abc2e7514f1b7e1b5
content_type: application/pdf
creator: dernst
date_created: 2020-11-06T07:41:03Z
date_updated: 2020-11-06T07:41:03Z
file_id: '8729'
file_name: 2020_LNCS_ATVA_Asadi_accepted.pdf
file_size: 726648
relation: main_file
success: 1
file_date_updated: 2020-11-06T07:41:03Z
has_accepted_license: '1'
intvolume: ' 12302'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 253-270
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies
publication: Automated Technology for Verification and Analysis
publication_identifier:
eisbn:
- '9783030591526'
eissn:
- 1611-3349
isbn:
- '9783030591519'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Faster algorithms for quantitative analysis of MCs and MDPs with small treewidth
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 12302
year: '2020'
...
---
_id: '8089'
abstract:
- lang: eng
text: "We consider the classical problem of invariant generation for programs with
polynomial assignments and focus on synthesizing invariants that are a conjunction
of strict polynomial inequalities. We present a sound and semi-complete method
based on positivstellensaetze, i.e. theorems in semi-algebraic geometry that characterize
positive polynomials over a semi-algebraic set.\r\n\r\nOn the theoretical side,
the worst-case complexity of our approach is subexponential, whereas the worst-case
complexity of the previous complete method (Kapur, ACA 2004) is doubly-exponential.
Even when restricted to linear invariants, the best previous complexity for complete
invariant generation is exponential (Colon et al, CAV 2003). On the practical
side, we reduce the invariant generation problem to quadratic programming (QCLP),
which is a classical optimization problem with many industrial solvers. We demonstrate
the applicability of our approach by providing experimental results on several
academic benchmarks. To the best of our knowledge, the only previous invariant
generation method that provides completeness guarantees for invariants consisting
of polynomial inequalities is (Kapur, ACA 2004), which relies on quantifier elimination
and cannot even handle toy programs such as our running example."
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: Hongfei
full_name: Fu, Hongfei
id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87
last_name: Fu
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Ehsan Kafshdar
full_name: Goharshady, Ehsan Kafshdar
last_name: Goharshady
citation:
ama: 'Chatterjee K, Fu H, Goharshady AK, Goharshady EK. Polynomial invariant generation
for non-deterministic recursive programs. In: Proceedings of the 41st ACM SIGPLAN
Conference on Programming Language Design and Implementation. Association
for Computing Machinery; 2020:672-687. doi:10.1145/3385412.3385969'
apa: 'Chatterjee, K., Fu, H., Goharshady, A. K., & Goharshady, E. K. (2020).
Polynomial invariant generation for non-deterministic recursive programs. In Proceedings
of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation
(pp. 672–687). London, United Kingdom: Association for Computing Machinery. https://doi.org/10.1145/3385412.3385969'
chicago: Chatterjee, Krishnendu, Hongfei Fu, Amir Kafshdar Goharshady, and Ehsan
Kafshdar Goharshady. “Polynomial Invariant Generation for Non-Deterministic Recursive
Programs.” In Proceedings of the 41st ACM SIGPLAN Conference on Programming
Language Design and Implementation, 672–87. Association for Computing Machinery,
2020. https://doi.org/10.1145/3385412.3385969.
ieee: K. Chatterjee, H. Fu, A. K. Goharshady, and E. K. Goharshady, “Polynomial
invariant generation for non-deterministic recursive programs,” in Proceedings
of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation,
London, United Kingdom, 2020, pp. 672–687.
ista: 'Chatterjee K, Fu H, Goharshady AK, Goharshady EK. 2020. Polynomial invariant
generation for non-deterministic recursive programs. Proceedings of the 41st ACM
SIGPLAN Conference on Programming Language Design and Implementation. PLDI: Programming
Language Design and Implementation, 672–687.'
mla: Chatterjee, Krishnendu, et al. “Polynomial Invariant Generation for Non-Deterministic
Recursive Programs.” Proceedings of the 41st ACM SIGPLAN Conference on Programming
Language Design and Implementation, Association for Computing Machinery, 2020,
pp. 672–87, doi:10.1145/3385412.3385969.
short: K. Chatterjee, H. Fu, A.K. Goharshady, E.K. Goharshady, in:, Proceedings
of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation,
Association for Computing Machinery, 2020, pp. 672–687.
conference:
end_date: 2020-06-20
location: London, United Kingdom
name: 'PLDI: Programming Language Design and Implementation'
start_date: 2020-06-15
date_created: 2020-07-05T22:00:45Z
date_published: 2020-06-11T00:00:00Z
date_updated: 2024-03-28T23:30:34Z
day: '11'
department:
- _id: KrCh
doi: 10.1145/3385412.3385969
external_id:
arxiv:
- '1902.04373'
isi:
- '000614622300045'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1902.04373
month: '06'
oa: 1
oa_version: Preprint
page: 672-687
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication: Proceedings of the 41st ACM SIGPLAN Conference on Programming Language
Design and Implementation
publication_identifier:
isbn:
- '9781450376136'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Polynomial invariant generation for non-deterministic recursive programs
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '6918'
abstract:
- lang: eng
text: "We consider the classic problem of Network Reliability. A network is given
together with a source vertex, one or more target vertices, and probabilities
assigned to each of the edges. Each edge of the network is operable with its associated
probability and the problem is to determine the probability of having at least
one source-to-target path that is entirely composed of operable edges. This problem
is known to be NP-hard.\r\n\r\nWe provide a novel scalable algorithm to solve
the Network Reliability problem when the treewidth of the underlying network is
small. We also show our algorithm’s applicability for real-world transit networks
that have small treewidth, including the metro networks of major cities, such
as London and Tokyo. Our algorithm leverages tree decompositions to shrink the
original graph into much smaller graphs, for which reliability can be efficiently
and exactly computed using a brute force method. To the best of our knowledge,
this is the first exact algorithm for Network Reliability that can scale to handle
real-world instances of the problem."
acknowledgement: We are grateful to the anonymous reviewers for their comments, which
significantly improved the present work. The research was partially supported by
the EPSRC Early Career Fellowship EP/R023379/1, grant no. SC7-1718-01 of the London
Mathematical Society, an IBM PhD Fellowship, and a DOC Fellowship of the Austrian
Academy of Sciences (ÖAW).
article_number: '106665'
article_processing_charge: No
article_type: original
author:
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Fatemeh
full_name: Mohammadi, Fatemeh
last_name: Mohammadi
citation:
ama: Goharshady AK, Mohammadi F. An efficient algorithm for computing network reliability
in small treewidth. Reliability Engineering and System Safety. 2020;193.
doi:10.1016/j.ress.2019.106665
apa: Goharshady, A. K., & Mohammadi, F. (2020). An efficient algorithm for computing
network reliability in small treewidth. Reliability Engineering and System
Safety. Elsevier. https://doi.org/10.1016/j.ress.2019.106665
chicago: Goharshady, Amir Kafshdar, and Fatemeh Mohammadi. “An Efficient Algorithm
for Computing Network Reliability in Small Treewidth.” Reliability Engineering
and System Safety. Elsevier, 2020. https://doi.org/10.1016/j.ress.2019.106665.
ieee: A. K. Goharshady and F. Mohammadi, “An efficient algorithm for computing network
reliability in small treewidth,” Reliability Engineering and System Safety,
vol. 193. Elsevier, 2020.
ista: Goharshady AK, Mohammadi F. 2020. An efficient algorithm for computing network
reliability in small treewidth. Reliability Engineering and System Safety. 193,
106665.
mla: Goharshady, Amir Kafshdar, and Fatemeh Mohammadi. “An Efficient Algorithm for
Computing Network Reliability in Small Treewidth.” Reliability Engineering
and System Safety, vol. 193, 106665, Elsevier, 2020, doi:10.1016/j.ress.2019.106665.
short: A.K. Goharshady, F. Mohammadi, Reliability Engineering and System Safety
193 (2020).
date_created: 2019-09-29T22:00:44Z
date_published: 2020-01-01T00:00:00Z
date_updated: 2024-03-28T23:30:34Z
day: '01'
department:
- _id: KrCh
doi: 10.1016/j.ress.2019.106665
external_id:
arxiv:
- '1712.09692'
isi:
- '000501641400050'
intvolume: ' 193'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1712.09692
month: '01'
oa: 1
oa_version: Preprint
project:
- _id: 266EEEC0-B435-11E9-9278-68D0E5697425
name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart
Contracts
publication: Reliability Engineering and System Safety
publication_identifier:
issn:
- '09518320'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: An efficient algorithm for computing network reliability in small treewidth
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 193
year: '2020'
...
---
_id: '7161'
abstract:
- lang: eng
text: In this paper, we introduce an inertial projection-type method with different
updating strategies for solving quasi-variational inequalities with strongly monotone
and Lipschitz continuous operators in real Hilbert spaces. Under standard assumptions,
we establish different strong convergence results for the proposed algorithm.
Primary numerical experiments demonstrate the potential applicability of our scheme
compared with some related methods in the literature.
acknowledgement: We are grateful to the anonymous referees and editor whose insightful
comments helped to considerably improve an earlier version of this paper. The research
of the first author is supported by an ERC Grant from the Institute of Science and
Technology (IST).
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: Aviv
full_name: Gibali, Aviv
last_name: Gibali
- first_name: Simone
full_name: Sagratella, Simone
last_name: Sagratella
citation:
ama: Shehu Y, Gibali A, Sagratella S. Inertial projection-type methods for solving
quasi-variational inequalities in real Hilbert spaces. Journal of Optimization
Theory and Applications. 2020;184:877–894. doi:10.1007/s10957-019-01616-6
apa: Shehu, Y., Gibali, A., & Sagratella, S. (2020). Inertial projection-type
methods for solving quasi-variational inequalities in real Hilbert spaces. Journal
of Optimization Theory and Applications. Springer Nature. https://doi.org/10.1007/s10957-019-01616-6
chicago: Shehu, Yekini, Aviv Gibali, and Simone Sagratella. “Inertial Projection-Type
Methods for Solving Quasi-Variational Inequalities in Real Hilbert Spaces.” Journal
of Optimization Theory and Applications. Springer Nature, 2020. https://doi.org/10.1007/s10957-019-01616-6.
ieee: Y. Shehu, A. Gibali, and S. Sagratella, “Inertial projection-type methods
for solving quasi-variational inequalities in real Hilbert spaces,” Journal
of Optimization Theory and Applications, vol. 184. Springer Nature, pp. 877–894,
2020.
ista: Shehu Y, Gibali A, Sagratella S. 2020. Inertial projection-type methods for
solving quasi-variational inequalities in real Hilbert spaces. Journal of Optimization
Theory and Applications. 184, 877–894.
mla: Shehu, Yekini, et al. “Inertial Projection-Type Methods for Solving Quasi-Variational
Inequalities in Real Hilbert Spaces.” Journal of Optimization Theory and Applications,
vol. 184, Springer Nature, 2020, pp. 877–894, doi:10.1007/s10957-019-01616-6.
short: Y. Shehu, A. Gibali, S. Sagratella, Journal of Optimization Theory and Applications
184 (2020) 877–894.
date_created: 2019-12-09T21:33:44Z
date_published: 2020-03-01T00:00:00Z
date_updated: 2023-09-06T11:27:15Z
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call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Journal of Optimization Theory and Applications
publication_identifier:
eissn:
- 1573-2878
issn:
- 0022-3239
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inertial projection-type methods for solving quasi-variational inequalities
in real Hilbert spaces
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 184
year: '2020'
...
---
_id: '7652'
abstract:
- lang: eng
text: Organisms cope with change by taking advantage of transcriptional regulators.
However, when faced with rare environments, the evolution of transcriptional regulators
and their promoters may be too slow. Here, we investigate whether the intrinsic
instability of gene duplication and amplification provides a generic alternative
to canonical gene regulation. Using real-time monitoring of gene-copy-number mutations
in Escherichia coli, we show that gene duplications and amplifications enable
adaptation to fluctuating environments by rapidly generating copy-number and,
therefore, expression-level polymorphisms. This amplification-mediated gene expression
tuning (AMGET) occurs on timescales that are similar to canonical gene regulation
and can respond to rapid environmental changes. Mathematical modelling shows that
amplifications also tune gene expression in stochastic environments in which transcription-factor-based
schemes are hard to evolve or maintain. The fleeting nature of gene amplifications
gives rise to a generic population-level mechanism that relies on genetic heterogeneity
to rapidly tune the expression of any gene, without leaving any genomic signature.
acknowledgement: We thank L. Hurst, N. Barton, M. Pleska, M. Steinrück, B. Kavcic
and A. Staron for input on the manuscript, and To. Bergmiller and R. Chait for help
with microfluidics experiments. I.T. is a recipient the OMV fellowship. R.G. is
a recipient of a DOC (Doctoral Fellowship Programme of the Austrian Academy of Sciences)
Fellowship of the Austrian Academy of Sciences.
article_processing_charge: No
article_type: original
author:
- first_name: Isabella
full_name: Tomanek, Isabella
id: 3981F020-F248-11E8-B48F-1D18A9856A87
last_name: Tomanek
orcid: 0000-0001-6197-363X
- first_name: Rok
full_name: Grah, Rok
id: 483E70DE-F248-11E8-B48F-1D18A9856A87
last_name: Grah
orcid: 0000-0003-2539-3560
- first_name: M.
full_name: Lagator, M.
last_name: Lagator
- first_name: A. M. C.
full_name: Andersson, A. M. C.
last_name: Andersson
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Tomanek I, Grah R, Lagator M, et al. Gene amplification as a form of population-level
gene expression regulation. Nature Ecology & Evolution. 2020;4(4):612-625.
doi:10.1038/s41559-020-1132-7
apa: Tomanek, I., Grah, R., Lagator, M., Andersson, A. M. C., Bollback, J. P., Tkačik,
G., & Guet, C. C. (2020). Gene amplification as a form of population-level
gene expression regulation. Nature Ecology & Evolution. Springer Nature.
https://doi.org/10.1038/s41559-020-1132-7
chicago: Tomanek, Isabella, Rok Grah, M. Lagator, A. M. C. Andersson, Jonathan P
Bollback, Gašper Tkačik, and Calin C Guet. “Gene Amplification as a Form of Population-Level
Gene Expression Regulation.” Nature Ecology & Evolution. Springer Nature,
2020. https://doi.org/10.1038/s41559-020-1132-7.
ieee: I. Tomanek et al., “Gene amplification as a form of population-level
gene expression regulation,” Nature Ecology & Evolution, vol. 4, no.
4. Springer Nature, pp. 612–625, 2020.
ista: Tomanek I, Grah R, Lagator M, Andersson AMC, Bollback JP, Tkačik G, Guet CC.
2020. Gene amplification as a form of population-level gene expression regulation.
Nature Ecology & Evolution. 4(4), 612–625.
mla: Tomanek, Isabella, et al. “Gene Amplification as a Form of Population-Level
Gene Expression Regulation.” Nature Ecology & Evolution, vol. 4, no.
4, Springer Nature, 2020, pp. 612–25, doi:10.1038/s41559-020-1132-7.
short: I. Tomanek, R. Grah, M. Lagator, A.M.C. Andersson, J.P. Bollback, G. Tkačik,
C.C. Guet, Nature Ecology & Evolution 4 (2020) 612–625.
date_created: 2020-04-08T15:20:53Z
date_published: 2020-04-01T00:00:00Z
date_updated: 2024-03-28T23:30:37Z
day: '01'
ddc:
- '570'
department:
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- _id: CaGu
doi: 10.1038/s41559-020-1132-7
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oa_version: Submitted Version
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- _id: 267C84F4-B435-11E9-9278-68D0E5697425
name: Biophysically realistic genotype-phenotype maps for regulatory networks
publication: Nature Ecology & Evolution
publication_identifier:
issn:
- 2397-334X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/how-to-thrive-without-gene-regulation/
record:
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relation: research_data
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- id: '7016'
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scopus_import: '1'
status: public
title: Gene amplification as a form of population-level gene expression regulation
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 4
year: '2020'
...
---
_id: '7258'
abstract:
- lang: eng
text: Many flows encountered in nature and applications are characterized by a chaotic
motion known as turbulence. Turbulent flows generate intense friction with pipe
walls and are responsible for considerable amounts of energy losses at world scale.
The nature of turbulent friction and techniques aimed at reducing it have been
subject of extensive research over the last century, but no definite answer has
been found yet. In this thesis we show that in pipes at moderate turbulent Reynolds
numbers friction is better described by the power law first introduced by Blasius
and not by the Prandtl–von Kármán formula. At higher Reynolds numbers, large scale
motions gradually become more important in the flow and can be related to the
change in scaling of friction. Next, we present a series of new techniques that
can relaminarize turbulence by suppressing a key mechanism that regenerates it
at walls, the lift–up effect. In addition, we investigate the process of turbulence
decay in several experiments and discuss the drag reduction potential. Finally,
we examine the behavior of friction under pulsating conditions inspired by the
human heart cycle and we show that under such circumstances turbulent friction
can be reduced to produce energy savings.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Davide
full_name: Scarselli, Davide
id: 40315C30-F248-11E8-B48F-1D18A9856A87
last_name: Scarselli
orcid: 0000-0001-5227-4271
citation:
ama: Scarselli D. New approaches to reduce friction in turbulent pipe flow. 2020.
doi:10.15479/AT:ISTA:7258
apa: Scarselli, D. (2020). New approaches to reduce friction in turbulent pipe
flow. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7258
chicago: Scarselli, Davide. “New Approaches to Reduce Friction in Turbulent Pipe
Flow.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7258.
ieee: D. Scarselli, “New approaches to reduce friction in turbulent pipe flow,”
Institute of Science and Technology Austria, 2020.
ista: Scarselli D. 2020. New approaches to reduce friction in turbulent pipe flow.
Institute of Science and Technology Austria.
mla: Scarselli, Davide. New Approaches to Reduce Friction in Turbulent Pipe Flow.
Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7258.
short: D. Scarselli, New Approaches to Reduce Friction in Turbulent Pipe Flow, Institute
of Science and Technology Austria, 2020.
date_created: 2020-01-12T16:07:26Z
date_published: 2020-01-13T00:00:00Z
date_updated: 2023-09-15T12:20:08Z
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degree_awarded: PhD
department:
- _id: BjHo
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ec_funded: 1
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oa_version: None
page: '174'
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
- _id: 25104D44-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '737549'
name: Eliminating turbulence in oil pipelines
- _id: 25136C54-B435-11E9-9278-68D0E5697425
grant_number: HO 4393/1-2
name: Experimental studies of the turbulence transition and transport processes
in turbulent Taylor-Couette currents
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6228'
relation: part_of_dissertation
status: public
- id: '6486'
relation: part_of_dissertation
status: public
- id: '461'
relation: part_of_dissertation
status: public
- id: '422'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
title: New approaches to reduce friction in turbulent pipe flow
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8653'
abstract:
- lang: eng
text: "Mutations are the raw material of evolution and come in many different flavors.
Point mutations change a single letter in the DNA sequence, while copy number
mutations like duplications or deletions add or remove many letters of the DNA
sequence simultaneously. Each type of mutation exhibits specific properties like
its rate of formation and reversal. \r\nGene expression is a fundamental phenotype
that can be altered by both, point and copy number mutations. The following thesis
is concerned with the dynamics of gene expression evolution and how it is affected
by the properties exhibited by point and copy number mutations. Specifically,
we are considering i) copy number mutations during adaptation to fluctuating environments
and ii) the interaction of copy number and point mutations during adaptation to
constant environments. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Isabella
full_name: Tomanek, Isabella
id: 3981F020-F248-11E8-B48F-1D18A9856A87
last_name: Tomanek
orcid: 0000-0001-6197-363X
citation:
ama: Tomanek I. The evolution of gene expression by copy number and point mutations.
2020. doi:10.15479/AT:ISTA:8653
apa: Tomanek, I. (2020). The evolution of gene expression by copy number and
point mutations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8653
chicago: Tomanek, Isabella. “The Evolution of Gene Expression by Copy Number and
Point Mutations.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8653.
ieee: I. Tomanek, “The evolution of gene expression by copy number and point mutations,”
Institute of Science and Technology Austria, 2020.
ista: Tomanek I. 2020. The evolution of gene expression by copy number and point
mutations. Institute of Science and Technology Austria.
mla: Tomanek, Isabella. The Evolution of Gene Expression by Copy Number and Point
Mutations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8653.
short: I. Tomanek, The Evolution of Gene Expression by Copy Number and Point Mutations,
Institute of Science and Technology Austria, 2020.
date_created: 2020-10-13T13:02:33Z
date_published: 2020-10-13T00:00:00Z
date_updated: 2023-09-07T13:22:42Z
day: '13'
ddc:
- '576'
degree_awarded: PhD
department:
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date_updated: 2021-10-20T22:30:03Z
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file_size: 15405675
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file_date_updated: 2021-10-20T22:30:03Z
has_accepted_license: '1'
keyword:
- duplication
- amplification
- promoter
- CNV
- AMGET
- experimental evolution
- Escherichia coli
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '117'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7652'
relation: research_data
status: public
status: public
supervisor:
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
title: The evolution of gene expression by copy number and point mutations
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '7427'
abstract:
- lang: eng
text: Plants, like other multicellular organisms, survive through a delicate balance
between growth and defense against pathogens. Salicylic acid (SA) is a major defense
signal in plants, and the perception mechanism as well as downstream signaling
activating the immune response are known. Here, we identify a parallel SA signaling
that mediates growth attenuation. SA directly binds to A subunits of protein phosphatase
2A (PP2A), inhibiting activity of this complex. Among PP2A targets, the PIN2 auxin
transporter is hyperphosphorylated in response to SA, leading to changed activity
of this important growth regulator. Accordingly, auxin transport and auxin-mediated
root development, including growth, gravitropic response, and lateral root organogenesis,
are inhibited. This study reveals how SA, besides activating immunity, concomitantly
attenuates growth through crosstalk with the auxin distribution network. Further
analysis of this dual role of SA and characterization of additional SA-regulated
PP2A targets will provide further insights into mechanisms maintaining a balance
between growth and defense.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: "We thank Shigeyuki Betsuyaku (University of Tsukuba), Alison Delong
(Brown University), Xinnian Dong (Duke University), Dolf Weijers (Wageningen University),
Yuelin Zhang (UBC), and Martine Pastuglia (Institut Jean-Pierre Bourgin) for sharing
published materials; Jana Riederer for help with cantharidin physiological analysis;
David Domjan for help with cloning pET28a-PIN2HL; Qing Lu for help with DARTS; Hana
Kozubı´kova´ for technical support on SA derivative synthesis; Zuzana Vondra´ kova´
for technical support with tobacco cells; Lucia Strader (Washington University),
Bert De Rybel (Ghent University), Bartel Vanholme (Ghent University), and Lukas
Mach (BOKU) for helpful discussions; and bioimaging and life science facilities
of IST Austria for continuous support. We gratefully acknowledge the Nottingham
Arabidopsis Stock Center (NASC) for providing T-DNA insertional mutants. The DSC
and SPR instruments were provided by the EQ-BOKU VIBT GmbH and the BOKU Core Facility
for Biomolecular and Cellular Analysis, with help of Irene Schaffner. The research
leading to these results has received funding from the European Union’s Horizon
2020 program (ERC grant agreement no. 742985 to J.F.) and the People Programme (Marie
Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013)
under REA grant agreement no. 291734. S.T. was supported by a European Molecular
Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). O.N.
was supported by the Ministry of Education, Youth and Sports of the Czech Republic
(European Regional Development Fund-Project ‘‘Centre for Experimental Plant Biology’’
no. CZ.02.1.01/0.0/0.0/16_019/0000738). J. Pospısil was supported by European Regional
Development Fund Project ‘‘Centre for Experimental Plant Biology’’\r\n(no. CZ.02.1.01/0.0/0.0/16_019/0000738).
J. Petrasek was supported by EU Operational Programme Prague-Competitiveness (no.
CZ.2.16/3.1.00/21519). "
article_processing_charge: No
article_type: original
author:
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Melinda F
full_name: Abas, Melinda F
id: 3CFB3B1C-F248-11E8-B48F-1D18A9856A87
last_name: Abas
- first_name: Inge
full_name: Verstraeten, Inge
id: 362BF7FE-F248-11E8-B48F-1D18A9856A87
last_name: Verstraeten
orcid: 0000-0001-7241-2328
- first_name: Matous
full_name: Glanc, Matous
id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2
last_name: Glanc
orcid: 0000-0003-0619-7783
- first_name: Gergely
full_name: Molnar, Gergely
id: 34F1AF46-F248-11E8-B48F-1D18A9856A87
last_name: Molnar
- first_name: Jakub
full_name: Hajny, Jakub
id: 4800CC20-F248-11E8-B48F-1D18A9856A87
last_name: Hajny
orcid: 0000-0003-2140-7195
- first_name: Pavel
full_name: Lasák, Pavel
last_name: Lasák
- first_name: Ivan
full_name: Petřík, Ivan
last_name: Petřík
- first_name: Eugenia
full_name: Russinova, Eugenia
last_name: Russinova
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Ondřej
full_name: Novák, Ondřej
last_name: Novák
- first_name: Jiří
full_name: Pospíšil, Jiří
last_name: Pospíšil
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Tan S, Abas MF, Verstraeten I, et al. Salicylic acid targets protein phosphatase
2A to attenuate growth in plants. Current Biology. 2020;30(3):381-395.e8.
doi:10.1016/j.cub.2019.11.058
apa: Tan, S., Abas, M. F., Verstraeten, I., Glanc, M., Molnar, G., Hajny, J., …
Friml, J. (2020). Salicylic acid targets protein phosphatase 2A to attenuate growth
in plants. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2019.11.058
chicago: Tan, Shutang, Melinda F Abas, Inge Verstraeten, Matous Glanc, Gergely Molnar,
Jakub Hajny, Pavel Lasák, et al. “Salicylic Acid Targets Protein Phosphatase 2A
to Attenuate Growth in Plants.” Current Biology. Cell Press, 2020. https://doi.org/10.1016/j.cub.2019.11.058.
ieee: S. Tan et al., “Salicylic acid targets protein phosphatase 2A to attenuate
growth in plants,” Current Biology, vol. 30, no. 3. Cell Press, p. 381–395.e8,
2020.
ista: Tan S, Abas MF, Verstraeten I, Glanc M, Molnar G, Hajny J, Lasák P, Petřík
I, Russinova E, Petrášek J, Novák O, Pospíšil J, Friml J. 2020. Salicylic acid
targets protein phosphatase 2A to attenuate growth in plants. Current Biology.
30(3), 381–395.e8.
mla: Tan, Shutang, et al. “Salicylic Acid Targets Protein Phosphatase 2A to Attenuate
Growth in Plants.” Current Biology, vol. 30, no. 3, Cell Press, 2020, p.
381–395.e8, doi:10.1016/j.cub.2019.11.058.
short: S. Tan, M.F. Abas, I. Verstraeten, M. Glanc, G. Molnar, J. Hajny, P. Lasák,
I. Petřík, E. Russinova, J. Petrášek, O. Novák, J. Pospíšil, J. Friml, Current
Biology 30 (2020) 381–395.e8.
date_created: 2020-02-02T23:01:00Z
date_published: 2020-02-03T00:00:00Z
date_updated: 2024-03-28T23:30:38Z
day: '03'
ddc:
- '580'
department:
- _id: JiFr
- _id: EvBe
doi: 10.1016/j.cub.2019.11.058
ec_funded: 1
external_id:
isi:
- '000511287900018'
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- '31956021'
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month: '02'
oa: 1
oa_version: Published Version
page: 381-395.e8
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: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 256FEF10-B435-11E9-9278-68D0E5697425
grant_number: 723-2015
name: Long Term Fellowship
publication: Current Biology
publication_identifier:
issn:
- '09609822'
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
record:
- id: '8822'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Salicylic acid targets protein phosphatase 2A to attenuate growth 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 30
year: '2020'
...
---
_id: '7500'
abstract:
- lang: eng
text: "Plant survival depends on vascular tissues, which originate in a self‐organizing
manner as strands of cells co‐directionally transporting the plant hormone auxin.
The latter phenomenon (also known as auxin canalization) is classically hypothesized
to be regulated by auxin itself via the effect of this hormone on the polarity
of its own intercellular transport. Correlative observations supported this concept,
but molecular insights remain limited.\r\nIn the current study, we established
an experimental system based on the model Arabidopsis thaliana, which exhibits
auxin transport channels and formation of vasculature strands in response to local
auxin application.\r\nOur methodology permits the genetic analysis of auxin canalization
under controllable experimental conditions. By utilizing this opportunity, we
confirmed the dependence of auxin canalization on a PIN‐dependent auxin transport
and nuclear, TIR1/AFB‐mediated auxin signaling. We also show that leaf venation
and auxin‐mediated PIN repolarization in the root require TIR1/AFB signaling.\r\nFurther
studies based on this experimental system are likely to yield better understanding
of the mechanisms underlying auxin transport polarization in other developmental
contexts."
acknowledgement: We thank Mark Estelle, José M. Alonso and the Arabidopsis Stock Centre
for providing seeds. We acknowledge the core facility CELLIM of CEITEC supported
by the MEYS CR (LM2015062 Czech‐BioImaging) and Plant Sciences Core Facility of
CEITEC Masaryk University for help in generating essential data. This project received
funding from the European Research Council (ERC) under the European Union's Horizon
2020 research and innovation program (grant agreement no. 742985) and the Czech
Science Foundation GAČR (GA13‐40637S and GA18‐26981S) to JF. JH is the recipient
of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science
and Technology. The authors declare no competing interests.
article_processing_charge: No
article_type: original
author:
- first_name: E
full_name: Mazur, E
last_name: Mazur
- first_name: Ivan
full_name: Kulik, Ivan
id: F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB
last_name: Kulik
- first_name: Jakub
full_name: Hajny, Jakub
id: 4800CC20-F248-11E8-B48F-1D18A9856A87
last_name: Hajny
orcid: 0000-0003-2140-7195
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Mazur E, Kulik I, Hajny J, Friml J. Auxin canalization and vascular tissue
formation by TIR1/AFB-mediated auxin signaling in arabidopsis. New Phytologist.
2020;226(5):1375-1383. doi:10.1111/nph.16446
apa: Mazur, E., Kulik, I., Hajny, J., & Friml, J. (2020). Auxin canalization
and vascular tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis.
New Phytologist. Wiley. https://doi.org/10.1111/nph.16446
chicago: Mazur, E, Ivan Kulik, Jakub Hajny, and Jiří Friml. “Auxin Canalization
and Vascular Tissue Formation by TIR1/AFB-Mediated Auxin Signaling in Arabidopsis.”
New Phytologist. Wiley, 2020. https://doi.org/10.1111/nph.16446.
ieee: E. Mazur, I. Kulik, J. Hajny, and J. Friml, “Auxin canalization and vascular
tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis,” New
Phytologist, vol. 226, no. 5. Wiley, pp. 1375–1383, 2020.
ista: Mazur E, Kulik I, Hajny J, Friml J. 2020. Auxin canalization and vascular
tissue formation by TIR1/AFB-mediated auxin signaling in arabidopsis. New Phytologist.
226(5), 1375–1383.
mla: Mazur, E., et al. “Auxin Canalization and Vascular Tissue Formation by TIR1/AFB-Mediated
Auxin Signaling in Arabidopsis.” New Phytologist, vol. 226, no. 5, Wiley,
2020, pp. 1375–83, doi:10.1111/nph.16446.
short: E. Mazur, I. Kulik, J. Hajny, J. Friml, New Phytologist 226 (2020) 1375–1383.
date_created: 2020-02-18T10:03:47Z
date_published: 2020-06-01T00:00:00Z
date_updated: 2024-03-28T23:30:38Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1111/nph.16446
ec_funded: 1
external_id:
isi:
- '000514939700001'
pmid:
- '31971254'
file:
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creator: dernst
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file_date_updated: 2020-11-20T09:32:10Z
has_accepted_license: '1'
intvolume: ' 226'
isi: 1
issue: '5'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1375-1383
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: 2699E3D2-B435-11E9-9278-68D0E5697425
grant_number: '25239'
name: Cell surface receptor complexes for PIN polarity and auxin-mediated development
publication: New Phytologist
publication_identifier:
eissn:
- 1469-8137
issn:
- 0028-646x
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '8822'
relation: dissertation_contains
status: public
status: public
title: Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin
signaling in arabidopsis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 226
year: '2020'
...
---
_id: '8822'
abstract:
- lang: eng
text: "Self-organization is a hallmark of plant development manifested e.g. by intricate
leaf vein patterns, flexible formation of vasculature during organogenesis or
its regeneration following wounding. Spontaneously arising channels transporting
the phytohormone auxin, created by coordinated polar localizations of PIN-FORMED
1 (PIN1) auxin exporter, provide positional cues for these as well as other plant
patterning processes. To find regulators acting downstream of auxin and the TIR1/AFB
auxin signaling pathway essential for PIN1 coordinated polarization during auxin
canalization, we performed microarray experiments. Besides the known components
of general PIN polarity maintenance, such as PID and PIP5K kinases, we identified
and characterized a new regulator of auxin canalization, the transcription factor
WRKY DNA-BINDING PROTEIN 23 (WRKY23).\r\nNext, we designed a subsequent microarray
experiment to further uncover other molecular players, downstream of auxin-TIR1/AFB-WRKY23
involved in the regulation of auxin-mediated PIN repolarization. We identified
a novel and crucial part of the molecular machinery underlying auxin canalization.
The auxin-regulated malectin-type receptor-like kinase CAMEL and the associated
leucine-rich repeat receptor-like kinase CANAR target and directly phosphorylate
PIN auxin transporters. camel and canar mutants are impaired in PIN1 subcellular
trafficking and auxin-mediated repolarization leading to defects in auxin transport,
ultimately to leaf venation and vasculature regeneration defects. Our results
describe the CAMEL-CANAR receptor complex, which is required for auxin feed-back
on its own transport and thus for coordinated tissue polarization during auxin
canalization."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Jakub
full_name: Hajny, Jakub
id: 4800CC20-F248-11E8-B48F-1D18A9856A87
last_name: Hajny
orcid: 0000-0003-2140-7195
citation:
ama: Hajny J. Identification and characterization of the molecular machinery of
auxin-dependent canalization during vasculature formation and regeneration. 2020.
doi:10.15479/AT:ISTA:8822
apa: Hajny, J. (2020). Identification and characterization of the molecular machinery
of auxin-dependent canalization during vasculature formation and regeneration.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8822
chicago: Hajny, Jakub. “Identification and Characterization of the Molecular Machinery
of Auxin-Dependent Canalization during Vasculature Formation and Regeneration.”
Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8822.
ieee: J. Hajny, “Identification and characterization of the molecular machinery
of auxin-dependent canalization during vasculature formation and regeneration,”
Institute of Science and Technology Austria, 2020.
ista: Hajny J. 2020. Identification and characterization of the molecular machinery
of auxin-dependent canalization during vasculature formation and regeneration.
Institute of Science and Technology Austria.
mla: Hajny, Jakub. Identification and Characterization of the Molecular Machinery
of Auxin-Dependent Canalization during Vasculature Formation and Regeneration.
Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8822.
short: J. Hajny, Identification and Characterization of the Molecular Machinery
of Auxin-Dependent Canalization during Vasculature Formation and Regeneration,
Institute of Science and Technology Austria, 2020.
date_created: 2020-12-01T12:38:18Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2023-09-19T10:39:33Z
day: '01'
ddc:
- '580'
degree_awarded: PhD
department:
- _id: JiFr
doi: 10.15479/AT:ISTA:8822
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checksum: 210a9675af5e4c78b0b56d920ac82866
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: jhajny
date_created: 2020-12-04T07:27:52Z
date_updated: 2021-07-16T22:30:03Z
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file_name: Jakub Hajný IST Austria final_JH.docx
file_size: 91279806
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language:
- iso: eng
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oa: 1
oa_version: Published Version
page: '249'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7427'
relation: part_of_dissertation
status: public
- id: '6260'
relation: part_of_dissertation
status: public
- id: '7500'
relation: part_of_dissertation
status: public
- id: '191'
relation: part_of_dissertation
status: public
- id: '449'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: Identification and characterization of the molecular machinery of auxin-dependent
canalization during vasculature formation and regeneration
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8350'
abstract:
- lang: eng
text: "Cytoplasm is a gel-like crowded environment composed of tens of thousands
of macromolecules, organelles, cytoskeletal networks and cytosol. The structure
of the cytoplasm is thought to be 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 is very restricted, an
effect that is further amplified by clustering and anchoring of molecules. Despite
the jammed nature of the cytoplasm at the microscopic scale, large-scale reorganization
of cytoplasm is essential for important cellular functions, such as nuclear positioning
and cell division. How such mesoscale reorganization of the cytoplasm is achieved,
especially for very large cells such as oocytes or syncytial tissues that can
span hundreds of micrometers in size, has only begun to be understood.\r\nIn this
thesis, I focus on the recent advances in elucidating the molecular, cellular
and biophysical principles underlying cytoplasmic organization across different
scales, structures and species. First, I outline which of these principles have
been identified by reductionist approaches, such as in vitro reconstitution assays,
where boundary conditions and components can be modulated at ease. I then describe
how the theoretical and experimental framework established in these reduced systems
have been applied to their more complex in vivo counterparts, in particular oocytes
and embryonic syncytial structures, and discuss how such complex biological systems
can initiate symmetry breaking and establish patterning.\r\nSpecifically, I examine
an example of large-scale reorganizations taking place in zebrafish embryos, where
extensive cytoplasmic streaming leads to the segregation of cytoplasm from yolk
granules along the animal-vegetal axis of the embryo. Using biophysical experimentation
and theory, I investigate the forces underlying this process, to show that this
process does not rely on cortical actin reorganization, as previously thought,
but instead on a cell-cycle-dependent bulk actin polymerization wave traveling
from the animal to the vegetal pole of the embryo. This wave functions in segregation
by both pulling cytoplasm animally and pushing yolk granules vegetally. Cytoplasm
pulling is mediated by bulk actin network flows exerting friction forces on the
cytoplasm, while yolk granule pushing is achieved by a mechanism closely resembling
actin comet formation on yolk granules. This study defines a novel role of bulk
actin polymerization waves in embryo polarization via cytoplasmic segregation.
Lastly, I describe the cytoplasmic reorganizations taking place during zebrafish
oocyte maturation, where the initial segregation of the cytoplasm and yolk granules
occurs. Here, I demonstrate a previously uncharacterized wave of microtubule aster
formation, traveling the oocyte along the animal-vegetal axis. Further research
is required to determine the role of such microtubule structures in cytoplasmic
reorganizations therein.\r\nCollectively, these studies provide further evidence
for the coupling between cell cytoskeleton and cell cycle machinery, which can
underlie a core self-organizing mechanism for orchestrating large-scale reorganizations
in a cell-cycle-tunable manner, where the modulations of the force-generating
machinery and cytoplasmic mechanics can be harbored to fulfill cellular functions."
acknowledged_ssus:
- _id: PreCl
- _id: Bio
- _id: EM-Fac
acknowledgement: "I would have had no fish and hence no results without our wonderful
fish facility crew, Verena Mayer, Eva Schlegl, Andreas Mlak and Matthias Nowak.
Special thanks to Verena for being always happy to help and dealing with our chaotic
schedules in the lab. Danke auch, Verena, für deine Geduld, mit mir auf Deutsch
zu sprechen. Das hat mir sehr geholfen.\r\nSpecial thanks to the Bioimaging and
EM facilities at IST Austria for supporting us every day. Very special thanks would
go to Robert Hauschild for his continuous support on data analysis and also to Jack
Merrin for designing and building microfabricated chambers for the project and for
the various discussions on making zebrafish extracts."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Shayan
full_name: Shamipour, Shayan
id: 40B34FE2-F248-11E8-B48F-1D18A9856A87
last_name: Shamipour
citation:
ama: Shamipour S. Bulk actin dynamics drive phase segregation in zebrafish oocytes
. 2020. doi:10.15479/AT:ISTA:8350
apa: Shamipour, S. (2020). Bulk actin dynamics drive phase segregation in zebrafish
oocytes . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8350
chicago: Shamipour, Shayan. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish
Oocytes .” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8350.
ieee: S. Shamipour, “Bulk actin dynamics drive phase segregation in zebrafish oocytes
,” Institute of Science and Technology Austria, 2020.
ista: Shamipour S. 2020. Bulk actin dynamics drive phase segregation in zebrafish
oocytes . Institute of Science and Technology Austria.
mla: Shamipour, Shayan. Bulk Actin Dynamics Drive Phase Segregation in Zebrafish
Oocytes . Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8350.
short: S. Shamipour, Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes
, Institute of Science and Technology Austria, 2020.
date_created: 2020-09-09T11:12:10Z
date_published: 2020-09-09T00:00:00Z
date_updated: 2023-09-27T14:16:45Z
day: '09'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: BjHo
- _id: CaHe
doi: 10.15479/AT:ISTA:8350
file:
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content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: sshamip
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date_updated: 2021-09-11T22:30:05Z
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file_size: 65194814
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creator: sshamip
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month: '09'
oa: 1
oa_version: None
page: '107'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '661'
relation: part_of_dissertation
status: public
- id: '6508'
relation: part_of_dissertation
status: public
- id: '7001'
relation: part_of_dissertation
status: public
- id: '735'
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
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
title: 'Bulk actin dynamics drive phase segregation in zebrafish oocytes '
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2020'
...
---
_id: '8569'
abstract:
- lang: eng
text: Concerted radial migration of newly born cortical projection neurons, from
their birthplace to their final target lamina, is a key step in the assembly of
the cerebral cortex. The cellular and molecular mechanisms regulating the specific
sequential steps of radial neuronal migration in vivo are however still unclear,
let alone the effects and interactions with the extracellular environment. In
any in vivo context, cells will always be exposed to a complex extracellular environment
consisting of (1) secreted factors acting as potential signaling cues, (2) the
extracellular matrix, and (3) other cells providing cell–cell interaction through
receptors and/or direct physical stimuli. Most studies so far have described and
focused mainly on intrinsic cell-autonomous gene functions in neuronal migration
but there is accumulating evidence that non-cell-autonomous-, local-, systemic-,
and/or whole tissue-wide effects substantially contribute to the regulation of
radial neuronal migration. These non-cell-autonomous effects may differentially
affect cortical neuron migration in distinct cellular environments. However, the
cellular and molecular natures of such non-cell-autonomous mechanisms are mostly
unknown. Furthermore, physical forces due to collective migration and/or community
effects (i.e., interactions with surrounding cells) may play important roles in
neocortical projection neuron migration. In this concise review, we first outline
distinct models of non-cell-autonomous interactions of cortical projection neurons
along their radial migration trajectory during development. We then summarize
experimental assays and platforms that can be utilized to visualize and potentially
probe non-cell-autonomous mechanisms. Lastly, we define key questions to address
in the future.
acknowledgement: AH was a recipient of a DOC Fellowship (24812) of the Austrian Academy
of Sciences. This work also received support from IST Austria institutional funds;
the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework
Programme (FP7/2007–2013) under REA Grant Agreement No. 618444 to SH.
article_number: '574382'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Andi H
full_name: Hansen, Andi H
id: 38853E16-F248-11E8-B48F-1D18A9856A87
last_name: Hansen
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Hansen AH, Hippenmeyer S. Non-cell-autonomous mechanisms in radial projection
neuron migration in the developing cerebral cortex. Frontiers in Cell and Developmental
Biology. 2020;8(9). doi:10.3389/fcell.2020.574382
apa: Hansen, A. H., & Hippenmeyer, S. (2020). Non-cell-autonomous mechanisms
in radial projection neuron migration in the developing cerebral cortex. Frontiers
in Cell and Developmental Biology. Frontiers. https://doi.org/10.3389/fcell.2020.574382
chicago: Hansen, Andi H, and Simon Hippenmeyer. “Non-Cell-Autonomous Mechanisms
in Radial Projection Neuron Migration in the Developing Cerebral Cortex.” Frontiers
in Cell and Developmental Biology. Frontiers, 2020. https://doi.org/10.3389/fcell.2020.574382.
ieee: A. H. Hansen and S. Hippenmeyer, “Non-cell-autonomous mechanisms in radial
projection neuron migration in the developing cerebral cortex,” Frontiers in
Cell and Developmental Biology, vol. 8, no. 9. Frontiers, 2020.
ista: Hansen AH, Hippenmeyer S. 2020. Non-cell-autonomous mechanisms in radial projection
neuron migration in the developing cerebral cortex. Frontiers in Cell and Developmental
Biology. 8(9), 574382.
mla: Hansen, Andi H., and Simon Hippenmeyer. “Non-Cell-Autonomous Mechanisms in
Radial Projection Neuron Migration in the Developing Cerebral Cortex.” Frontiers
in Cell and Developmental Biology, vol. 8, no. 9, 574382, Frontiers, 2020,
doi:10.3389/fcell.2020.574382.
short: A.H. Hansen, S. Hippenmeyer, Frontiers in Cell and Developmental Biology
8 (2020).
date_created: 2020-09-26T06:11:07Z
date_published: 2020-09-25T00:00:00Z
date_updated: 2024-03-28T23:30:41Z
day: '25'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.3389/fcell.2020.574382
ec_funded: 1
external_id:
isi:
- '000577915900001'
pmid:
- '33102480'
file:
- access_level: open_access
checksum: 01f731824194c94c81a5da360d997073
content_type: application/pdf
creator: dernst
date_created: 2020-09-28T13:11:17Z
date_updated: 2020-09-28T13:11:17Z
file_id: '8584'
file_name: 2020_Frontiers_Hansen.pdf
file_size: 5527139
relation: main_file
success: 1
file_date_updated: 2020-09-28T13:11:17Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2625A13E-B435-11E9-9278-68D0E5697425
grant_number: '24812'
name: Molecular Mechanisms of Radial Neuronal Migration
- _id: 25D61E48-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618444'
name: Molecular Mechanisms of Cerebral Cortex Development
publication: Frontiers in Cell and Developmental Biology
publication_identifier:
issn:
- 2296-634X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
related_material:
record:
- id: '9962'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Non-cell-autonomous mechanisms in radial projection neuron migration in the
developing cerebral cortex
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: 8
year: '2020'
...
---
_id: '7815'
abstract:
- lang: eng
text: Beginning from a limited pool of progenitors, the mammalian cerebral cortex
forms highly organized functional neural circuits. However, the underlying cellular
and molecular mechanisms regulating lineage transitions of neural stem cells (NSCs)
and eventual production of neurons and glia in the developing neuroepithelium
remains unclear. Methods to trace NSC division patterns and map the lineage of
clonally related cells have advanced dramatically. However, many contemporary
lineage tracing techniques suffer from the lack of cellular resolution of progeny
cell fate, which is essential for deciphering progenitor cell division patterns.
Presented is a protocol using mosaic analysis with double markers (MADM) to perform
in vivo clonal analysis. MADM concomitantly manipulates individual progenitor
cells and visualizes precise division patterns and lineage progression at unprecedented
single cell resolution. MADM-based interchromosomal recombination events during
the G2-X phase of mitosis, together with temporally inducible CreERT2, provide
exact information on the birth dates of clones and their division patterns. Thus,
MADM lineage tracing provides unprecedented qualitative and quantitative optical
readouts of the proliferation mode of stem cell progenitors at the single cell
level. MADM also allows for examination of the mechanisms and functional requirements
of candidate genes in NSC lineage progression. This method is unique in that comparative
analysis of control and mutant subclones can be performed in the same tissue environment
in vivo. Here, the protocol is described in detail, and experimental paradigms
to employ MADM for clonal analysis and lineage tracing in the developing cerebral
cortex are demonstrated. Importantly, this protocol can be adapted to perform
MADM clonal analysis in any murine stem cell niche, as long as the CreERT2 driver
is present.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: PreCl
article_number: e61147
article_processing_charge: No
article_type: original
author:
- first_name: Robert J
full_name: Beattie, Robert J
id: 2E26DF60-F248-11E8-B48F-1D18A9856A87
last_name: Beattie
orcid: 0000-0002-8483-8753
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Nicole
full_name: Amberg, Nicole
id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87
last_name: Amberg
orcid: 0000-0002-3183-8207
- first_name: Giselle T
full_name: Cheung, Giselle T
id: 471195F6-F248-11E8-B48F-1D18A9856A87
last_name: Cheung
orcid: 0000-0001-8457-2572
- first_name: Ximena
full_name: Contreras, Ximena
id: 475990FE-F248-11E8-B48F-1D18A9856A87
last_name: Contreras
- first_name: Andi H
full_name: Hansen, Andi H
id: 38853E16-F248-11E8-B48F-1D18A9856A87
last_name: Hansen
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Beattie RJ, Streicher C, Amberg N, et al. Lineage tracing and clonal analysis
in developing cerebral cortex using mosaic analysis with double markers (MADM).
Journal of Visual Experiments. 2020;(159). doi:10.3791/61147
apa: Beattie, R. J., Streicher, C., Amberg, N., Cheung, G. T., Contreras, X., Hansen,
A. H., & Hippenmeyer, S. (2020). Lineage tracing and clonal analysis in developing
cerebral cortex using mosaic analysis with double markers (MADM). Journal of
Visual Experiments. MyJove Corporation. https://doi.org/10.3791/61147
chicago: Beattie, Robert J, Carmen Streicher, Nicole Amberg, Giselle T Cheung, Ximena
Contreras, Andi H Hansen, and Simon Hippenmeyer. “Lineage Tracing and Clonal Analysis
in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM).”
Journal of Visual Experiments. MyJove Corporation, 2020. https://doi.org/10.3791/61147.
ieee: R. J. Beattie et al., “Lineage tracing and clonal analysis in developing
cerebral cortex using mosaic analysis with double markers (MADM),” Journal
of Visual Experiments, no. 159. MyJove Corporation, 2020.
ista: Beattie RJ, Streicher C, Amberg N, Cheung GT, Contreras X, Hansen AH, Hippenmeyer
S. 2020. Lineage tracing and clonal analysis in developing cerebral cortex using
mosaic analysis with double markers (MADM). Journal of Visual Experiments. (159),
e61147.
mla: Beattie, Robert J., et al. “Lineage Tracing and Clonal Analysis in Developing
Cerebral Cortex Using Mosaic Analysis with Double Markers (MADM).” Journal
of Visual Experiments, no. 159, e61147, MyJove Corporation, 2020, doi:10.3791/61147.
short: R.J. Beattie, C. Streicher, N. Amberg, G.T. Cheung, X. Contreras, A.H. Hansen,
S. Hippenmeyer, Journal of Visual Experiments (2020).
date_created: 2020-05-11T08:31:20Z
date_published: 2020-05-08T00:00:00Z
date_updated: 2024-03-28T23:30:42Z
day: '08'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.3791/61147
ec_funded: 1
external_id:
isi:
- '000546406600043'
file:
- access_level: open_access
checksum: 3154ea7f90b9fb45e084cd1c2770597d
content_type: application/pdf
creator: rbeattie
date_created: 2020-05-11T08:28:38Z
date_updated: 2020-07-14T12:48:03Z
file_id: '7816'
file_name: jove-protocol-61147-lineage-tracing-clonal-analysis-developing-cerebral-cortex-using.pdf
file_size: 1352186
relation: main_file
file_date_updated: 2020-07-14T12:48:03Z
has_accepted_license: '1'
isi: 1
issue: '159'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 264E56E2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02416
name: Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex
- _id: 268F8446-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: T0101031
name: Role of Eed in neural stem cell lineage progression
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 2625A13E-B435-11E9-9278-68D0E5697425
grant_number: '24812'
name: Molecular Mechanisms of Radial Neuronal Migration
- _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: Journal of Visual Experiments
publication_identifier:
issn:
- 1940-087X
publication_status: published
publisher: MyJove Corporation
quality_controlled: '1'
related_material:
record:
- id: '7902'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: Lineage tracing and clonal analysis in developing cerebral cortex using mosaic
analysis with double markers (MADM)
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
year: '2020'
...
---
_id: '7902'
abstract:
- lang: eng
text: "Mosaic genetic analysis has been widely used in different model organisms
such as the fruit fly to study gene-function in a cell-autonomous or tissue-specific
fashion. More recently, and less easily conducted, mosaic genetic analysis in
mice has also been enabled with the ambition to shed light on human gene function
and disease. These genetic tools are of particular interest, but not restricted
to, the study of the brain. Notably, the MADM technology offers a genetic approach
in mice to visualize and concomitantly manipulate small subsets of genetically
defined cells at a clonal level and single cell resolution. MADM-based analysis
has already advanced the study of genetic mechanisms regulating brain development
and is expected that further MADM-based analysis of genetic alterations will continue
to reveal important insights on the fundamental principles of development and
disease to potentially assist in the development of new therapies or treatments.\r\nIn
summary, this work completed and characterized the necessary genome-wide genetic
tools to perform MADM-based analysis at single cell level of the vast majority
of mouse genes in virtually any cell type and provided a protocol to perform lineage
tracing using the novel MADM resource. Importantly, this work also explored and
revealed novel aspects of biologically relevant events in an in vivo context,
such as the chromosome-specific bias of chromatid sister segregation pattern,
the generation of cell-type diversity in the cerebral cortex and in the cerebellum
and finally, the relevance of the interplay between the cell-autonomous gene function
and cell-non-autonomous (community) effects in radial glial progenitor lineage
progression.\r\nThis work provides a foundation and opens the door to further
elucidating the molecular mechanisms underlying neuronal diversity and astrocyte
generation."
acknowledged_ssus:
- _id: PreCl
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Ximena
full_name: Contreras, Ximena
id: 475990FE-F248-11E8-B48F-1D18A9856A87
last_name: Contreras
citation:
ama: Contreras X. Genetic dissection of neural development in health and disease
at single cell resolution. 2020. doi:10.15479/AT:ISTA:7902
apa: Contreras, X. (2020). Genetic dissection of neural development in health
and disease at single cell resolution. Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:7902
chicago: Contreras, Ximena. “Genetic Dissection of Neural Development in Health
and Disease at Single Cell Resolution.” Institute of Science and Technology Austria,
2020. https://doi.org/10.15479/AT:ISTA:7902.
ieee: X. Contreras, “Genetic dissection of neural development in health and disease
at single cell resolution,” Institute of Science and Technology Austria, 2020.
ista: Contreras X. 2020. Genetic dissection of neural development in health and
disease at single cell resolution. Institute of Science and Technology Austria.
mla: Contreras, Ximena. Genetic Dissection of Neural Development in Health and
Disease at Single Cell Resolution. Institute of Science and Technology Austria,
2020, doi:10.15479/AT:ISTA:7902.
short: X. Contreras, Genetic Dissection of Neural Development in Health and Disease
at Single Cell Resolution, Institute of Science and Technology Austria, 2020.
date_created: 2020-05-29T08:27:32Z
date_published: 2020-06-05T00:00:00Z
date_updated: 2023-10-18T08:45:16Z
day: '05'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: SiHi
doi: 10.15479/AT:ISTA:7902
ec_funded: 1
file:
- access_level: closed
checksum: 43c172bf006c95b65992d473c7240d13
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: xcontreras
date_created: 2020-06-05T08:18:08Z
date_updated: 2021-06-07T22:30:03Z
embargo_to: open_access
file_id: '7927'
file_name: PhDThesis_Contreras.docx
file_size: 53134142
relation: source_file
- access_level: open_access
checksum: addfed9128271be05cae3608e03a6ec0
content_type: application/pdf
creator: xcontreras
date_created: 2020-06-05T08:18:07Z
date_updated: 2021-06-07T22:30:03Z
embargo: 2021-06-06
file_id: '7928'
file_name: PhDThesis_Contreras.pdf
file_size: 35117191
relation: main_file
file_date_updated: 2021-06-07T22:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '214'
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_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6830'
relation: dissertation_contains
status: public
- id: '28'
relation: dissertation_contains
status: public
- id: '7815'
relation: dissertation_contains
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: Genetic dissection of neural development in health and disease at single cell
resolution
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8190'
article_number: e202007029
article_processing_charge: No
article_type: letter_note
author:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Anna
full_name: Huttenlocher, Anna
last_name: Huttenlocher
citation:
ama: 'Sixt MK, Huttenlocher A. Zena Werb (1945-2020): Cell biology in context. The
Journal of Cell Biology. 2020;219(8). doi:10.1083/jcb.202007029'
apa: 'Sixt, M. K., & Huttenlocher, A. (2020). Zena Werb (1945-2020): Cell biology
in context. The Journal of Cell Biology. Rockefeller University Press.
https://doi.org/10.1083/jcb.202007029'
chicago: 'Sixt, Michael K, and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology
in Context.” The Journal of Cell Biology. Rockefeller University Press,
2020. https://doi.org/10.1083/jcb.202007029.'
ieee: 'M. K. Sixt and A. Huttenlocher, “Zena Werb (1945-2020): Cell biology in context,”
The Journal of Cell Biology, vol. 219, no. 8. Rockefeller University Press,
2020.'
ista: 'Sixt MK, Huttenlocher A. 2020. Zena Werb (1945-2020): Cell biology in context.
The Journal of Cell Biology. 219(8), e202007029.'
mla: 'Sixt, Michael K., and Anna Huttenlocher. “Zena Werb (1945-2020): Cell Biology
in Context.” The Journal of Cell Biology, vol. 219, no. 8, e202007029,
Rockefeller University Press, 2020, doi:10.1083/jcb.202007029.'
short: M.K. Sixt, A. Huttenlocher, The Journal of Cell Biology 219 (2020).
date_created: 2020-08-02T22:00:57Z
date_published: 2020-07-22T00:00:00Z
date_updated: 2023-10-17T10:04:49Z
day: '22'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1083/jcb.202007029
external_id:
isi:
- '000573631000004'
file:
- access_level: open_access
checksum: 30016d778d266b8e17d01094917873b8
content_type: application/pdf
creator: dernst
date_created: 2020-08-04T13:11:52Z
date_updated: 2021-02-02T23:30:03Z
embargo: 2021-02-01
file_id: '8200'
file_name: 2020_JCB_Sixt.pdf
file_size: 830725
relation: main_file
file_date_updated: 2021-02-02T23:30:03Z
has_accepted_license: '1'
intvolume: ' 219'
isi: 1
issue: '8'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '07'
oa: 1
oa_version: Published Version
publication: The Journal of Cell Biology
publication_identifier:
eissn:
- 1540-8140
publication_status: published
publisher: Rockefeller University Press
scopus_import: '1'
status: public
title: 'Zena Werb (1945-2020): Cell biology in context'
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 219
year: '2020'
...
---
_id: '8986'
abstract:
- lang: eng
text: 'Flowering plants display the highest diversity among plant species and have
notably shaped terrestrial landscapes. Nonetheless, the evolutionary origin of
their unprecedented morphological complexity remains largely an enigma. Here,
we show that the coevolution of cis-regulatory and coding regions of PIN-FORMED
(PIN) auxin transporters confined their expression to certain cell types and directed
their subcellular localization to particular cell sides, which together enabled
dynamic auxin gradients across tissues critical to the complex architecture of
flowering plants. Extensive intraspecies and interspecies genetic complementation
experiments with PINs from green alga up to flowering plant lineages showed that
PIN genes underwent three subsequent, critical evolutionary innovations and thus
acquired a triple function to regulate the development of three essential components
of the flowering plant Arabidopsis: shoot/root, inflorescence, and floral organ.
Our work highlights the critical role of functional innovations within the PIN
gene family as essential prerequisites for the origin of flowering plants.'
acknowledgement: 'We thank C.Löhne (Botanic Gardens, University of Bonn) for providing
us with A. trichopoda. We would like to thank T.Han, A.Mally (IST, Austria), and
C.Hartinger (University of Oxford) for constructive comment and careful reading.
Funding: The research leading to these results has received funding from the European
Union’s Horizon 2020 Research and Innovation Programme (ERC grant agreement number
742985), Austrian Science Fund (FWF, grant number I 3630-B25), DOC Fellowship of
the Austrian Academy of Sciences, and IST Fellow program. '
article_number: eabc8895
article_processing_charge: No
article_type: original
author:
- first_name: Yuzhou
full_name: Zhang, Yuzhou
id: 3B6137F2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0003-2627-6956
- 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: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: Xixi
full_name: Zhang, Xixi
id: 61A66458-47E9-11EA-85BA-8AEAAF14E49A
last_name: Zhang
orcid: 0000-0001-7048-4627
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Zhang Y, Rodriguez Solovey L, Li L, Zhang X, Friml J. Functional innovations
of PIN auxin transporters mark crucial evolutionary transitions during rise of
flowering plants. Science Advances. 2020;6(50). doi:10.1126/sciadv.abc8895
apa: Zhang, Y., Rodriguez Solovey, L., Li, L., Zhang, X., & Friml, J. (2020).
Functional innovations of PIN auxin transporters mark crucial evolutionary transitions
during rise of flowering plants. Science Advances. AAAS. https://doi.org/10.1126/sciadv.abc8895
chicago: Zhang, Yuzhou, Lesia Rodriguez Solovey, Lanxin Li, Xixi Zhang, and Jiří
Friml. “Functional Innovations of PIN Auxin Transporters Mark Crucial Evolutionary
Transitions during Rise of Flowering Plants.” Science Advances. AAAS, 2020.
https://doi.org/10.1126/sciadv.abc8895.
ieee: Y. Zhang, L. Rodriguez Solovey, L. Li, X. Zhang, and J. Friml, “Functional
innovations of PIN auxin transporters mark crucial evolutionary transitions during
rise of flowering plants,” Science Advances, vol. 6, no. 50. AAAS, 2020.
ista: Zhang Y, Rodriguez Solovey L, Li L, Zhang X, Friml J. 2020. Functional innovations
of PIN auxin transporters mark crucial evolutionary transitions during rise of
flowering plants. Science Advances. 6(50), eabc8895.
mla: Zhang, Yuzhou, et al. “Functional Innovations of PIN Auxin Transporters Mark
Crucial Evolutionary Transitions during Rise of Flowering Plants.” Science
Advances, vol. 6, no. 50, eabc8895, AAAS, 2020, doi:10.1126/sciadv.abc8895.
short: Y. Zhang, L. Rodriguez Solovey, L. Li, X. Zhang, J. Friml, Science Advances
6 (2020).
date_created: 2021-01-03T23:01:23Z
date_published: 2020-12-11T00:00:00Z
date_updated: 2024-03-28T23:30:44Z
day: '11'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1126/sciadv.abc8895
ec_funded: 1
external_id:
isi:
- '000599903600014'
pmid:
- '33310852'
file:
- access_level: open_access
checksum: 5ac2500b191c08ef6dab5327f40ff663
content_type: application/pdf
creator: dernst
date_created: 2021-01-07T12:44:33Z
date_updated: 2021-01-07T12:44:33Z
file_id: '8994'
file_name: 2020_ScienceAdvances_Zhang.pdf
file_size: 10578145
relation: main_file
success: 1
file_date_updated: 2021-01-07T12:44:33Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: '50'
language:
- iso: eng
month: '12'
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: Science Advances
publication_identifier:
eissn:
- 2375-2548
publication_status: published
publisher: AAAS
quality_controlled: '1'
related_material:
record:
- id: '10083'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Functional innovations of PIN auxin transporters mark crucial evolutionary
transitions during rise of flowering plants
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 6
year: '2020'
...
---
_id: '8283'
abstract:
- lang: eng
text: 'Drought and salt stress are the main environmental cues affecting the survival,
development, distribution, and yield of crops worldwide. MYB transcription factors
play a crucial role in plants’ biological processes, but the function of pineapple
MYB genes is still obscure. In this study, one of the pineapple MYB transcription
factors, AcoMYB4, was isolated and characterized. The results showed that AcoMYB4
is localized in the cell nucleus, and its expression is induced by low temperature,
drought, salt stress, and hormonal stimulation, especially by abscisic acid (ABA).
Overexpression of AcoMYB4 in rice and Arabidopsis enhanced plant sensitivity to
osmotic stress; it led to an increase in the number stomata on leaf surfaces and
lower germination rate under salt and drought stress. Furthermore, in AcoMYB4
OE lines, the membrane oxidation index, free proline, and soluble sugar contents
were decreased. In contrast, electrolyte leakage and malondialdehyde (MDA) content
increased significantly due to membrane injury, indicating higher sensitivity
to drought and salinity stresses. Besides the above, both the expression level
and activities of several antioxidant enzymes were decreased, indicating lower
antioxidant activity in AcoMYB4 transgenic plants. Moreover, under osmotic stress,
overexpression of AcoMYB4 inhibited ABA biosynthesis through a decrease in the
transcription of genes responsible for ABA synthesis (ABA1 and ABA2) and ABA signal
transduction factor ABI5. These results suggest that AcoMYB4 negatively regulates
osmotic stress by attenuating cellular ABA biosynthesis and signal transduction
pathways. '
acknowledgement: 'We would like to thank the reviewers for their helpful comments
on the original manuscript. '
article_number: '5272'
article_processing_charge: No
article_type: original
author:
- first_name: Huihuang
full_name: Chen, Huihuang
last_name: Chen
- first_name: Linyi
full_name: Lai, Linyi
last_name: Lai
- first_name: Lanxin
full_name: Li, Lanxin
id: 367EF8FA-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0002-5607-272X
- first_name: Liping
full_name: Liu, Liping
last_name: Liu
- first_name: Bello Hassan
full_name: Jakada, Bello Hassan
last_name: Jakada
- first_name: Youmei
full_name: Huang, Youmei
last_name: Huang
- first_name: Qing
full_name: He, Qing
last_name: He
- first_name: Mengnan
full_name: Chai, Mengnan
last_name: Chai
- first_name: Xiaoping
full_name: Niu, Xiaoping
last_name: Niu
- first_name: Yuan
full_name: Qin, Yuan
last_name: Qin
citation:
ama: Chen H, Lai L, Li L, et al. AcoMYB4, an Ananas comosus L. MYB transcription
factor, functions in osmotic stress through negative regulation of ABA signaling.
International Journal of Molecular Sciences. 2020;21(16). doi:10.3390/ijms21165727
apa: Chen, H., Lai, L., Li, L., Liu, L., Jakada, B. H., Huang, Y., … Qin, Y. (2020).
AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic stress
through negative regulation of ABA signaling. International Journal of Molecular
Sciences. MDPI. https://doi.org/10.3390/ijms21165727
chicago: Chen, Huihuang, Linyi Lai, Lanxin Li, Liping Liu, Bello Hassan Jakada,
Youmei Huang, Qing He, Mengnan Chai, Xiaoping Niu, and Yuan Qin. “AcoMYB4, an
Ananas Comosus L. MYB Transcription Factor, Functions in Osmotic Stress through
Negative Regulation of ABA Signaling.” International Journal of Molecular Sciences.
MDPI, 2020. https://doi.org/10.3390/ijms21165727.
ieee: H. Chen et al., “AcoMYB4, an Ananas comosus L. MYB transcription factor,
functions in osmotic stress through negative regulation of ABA signaling,” International
Journal of Molecular Sciences, vol. 21, no. 16. MDPI, 2020.
ista: Chen H, Lai L, Li L, Liu L, Jakada BH, Huang Y, He Q, Chai M, Niu X, Qin Y.
2020. AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic
stress through negative regulation of ABA signaling. International Journal of
Molecular Sciences. 21(16), 5272.
mla: Chen, Huihuang, et al. “AcoMYB4, an Ananas Comosus L. MYB Transcription Factor,
Functions in Osmotic Stress through Negative Regulation of ABA Signaling.” International
Journal of Molecular Sciences, vol. 21, no. 16, 5272, MDPI, 2020, doi:10.3390/ijms21165727.
short: H. Chen, L. Lai, L. Li, L. Liu, B.H. Jakada, Y. Huang, Q. He, M. Chai, X.
Niu, Y. Qin, International Journal of Molecular Sciences 21 (2020).
date_created: 2020-08-24T06:24:03Z
date_published: 2020-08-10T00:00:00Z
date_updated: 2024-03-28T23:30:44Z
day: '10'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.3390/ijms21165727
external_id:
isi:
- '000565090300001'
pmid:
- '32785037'
file:
- access_level: open_access
checksum: 03b039244e6ae80580385fd9f577e2b2
content_type: application/pdf
creator: cziletti
date_created: 2020-08-25T09:53:50Z
date_updated: 2020-08-25T09:53:50Z
file_id: '8292'
file_name: 2020_IntMolecSciences_Chen.pdf
file_size: 5718755
relation: main_file
success: 1
file_date_updated: 2020-08-25T09:53:50Z
has_accepted_license: '1'
intvolume: ' 21'
isi: 1
issue: '16'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: International Journal of Molecular Sciences
publication_identifier:
eissn:
- '14220067'
issn:
- '16616596'
publication_status: published
publisher: MDPI
quality_controlled: '1'
related_material:
record:
- id: '10083'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: AcoMYB4, an Ananas comosus L. MYB transcription factor, functions in osmotic
stress through negative regulation of ABA signaling
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 21
year: '2020'
...
---
_id: '8139'
abstract:
- lang: eng
text: 'Clathrin-mediated endocytosis (CME) is a crucial cellular process implicated
in many aspects of plant growth, development, intra- and inter-cellular signaling,
nutrient uptake and pathogen defense. Despite these significant roles, little
is known about the precise molecular details of how it functions in planta. In
order to facilitate the direct quantitative study of plant CME, here we review
current routinely used methods and present refined, standardized quantitative
imaging protocols which allow the detailed characterization of CME at multiple
scales in plant tissues. These include: (i) an efficient electron microscopy protocol
for the imaging of Arabidopsis CME vesicles in situ, thus providing a method for
the detailed characterization of the ultra-structure of clathrin-coated vesicles;
(ii) a detailed protocol and analysis for quantitative live-cell fluorescence
microscopy to precisely examine the temporal interplay of endocytosis components
during single CME events; (iii) a semi-automated analysis to allow the quantitative
characterization of global internalization of cargos in whole plant tissues; and
(iv) an overview and validation of useful genetic and pharmacological tools to
interrogate the molecular mechanisms and function of CME in intact plant samples.'
acknowledged_ssus:
- _id: EM-Fac
- _id: Bio
acknowledgement: "This paper is dedicated to the memory of Christien Merrifield. He
pioneered quantitative\r\nimaging approaches in mammalian CME and his mentorship
inspired the development of all\r\nthe analysis methods presented here. His joy
in research, pure scientific curiosity and\r\nmicroscopy excellence remain a constant
inspiration. We thank Daniel Van Damme for gifting\r\nus the CLC2-GFP x TPLATE-TagRFP
plants used in this manuscript. We further thank the\r\nScientific Service Units
at IST Austria; specifically, the Electron Microscopy Facility for\r\ntechnical
assistance (in particular Vanessa Zheden) and the BioImaging Facility BioImaging\r\nFacility
for access to equipment. "
article_number: jcs248062
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: 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: Madhumitha
full_name: Narasimhan, Madhumitha
id: 44BF24D0-F248-11E8-B48F-1D18A9856A87
last_name: Narasimhan
orcid: 0000-0002-8600-0671
- first_name: G
full_name: Vert, G
last_name: Vert
- first_name: SY
full_name: Bednarek, SY
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, Gnyliukh N, Kaufmann W, et al. Experimental toolbox for quantitative
evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. Journal
of Cell Science. 2020;133(15). doi:10.1242/jcs.248062
apa: Johnson, A. J., Gnyliukh, N., Kaufmann, W., Narasimhan, M., Vert, G., Bednarek,
S., & Friml, J. (2020). Experimental toolbox for quantitative evaluation of
clathrin-mediated endocytosis in the plant model Arabidopsis. Journal of Cell
Science. The Company of Biologists. https://doi.org/10.1242/jcs.248062
chicago: Johnson, Alexander J, Nataliia Gnyliukh, Walter Kaufmann, Madhumitha Narasimhan,
G Vert, SY Bednarek, and Jiří Friml. “Experimental Toolbox for Quantitative Evaluation
of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” Journal of
Cell Science. The Company of Biologists, 2020. https://doi.org/10.1242/jcs.248062.
ieee: A. J. Johnson et al., “Experimental toolbox for quantitative evaluation
of clathrin-mediated endocytosis in the plant model Arabidopsis,” Journal of
Cell Science, vol. 133, no. 15. The Company of Biologists, 2020.
ista: Johnson AJ, Gnyliukh N, Kaufmann W, Narasimhan M, Vert G, Bednarek S, Friml
J. 2020. Experimental toolbox for quantitative evaluation of clathrin-mediated
endocytosis in the plant model Arabidopsis. Journal of Cell Science. 133(15),
jcs248062.
mla: Johnson, Alexander J., et al. “Experimental Toolbox for Quantitative Evaluation
of Clathrin-Mediated Endocytosis in the Plant Model Arabidopsis.” Journal of
Cell Science, vol. 133, no. 15, jcs248062, The Company of Biologists, 2020,
doi:10.1242/jcs.248062.
short: A.J. Johnson, N. Gnyliukh, W. Kaufmann, M. Narasimhan, G. Vert, S. Bednarek,
J. Friml, Journal of Cell Science 133 (2020).
date_created: 2020-07-21T08:58:19Z
date_published: 2020-08-06T00:00:00Z
date_updated: 2023-12-01T13:51:07Z
day: '06'
ddc:
- '575'
department:
- _id: JiFr
- _id: EM-Fac
doi: 10.1242/jcs.248062
ec_funded: 1
external_id:
isi:
- '000561047900021'
pmid:
- '32616560'
file:
- access_level: open_access
checksum: 2d11f79a0b4e0a380fb002b933da331a
content_type: application/pdf
creator: ajohnson
date_created: 2020-11-26T17:12:51Z
date_updated: 2021-08-08T22:30:03Z
embargo: 2021-08-07
file_id: '8815'
file_name: 2020 - Johnson - JSC - plant CME toolbox.pdf
file_size: 15150403
relation: main_file
file_date_updated: 2021-08-08T22:30:03Z
has_accepted_license: '1'
intvolume: ' 133'
isi: 1
issue: '15'
language:
- iso: eng
month: '08'
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
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Journal of Cell Science
publication_identifier:
eissn:
- 1477-9137
issn:
- 0021-9533
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
related_material:
record:
- id: '14510'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis
in the plant model Arabidopsis
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 133
year: '2020'
...
---
_id: '9160'
abstract:
- lang: eng
text: Auxin is a key hormonal regulator, that governs plant growth and development
in concert with other hormonal pathways. The unique feature of auxin is its polar,
cell-to-cell transport that leads to the formation of local auxin maxima and gradients,
which coordinate initiation and patterning of plant organs. The molecular machinery
mediating polar auxin transport is one of the important points of interaction
with other hormones. Multiple hormonal pathways converge at the regulation of
auxin transport and form a regulatory network that integrates various developmental
and environmental inputs to steer plant development. In this review, we discuss
recent advances in understanding the mechanisms that underlie regulation of polar
auxin transport by multiple hormonal pathways. Specifically, we focus on the post-translational
mechanisms that contribute to fine-tuning of the abundance and polarity of auxin
transporters at the plasma membrane and thereby enable rapid modification of the
auxin flow to coordinate plant growth and development.
acknowledgement: H.S. is the recipient of a DOC Fellowship of the Austrian Academy
of Sciences at the Institute of Science and Technology, Austria. J.C.M. is the recipient
of an EMBO Long-Term Fellowship (ALTF number 710-2016). We would like to thank Jiri
Friml and Carina Baskett for critical reading of the manuscript and Shutang Tan
and Maciek Adamowski for helpful discussions. No conflict of interest declared.
article_number: '100048'
article_processing_charge: No
article_type: original
author:
- first_name: Hana
full_name: Semeradova, Hana
id: 42FE702E-F248-11E8-B48F-1D18A9856A87
last_name: Semeradova
- 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: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: 'Semerádová H, Montesinos López JC, Benková E. All roads lead to auxin: Post-translational
regulation of auxin transport by multiple hormonal pathways. Plant Communications.
2020;1(3). doi:10.1016/j.xplc.2020.100048'
apa: 'Semerádová, H., Montesinos López, J. C., & Benková, E. (2020). All roads
lead to auxin: Post-translational regulation of auxin transport by multiple hormonal
pathways. Plant Communications. Elsevier. https://doi.org/10.1016/j.xplc.2020.100048'
chicago: 'Semerádová, Hana, Juan C Montesinos López, and Eva Benková. “All Roads
Lead to Auxin: Post-Translational Regulation of Auxin Transport by Multiple Hormonal
Pathways.” Plant Communications. Elsevier, 2020. https://doi.org/10.1016/j.xplc.2020.100048.'
ieee: 'H. Semerádová, J. C. Montesinos López, and E. Benková, “All roads lead to
auxin: Post-translational regulation of auxin transport by multiple hormonal pathways,”
Plant Communications, vol. 1, no. 3. Elsevier, 2020.'
ista: 'Semerádová H, Montesinos López JC, Benková E. 2020. All roads lead to auxin:
Post-translational regulation of auxin transport by multiple hormonal pathways.
Plant Communications. 1(3), 100048.'
mla: 'Semerádová, Hana, et al. “All Roads Lead to Auxin: Post-Translational Regulation
of Auxin Transport by Multiple Hormonal Pathways.” Plant Communications,
vol. 1, no. 3, 100048, Elsevier, 2020, doi:10.1016/j.xplc.2020.100048.'
short: H. Semerádová, J.C. Montesinos López, E. Benková, Plant Communications 1
(2020).
date_created: 2021-02-18T10:18:43Z
date_published: 2020-05-11T00:00:00Z
date_updated: 2024-03-28T23:30:47Z
day: '11'
ddc:
- '580'
department:
- _id: EvBe
doi: 10.1016/j.xplc.2020.100048
external_id:
isi:
- '000654052800010'
pmid:
- '33367243'
file:
- access_level: open_access
checksum: 785b266d82a94b007cf40dbbe7c4847e
content_type: application/pdf
creator: dernst
date_created: 2021-02-18T10:23:59Z
date_updated: 2021-02-18T10:23:59Z
file_id: '9161'
file_name: 2020_PlantComm_Semeradova.pdf
file_size: 840289
relation: main_file
success: 1
file_date_updated: 2021-02-18T10:23:59Z
has_accepted_license: '1'
intvolume: ' 1'
isi: 1
issue: '3'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 261821BC-B435-11E9-9278-68D0E5697425
grant_number: '24746'
name: Molecular mechanisms of the cytokinin regulated endomembrane trafficking to
coordinate plant organogenesis.
- _id: 253E54C8-B435-11E9-9278-68D0E5697425
grant_number: ALTF710-2016
name: Molecular mechanism of auxindriven formative divisions delineating lateral
root organogenesis in plants
publication: Plant Communications
publication_identifier:
issn:
- 2590-3462
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '10135'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'All roads lead to auxin: Post-translational regulation of auxin transport
by multiple hormonal pathways'
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 1
year: '2020'
...
---
_id: '10877'
abstract:
- lang: eng
text: 'This report presents the results of a friendly competition for formal verification
of continuous and hybrid systems with piecewise constant dynamics. The friendly
competition took place as part of the workshop Applied Verification for Continuous
and Hybrid Systems (ARCH) in 2019. In this third edition, six tools have been
applied to solve five different benchmark problems in the category for piecewise
constant dynamics: BACH, Lyse, Hy- COMP, PHAVer/SX, PHAVerLite, and VeriSiMPL.
Compared to last year, a new tool has participated (HyCOMP) and PHAVerLite has
replaced PHAVer-lite. The result is a snap- shot of the current landscape of tools
and the types of benchmarks they are particularly suited for. Due to the diversity
of problems, we are not ranking tools, yet the presented results probably provide
the most complete assessment of tools for the safety verification of continuous
and hybrid systems with piecewise constant dynamics up to this date.'
acknowledgement: "The authors gratefully acknowledge \fnancial support by the European
Commission project\r\nUnCoVerCPS under grant number 643921. Lei Bu is supported
by the National Natural Science\r\nFoundation of China (No.61572249)."
alternative_title:
- EPiC Series in Computing
article_processing_charge: No
author:
- first_name: Goran
full_name: Frehse, Goran
last_name: Frehse
- first_name: Alessandro
full_name: Abate, Alessandro
last_name: Abate
- first_name: Dieky
full_name: Adzkiya, Dieky
last_name: Adzkiya
- first_name: Anna
full_name: Becchi, Anna
last_name: Becchi
- first_name: Lei
full_name: Bu, Lei
last_name: Bu
- first_name: Alessandro
full_name: Cimatti, Alessandro
last_name: Cimatti
- first_name: Mirco
full_name: Giacobbe, Mirco
id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
last_name: Giacobbe
orcid: 0000-0001-8180-0904
- first_name: Alberto
full_name: Griggio, Alberto
last_name: Griggio
- first_name: Sergio
full_name: Mover, Sergio
last_name: Mover
- first_name: Muhammad Syifa'ul
full_name: Mufid, Muhammad Syifa'ul
last_name: Mufid
- first_name: Idriss
full_name: Riouak, Idriss
last_name: Riouak
- first_name: Stefano
full_name: Tonetta, Stefano
last_name: Tonetta
- first_name: Enea
full_name: Zaffanella, Enea
last_name: Zaffanella
citation:
ama: 'Frehse G, Abate A, Adzkiya D, et al. ARCH-COMP19 Category Report: Hybrid systems
with piecewise constant dynamics. In: Frehse G, Althoff M, eds. ARCH19. 6th
International Workshop on Applied Verification of Continuous and Hybrid Systems.
Vol 61. EasyChair; 2019:1-13. doi:10.29007/rjwn'
apa: 'Frehse, G., Abate, A., Adzkiya, D., Becchi, A., Bu, L., Cimatti, A., … Zaffanella,
E. (2019). ARCH-COMP19 Category Report: Hybrid systems with piecewise constant
dynamics. In G. Frehse & M. Althoff (Eds.), ARCH19. 6th International Workshop
on Applied Verification of Continuous and Hybrid Systems (Vol. 61, pp. 1–13).
Montreal, Canada: EasyChair. https://doi.org/10.29007/rjwn'
chicago: 'Frehse, Goran, Alessandro Abate, Dieky Adzkiya, Anna Becchi, Lei Bu, Alessandro
Cimatti, Mirco Giacobbe, et al. “ARCH-COMP19 Category Report: Hybrid Systems with
Piecewise Constant Dynamics.” In ARCH19. 6th International Workshop on Applied
Verification of Continuous and Hybrid Systems, edited by Goran Frehse and
Matthias Althoff, 61:1–13. EasyChair, 2019. https://doi.org/10.29007/rjwn.'
ieee: 'G. Frehse et al., “ARCH-COMP19 Category Report: Hybrid systems with
piecewise constant dynamics,” in ARCH19. 6th International Workshop on Applied
Verification of Continuous and Hybrid Systems, Montreal, Canada, 2019, vol.
61, pp. 1–13.'
ista: 'Frehse G, Abate A, Adzkiya D, Becchi A, Bu L, Cimatti A, Giacobbe M, Griggio
A, Mover S, Mufid MS, Riouak I, Tonetta S, Zaffanella E. 2019. ARCH-COMP19 Category
Report: Hybrid systems with piecewise constant dynamics. ARCH19. 6th International
Workshop on Applied Verification of Continuous and Hybrid Systems. ARCH: International
Workshop on Applied Verification on Continuous and Hybrid Systems, EPiC Series
in Computing, vol. 61, 1–13.'
mla: 'Frehse, Goran, et al. “ARCH-COMP19 Category Report: Hybrid Systems with Piecewise
Constant Dynamics.” ARCH19. 6th International Workshop on Applied Verification
of Continuous and Hybrid Systems, edited by Goran Frehse and Matthias Althoff,
vol. 61, EasyChair, 2019, pp. 1–13, doi:10.29007/rjwn.'
short: G. Frehse, A. Abate, D. Adzkiya, A. Becchi, L. Bu, A. Cimatti, M. Giacobbe,
A. Griggio, S. Mover, M.S. Mufid, I. Riouak, S. Tonetta, E. Zaffanella, in:, G.
Frehse, M. Althoff (Eds.), ARCH19. 6th International Workshop on Applied Verification
of Continuous and Hybrid Systems, EasyChair, 2019, pp. 1–13.
conference:
end_date: 2019-04-15
location: Montreal, Canada
name: 'ARCH: International Workshop on Applied Verification on Continuous and Hybrid
Systems'
start_date: 2019-04-15
date_created: 2022-03-18T12:29:23Z
date_published: 2019-05-25T00:00:00Z
date_updated: 2022-05-17T07:09:47Z
day: '25'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.29007/rjwn
editor:
- first_name: Goran
full_name: Frehse, Goran
last_name: Frehse
- first_name: Matthias
full_name: Althoff, Matthias
last_name: Althoff
file:
- access_level: open_access
checksum: 4b92e333db7b4e2349501a804dfede69
content_type: application/pdf
creator: dernst
date_created: 2022-05-17T06:55:49Z
date_updated: 2022-05-17T06:55:49Z
file_id: '11391'
file_name: 2019_EPiCs_Frehse.pdf
file_size: 346415
relation: main_file
success: 1
file_date_updated: 2022-05-17T06:55:49Z
has_accepted_license: '1'
intvolume: ' 61'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1-13
publication: ARCH19. 6th International Workshop on Applied Verification of Continuous
and Hybrid Systems
publication_identifier:
issn:
- 2398-7340
publication_status: published
publisher: EasyChair
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'ARCH-COMP19 Category Report: Hybrid systems with piecewise constant dynamics'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 61
year: '2019'
...
---
_id: '441'
article_processing_charge: No
article_type: original
author:
- first_name: Nikita
full_name: Kalinin, Nikita
last_name: Kalinin
- first_name: Mikhail
full_name: Shkolnikov, Mikhail
id: 35084A62-F248-11E8-B48F-1D18A9856A87
last_name: Shkolnikov
orcid: 0000-0002-4310-178X
citation:
ama: Kalinin N, Shkolnikov M. Tropical formulae for summation over a part of SL(2,Z).
European Journal of Mathematics. 2019;5(3):909–928. doi:10.1007/s40879-018-0218-0
apa: Kalinin, N., & Shkolnikov, M. (2019). Tropical formulae for summation over
a part of SL(2,Z). European Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s40879-018-0218-0
chicago: Kalinin, Nikita, and Mikhail Shkolnikov. “Tropical Formulae for Summation
over a Part of SL(2,Z).” European Journal of Mathematics. Springer Nature,
2019. https://doi.org/10.1007/s40879-018-0218-0.
ieee: N. Kalinin and M. Shkolnikov, “Tropical formulae for summation over a part
of SL(2,Z),” European Journal of Mathematics, vol. 5, no. 3. Springer Nature,
pp. 909–928, 2019.
ista: Kalinin N, Shkolnikov M. 2019. Tropical formulae for summation over a part
of SL(2,Z). European Journal of Mathematics. 5(3), 909–928.
mla: Kalinin, Nikita, and Mikhail Shkolnikov. “Tropical Formulae for Summation over
a Part of SL(2,Z).” European Journal of Mathematics, vol. 5, no. 3, Springer
Nature, 2019, pp. 909–928, doi:10.1007/s40879-018-0218-0.
short: N. Kalinin, M. Shkolnikov, European Journal of Mathematics 5 (2019) 909–928.
date_created: 2018-12-11T11:46:29Z
date_published: 2019-09-15T00:00:00Z
date_updated: 2021-01-12T07:56:46Z
day: '15'
department:
- _id: TaHa
doi: 10.1007/s40879-018-0218-0
ec_funded: 1
external_id:
arxiv:
- '1711.02089'
intvolume: ' 5'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1711.02089
month: '09'
oa: 1
oa_version: Preprint
page: 909–928
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: European Journal of Mathematics
publication_identifier:
eissn:
- 2199-6768
issn:
- 2199-675X
publication_status: published
publisher: Springer Nature
publist_id: '7382'
quality_controlled: '1'
scopus_import: 1
status: public
title: Tropical formulae for summation over a part of SL(2,Z)
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 5
year: '2019'
...
---
_id: '5793'
abstract:
- lang: eng
text: The transcription coactivator, Yes-associated protein (YAP), which is a nuclear
effector of the Hippo signaling pathway, has been shown to be a mechano-transducer.
By using mutant fish and human 3D spheroids, we have recently demonstrated that
YAP is also a mechano-effector. YAP functions in three-dimensional (3D) morphogenesis
of organ and global body shape by controlling actomyosin-mediated tissue tension.
In this chapter, we present a platform that links the findings in fish embryos
with human cells. The protocols for analyzing tissue tension-mediated global body
shape/organ morphogenesis in vivo and ex vivo using medaka fish embryos and in
vitro using human cell spheroids represent useful tools for unraveling the molecular
mechanisms by which YAP functions in regulating global body/organ morphogenesis.
alternative_title:
- MIMB
author:
- first_name: Yoichi
full_name: Asaoka, Yoichi
last_name: Asaoka
- first_name: Hitoshi
full_name: Morita, Hitoshi
last_name: Morita
- first_name: Hiroko
full_name: Furumoto, Hiroko
last_name: Furumoto
- 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
- first_name: Makoto
full_name: Furutani-Seiki, Makoto
last_name: Furutani-Seiki
citation:
ama: 'Asaoka Y, Morita H, Furumoto H, Heisenberg C-PJ, Furutani-Seiki M. Studying
YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In: Hergovich
A, ed. The Hippo Pathway. Vol 1893. Methods in Molecular Biology. Springer;
2019:167-181. doi:10.1007/978-1-4939-8910-2_14'
apa: Asaoka, Y., Morita, H., Furumoto, H., Heisenberg, C.-P. J., & Furutani-Seiki,
M. (2019). Studying YAP-mediated 3D morphogenesis using fish embryos and human
spheroids. In A. Hergovich (Ed.), The hippo pathway (Vol. 1893, pp. 167–181).
Springer. https://doi.org/10.1007/978-1-4939-8910-2_14
chicago: Asaoka, Yoichi, Hitoshi Morita, Hiroko Furumoto, Carl-Philipp J Heisenberg,
and Makoto Furutani-Seiki. “Studying YAP-Mediated 3D Morphogenesis Using Fish
Embryos and Human Spheroids.” In The Hippo Pathway, edited by Alexander
Hergovich, 1893:167–81. Methods in Molecular Biology. Springer, 2019. https://doi.org/10.1007/978-1-4939-8910-2_14.
ieee: Y. Asaoka, H. Morita, H. Furumoto, C.-P. J. Heisenberg, and M. Furutani-Seiki,
“Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids,”
in The hippo pathway, vol. 1893, A. Hergovich, Ed. Springer, 2019, pp.
167–181.
ista: 'Asaoka Y, Morita H, Furumoto H, Heisenberg C-PJ, Furutani-Seiki M. 2019.Studying
YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In: The
hippo pathway. MIMB, vol. 1893, 167–181.'
mla: Asaoka, Yoichi, et al. “Studying YAP-Mediated 3D Morphogenesis Using Fish Embryos
and Human Spheroids.” The Hippo Pathway, edited by Alexander Hergovich,
vol. 1893, Springer, 2019, pp. 167–81, doi:10.1007/978-1-4939-8910-2_14.
short: Y. Asaoka, H. Morita, H. Furumoto, C.-P.J. Heisenberg, M. Furutani-Seiki,
in:, A. Hergovich (Ed.), The Hippo Pathway, Springer, 2019, pp. 167–181.
date_created: 2019-01-06T22:59:11Z
date_published: 2019-01-01T00:00:00Z
date_updated: 2021-01-12T08:03:30Z
day: '01'
department:
- _id: CaHe
doi: 10.1007/978-1-4939-8910-2_14
editor:
- first_name: Alexander
full_name: Hergovich, Alexander
last_name: Hergovich
intvolume: ' 1893'
language:
- iso: eng
month: '01'
oa_version: None
page: 167-181
publication: The hippo pathway
publication_identifier:
isbn:
- 978-1-4939-8909-6
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: 1
series_title: Methods in Molecular Biology
status: public
title: Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1893
year: '2019'
...
---
_id: '5887'
abstract:
- lang: eng
text: 'Cryptographic security is usually defined as a guarantee that holds except
when a bad event with negligible probability occurs, and nothing is guaranteed
in that bad case. However, in settings where such failure can happen with substantial
probability, one needs to provide guarantees even for the bad case. A typical
example is where a (possibly weak) password is used instead of a secure cryptographic
key to protect a session, the bad event being that the adversary correctly guesses
the password. In a situation with multiple such sessions, a per-session guarantee
is desired: any session for which the password has not been guessed remains secure,
independently of whether other sessions have been compromised. A new formalism
for stating such gracefully degrading security guarantees is introduced and applied
to analyze the examples of password-based message authentication and password-based
encryption. While a natural per-message guarantee is achieved for authentication,
the situation of password-based encryption is more delicate: a per-session confidentiality
guarantee only holds against attackers for which the distribution of password-guessing
effort over the sessions is known in advance. In contrast, for more general attackers
without such a restriction, a strong, composable notion of security cannot be
achieved.'
article_processing_charge: No
article_type: original
author:
- first_name: Gregory
full_name: Demay, Gregory
last_name: Demay
- first_name: Peter
full_name: Gazi, Peter
id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87
last_name: Gazi
- first_name: Ueli
full_name: Maurer, Ueli
last_name: Maurer
- first_name: Bjorn
full_name: Tackmann, Bjorn
last_name: Tackmann
citation:
ama: 'Demay G, Gazi P, Maurer U, Tackmann B. Per-session security: Password-based
cryptography revisited. Journal of Computer Security. 2019;27(1):75-111.
doi:10.3233/JCS-181131'
apa: 'Demay, G., Gazi, P., Maurer, U., & Tackmann, B. (2019). Per-session security:
Password-based cryptography revisited. Journal of Computer Security. IOS
Press. https://doi.org/10.3233/JCS-181131'
chicago: 'Demay, Gregory, Peter Gazi, Ueli Maurer, and Bjorn Tackmann. “Per-Session
Security: Password-Based Cryptography Revisited.” Journal of Computer Security.
IOS Press, 2019. https://doi.org/10.3233/JCS-181131.'
ieee: 'G. Demay, P. Gazi, U. Maurer, and B. Tackmann, “Per-session security: Password-based
cryptography revisited,” Journal of Computer Security, vol. 27, no. 1.
IOS Press, pp. 75–111, 2019.'
ista: 'Demay G, Gazi P, Maurer U, Tackmann B. 2019. Per-session security: Password-based
cryptography revisited. Journal of Computer Security. 27(1), 75–111.'
mla: 'Demay, Gregory, et al. “Per-Session Security: Password-Based Cryptography
Revisited.” Journal of Computer Security, vol. 27, no. 1, IOS Press, 2019,
pp. 75–111, doi:10.3233/JCS-181131.'
short: G. Demay, P. Gazi, U. Maurer, B. Tackmann, Journal of Computer Security 27
(2019) 75–111.
date_created: 2019-01-27T22:59:10Z
date_published: 2019-01-01T00:00:00Z
date_updated: 2021-01-12T08:05:08Z
day: '1'
department:
- _id: KrPi
doi: 10.3233/JCS-181131
ec_funded: 1
intvolume: ' 27'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2016/166
month: '01'
oa: 1
oa_version: Preprint
page: 75-111
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication: Journal of Computer Security
publication_identifier:
issn:
- 0926227X
publication_status: published
publisher: IOS Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Per-session security: Password-based cryptography revisited'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2019'
...
---
_id: '6515'
abstract:
- lang: eng
text: We give non-degeneracy criteria for Riemannian simplices based on simplices
in spaces of constant sectional curvature. It extends previous work on Riemannian
simplices, where we developed Riemannian simplices with respect to Euclidean reference
simplices. The criteria we give in this article are in terms of quality measures
for spaces of constant curvature that we develop here. We see that simplices in
spaces that have nearly constant curvature, are already non-degenerate under very
weak quality demands. This is of importance because it allows for sampling of
Riemannian manifolds based on anisotropy of the manifold and not (absolute) curvature.
author:
- first_name: Ramsay
full_name: Dyer, Ramsay
last_name: Dyer
- first_name: Gert
full_name: Vegter, Gert
last_name: Vegter
- first_name: Mathijs
full_name: Wintraecken, Mathijs
id: 307CFBC8-F248-11E8-B48F-1D18A9856A87
last_name: Wintraecken
orcid: 0000-0002-7472-2220
citation:
ama: Dyer R, Vegter G, Wintraecken M. Simplices modelled on spaces of constant curvature.
Journal of Computational Geometry . 2019;10(1):223–256. doi:10.20382/jocg.v10i1a9
apa: Dyer, R., Vegter, G., & Wintraecken, M. (2019). Simplices modelled on spaces
of constant curvature. Journal of Computational Geometry . Carleton University.
https://doi.org/10.20382/jocg.v10i1a9
chicago: Dyer, Ramsay, Gert Vegter, and Mathijs Wintraecken. “Simplices Modelled
on Spaces of Constant Curvature.” Journal of Computational Geometry . Carleton
University, 2019. https://doi.org/10.20382/jocg.v10i1a9.
ieee: R. Dyer, G. Vegter, and M. Wintraecken, “Simplices modelled on spaces of constant
curvature,” Journal of Computational Geometry , vol. 10, no. 1. Carleton
University, pp. 223–256, 2019.
ista: Dyer R, Vegter G, Wintraecken M. 2019. Simplices modelled on spaces of constant
curvature. Journal of Computational Geometry . 10(1), 223–256.
mla: Dyer, Ramsay, et al. “Simplices Modelled on Spaces of Constant Curvature.”
Journal of Computational Geometry , vol. 10, no. 1, Carleton University,
2019, pp. 223–256, doi:10.20382/jocg.v10i1a9.
short: R. Dyer, G. Vegter, M. Wintraecken, Journal of Computational Geometry 10
(2019) 223–256.
date_created: 2019-06-03T09:35:33Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2021-01-12T08:07:50Z
day: '01'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.20382/jocg.v10i1a9
ec_funded: 1
file:
- access_level: open_access
checksum: 57b4df2f16a74eb499734ec8ee240178
content_type: application/pdf
creator: mwintrae
date_created: 2019-06-03T09:30:01Z
date_updated: 2020-07-14T12:47:32Z
file_id: '6516'
file_name: mainJournalFinal.pdf
file_size: 2170882
relation: main_file
file_date_updated: 2020-07-14T12:47:32Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 223–256
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: 'Journal of Computational Geometry '
publication_identifier:
issn:
- 1920-180X
publication_status: published
publisher: Carleton University
quality_controlled: '1'
scopus_import: 1
status: public
title: Simplices modelled on spaces of constant curvature
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: 10
year: '2019'
...
---
_id: '6528'
abstract:
- lang: eng
text: We construct a verifiable delay function (VDF) by showing how the Rivest-Shamir-Wagner
time-lock puzzle can be made publicly verifiable. Concretely, we give a statistically
sound public-coin protocol to prove that a tuple (N,x,T,y) satisfies y=x2T (mod
N) where the prover doesn’t know the factorization of N and its running time is
dominated by solving the puzzle, that is, compute x2T, which is conjectured to
require T sequential squarings. To get a VDF we make this protocol non-interactive
using the Fiat-Shamir heuristic.The motivation for this work comes from the Chia
blockchain design, which uses a VDF as akey ingredient. For typical parameters
(T≤2 40, N= 2048), our proofs are of size around 10K B, verification cost around
three RSA exponentiations and computing the proof is 8000 times faster than solving
the puzzle even without any parallelism.
alternative_title:
- LIPIcs
article_number: '60'
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
citation:
ama: 'Pietrzak KZ. Simple verifiable delay functions. In: 10th Innovations in
Theoretical Computer Science Conference. Vol 124. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik; 2019. doi:10.4230/LIPICS.ITCS.2019.60'
apa: 'Pietrzak, K. Z. (2019). Simple verifiable delay functions. In 10th Innovations
in Theoretical Computer Science Conference (Vol. 124). San Diego, CA, United
States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ITCS.2019.60'
chicago: Pietrzak, Krzysztof Z. “Simple Verifiable Delay Functions.” In 10th
Innovations in Theoretical Computer Science Conference, Vol. 124. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.ITCS.2019.60.
ieee: K. Z. Pietrzak, “Simple verifiable delay functions,” in 10th Innovations
in Theoretical Computer Science Conference, San Diego, CA, United States,
2019, vol. 124.
ista: 'Pietrzak KZ. 2019. Simple verifiable delay functions. 10th Innovations in
Theoretical Computer Science Conference. ITCS 2019: Innovations in Theoretical
Computer Science, LIPIcs, vol. 124, 60.'
mla: Pietrzak, Krzysztof Z. “Simple Verifiable Delay Functions.” 10th Innovations
in Theoretical Computer Science Conference, vol. 124, 60, Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.ITCS.2019.60.
short: K.Z. Pietrzak, in:, 10th Innovations in Theoretical Computer Science Conference,
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.
conference:
end_date: 2019-01-12
location: San Diego, CA, United States
name: 'ITCS 2019: Innovations in Theoretical Computer Science'
start_date: 2019-01-10
date_created: 2019-06-06T14:12:36Z
date_published: 2019-01-10T00:00:00Z
date_updated: 2021-01-12T08:07:53Z
day: '10'
ddc:
- '000'
department:
- _id: KrPi
doi: 10.4230/LIPICS.ITCS.2019.60
ec_funded: 1
file:
- access_level: open_access
checksum: f0ae1bb161431d9db3dea5ace082bfb5
content_type: application/pdf
creator: dernst
date_created: 2019-06-06T14:22:04Z
date_updated: 2020-07-14T12:47:33Z
file_id: '6529'
file_name: 2019_LIPIcs_Pietrzak.pdf
file_size: 558770
relation: main_file
file_date_updated: 2020-07-14T12:47:33Z
has_accepted_license: '1'
intvolume: ' 124'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2018/627
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication: 10th Innovations in Theoretical Computer Science Conference
publication_identifier:
isbn:
- 978-3-95977-095-8
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: 1
status: public
title: Simple verifiable delay functions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 124
year: '2019'
...
---
_id: '6565'
abstract:
- lang: eng
text: In this paper, we address the problem of synthesizing periodic switching controllers
for stabilizing a family of linear systems. Our broad approach consists of constructing
a finite game graph based on the family of linear systems such that every winning
strategy on the game graph corresponds to a stabilizing switching controller for
the family of linear systems. The construction of a (finite) game graph, the synthesis
of a winning strategy and the extraction of a stabilizing controller are all computationally
feasible. We illustrate our method on an example.
article_number: '8715598'
article_processing_charge: No
author:
- first_name: Atreyee
full_name: Kundu, Atreyee
last_name: Kundu
- first_name: Miriam
full_name: Garcia Soto, Miriam
id: 4B3207F6-F248-11E8-B48F-1D18A9856A87
last_name: Garcia Soto
orcid: 0000−0003−2936−5719
- first_name: Pavithra
full_name: Prabhakar, Pavithra
last_name: Prabhakar
citation:
ama: 'Kundu A, Garcia Soto M, Prabhakar P. Formal synthesis of stabilizing controllers
for periodically controlled linear switched systems. In: 5th Indian Control
Conference Proceedings. IEEE; 2019. doi:10.1109/INDIANCC.2019.8715598'
apa: 'Kundu, A., Garcia Soto, M., & Prabhakar, P. (2019). Formal synthesis of
stabilizing controllers for periodically controlled linear switched systems. In
5th Indian Control Conference Proceedings. Delhi, India: IEEE. https://doi.org/10.1109/INDIANCC.2019.8715598'
chicago: Kundu, Atreyee, Miriam Garcia Soto, and Pavithra Prabhakar. “Formal Synthesis
of Stabilizing Controllers for Periodically Controlled Linear Switched Systems.”
In 5th Indian Control Conference Proceedings. IEEE, 2019. https://doi.org/10.1109/INDIANCC.2019.8715598.
ieee: A. Kundu, M. Garcia Soto, and P. Prabhakar, “Formal synthesis of stabilizing
controllers for periodically controlled linear switched systems,” in 5th Indian
Control Conference Proceedings, Delhi, India, 2019.
ista: Kundu A, Garcia Soto M, Prabhakar P. 2019. Formal synthesis of stabilizing
controllers for periodically controlled linear switched systems. 5th Indian Control
Conference Proceedings. ICC 2019 - Indian Control Conference, 8715598.
mla: Kundu, Atreyee, et al. “Formal Synthesis of Stabilizing Controllers for Periodically
Controlled Linear Switched Systems.” 5th Indian Control Conference Proceedings,
8715598, IEEE, 2019, doi:10.1109/INDIANCC.2019.8715598.
short: A. Kundu, M. Garcia Soto, P. Prabhakar, in:, 5th Indian Control Conference
Proceedings, IEEE, 2019.
conference:
end_date: 2019-01-11
location: Delhi, India
name: ICC 2019 - Indian Control Conference
start_date: 2019-01-09
date_created: 2019-06-17T06:57:33Z
date_published: 2019-05-16T00:00:00Z
date_updated: 2021-01-12T08:08:01Z
day: '16'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1109/INDIANCC.2019.8715598
file:
- access_level: open_access
checksum: d622a91af1e427f6b1e0ba8e18a2b767
content_type: application/pdf
creator: dernst
date_created: 2020-10-21T13:13:49Z
date_updated: 2020-10-21T13:13:49Z
file_id: '8687'
file_name: 2019_ICC_Kundu.pdf
file_size: 396031
relation: main_file
success: 1
file_date_updated: 2020-10-21T13:13:49Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: 5th Indian Control Conference Proceedings
publication_identifier:
isbn:
- 978-153866246-5
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Formal synthesis of stabilizing controllers for periodically controlled linear
switched systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6628'
abstract:
- lang: eng
text: Fejes Tóth [5] and Schneider [9] studied approximations of smooth convex hypersurfaces
in Euclidean space by piecewise flat triangular meshes with a given number
of vertices on the hypersurface that are optimal with respect to Hausdorff distance. They proved that this
Hausdorff distance decreases inversely proportional with m 2/(d−1), where m is the number of vertices and
d is the dimension of Euclidean space. Moreover the pro-portionality constant
can be expressed in terms of the Gaussian curvature, an intrinsic quantity. In
this short note, we prove the extrinsic nature of this constant for manifolds
of sufficiently high codimension. We do so by constructing an family of isometric
embeddings of the flat torus in Euclidean space.
author:
- first_name: Gert
full_name: Vegter, Gert
last_name: Vegter
- first_name: Mathijs
full_name: Wintraecken, Mathijs
id: 307CFBC8-F248-11E8-B48F-1D18A9856A87
last_name: Wintraecken
orcid: 0000-0002-7472-2220
citation:
ama: 'Vegter G, Wintraecken M. The extrinsic nature of the Hausdorff distance of
optimal triangulations of manifolds. In: The 31st Canadian Conference in Computational
Geometry. ; 2019:275-279.'
apa: Vegter, G., & Wintraecken, M. (2019). The extrinsic nature of the Hausdorff
distance of optimal triangulations of manifolds. In The 31st Canadian Conference
in Computational Geometry (pp. 275–279). Edmonton, Canada.
chicago: Vegter, Gert, and Mathijs Wintraecken. “The Extrinsic Nature of the Hausdorff
Distance of Optimal Triangulations of Manifolds.” In The 31st Canadian Conference
in Computational Geometry, 275–79, 2019.
ieee: G. Vegter and M. Wintraecken, “The extrinsic nature of the Hausdorff distance
of optimal triangulations of manifolds,” in The 31st Canadian Conference in
Computational Geometry, Edmonton, Canada, 2019, pp. 275–279.
ista: 'Vegter G, Wintraecken M. 2019. The extrinsic nature of the Hausdorff distance
of optimal triangulations of manifolds. The 31st Canadian Conference in Computational
Geometry. CCCG: Canadian Conference in Computational Geometry, 275–279.'
mla: Vegter, Gert, and Mathijs Wintraecken. “The Extrinsic Nature of the Hausdorff
Distance of Optimal Triangulations of Manifolds.” The 31st Canadian Conference
in Computational Geometry, 2019, pp. 275–79.
short: G. Vegter, M. Wintraecken, in:, The 31st Canadian Conference in Computational
Geometry, 2019, pp. 275–279.
conference:
end_date: 2019-08-10
location: Edmonton, Canada
name: 'CCCG: Canadian Conference in Computational Geometry'
start_date: 2019-08-08
date_created: 2019-07-12T08:34:57Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2021-01-12T08:08:16Z
day: '01'
ddc:
- '004'
department:
- _id: HeEd
ec_funded: 1
file:
- access_level: open_access
checksum: ceabd152cfa55170d57763f9c6c60a53
content_type: application/pdf
creator: mwintrae
date_created: 2019-07-12T08:32:46Z
date_updated: 2020-07-14T12:47:34Z
file_id: '6629'
file_name: IntrinsicExtrinsicCCCG2019.pdf
file_size: 321176
relation: main_file
file_date_updated: 2020-07-14T12:47:34Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 275-279
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: The 31st Canadian Conference in Computational Geometry
publication_status: published
quality_controlled: '1'
scopus_import: 1
status: public
title: The extrinsic nature of the Hausdorff distance of optimal triangulations of
manifolds
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6648'
abstract:
- lang: eng
text: "Various kinds of data are routinely represented as discrete probability distributions.
Examples include text documents summarized by histograms of word occurrences and
images represented as histograms of oriented gradients. Viewing a discrete probability
distribution as a point in the standard simplex of the appropriate dimension,
we can understand collections of such objects in geometric and topological terms.
Importantly, instead of using the standard Euclidean distance, we look into dissimilarity
measures with information-theoretic justification, and we develop the theory\r\nneeded
for applying topological data analysis in this setting. In doing so, we emphasize
constructions that enable the usage of existing computational topology software
in this context."
alternative_title:
- LIPIcs
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Ziga
full_name: Virk, Ziga
last_name: Virk
- first_name: Hubert
full_name: Wagner, Hubert
id: 379CA8B8-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
citation:
ama: 'Edelsbrunner H, Virk Z, Wagner H. Topological data analysis in information
space. In: 35th International Symposium on Computational Geometry. Vol
129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:31:1-31:14. doi:10.4230/LIPICS.SOCG.2019.31'
apa: 'Edelsbrunner, H., Virk, Z., & Wagner, H. (2019). Topological data analysis
in information space. In 35th International Symposium on Computational Geometry
(Vol. 129, p. 31:1-31:14). Portland, OR, United States: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPICS.SOCG.2019.31'
chicago: Edelsbrunner, Herbert, Ziga Virk, and Hubert Wagner. “Topological Data
Analysis in Information Space.” In 35th International Symposium on Computational
Geometry, 129:31:1-31:14. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2019. https://doi.org/10.4230/LIPICS.SOCG.2019.31.
ieee: H. Edelsbrunner, Z. Virk, and H. Wagner, “Topological data analysis in information
space,” in 35th International Symposium on Computational Geometry, Portland,
OR, United States, 2019, vol. 129, p. 31:1-31:14.
ista: 'Edelsbrunner H, Virk Z, Wagner H. 2019. Topological data analysis in information
space. 35th International Symposium on Computational Geometry. SoCG 2019: Symposium
on Computational Geometry, LIPIcs, vol. 129, 31:1-31:14.'
mla: Edelsbrunner, Herbert, et al. “Topological Data Analysis in Information Space.”
35th International Symposium on Computational Geometry, vol. 129, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 31:1-31:14, doi:10.4230/LIPICS.SOCG.2019.31.
short: H. Edelsbrunner, Z. Virk, H. Wagner, in:, 35th International Symposium on
Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019,
p. 31:1-31:14.
conference:
end_date: 2019-06-21
location: Portland, OR, United States
name: 'SoCG 2019: Symposium on Computational Geometry'
start_date: 2019-06-18
date_created: 2019-07-17T10:36:09Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2021-01-12T08:08:23Z
day: '01'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.4230/LIPICS.SOCG.2019.31
external_id:
arxiv:
- '1903.08510'
file:
- access_level: open_access
checksum: 8ec8720730d4c789bf7b06540f1c29f4
content_type: application/pdf
creator: dernst
date_created: 2019-07-24T06:40:01Z
date_updated: 2020-07-14T12:47:35Z
file_id: '6666'
file_name: 2019_LIPICS_Edelsbrunner.pdf
file_size: 1355179
relation: main_file
file_date_updated: 2020-07-14T12:47:35Z
has_accepted_license: '1'
intvolume: ' 129'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 31:1-31:14
project:
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: 35th International Symposium on Computational Geometry
publication_identifier:
isbn:
- '9783959771047'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: 1
status: public
title: Topological data analysis in information 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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 129
year: '2019'
...
---
_id: '6659'
abstract:
- lang: eng
text: Chemical labeling of proteins with synthetic molecular probes offers the possibility
to probe the functions of proteins of interest in living cells. However, the methods
for covalently labeling targeted proteins using complementary peptide tag-probe
pairs are still limited, irrespective of the versatility of such pairs in biological
research. Herein, we report the new CysHis tag-Ni(II) probe pair for the specific
covalent labeling of proteins. A broad-range evaluation of the reactivity profiles
of the probe and the CysHis peptide tag afforded a tag-probe pair with an optimized
and high labeling selectivity and reactivity. In particular, the labeling specificity
of this pair was notably improved compared to the previously reported one. This
pair was successfully utilized for the fluorescence imaging of membrane proteins
on the surfaces of living cells, demonstrating its potential utility in biological
research.
acknowledgement: his work was supported by the Grant-in-Aid for Scientific Research
B (JSPS KAKENHI grant no. JP17H03090 to A. O.); the Scientific Research on Innovative
Areas “Chemistry for Multimolecular Crowding Biosystems” (JSPS KAKENHI grant no.
JP17H06349 to A. O.); and the European Union (European Research Council Advanced
grant no. 694539 and Human Brain Project Ref. 720270 to R. S.). A. O. acknowledges
the financial support of the Takeda Science Foundation.
article_processing_charge: No
article_type: original
author:
- first_name: Naoki
full_name: Zenmyo, Naoki
last_name: Zenmyo
- first_name: Hiroki
full_name: Tokumaru, Hiroki
last_name: Tokumaru
- first_name: Shohei
full_name: Uchinomiya, Shohei
last_name: Uchinomiya
- first_name: Hirokazu
full_name: Fuchida, Hirokazu
last_name: Fuchida
- first_name: Shigekazu
full_name: Tabata, Shigekazu
id: 4427179E-F248-11E8-B48F-1D18A9856A87
last_name: Tabata
- first_name: Itaru
full_name: Hamachi, Itaru
last_name: Hamachi
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Akio
full_name: Ojida, Akio
last_name: Ojida
citation:
ama: Zenmyo N, Tokumaru H, Uchinomiya S, et al. Optimized reaction pair of the CysHis
tag and Ni(II)-NTA probe for highly selective chemical labeling of membrane proteins.
Bulletin of the Chemical Society of Japan. 2019;92(5):995-1000. doi:10.1246/bcsj.20190034
apa: Zenmyo, N., Tokumaru, H., Uchinomiya, S., Fuchida, H., Tabata, S., Hamachi,
I., … Ojida, A. (2019). Optimized reaction pair of the CysHis tag and Ni(II)-NTA
probe for highly selective chemical labeling of membrane proteins. Bulletin
of the Chemical Society of Japan. Bulletin of the Chemical Society of Japan.
https://doi.org/10.1246/bcsj.20190034
chicago: Zenmyo, Naoki, Hiroki Tokumaru, Shohei Uchinomiya, Hirokazu Fuchida, Shigekazu
Tabata, Itaru Hamachi, Ryuichi Shigemoto, and Akio Ojida. “Optimized Reaction
Pair of the CysHis Tag and Ni(II)-NTA Probe for Highly Selective Chemical Labeling
of Membrane Proteins.” Bulletin of the Chemical Society of Japan. Bulletin
of the Chemical Society of Japan, 2019. https://doi.org/10.1246/bcsj.20190034.
ieee: N. Zenmyo et al., “Optimized reaction pair of the CysHis tag and Ni(II)-NTA
probe for highly selective chemical labeling of membrane proteins,” Bulletin
of the Chemical Society of Japan, vol. 92, no. 5. Bulletin of the Chemical
Society of Japan, pp. 995–1000, 2019.
ista: Zenmyo N, Tokumaru H, Uchinomiya S, Fuchida H, Tabata S, Hamachi I, Shigemoto
R, Ojida A. 2019. Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe
for highly selective chemical labeling of membrane proteins. Bulletin of the Chemical
Society of Japan. 92(5), 995–1000.
mla: Zenmyo, Naoki, et al. “Optimized Reaction Pair of the CysHis Tag and Ni(II)-NTA
Probe for Highly Selective Chemical Labeling of Membrane Proteins.” Bulletin
of the Chemical Society of Japan, vol. 92, no. 5, Bulletin of the Chemical
Society of Japan, 2019, pp. 995–1000, doi:10.1246/bcsj.20190034.
short: N. Zenmyo, H. Tokumaru, S. Uchinomiya, H. Fuchida, S. Tabata, I. Hamachi,
R. Shigemoto, A. Ojida, Bulletin of the Chemical Society of Japan 92 (2019) 995–1000.
date_created: 2019-07-21T21:59:16Z
date_published: 2019-05-15T00:00:00Z
date_updated: 2021-01-12T08:08:26Z
day: '15'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1246/bcsj.20190034
ec_funded: 1
file:
- access_level: open_access
checksum: 186de511d6e0ca93f5d981e2443eb8cd
content_type: application/pdf
creator: dernst
date_created: 2020-10-02T08:49:58Z
date_updated: 2020-10-02T08:49:58Z
file_id: '8594'
file_name: 2019_BCSJ_Zenmyo.pdf
file_size: 2464903
relation: main_file
success: 1
file_date_updated: 2020-10-02T08:49:58Z
has_accepted_license: '1'
intvolume: ' 92'
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 995-1000
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'
publication: Bulletin of the Chemical Society of Japan
publication_identifier:
issn:
- '00092673'
publication_status: published
publisher: Bulletin of the Chemical Society of Japan
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optimized reaction pair of the CysHis tag and Ni(II)-NTA probe for highly selective
chemical labeling of membrane proteins
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 92
year: '2019'
...
---
_id: '6725'
abstract:
- lang: eng
text: "A Valued Constraint Satisfaction Problem (VCSP) provides a common framework
that can express a wide range of discrete optimization problems. A VCSP instance
is given by a finite set of variables, a finite domain of labels, and an objective
function to be minimized. This function is represented as a sum of terms where
each term depends on a subset of the variables. To obtain different classes of
optimization problems, one can restrict all terms to come from a fixed set Γ of
cost functions, called a language. \r\nRecent breakthrough results have established
a complete complexity classification of such classes with respect to language
Γ: if all cost functions in Γ satisfy a certain algebraic condition then all Γ-instances
can be solved in polynomial time, otherwise the problem is NP-hard. Unfortunately,
testing this condition for a given language Γ is known to be NP-hard. We thus
study exponential algorithms for this meta-problem. We show that the tractability
condition of a finite-valued language Γ can be tested in O(3‾√3|D|⋅poly(size(Γ)))
time, where D is the domain of Γ and poly(⋅) is some fixed polynomial. We also
obtain a matching lower bound under the Strong Exponential Time Hypothesis (SETH).
More precisely, we prove that for any constant δ<1 there is no O(3‾√3δ|D|) algorithm,
assuming that SETH holds."
alternative_title:
- LIPIcs
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Kolmogorov V. Testing the complexity of a valued CSP language. In: 46th
International Colloquium on Automata, Languages and Programming. Vol 132.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:77:1-77:12. doi:10.4230/LIPICS.ICALP.2019.77'
apa: 'Kolmogorov, V. (2019). Testing the complexity of a valued CSP language. In
46th International Colloquium on Automata, Languages and Programming (Vol.
132, p. 77:1-77:12). Patras, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPICS.ICALP.2019.77'
chicago: Kolmogorov, Vladimir. “Testing the Complexity of a Valued CSP Language.”
In 46th International Colloquium on Automata, Languages and Programming,
132:77:1-77:12. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.ICALP.2019.77.
ieee: V. Kolmogorov, “Testing the complexity of a valued CSP language,” in 46th
International Colloquium on Automata, Languages and Programming, Patras, Greece,
2019, vol. 132, p. 77:1-77:12.
ista: 'Kolmogorov V. 2019. Testing the complexity of a valued CSP language. 46th
International Colloquium on Automata, Languages and Programming. ICALP 2019: International
Colloquim on Automata, Languages and Programming, LIPIcs, vol. 132, 77:1-77:12.'
mla: Kolmogorov, Vladimir. “Testing the Complexity of a Valued CSP Language.” 46th
International Colloquium on Automata, Languages and Programming, vol. 132,
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 77:1-77:12, doi:10.4230/LIPICS.ICALP.2019.77.
short: V. Kolmogorov, in:, 46th International Colloquium on Automata, Languages
and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 77:1-77:12.
conference:
end_date: 2019-07-12
location: Patras, Greece
name: 'ICALP 2019: International Colloquim on Automata, Languages and Programming'
start_date: 2019-07-08
date_created: 2019-07-29T12:23:29Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2021-01-12T08:08:40Z
day: '01'
ddc:
- '000'
department:
- _id: VlKo
doi: 10.4230/LIPICS.ICALP.2019.77
ec_funded: 1
external_id:
arxiv:
- '1803.02289'
file:
- access_level: open_access
checksum: f5ebee8eec6ae09e30365578ee63a492
content_type: application/pdf
creator: dernst
date_created: 2019-07-31T07:01:45Z
date_updated: 2020-07-14T12:47:38Z
file_id: '6738'
file_name: 2019_LIPICS_Kolmogorov.pdf
file_size: 575475
relation: main_file
file_date_updated: 2020-07-14T12:47:38Z
has_accepted_license: '1'
intvolume: ' 132'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 77:1-77:12
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: 46th International Colloquium on Automata, Languages and Programming
publication_identifier:
isbn:
- 978-3-95977-109-2
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: 1
status: public
title: Testing the complexity of a valued CSP language
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 132
year: '2019'
...
---
_id: '6726'
abstract:
- lang: eng
text: Randomness is an essential part of any secure cryptosystem, but many constructions
rely on distributions that are not uniform. This is particularly true for lattice
based cryptosystems, which more often than not make use of discrete Gaussian distributions
over the integers. For practical purposes it is crucial to evaluate the impact
that approximation errors have on the security of a scheme to provide the best
possible trade-off between security and performance. Recent years have seen surprising
results allowing to use relatively low precision while maintaining high levels
of security. A key insight in these results is that sampling a distribution with
low relative error can provide very strong security guarantees. Since floating
point numbers provide guarantees on the relative approximation error, they seem
a suitable tool in this setting, but it is not obvious which sampling algorithms
can actually profit from them. While previous works have shown that inversion
sampling can be adapted to provide a low relative error (Pöppelmann et al., CHES
2014; Prest, ASIACRYPT 2017), other works have called into question if this is
possible for other sampling techniques (Zheng et al., Eprint report 2018/309).
In this work, we consider all sampling algorithms that are popular in the cryptographic
setting and analyze the relationship of floating point precision and the resulting
relative error. We show that all of the algorithms either natively achieve a low
relative error or can be adapted to do so.
article_processing_charge: No
author:
- first_name: Michael
full_name: Walter, Michael
id: 488F98B0-F248-11E8-B48F-1D18A9856A87
last_name: Walter
orcid: 0000-0003-3186-2482
citation:
ama: 'Walter M. Sampling the integers with low relative error. In: Buchmann J, Nitaj
A, Rachidi T, eds. Progress in Cryptology – AFRICACRYPT 2019. Vol 11627.
LNCS. Cham: Springer Nature; 2019:157-180. doi:10.1007/978-3-030-23696-0_9'
apa: 'Walter, M. (2019). Sampling the integers with low relative error. In J. Buchmann,
A. Nitaj, & T. Rachidi (Eds.), Progress in Cryptology – AFRICACRYPT 2019
(Vol. 11627, pp. 157–180). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-23696-0_9'
chicago: 'Walter, Michael. “Sampling the Integers with Low Relative Error.” In Progress
in Cryptology – AFRICACRYPT 2019, edited by J Buchmann, A Nitaj, and T Rachidi,
11627:157–80. LNCS. Cham: Springer Nature, 2019. https://doi.org/10.1007/978-3-030-23696-0_9.'
ieee: 'M. Walter, “Sampling the integers with low relative error,” in Progress
in Cryptology – AFRICACRYPT 2019, vol. 11627, J. Buchmann, A. Nitaj, and T.
Rachidi, Eds. Cham: Springer Nature, 2019, pp. 157–180.'
ista: 'Walter M. 2019.Sampling the integers with low relative error. In: Progress
in Cryptology – AFRICACRYPT 2019. vol. 11627, 157–180.'
mla: Walter, Michael. “Sampling the Integers with Low Relative Error.” Progress
in Cryptology – AFRICACRYPT 2019, edited by J Buchmann et al., vol. 11627,
Springer Nature, 2019, pp. 157–80, doi:10.1007/978-3-030-23696-0_9.
short: M. Walter, in:, J. Buchmann, A. Nitaj, T. Rachidi (Eds.), Progress in Cryptology
– AFRICACRYPT 2019, Springer Nature, Cham, 2019, pp. 157–180.
conference:
end_date: 2019-07-11
location: Rabat, Morocco
name: 'AFRICACRYPT: International Conference on Cryptology in Africa'
start_date: 2019-07-09
date_created: 2019-07-29T12:25:31Z
date_published: 2019-06-29T00:00:00Z
date_updated: 2023-02-23T12:50:15Z
day: '29'
department:
- _id: KrPi
doi: 10.1007/978-3-030-23696-0_9
ec_funded: 1
editor:
- first_name: J
full_name: Buchmann, J
last_name: Buchmann
- first_name: A
full_name: Nitaj, A
last_name: Nitaj
- first_name: T
full_name: Rachidi, T
last_name: Rachidi
intvolume: ' 11627'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2019/068
month: '06'
oa: 1
oa_version: Preprint
page: 157-180
place: Cham
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication: Progress in Cryptology – AFRICACRYPT 2019
publication_identifier:
eisbn:
- 978-3-0302-3696-0
isbn:
- 978-3-0302-3695-3
issn:
- 0302-9743
- 1611-3349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: LNCS
status: public
title: Sampling the integers with low relative error
type: book_chapter
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 11627
year: '2019'
...
---
_id: '6750'
abstract:
- lang: eng
text: 'Polar codes have gained extensive attention during the past few years and
recently they have been selected for the next generation of wireless communications
standards (5G). Successive-cancellation-based (SC-based) decoders, such as SC
list (SCL) and SC flip (SCF), provide a reasonable error performance for polar
codes at the cost of low decoding speed. Fast SC-based decoders, such as Fast-SSC,
Fast-SSCL, and Fast-SSCF, identify the special constituent codes in a polar code
graph off-line, produce a list of operations, store the list in memory, and feed
the list to the decoder to decode the constituent codes in order efficiently,
thus increasing the decoding speed. However, the list of operations is dependent
on the code rate and as the rate changes, a new list is produced, making fast
SC-based decoders not rate-flexible. In this paper, we propose a completely rate-flexible
fast SC-based decoder by creating the list of operations directly in hardware,
with low implementation complexity. We further propose a hardware architecture
implementing the proposed method and show that the area occupation of the rate-flexible
fast SC-based decoder in this paper is only 38% of the total area of the memory-based
base-line decoder when 5G code rates are supported. '
article_number: '8854897'
article_processing_charge: No
article_type: original
author:
- first_name: Seyyed Ali
full_name: Hashemi, Seyyed Ali
last_name: Hashemi
- first_name: Carlo
full_name: Condo, Carlo
last_name: Condo
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Warren J
full_name: Gross, Warren J
last_name: Gross
citation:
ama: Hashemi SA, Condo C, Mondelli M, Gross WJ. Rate-flexible fast polar decoders.
IEEE Transactions on Signal Processing. 2019;67(22). doi:10.1109/TSP.2019.2944738
apa: Hashemi, S. A., Condo, C., Mondelli, M., & Gross, W. J. (2019). Rate-flexible
fast polar decoders. IEEE Transactions on Signal Processing. IEEE. https://doi.org/10.1109/TSP.2019.2944738
chicago: Hashemi, Seyyed Ali, Carlo Condo, Marco Mondelli, and Warren J Gross. “Rate-Flexible
Fast Polar Decoders.” IEEE Transactions on Signal Processing. IEEE, 2019.
https://doi.org/10.1109/TSP.2019.2944738.
ieee: S. A. Hashemi, C. Condo, M. Mondelli, and W. J. Gross, “Rate-flexible fast
polar decoders,” IEEE Transactions on Signal Processing, vol. 67, no. 22.
IEEE, 2019.
ista: Hashemi SA, Condo C, Mondelli M, Gross WJ. 2019. Rate-flexible fast polar
decoders. IEEE Transactions on Signal Processing. 67(22), 8854897.
mla: Hashemi, Seyyed Ali, et al. “Rate-Flexible Fast Polar Decoders.” IEEE Transactions
on Signal Processing, vol. 67, no. 22, 8854897, IEEE, 2019, doi:10.1109/TSP.2019.2944738.
short: S.A. Hashemi, C. Condo, M. Mondelli, W.J. Gross, IEEE Transactions on Signal
Processing 67 (2019).
date_created: 2019-07-31T09:51:14Z
date_published: 2019-11-15T00:00:00Z
date_updated: 2021-01-12T08:08:51Z
day: '15'
department:
- _id: MaMo
doi: 10.1109/TSP.2019.2944738
external_id:
arxiv:
- '1903.09203'
intvolume: ' 67'
issue: '22'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1903.09203
month: '11'
oa: 1
oa_version: Preprint
publication: IEEE Transactions on Signal Processing
publication_identifier:
issn:
- 1053587X
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: 1
status: public
title: Rate-flexible fast polar decoders
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 67
year: '2019'
...
---
_id: '6759'
abstract:
- lang: eng
text: "We consider the graph class Grounded-L corresponding to graphs that admit
an intersection representation by L-shaped curves, where additionally the topmost
points of each curve are assumed to belong to a common horizontal line. We prove
that Grounded-L graphs admit an equivalent characterisation in terms of vertex
ordering with forbidden patterns. \r\nWe also compare this class to related intersection
classes, such as the grounded segment graphs, the monotone L-graphs (a.k.a. max
point-tolerance graphs), or the outer-1-string graphs. We give constructions showing
that these classes are all distinct and satisfy only trivial or previously known
inclusions."
article_number: P3.17
article_processing_charge: No
article_type: original
author:
- first_name: Vít
full_name: Jelínek, Vít
last_name: Jelínek
- first_name: Martin
full_name: Töpfer, Martin
id: 4B865388-F248-11E8-B48F-1D18A9856A87
last_name: Töpfer
citation:
ama: Jelínek V, Töpfer M. On grounded L-graphs and their relatives. Electronic
Journal of Combinatorics. 2019;26(3). doi:10.37236/8096
apa: Jelínek, V., & Töpfer, M. (2019). On grounded L-graphs and their relatives.
Electronic Journal of Combinatorics. Electronic Journal of Combinatorics.
https://doi.org/10.37236/8096
chicago: Jelínek, Vít, and Martin Töpfer. “On Grounded L-Graphs and Their Relatives.”
Electronic Journal of Combinatorics. Electronic Journal of Combinatorics,
2019. https://doi.org/10.37236/8096.
ieee: V. Jelínek and M. Töpfer, “On grounded L-graphs and their relatives,” Electronic
Journal of Combinatorics, vol. 26, no. 3. Electronic Journal of Combinatorics,
2019.
ista: Jelínek V, Töpfer M. 2019. On grounded L-graphs and their relatives. Electronic
Journal of Combinatorics. 26(3), P3.17.
mla: Jelínek, Vít, and Martin Töpfer. “On Grounded L-Graphs and Their Relatives.”
Electronic Journal of Combinatorics, vol. 26, no. 3, P3.17, Electronic
Journal of Combinatorics, 2019, doi:10.37236/8096.
short: V. Jelínek, M. Töpfer, Electronic Journal of Combinatorics 26 (2019).
date_created: 2019-08-04T21:59:20Z
date_published: 2019-07-19T00:00:00Z
date_updated: 2022-03-18T12:32:02Z
day: '19'
ddc:
- '510'
department:
- _id: DaAl
doi: 10.37236/8096
ec_funded: 1
external_id:
arxiv:
- '1808.04148'
file:
- access_level: open_access
checksum: 20fc366fc6683ef0b074a019b73a663a
content_type: application/pdf
creator: dernst
date_created: 2019-08-05T06:46:55Z
date_updated: 2020-07-14T12:47:39Z
file_id: '6764'
file_name: 2019_eJourCombinatorics_Jelinek.pdf
file_size: 533697
relation: main_file
file_date_updated: 2020-07-14T12:47:39Z
has_accepted_license: '1'
intvolume: ' 26'
issue: '3'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Electronic Journal of Combinatorics
publication_identifier:
eissn:
- '10778926'
publication_status: published
publisher: Electronic Journal of Combinatorics
quality_controlled: '1'
scopus_import: '1'
status: public
title: On grounded L-graphs and their relatives
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: 26
year: '2019'
...
---
_id: '6822'
abstract:
- lang: eng
text: "In two-player games on graphs, the players move a token through a graph to
produce an infinite path, which determines the qualitative winner or quantitative
payoff of the game. In bidding games, in each turn, we hold an auction between
the two players to determine which player moves the token. Bidding games have
largely been studied with concrete bidding mechanisms that are variants of a first-price
auction: in each turn both players simultaneously submit bids, the higher\r\nbidder
moves the token, and pays his bid to the lower bidder in Richman bidding, to the
bank in poorman bidding, and in taxman bidding, the bid is split between the other
player and the bank according to a predefined constant factor. Bidding games are
deterministic games. They have an intriguing connection with a fragment of stochastic
games called \r\n randomturn games. We study, for the first time, a combination
of bidding games with probabilistic behavior; namely, we study bidding games that
are played on Markov decision processes, where the players bid for the right to
choose the next action, which determines the probability distribution according
to which the next vertex is chosen. We study parity and meanpayoff bidding games
on MDPs and extend results from the deterministic bidding setting to the probabilistic
one."
alternative_title:
- LNCS
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Petr
full_name: Novotny, Petr
last_name: Novotny
citation:
ama: 'Avni G, Henzinger TA, Ibsen-Jensen R, Novotny P. Bidding games on Markov decision
processes. In: Proceedings of the 13th International Conference of Reachability
Problems. Vol 11674. Springer; 2019:1-12. doi:10.1007/978-3-030-30806-3_1'
apa: 'Avni, G., Henzinger, T. A., Ibsen-Jensen, R., & Novotny, P. (2019). Bidding
games on Markov decision processes. In Proceedings of the 13th International
Conference of Reachability Problems (Vol. 11674, pp. 1–12). Brussels, Belgium:
Springer. https://doi.org/10.1007/978-3-030-30806-3_1'
chicago: Avni, Guy, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Petr Novotny. “Bidding
Games on Markov Decision Processes.” In Proceedings of the 13th International
Conference of Reachability Problems, 11674:1–12. Springer, 2019. https://doi.org/10.1007/978-3-030-30806-3_1.
ieee: G. Avni, T. A. Henzinger, R. Ibsen-Jensen, and P. Novotny, “Bidding games
on Markov decision processes,” in Proceedings of the 13th International Conference
of Reachability Problems, Brussels, Belgium, 2019, vol. 11674, pp. 1–12.
ista: 'Avni G, Henzinger TA, Ibsen-Jensen R, Novotny P. 2019. Bidding games on Markov
decision processes. Proceedings of the 13th International Conference of Reachability
Problems. RP: Reachability Problems, LNCS, vol. 11674, 1–12.'
mla: Avni, Guy, et al. “Bidding Games on Markov Decision Processes.” Proceedings
of the 13th International Conference of Reachability Problems, vol. 11674,
Springer, 2019, pp. 1–12, doi:10.1007/978-3-030-30806-3_1.
short: G. Avni, T.A. Henzinger, R. Ibsen-Jensen, P. Novotny, in:, Proceedings of
the 13th International Conference of Reachability Problems, Springer, 2019, pp.
1–12.
conference:
end_date: 2019-09-13
location: Brussels, Belgium
name: 'RP: Reachability Problems'
start_date: 2019-09-11
date_created: 2019-08-19T07:58:10Z
date_published: 2019-09-06T00:00:00Z
date_updated: 2021-01-12T08:09:12Z
day: '06'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-030-30806-3_1
file:
- access_level: open_access
checksum: 45ebbc709af2b247d28c7c293c01504b
content_type: application/pdf
creator: gavni
date_created: 2019-08-19T07:56:40Z
date_updated: 2020-07-14T12:47:41Z
file_id: '6823'
file_name: prob.pdf
file_size: 436635
relation: main_file
file_date_updated: 2020-07-14T12:47:41Z
has_accepted_license: '1'
intvolume: ' 11674'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 1-12
project:
- _id: 264B3912-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02369
name: Formal Methods meets Algorithmic Game Theory
- _id: 25F2ACDE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: ' Proceedings of the 13th International Conference of Reachability Problems'
publication_identifier:
isbn:
- 978-303030805-6
issn:
- 0302-9743
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: 1
status: public
title: Bidding games on Markov decision processes
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11674
year: '2019'
...
---
_id: '6887'
abstract:
- lang: eng
text: 'The fundamental model-checking problem, given as input a model and a specification,
asks for the algorithmic verification of whether the model satisfies the specification.
Two classical models for reactive systems are graphs and Markov decision processes
(MDPs). A basic specification formalism in the verification of reactive systems
is the strong fairness (aka Streett) objective, where given different types of
requests and corresponding grants, the requirement is that for each type, if the
request event happens infinitely often, then the corresponding grant event must
also happen infinitely often. All omega-regular objectives can be expressed as
Streett objectives and hence they are canonical in verification. Consider graphs/MDPs
with n vertices, m edges, and a Streett objectives with k pairs, and let b denote
the size of the description of the Streett objective for the sets of requests
and grants. The current best-known algorithm for the problem requires time O(min(n^2,
m sqrt{m log n}) + b log n). In this work we present randomized near-linear time
algorithms, with expected running time O~(m + b), where the O~ notation hides
poly-log factors. Our randomized algorithms are near-linear in the size of the
input, and hence optimal up to poly-log factors. '
alternative_title:
- LIPIcs
article_number: '7'
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: Wolfgang
full_name: Dvorák, Wolfgang
last_name: Dvorák
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
- first_name: Alexander
full_name: Svozil, Alexander
last_name: Svozil
citation:
ama: 'Chatterjee K, Dvorák W, Henzinger MH, Svozil A. Near-linear time algorithms
for Streett objectives in graphs and MDPs. In: Leibniz International Proceedings
in Informatics. Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2019. doi:10.4230/LIPICS.CONCUR.2019.7'
apa: 'Chatterjee, K., Dvorák, W., Henzinger, M. H., & Svozil, A. (2019). Near-linear
time algorithms for Streett objectives in graphs and MDPs. In Leibniz International
Proceedings in Informatics (Vol. 140). Amsterdam, Netherlands: Schloss Dagstuhl
- Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.CONCUR.2019.7'
chicago: Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Alexander
Svozil. “Near-Linear Time Algorithms for Streett Objectives in Graphs and MDPs.”
In Leibniz International Proceedings in Informatics, Vol. 140. Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.CONCUR.2019.7.
ieee: K. Chatterjee, W. Dvorák, M. H. Henzinger, and A. Svozil, “Near-linear time
algorithms for Streett objectives in graphs and MDPs,” in Leibniz International
Proceedings in Informatics, Amsterdam, Netherlands, 2019, vol. 140.
ista: 'Chatterjee K, Dvorák W, Henzinger MH, Svozil A. 2019. Near-linear time algorithms
for Streett objectives in graphs and MDPs. Leibniz International Proceedings in
Informatics. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol.
140, 7.'
mla: Chatterjee, Krishnendu, et al. “Near-Linear Time Algorithms for Streett Objectives
in Graphs and MDPs.” Leibniz International Proceedings in Informatics,
vol. 140, 7, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.CONCUR.2019.7.
short: K. Chatterjee, W. Dvorák, M.H. Henzinger, A. Svozil, in:, Leibniz International
Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2019.
conference:
end_date: 2019-08-30
location: Amsterdam, Netherlands
name: 'CONCUR: International Conference on Concurrency Theory'
start_date: 2019-08-27
date_created: 2019-09-18T08:07:58Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2022-08-12T10:54:34Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.4230/LIPICS.CONCUR.2019.7
ec_funded: 1
file:
- access_level: open_access
checksum: e1f0e4061212454574f34a1368d018ec
content_type: application/pdf
creator: kschuh
date_created: 2019-10-01T08:20:30Z
date_updated: 2020-07-14T12:47:43Z
file_id: '6922'
file_name: 2019_LIPIcs_Chatterjee.pdf
file_size: 730112
relation: main_file
file_date_updated: 2020-07-14T12:47:43Z
has_accepted_license: '1'
intvolume: ' 140'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Leibniz International Proceedings in Informatics
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Near-linear time algorithms for Streett objectives in graphs and MDPs
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 140
year: '2019'
...
---
_id: '6888'
abstract:
- lang: eng
text: In this paper, we design novel liquid time-constant recurrent neural networks
for robotic control, inspired by the brain of the nematode, C. elegans. In the
worm's nervous system, neurons communicate through nonlinear time-varying synaptic
links established amongst them by their particular wiring structure. This property
enables neurons to express liquid time-constants dynamics and therefore allows
the network to originate complex behaviors with a small number of neurons. We
identify neuron-pair communication motifs as design operators and use them to
configure compact neuronal network structures to govern sequential robotic tasks.
The networks are systematically designed to map the environmental observations
to motor actions, by their hierarchical topology from sensory neurons, through
recurrently-wired interneurons, to motor neurons. The networks are then parametrized
in a supervised-learning scheme by a search-based algorithm. We demonstrate that
obtained networks realize interpretable dynamics. We evaluate their performance
in controlling mobile and arm robots, and compare their attributes to other artificial
neural network-based control agents. Finally, we experimentally show their superior
resilience to environmental noise, compared to the existing machine learning-based
methods.
alternative_title:
- ICRA
article_number: '8793840'
article_processing_charge: No
author:
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Ramin
full_name: Hasani, Ramin
last_name: Hasani
- first_name: Manuel
full_name: Zimmer, Manuel
last_name: Zimmer
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Radu
full_name: Grosu, Radu
last_name: Grosu
citation:
ama: 'Lechner M, Hasani R, Zimmer M, Henzinger TA, Grosu R. Designing worm-inspired
neural networks for interpretable robotic control. In: Proceedings - IEEE International
Conference on Robotics and Automation. Vol 2019-May. IEEE; 2019. doi:10.1109/icra.2019.8793840'
apa: 'Lechner, M., Hasani, R., Zimmer, M., Henzinger, T. A., & Grosu, R. (2019).
Designing worm-inspired neural networks for interpretable robotic control. In
Proceedings - IEEE International Conference on Robotics and Automation
(Vol. 2019–May). Montreal, QC, Canada: IEEE. https://doi.org/10.1109/icra.2019.8793840'
chicago: Lechner, Mathias, Ramin Hasani, Manuel Zimmer, Thomas A Henzinger, and
Radu Grosu. “Designing Worm-Inspired Neural Networks for Interpretable Robotic
Control.” In Proceedings - IEEE International Conference on Robotics and Automation,
Vol. 2019–May. IEEE, 2019. https://doi.org/10.1109/icra.2019.8793840.
ieee: M. Lechner, R. Hasani, M. Zimmer, T. A. Henzinger, and R. Grosu, “Designing
worm-inspired neural networks for interpretable robotic control,” in Proceedings
- IEEE International Conference on Robotics and Automation, Montreal, QC,
Canada, 2019, vol. 2019–May.
ista: 'Lechner M, Hasani R, Zimmer M, Henzinger TA, Grosu R. 2019. Designing worm-inspired
neural networks for interpretable robotic control. Proceedings - IEEE International
Conference on Robotics and Automation. ICRA: International Conference on Robotics
and Automation, ICRA, vol. 2019–May, 8793840.'
mla: Lechner, Mathias, et al. “Designing Worm-Inspired Neural Networks for Interpretable
Robotic Control.” Proceedings - IEEE International Conference on Robotics and
Automation, vol. 2019–May, 8793840, IEEE, 2019, doi:10.1109/icra.2019.8793840.
short: M. Lechner, R. Hasani, M. Zimmer, T.A. Henzinger, R. Grosu, in:, Proceedings
- IEEE International Conference on Robotics and Automation, IEEE, 2019.
conference:
end_date: 2019-05-24
location: Montreal, QC, Canada
name: 'ICRA: International Conference on Robotics and Automation'
start_date: 2019-05-20
date_created: 2019-09-18T08:09:51Z
date_published: 2019-05-01T00:00:00Z
date_updated: 2021-01-12T08:09:28Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1109/icra.2019.8793840
file:
- access_level: open_access
checksum: f5545a6b60c3ffd01feb3613f81d03b6
content_type: application/pdf
creator: dernst
date_created: 2020-10-08T17:30:38Z
date_updated: 2020-10-08T17:30:38Z
file_id: '8636'
file_name: 2019_ICRA_Lechner.pdf
file_size: 3265107
relation: main_file
success: 1
file_date_updated: 2020-10-08T17:30:38Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Proceedings - IEEE International Conference on Robotics and Automation
publication_identifier:
isbn:
- '9781538660270'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Designing worm-inspired neural networks for interpretable robotic control
type: conference
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 2019-May
year: '2019'
...
---
_id: '6886'
abstract:
- lang: eng
text: 'In two-player games on graphs, the players move a token through a graph to
produce an infinite path, which determines the winner of the game. Such games
are central in formal methods since they model the interaction between a non-terminating
system and its environment. In bidding games the players bid for the right to
move the token: in each round, the players simultaneously submit bids, and the
higher bidder moves the token and pays the other player. Bidding games are known
to have a clean and elegant mathematical structure that relies on the ability
of the players to submit arbitrarily small bids. Many applications, however, require
a fixed granularity for the bids, which can represent, for example, the monetary
value expressed in cents. We study, for the first time, the combination of discrete-bidding
and infinite-duration games. Our most important result proves that these games
form a large determined subclass of concurrent games, where determinacy is the
strong property that there always exists exactly one player who can guarantee
winning the game. In particular, we show that, in contrast to non-discrete bidding
games, the mechanism with which tied bids are resolved plays an important role
in discrete-bidding games. We study several natural tie-breaking mechanisms and
show that, while some do not admit determinacy, most natural mechanisms imply
determinacy for every pair of initial budgets. '
alternative_title:
- LIPIcs
article_number: '20'
article_processing_charge: No
author:
- first_name: Milad
full_name: Aghajohari, Milad
last_name: Aghajohari
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- 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: 'Aghajohari M, Avni G, Henzinger TA. Determinacy in discrete-bidding infinite-duration
games. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.CONCUR.2019.20'
apa: 'Aghajohari, M., Avni, G., & Henzinger, T. A. (2019). Determinacy in discrete-bidding
infinite-duration games (Vol. 140). Presented at the CONCUR: International Conference
on Concurrency Theory, Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPICS.CONCUR.2019.20'
chicago: Aghajohari, Milad, Guy Avni, and Thomas A Henzinger. “Determinacy in Discrete-Bidding
Infinite-Duration Games,” Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2019. https://doi.org/10.4230/LIPICS.CONCUR.2019.20.
ieee: 'M. Aghajohari, G. Avni, and T. A. Henzinger, “Determinacy in discrete-bidding
infinite-duration games,” presented at the CONCUR: International Conference on
Concurrency Theory, Amsterdam, Netherlands, 2019, vol. 140.'
ista: 'Aghajohari M, Avni G, Henzinger TA. 2019. Determinacy in discrete-bidding
infinite-duration games. CONCUR: International Conference on Concurrency Theory,
LIPIcs, vol. 140, 20.'
mla: Aghajohari, Milad, et al. Determinacy in Discrete-Bidding Infinite-Duration
Games. Vol. 140, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019,
doi:10.4230/LIPICS.CONCUR.2019.20.
short: M. Aghajohari, G. Avni, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2019.
conference:
end_date: 2019-08-30
location: Amsterdam, Netherlands
name: 'CONCUR: International Conference on Concurrency Theory'
start_date: 2019-08-27
date_created: 2019-09-18T08:06:58Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2022-01-26T08:27:10Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.4230/LIPICS.CONCUR.2019.20
external_id:
arxiv:
- '1905.03588'
file:
- access_level: open_access
checksum: 4df6d3575c506edb17215adada03cc8e
content_type: application/pdf
creator: kschuh
date_created: 2019-09-27T12:21:38Z
date_updated: 2020-07-14T12:47:43Z
file_id: '6915'
file_name: 2019_LIPIcs_Aghajohari.pdf
file_size: 741425
relation: main_file
file_date_updated: 2020-07-14T12:47:43Z
has_accepted_license: '1'
intvolume: ' 140'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25F2ACDE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Rigorous Systems Engineering
- _id: 264B3912-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02369
name: Formal Methods meets Algorithmic Game Theory
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: '1'
status: public
title: Determinacy in discrete-bidding infinite-duration games
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 140
year: '2019'
...
---
_id: '6885'
abstract:
- lang: eng
text: 'A vector addition system with states (VASS) consists of a finite set of states
and counters. A configuration is a state and a value for each counter; a transition
changes the state and each counter is incremented, decremented, or left unchanged.
While qualitative properties such as state and configuration reachability have
been studied for VASS, we consider the long-run average cost of infinite computations
of VASS. The cost of a configuration is for each state, a linear combination of
the counter values. In the special case of uniform cost functions, the linear
combination is the same for all states. The (regular) long-run emptiness problem
is, given a VASS, a cost function, and a threshold value, if there is a (lasso-shaped)
computation such that the long-run average value of the cost function does not
exceed the threshold. For uniform cost functions, we show that the regular long-run
emptiness problem is (a) decidable in polynomial time for integer-valued VASS,
and (b) decidable but nonelementarily hard for natural-valued VASS (i.e., nonnegative
counters). For general cost functions, we show that the problem is (c) NP-complete
for integer-valued VASS, and (d) undecidable for natural-valued VASS. Our most
interesting result is for (c) integer-valued VASS with general cost functions,
where we establish a connection between the regular long-run emptiness problem
and quadratic Diophantine inequalities. The general (nonregular) long-run emptiness
problem is equally hard as the regular problem in all cases except (c), where
it remains open. '
alternative_title:
- LIPIcs
article_number: '27'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
last_name: Otop
citation:
ama: 'Chatterjee K, Henzinger TA, Otop J. Long-run average behavior of vector addition
systems with states. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2019. doi:10.4230/LIPICS.CONCUR.2019.27'
apa: 'Chatterjee, K., Henzinger, T. A., & Otop, J. (2019). Long-run average
behavior of vector addition systems with states (Vol. 140). Presented at the CONCUR:
International Conference on Concurrency Theory, Amsterdam, Netherlands: Schloss
Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.CONCUR.2019.27'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Long-Run Average
Behavior of Vector Addition Systems with States,” Vol. 140. Schloss Dagstuhl -
Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.CONCUR.2019.27.
ieee: 'K. Chatterjee, T. A. Henzinger, and J. Otop, “Long-run average behavior of
vector addition systems with states,” presented at the CONCUR: International Conference
on Concurrency Theory, Amsterdam, Netherlands, 2019, vol. 140.'
ista: 'Chatterjee K, Henzinger TA, Otop J. 2019. Long-run average behavior of vector
addition systems with states. CONCUR: International Conference on Concurrency
Theory, LIPIcs, vol. 140, 27.'
mla: Chatterjee, Krishnendu, et al. Long-Run Average Behavior of Vector Addition
Systems with States. Vol. 140, 27, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2019, doi:10.4230/LIPICS.CONCUR.2019.27.
short: K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2019.
conference:
end_date: 2019-08-30
location: Amsterdam, Netherlands
name: 'CONCUR: International Conference on Concurrency Theory'
start_date: 2019-08-27
date_created: 2019-09-18T08:06:14Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2021-01-12T08:09:27Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
- _id: KrCh
doi: 10.4230/LIPICS.CONCUR.2019.27
file:
- access_level: open_access
checksum: 4985e26e1572d1575d64d38acabd71d6
content_type: application/pdf
creator: kschuh
date_created: 2019-09-27T12:09:35Z
date_updated: 2020-07-14T12:47:43Z
file_id: '6914'
file_name: 2019_LIPIcs_Chatterjee.pdf
file_size: 538120
relation: main_file
file_date_updated: 2020-07-14T12:47:43Z
has_accepted_license: '1'
intvolume: ' 140'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 25F2ACDE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: 1
status: public
title: Long-run average behavior of vector addition systems with states
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 140
year: '2019'
...
---
_id: '6889'
abstract:
- lang: eng
text: 'We study Markov decision processes and turn-based stochastic games with parity
conditions. There are three qualitative winning criteria, namely, sure winning,
which requires all paths to satisfy the condition, almost-sure winning, which
requires the condition to be satisfied with probability 1, and limit-sure winning,
which requires the condition to be satisfied with probability arbitrarily close
to 1. We study the combination of two of these criteria for parity conditions,
e.g., there are two parity conditions one of which must be won surely, and the
other almost-surely. The problem has been studied recently by Berthon et al. for
MDPs with combination of sure and almost-sure winning, under infinite-memory strategies,
and the problem has been established to be in NP cap co-NP. Even in MDPs there
is a difference between finite-memory and infinite-memory strategies. Our main
results for combination of sure and almost-sure winning are as follows: (a) we
show that for MDPs with finite-memory strategies the problem is in NP cap co-NP;
(b) we show that for turn-based stochastic games the problem is co-NP-complete,
both for finite-memory and infinite-memory strategies; and (c) we present algorithmic
results for the finite-memory case, both for MDPs and turn-based stochastic games,
by reduction to non-stochastic parity games. In addition we show that all the
above complexity results also carry over to combination of sure and limit-sure
winning, and results for all other combinations can be derived from existing results
in the literature. Thus we present a complete picture for the study of combinations
of two qualitative winning criteria for parity conditions in MDPs and turn-based
stochastic games. '
alternative_title:
- LIPIcs
article_number: '6'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Nir
full_name: Piterman, Nir
last_name: Piterman
citation:
ama: 'Chatterjee K, Piterman N. Combinations of Qualitative Winning for Stochastic
Parity Games. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2019. doi:10.4230/LIPICS.CONCUR.2019.6'
apa: 'Chatterjee, K., & Piterman, N. (2019). Combinations of Qualitative Winning
for Stochastic Parity Games (Vol. 140). Presented at the CONCUR: International
Conference on Concurrency Theory, Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPICS.CONCUR.2019.6'
chicago: Chatterjee, Krishnendu, and Nir Piterman. “Combinations of Qualitative
Winning for Stochastic Parity Games,” Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2019. https://doi.org/10.4230/LIPICS.CONCUR.2019.6.
ieee: 'K. Chatterjee and N. Piterman, “Combinations of Qualitative Winning for Stochastic
Parity Games,” presented at the CONCUR: International Conference on Concurrency
Theory, Amsterdam, Netherlands, 2019, vol. 140.'
ista: 'Chatterjee K, Piterman N. 2019. Combinations of Qualitative Winning for Stochastic
Parity Games. CONCUR: International Conference on Concurrency Theory, LIPIcs,
vol. 140, 6.'
mla: Chatterjee, Krishnendu, and Nir Piterman. Combinations of Qualitative Winning
for Stochastic Parity Games. Vol. 140, 6, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2019, doi:10.4230/LIPICS.CONCUR.2019.6.
short: K. Chatterjee, N. Piterman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2019.
conference:
end_date: 2019-08-30
location: Amsterdam, Netherlands
name: 'CONCUR: International Conference on Concurrency Theory'
start_date: 2019-08-27
date_created: 2019-09-18T08:11:43Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2021-01-12T08:09:28Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.4230/LIPICS.CONCUR.2019.6
file:
- access_level: open_access
checksum: 7b2ecfd4d9d02360308c0ca986fc10a7
content_type: application/pdf
creator: kschuh
date_created: 2019-10-01T08:49:45Z
date_updated: 2020-07-14T12:47:43Z
file_id: '6923'
file_name: 2019_LIPIcs_Chatterjee.pdf
file_size: 509163
relation: main_file
file_date_updated: 2020-07-14T12:47:43Z
has_accepted_license: '1'
intvolume: ' 140'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: 1
status: public
title: Combinations of Qualitative Winning for Stochastic Parity 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: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 140
year: '2019'
...
---
_id: '6931'
abstract:
- lang: eng
text: "Consider a distributed system with n processors out of which f can be Byzantine
faulty. In the\r\napproximate agreement task, each processor i receives an input
value xi and has to decide on an\r\noutput value yi such that\r\n1. the output
values are in the convex hull of the non-faulty processors’ input values,\r\n2.
the output values are within distance d of each other.\r\n\r\n\r\nClassically,
the values are assumed to be from an m-dimensional Euclidean space, where m ≥
1.\r\nIn this work, we study the task in a discrete setting, where input values
with some structure\r\nexpressible as a graph. Namely, the input values are vertices
of a finite graph G and the goal is to\r\noutput vertices that are within distance
d of each other in G, but still remain in the graph-induced\r\nconvex hull of
the input values. For d = 0, the task reduces to consensus and cannot be solved
with\r\na deterministic algorithm in an asynchronous system even with a single
crash fault. For any d ≥ 1,\r\nwe show that the task is solvable in asynchronous
systems when G is chordal and n > (ω + 1)f,\r\nwhere ω is the clique number of
G. In addition, we give the first Byzantine-tolerant algorithm for a\r\nvariant
of lattice agreement. For synchronous systems, we show tight resilience bounds
for the exact\r\nvariants of these and related tasks over a large class of combinatorial
structures."
alternative_title:
- LIPIcs
article_processing_charge: No
author:
- first_name: Thomas
full_name: Nowak, Thomas
last_name: Nowak
- first_name: Joel
full_name: Rybicki, Joel
id: 334EFD2E-F248-11E8-B48F-1D18A9856A87
last_name: Rybicki
orcid: 0000-0002-6432-6646
citation:
ama: 'Nowak T, Rybicki J. Byzantine approximate agreement on graphs. In: 33rd
International Symposium on Distributed Computing. Vol 146. Schloss Dagstuhl
- Leibniz-Zentrum für Informatik; 2019:29:1--29:17. doi:10.4230/LIPICS.DISC.2019.29'
apa: 'Nowak, T., & Rybicki, J. (2019). Byzantine approximate agreement on graphs.
In 33rd International Symposium on Distributed Computing (Vol. 146, p.
29:1--29:17). Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik.
https://doi.org/10.4230/LIPICS.DISC.2019.29'
chicago: Nowak, Thomas, and Joel Rybicki. “Byzantine Approximate Agreement on Graphs.”
In 33rd International Symposium on Distributed Computing, 146:29:1--29:17.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.DISC.2019.29.
ieee: T. Nowak and J. Rybicki, “Byzantine approximate agreement on graphs,” in 33rd
International Symposium on Distributed Computing, Budapest, Hungary, 2019,
vol. 146, p. 29:1--29:17.
ista: 'Nowak T, Rybicki J. 2019. Byzantine approximate agreement on graphs. 33rd
International Symposium on Distributed Computing. DISC: International Symposium
on Distributed Computing, LIPIcs, vol. 146, 29:1--29:17.'
mla: Nowak, Thomas, and Joel Rybicki. “Byzantine Approximate Agreement on Graphs.”
33rd International Symposium on Distributed Computing, vol. 146, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 29:1--29:17, doi:10.4230/LIPICS.DISC.2019.29.
short: T. Nowak, J. Rybicki, in:, 33rd International Symposium on Distributed Computing,
Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 29:1--29:17.
conference:
end_date: 2019-10-18
location: Budapest, Hungary
name: 'DISC: International Symposium on Distributed Computing'
start_date: 2019-10-14
date_created: 2019-10-08T12:41:38Z
date_published: 2019-01-01T00:00:00Z
date_updated: 2021-01-12T08:09:38Z
ddc:
- '004'
department:
- _id: DaAl
doi: 10.4230/LIPICS.DISC.2019.29
ec_funded: 1
external_id:
arxiv:
- '1908.02743'
file:
- access_level: open_access
checksum: 2d2202f90c6ac991e50876451627c4b5
content_type: application/pdf
creator: jrybicki
date_created: 2019-10-08T12:47:19Z
date_updated: 2020-07-14T12:47:44Z
file_id: '6934'
file_name: LIPIcs-DISC-2019-29.pdf
file_size: 639378
relation: main_file
file_date_updated: 2020-07-14T12:47:44Z
has_accepted_license: '1'
intvolume: ' 146'
keyword:
- consensus
- approximate agreement
- Byzantine faults
- chordal graphs
- lattice agreement
language:
- iso: eng
oa: 1
oa_version: Published Version
page: 29:1--29:17
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: 33rd International Symposium on Distributed Computing
publication_identifier:
eisbn:
- 978-3-95977-126-9
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: 1
status: public
title: Byzantine approximate agreement on graphs
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 146
year: '2019'
...
---
_id: '6985'
abstract:
- lang: eng
text: In this paper, we introduce a novel method to interpret recurrent neural networks
(RNNs), particularly long short-term memory networks (LSTMs) at the cellular level.
We propose a systematic pipeline for interpreting individual hidden state dynamics
within the network using response characterization methods. The ranked contribution
of individual cells to the network's output is computed by analyzing a set of
interpretable metrics of their decoupled step and sinusoidal responses. As a result,
our method is able to uniquely identify neurons with insightful dynamics, quantify
relationships between dynamical properties and test accuracy through ablation
analysis, and interpret the impact of network capacity on a network's dynamical
distribution. Finally, we demonstrate the generalizability and scalability of
our method by evaluating a series of different benchmark sequential datasets.
article_number: '8851954'
author:
- first_name: Ramin
full_name: Hasani, Ramin
last_name: Hasani
- first_name: Alexander
full_name: Amini, Alexander
last_name: Amini
- first_name: Mathias
full_name: Lechner, Mathias
id: 3DC22916-F248-11E8-B48F-1D18A9856A87
last_name: Lechner
- first_name: Felix
full_name: Naser, Felix
last_name: Naser
- first_name: Radu
full_name: Grosu, Radu
last_name: Grosu
- first_name: Daniela
full_name: Rus, Daniela
last_name: Rus
citation:
ama: 'Hasani R, Amini A, Lechner M, Naser F, Grosu R, Rus D. Response characterization
for auditing cell dynamics in long short-term memory networks. In: Proceedings
of the International Joint Conference on Neural Networks. IEEE; 2019. doi:10.1109/ijcnn.2019.8851954'
apa: 'Hasani, R., Amini, A., Lechner, M., Naser, F., Grosu, R., & Rus, D. (2019).
Response characterization for auditing cell dynamics in long short-term memory
networks. In Proceedings of the International Joint Conference on Neural Networks.
Budapest, Hungary: IEEE. https://doi.org/10.1109/ijcnn.2019.8851954'
chicago: Hasani, Ramin, Alexander Amini, Mathias Lechner, Felix Naser, Radu Grosu,
and Daniela Rus. “Response Characterization for Auditing Cell Dynamics in Long
Short-Term Memory Networks.” In Proceedings of the International Joint Conference
on Neural Networks. IEEE, 2019. https://doi.org/10.1109/ijcnn.2019.8851954.
ieee: R. Hasani, A. Amini, M. Lechner, F. Naser, R. Grosu, and D. Rus, “Response
characterization for auditing cell dynamics in long short-term memory networks,”
in Proceedings of the International Joint Conference on Neural Networks,
Budapest, Hungary, 2019.
ista: 'Hasani R, Amini A, Lechner M, Naser F, Grosu R, Rus D. 2019. Response characterization
for auditing cell dynamics in long short-term memory networks. Proceedings of
the International Joint Conference on Neural Networks. IJCNN: International Joint
Conference on Neural Networks, 8851954.'
mla: Hasani, Ramin, et al. “Response Characterization for Auditing Cell Dynamics
in Long Short-Term Memory Networks.” Proceedings of the International Joint
Conference on Neural Networks, 8851954, IEEE, 2019, doi:10.1109/ijcnn.2019.8851954.
short: R. Hasani, A. Amini, M. Lechner, F. Naser, R. Grosu, D. Rus, in:, Proceedings
of the International Joint Conference on Neural Networks, IEEE, 2019.
conference:
end_date: 2019-07-19
location: Budapest, Hungary
name: 'IJCNN: International Joint Conference on Neural Networks'
start_date: 2019-07-14
date_created: 2019-11-04T15:59:58Z
date_published: 2019-09-30T00:00:00Z
date_updated: 2021-01-12T08:11:19Z
day: '30'
department:
- _id: ToHe
doi: 10.1109/ijcnn.2019.8851954
external_id:
arxiv:
- '1809.03864'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1809.03864
month: '09'
oa: 1
oa_version: Preprint
publication: Proceedings of the International Joint Conference on Neural Networks
publication_identifier:
isbn:
- '9781728119854'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: 1
status: public
title: Response characterization for auditing cell dynamics in long short-term memory
networks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '7007'
abstract:
- lang: eng
text: 'We consider the primitive relay channel, where the source sends a message
to the relay and to the destination, and the relay helps the communication by
transmitting an additional message to the destination via a separate channel.
Two well-known coding techniques have been introduced for this setting: decode-and-forward
and compress-and-forward. In decode-and-forward, the relay completely decodes
the message and sends some information to the destination; in compress-and-forward,
the relay does not decode, and it sends a compressed version of the received signal
to the destination using Wyner–Ziv coding. In this paper, we present a novel coding
paradigm that provides an improved achievable rate for the primitive relay channel.
The idea is to combine compress-and-forward and decode-and-forward via a chaining
construction. We transmit over pairs of blocks: in the first block, we use compress-and-forward;
and, in the second block, we use decode-and-forward. More specifically, in the
first block, the relay does not decode, it compresses the received signal via
Wyner–Ziv, and it sends only part of the compression to the destination. In the
second block, the relay completely decodes the message, it sends some information
to the destination, and it also sends the remaining part of the compression coming
from the first block. By doing so, we are able to strictly outperform both compress-and-forward
and decode-and-forward. Note that the proposed coding scheme can be implemented
with polar codes. As such, it has the typical attractive properties of polar coding
schemes, namely, quasi-linear encoding and decoding complexity, and error probability
that decays at super-polynomial speed. As a running example, we take into account
the special case of the erasure relay channel, and we provide a comparison between
the rates achievable by our proposed scheme and the existing upper and lower bounds.'
article_number: '218'
article_type: original
author:
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: S. Hamed
full_name: Hassani, S. Hamed
last_name: Hassani
- first_name: Rüdiger
full_name: Urbanke, Rüdiger
last_name: Urbanke
citation:
ama: Mondelli M, Hassani SH, Urbanke R. A new coding paradigm for the primitive
relay channel. Algorithms. 2019;12(10). doi:10.3390/a12100218
apa: Mondelli, M., Hassani, S. H., & Urbanke, R. (2019). A new coding paradigm
for the primitive relay channel. Algorithms. MDPI. https://doi.org/10.3390/a12100218
chicago: Mondelli, Marco, S. Hamed Hassani, and Rüdiger Urbanke. “A New Coding Paradigm
for the Primitive Relay Channel.” Algorithms. MDPI, 2019. https://doi.org/10.3390/a12100218.
ieee: M. Mondelli, S. H. Hassani, and R. Urbanke, “A new coding paradigm for the
primitive relay channel,” Algorithms, vol. 12, no. 10. MDPI, 2019.
ista: Mondelli M, Hassani SH, Urbanke R. 2019. A new coding paradigm for the primitive
relay channel. Algorithms. 12(10), 218.
mla: Mondelli, Marco, et al. “A New Coding Paradigm for the Primitive Relay Channel.”
Algorithms, vol. 12, no. 10, 218, MDPI, 2019, doi:10.3390/a12100218.
short: M. Mondelli, S.H. Hassani, R. Urbanke, Algorithms 12 (2019).
date_created: 2019-11-12T14:46:19Z
date_published: 2019-10-18T00:00:00Z
date_updated: 2023-02-23T12:49:28Z
day: '18'
ddc:
- '510'
department:
- _id: MaMo
doi: 10.3390/a12100218
external_id:
arxiv:
- '1801.03153'
file:
- access_level: open_access
checksum: 267756d8f9db572f496cd1663c89d59a
content_type: application/pdf
creator: dernst
date_created: 2019-11-12T14:48:45Z
date_updated: 2020-07-14T12:47:47Z
file_id: '7008'
file_name: 2019_Algorithms_Mondelli.pdf
file_size: 696791
relation: main_file
file_date_updated: 2020-07-14T12:47:47Z
has_accepted_license: '1'
intvolume: ' 12'
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: Algorithms
publication_identifier:
issn:
- 1999-4893
publication_status: published
publisher: MDPI
quality_controlled: '1'
related_material:
record:
- id: '6675'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: A new coding paradigm for the primitive relay channel
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: 12
year: '2019'
...
---
_id: '7035'
abstract:
- lang: eng
text: 'The aim of this short note is to expound one particular issue that was discussed
during the talk [10] given at the symposium ”Researches on isometries as preserver
problems and related topics” at Kyoto RIMS. That is, the role of Dirac masses
by describing the isometry group of various metric spaces of probability measures. This article is of survey character, and it does not contain any essentially new
results.From an isometric point of view, in some cases, metric spaces of measures
are similar to C(K)-type function spaces. Similarity means here that their isometries are driven by some nice transformations
of the underlying space. Of course, it depends on the particular choice of the metric how nice these
transformations should be. Sometimes, as we will see, being a homeomorphism is
enough to generate an isometry. But sometimes we need more: the transformation
must preserve the underlying distance as well. Statements claiming that isometries
in questions are necessarily induced by homeomorphisms are called Banach-Stone-type
results, while results asserting that the underlying transformation is necessarily
an isometry are termed as isometric rigidity results.As Dirac masses can be considered as building bricks of the set of all Borel measures, a natural
question arises:Is it enough to understand how an isometry acts on the set of
Dirac masses? Does this action extend uniquely to all measures?In what follows,
we will thoroughly investigate this question.'
article_processing_charge: No
author:
- first_name: Gyorgy Pal
full_name: Geher, Gyorgy Pal
last_name: Geher
- first_name: Tamas
full_name: Titkos, Tamas
last_name: Titkos
- first_name: Daniel
full_name: Virosztek, Daniel
id: 48DB45DA-F248-11E8-B48F-1D18A9856A87
last_name: Virosztek
orcid: 0000-0003-1109-5511
citation:
ama: 'Geher GP, Titkos T, Virosztek D. Dirac masses and isometric rigidity. In:
Kyoto RIMS Kôkyûroku. Vol 2125. Research Institute for Mathematical Sciences,
Kyoto University; 2019:34-41.'
apa: 'Geher, G. P., Titkos, T., & Virosztek, D. (2019). Dirac masses and isometric
rigidity. In Kyoto RIMS Kôkyûroku (Vol. 2125, pp. 34–41). Kyoto, Japan:
Research Institute for Mathematical Sciences, Kyoto University.'
chicago: Geher, Gyorgy Pal, Tamas Titkos, and Daniel Virosztek. “Dirac Masses and
Isometric Rigidity.” In Kyoto RIMS Kôkyûroku, 2125:34–41. Research Institute
for Mathematical Sciences, Kyoto University, 2019.
ieee: G. P. Geher, T. Titkos, and D. Virosztek, “Dirac masses and isometric rigidity,”
in Kyoto RIMS Kôkyûroku, Kyoto, Japan, 2019, vol. 2125, pp. 34–41.
ista: Geher GP, Titkos T, Virosztek D. 2019. Dirac masses and isometric rigidity.
Kyoto RIMS Kôkyûroku. Research on isometries as preserver problems and related
topics vol. 2125, 34–41.
mla: Geher, Gyorgy Pal, et al. “Dirac Masses and Isometric Rigidity.” Kyoto RIMS
Kôkyûroku, vol. 2125, Research Institute for Mathematical Sciences, Kyoto
University, 2019, pp. 34–41.
short: G.P. Geher, T. Titkos, D. Virosztek, in:, Kyoto RIMS Kôkyûroku, Research
Institute for Mathematical Sciences, Kyoto University, 2019, pp. 34–41.
conference:
end_date: 2019-01-30
location: Kyoto, Japan
name: Research on isometries as preserver problems and related topics
start_date: 2019-01-28
date_created: 2019-11-18T15:39:53Z
date_published: 2019-01-30T00:00:00Z
date_updated: 2021-01-12T08:11:33Z
day: '30'
department:
- _id: LaEr
intvolume: ' 2125'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.kurims.kyoto-u.ac.jp/~kyodo/kokyuroku/contents/2125.html
month: '01'
oa: 1
oa_version: Submitted Version
page: 34-41
publication: Kyoto RIMS Kôkyûroku
publication_status: published
publisher: Research Institute for Mathematical Sciences, Kyoto University
quality_controlled: '1'
status: public
title: Dirac masses and isometric rigidity
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2125
year: '2019'
...
---
_id: '7171'
abstract:
- lang: ger
text: "Wissen Sie, was sich hinter künstlicher Intelligenz und maschinellem Lernen
verbirgt? \r\nDieses Sachbuch erklärt Ihnen leicht verständlich und ohne komplizierte
Formeln die grundlegenden Methoden und Vorgehensweisen des maschinellen Lernens.
Mathematisches Vorwissen ist dafür nicht nötig. Kurzweilig und informativ illustriert
Lisa, die Protagonistin des Buches, diese anhand von Alltagssituationen. \r\nEin
Buch für alle, die in Diskussionen über Chancen und Risiken der aktuellen Entwicklung
der künstlichen Intelligenz und des maschinellen Lernens mit Faktenwissen punkten
möchten. Auch für Schülerinnen und Schüler geeignet!"
article_processing_charge: No
citation:
ama: 'Kersting K, Lampert C, Rothkopf C, eds. Wie Maschinen Lernen: Künstliche
Intelligenz Verständlich Erklärt. 1st ed. Wiesbaden: Springer Nature; 2019.
doi:10.1007/978-3-658-26763-6'
apa: 'Kersting, K., Lampert, C., & Rothkopf, C. (Eds.). (2019). Wie Maschinen
Lernen: Künstliche Intelligenz Verständlich Erklärt (1st ed.). Wiesbaden:
Springer Nature. https://doi.org/10.1007/978-3-658-26763-6'
chicago: 'Kersting, Kristian, Christoph Lampert, and Constantin Rothkopf, eds. Wie
Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt. 1st ed. Wiesbaden:
Springer Nature, 2019. https://doi.org/10.1007/978-3-658-26763-6.'
ieee: 'K. Kersting, C. Lampert, and C. Rothkopf, Eds., Wie Maschinen Lernen:
Künstliche Intelligenz Verständlich Erklärt, 1st ed. Wiesbaden: Springer Nature,
2019.'
ista: 'Kersting K, Lampert C, Rothkopf C eds. 2019. Wie Maschinen Lernen: Künstliche
Intelligenz Verständlich Erklärt 1st ed., Wiesbaden: Springer Nature, XIV, 245p.'
mla: 'Kersting, Kristian, et al., editors. Wie Maschinen Lernen: Künstliche Intelligenz
Verständlich Erklärt. 1st ed., Springer Nature, 2019, doi:10.1007/978-3-658-26763-6.'
short: 'K. Kersting, C. Lampert, C. Rothkopf, eds., Wie Maschinen Lernen: Künstliche
Intelligenz Verständlich Erklärt, 1st ed., Springer Nature, Wiesbaden, 2019.'
date_created: 2019-12-11T14:15:56Z
date_published: 2019-10-30T00:00:00Z
date_updated: 2021-12-22T14:40:58Z
day: '30'
department:
- _id: ChLa
doi: 10.1007/978-3-658-26763-6
edition: '1'
editor:
- first_name: Kristian
full_name: Kersting, Kristian
last_name: Kersting
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Constantin
full_name: Rothkopf, Constantin
last_name: Rothkopf
language:
- iso: ger
month: '10'
oa_version: None
page: XIV, 245
place: Wiesbaden
publication_identifier:
eisbn:
- 978-3-658-26763-6
isbn:
- 978-3-658-26762-9
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Website
relation: press_release
url: https://ist.ac.at/en/news/book-release-how-machines-learn/
status: public
title: 'Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt'
type: book_editor
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2019'
...
---
_id: '7401'
abstract:
- lang: eng
text: 'The genus g(G) of a graph G is the minimum g such that G has an embedding
on the orientable surface M_g of genus g. A drawing of a graph on a surface is
independently even if every pair of nonadjacent edges in the drawing crosses an
even number of times. The Z_2-genus of a graph G, denoted by g_0(G), is the minimum
g such that G has an independently even drawing on M_g. By a result of Battle,
Harary, Kodama and Youngs from 1962, the graph genus is additive over 2-connected
blocks. In 2013, Schaefer and Stefankovic proved that the Z_2-genus of a graph
is additive over 2-connected blocks as well, and asked whether this result can
be extended to so-called 2-amalgamations, as an analogue of results by Decker,
Glover, Huneke, and Stahl for the genus. We give the following partial answer.
If G=G_1 cup G_2, G_1 and G_2 intersect in two vertices u and v, and G-u-v has
k connected components (among which we count the edge uv if present), then |g_0(G)-(g_0(G_1)+g_0(G_2))|<=k+1.
For complete bipartite graphs K_{m,n}, with n >= m >= 3, we prove that g_0(K_{m,n})/g(K_{m,n})=1-O(1/n).
Similar results are proved also for the Euler Z_2-genus. We express the Z_2-genus
of a graph using the minimum rank of partial symmetric matrices over Z_2; a problem
that might be of independent interest. '
alternative_title:
- LIPIcs
article_number: '39'
article_processing_charge: No
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Jan
full_name: Kyncl, Jan
last_name: Kyncl
citation:
ama: 'Fulek R, Kyncl J. Z_2-Genus of graphs and minimum rank of partial symmetric
matrices. In: 35th International Symposium on Computational Geometry (SoCG
2019). Vol 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.SOCG.2019.39'
apa: 'Fulek, R., & Kyncl, J. (2019). Z_2-Genus of graphs and minimum rank of
partial symmetric matrices. In 35th International Symposium on Computational
Geometry (SoCG 2019) (Vol. 129). Portland, OR, United States: Schloss Dagstuhl
- Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.SOCG.2019.39'
chicago: Fulek, Radoslav, and Jan Kyncl. “Z_2-Genus of Graphs and Minimum Rank of
Partial Symmetric Matrices.” In 35th International Symposium on Computational
Geometry (SoCG 2019), Vol. 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2019. https://doi.org/10.4230/LIPICS.SOCG.2019.39.
ieee: R. Fulek and J. Kyncl, “Z_2-Genus of graphs and minimum rank of partial symmetric
matrices,” in 35th International Symposium on Computational Geometry (SoCG
2019), Portland, OR, United States, 2019, vol. 129.
ista: 'Fulek R, Kyncl J. 2019. Z_2-Genus of graphs and minimum rank of partial symmetric
matrices. 35th International Symposium on Computational Geometry (SoCG 2019).
SoCG: Symposium on Computational Geometry, LIPIcs, vol. 129, 39.'
mla: Fulek, Radoslav, and Jan Kyncl. “Z_2-Genus of Graphs and Minimum Rank of Partial
Symmetric Matrices.” 35th International Symposium on Computational Geometry
(SoCG 2019), vol. 129, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2019, doi:10.4230/LIPICS.SOCG.2019.39.
short: R. Fulek, J. Kyncl, in:, 35th International Symposium on Computational Geometry
(SoCG 2019), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.
conference:
end_date: 2019-06-21
location: Portland, OR, United States
name: 'SoCG: Symposium on Computational Geometry'
start_date: 2019-06-18
date_created: 2020-01-29T16:17:05Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2021-01-12T08:13:24Z
day: '01'
ddc:
- '000'
department:
- _id: UlWa
doi: 10.4230/LIPICS.SOCG.2019.39
external_id:
arxiv:
- '1903.08637'
file:
- access_level: open_access
checksum: aac37b09118cc0ab58cf77129e691f8c
content_type: application/pdf
creator: dernst
date_created: 2020-02-04T09:14:31Z
date_updated: 2020-07-14T12:47:57Z
file_id: '7445'
file_name: 2019_LIPIcs_Fulek.pdf
file_size: 628347
relation: main_file
file_date_updated: 2020-07-14T12:47:57Z
has_accepted_license: '1'
intvolume: ' 129'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 261FA626-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02281
name: Eliminating intersections in drawings of graphs
publication: 35th International Symposium on Computational Geometry (SoCG 2019)
publication_identifier:
isbn:
- 978-3-95977-104-7
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
scopus_import: 1
status: public
title: Z_2-Genus of graphs and minimum rank of partial symmetric 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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 129
year: '2019'
...
---
_id: '7453'
abstract:
- lang: eng
text: We illustrate the ingredients of the state-of-the-art of model-based approach
for the formal design and verification of cyber-physical systems. To capture the
interaction between a discrete controller and its continuously evolving environment,
we use the formal models of timed and hybrid automata. We explain the steps of
modeling and verification in the tools Uppaal and SpaceEx using a case study based
on a dual-chamber implantable pacemaker monitoring a human heart. We show how
to design a model as a composition of components, how to construct models at varying
levels of detail, how to establish that one model is an abstraction of another,
how to specify correctness requirements using temporal logic, and how to verify
that a model satisfies a logical requirement.
acknowledgement: This research was supported in part by the Austrian Science Fund
(FWF) under grants S11402-N23(RiSE/SHiNE) and Z211-N23 (Wittgenstein Award). This
research has received funding from the Sino-Danish Basic Research Centre, IDEA4CPS,
funded by the Danish National Research Foundation and the National Science Foundation,
China, the Innovation Fund Denmark centre DiCyPS, as well as the ERC Advanced Grant
LASSO.
alternative_title:
- Lecture Notes in Computer Science
article_processing_charge: No
author:
- first_name: Rajeev
full_name: Alur, Rajeev
last_name: Alur
- first_name: Mirco
full_name: Giacobbe, Mirco
id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
last_name: Giacobbe
orcid: 0000-0001-8180-0904
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Kim G.
full_name: Larsen, Kim G.
last_name: Larsen
- first_name: Marius
full_name: Mikučionis, Marius
last_name: Mikučionis
citation:
ama: 'Alur R, Giacobbe M, Henzinger TA, Larsen KG, Mikučionis M. Continuous-time
models for system design and analysis. In: Steffen B, Woeginger G, eds. Computing
and Software Science. Vol 10000. LNCS. Springer Nature; 2019:452-477. doi:10.1007/978-3-319-91908-9_22'
apa: Alur, R., Giacobbe, M., Henzinger, T. A., Larsen, K. G., & Mikučionis,
M. (2019). Continuous-time models for system design and analysis. In B. Steffen
& G. Woeginger (Eds.), Computing and Software Science (Vol. 10000,
pp. 452–477). Springer Nature. https://doi.org/10.1007/978-3-319-91908-9_22
chicago: Alur, Rajeev, Mirco Giacobbe, Thomas A Henzinger, Kim G. Larsen, and Marius
Mikučionis. “Continuous-Time Models for System Design and Analysis.” In Computing
and Software Science, edited by Bernhard Steffen and Gerhard Woeginger, 10000:452–77.
LNCS. Springer Nature, 2019. https://doi.org/10.1007/978-3-319-91908-9_22.
ieee: R. Alur, M. Giacobbe, T. A. Henzinger, K. G. Larsen, and M. Mikučionis, “Continuous-time
models for system design and analysis,” in Computing and Software Science,
vol. 10000, B. Steffen and G. Woeginger, Eds. Springer Nature, 2019, pp. 452–477.
ista: 'Alur R, Giacobbe M, Henzinger TA, Larsen KG, Mikučionis M. 2019.Continuous-time
models for system design and analysis. In: Computing and Software Science. Lecture
Notes in Computer Science, vol. 10000, 452–477.'
mla: Alur, Rajeev, et al. “Continuous-Time Models for System Design and Analysis.”
Computing and Software Science, edited by Bernhard Steffen and Gerhard
Woeginger, vol. 10000, Springer Nature, 2019, pp. 452–77, doi:10.1007/978-3-319-91908-9_22.
short: R. Alur, M. Giacobbe, T.A. Henzinger, K.G. Larsen, M. Mikučionis, in:, B.
Steffen, G. Woeginger (Eds.), Computing and Software Science, Springer Nature,
2019, pp. 452–477.
date_created: 2020-02-05T10:51:44Z
date_published: 2019-10-05T00:00:00Z
date_updated: 2022-09-06T08:25:52Z
day: '05'
department:
- _id: ToHe
doi: 10.1007/978-3-319-91908-9_22
editor:
- first_name: Bernhard
full_name: Steffen, Bernhard
last_name: Steffen
- first_name: Gerhard
full_name: Woeginger, Gerhard
last_name: Woeginger
intvolume: ' 10000'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1007/978-3-319-91908-9_22
month: '10'
oa: 1
oa_version: Published Version
page: 452-477
project:
- _id: 25F2ACDE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Computing and Software Science
publication_identifier:
eisbn:
- '9783319919089'
eissn:
- 0302-9743
isbn:
- '9783319919072'
issn:
- 1611-3349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: LNCS
status: public
title: Continuous-time models for system design and analysis
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10000
year: '2019'
...
---
_id: '7550'
abstract:
- lang: eng
text: 'We consider an optimal control problem for an abstract nonlinear dissipative
evolution equation. The differential constraint is penalized by augmenting the
target functional by a nonnegative global-in-time functional which is null-minimized
in the evolution equation is satisfied. Different variational settings are presented,
leading to the convergence of the penalization method for gradient flows, noncyclic
and semimonotone flows, doubly nonlinear evolutions, and GENERIC systems. '
acknowledgement: This work is supported by Vienna Science and Technology Fund (WWTF)
through Project MA14-009 and by the Austrian Science Fund (FWF) projects F 65 and
I 2375.
article_processing_charge: No
article_type: original
author:
- first_name: Lorenzo
full_name: Portinale, Lorenzo
id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87
last_name: Portinale
- first_name: Ulisse
full_name: Stefanelli, Ulisse
last_name: Stefanelli
citation:
ama: Portinale L, Stefanelli U. Penalization via global functionals of optimal-control
problems for dissipative evolution. Advances in Mathematical Sciences and Applications.
2019;28(2):425-447.
apa: Portinale, L., & Stefanelli, U. (2019). Penalization via global functionals
of optimal-control problems for dissipative evolution. Advances in Mathematical
Sciences and Applications. Gakko Tosho.
chicago: Portinale, Lorenzo, and Ulisse Stefanelli. “Penalization via Global Functionals
of Optimal-Control Problems for Dissipative Evolution.” Advances in Mathematical
Sciences and Applications. Gakko Tosho, 2019.
ieee: L. Portinale and U. Stefanelli, “Penalization via global functionals of optimal-control
problems for dissipative evolution,” Advances in Mathematical Sciences and
Applications, vol. 28, no. 2. Gakko Tosho, pp. 425–447, 2019.
ista: Portinale L, Stefanelli U. 2019. Penalization via global functionals of optimal-control
problems for dissipative evolution. Advances in Mathematical Sciences and Applications.
28(2), 425–447.
mla: Portinale, Lorenzo, and Ulisse Stefanelli. “Penalization via Global Functionals
of Optimal-Control Problems for Dissipative Evolution.” Advances in Mathematical
Sciences and Applications, vol. 28, no. 2, Gakko Tosho, 2019, pp. 425–47.
short: L. Portinale, U. Stefanelli, Advances in Mathematical Sciences and Applications
28 (2019) 425–447.
date_created: 2020-02-28T10:54:41Z
date_published: 2019-10-22T00:00:00Z
date_updated: 2022-06-17T07:52:41Z
day: '22'
department:
- _id: JaMa
external_id:
arxiv:
- '1910.10050'
intvolume: ' 28'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.1910.10050'
month: '10'
oa: 1
oa_version: Preprint
page: 425-447
project:
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication: Advances in Mathematical Sciences and Applications
publication_identifier:
issn:
- 1343-4373
publication_status: published
publisher: Gakko Tosho
quality_controlled: '1'
status: public
title: Penalization via global functionals of optimal-control problems for dissipative
evolution
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2019'
...
---
_id: '7552'
abstract:
- lang: eng
text: 'There is increasing evidence that protein binding to specific sites along
DNA can activate the reading out of genetic information without coming into direct
physical contact with the gene. There also is evidence that these distant but
interacting sites are embedded in a liquid droplet of proteins which condenses
out of the surrounding solution. We argue that droplet-mediated interactions can
account for crucial features of gene regulation only if the droplet is poised
at a non-generic point in its phase diagram. We explore a minimal model that embodies
this idea, show that this model has a natural mechanism for self-tuning, and suggest
direct experimental tests. '
article_processing_charge: No
author:
- first_name: William
full_name: Bialek, William
last_name: Bialek
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation.
arXiv:191208579.
apa: Bialek, W., Gregor, T., & Tkačik, G. (n.d.). Action at a distance in transcriptional
regulation. arXiv:1912.08579. ArXiv.
chicago: Bialek, William, Thomas Gregor, and Gašper Tkačik. “Action at a Distance
in Transcriptional Regulation.” ArXiv:1912.08579. ArXiv, n.d.
ieee: W. Bialek, T. Gregor, and G. Tkačik, “Action at a distance in transcriptional
regulation,” arXiv:1912.08579. ArXiv.
ista: Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation.
arXiv:1912.08579, .
mla: Bialek, William, et al. “Action at a Distance in Transcriptional Regulation.”
ArXiv:1912.08579, ArXiv.
short: W. Bialek, T. Gregor, G. Tkačik, ArXiv:1912.08579 (n.d.).
date_created: 2020-02-28T10:57:08Z
date_published: 2019-12-18T00:00:00Z
date_updated: 2021-01-12T08:14:09Z
day: '18'
department:
- _id: GaTk
external_id:
arxiv:
- '1912.08579'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1912.08579
month: '12'
oa: 1
oa_version: Preprint
page: '5'
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: arXiv:1912.08579
publication_status: submitted
publisher: ArXiv
status: public
title: Action at a distance in transcriptional regulation
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '7576'
abstract:
- lang: eng
text: We present the results of a friendly competition for formal verification of
continuous and hybrid systems with nonlinear continuous dynamics. The friendly
competition took place as part of the workshop Applied Verification for Continuous
and Hybrid Systems (ARCH) in 2019. In this year, 6 tools Ariadne, CORA, DynIbex,
Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. They are
applied to solve reachability analysis problems on four benchmark problems, one
of them with hybrid dynamics. We do not rank the tools based on the results, but
show the current status and discover the potential advantages of different tools.
article_processing_charge: No
author:
- first_name: Fabian
full_name: Immler, Fabian
last_name: Immler
- first_name: Matthias
full_name: Althoff, Matthias
last_name: Althoff
- first_name: Luis
full_name: Benet, Luis
last_name: Benet
- first_name: Alexandre
full_name: Chapoutot, Alexandre
last_name: Chapoutot
- first_name: Xin
full_name: Chen, Xin
last_name: Chen
- first_name: Marcelo
full_name: Forets, Marcelo
last_name: Forets
- first_name: Luca
full_name: Geretti, Luca
last_name: Geretti
- first_name: Niklas
full_name: Kochdumper, Niklas
last_name: Kochdumper
- first_name: David P.
full_name: Sanders, David P.
last_name: Sanders
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
citation:
ama: 'Immler F, Althoff M, Benet L, et al. ARCH-COMP19 Category Report: Continuous
and hybrid systems with nonlinear dynamics. In: EPiC Series in Computing.
Vol 61. EasyChair Publications; 2019:41-61. doi:10.29007/m75b'
apa: 'Immler, F., Althoff, M., Benet, L., Chapoutot, A., Chen, X., Forets, M., …
Schilling, C. (2019). ARCH-COMP19 Category Report: Continuous and hybrid systems
with nonlinear dynamics. In EPiC Series in Computing (Vol. 61, pp. 41–61).
Montreal, Canada: EasyChair Publications. https://doi.org/10.29007/m75b'
chicago: 'Immler, Fabian, Matthias Althoff, Luis Benet, Alexandre Chapoutot, Xin
Chen, Marcelo Forets, Luca Geretti, Niklas Kochdumper, David P. Sanders, and Christian
Schilling. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Nonlinear
Dynamics.” In EPiC Series in Computing, 61:41–61. EasyChair Publications,
2019. https://doi.org/10.29007/m75b.'
ieee: 'F. Immler et al., “ARCH-COMP19 Category Report: Continuous and hybrid
systems with nonlinear dynamics,” in EPiC Series in Computing, Montreal,
Canada, 2019, vol. 61, pp. 41–61.'
ista: 'Immler F, Althoff M, Benet L, Chapoutot A, Chen X, Forets M, Geretti L, Kochdumper
N, Sanders DP, Schilling C. 2019. ARCH-COMP19 Category Report: Continuous and
hybrid systems with nonlinear dynamics. EPiC Series in Computing. ARCH: International
Workshop on Applied Verification on Continuous and Hybrid Systems vol. 61, 41–61.'
mla: 'Immler, Fabian, et al. “ARCH-COMP19 Category Report: Continuous and Hybrid
Systems with Nonlinear Dynamics.” EPiC Series in Computing, vol. 61, EasyChair
Publications, 2019, pp. 41–61, doi:10.29007/m75b.'
short: F. Immler, M. Althoff, L. Benet, A. Chapoutot, X. Chen, M. Forets, L. Geretti,
N. Kochdumper, D.P. Sanders, C. Schilling, in:, EPiC Series in Computing, EasyChair
Publications, 2019, pp. 41–61.
conference:
end_date: 2019-04-15
location: Montreal, Canada
name: 'ARCH: International Workshop on Applied Verification on Continuous and Hybrid
Systems'
start_date: 2019-04-15
date_created: 2020-03-08T23:00:49Z
date_published: 2019-05-25T00:00:00Z
date_updated: 2021-01-12T08:14:17Z
day: '25'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.29007/m75b
file:
- access_level: open_access
checksum: 9138977a06fcd6a95976eb4bca875f0c
content_type: application/pdf
creator: dernst
date_created: 2020-03-24T07:36:36Z
date_updated: 2020-07-14T12:48:00Z
file_id: '7617'
file_name: 2019_ARCH19_Immler.pdf
file_size: 1934830
relation: main_file
file_date_updated: 2020-07-14T12:48:00Z
has_accepted_license: '1'
intvolume: ' 61'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 41-61
publication: EPiC Series in Computing
publication_identifier:
eissn:
- '23987340'
publication_status: published
publisher: EasyChair Publications
quality_controlled: '1'
scopus_import: 1
status: public
title: 'ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear
dynamics'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 61
year: '2019'
...
---
_id: '8175'
abstract:
- lang: eng
text: We study edge asymptotics of poissonized Plancherel-type measures on skew
Young diagrams (integer partitions). These measures can be seen as generalizations
of those studied by Baik--Deift--Johansson and Baik--Rains in resolving Ulam's
problem on longest increasing subsequences of random permutations and the last
passage percolation (corner growth) discrete versions thereof. Moreover they interpolate
between said measures and the uniform measure on partitions. In the new KPZ-like
1/3 exponent edge scaling limit with logarithmic corrections, we find new probability
distributions generalizing the classical Tracy--Widom GUE, GOE and GSE distributions
from the theory of random matrices.
acknowledgement: "D.B. is especially grateful to Patrik Ferrari for suggesting simplifications
in Section 3 and\r\nto Alessandra Occelli for suggesting the name for the models
of Section 2.\r\n"
article_number: '34'
article_processing_charge: No
author:
- first_name: Dan
full_name: Betea, Dan
last_name: Betea
- first_name: Jérémie
full_name: Bouttier, Jérémie
last_name: Bouttier
- first_name: Peter
full_name: Nejjar, Peter
id: 4BF426E2-F248-11E8-B48F-1D18A9856A87
last_name: Nejjar
- first_name: Mirjana
full_name: Vuletíc, Mirjana
last_name: Vuletíc
citation:
ama: 'Betea D, Bouttier J, Nejjar P, Vuletíc M. New edge asymptotics of skew Young
diagrams via free boundaries. In: Proceedings on the 31st International Conference
on Formal Power Series and Algebraic Combinatorics. Formal Power Series and
Algebraic Combinatorics; 2019.'
apa: 'Betea, D., Bouttier, J., Nejjar, P., & Vuletíc, M. (2019). New edge asymptotics
of skew Young diagrams via free boundaries. In Proceedings on the 31st International
Conference on Formal Power Series and Algebraic Combinatorics. Ljubljana,
Slovenia: Formal Power Series and Algebraic Combinatorics.'
chicago: Betea, Dan, Jérémie Bouttier, Peter Nejjar, and Mirjana Vuletíc. “New Edge
Asymptotics of Skew Young Diagrams via Free Boundaries.” In Proceedings on
the 31st International Conference on Formal Power Series and Algebraic Combinatorics.
Formal Power Series and Algebraic Combinatorics, 2019.
ieee: D. Betea, J. Bouttier, P. Nejjar, and M. Vuletíc, “New edge asymptotics of
skew Young diagrams via free boundaries,” in Proceedings on the 31st International
Conference on Formal Power Series and Algebraic Combinatorics, Ljubljana,
Slovenia, 2019.
ista: 'Betea D, Bouttier J, Nejjar P, Vuletíc M. 2019. New edge asymptotics of skew
Young diagrams via free boundaries. Proceedings on the 31st International Conference
on Formal Power Series and Algebraic Combinatorics. FPSAC: International Conference
on Formal Power Series and Algebraic Combinatorics, 34.'
mla: Betea, Dan, et al. “New Edge Asymptotics of Skew Young Diagrams via Free Boundaries.”
Proceedings on the 31st International Conference on Formal Power Series and
Algebraic Combinatorics, 34, Formal Power Series and Algebraic Combinatorics,
2019.
short: D. Betea, J. Bouttier, P. Nejjar, M. Vuletíc, in:, Proceedings on the 31st
International Conference on Formal Power Series and Algebraic Combinatorics, Formal
Power Series and Algebraic Combinatorics, 2019.
conference:
end_date: 2019-07-05
location: Ljubljana, Slovenia
name: 'FPSAC: International Conference on Formal Power Series and Algebraic Combinatorics'
start_date: 2019-07-01
date_created: 2020-07-26T22:01:04Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2021-01-12T08:17:18Z
day: '01'
department:
- _id: LaEr
ec_funded: 1
external_id:
arxiv:
- '1902.08750'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1902.08750
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
publication: Proceedings on the 31st International Conference on Formal Power Series
and Algebraic Combinatorics
publication_status: published
publisher: Formal Power Series and Algebraic Combinatorics
quality_controlled: '1'
scopus_import: '1'
status: public
title: New edge asymptotics of skew Young diagrams via free boundaries
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...