---
_id: '2050'
abstract:
- lang: eng
text: The flow instability and further transition to turbulence in a toroidal pipe
(torus) with curvature ratio (tube-to-coiling diameter) 0.049 is investigated
experimentally. The flow inside the toroidal pipe is driven by a steel sphere
fitted to the inner pipe diameter. The sphere is moved with constant azimuthal
velocity from outside the torus by a moving magnet. The experiment is designed
to investigate curved pipe flow by optical measurement techniques. Using stereoscopic
particle image velocimetry, laser Doppler velocimetry and pressure drop measurements,
the flow is measured for Reynolds numbers ranging from 1000 to 15 000. Time- and
space-resolved velocity fields are obtained and analysed. The steady axisymmetric
basic flow is strongly influenced by centrifugal effects. On an increase of the
Reynolds number we find a sequence of bifurcations. For Re=4075±2% a supercritical
bifurcation to an oscillatory flow is found in which waves travel in the streamwise
direction with a phase velocity slightly faster than the mean flow. The oscillatory
flow is superseded by a presumably quasi-periodic flow at a further increase of
the Reynolds number before turbulence sets in. The results are found to be compatible,
in general, with earlier experimental and numerical investigations on transition
to turbulence in helical and curved pipes. However, important aspects of the bifurcation
scenario differ considerably.
article_processing_charge: No
arxiv: 1
author:
- first_name: Jakob
full_name: Kühnen, Jakob
id: 3A47AE32-F248-11E8-B48F-1D18A9856A87
last_name: Kühnen
orcid: 0000-0003-4312-0179
- first_name: Markus
full_name: Holzner, Markus
last_name: Holzner
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Hendrik
full_name: Kuhlmann, Hendrik
last_name: Kuhlmann
citation:
ama: Kühnen J, Holzner M, Hof B, Kuhlmann H. Experimental investigation of transitional
flow in a toroidal pipe. Journal of Fluid Mechanics. 2014;738:463-491.
doi:10.1017/jfm.2013.603
apa: Kühnen, J., Holzner, M., Hof, B., & Kuhlmann, H. (2014). Experimental investigation
of transitional flow in a toroidal pipe. Journal of Fluid Mechanics. Cambridge
University Press. https://doi.org/10.1017/jfm.2013.603
chicago: Kühnen, Jakob, Markus Holzner, Björn Hof, and Hendrik Kuhlmann. “Experimental
Investigation of Transitional Flow in a Toroidal Pipe.” Journal of Fluid Mechanics.
Cambridge University Press, 2014. https://doi.org/10.1017/jfm.2013.603.
ieee: J. Kühnen, M. Holzner, B. Hof, and H. Kuhlmann, “Experimental investigation
of transitional flow in a toroidal pipe,” Journal of Fluid Mechanics, vol.
738. Cambridge University Press, pp. 463–491, 2014.
ista: Kühnen J, Holzner M, Hof B, Kuhlmann H. 2014. Experimental investigation of
transitional flow in a toroidal pipe. Journal of Fluid Mechanics. 738, 463–491.
mla: Kühnen, Jakob, et al. “Experimental Investigation of Transitional Flow in a
Toroidal Pipe.” Journal of Fluid Mechanics, vol. 738, Cambridge University
Press, 2014, pp. 463–91, doi:10.1017/jfm.2013.603.
short: J. Kühnen, M. Holzner, B. Hof, H. Kuhlmann, Journal of Fluid Mechanics 738
(2014) 463–491.
corr_author: '1'
date_created: 2018-12-11T11:55:25Z
date_published: 2014-01-10T00:00:00Z
date_updated: 2025-09-29T11:51:23Z
day: '10'
department:
- _id: BjHo
doi: 10.1017/jfm.2013.603
external_id:
arxiv:
- '1508.06546'
isi:
- '000328486400021'
intvolume: ' 738'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1508.06546
month: '01'
oa: 1
oa_version: Submitted Version
page: 463 - 491
publication: Journal of Fluid Mechanics
publication_status: published
publisher: Cambridge University Press
publist_id: '5001'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Experimental investigation of transitional flow in a toroidal pipe
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 738
year: '2014'
...
---
OA_place: repository
OA_type: gold
_id: '2051'
abstract:
- lang: eng
text: We show that the usual score function for conditional Markov networks can
be written as the expectation over the scores of their spanning trees. We also
show that a small random sample of these output trees can attain a significant
fraction of the margin obtained by the complete graph and we provide conditions
under which we can perform tractable inference. The experimental results confirm
that practical learning is scalable to realistic datasets using this approach.
article_processing_charge: No
author:
- first_name: Mario
full_name: Marchand, Mario
last_name: Marchand
- first_name: Su
full_name: Hongyu, Su
last_name: Hongyu
- first_name: Emilie
full_name: Morvant, Emilie
id: 4BAC2A72-F248-11E8-B48F-1D18A9856A87
last_name: Morvant
orcid: 0000-0002-8301-7240
- first_name: Juho
full_name: Rousu, Juho
last_name: Rousu
- first_name: John
full_name: Shawe Taylor, John
last_name: Shawe Taylor
citation:
ama: 'Marchand M, Hongyu S, Morvant E, Rousu J, Shawe Taylor J. Multilabel structured
output learning with random spanning trees of max-margin Markov networks. In:
Advances in Neural Information Processing Systems. Vol 27. Neural Information
Processing Systems Foundation; 2014.'
apa: 'Marchand, M., Hongyu, S., Morvant, E., Rousu, J., & Shawe Taylor, J. (2014).
Multilabel structured output learning with random spanning trees of max-margin
Markov networks. In Advances in Neural Information Processing Systems (Vol.
27). Montreal, Canada: Neural Information Processing Systems Foundation.'
chicago: Marchand, Mario, Su Hongyu, Emilie Morvant, Juho Rousu, and John Shawe
Taylor. “Multilabel Structured Output Learning with Random Spanning Trees of Max-Margin
Markov Networks.” In Advances in Neural Information Processing Systems,
Vol. 27. Neural Information Processing Systems Foundation, 2014.
ieee: M. Marchand, S. Hongyu, E. Morvant, J. Rousu, and J. Shawe Taylor, “Multilabel
structured output learning with random spanning trees of max-margin Markov networks,”
in Advances in Neural Information Processing Systems, Montreal, Canada,
2014, vol. 27.
ista: 'Marchand M, Hongyu S, Morvant E, Rousu J, Shawe Taylor J. 2014. Multilabel
structured output learning with random spanning trees of max-margin Markov networks.
Advances in Neural Information Processing Systems. NIPS: Neural Information Processing
Systems vol. 27.'
mla: Marchand, Mario, et al. “Multilabel Structured Output Learning with Random
Spanning Trees of Max-Margin Markov Networks.” Advances in Neural Information
Processing Systems, vol. 27, Neural Information Processing Systems Foundation,
2014.
short: M. Marchand, S. Hongyu, E. Morvant, J. Rousu, J. Shawe Taylor, in:, Advances
in Neural Information Processing Systems, Neural Information Processing Systems
Foundation, 2014.
conference:
end_date: 2014-12-13
location: Montreal, Canada
name: 'NIPS: Neural Information Processing Systems'
start_date: 2014-12-08
date_created: 2018-12-11T11:55:26Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2026-06-18T18:24:19Z
day: '01'
ddc:
- '000'
department:
- _id: ChLa
intvolume: ' 27'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-01065586
month: '01'
oa: 1
oa_version: Published Version
publication: Advances in Neural Information Processing Systems
publication_identifier:
isbn:
- '9781510800410'
publication_status: published
publisher: Neural Information Processing Systems Foundation
publist_id: '4996'
status: public
title: Multilabel structured output learning with random spanning trees of max-margin
Markov networks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2014'
...
---
_id: '2052'
abstract:
- lang: eng
text: A standard technique for solving the parameterized model checking problem
is to reduce it to the classic model checking problem of finitely many finite-state
systems. This work considers some of the theoretical power and limitations of
this technique. We focus on concurrent systems in which processes communicate
via pairwise rendezvous, as well as the special cases of disjunctive guards and
token passing; specifications are expressed in indexed temporal logic without
the next operator; and the underlying network topologies are generated by suitable
Monadic Second Order Logic formulas and graph operations. First, we settle the
exact computational complexity of the parameterized model checking problem for
some of our concurrent systems, and establish new decidability results for others.
Second, we consider the cases that model checking the parameterized system can
be reduced to model checking some fixed number of processes, the number is known
as a cutoff. We provide many cases for when such cutoffs can be computed, establish
lower bounds on the size of such cutoffs, and identify cases where no cutoff exists.
Third, we consider cases for which the parameterized system is equivalent to a
single finite-state system (more precisely a Büchi word automaton), and establish
tight bounds on the sizes of such automata.
acknowledgement: The second, third, fourth and fifth authors were supported by the
Austrian National Research Network S11403-N23 (RiSE) of the Austrian Science Fund
(FWF) and by the Vienna Science and Technology Fund (WWTF) through grants PROSEED,
ICT12-059, and VRG11-005.
alternative_title:
- LNCS
author:
- first_name: Benjamin
full_name: Aminof, Benjamin
id: 4A55BD00-F248-11E8-B48F-1D18A9856A87
last_name: Aminof
- first_name: Tomer
full_name: Kotek, Tomer
last_name: Kotek
- first_name: Sacha
full_name: Rubin, Sacha
last_name: Rubin
- first_name: Francesco
full_name: Spegni, Francesco
last_name: Spegni
- first_name: Helmut
full_name: Veith, Helmut
last_name: Veith
citation:
ama: 'Aminof B, Kotek T, Rubin S, Spegni F, Veith H. Parameterized model checking
of rendezvous systems. In: Baldan P, Gorla D, eds. Lecture Notes in Computer
Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture
Notes in Bioinformatics). Vol 8704. Schloss Dagstuhl - Leibniz-Zentrum für
Informatik; 2014:109-124. doi:10.1007/978-3-662-44584-6_9'
apa: 'Aminof, B., Kotek, T., Rubin, S., Spegni, F., & Veith, H. (2014). Parameterized
model checking of rendezvous systems. In P. Baldan & D. Gorla (Eds.), Lecture
Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence
and Lecture Notes in Bioinformatics) (Vol. 8704, pp. 109–124). Rome, Italy:
Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-662-44584-6_9'
chicago: Aminof, Benjamin, Tomer Kotek, Sacha Rubin, Francesco Spegni, and Helmut
Veith. “Parameterized Model Checking of Rendezvous Systems.” In Lecture Notes
in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence
and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla,
8704:109–24. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014. https://doi.org/10.1007/978-3-662-44584-6_9.
ieee: B. Aminof, T. Kotek, S. Rubin, F. Spegni, and H. Veith, “Parameterized model
checking of rendezvous systems,” in Lecture Notes in Computer Science (including
subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics),
Rome, Italy, 2014, vol. 8704, pp. 109–124.
ista: 'Aminof B, Kotek T, Rubin S, Spegni F, Veith H. 2014. Parameterized model
checking of rendezvous systems. Lecture Notes in Computer Science (including subseries
Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics).
CONCUR: Concurrency Theory, LNCS, vol. 8704, 109–124.'
mla: Aminof, Benjamin, et al. “Parameterized Model Checking of Rendezvous Systems.”
Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial
Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan
and Daniele Gorla, vol. 8704, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2014, pp. 109–24, doi:10.1007/978-3-662-44584-6_9.
short: B. Aminof, T. Kotek, S. Rubin, F. Spegni, H. Veith, in:, P. Baldan, D. Gorla
(Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in
Artificial Intelligence and Lecture Notes in Bioinformatics), Schloss Dagstuhl
- Leibniz-Zentrum für Informatik, 2014, pp. 109–124.
conference:
end_date: 2014-09-05
location: Rome, Italy
name: 'CONCUR: Concurrency Theory'
start_date: 2014-09-02
date_created: 2018-12-11T11:55:26Z
date_published: 2014-09-01T00:00:00Z
date_updated: 2024-10-21T06:02:50Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-662-44584-6_9
editor:
- first_name: Paolo
full_name: Baldan, Paolo
last_name: Baldan
- first_name: Daniele
full_name: Gorla, Daniele
last_name: Gorla
intvolume: ' 8704'
language:
- iso: eng
month: '09'
oa_version: None
page: 109 - 124
publication: Lecture Notes in Computer Science (including subseries Lecture Notes
in Artificial Intelligence and Lecture Notes in Bioinformatics)
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '4994'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Parameterized model checking of rendezvous systems
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 8704
year: '2014'
...
---
_id: '2053'
abstract:
- lang: eng
text: In contrast to the usual understanding of probabilistic systems as stochastic
processes, recently these systems have also been regarded as transformers of probabilities.
In this paper, we give a natural definition of strong bisimulation for probabilistic
systems corresponding to this view that treats probability distributions as first-class
citizens. Our definition applies in the same way to discrete systems as well as
to systems with uncountable state and action spaces. Several examples demonstrate
that our definition refines the understanding of behavioural equivalences of probabilistic
systems. In particular, it solves a longstanding open problem concerning the representation
of memoryless continuous time by memoryfull continuous time. Finally, we give
algorithms for computing this bisimulation not only for finite but also for classes
of uncountably infinite systems.
acknowledgement: This work is supported by the EU 7th Framework Programme under grant
agreements 295261 (MEALS) and 318490 (SENSATION), Czech Science Foundation under
grant agreement P202/12/G061, the DFG Transregional Collaborative Research Centre
SFB/TR 14 AVACS, and by the CAS/SAFEA International Partnership Program for Creative
Research Teams.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Holger
full_name: Hermanns, Holger
last_name: Hermanns
- first_name: Jan
full_name: Krčál, Jan
last_name: Krčál
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
citation:
ama: 'Hermanns H, Krčál J, Kretinsky J. Probabilistic bisimulation: Naturally on
distributions. In: Baldan P, Gorla D, eds. Lecture Notes in Computer Science
(Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes
in Bioinformatics). Vol 8704. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2014:249-265. doi:10.1007/978-3-662-44584-6_18'
apa: 'Hermanns, H., Krčál, J., & Kretinsky, J. (2014). Probabilistic bisimulation:
Naturally on distributions. In P. Baldan & D. Gorla (Eds.), Lecture Notes
in Computer Science (including subseries Lecture Notes in Artificial Intelligence
and Lecture Notes in Bioinformatics) (Vol. 8704, pp. 249–265). Rome, Italy:
Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-662-44584-6_18'
chicago: 'Hermanns, Holger, Jan Krčál, and Jan Kretinsky. “Probabilistic Bisimulation:
Naturally on Distributions.” In Lecture Notes in Computer Science (Including
Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics),
edited by Paolo Baldan and Daniele Gorla, 8704:249–65. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2014. https://doi.org/10.1007/978-3-662-44584-6_18.'
ieee: 'H. Hermanns, J. Krčál, and J. Kretinsky, “Probabilistic bisimulation: Naturally
on distributions,” in Lecture Notes in Computer Science (including subseries
Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics),
Rome, Italy, 2014, vol. 8704, pp. 249–265.'
ista: 'Hermanns H, Krčál J, Kretinsky J. 2014. Probabilistic bisimulation: Naturally
on distributions. Lecture Notes in Computer Science (including subseries Lecture
Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). CONCUR:
Concurrency Theory, LNCS, vol. 8704, 249–265.'
mla: 'Hermanns, Holger, et al. “Probabilistic Bisimulation: Naturally on Distributions.”
Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial
Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan
and Daniele Gorla, vol. 8704, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2014, pp. 249–65, doi:10.1007/978-3-662-44584-6_18.'
short: H. Hermanns, J. Krčál, J. Kretinsky, in:, P. Baldan, D. Gorla (Eds.), Lecture
Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence
and Lecture Notes in Bioinformatics), Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2014, pp. 249–265.
conference:
end_date: 2014-09-05
location: Rome, Italy
name: 'CONCUR: Concurrency Theory'
start_date: 2014-09-02
date_created: 2018-12-11T11:55:27Z
date_published: 2014-09-01T00:00:00Z
date_updated: 2025-06-11T07:57:15Z
day: '01'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1007/978-3-662-44584-6_18
ec_funded: 1
editor:
- first_name: Paolo
full_name: Baldan, Paolo
last_name: Baldan
- first_name: Daniele
full_name: Gorla, Daniele
last_name: Gorla
external_id:
arxiv:
- '1404.5084'
intvolume: ' 8704'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1404.5084
month: '09'
oa: 1
oa_version: Submitted Version
page: 249 - 265
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
publication: Lecture Notes in Computer Science (including subseries Lecture Notes
in Artificial Intelligence and Lecture Notes in Bioinformatics)
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '4993'
scopus_import: '1'
status: public
title: 'Probabilistic bisimulation: Naturally on distributions'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8704
year: '2014'
...
---
_id: '2054'
abstract:
- lang: eng
text: 'We study two-player concurrent games on finite-state graphs played for an
infinite number of rounds, where in each round, the two players (player 1 and
player 2) choose their moves independently and simultaneously; the current state
and the two moves determine the successor state. The objectives are ω-regular
winning conditions specified as parity objectives. We consider the qualitative
analysis problems: the computation of the almost-sure and limit-sure winning set
of states, where player 1 can ensure to win with probability 1 and with probability
arbitrarily close to 1, respectively. In general the almost-sure and limit-sure
winning strategies require both infinite-memory as well as infinite-precision
(to describe probabilities). While the qualitative analysis problem for concurrent
parity games with infinite-memory, infinite-precision randomized strategies was
studied before, we study the bounded-rationality problem for qualitative analysis
of concurrent parity games, where the strategy set for player 1 is restricted
to bounded-resource strategies. In terms of precision, strategies can be deterministic,
uniform, finite-precision, or infinite-precision; and in terms of memory, strategies
can be memoryless, finite-memory, or infinite-memory. We present a precise and
complete characterization of the qualitative winning sets for all combinations
of classes of strategies. In particular, we show that uniform memoryless strategies
are as powerful as finite-precision infinite-memory strategies, and infinite-precision
memoryless strategies are as powerful as infinite-precision finite-memory strategies.
We show that the winning sets can be computed in (n2d+3) time, where n is the
size of the game structure and 2d is the number of priorities (or colors), and
our algorithms are symbolic. The membership problem of whether a state belongs
to a winning set can be decided in NP ∩ coNP. Our symbolic algorithms are based
on a characterization of the winning sets as μ-calculus formulas, however, our
μ-calculus formulas are crucially different from the ones for concurrent parity
games (without bounded rationality); and our memoryless witness strategy constructions
are significantly different from the infinite-memory witness strategy constructions
for concurrent parity games.'
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Chatterjee K. Qualitative concurrent parity games: Bounded rationality. In:
Baldan P, Gorla D, eds. Lecture Notes in Computer Science (Including Subseries
Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics).
Vol 8704. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:544-559. doi:10.1007/978-3-662-44584-6_37'
apa: 'Chatterjee, K. (2014). Qualitative concurrent parity games: Bounded rationality.
In P. Baldan & D. Gorla (Eds.), Lecture Notes in Computer Science (including
subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
(Vol. 8704, pp. 544–559). Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für
Informatik. https://doi.org/10.1007/978-3-662-44584-6_37'
chicago: 'Chatterjee, Krishnendu. “Qualitative Concurrent Parity Games: Bounded
Rationality.” In Lecture Notes in Computer Science (Including Subseries Lecture
Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited
by Paolo Baldan and Daniele Gorla, 8704:544–59. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2014. https://doi.org/10.1007/978-3-662-44584-6_37.'
ieee: 'K. Chatterjee, “Qualitative concurrent parity games: Bounded rationality,”
in Lecture Notes in Computer Science (including subseries Lecture Notes in
Artificial Intelligence and Lecture Notes in Bioinformatics), Rome, Italy,
2014, vol. 8704, pp. 544–559.'
ista: 'Chatterjee K. 2014. Qualitative concurrent parity games: Bounded rationality.
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial
Intelligence and Lecture Notes in Bioinformatics). CONCUR: Concurrency Theory,
LNCS, vol. 8704, 544–559.'
mla: 'Chatterjee, Krishnendu. “Qualitative Concurrent Parity Games: Bounded Rationality.”
Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial
Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan
and Daniele Gorla, vol. 8704, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2014, pp. 544–59, doi:10.1007/978-3-662-44584-6_37.'
short: K. Chatterjee, in:, P. Baldan, D. Gorla (Eds.), Lecture Notes in Computer
Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture
Notes in Bioinformatics), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014,
pp. 544–559.
conference:
end_date: 2014-09-05
location: Rome, Italy
name: 'CONCUR: Concurrency Theory'
start_date: 2014-09-02
corr_author: '1'
date_created: 2018-12-11T11:55:27Z
date_published: 2014-09-01T00:00:00Z
date_updated: 2025-09-30T09:05:12Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-662-44584-6_37
ec_funded: 1
editor:
- first_name: Paolo
full_name: Baldan, Paolo
last_name: Baldan
- first_name: Daniele
full_name: Gorla, Daniele
last_name: Gorla
intvolume: ' 8704'
language:
- iso: eng
month: '09'
oa_version: None
page: 544 - 559
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _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'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Lecture Notes in Computer Science (including subseries Lecture Notes
in Artificial Intelligence and Lecture Notes in Bioinformatics)
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '4992'
quality_controlled: '1'
related_material:
record:
- id: '3354'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: 'Qualitative concurrent parity games: Bounded rationality'
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 8704
year: '2014'
...
---
_id: '2056'
abstract:
- lang: eng
text: 'We consider a continuous-time Markov chain (CTMC) whose state space is partitioned
into aggregates, and each aggregate is assigned a probability measure. A sufficient
condition for defining a CTMC over the aggregates is presented as a variant of
weak lumpability, which also characterizes that the measure over the original
process can be recovered from that of the aggregated one. We show how the applicability
of de-aggregation depends on the initial distribution. The application section
is devoted to illustrate how the developed theory aids in reducing CTMC models
of biochemical systems particularly in connection to protein-protein interactions.
We assume that the model is written by a biologist in form of site-graph-rewrite
rules. Site-graph-rewrite rules compactly express that, often, only a local context
of a protein (instead of a full molecular species) needs to be in a certain configuration
in order to trigger a reaction event. This observation leads to suitable aggregate
Markov chains with smaller state spaces, thereby providing sufficient reduction
in computational complexity. This is further exemplified in two case studies:
simple unbounded polymerization and early EGFR/insulin crosstalk.'
acknowledgement: T. Petrov is supported by SystemsX.ch—the Swiss Inititative for Systems
Biology.
article_processing_charge: No
arxiv: 1
author:
- first_name: Arnab
full_name: Ganguly, Arnab
last_name: Ganguly
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
- first_name: Heinz
full_name: Koeppl, Heinz
last_name: Koeppl
citation:
ama: Ganguly A, Petrov T, Koeppl H. Markov chain aggregation and its applications
to combinatorial reaction networks. Journal of Mathematical Biology. 2014;69(3):767-797.
doi:10.1007/s00285-013-0738-7
apa: Ganguly, A., Petrov, T., & Koeppl, H. (2014). Markov chain aggregation
and its applications to combinatorial reaction networks. Journal of Mathematical
Biology. Springer. https://doi.org/10.1007/s00285-013-0738-7
chicago: Ganguly, Arnab, Tatjana Petrov, and Heinz Koeppl. “Markov Chain Aggregation
and Its Applications to Combinatorial Reaction Networks.” Journal of Mathematical
Biology. Springer, 2014. https://doi.org/10.1007/s00285-013-0738-7.
ieee: A. Ganguly, T. Petrov, and H. Koeppl, “Markov chain aggregation and its applications
to combinatorial reaction networks,” Journal of Mathematical Biology, vol.
69, no. 3. Springer, pp. 767–797, 2014.
ista: Ganguly A, Petrov T, Koeppl H. 2014. Markov chain aggregation and its applications
to combinatorial reaction networks. Journal of Mathematical Biology. 69(3), 767–797.
mla: Ganguly, Arnab, et al. “Markov Chain Aggregation and Its Applications to Combinatorial
Reaction Networks.” Journal of Mathematical Biology, vol. 69, no. 3, Springer,
2014, pp. 767–97, doi:10.1007/s00285-013-0738-7.
short: A. Ganguly, T. Petrov, H. Koeppl, Journal of Mathematical Biology 69 (2014)
767–797.
date_created: 2018-12-11T11:55:28Z
date_published: 2014-11-20T00:00:00Z
date_updated: 2025-09-29T11:50:22Z
day: '20'
department:
- _id: CaGu
- _id: ToHe
doi: 10.1007/s00285-013-0738-7
external_id:
arxiv:
- '1303.4532'
isi:
- '000340588700008'
intvolume: ' 69'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1303.4532
month: '11'
oa: 1
oa_version: Submitted Version
page: 767 - 797
publication: Journal of Mathematical Biology
publication_status: published
publisher: Springer
publist_id: '4990'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Markov chain aggregation and its applications to combinatorial reaction networks
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 69
year: '2014'
...
---
_id: '2057'
abstract:
- lang: eng
text: 'In the past few years, a lot of attention has been devoted to multimedia
indexing by fusing multimodal informations. Two kinds of fusion schemes are generally
considered: The early fusion and the late fusion. We focus on late classifier
fusion, where one combines the scores of each modality at the decision level.
To tackle this problem, we investigate a recent and elegant well-founded quadratic
program named MinCq coming from the machine learning PAC-Bayesian theory. MinCq
looks for the weighted combination, over a set of real-valued functions seen as
voters, leading to the lowest misclassification rate, while maximizing the voters’
diversity. We propose an extension of MinCq tailored to multimedia indexing. Our
method is based on an order-preserving pairwise loss adapted to ranking that allows
us to improve Mean Averaged Precision measure while taking into account the diversity
of the voters that we want to fuse. We provide evidence that this method is naturally
adapted to late fusion procedures and confirm the good behavior of our approach
on the challenging PASCAL VOC’07 benchmark.'
alternative_title:
- LNCS
arxiv: 1
author:
- first_name: Emilie
full_name: Morvant, Emilie
id: 4BAC2A72-F248-11E8-B48F-1D18A9856A87
last_name: Morvant
orcid: 0000-0002-8301-7240
- first_name: Amaury
full_name: Habrard, Amaury
last_name: Habrard
- first_name: Stéphane
full_name: Ayache, Stéphane
last_name: Ayache
citation:
ama: 'Morvant E, Habrard A, Ayache S. Majority vote of diverse classifiers for late
fusion. In: Lecture Notes in Computer Science (Including Subseries Lecture
Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol
8621. Springer; 2014:153-162. doi:10.1007/978-3-662-44415-3_16'
apa: 'Morvant, E., Habrard, A., & Ayache, S. (2014). Majority vote of diverse
classifiers for late fusion. In Lecture Notes in Computer Science (including
subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
(Vol. 8621, pp. 153–162). Joensuu, Finland: Springer. https://doi.org/10.1007/978-3-662-44415-3_16'
chicago: Morvant, Emilie, Amaury Habrard, and Stéphane Ayache. “Majority Vote of
Diverse Classifiers for Late Fusion.” In Lecture Notes in Computer Science
(Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes
in Bioinformatics), 8621:153–62. Springer, 2014. https://doi.org/10.1007/978-3-662-44415-3_16.
ieee: E. Morvant, A. Habrard, and S. Ayache, “Majority vote of diverse classifiers
for late fusion,” in Lecture Notes in Computer Science (including subseries
Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics),
Joensuu, Finland, 2014, vol. 8621, pp. 153–162.
ista: 'Morvant E, Habrard A, Ayache S. 2014. Majority vote of diverse classifiers
for late fusion. Lecture Notes in Computer Science (including subseries Lecture
Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). IAPR: International
Workshop on Structural, Syntactic, and Statistical Pattern Recognition, LNCS,
vol. 8621, 153–162.'
mla: Morvant, Emilie, et al. “Majority Vote of Diverse Classifiers for Late Fusion.”
Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial
Intelligence and Lecture Notes in Bioinformatics), vol. 8621, Springer, 2014,
pp. 153–62, doi:10.1007/978-3-662-44415-3_16.
short: E. Morvant, A. Habrard, S. Ayache, in:, Lecture Notes in Computer Science
(Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes
in Bioinformatics), Springer, 2014, pp. 153–162.
conference:
end_date: 2014-08-22
location: Joensuu, Finland
name: 'IAPR: International Workshop on Structural, Syntactic, and Statistical Pattern
Recognition'
start_date: 2014-08-20
date_created: 2018-12-11T11:55:28Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:55:01Z
day: '01'
department:
- _id: ChLa
doi: 10.1007/978-3-662-44415-3_16
ec_funded: 1
external_id:
arxiv:
- '1404.7796'
intvolume: ' 8621'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1404.7796
month: '01'
oa: 1
oa_version: Preprint
page: 153 - 162
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication: Lecture Notes in Computer Science (including subseries Lecture Notes
in Artificial Intelligence and Lecture Notes in Bioinformatics)
publication_status: published
publisher: Springer
publist_id: '4989'
quality_controlled: '1'
scopus_import: 1
status: public
title: Majority vote of diverse classifiers for late fusion
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8621
year: '2014'
...
---
_id: '2058'
abstract:
- lang: eng
text: We present a method for smoothly blending between existing liquid animations.
We introduce a semi-automatic method for matching two existing liquid animations,
which we use to create new fluid motion that plausibly interpolates the input.
Our contributions include a new space-time non-rigid iterative closest point algorithm
that incorporates user guidance, a subsampling technique for efficient registration
of meshes with millions of vertices, and a fast surface extraction algorithm that
produces 3D triangle meshes from a 4D space-time surface. Our technique can be
used to instantly create hundreds of new simulations, or to interactively explore
complex parameter spaces. Our method is guaranteed to produce output that does
not deviate from the input animations, and it generalizes to multiple dimensions.
Because our method runs at interactive rates after the initial precomputation
step, it has potential applications in games and training simulations.
article_number: '137'
article_processing_charge: No
author:
- first_name: Karthik
full_name: Raveendran, Karthik
last_name: Raveendran
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Nils
full_name: Thuerey, Nils
last_name: Thuerey
- first_name: Greg
full_name: Türk, Greg
last_name: Türk
citation:
ama: 'Raveendran K, Wojtan C, Thuerey N, Türk G. Blending liquids. In: ACM Transactions
on Graphics. Vol 33. ACM; 2014. doi:10.1145/2601097.2601126'
apa: 'Raveendran, K., Wojtan, C., Thuerey, N., & Türk, G. (2014). Blending liquids.
In ACM Transactions on Graphics (Vol. 33). Vancouver, Canada: ACM. https://doi.org/10.1145/2601097.2601126'
chicago: Raveendran, Karthik, Chris Wojtan, Nils Thuerey, and Greg Türk. “Blending
Liquids.” In ACM Transactions on Graphics, Vol. 33. ACM, 2014. https://doi.org/10.1145/2601097.2601126.
ieee: K. Raveendran, C. Wojtan, N. Thuerey, and G. Türk, “Blending liquids,” in
ACM Transactions on Graphics, Vancouver, Canada, 2014, vol. 33, no. 4.
ista: 'Raveendran K, Wojtan C, Thuerey N, Türk G. 2014. Blending liquids. ACM Transactions
on Graphics. SIGGRAPH: International Conference and Exhibition on Computer Graphics
and Interactive Techniques vol. 33, 137.'
mla: Raveendran, Karthik, et al. “Blending Liquids.” ACM Transactions on Graphics,
vol. 33, no. 4, 137, ACM, 2014, doi:10.1145/2601097.2601126.
short: K. Raveendran, C. Wojtan, N. Thuerey, G. Türk, in:, ACM Transactions on Graphics,
ACM, 2014.
conference:
end_date: 2014-08-14
location: Vancouver, Canada
name: 'SIGGRAPH: International Conference and Exhibition on Computer Graphics and
Interactive Techniques'
start_date: 2014-08-10
date_created: 2018-12-11T11:55:28Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2025-09-29T11:49:44Z
day: '01'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2601097.2601126
external_id:
isi:
- '000340000100104'
file:
- access_level: open_access
checksum: 1752760a2e71e254537f31c0d10d9c6c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:27Z
date_updated: 2020-07-14T12:45:27Z
file_id: '4688'
file_name: IST-2016-606-v1+1_BlendingLiquids-Preprint.pdf
file_size: 8387384
relation: main_file
file_date_updated: 2020-07-14T12:45:27Z
has_accepted_license: '1'
intvolume: ' 33'
isi: 1
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
project:
- _id: 25636330-B435-11E9-9278-68D0E5697425
grant_number: 11-NSF-1070
name: Genome-wide Analysis of Root Traits
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '4988'
pubrep_id: '606'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Blending liquids
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 33
year: '2014'
...
---
_id: '2059'
abstract:
- lang: eng
text: Plant embryogenesis is regulated by differential distribution of the plant
hormone auxin. However, the cells establishing these gradients during microspore
embryogenesis remain to be identified. For the first time, we describe, using
the DR5 or DR5rev reporter gene systems, the GFP- and GUS-based auxin biosensors
to monitor auxin during Brassica napus androgenesis at cellular resolution in
the initial stages. Our study provides evidence that the distribution of auxin
changes during embryo development and depends on the temperature-inducible in
vitro culture conditions. For this, microspores (mcs) were induced to embryogenesis
by heat treatment and then subjected to genetic modification via Agrobacterium
tumefaciens. The duration of high temperature treatment had a significant influence
on auxin distribution in isolated and in vitro-cultured microspores and on microspore-derived
embryo development. In the “mild” heat-treated (1 day at 32 °C) mcs, auxin localized
in a polar way already at the uni-nucleate microspore, which was critical for
the initiation of embryos with suspensor-like structure. Assuming a mean mcs radius
of 20 μm, endogenous auxin content in a single cell corresponded to concentration
of 1.01 μM. In mcs subjected to a prolonged heat (5 days at 32 °C), although auxin
concentration increased dozen times, auxin polarization was set up at a few-celled
pro-embryos without suspensor. Those embryos were enclosed in the outer wall called
the exine. The exine rupture was accompanied by the auxin gradient polarization.
Relative quantitative estimation of auxin, using time-lapse imaging, revealed
that primordia possess up to 1.3-fold higher amounts than those found in the root
apices of transgenic MDEs in the presence of exogenous auxin. Our results show,
for the first time, which concentration of endogenous auxin coincides with the
first cell division and how the high temperature interplays with auxin, by what
affects delay early establishing microspore polarity. Moreover, we present how
the local auxin accumulation demonstrates the apical–basal axis formation of the
androgenic embryo and directs the axiality of the adult haploid plant.
acknowledgement: The research was supported by the IPP PAS-IPGB SAS bilateral project
(“Molecular analysis of auxin distribution in oilseed androgenic embryos”), IPP
PAS-FWO VIB bilateral project (“Auxin as signaling molecule in doubled haploid production
of rape (B. napus var. oleifera)”), individual national research project 2011/01/D/NZ9/02547,
and VEGA 2-0090-14.
article_processing_charge: No
author:
- first_name: Ewa
full_name: Dubas, Ewa
last_name: Dubas
- first_name: Jana
full_name: Moravčíková, Jana
last_name: Moravčíková
- first_name: Jana
full_name: Libantová, Jana
last_name: Libantová
- first_name: Ildikó
full_name: Matušíková, Ildikó
last_name: Matušíková
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Iwona
full_name: Zur, Iwona
last_name: Zur
- first_name: Monika
full_name: Krzewska, Monika
last_name: Krzewska
citation:
ama: Dubas E, Moravčíková J, Libantová J, et al. The influence of heat stress on
auxin distribution in transgenic B napus microspores and microspore derived embryos.
Protoplasma. 2014;251(5):1077-1087. doi:10.1007/s00709-014-0616-1
apa: Dubas, E., Moravčíková, J., Libantová, J., Matušíková, I., Benková, E., Zur,
I., & Krzewska, M. (2014). The influence of heat stress on auxin distribution
in transgenic B napus microspores and microspore derived embryos. Protoplasma.
Springer. https://doi.org/10.1007/s00709-014-0616-1
chicago: Dubas, Ewa, Jana Moravčíková, Jana Libantová, Ildikó Matušíková, Eva Benková,
Iwona Zur, and Monika Krzewska. “The Influence of Heat Stress on Auxin Distribution
in Transgenic B Napus Microspores and Microspore Derived Embryos.” Protoplasma.
Springer, 2014. https://doi.org/10.1007/s00709-014-0616-1.
ieee: E. Dubas et al., “The influence of heat stress on auxin distribution
in transgenic B napus microspores and microspore derived embryos,” Protoplasma,
vol. 251, no. 5. Springer, pp. 1077–1087, 2014.
ista: Dubas E, Moravčíková J, Libantová J, Matušíková I, Benková E, Zur I, Krzewska
M. 2014. The influence of heat stress on auxin distribution in transgenic B napus
microspores and microspore derived embryos. Protoplasma. 251(5), 1077–1087.
mla: Dubas, Ewa, et al. “The Influence of Heat Stress on Auxin Distribution in Transgenic
B Napus Microspores and Microspore Derived Embryos.” Protoplasma, vol.
251, no. 5, Springer, 2014, pp. 1077–87, doi:10.1007/s00709-014-0616-1.
short: E. Dubas, J. Moravčíková, J. Libantová, I. Matušíková, E. Benková, I. Zur,
M. Krzewska, Protoplasma 251 (2014) 1077–1087.
date_created: 2018-12-11T11:55:29Z
date_published: 2014-02-20T00:00:00Z
date_updated: 2025-09-29T11:49:12Z
day: '20'
ddc:
- '580'
department:
- _id: EvBe
doi: 10.1007/s00709-014-0616-1
external_id:
isi:
- '000340480300008'
file:
- access_level: open_access
checksum: d570a6073765118fc0bb83c31d96fa53
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:31Z
date_updated: 2020-07-14T12:45:27Z
file_id: '5353'
file_name: IST-2015-394-v1+1_s00709-014-0616-1.pdf
file_size: 6377990
relation: main_file
file_date_updated: 2020-07-14T12:45:27Z
has_accepted_license: '1'
intvolume: ' 251'
isi: 1
issue: '5'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 1077 - 1087
publication: Protoplasma
publication_status: published
publisher: Springer
publist_id: '4987'
pubrep_id: '394'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The influence of heat stress on auxin distribution in transgenic B napus microspores
and microspore derived embryos
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 251
year: '2014'
...
---
_id: '2061'
abstract:
- lang: eng
text: 'Development of cambium and its activity is important for our knowledge of
the mechanism of secondary growth. Arabidopsis thaliana emerges as a good model
plant for such a kind of study. Thus, this paper reports on cellular events taking
place in the interfascicular regions of inflorescence stems of A. thaliana, leading
to the development of interfascicular cambium from differentiated interfascicular
parenchyma cells (IPC). These events are as follows: appearance of auxin accumulation,
PIN1 gene expression, polar PIN1 protein localization in the basal plasma membrane
and periclinal divisions. Distribution of auxin was observed to be higher in differentiating
into cambium parenchyma cells compared to cells within the pith and cortex. Expression
of PIN1 in IPC was always preceded by auxin accumulation. Basal localization of
PIN1 was already established in the cells prior to their periclinal division.
These cellular events initiated within parenchyma cells adjacent to the vascular
bundles and successively extended from that point towards the middle region of
the interfascicular area, located between neighboring vascular bundles. The final
consequence of which was the closure of the cambial ring within the stem. Changes
in the chemical composition of IPC walls were also detected and included changes
of pectic epitopes, xyloglucans (XG) and extensins rich in hydroxyproline (HRGPs).
In summary, results presented in this paper describe interfascicular cambium ontogenesis
in terms of successive cellular events in the interfascicular regions of inflorescence
stems of Arabidopsis.'
article_processing_charge: No
author:
- first_name: Ewa
full_name: Mazur, Ewa
last_name: Mazur
- first_name: Ewa
full_name: Kurczyñska, Ewa
last_name: Kurczyñska
- 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, Kurczyñska E, Friml J. Cellular events during interfascicular cambium
ontogenesis in inflorescence stems of Arabidopsis. Protoplasma. 2014;251(5):1125-1139.
doi:10.1007/s00709-014-0620-5
apa: Mazur, E., Kurczyñska, E., & Friml, J. (2014). Cellular events during interfascicular
cambium ontogenesis in inflorescence stems of Arabidopsis. Protoplasma.
Springer. https://doi.org/10.1007/s00709-014-0620-5
chicago: Mazur, Ewa, Ewa Kurczyñska, and Jiří Friml. “Cellular Events during Interfascicular
Cambium Ontogenesis in Inflorescence Stems of Arabidopsis.” Protoplasma.
Springer, 2014. https://doi.org/10.1007/s00709-014-0620-5.
ieee: E. Mazur, E. Kurczyñska, and J. Friml, “Cellular events during interfascicular
cambium ontogenesis in inflorescence stems of Arabidopsis,” Protoplasma,
vol. 251, no. 5. Springer, pp. 1125–1139, 2014.
ista: Mazur E, Kurczyñska E, Friml J. 2014. Cellular events during interfascicular
cambium ontogenesis in inflorescence stems of Arabidopsis. Protoplasma. 251(5),
1125–1139.
mla: Mazur, Ewa, et al. “Cellular Events during Interfascicular Cambium Ontogenesis
in Inflorescence Stems of Arabidopsis.” Protoplasma, vol. 251, no. 5, Springer,
2014, pp. 1125–39, doi:10.1007/s00709-014-0620-5.
short: E. Mazur, E. Kurczyñska, J. Friml, Protoplasma 251 (2014) 1125–1139.
date_created: 2018-12-11T11:55:29Z
date_published: 2014-02-14T00:00:00Z
date_updated: 2025-09-29T11:48:32Z
day: '14'
department:
- _id: JiFr
doi: 10.1007/s00709-014-0620-5
external_id:
isi:
- '000340480300012'
intvolume: ' 251'
isi: 1
issue: '5'
language:
- iso: eng
month: '02'
oa_version: None
page: 1125 - 1139
publication: Protoplasma
publication_status: published
publisher: Springer
publist_id: '4985'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cellular events during interfascicular cambium ontogenesis in inflorescence
stems of Arabidopsis
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 251
year: '2014'
...
---
_id: '2062'
abstract:
- lang: eng
text: The success story of fast-spiking, parvalbumin-positive (PV+) GABAergic interneurons
(GABA, γ-aminobutyric acid) in the mammalian central nervous system is noteworthy.
In 1995, the properties of these interneurons were completely unknown. Twenty
years later, thanks to the massive use of subcellular patch-clamp techniques,
simultaneous multiple-cell recording, optogenetics, in vivo measurements, and
computational approaches, our knowledge about PV+ interneurons became more extensive
than for several types of pyramidal neurons. These findings have implications
beyond the “small world” of basic research on GABAergic cells. For example, the
results provide a first proof of principle that neuroscientists might be able
to close the gaps between the molecular, cellular, network, and behavioral levels,
representing one of the main challenges at the present time. Furthermore, the
results may form the basis for PV+ interneurons as therapeutic targets for brain
disease in the future. However, much needs to be learned about the basic function
of these interneurons before clinical neuroscientists will be able to use PV+
interneurons for therapeutic purposes.
article_number: '1255263'
article_processing_charge: No
author:
- first_name: Hua
full_name: Hu, Hua
id: 4AC0145C-F248-11E8-B48F-1D18A9856A87
last_name: Hu
- first_name: Jian
full_name: Gan, Jian
id: 3614E438-F248-11E8-B48F-1D18A9856A87
last_name: Gan
- 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: 'Hu H, Gan J, Jonas PM. Fast-spiking parvalbumin^+ GABAergic interneurons:
From cellular design to microcircuit function. Science. 2014;345(6196).
doi:10.1126/science.1255263'
apa: 'Hu, H., Gan, J., & Jonas, P. M. (2014). Fast-spiking parvalbumin^+ GABAergic
interneurons: From cellular design to microcircuit function. Science. American
Association for the Advancement of Science. https://doi.org/10.1126/science.1255263'
chicago: 'Hu, Hua, Jian Gan, and Peter M Jonas. “Fast-Spiking Parvalbumin^+ GABAergic
Interneurons: From Cellular Design to Microcircuit Function.” Science.
American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1255263.'
ieee: 'H. Hu, J. Gan, and P. M. Jonas, “Fast-spiking parvalbumin^+ GABAergic interneurons:
From cellular design to microcircuit function,” Science, vol. 345, no.
6196. American Association for the Advancement of Science, 2014.'
ista: 'Hu H, Gan J, Jonas PM. 2014. Fast-spiking parvalbumin^+ GABAergic interneurons:
From cellular design to microcircuit function. Science. 345(6196), 1255263.'
mla: 'Hu, Hua, et al. “Fast-Spiking Parvalbumin^+ GABAergic Interneurons: From Cellular
Design to Microcircuit Function.” Science, vol. 345, no. 6196, 1255263,
American Association for the Advancement of Science, 2014, doi:10.1126/science.1255263.'
short: H. Hu, J. Gan, P.M. Jonas, Science 345 (2014).
corr_author: '1'
date_created: 2018-12-11T11:55:29Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2025-09-29T11:48:03Z
day: '01'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1126/science.1255263
ec_funded: 1
external_id:
isi:
- '000339651300036'
file:
- access_level: open_access
checksum: a0036a589037d37e86364fa25cc0a82f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:00Z
date_updated: 2020-07-14T12:45:27Z
file_id: '5185'
file_name: IST-2017-821-v1+1_1255263JonasPVReviewTextR_Final.pdf
file_size: 215514
relation: main_file
- access_level: open_access
checksum: e1f57d2713725449cb898fdcb8ef47b8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:01Z
date_updated: 2020-07-14T12:45:27Z
file_id: '5186'
file_name: IST-2017-821-v1+2_1255263JonasPVReviewFigures_Final.pdf
file_size: 1732723
relation: main_file
file_date_updated: 2020-07-14T12:45:27Z
has_accepted_license: '1'
intvolume: ' 345'
isi: 1
issue: '6196'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
project:
- _id: 25C26B1E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P24909-B24
name: Mechanisms of transmitter release at GABAergic synapses
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '4984'
pubrep_id: '821'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to
microcircuit function'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 345
year: '2014'
...
---
_id: '2063'
abstract:
- lang: eng
text: We consider Markov decision processes (MDPs) which are a standard model for
probabilistic systems.We focus on qualitative properties forMDPs that can express
that desired behaviors of the system arise almost-surely (with probability 1)
or with positive probability. We introduce a new simulation relation to capture
the refinement relation ofMDPs with respect to qualitative properties, and present
discrete graph theoretic algorithms with quadratic complexity to compute the simulation
relation.We present an automated technique for assume-guarantee style reasoning
for compositional analysis ofMDPs with qualitative properties by giving a counterexample
guided abstraction-refinement approach to compute our new simulation relation.
We have implemented our algorithms and show that the compositional analysis leads
to significant improvements.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Przemyslaw
full_name: Daca, Przemyslaw
id: 49351290-F248-11E8-B48F-1D18A9856A87
last_name: Daca
citation:
ama: 'Chatterjee K, Chmelik M, Daca P. CEGAR for qualitative analysis of probabilistic
systems. In: Vol 8559. Springer; 2014:473-490. doi:10.1007/978-3-319-08867-9_31'
apa: 'Chatterjee, K., Chmelik, M., & Daca, P. (2014). CEGAR for qualitative
analysis of probabilistic systems (Vol. 8559, pp. 473–490). Presented at the CAV:
Computer Aided Verification, Vienna, Austria: Springer. https://doi.org/10.1007/978-3-319-08867-9_31'
chicago: Chatterjee, Krishnendu, Martin Chmelik, and Przemyslaw Daca. “CEGAR for
Qualitative Analysis of Probabilistic Systems,” 8559:473–90. Springer, 2014. https://doi.org/10.1007/978-3-319-08867-9_31.
ieee: 'K. Chatterjee, M. Chmelik, and P. Daca, “CEGAR for qualitative analysis of
probabilistic systems,” presented at the CAV: Computer Aided Verification, Vienna,
Austria, 2014, vol. 8559, pp. 473–490.'
ista: 'Chatterjee K, Chmelik M, Daca P. 2014. CEGAR for qualitative analysis of
probabilistic systems. CAV: Computer Aided Verification, LNCS, vol. 8559, 473–490.'
mla: Chatterjee, Krishnendu, et al. CEGAR for Qualitative Analysis of Probabilistic
Systems. Vol. 8559, Springer, 2014, pp. 473–90, doi:10.1007/978-3-319-08867-9_31.
short: K. Chatterjee, M. Chmelik, P. Daca, in:, Springer, 2014, pp. 473–490.
conference:
end_date: 2014-07-22
location: Vienna, Austria
name: 'CAV: Computer Aided Verification'
start_date: 2014-07-18
corr_author: '1'
date_created: 2018-12-11T11:55:30Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2026-04-15T10:02:12Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-319-08867-9_31
ec_funded: 1
intvolume: ' 8559'
language:
- iso: eng
month: '07'
oa_version: None
page: 473 - 490
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication_status: published
publisher: Springer
publist_id: '4978'
quality_controlled: '1'
related_material:
record:
- id: '5412'
relation: earlier_version
status: public
- id: '5413'
relation: earlier_version
status: public
- id: '5414'
relation: earlier_version
status: public
- id: '1155'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: CEGAR for qualitative analysis of probabilistic systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8559
year: '2014'
...
---
_id: '2064'
abstract:
- lang: eng
text: We examined the synaptic structure, quantity, and distribution of α-amino-3-hydroxy-5-methylisoxazole-4-propionic
acid (AMPA)- and N-methyl-D-aspartate (NMDA)-type glutamate receptors (AMPARs
and NMDARs, respectively) in rat cochlear nuclei by a highly sensitive freeze-fracture
replica labeling technique. Four excitatory synapses formed by two distinct inputs,
auditory nerve (AN) and parallel fibers (PF), on different cell types were analyzed.
These excitatory synapse types included AN synapses on bushy cells (AN-BC synapses)
and fusiform cells (AN-FC synapses) and PF synapses on FC (PF-FC synapses) and
cartwheel cell spines (PF-CwC synapses). Immunogold labeling revealed differences
in synaptic structure as well as AMPAR and NMDAR number and/or density in both
AN and PF synapses, indicating a target-dependent organization. The immunogold
receptor labeling also identified differences in the synaptic organization of
FCs based on AN or PF connections, indicating an input-dependent organization
in FCs. Among the four excitatory synapse types, the AN-BC synapses were the smallest
and had the most densely packed intramembrane particles (IMPs), whereas the PF-CwC
synapses were the largest and had sparsely packed IMPs. All four synapse types
showed positive correlations between the IMP-cluster area and the AMPAR number,
indicating a common intrasynapse-type relationship for glutamatergic synapses.
Immunogold particles for AMPARs were distributed over the entire area of individual
AN synapses; PF synapses often showed synaptic areas devoid of labeling. The gold-labeling
for NMDARs occurred in a mosaic fashion, with less positive correlations between
the IMP-cluster area and the NMDAR number. Our observations reveal target- and
input-dependent features in the structure, number, and organization of AMPARs
and NMDARs in AN and PF synapses.
acknowledgement: "National Institutes of Health (NIH) Grant Number: 1R01DC013048‐0;
Biotechnology and Biological Sciences Research Council, UK Grant Number: BB/J015938/1\r\n"
article_processing_charge: No
author:
- first_name: Maía
full_name: Rubio, Maía
last_name: Rubio
- first_name: Yugo
full_name: Fukazawa, Yugo
last_name: Fukazawa
- first_name: Naomi
full_name: Kamasawa, Naomi
last_name: Kamasawa
- first_name: Cheryl
full_name: Clarkson, Cheryl
last_name: Clarkson
- first_name: Elek
full_name: Molnár, Elek
last_name: Molnár
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
citation:
ama: Rubio M, Fukazawa Y, Kamasawa N, Clarkson C, Molnár E, Shigemoto R. Target-
and input-dependent organization of AMPA and NMDA receptors in synaptic connections
of the cochlear nucleus. Journal of Comparative Neurology. 2014;522(18):4023-4042.
doi:10.1002/cne.23654
apa: Rubio, M., Fukazawa, Y., Kamasawa, N., Clarkson, C., Molnár, E., & Shigemoto,
R. (2014). Target- and input-dependent organization of AMPA and NMDA receptors
in synaptic connections of the cochlear nucleus. Journal of Comparative Neurology.
Wiley-Blackwell. https://doi.org/10.1002/cne.23654
chicago: Rubio, Maía, Yugo Fukazawa, Naomi Kamasawa, Cheryl Clarkson, Elek Molnár,
and Ryuichi Shigemoto. “Target- and Input-Dependent Organization of AMPA and NMDA
Receptors in Synaptic Connections of the Cochlear Nucleus.” Journal of Comparative
Neurology. Wiley-Blackwell, 2014. https://doi.org/10.1002/cne.23654.
ieee: M. Rubio, Y. Fukazawa, N. Kamasawa, C. Clarkson, E. Molnár, and R. Shigemoto,
“Target- and input-dependent organization of AMPA and NMDA receptors in synaptic
connections of the cochlear nucleus,” Journal of Comparative Neurology,
vol. 522, no. 18. Wiley-Blackwell, pp. 4023–4042, 2014.
ista: Rubio M, Fukazawa Y, Kamasawa N, Clarkson C, Molnár E, Shigemoto R. 2014.
Target- and input-dependent organization of AMPA and NMDA receptors in synaptic
connections of the cochlear nucleus. Journal of Comparative Neurology. 522(18),
4023–4042.
mla: Rubio, Maía, et al. “Target- and Input-Dependent Organization of AMPA and NMDA
Receptors in Synaptic Connections of the Cochlear Nucleus.” Journal of Comparative
Neurology, vol. 522, no. 18, Wiley-Blackwell, 2014, pp. 4023–42, doi:10.1002/cne.23654.
short: M. Rubio, Y. Fukazawa, N. Kamasawa, C. Clarkson, E. Molnár, R. Shigemoto,
Journal of Comparative Neurology 522 (2014) 4023–4042.
date_created: 2018-12-11T11:55:30Z
date_published: 2014-07-29T00:00:00Z
date_updated: 2025-09-29T11:47:23Z
day: '29'
department:
- _id: RySh
doi: 10.1002/cne.23654
external_id:
isi:
- '000343973100005'
intvolume: ' 522'
isi: 1
issue: '18'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4198489/
month: '07'
oa: 1
oa_version: Submitted Version
page: 4023 - 4042
publication: Journal of Comparative Neurology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4974'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Target- and input-dependent organization of AMPA and NMDA receptors in synaptic
connections of the cochlear nucleus
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 522
year: '2014'
...
---
_id: '2080'
abstract:
- lang: eng
text: 'Spinning tops and yo-yos have long fascinated cultures around the world with
their unexpected, graceful motions that seemingly elude gravity. We present an
algorithm to generate designs for spinning objects by optimizing rotational dynamics
properties. As input, the user provides a solid 3D model and a desired axis of
rotation. Our approach then modifies the mass distribution such that the principal
directions of the moment of inertia align with the target rotation frame. We augment
the model by creating voids inside its volume, with interior fill represented
by an adaptive multi-resolution vox-elization. The discrete voxel fill values
are optimized using a continuous, nonlinear formulation. Further, we optimize
for rotational stability by maximizing the dominant principal moment. We extend
our technique to incorporate deformation and multiple materials for cases where
internal voids alone are insufficient. Our method is well-suited for a variety
of 3D printed models, ranging from characters to abstract shapes. We demonstrate
tops and yo-yos that spin surprisingly stably despite their asymmetric appearance. '
acknowledgement: This project was supported in part by the ERC Starting Grant iModel
(StG-2012-306877). Emily Whiting is supported by the ETH Zurich / Marie Curie COFUND
Postdoctoral Fellowship.
article_number: '96'
article_processing_charge: No
article_type: original
author:
- first_name: Moritz
full_name: Bächer, Moritz
last_name: Bächer
- first_name: Emily
full_name: Whiting, Emily
last_name: Whiting
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Olga
full_name: Sorkine Hornung, Olga
last_name: Sorkine Hornung
citation:
ama: 'Bächer M, Whiting E, Bickel B, Sorkine Hornung O. Spin-It: Optimizing moment
of inertia for spinnable objects. ACM Transactions on Graphics. 2014;33(4).
doi:10.1145/2601097.2601157'
apa: 'Bächer, M., Whiting, E., Bickel, B., & Sorkine Hornung, O. (2014). Spin-It:
Optimizing moment of inertia for spinnable objects. ACM Transactions on Graphics.
ACM. https://doi.org/10.1145/2601097.2601157'
chicago: 'Bächer, Moritz, Emily Whiting, Bernd Bickel, and Olga Sorkine Hornung.
“Spin-It: Optimizing Moment of Inertia for Spinnable Objects.” ACM Transactions
on Graphics. ACM, 2014. https://doi.org/10.1145/2601097.2601157.'
ieee: 'M. Bächer, E. Whiting, B. Bickel, and O. Sorkine Hornung, “Spin-It: Optimizing
moment of inertia for spinnable objects,” ACM Transactions on Graphics,
vol. 33, no. 4. ACM, 2014.'
ista: 'Bächer M, Whiting E, Bickel B, Sorkine Hornung O. 2014. Spin-It: Optimizing
moment of inertia for spinnable objects. ACM Transactions on Graphics. 33(4),
96.'
mla: 'Bächer, Moritz, et al. “Spin-It: Optimizing Moment of Inertia for Spinnable
Objects.” ACM Transactions on Graphics, vol. 33, no. 4, 96, ACM, 2014,
doi:10.1145/2601097.2601157.'
short: M. Bächer, E. Whiting, B. Bickel, O. Sorkine Hornung, ACM Transactions on
Graphics 33 (2014).
date_created: 2018-12-11T11:55:35Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2025-08-05T14:20:24Z
day: '01'
doi: 10.1145/2601097.2601157
extern: '1'
intvolume: ' 33'
issue: '4'
language:
- iso: eng
month: '07'
oa_version: None
publication: ACM Transactions on Graphics
publication_identifier:
eissn:
- 1557-7368
issn:
- 0730-0301
publication_status: published
publisher: ACM
publist_id: '4958'
quality_controlled: '1'
related_material:
record:
- id: '452'
relation: later_version
status: public
scopus_import: '1'
status: public
title: 'Spin-It: Optimizing moment of inertia for spinnable objects'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2014'
...
---
_id: '2081'
abstract:
- lang: eng
text: We propose an interactive, optimization-in-the-loop tool for designing inflatable
structures. Given a target shape, the user draws a network of seams defining desired
segment boundaries in 3D. Our method computes optimally-shaped flat panels for
the segments, such that the inflated structure is as close as possible to the
target while satisfying the desired seam positions. Our approach is underpinned
by physics-based pattern optimization, accurate coarse-scale simulation using
tension field theory, and a specialized constraint-optimization method. Our system
is fast enough to warrant interactive exploration of different seam layouts, including
internal connections, and their effects on the inflated shape. We demonstrate
the resulting design process on a varied set of simulation examples, some of which
we have fabricated, demonstrating excellent agreement with the design intent.
acknowledgement: This work was partly funded by the NCCR Co-Me of the Swiss NSF.
article_number: '63'
author:
- first_name: Mélina
full_name: Skouras, Mélina
last_name: Skouras
- first_name: Bernhard
full_name: Thomaszewski, Bernhard
last_name: Thomaszewski
- first_name: Peter
full_name: Kaufmann, Peter
last_name: Kaufmann
- first_name: Akash
full_name: Garg, Akash
last_name: Garg
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Eitan
full_name: Grinspun, Eitan
last_name: Grinspun
- first_name: Markus
full_name: Gross, Markus
last_name: Gross
citation:
ama: 'Skouras M, Thomaszewski B, Kaufmann P, et al. Designing inflatable structures.
In: Vol 33. ACM; 2014. doi:10.1145/2601097.2601166'
apa: 'Skouras, M., Thomaszewski, B., Kaufmann, P., Garg, A., Bickel, B., Grinspun,
E., & Gross, M. (2014). Designing inflatable structures (Vol. 33). Presented
at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques,
ACM. https://doi.org/10.1145/2601097.2601166'
chicago: Skouras, Mélina, Bernhard Thomaszewski, Peter Kaufmann, Akash Garg, Bernd
Bickel, Eitan Grinspun, and Markus Gross. “Designing Inflatable Structures,” Vol.
33. ACM, 2014. https://doi.org/10.1145/2601097.2601166.
ieee: 'M. Skouras et al., “Designing inflatable structures,” presented at
the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques,
2014, vol. 33, no. 4.'
ista: 'Skouras M, Thomaszewski B, Kaufmann P, Garg A, Bickel B, Grinspun E, Gross
M. 2014. Designing inflatable structures. SIGGRAPH: Special Interest Group on
Computer Graphics and Interactive Techniques vol. 33, 63.'
mla: Skouras, Mélina, et al. Designing Inflatable Structures. Vol. 33, no.
4, 63, ACM, 2014, doi:10.1145/2601097.2601166.
short: M. Skouras, B. Thomaszewski, P. Kaufmann, A. Garg, B. Bickel, E. Grinspun,
M. Gross, in:, ACM, 2014.
conference:
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
date_created: 2018-12-11T11:55:36Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2021-01-12T06:55:11Z
day: '01'
doi: 10.1145/2601097.2601166
extern: '1'
intvolume: ' 33'
issue: '4'
language:
- iso: eng
month: '07'
oa_version: None
publication_status: published
publisher: ACM
publist_id: '4957'
status: public
title: Designing inflatable structures
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2014'
...
---
_id: '10382'
abstract:
- lang: eng
text: 'Protein oligomers have been implicated as toxic agents in a wide range of
amyloid-related diseases. However, it has remained unsolved whether the oligomers
are a necessary step in the formation of amyloid fibrils or just a dangerous byproduct.
Analogously, it has not been resolved if the amyloid nucleation process is a classical
one-step nucleation process or a two-step process involving prenucleation clusters.
We use coarse-grained computer simulations to study the effect of nonspecific
attractions between peptides on the primary nucleation process underlying amyloid
fibrillization. We find that, for peptides that do not attract, the classical
one-step nucleation mechanism is possible but only at nonphysiologically high
peptide concentrations. At low peptide concentrations, which mimic the physiologically
relevant regime, attractive interpeptide interactions are essential for fibril
formation. Nucleation then inevitably takes place through a two-step mechanism
involving prefibrillar oligomers. We show that oligomers not only help peptides
meet each other but also, create an environment that facilitates the conversion
of monomers into the β-sheet–rich form characteristic of fibrils. Nucleation typically
does not proceed through the most prevalent oligomers but through an oligomer
size that is only observed in rare fluctuations, which is why such aggregates
might be hard to capture experimentally. Finally, we find that the nucleation
of amyloid fibrils cannot be described by classical nucleation theory: in the
two-step mechanism, the critical nucleus size increases with increases in both
concentration and interpeptide interactions, which is in direct contrast with
predictions from classical nucleation theory.'
acknowledgement: We thank Michele Vendruscolo, Iskra Staneva, and William M. Jacobs,
for helpful discussions. A.Š. acknowledges support from the Human Frontier Science
Program and Emmanuel College. Y.C.C. and D.F. are supported by Engineering and Physical
Sciences Research Council Programme Grant EP/I001352/1. T.P.J.K. acknowledges the
Frances and Augustus Newman Foundation, the European Research Council, and the Biotechnology
and Biological Sciences Research Council. D.F. acknowledges European Research Council
Advanced Grant 227758.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Yassmine C.
full_name: Chebaro, Yassmine C.
last_name: Chebaro
- first_name: Tuomas P. J.
full_name: Knowles, Tuomas P. J.
last_name: Knowles
- first_name: Daan
full_name: Frenkel, Daan
last_name: Frenkel
citation:
ama: Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. Crucial role of nonspecific interactions
in amyloid nucleation. Proceedings of the National Academy of Sciences.
2014;111(50):17869-17874. doi:10.1073/pnas.1410159111
apa: Šarić, A., Chebaro, Y. C., Knowles, T. P. J., & Frenkel, D. (2014). Crucial
role of nonspecific interactions in amyloid nucleation. Proceedings of the
National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1410159111
chicago: Šarić, Anđela, Yassmine C. Chebaro, Tuomas P. J. Knowles, and Daan Frenkel.
“Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1410159111.
ieee: A. Šarić, Y. C. Chebaro, T. P. J. Knowles, and D. Frenkel, “Crucial role of
nonspecific interactions in amyloid nucleation,” Proceedings of the National
Academy of Sciences, vol. 111, no. 50. National Academy of Sciences, pp. 17869–17874,
2014.
ista: Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. 2014. Crucial role of nonspecific
interactions in amyloid nucleation. Proceedings of the National Academy of Sciences.
111(50), 17869–17874.
mla: Šarić, Anđela, et al. “Crucial Role of Nonspecific Interactions in Amyloid
Nucleation.” Proceedings of the National Academy of Sciences, vol. 111,
no. 50, National Academy of Sciences, 2014, pp. 17869–74, doi:10.1073/pnas.1410159111.
short: A. Šarić, Y.C. Chebaro, T.P.J. Knowles, D. Frenkel, Proceedings of the National
Academy of Sciences 111 (2014) 17869–17874.
date_created: 2021-11-29T13:09:53Z
date_published: 2014-12-01T00:00:00Z
date_updated: 2021-11-29T13:29:05Z
day: '01'
doi: 10.1073/pnas.1410159111
extern: '1'
external_id:
arxiv:
- '1412.0897'
pmid:
- '25453085'
intvolume: ' 111'
issue: '50'
keyword:
- multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.pnas.org/content/111/50/17869
month: '12'
oa: 1
oa_version: Published Version
page: 17869-17874
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Crucial role of nonspecific interactions in amyloid nucleation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 111
year: '2014'
...
---
_id: '10383'
abstract:
- lang: eng
text: We use numerical simulations to compute the equation of state of a suspension
of spherical self-propelled nanoparticles in two and three dimensions. We study
in detail the effect of excluded volume interactions and confinement as a function
of the system's temperature, concentration, and strength of the propulsion. We
find a striking nonmonotonic dependence of the pressure on the temperature and
provide simple scaling arguments to predict and explain the occurrence of such
anomalous behavior. We explicitly show how our results have important implications
for the effective forces on passive components suspended in a bath of active particles.
article_number: '052303'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: S. A.
full_name: Mallory, S. A.
last_name: Mallory
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: C.
full_name: Valeriani, C.
last_name: Valeriani
- first_name: A.
full_name: Cacciuto, A.
last_name: Cacciuto
citation:
ama: Mallory SA, Šarić A, Valeriani C, Cacciuto A. Anomalous thermomechanical properties
of a self-propelled colloidal fluid. Physical Review E. 2014;89(5). doi:10.1103/physreve.89.052303
apa: Mallory, S. A., Šarić, A., Valeriani, C., & Cacciuto, A. (2014). Anomalous
thermomechanical properties of a self-propelled colloidal fluid. Physical Review
E. American Physical Society. https://doi.org/10.1103/physreve.89.052303
chicago: Mallory, S. A., Anđela Šarić, C. Valeriani, and A. Cacciuto. “Anomalous
Thermomechanical Properties of a Self-Propelled Colloidal Fluid.” Physical
Review E. American Physical Society, 2014. https://doi.org/10.1103/physreve.89.052303.
ieee: S. A. Mallory, A. Šarić, C. Valeriani, and A. Cacciuto, “Anomalous thermomechanical
properties of a self-propelled colloidal fluid,” Physical Review E, vol.
89, no. 5. American Physical Society, 2014.
ista: Mallory SA, Šarić A, Valeriani C, Cacciuto A. 2014. Anomalous thermomechanical
properties of a self-propelled colloidal fluid. Physical Review E. 89(5), 052303.
mla: Mallory, S. A., et al. “Anomalous Thermomechanical Properties of a Self-Propelled
Colloidal Fluid.” Physical Review E, vol. 89, no. 5, 052303, American Physical
Society, 2014, doi:10.1103/physreve.89.052303.
short: S.A. Mallory, A. Šarić, C. Valeriani, A. Cacciuto, Physical Review E 89 (2014).
date_created: 2021-11-29T13:10:33Z
date_published: 2014-05-06T00:00:00Z
date_updated: 2021-11-29T13:29:01Z
day: '06'
doi: 10.1103/physreve.89.052303
extern: '1'
external_id:
arxiv:
- '1310.0826'
pmid:
- '25353796'
intvolume: ' 89'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1310.0826
month: '05'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review E
publication_identifier:
eissn:
- 1550-2376
issn:
- 1539-3755
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Anomalous thermomechanical properties of a self-propelled colloidal fluid
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 89
year: '2014'
...
---
_id: '1058'
abstract:
- lang: eng
text: Diffraction-unlimited far-field super-resolution fluorescence (nanoscopy)
methods typically rely on transiently transferring fluorophores between two states,
whereby this transfer is usually laid out as a switch. However, depending on whether
this is induced in a spatially controlled manner using a pattern of light (coordinate-targeted)
or stochastically on a single-molecule basis, specific requirements on the fluorophores
are imposed. Therefore, the fluorophores are usually utilized just for one class
of methods only. In this study we demonstrate that the reversibly switchable fluorescent
protein Dreiklang enables live-cell recordings in both spatially controlled and
stochastic modes. We show that the Dreiklang chromophore entails three different
light-induced switching mechanisms, namely a reversible photochemical one, off-switching
by stimulated emission, and a reversible transfer to a long-lived dark state from
the S1 state, all of which can be utilized to overcome the diffraction barrier.
We also find that for the single-molecule- based stochastic GSDIM approach (ground-state
depletion followed by individual molecule return), Dreiklang provides a larger
number of on-off localization events as compared to its progenitor Citrine. Altogether,
Dreiklang is a versatile probe for essentially all popular forms of live-cell
fluorescence nanoscopy.
article_processing_charge: No
author:
- first_name: Nickels
full_name: Jensen, Nickels
last_name: Jensen
- 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: Katrin
full_name: Willig, Katrin
last_name: Willig
- first_name: Flavie
full_name: Lavoie Cardinal, Flavie
last_name: Lavoie Cardinal
- first_name: Tanja
full_name: Brakemann, Tanja
last_name: Brakemann
- first_name: Stefan
full_name: Hell, Stefan
last_name: Hell
- first_name: Stefan
full_name: Jakobs, Stefan
last_name: Jakobs
citation:
ama: Jensen N, Danzl JG, Willig K, et al. Coordinate-targeted and coordinate-stochastic
super-resolution microscopy with the reversibly switchable fluorescent protein
dreiklang. ChemPhysChem. 2014;15(4):756-762. doi:10.1002/cphc.201301034
apa: Jensen, N., Danzl, J. G., Willig, K., Lavoie Cardinal, F., Brakemann, T., Hell,
S., & Jakobs, S. (2014). Coordinate-targeted and coordinate-stochastic super-resolution
microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem.
Wiley-Blackwell. https://doi.org/10.1002/cphc.201301034
chicago: Jensen, Nickels, Johann G Danzl, Katrin Willig, Flavie Lavoie Cardinal,
Tanja Brakemann, Stefan Hell, and Stefan Jakobs. “Coordinate-Targeted and Coordinate-Stochastic
Super-Resolution Microscopy with the Reversibly Switchable Fluorescent Protein
Dreiklang.” ChemPhysChem. Wiley-Blackwell, 2014. https://doi.org/10.1002/cphc.201301034.
ieee: N. Jensen et al., “Coordinate-targeted and coordinate-stochastic super-resolution
microscopy with the reversibly switchable fluorescent protein dreiklang,” ChemPhysChem,
vol. 15, no. 4. Wiley-Blackwell, pp. 756–762, 2014.
ista: Jensen N, Danzl JG, Willig K, Lavoie Cardinal F, Brakemann T, Hell S, Jakobs
S. 2014. Coordinate-targeted and coordinate-stochastic super-resolution microscopy
with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. 15(4),
756–762.
mla: Jensen, Nickels, et al. “Coordinate-Targeted and Coordinate-Stochastic Super-Resolution
Microscopy with the Reversibly Switchable Fluorescent Protein Dreiklang.” ChemPhysChem,
vol. 15, no. 4, Wiley-Blackwell, 2014, pp. 756–62, doi:10.1002/cphc.201301034.
short: N. Jensen, J.G. Danzl, K. Willig, F. Lavoie Cardinal, T. Brakemann, S. Hell,
S. Jakobs, ChemPhysChem 15 (2014) 756–762.
date_created: 2018-12-11T11:49:55Z
date_published: 2014-03-17T00:00:00Z
date_updated: 2021-01-12T06:47:58Z
day: '17'
doi: 10.1002/cphc.201301034
extern: '1'
intvolume: ' 15'
issue: '4'
language:
- iso: eng
month: '03'
oa_version: None
page: 756 - 762
publication: ChemPhysChem
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6332'
status: public
title: Coordinate-targeted and coordinate-stochastic super-resolution microscopy with
the reversibly switchable fluorescent protein dreiklang
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2014'
...
---
OA_place: repository
OA_type: green
_id: '10793'
abstract:
- lang: eng
text: "The Hanani–Tutte theorem is a classical result proved for the first time
in the 1930s that characterizes planar graphs as graphs that admit a drawing in
the plane in which every pair of edges not sharing a vertex cross an even number
of times. We generalize this classical result to clustered graphs with two disjoint
clusters, and show that a straightforward extension of our result to flat clustered
graphs with three or more disjoint clusters is not possible.\r\n\r\nWe also give
a new and short proof for a related result by Di Battista and Frati based on the
matroid intersection algorithm."
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
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: Kynčl, Jan
last_name: Kynčl
- first_name: Igor
full_name: Malinović, Igor
last_name: Malinović
- first_name: Dömötör
full_name: Pálvölgyi, Dömötör
last_name: Pálvölgyi
citation:
ama: 'Fulek R, Kynčl J, Malinović I, Pálvölgyi D. Clustered planarity testing revisited.
In: International Symposium on Graph Drawing. Vol 8871. Cham: Springer
Nature; 2014:428-436. doi:10.1007/978-3-662-45803-7_36'
apa: 'Fulek, R., Kynčl, J., Malinović, I., & Pálvölgyi, D. (2014). Clustered
planarity testing revisited. In International Symposium on Graph Drawing
(Vol. 8871, pp. 428–436). Cham: Springer Nature. https://doi.org/10.1007/978-3-662-45803-7_36'
chicago: 'Fulek, Radoslav, Jan Kynčl, Igor Malinović, and Dömötör Pálvölgyi. “Clustered
Planarity Testing Revisited.” In International Symposium on Graph Drawing,
8871:428–36. Cham: Springer Nature, 2014. https://doi.org/10.1007/978-3-662-45803-7_36.'
ieee: R. Fulek, J. Kynčl, I. Malinović, and D. Pálvölgyi, “Clustered planarity testing
revisited,” in International Symposium on Graph Drawing, 2014, vol. 8871,
pp. 428–436.
ista: Fulek R, Kynčl J, Malinović I, Pálvölgyi D. 2014. Clustered planarity testing
revisited. International Symposium on Graph Drawing. , LNCS, vol. 8871, 428–436.
mla: Fulek, Radoslav, et al. “Clustered Planarity Testing Revisited.” International
Symposium on Graph Drawing, vol. 8871, Springer Nature, 2014, pp. 428–36,
doi:10.1007/978-3-662-45803-7_36.
short: R. Fulek, J. Kynčl, I. Malinović, D. Pálvölgyi, in:, International Symposium
on Graph Drawing, Springer Nature, Cham, 2014, pp. 428–436.
date_created: 2022-02-25T10:32:14Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2025-06-26T07:57:46Z
day: '01'
department:
- _id: UlWa
doi: 10.1007/978-3-662-45803-7_36
external_id:
arxiv:
- '1305.4519'
intvolume: ' 8871'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1305.4519
month: '01'
oa: 1
oa_version: Preprint
page: 428-436
place: Cham
publication: International Symposium on Graph Drawing
publication_identifier:
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '1642'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Clustered planarity testing revisited
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8871
year: '2014'
...
---
_id: '10811'
abstract:
- lang: eng
text: Auxin is an important signaling compound in plants and vital for plant development
and growth. The present book, Auxin and its Role in Plant Development, provides
the reader with detailed and comprehensive insight into the functioning of the
molecule on the whole and specifically in plant development. In the first part,
the functioning, metabolism and signaling pathways of auxin in plants are explained,
the second part depicts the specific role of auxin in plant development and the
third part describes the interaction and functioning of the signaling compound upon
stimuli of the environment. Each chapter is written by international experts in
the respective field and designed for scientists and researchers in plant biology,
plant development and cell biology to summarize the recent progress in understanding
the role of auxin and suggest future perspectives for auxin research.
article_processing_charge: No
citation:
ama: 'Zažímalová E, Petrášek J, Benková E, eds. Auxin and Its Role in Plant Development.
1st ed. Vienna: Springer Nature; 2014. doi:10.1007/978-3-7091-1526-8'
apa: 'Zažímalová, E., Petrášek, J., & Benková, E. (Eds.). (2014). Auxin and
Its Role in Plant Development (1st ed.). Vienna: Springer Nature. https://doi.org/10.1007/978-3-7091-1526-8'
chicago: 'Zažímalová, Eva, Jan Petrášek, and Eva Benková, eds. Auxin and Its
Role in Plant Development. 1st ed. Vienna: Springer Nature, 2014. https://doi.org/10.1007/978-3-7091-1526-8.'
ieee: 'E. Zažímalová, J. Petrášek, and E. Benková, Eds., Auxin and Its Role in
Plant Development, 1st ed. Vienna: Springer Nature, 2014.'
ista: 'Zažímalová E, Petrášek J, Benková E eds. 2014. Auxin and Its Role in Plant
Development 1st ed., Vienna: Springer Nature, 444p.'
mla: Zažímalová, Eva, et al., editors. Auxin and Its Role in Plant Development.
1st ed., Springer Nature, 2014, doi:10.1007/978-3-7091-1526-8.
short: E. Zažímalová, J. Petrášek, E. Benková, eds., Auxin and Its Role in Plant
Development, 1st ed., Springer Nature, Vienna, 2014.
date_created: 2022-03-03T11:52:44Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2022-03-04T07:38:15Z
day: '01'
department:
- _id: EvBe
doi: 10.1007/978-3-7091-1526-8
edition: '1'
editor:
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
language:
- iso: eng
month: '04'
oa_version: None
page: '444'
place: Vienna
publication_identifier:
eisbn:
- '9783709115268'
isbn:
- '9783709115251'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Auxin and Its Role in Plant Development
type: book_editor
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...