---
_id: '2212'
abstract:
- lang: eng
text: 'The theory of graph games is the foundation for modeling and synthesizing
reactive processes. In the synthesis of stochastic processes, we use 2 1/2-player
games where some transitions of the game graph are controlled by two adversarial
players, the System and the Environment, and the other transitions are determined
probabilistically. We consider 2 1/2-player games where the objective of the System
is the conjunction of a qualitative objective (specified as a parity condition)
and a quantitative objective (specified as a mean-payoff condition). We establish
that the problem of deciding whether the System can ensure that the probability
to satisfy the mean-payoff parity objective is at least a given threshold is in
NP ∩ coNP, matching the best known bound in the special case of 2-player games
(where all transitions are deterministic). We present an algorithm running in
time O(d·n2d·MeanGame) to compute the set of almost-sure winning states from which
the objective can be ensured with probability 1, where n is the number of states
of the game, d the number of priorities of the parity objective, and MeanGame
is the complexity to compute the set of almost-sure winning states in 2 1/2-player
mean-payoff games. Our results are useful in the synthesis of stochastic reactive
systems with both functional requirement (given as a qualitative objective) and
performance requirement (given as a quantitative objective). '
acknowledgement: "This research was supported by European project Cassting (FP7-601148).\r\nA
Technical Report of this paper is available at: \r\nhttps://repository.ist.ac.at/id/eprint/128."
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: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Hugo
full_name: Gimbert, Hugo
last_name: Gimbert
- first_name: Youssouf
full_name: Oualhadj, Youssouf
last_name: Oualhadj
citation:
ama: 'Chatterjee K, Doyen L, Gimbert H, Oualhadj Y. Perfect-information stochastic
mean-payoff parity games. In: Vol 8412. Springer; 2014:210-225. doi:10.1007/978-3-642-54830-7_14'
apa: 'Chatterjee, K., Doyen, L., Gimbert, H., & Oualhadj, Y. (2014). Perfect-information
stochastic mean-payoff parity games (Vol. 8412, pp. 210–225). Presented at the
FoSSaCS: Foundations of Software Science and Computation Structures, Grenoble,
France: Springer. https://doi.org/10.1007/978-3-642-54830-7_14'
chicago: Chatterjee, Krishnendu, Laurent Doyen, Hugo Gimbert, and Youssouf Oualhadj.
“Perfect-Information Stochastic Mean-Payoff Parity Games,” 8412:210–25. Springer,
2014. https://doi.org/10.1007/978-3-642-54830-7_14.
ieee: 'K. Chatterjee, L. Doyen, H. Gimbert, and Y. Oualhadj, “Perfect-information
stochastic mean-payoff parity games,” presented at the FoSSaCS: Foundations of
Software Science and Computation Structures, Grenoble, France, 2014, vol. 8412,
pp. 210–225.'
ista: 'Chatterjee K, Doyen L, Gimbert H, Oualhadj Y. 2014. Perfect-information stochastic
mean-payoff parity games. FoSSaCS: Foundations of Software Science and Computation
Structures, LNCS, vol. 8412, 210–225.'
mla: Chatterjee, Krishnendu, et al. Perfect-Information Stochastic Mean-Payoff
Parity Games. Vol. 8412, Springer, 2014, pp. 210–25, doi:10.1007/978-3-642-54830-7_14.
short: K. Chatterjee, L. Doyen, H. Gimbert, Y. Oualhadj, in:, Springer, 2014, pp.
210–225.
conference:
end_date: 2014-04-13
location: Grenoble, France
name: 'FoSSaCS: Foundations of Software Science and Computation Structures'
start_date: 2014-04-05
date_created: 2018-12-11T11:56:21Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2023-02-23T12:24:50Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-642-54830-7_14
ec_funded: 1
intvolume: ' 8412'
language:
- iso: eng
month: '04'
oa_version: None
page: 210 - 225
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_status: published
publisher: Springer
publist_id: '4758'
quality_controlled: '1'
related_material:
record:
- id: '5405'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Perfect-information stochastic mean-payoff parity games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8412
year: '2014'
...
---
_id: '2213'
abstract:
- lang: eng
text: We consider two-player partial-observation stochastic games on finitestate
graphs where player 1 has partial observation and player 2 has perfect observation.
The winning condition we study are ε-regular conditions specified as parity objectives.
The qualitative-analysis problem given a partial-observation stochastic game and
a parity objective asks whether there is a strategy to ensure that the objective
is satisfied with probability 1 (resp. positive probability). These qualitative-analysis
problems are known to be undecidable. However in many applications the relevant
question is the existence of finite-memory strategies, and the qualitative-analysis
problems under finite-memory strategies was recently shown to be decidable in
2EXPTIME.We improve the complexity and show that the qualitative-analysis problems
for partial-observation stochastic parity games under finite-memory strategies
are EXPTIME-complete; and also establish optimal (exponential) memory bounds for
finite-memory strategies required for qualitative analysis.
acknowledgement: 'This research was supported by European project Cassting (FP7-601148),
NSF grants CNS 1049862 and CCF-1139011, by NSF Expe ditions in Computing project
“ExCAPE: Expeditions in Computer Augmented Program Engineering”, by BSF grant 9800096,
and by gift from Intel.'
alternative_title:
- LNCS
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Sumit
full_name: Nain, Sumit
last_name: Nain
- first_name: Moshe
full_name: Vardi, Moshe
last_name: Vardi
citation:
ama: 'Chatterjee K, Doyen L, Nain S, Vardi M. The complexity of partial-observation
stochastic parity games with finite-memory strategies. In: Vol 8412. Springer;
2014:242-257. doi:10.1007/978-3-642-54830-7_16'
apa: 'Chatterjee, K., Doyen, L., Nain, S., & Vardi, M. (2014). The complexity
of partial-observation stochastic parity games with finite-memory strategies (Vol.
8412, pp. 242–257). Presented at the FoSSaCS: Foundations of Software Science
and Computation Structures, Grenoble, France: Springer. https://doi.org/10.1007/978-3-642-54830-7_16'
chicago: Chatterjee, Krishnendu, Laurent Doyen, Sumit Nain, and Moshe Vardi. “The
Complexity of Partial-Observation Stochastic Parity Games with Finite-Memory Strategies,”
8412:242–57. Springer, 2014. https://doi.org/10.1007/978-3-642-54830-7_16.
ieee: 'K. Chatterjee, L. Doyen, S. Nain, and M. Vardi, “The complexity of partial-observation
stochastic parity games with finite-memory strategies,” presented at the FoSSaCS:
Foundations of Software Science and Computation Structures, Grenoble, France,
2014, vol. 8412, pp. 242–257.'
ista: 'Chatterjee K, Doyen L, Nain S, Vardi M. 2014. The complexity of partial-observation
stochastic parity games with finite-memory strategies. FoSSaCS: Foundations of
Software Science and Computation Structures, LNCS, vol. 8412, 242–257.'
mla: Chatterjee, Krishnendu, et al. The Complexity of Partial-Observation Stochastic
Parity Games with Finite-Memory Strategies. Vol. 8412, Springer, 2014, pp.
242–57, doi:10.1007/978-3-642-54830-7_16.
short: K. Chatterjee, L. Doyen, S. Nain, M. Vardi, in:, Springer, 2014, pp. 242–257.
conference:
end_date: 2014-04-13
location: Grenoble, France
name: 'FoSSaCS: Foundations of Software Science and Computation Structures'
start_date: 2014-04-05
date_created: 2018-12-11T11:56:21Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2023-02-23T12:24:58Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-642-54830-7_16
ec_funded: 1
external_id:
arxiv:
- '1401.3289'
intvolume: ' 8412'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1401.3289
month: '04'
oa: 1
oa_version: Preprint
page: 242 - 257
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_status: published
publisher: Springer
publist_id: '4757'
quality_controlled: '1'
related_material:
record:
- id: '5408'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: The complexity of partial-observation stochastic parity games with finite-memory
strategies
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8412
year: '2014'
...
---
_id: '2214'
abstract:
- lang: eng
text: A hallmark of immune cell trafficking is directional guidance via gradients
of soluble or surface bound chemokines. Vascular endothelial cells produce, transport
and deposit either their own chemokines or chemokines produced by the underlying
stroma. Endothelial heparan sulfate (HS) was suggested to be a critical scaffold
for these chemokine pools, but it is unclear how steep chemokine gradients are
sustained between the lumenal and ablumenal aspects of blood vessels. Addressing
this question by semi-quantitative immunostaining of HS moieties around blood
vessels with a pan anti-HS IgM mAb, we found a striking HS enrichment in the basal
lamina of resting and inflamed post capillary skin venules, as well as in high
endothelial venules (HEVs) of lymph nodes. Staining of skin vessels with a glycocalyx
probe further suggested that their lumenal glycocalyx contains much lower HS density
than their basolateral extracellular matrix (ECM). This polarized HS pattern was
observed also in isolated resting and inflamed microvascular dermal cells. Notably,
progressive skin inflammation resulted in massive ECM deposition and in further
HS enrichment around skin post capillary venules and their associated pericytes.
Inflammation-dependent HS enrichment was not compromised in mice deficient in
the main HS degrading enzyme, heparanase. Our results suggest that the blood vasculature
patterns steep gradients of HS scaffolds between their lumenal and basolateral
endothelial aspects, and that inflammatory processes can further enrich the HS
content nearby inflamed vessels. We propose that chemokine gradients between the
lumenal and ablumenal sides of vessels could be favored by these sharp HS scaffold
gradients.
acknowledgement: Michael Sixt's research is supported by the European Research Council
(ERC Starting grant).
article_number: e85699
author:
- first_name: Liat
full_name: Stoler Barak, Liat
last_name: Stoler Barak
- first_name: Christine
full_name: Moussion, Christine
id: 3356F664-F248-11E8-B48F-1D18A9856A87
last_name: Moussion
- first_name: Elias
full_name: Shezen, Elias
last_name: Shezen
- first_name: Miki
full_name: Hatzav, Miki
last_name: Hatzav
- 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: Ronen
full_name: Alon, Ronen
last_name: Alon
citation:
ama: Stoler Barak L, Moussion C, Shezen E, Hatzav M, Sixt MK, Alon R. Blood vessels
pattern heparan sulfate gradients between their apical and basolateral aspects.
PLoS One. 2014;9(1). doi:10.1371/journal.pone.0085699
apa: Stoler Barak, L., Moussion, C., Shezen, E., Hatzav, M., Sixt, M. K., &
Alon, R. (2014). Blood vessels pattern heparan sulfate gradients between their
apical and basolateral aspects. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0085699
chicago: Stoler Barak, Liat, Christine Moussion, Elias Shezen, Miki Hatzav, Michael
K Sixt, and Ronen Alon. “Blood Vessels Pattern Heparan Sulfate Gradients between
Their Apical and Basolateral Aspects.” PLoS One. Public Library of Science,
2014. https://doi.org/10.1371/journal.pone.0085699.
ieee: L. Stoler Barak, C. Moussion, E. Shezen, M. Hatzav, M. K. Sixt, and R. Alon,
“Blood vessels pattern heparan sulfate gradients between their apical and basolateral
aspects,” PLoS One, vol. 9, no. 1. Public Library of Science, 2014.
ista: Stoler Barak L, Moussion C, Shezen E, Hatzav M, Sixt MK, Alon R. 2014. Blood
vessels pattern heparan sulfate gradients between their apical and basolateral
aspects. PLoS One. 9(1), e85699.
mla: Stoler Barak, Liat, et al. “Blood Vessels Pattern Heparan Sulfate Gradients
between Their Apical and Basolateral Aspects.” PLoS One, vol. 9, no. 1,
e85699, Public Library of Science, 2014, doi:10.1371/journal.pone.0085699.
short: L. Stoler Barak, C. Moussion, E. Shezen, M. Hatzav, M.K. Sixt, R. Alon, PLoS
One 9 (2014).
date_created: 2018-12-11T11:56:22Z
date_published: 2014-01-22T00:00:00Z
date_updated: 2021-01-12T06:56:03Z
day: '22'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1371/journal.pone.0085699
ec_funded: 1
file:
- access_level: open_access
checksum: 84a8033bda2e07e39405f5acc85f4eca
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:48Z
date_updated: 2020-07-14T12:45:33Z
file_id: '4646'
file_name: IST-2016-433-v1+1_journal.pone.0085699.pdf
file_size: 12634775
relation: main_file
file_date_updated: 2020-07-14T12:45:33Z
has_accepted_license: '1'
intvolume: ' 9'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25A76F58-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '289720'
name: Stromal Cell-immune Cell Interactions in Health and Disease
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '4756'
pubrep_id: '433'
quality_controlled: '1'
scopus_import: 1
status: public
title: Blood vessels pattern heparan sulfate gradients between their apical and basolateral
aspects
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2014'
...
---
_id: '2215'
abstract:
- lang: eng
text: Homologous recombination is crucial for genome stability and for genetic exchange.
Although our knowledge of the principle steps in recombination and its machinery
is well advanced, homology search, the critical step of exploring the genome for
homologous sequences to enable recombination, has remained mostly enigmatic. However,
recent methodological advances have provided considerable new insights into this
fundamental step in recombination that can be integrated into a mechanistic model.
These advances emphasize the importance of genomic proximity and nuclear organization
for homology search and the critical role of homology search mediators in this
process. They also aid our understanding of how homology search might lead to
unwanted and potentially disease-promoting recombination events.
acknowledgement: J.R. was supported by a Boehringer Ingelheim Fonds PhD stipend.
author:
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
- first_name: Claudio
full_name: Lademann, Claudio
last_name: Lademann
- first_name: Stefan
full_name: Jentsch, Stefan
last_name: Jentsch
citation:
ama: Renkawitz J, Lademann C, Jentsch S. Mechanisms and principles of homology search
during recombination. Nature Reviews Molecular Cell Biology. 2014;15(6):369-383.
doi:10.1038/nrm3805
apa: Renkawitz, J., Lademann, C., & Jentsch, S. (2014). Mechanisms and principles
of homology search during recombination. Nature Reviews Molecular Cell Biology.
Nature Publishing Group. https://doi.org/10.1038/nrm3805
chicago: Renkawitz, Jörg, Claudio Lademann, and Stefan Jentsch. “Mechanisms and
Principles of Homology Search during Recombination.” Nature Reviews Molecular
Cell Biology. Nature Publishing Group, 2014. https://doi.org/10.1038/nrm3805.
ieee: J. Renkawitz, C. Lademann, and S. Jentsch, “Mechanisms and principles of homology
search during recombination,” Nature Reviews Molecular Cell Biology, vol.
15, no. 6. Nature Publishing Group, pp. 369–383, 2014.
ista: Renkawitz J, Lademann C, Jentsch S. 2014. Mechanisms and principles of homology
search during recombination. Nature Reviews Molecular Cell Biology. 15(6), 369–383.
mla: Renkawitz, Jörg, et al. “Mechanisms and Principles of Homology Search during
Recombination.” Nature Reviews Molecular Cell Biology, vol. 15, no. 6,
Nature Publishing Group, 2014, pp. 369–83, doi:10.1038/nrm3805.
short: J. Renkawitz, C. Lademann, S. Jentsch, Nature Reviews Molecular Cell Biology
15 (2014) 369–383.
date_created: 2018-12-11T11:56:22Z
date_published: 2014-05-14T00:00:00Z
date_updated: 2021-01-12T06:56:03Z
day: '14'
department:
- _id: MiSi
doi: 10.1038/nrm3805
intvolume: ' 15'
issue: '6'
language:
- iso: eng
month: '05'
oa_version: None
page: 369 - 383
publication: Nature Reviews Molecular Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '4755'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mechanisms and principles of homology search during recombination
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2014'
...
---
_id: '2216'
abstract:
- lang: eng
text: The edit distance between two (untimed) traces is the minimum cost of a sequence
of edit operations (insertion, deletion, or substitution) needed to transform
one trace to the other. Edit distances have been extensively studied in the untimed
setting, and form the basis for approximate matching of sequences in different
domains such as coding theory, parsing, and speech recognition. In this paper,
we lift the study of edit distances from untimed languages to the timed setting.
We define an edit distance between timed words which incorporates both the edit
distance between the untimed words and the absolute difference in time stamps.
Our edit distance between two timed words is computable in polynomial time. Further,
we show that the edit distance between a timed word and a timed language generated
by a timed automaton, defined as the edit distance between the word and the closest
word in the language, is PSPACE-complete. While computing the edit distance between
two timed automata is undecidable, we show that the approximate version, where
we decide if the edit distance between two timed automata is either less than
a given parameter or more than δ away from the parameter, for δ > 0, can be
solved in exponential space and is EXPSPACE-hard. Our definitions and techniques
can be generalized to the setting of hybrid systems, and analogous decidability
results hold for rectangular automata.
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- 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: Ritankar
full_name: Majumdar, Ritankar
last_name: Majumdar
citation:
ama: 'Chatterjee K, Ibsen-Jensen R, Majumdar R. Edit distance for timed automata.
In: Springer; 2014:303-312. doi:10.1145/2562059.2562141'
apa: 'Chatterjee, K., Ibsen-Jensen, R., & Majumdar, R. (2014). Edit distance
for timed automata (pp. 303–312). Presented at the HSCC: Hybrid Systems - Computation
and Control, Berlin, Germany: Springer. https://doi.org/10.1145/2562059.2562141'
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Ritankar Majumdar. “Edit
Distance for Timed Automata,” 303–12. Springer, 2014. https://doi.org/10.1145/2562059.2562141.
ieee: 'K. Chatterjee, R. Ibsen-Jensen, and R. Majumdar, “Edit distance for timed
automata,” presented at the HSCC: Hybrid Systems - Computation and Control, Berlin,
Germany, 2014, pp. 303–312.'
ista: 'Chatterjee K, Ibsen-Jensen R, Majumdar R. 2014. Edit distance for timed automata.
HSCC: Hybrid Systems - Computation and Control, 303–312.'
mla: Chatterjee, Krishnendu, et al. Edit Distance for Timed Automata. Springer,
2014, pp. 303–12, doi:10.1145/2562059.2562141.
short: K. Chatterjee, R. Ibsen-Jensen, R. Majumdar, in:, Springer, 2014, pp. 303–312.
conference:
end_date: 2017-04-17
location: Berlin, Germany
name: 'HSCC: Hybrid Systems - Computation and Control'
start_date: 2017-04-15
date_created: 2018-12-11T11:56:22Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-02-23T12:25:01Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/2562059.2562141
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://dl.acm.org/citation.cfm?doid=2562059.2562141
month: '01'
oa: 1
oa_version: Submitted Version
page: 303 - 312
publication_status: published
publisher: Springer
publist_id: '4752'
quality_controlled: '1'
related_material:
record:
- id: '5409'
relation: earlier_version
status: public
status: public
title: Edit distance for timed automata
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '2217'
abstract:
- lang: eng
text: "As hybrid systems involve continuous behaviors, they should be evaluated
by quantitative methods, rather than qualitative methods. In this paper we adapt
a quantitative framework, called model measuring, to the hybrid systems domain.
The model-measuring problem asks, given a model M and a specification, what is
the maximal distance such that all models within that distance from M satisfy
(or violate) the specification. A distance function on models is given as part
of the input of the problem. Distances, especially related to continuous behaviors
are more natural in the hybrid case than the discrete case. We are interested
in distances represented by monotonic hybrid automata, a hybrid counterpart of
(discrete) weighted automata, whose recognized timed languages are monotone (w.r.t.
inclusion) in the values of parameters.\r\n\r\nThe contributions of this paper
are twofold. First, we give sufficient conditions under which the model-measuring
problem can be solved. Second, we discuss the modeling of distances and applications
of the model-measuring problem."
acknowledgement: "This work was supported in part by the Austrian Science
Fund NFN RiSE (Rigorous Systems Engineering) and by the ERC Advanced Grant
QUAREM (Quantitative Reactive Modeling).\r\nA Technical Report of this paper is
available at: \r\nhttps://repository.ist.ac.at/id/eprint/171"
article_processing_charge: No
author:
- 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
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: 'Henzinger TA, Otop J. Model measuring for hybrid systems. In: Proceedings
of the 17th International Conference on Hybrid Systems: Computation and Control.
Springer; 2014:213-222. doi:10.1145/2562059.2562130'
apa: 'Henzinger, T. A., & Otop, J. (2014). Model measuring for hybrid systems.
In Proceedings of the 17th international conference on Hybrid systems: computation
and control (pp. 213–222). Berlin, Germany: Springer. https://doi.org/10.1145/2562059.2562130'
chicago: 'Henzinger, Thomas A, and Jan Otop. “Model Measuring for Hybrid Systems.”
In Proceedings of the 17th International Conference on Hybrid Systems: Computation
and Control, 213–22. Springer, 2014. https://doi.org/10.1145/2562059.2562130.'
ieee: 'T. A. Henzinger and J. Otop, “Model measuring for hybrid systems,” in Proceedings
of the 17th international conference on Hybrid systems: computation and control,
Berlin, Germany, 2014, pp. 213–222.'
ista: 'Henzinger TA, Otop J. 2014. Model measuring for hybrid systems. Proceedings
of the 17th international conference on Hybrid systems: computation and control.
HSCC: Hybrid Systems - Computation and Control, 213–222.'
mla: 'Henzinger, Thomas A., and Jan Otop. “Model Measuring for Hybrid Systems.”
Proceedings of the 17th International Conference on Hybrid Systems: Computation
and Control, Springer, 2014, pp. 213–22, doi:10.1145/2562059.2562130.'
short: 'T.A. Henzinger, J. Otop, in:, Proceedings of the 17th International Conference
on Hybrid Systems: Computation and Control, Springer, 2014, pp. 213–222.'
conference:
end_date: 2014-04-17
location: Berlin, Germany
name: 'HSCC: Hybrid Systems - Computation and Control'
start_date: 2014-04-15
date_created: 2018-12-11T11:56:23Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2023-02-23T12:25:23Z
day: '01'
department:
- _id: ToHe
doi: 10.1145/2562059.2562130
ec_funded: 1
language:
- iso: eng
month: '04'
oa_version: None
page: 213 - 222
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: 'Proceedings of the 17th international conference on Hybrid systems:
computation and control'
publication_status: published
publisher: Springer
publist_id: '4751'
quality_controlled: '1'
related_material:
record:
- id: '5416'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Model measuring for hybrid systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '2218'
abstract:
- lang: eng
text: While fixing concurrency bugs, program repair algorithms may introduce new
concurrency bugs. We present an algorithm that avoids such regressions. The solution
space is given by a set of program transformations we consider in the repair process.
These include reordering of instructions within a thread and inserting atomic
sections. The new algorithm learns a constraint on the space of candidate solutions,
from both positive examples (error-free traces) and counterexamples (error traces).
From each counterexample, the algorithm learns a constraint necessary to remove
the errors. From each positive examples, it learns a constraint that is necessary
in order to prevent the repair from turning the trace into an error trace. We
implemented the algorithm and evaluated it on simplified Linux device drivers
with known bugs.
alternative_title:
- LNCS
author:
- first_name: Pavol
full_name: Cerny, Pavol
last_name: Cerny
- 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: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
- first_name: Leonid
full_name: Ryzhyk, Leonid
last_name: Ryzhyk
- first_name: Thorsten
full_name: Tarrach, Thorsten
id: 3D6E8F2C-F248-11E8-B48F-1D18A9856A87
last_name: Tarrach
orcid: 0000-0003-4409-8487
citation:
ama: 'Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. Regression-free
synthesis for concurrency. In: Vol 8559. Springer; 2014:568-584. doi:10.1007/978-3-319-08867-9_38'
apa: 'Cerny, P., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., & Tarrach,
T. (2014). Regression-free synthesis for concurrency (Vol. 8559, pp. 568–584).
Presented at the CAV: Computer Aided Verification, Vienna, Austria: Springer.
https://doi.org/10.1007/978-3-319-08867-9_38'
chicago: Cerny, Pavol, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, and
Thorsten Tarrach. “Regression-Free Synthesis for Concurrency,” 8559:568–84. Springer,
2014. https://doi.org/10.1007/978-3-319-08867-9_38.
ieee: 'P. Cerny, T. A. Henzinger, A. Radhakrishna, L. Ryzhyk, and T. Tarrach, “Regression-free
synthesis for concurrency,” presented at the CAV: Computer Aided Verification,
Vienna, Austria, 2014, vol. 8559, pp. 568–584.'
ista: 'Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. 2014. Regression-free
synthesis for concurrency. CAV: Computer Aided Verification, LNCS, vol. 8559,
568–584.'
mla: Cerny, Pavol, et al. Regression-Free Synthesis for Concurrency. Vol.
8559, Springer, 2014, pp. 568–84, doi:10.1007/978-3-319-08867-9_38.
short: P. Cerny, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, T. Tarrach, in:, Springer,
2014, pp. 568–584.
conference:
end_date: 2014-07-22
location: Vienna, Austria
name: 'CAV: Computer Aided Verification'
start_date: 2014-07-18
date_created: 2018-12-11T11:56:23Z
date_published: 2014-07-22T00:00:00Z
date_updated: 2023-09-07T11:57:01Z
day: '22'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-319-08867-9_38
ec_funded: 1
file:
- access_level: open_access
checksum: a631d3105509f239724644e77a1212e2
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:14Z
date_updated: 2020-07-14T12:45:33Z
file_id: '4995'
file_name: IST-2014-297-v1+1_cav14-final.pdf
file_size: 416732
relation: main_file
- access_level: open_access
checksum: f8b0f748cc9fa697ca992cc56c87bc4e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:15Z
date_updated: 2020-07-14T12:45:33Z
file_id: '4996'
file_name: IST-2014-297-v2+1_cav14-final2.pdf
file_size: 616293
relation: main_file
file_date_updated: 2020-07-14T12:45:33Z
has_accepted_license: '1'
intvolume: ' 8559'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://link.springer.com/chapter/10.1007%2F978-3-319-08867-9_38
month: '07'
oa: 1
oa_version: Submitted Version
page: 568 - 584
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_identifier:
isbn:
- 978-331908866-2
publication_status: published
publisher: Springer
publist_id: '4749'
pubrep_id: '297'
quality_controlled: '1'
related_material:
record:
- id: '1130'
relation: dissertation_contains
status: public
status: public
title: Regression-free synthesis for concurrency
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8559
year: '2014'
...
---
_id: '2219'
abstract:
- lang: eng
text: Recently, Döttling et al. (ASIACRYPT 2012) proposed the first chosen-ciphertext
(IND-CCA) secure public-key encryption scheme from the learning parity with noise
(LPN) assumption. In this work we give an alternative scheme which is conceptually
simpler and more efficient. At the core of our construction is a trapdoor technique
originally proposed for lattices by Micciancio and Peikert (EUROCRYPT 2012), which
we adapt to the LPN setting. The main technical tool is a new double-trapdoor
mechanism, together with a trapdoor switching lemma based on a computational variant
of the leftover hash lemma.
alternative_title:
- LNCS
author:
- first_name: Eike
full_name: Kiltz, Eike
last_name: Kiltz
- first_name: Daniel
full_name: Masny, Daniel
last_name: Masny
- 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: 'Kiltz E, Masny D, Pietrzak KZ. Simple chosen-ciphertext security from low
noise LPN. In: Vol 8383. Springer; 2014:1-18. doi:10.1007/978-3-642-54631-0_1'
apa: 'Kiltz, E., Masny, D., & Pietrzak, K. Z. (2014). Simple chosen-ciphertext
security from low noise LPN (Vol. 8383, pp. 1–18). Presented at the IACR: International
Conference on Practice and Theory in Public-Key Cryptography, Springer. https://doi.org/10.1007/978-3-642-54631-0_1'
chicago: Kiltz, Eike, Daniel Masny, and Krzysztof Z Pietrzak. “Simple Chosen-Ciphertext
Security from Low Noise LPN,” 8383:1–18. Springer, 2014. https://doi.org/10.1007/978-3-642-54631-0_1.
ieee: 'E. Kiltz, D. Masny, and K. Z. Pietrzak, “Simple chosen-ciphertext security
from low noise LPN,” presented at the IACR: International Conference on Practice
and Theory in Public-Key Cryptography, 2014, vol. 8383, pp. 1–18.'
ista: 'Kiltz E, Masny D, Pietrzak KZ. 2014. Simple chosen-ciphertext security from
low noise LPN. IACR: International Conference on Practice and Theory in Public-Key
Cryptography, LNCS, vol. 8383, 1–18.'
mla: Kiltz, Eike, et al. Simple Chosen-Ciphertext Security from Low Noise LPN.
Vol. 8383, Springer, 2014, pp. 1–18, doi:10.1007/978-3-642-54631-0_1.
short: E. Kiltz, D. Masny, K.Z. Pietrzak, in:, Springer, 2014, pp. 1–18.
conference:
name: 'IACR: International Conference on Practice and Theory in Public-Key Cryptography'
date_created: 2018-12-11T11:56:24Z
date_published: 2014-03-01T00:00:00Z
date_updated: 2021-01-12T06:56:05Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/978-3-642-54631-0_1
intvolume: ' 8383'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2015/401
month: '03'
oa: 1
oa_version: Submitted Version
page: 1 - 18
publication_identifier:
isbn:
- 978-364254630-3
publication_status: published
publisher: Springer
publist_id: '4748'
quality_controlled: '1'
scopus_import: 1
status: public
title: Simple chosen-ciphertext security from low noise LPN
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 8383
year: '2014'
...
---
_id: '2220'
abstract:
- lang: eng
text: In this issue of Chemistry & Biology, Cokol and colleagues report a systematic
study of drug interactions between antifungal compounds. Suppressive drug interactions
occur more frequently than previously realized and come in different flavors with
interesting implications.
author:
- first_name: Marjon
full_name: De Vos, Marjon
id: 3111FFAC-F248-11E8-B48F-1D18A9856A87
last_name: De Vos
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: de Vos M, Bollenbach MT. Suppressive drug interactions between antifungals.
Chemistry and Biology. 2014;21(4):439-440. doi:10.1016/j.chembiol.2014.04.004
apa: de Vos, M., & Bollenbach, M. T. (2014). Suppressive drug interactions between
antifungals. Chemistry and Biology. Cell Press. https://doi.org/10.1016/j.chembiol.2014.04.004
chicago: Vos, Marjon de, and Mark Tobias Bollenbach. “Suppressive Drug Interactions
between Antifungals.” Chemistry and Biology. Cell Press, 2014. https://doi.org/10.1016/j.chembiol.2014.04.004.
ieee: M. de Vos and M. T. Bollenbach, “Suppressive drug interactions between antifungals,”
Chemistry and Biology, vol. 21, no. 4. Cell Press, pp. 439–440, 2014.
ista: de Vos M, Bollenbach MT. 2014. Suppressive drug interactions between antifungals.
Chemistry and Biology. 21(4), 439–440.
mla: de Vos, Marjon, and Mark Tobias Bollenbach. “Suppressive Drug Interactions
between Antifungals.” Chemistry and Biology, vol. 21, no. 4, Cell Press,
2014, pp. 439–40, doi:10.1016/j.chembiol.2014.04.004.
short: M. de Vos, M.T. Bollenbach, Chemistry and Biology 21 (2014) 439–440.
date_created: 2018-12-11T11:56:24Z
date_published: 2014-04-24T00:00:00Z
date_updated: 2021-01-12T06:56:06Z
day: '24'
department:
- _id: ToBo
doi: 10.1016/j.chembiol.2014.04.004
external_id:
pmid:
- '24766845'
intvolume: ' 21'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/24766845
month: '04'
oa: 1
oa_version: Published Version
page: 439 - 440
pmid: 1
publication: Chemistry and Biology
publication_identifier:
issn:
- '10745521'
publication_status: published
publisher: Cell Press
publist_id: '4747'
quality_controlled: '1'
scopus_import: 1
status: public
title: Suppressive drug interactions between antifungals
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2014'
...
---
_id: '2222'
abstract:
- lang: eng
text: Leaf venation develops complex patterns in angiosperms, but the mechanism
underlying this process is largely unknown. To elucidate the molecular mechanisms
governing vein pattern formation, we previously isolated vascular network defective
(van) mutants that displayed venation discontinuities. Here, we report the phenotypic
analysis of van4 mutants, and we identify and characterize the VAN4 gene. Detailed
phenotypic analysis shows that van4 mutants are defective in procambium cell differentiation
and subsequent vascular cell differentiation. Reduced shoot and root cell growth
is observed in van4 mutants, suggesting that VAN4 function is important for cell
growth and the establishment of venation continuity. Consistent with these phenotypes,
the VAN4 gene is strongly expressed in vascular and meristematic cells. VAN4 encodes
a putative TRS120, which is a known guanine nucleotide exchange factor (GEF) for
Rab GTPase involved in regulating vesicle transport, and a known tethering factor
that determines the specificity of membrane fusion. VAN4 protein localizes at
the trans-Golgi network/early endosome (TGN/EE). Aberrant recycling of the auxin
efflux carrier PIN proteins is observed in van4 mutants. These results suggest
that VAN4-mediated exocytosis at the TGN plays important roles in plant vascular
development and cell growth in shoot and root. Our identification of VAN4 as a
putative TRS120 shows that Rab GTPases are crucial (in addition to ARF GTPases)
for continuous vascular development, and provides further evidence for the importance
of vesicle transport in leaf vascular formation.
author:
- first_name: Satoshi
full_name: Naramoto, Satoshi
last_name: Naramoto
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- first_name: Tomoko
full_name: Dainobu, Tomoko
last_name: Dainobu
- first_name: Hirotomo
full_name: Takatsuka, Hirotomo
last_name: Takatsuka
- first_name: Teruyo
full_name: Okada, Teruyo
last_name: Okada
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Hiroo
full_name: Fukuda, Hiroo
last_name: Fukuda
citation:
ama: Naramoto S, Nodzyński T, Dainobu T, et al. VAN4 encodes a putative TRS120 that
is required for normal cell growth and vein development in arabidopsis. Plant
and Cell Physiology. 2014;55(4):750-763. doi:10.1093/pcp/pcu012
apa: Naramoto, S., Nodzyński, T., Dainobu, T., Takatsuka, H., Okada, T., Friml,
J., & Fukuda, H. (2014). VAN4 encodes a putative TRS120 that is required for
normal cell growth and vein development in arabidopsis. Plant and Cell Physiology.
Oxford University Press. https://doi.org/10.1093/pcp/pcu012
chicago: Naramoto, Satoshi, Tomasz Nodzyński, Tomoko Dainobu, Hirotomo Takatsuka,
Teruyo Okada, Jiří Friml, and Hiroo Fukuda. “VAN4 Encodes a Putative TRS120 That
Is Required for Normal Cell Growth and Vein Development in Arabidopsis.” Plant
and Cell Physiology. Oxford University Press, 2014. https://doi.org/10.1093/pcp/pcu012.
ieee: S. Naramoto et al., “VAN4 encodes a putative TRS120 that is required
for normal cell growth and vein development in arabidopsis,” Plant and Cell
Physiology, vol. 55, no. 4. Oxford University Press, pp. 750–763, 2014.
ista: Naramoto S, Nodzyński T, Dainobu T, Takatsuka H, Okada T, Friml J, Fukuda
H. 2014. VAN4 encodes a putative TRS120 that is required for normal cell growth
and vein development in arabidopsis. Plant and Cell Physiology. 55(4), 750–763.
mla: Naramoto, Satoshi, et al. “VAN4 Encodes a Putative TRS120 That Is Required
for Normal Cell Growth and Vein Development in Arabidopsis.” Plant and Cell
Physiology, vol. 55, no. 4, Oxford University Press, 2014, pp. 750–63, doi:10.1093/pcp/pcu012.
short: S. Naramoto, T. Nodzyński, T. Dainobu, H. Takatsuka, T. Okada, J. Friml,
H. Fukuda, Plant and Cell Physiology 55 (2014) 750–763.
date_created: 2018-12-11T11:56:24Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2021-01-12T06:56:06Z
day: '01'
department:
- _id: JiFr
doi: 10.1093/pcp/pcu012
ec_funded: 1
intvolume: ' 55'
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
page: 750 - 763
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Plant and Cell Physiology
publication_identifier:
issn:
- '00320781'
publication_status: published
publisher: Oxford University Press
publist_id: '4742'
quality_controlled: '1'
scopus_import: 1
status: public
title: VAN4 encodes a putative TRS120 that is required for normal cell growth and
vein development in arabidopsis
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2014'
...
---
_id: '2223'
abstract:
- lang: eng
text: Correct positioning of membrane proteins is an essential process in eukaryotic
organisms. The plant hormone auxin is distributed through intercellular transport
and triggers various cellular responses. Auxin transporters of the PIN-FORMED
(PIN) family localize asymmetrically at the plasma membrane (PM) and mediate the
directional transport of auxin between cells. A fungal toxin, brefeldin A (BFA),
inhibits a subset of guanine nucleotide exchange factors for ADP-ribosylation
factor small GTPases (ARF GEFs) including GNOM, which plays a major role in localization
of PIN1 predominantly to the basal side of the PM. The Arabidopsis genome encodes
19 ARF-related putative GTPases. However, ARF components involved in PIN1 localization
have been genetically poorly defined. Using a fluorescence imaging-based forward
genetic approach, we identified an Arabidopsis mutant, bfa-visualized exocytic
trafficking defective1 (bex1), in which PM localization of PIN1-green fluorescent
protein (GFP) as well as development is hypersensitive to BFA. We found that in
bex1 a member of the ARF1 gene family, ARF1A1C, was mutated. ARF1A1C localizes
to the trans-Golgi network/early endosome and Golgi apparatus, acts synergistically
to BEN1/MIN7 ARF GEF and is important for PIN recycling to the PM. Consistent
with the developmental importance of PIN proteins, functional interference with
ARF1 resulted in an impaired auxin response gradient and various developmental
defects including embryonic patterning defects and growth arrest. Our results
show that ARF1A1C is essential for recycling of PIN auxin transporters and for
various auxin-dependent developmental processes.
author:
- first_name: Hirokazu
full_name: Tanaka, Hirokazu
last_name: Tanaka
- first_name: Tomasz
full_name: Nodzyński, Tomasz
last_name: Nodzyński
- first_name: Saeko
full_name: Kitakura, Saeko
last_name: Kitakura
- first_name: Mugurel
full_name: Feraru, Mugurel
last_name: Feraru
- first_name: Michiko
full_name: Sasabe, Michiko
last_name: Sasabe
- first_name: Tomomi
full_name: Ishikawa, Tomomi
last_name: Ishikawa
- first_name: Jürgen
full_name: Kleine Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Tatsuo
full_name: Kakimoto, Tatsuo
last_name: Kakimoto
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Tanaka H, Nodzyński T, Kitakura S, et al. BEX1/ARF1A1C is required for BFA-sensitive
recycling of PIN auxin transporters and auxin-mediated development in arabidopsis.
Plant and Cell Physiology. 2014;55(4):737-749. doi:10.1093/pcp/pct196
apa: Tanaka, H., Nodzyński, T., Kitakura, S., Feraru, M., Sasabe, M., Ishikawa,
T., … Friml, J. (2014). BEX1/ARF1A1C is required for BFA-sensitive recycling of
PIN auxin transporters and auxin-mediated development in arabidopsis. Plant
and Cell Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pct196
chicago: Tanaka, Hirokazu, Tomasz Nodzyński, Saeko Kitakura, Mugurel Feraru, Michiko
Sasabe, Tomomi Ishikawa, Jürgen Kleine Vehn, Tatsuo Kakimoto, and Jiří Friml.
“BEX1/ARF1A1C Is Required for BFA-Sensitive Recycling of PIN Auxin Transporters
and Auxin-Mediated Development in Arabidopsis.” Plant and Cell Physiology.
Oxford University Press, 2014. https://doi.org/10.1093/pcp/pct196.
ieee: H. Tanaka et al., “BEX1/ARF1A1C is required for BFA-sensitive recycling
of PIN auxin transporters and auxin-mediated development in arabidopsis,” Plant
and Cell Physiology, vol. 55, no. 4. Oxford University Press, pp. 737–749,
2014.
ista: Tanaka H, Nodzyński T, Kitakura S, Feraru M, Sasabe M, Ishikawa T, Kleine
Vehn J, Kakimoto T, Friml J. 2014. BEX1/ARF1A1C is required for BFA-sensitive
recycling of PIN auxin transporters and auxin-mediated development in arabidopsis.
Plant and Cell Physiology. 55(4), 737–749.
mla: Tanaka, Hirokazu, et al. “BEX1/ARF1A1C Is Required for BFA-Sensitive Recycling
of PIN Auxin Transporters and Auxin-Mediated Development in Arabidopsis.” Plant
and Cell Physiology, vol. 55, no. 4, Oxford University Press, 2014, pp. 737–49,
doi:10.1093/pcp/pct196.
short: H. Tanaka, T. Nodzyński, S. Kitakura, M. Feraru, M. Sasabe, T. Ishikawa,
J. Kleine Vehn, T. Kakimoto, J. Friml, Plant and Cell Physiology 55 (2014) 737–749.
date_created: 2018-12-11T11:56:25Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2021-01-12T06:56:07Z
day: '01'
ddc:
- '570'
department:
- _id: JiFr
doi: 10.1093/pcp/pct196
ec_funded: 1
file:
- access_level: open_access
checksum: b781a76b32ac35a520256453c3ba9433
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:25Z
date_updated: 2020-07-14T12:45:34Z
file_id: '5076'
file_name: IST-2016-431-v1+1_Plant_Cell_Physiol-2014-Tanaka-737-49.pdf
file_size: 2028111
relation: main_file
file_date_updated: 2020-07-14T12:45:34Z
has_accepted_license: '1'
intvolume: ' 55'
issue: '4'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
main_file_link:
- open_access: '1'
url: http://repository.ist.ac.at/id/eprint/431
month: '04'
oa: 1
oa_version: Published Version
page: 737 - 749
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
- _id: 256BDAB0-B435-11E9-9278-68D0E5697425
name: Innovationsförderung in der Grenzregion Österreich – Tschechische Republik
durch die Schaffung von Synergien im Bereich der Forschungsinfrastruktur
publication: Plant and Cell Physiology
publication_identifier:
issn:
- '00320781'
publication_status: published
publisher: Oxford University Press
publist_id: '4741'
pubrep_id: '431'
quality_controlled: '1'
scopus_import: 1
status: public
title: BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters
and auxin-mediated development in arabidopsis
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2014'
...
---
_id: '2224'
abstract:
- lang: eng
text: This work investigates the transition between different traveling helical
waves (spirals, SPIs) in the setup of differentially independent rotating cylinders.
We use direct numerical simulations to consider an infinite long and periodic
Taylor-Couette apparatus with fixed axial periodicity length. We find so-called
mixed-cross-spirals (MCSs), that can be seen as nonlinear superpositions of SPIs,
to establish stable footbridges connecting SPI states. While bridging the bifurcation
branches of SPIs, the corresponding contributions within the MCS vary continuously
with the control parameters. Here discussed MCSs presenting footbridge solutions
start and end in different SPI branches. Therefore they differ significantly from
the already known MCSs that present bypass solutions (Altmeyer and Hoffmann 2010
New J. Phys. 12 113035). The latter start and end in the same SPI branch, while
they always bifurcate out of those SPI branches with the larger mode amplitude.
Meanwhile, these only appear within the coexisting region of both SPIs. In contrast,
the footbridge solutions can also bifurcate out of the minor SPI contribution.
We also find they exist in regions where only one of the SPIs contributions exists.
In addition, MCS as footbridge solution can appear either stable or unstable.
The latter detected transient solutions offer similar spatio-temporal characteristics
to the flow establishing stable footbridges. Such transition processes are interesting
for pattern-forming systems in general because they accomplish transitions between
traveling waves of different azimuthal wave numbers and have not been described
in the literature yet.
article_number: '025503'
author:
- first_name: Sebastian
full_name: Altmeyer, Sebastian
id: 2EE67FDC-F248-11E8-B48F-1D18A9856A87
last_name: Altmeyer
orcid: 0000-0001-5964-0203
citation:
ama: Altmeyer S. On secondary instabilities generating footbridges between spiral
vortex flow. Fluid Dynamics Research. 2014;46(2). doi:10.1088/0169-5983/46/2/025503
apa: Altmeyer, S. (2014). On secondary instabilities generating footbridges between
spiral vortex flow. Fluid Dynamics Research. IOP Publishing Ltd. https://doi.org/10.1088/0169-5983/46/2/025503
chicago: Altmeyer, Sebastian. “On Secondary Instabilities Generating Footbridges
between Spiral Vortex Flow.” Fluid Dynamics Research. IOP Publishing Ltd.,
2014. https://doi.org/10.1088/0169-5983/46/2/025503.
ieee: S. Altmeyer, “On secondary instabilities generating footbridges between spiral
vortex flow,” Fluid Dynamics Research, vol. 46, no. 2. IOP Publishing Ltd.,
2014.
ista: Altmeyer S. 2014. On secondary instabilities generating footbridges between
spiral vortex flow. Fluid Dynamics Research. 46(2), 025503.
mla: Altmeyer, Sebastian. “On Secondary Instabilities Generating Footbridges between
Spiral Vortex Flow.” Fluid Dynamics Research, vol. 46, no. 2, 025503, IOP
Publishing Ltd., 2014, doi:10.1088/0169-5983/46/2/025503.
short: S. Altmeyer, Fluid Dynamics Research 46 (2014).
date_created: 2018-12-11T11:56:25Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2021-01-12T06:56:07Z
day: '01'
department:
- _id: BjHo
doi: 10.1088/0169-5983/46/2/025503
intvolume: ' 46'
issue: '2'
language:
- iso: eng
month: '04'
oa_version: None
publication: Fluid Dynamics Research
publication_identifier:
issn:
- '01695983'
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '4740'
quality_controlled: '1'
scopus_import: 1
status: public
title: On secondary instabilities generating footbridges between spiral vortex flow
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 46
year: '2014'
...
---
_id: '2225'
abstract:
- lang: eng
text: "We consider sample covariance matrices of the form X∗X, where X is an M×N
matrix with independent random entries. We prove the isotropic local Marchenko-Pastur
law, i.e. we prove that the resolvent (X∗X−z)−1 converges to a multiple of the
identity in the sense of quadratic forms. More precisely, we establish sharp high-probability
bounds on the quantity ⟨v,(X∗X−z)−1w⟩−⟨v,w⟩m(z), where m is the Stieltjes transform
of the Marchenko-Pastur law and v,w∈CN. We require the logarithms of the dimensions
M and N to be comparable. Our result holds down to scales Iz≥N−1+ε and throughout
the entire spectrum away from 0. We also prove analogous results for generalized
Wigner matrices.\r\n"
article_number: '33'
author:
- first_name: Alex
full_name: Bloemendal, Alex
last_name: Bloemendal
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Antti
full_name: Knowles, Antti
last_name: Knowles
- first_name: Horng
full_name: Yau, Horng
last_name: Yau
- first_name: Jun
full_name: Yin, Jun
last_name: Yin
citation:
ama: Bloemendal A, Erdös L, Knowles A, Yau H, Yin J. Isotropic local laws for sample
covariance and generalized Wigner matrices. Electronic Journal of Probability.
2014;19. doi:10.1214/EJP.v19-3054
apa: Bloemendal, A., Erdös, L., Knowles, A., Yau, H., & Yin, J. (2014). Isotropic
local laws for sample covariance and generalized Wigner matrices. Electronic
Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/EJP.v19-3054
chicago: Bloemendal, Alex, László Erdös, Antti Knowles, Horng Yau, and Jun Yin.
“Isotropic Local Laws for Sample Covariance and Generalized Wigner Matrices.”
Electronic Journal of Probability. Institute of Mathematical Statistics,
2014. https://doi.org/10.1214/EJP.v19-3054.
ieee: A. Bloemendal, L. Erdös, A. Knowles, H. Yau, and J. Yin, “Isotropic local
laws for sample covariance and generalized Wigner matrices,” Electronic Journal
of Probability, vol. 19. Institute of Mathematical Statistics, 2014.
ista: Bloemendal A, Erdös L, Knowles A, Yau H, Yin J. 2014. Isotropic local laws
for sample covariance and generalized Wigner matrices. Electronic Journal of Probability.
19, 33.
mla: Bloemendal, Alex, et al. “Isotropic Local Laws for Sample Covariance and Generalized
Wigner Matrices.” Electronic Journal of Probability, vol. 19, 33, Institute
of Mathematical Statistics, 2014, doi:10.1214/EJP.v19-3054.
short: A. Bloemendal, L. Erdös, A. Knowles, H. Yau, J. Yin, Electronic Journal of
Probability 19 (2014).
date_created: 2018-12-11T11:56:25Z
date_published: 2014-03-15T00:00:00Z
date_updated: 2021-01-12T06:56:07Z
day: '15'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1214/EJP.v19-3054
ec_funded: 1
file:
- access_level: open_access
checksum: 7eb297ff367a2ee73b21b6dd1e1948e4
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:06Z
date_updated: 2020-07-14T12:45:34Z
file_id: '5055'
file_name: IST-2016-427-v1+1_3054-16624-4-PB.pdf
file_size: 810150
relation: main_file
file_date_updated: 2020-07-14T12:45:34Z
has_accepted_license: '1'
intvolume: ' 19'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Electronic Journal of Probability
publication_identifier:
issn:
- '10836489'
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '4739'
pubrep_id: '427'
quality_controlled: '1'
status: public
title: Isotropic local laws for sample covariance and generalized Wigner matrices
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2014'
...
---
_id: '2226'
abstract:
- lang: eng
text: Coriolis force effects on shear flows are important in geophysical and astrophysical
contexts. We report a study on the linear stability and the transient energy growth
of the plane Couette flow with system rotation perpendicular to the shear direction.
External rotation causes linear instability. At small rotation rates, the onset
of linear instability scales inversely with the rotation rate and the optimal
transient growth in the linearly stable region is slightly enhanced ∼Re2. The
corresponding optimal initial perturbations are characterized by roll structures
inclined in the streamwise direction and are twisted under external rotation.
At large rotation rates, the transient growth is significantly inhibited and hence
linear stability analysis is a reliable indicator for instability.
article_number: '013001'
author:
- first_name: Liang
full_name: Shi, Liang
last_name: Shi
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Andreas
full_name: Tilgner, Andreas
last_name: Tilgner
citation:
ama: Shi L, Hof B, Tilgner A. Transient growth of Ekman-Couette flow. Physical
Review E Statistical Nonlinear and Soft Matter Physics. 2014;89(1). doi:10.1103/PhysRevE.89.013001
apa: Shi, L., Hof, B., & Tilgner, A. (2014). Transient growth of Ekman-Couette
flow. Physical Review E Statistical Nonlinear and Soft Matter Physics.
American Institute of Physics. https://doi.org/10.1103/PhysRevE.89.013001
chicago: Shi, Liang, Björn Hof, and Andreas Tilgner. “Transient Growth of Ekman-Couette
Flow.” Physical Review E Statistical Nonlinear and Soft Matter Physics.
American Institute of Physics, 2014. https://doi.org/10.1103/PhysRevE.89.013001.
ieee: L. Shi, B. Hof, and A. Tilgner, “Transient growth of Ekman-Couette flow,”
Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89,
no. 1. American Institute of Physics, 2014.
ista: Shi L, Hof B, Tilgner A. 2014. Transient growth of Ekman-Couette flow. Physical
Review E Statistical Nonlinear and Soft Matter Physics. 89(1), 013001.
mla: Shi, Liang, et al. “Transient Growth of Ekman-Couette Flow.” Physical Review
E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 1, 013001, American
Institute of Physics, 2014, doi:10.1103/PhysRevE.89.013001.
short: L. Shi, B. Hof, A. Tilgner, Physical Review E Statistical Nonlinear and Soft
Matter Physics 89 (2014).
date_created: 2018-12-11T11:56:26Z
date_published: 2014-01-06T00:00:00Z
date_updated: 2021-01-12T06:56:08Z
day: '06'
department:
- _id: BjHo
doi: 10.1103/PhysRevE.89.013001
intvolume: ' 89'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1312.5095
month: '01'
oa: 1
oa_version: Submitted Version
project:
- _id: 25BDE9A4-B435-11E9-9278-68D0E5697425
grant_number: SFB-TR3-TP10B
name: Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_identifier:
issn:
- '15393755'
publication_status: published
publisher: American Institute of Physics
publist_id: '4737'
quality_controlled: '1'
scopus_import: 1
status: public
title: Transient growth of Ekman-Couette flow
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 89
year: '2014'
...
---
_id: '2227'
abstract:
- lang: eng
text: The Balkan Peninsula, characterized by high rates of endemism, is recognised
as one of the most diverse and species-rich areas of Europe. However, little is
known about the origin of Balkan endemics. The present study addresses the phylogenetic
position of the Balkan endemic Ranunculus wettsteinii, as well as its taxonomic
status and relationship with the widespread R. parnassiifolius, based on nuclear
DNA (internal transcribed spacer, ITS) and plastid regions (rpl32-trnL, rps16-trnQ,
trnK-matK and ycf6-psbM). Maximum parsimony and Bayesian inference analyses revealed
a well-supported clade formed by accessions of R. wettsteinii. Furthermore, our
phylogenetic and network analyses supported previous hypotheses of a likely allopolyploid
origin for R. wettsteinii between R. montenegrinus and R. parnassiifolius, with
the latter as the maternal parent.
article_processing_charge: No
author:
- first_name: Eduardo
full_name: Cires Rodriguez, Eduardo
id: 2AD56A7A-F248-11E8-B48F-1D18A9856A87
last_name: Cires Rodriguez
- first_name: Matthias
full_name: Baltisberger, Matthias
last_name: Baltisberger
- first_name: Candela
full_name: Cuesta, Candela
id: 33A3C818-F248-11E8-B48F-1D18A9856A87
last_name: Cuesta
orcid: 0000-0003-1923-2410
- first_name: Pablo
full_name: Vargas, Pablo
last_name: Vargas
- first_name: José
full_name: Prieto, José
last_name: Prieto
citation:
ama: Cires Rodriguez E, Baltisberger M, Cuesta C, Vargas P, Prieto J. Allopolyploid
origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from
nuclear and plastid DNA sequences. Organisms Diversity and Evolution. 2014;14(1):1-10.
doi:10.1007/s13127-013-0150-6
apa: Cires Rodriguez, E., Baltisberger, M., Cuesta, C., Vargas, P., & Prieto,
J. (2014). Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae)
inferred from nuclear and plastid DNA sequences. Organisms Diversity and Evolution.
Springer. https://doi.org/10.1007/s13127-013-0150-6
chicago: Cires Rodriguez, Eduardo, Matthias Baltisberger, Candela Cuesta, Pablo
Vargas, and José Prieto. “Allopolyploid Origin of the Balkan Endemic Ranunculus
Wettsteinii (Ranunculaceae) Inferred from Nuclear and Plastid DNA Sequences.”
Organisms Diversity and Evolution. Springer, 2014. https://doi.org/10.1007/s13127-013-0150-6.
ieee: E. Cires Rodriguez, M. Baltisberger, C. Cuesta, P. Vargas, and J. Prieto,
“Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae)
inferred from nuclear and plastid DNA sequences,” Organisms Diversity and Evolution,
vol. 14, no. 1. Springer, pp. 1–10, 2014.
ista: Cires Rodriguez E, Baltisberger M, Cuesta C, Vargas P, Prieto J. 2014. Allopolyploid
origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from
nuclear and plastid DNA sequences. Organisms Diversity and Evolution. 14(1), 1–10.
mla: Cires Rodriguez, Eduardo, et al. “Allopolyploid Origin of the Balkan Endemic
Ranunculus Wettsteinii (Ranunculaceae) Inferred from Nuclear and Plastid DNA Sequences.”
Organisms Diversity and Evolution, vol. 14, no. 1, Springer, 2014, pp.
1–10, doi:10.1007/s13127-013-0150-6.
short: E. Cires Rodriguez, M. Baltisberger, C. Cuesta, P. Vargas, J. Prieto, Organisms
Diversity and Evolution 14 (2014) 1–10.
date_created: 2018-12-11T11:56:26Z
date_published: 2014-03-01T00:00:00Z
date_updated: 2022-08-25T14:42:46Z
day: '01'
department:
- _id: JiFr
- _id: EvBe
doi: 10.1007/s13127-013-0150-6
intvolume: ' 14'
issue: '1'
language:
- iso: eng
month: '03'
oa_version: None
page: 1 - 10
publication: Organisms Diversity and Evolution
publication_identifier:
issn:
- '14396092'
publication_status: published
publisher: Springer
publist_id: '4734'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae)
inferred from nuclear and plastid DNA sequences
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2014'
...
---
_id: '2228'
abstract:
- lang: eng
text: Fast-spiking, parvalbumin-expressing GABAergic interneurons, a large proportion
of which are basket cells (BCs), have a key role in feedforward and feedback inhibition,
gamma oscillations and complex information processing. For these functions, fast
propagation of action potentials (APs) from the soma to the presynaptic terminals
is important. However, the functional properties of interneuron axons remain elusive.
We examined interneuron axons by confocally targeted subcellular patch-clamp recording
in rat hippocampal slices. APs were initiated in the proximal axon ∼20 μm from
the soma and propagated to the distal axon with high reliability and speed. Subcellular
mapping revealed a stepwise increase of Na^+ conductance density from the soma
to the proximal axon, followed by a further gradual increase in the distal axon.
Active cable modeling and experiments with partial channel block revealed that
low axonal Na^+ conductance density was sufficient for reliability, but high Na^+
density was necessary for both speed of propagation and fast-spiking AP phenotype.
Our results suggest that a supercritical density of Na^+ channels compensates
for the morphological properties of interneuron axons (small segmental diameter,
extensive branching and high bouton density), ensuring fast AP propagation and
high-frequency repetitive firing.
author:
- first_name: Hua
full_name: Hu, Hua
id: 4AC0145C-F248-11E8-B48F-1D18A9856A87
last_name: Hu
- 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, Jonas PM. A supercritical density of Na^+ channels ensures fast signaling
in GABAergic interneuron axons. Nature Neuroscience. 2014;17(5):686-693.
doi:10.1038/nn.3678
apa: Hu, H., & Jonas, P. M. (2014). A supercritical density of Na^+ channels
ensures fast signaling in GABAergic interneuron axons. Nature Neuroscience.
Nature Publishing Group. https://doi.org/10.1038/nn.3678
chicago: Hu, Hua, and Peter M Jonas. “A Supercritical Density of Na^+ Channels Ensures
Fast Signaling in GABAergic Interneuron Axons.” Nature Neuroscience. Nature
Publishing Group, 2014. https://doi.org/10.1038/nn.3678.
ieee: H. Hu and P. M. Jonas, “A supercritical density of Na^+ channels ensures fast
signaling in GABAergic interneuron axons,” Nature Neuroscience, vol. 17,
no. 5. Nature Publishing Group, pp. 686–693, 2014.
ista: Hu H, Jonas PM. 2014. A supercritical density of Na^+ channels ensures fast
signaling in GABAergic interneuron axons. Nature Neuroscience. 17(5), 686–693.
mla: Hu, Hua, and Peter M. Jonas. “A Supercritical Density of Na^+ Channels Ensures
Fast Signaling in GABAergic Interneuron Axons.” Nature Neuroscience, vol.
17, no. 5, Nature Publishing Group, 2014, pp. 686–93, doi:10.1038/nn.3678.
short: H. Hu, P.M. Jonas, Nature Neuroscience 17 (2014) 686–693.
date_created: 2018-12-11T11:56:26Z
date_published: 2014-03-23T00:00:00Z
date_updated: 2021-01-12T06:56:08Z
day: '23'
department:
- _id: PeJo
doi: 10.1038/nn.3678
ec_funded: 1
intvolume: ' 17'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286295/
month: '03'
oa: 1
oa_version: Submitted Version
page: 686-693
project:
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
- _id: 25C26B1E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P24909-B24
name: Mechanisms of transmitter release at GABAergic synapses
publication: Nature Neuroscience
publication_identifier:
issn:
- '10976256'
publication_status: published
publisher: Nature Publishing Group
publist_id: '4733'
quality_controlled: '1'
scopus_import: 1
status: public
title: A supercritical density of Na^+ channels ensures fast signaling in GABAergic
interneuron axons
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2014'
...
---
_id: '2229'
abstract:
- lang: eng
text: The distance between Ca^2+ channels and release sensors determines the speed
and efficacy of synaptic transmission. Tight "nanodomain" channel-sensor
coupling initiates transmitter release at synapses in the mature brain, whereas
loose "microdomain" coupling appears restricted to early developmental
stages. To probe the coupling configuration at a plastic synapse in the mature
central nervous system, we performed paired recordings between mossy fiber terminals
and CA3 pyramidal neurons in rat hippocampus. Millimolar concentrations of both
the fast Ca^2+ chelator BAPTA [1,2-bis(2-aminophenoxy)ethane- N,N, N′,N′-tetraacetic
acid] and the slow chelator EGTA efficiently suppressed transmitter release, indicating
loose coupling between Ca^2+ channels and release sensors. Loose coupling enabled
the control of initial release probability by fast endogenous Ca^2+ buffers and
the generation of facilitation by buffer saturation. Thus, loose coupling provides
the molecular framework for presynaptic plasticity.
author:
- first_name: Nicholas
full_name: Vyleta, Nicholas
id: 36C4978E-F248-11E8-B48F-1D18A9856A87
last_name: Vyleta
- 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: Vyleta N, Jonas PM. Loose coupling between Ca^2+ channels and release sensors
at a plastic hippocampal synapse. Science. 2014;343(6171):665-670. doi:10.1126/science.1244811
apa: Vyleta, N., & Jonas, P. M. (2014). Loose coupling between Ca^2+ channels
and release sensors at a plastic hippocampal synapse. Science. American
Association for the Advancement of Science. https://doi.org/10.1126/science.1244811
chicago: Vyleta, Nicholas, and Peter M Jonas. “Loose Coupling between Ca^2+ Channels
and Release Sensors at a Plastic Hippocampal Synapse.” Science. American
Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1244811.
ieee: N. Vyleta and P. M. Jonas, “Loose coupling between Ca^2+ channels and release
sensors at a plastic hippocampal synapse,” Science, vol. 343, no. 6171.
American Association for the Advancement of Science, pp. 665–670, 2014.
ista: Vyleta N, Jonas PM. 2014. Loose coupling between Ca^2+ channels and release
sensors at a plastic hippocampal synapse. Science. 343(6171), 665–670.
mla: Vyleta, Nicholas, and Peter M. Jonas. “Loose Coupling between Ca^2+ Channels
and Release Sensors at a Plastic Hippocampal Synapse.” Science, vol. 343,
no. 6171, American Association for the Advancement of Science, 2014, pp. 665–70,
doi:10.1126/science.1244811.
short: N. Vyleta, P.M. Jonas, Science 343 (2014) 665–670.
date_created: 2018-12-11T11:56:27Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2021-01-12T06:56:09Z
day: '01'
department:
- _id: PeJo
doi: 10.1126/science.1244811
ec_funded: 1
intvolume: ' 343'
issue: '6171'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617475/
month: '02'
oa: 1
oa_version: Submitted Version
page: 665 - 670
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_identifier:
issn:
- '00368075'
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '4732'
quality_controlled: '1'
scopus_import: 1
status: public
title: Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal
synapse
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 343
year: '2014'
...
---
_id: '2230'
abstract:
- lang: eng
text: Intracellular electrophysiological recordings provide crucial insights into
elementary neuronal signals such as action potentials and synaptic currents. Analyzing
and interpreting these signals is essential for a quantitative understanding of
neuronal information processing, and requires both fast data visualization and
ready access to complex analysis routines. To achieve this goal, we have developed
Stimfit, a free software package for cellular neurophysiology with a Python scripting
interface and a built-in Python shell. The program supports most standard file
formats for cellular neurophysiology and other biomedical signals through the
Biosig library. To quantify and interpret the activity of single neurons and communication
between neurons, the program includes algorithms to characterize the kinetics
of presynaptic action potentials and postsynaptic currents, estimate latencies
between pre- and postsynaptic events, and detect spontaneously occurring events.
We validate and benchmark these algorithms, give estimation errors, and provide
sample use cases, showing that Stimfit represents an efficient, accessible and
extensible way to accurately analyze and interpret neuronal signals.
article_number: '16'
author:
- first_name: José
full_name: Guzmán, José
id: 30CC5506-F248-11E8-B48F-1D18A9856A87
last_name: Guzmán
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Christoph
full_name: Schmidt Hieber, Christoph
last_name: Schmidt Hieber
citation:
ama: 'Guzmán J, Schlögl A, Schmidt Hieber C. Stimfit: Quantifying electrophysiological
data with Python. Frontiers in Neuroinformatics. 2014;8(FEB). doi:10.3389/fninf.2014.00016'
apa: 'Guzmán, J., Schlögl, A., & Schmidt Hieber, C. (2014). Stimfit: Quantifying
electrophysiological data with Python. Frontiers in Neuroinformatics. Frontiers
Research Foundation. https://doi.org/10.3389/fninf.2014.00016'
chicago: 'Guzmán, José, Alois Schlögl, and Christoph Schmidt Hieber. “Stimfit: Quantifying
Electrophysiological Data with Python.” Frontiers in Neuroinformatics.
Frontiers Research Foundation, 2014. https://doi.org/10.3389/fninf.2014.00016.'
ieee: 'J. Guzmán, A. Schlögl, and C. Schmidt Hieber, “Stimfit: Quantifying electrophysiological
data with Python,” Frontiers in Neuroinformatics, vol. 8, no. FEB. Frontiers
Research Foundation, 2014.'
ista: 'Guzmán J, Schlögl A, Schmidt Hieber C. 2014. Stimfit: Quantifying electrophysiological
data with Python. Frontiers in Neuroinformatics. 8(FEB), 16.'
mla: 'Guzmán, José, et al. “Stimfit: Quantifying Electrophysiological Data with
Python.” Frontiers in Neuroinformatics, vol. 8, no. FEB, 16, Frontiers
Research Foundation, 2014, doi:10.3389/fninf.2014.00016.'
short: J. Guzmán, A. Schlögl, C. Schmidt Hieber, Frontiers in Neuroinformatics 8
(2014).
date_created: 2018-12-11T11:56:27Z
date_published: 2014-02-21T00:00:00Z
date_updated: 2021-01-12T06:56:09Z
day: '21'
ddc:
- '570'
department:
- _id: ScienComp
- _id: PeJo
doi: 10.3389/fninf.2014.00016
file:
- access_level: open_access
checksum: eeca00bba7232ff7d27db83321f6ea30
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:17Z
date_updated: 2020-07-14T12:45:34Z
file_id: '4935'
file_name: IST-2016-425-v1+1_fninf-08-00016.pdf
file_size: 2883372
relation: main_file
file_date_updated: 2020-07-14T12:45:34Z
has_accepted_license: '1'
intvolume: ' 8'
issue: FEB
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: Frontiers in Neuroinformatics
publication_identifier:
issn:
- '16625196'
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '4731'
pubrep_id: '425'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Stimfit: Quantifying electrophysiological data with Python'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2014'
...
---
_id: '2231'
abstract:
- lang: eng
text: Based on the measurements of noise in gene expression performed during the
past decade, it has become customary to think of gene regulation in terms of a
two-state model, where the promoter of a gene can stochastically switch between
an ON and an OFF state. As experiments are becoming increasingly precise and the
deviations from the two-state model start to be observable, we ask about the experimental
signatures of complex multistate promoters, as well as the functional consequences
of this additional complexity. In detail, we i), extend the calculations for noise
in gene expression to promoters described by state transition diagrams with multiple
states, ii), systematically compute the experimentally accessible noise characteristics
for these complex promoters, and iii), use information theory to evaluate the
channel capacities of complex promoter architectures and compare them with the
baseline provided by the two-state model. We find that adding internal states
to the promoter generically decreases channel capacity, except in certain cases,
three of which (cooperativity, dual-role regulation, promoter cycling) we analyze
in detail.
author:
- first_name: Georg
full_name: Rieckh, Georg
id: 34DA8BD6-F248-11E8-B48F-1D18A9856A87
last_name: Rieckh
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Rieckh G, Tkačik G. Noise and information transmission in promoters with multiple
internal states. Biophysical Journal. 2014;106(5):1194-1204. doi:10.1016/j.bpj.2014.01.014
apa: Rieckh, G., & Tkačik, G. (2014). Noise and information transmission in
promoters with multiple internal states. Biophysical Journal. Biophysical
Society. https://doi.org/10.1016/j.bpj.2014.01.014
chicago: Rieckh, Georg, and Gašper Tkačik. “Noise and Information Transmission in
Promoters with Multiple Internal States.” Biophysical Journal. Biophysical
Society, 2014. https://doi.org/10.1016/j.bpj.2014.01.014.
ieee: G. Rieckh and G. Tkačik, “Noise and information transmission in promoters
with multiple internal states,” Biophysical Journal, vol. 106, no. 5. Biophysical
Society, pp. 1194–1204, 2014.
ista: Rieckh G, Tkačik G. 2014. Noise and information transmission in promoters
with multiple internal states. Biophysical Journal. 106(5), 1194–1204.
mla: Rieckh, Georg, and Gašper Tkačik. “Noise and Information Transmission in Promoters
with Multiple Internal States.” Biophysical Journal, vol. 106, no. 5, Biophysical
Society, 2014, pp. 1194–204, doi:10.1016/j.bpj.2014.01.014.
short: G. Rieckh, G. Tkačik, Biophysical Journal 106 (2014) 1194–1204.
date_created: 2018-12-11T11:56:28Z
date_published: 2014-03-04T00:00:00Z
date_updated: 2021-01-12T06:56:10Z
day: '04'
department:
- _id: GaTk
doi: 10.1016/j.bpj.2014.01.014
external_id:
pmid:
- '24606943'
intvolume: ' 106'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4026790/
month: '03'
oa: 1
oa_version: Submitted Version
page: 1194 - 1204
pmid: 1
publication: Biophysical Journal
publication_identifier:
issn:
- '00063495'
publication_status: published
publisher: Biophysical Society
publist_id: '4730'
quality_controlled: '1'
scopus_import: 1
status: public
title: Noise and information transmission in promoters with multiple internal states
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 106
year: '2014'
...
---
_id: '2232'
abstract:
- lang: eng
text: The purpose of this contribution is to summarize and discuss recent advances
regarding the onset of turbulence in shear flows. The absence of a clear-cut instability
mechanism, the spatio-temporal intermittent character and extremely long lived
transients are some of the major difficulties encountered in these flows and have
hindered progress towards understanding the transition process. We will show for
the case of pipe flow that concepts from nonlinear dynamics and statistical physics
can help to explain the onset of turbulence. In particular, the turbulent structures
(puffs) observed close to onset are spatially localized chaotic transients and
their lifetimes increase super-exponentially with Reynolds number. At the same
time fluctuations of individual turbulent puffs can (although very rarely) lead
to the nucleation of new puffs. The competition between these two stochastic processes
gives rise to a non-equilibrium phase transition where turbulence changes from
a super-transient to a sustained state.
article_number: P02001
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Baofang
full_name: Song, Baofang
id: a79e57f5-e8a5-11ec-9dc9-83fb8c81cf72
last_name: Song
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Song B, Hof B. Deterministic and stochastic aspects of the transition to turbulence.
Journal of Statistical Mechanics Theory and Experiment. 2014;2014(2). doi:10.1088/1742-5468/2014/02/P02001
apa: Song, B., & Hof, B. (2014). Deterministic and stochastic aspects of the
transition to turbulence. Journal of Statistical Mechanics Theory and Experiment.
IOP Publishing. https://doi.org/10.1088/1742-5468/2014/02/P02001
chicago: Song, Baofang, and Björn Hof. “Deterministic and Stochastic Aspects of
the Transition to Turbulence.” Journal of Statistical Mechanics Theory and
Experiment. IOP Publishing, 2014. https://doi.org/10.1088/1742-5468/2014/02/P02001.
ieee: B. Song and B. Hof, “Deterministic and stochastic aspects of the transition
to turbulence,” Journal of Statistical Mechanics Theory and Experiment,
vol. 2014, no. 2. IOP Publishing, 2014.
ista: Song B, Hof B. 2014. Deterministic and stochastic aspects of the transition
to turbulence. Journal of Statistical Mechanics Theory and Experiment. 2014(2),
P02001.
mla: Song, Baofang, and Björn Hof. “Deterministic and Stochastic Aspects of the
Transition to Turbulence.” Journal of Statistical Mechanics Theory and Experiment,
vol. 2014, no. 2, P02001, IOP Publishing, 2014, doi:10.1088/1742-5468/2014/02/P02001.
short: B. Song, B. Hof, Journal of Statistical Mechanics Theory and Experiment 2014
(2014).
date_created: 2018-12-11T11:56:28Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2022-06-10T10:13:15Z
day: '01'
department:
- _id: BjHo
doi: 10.1088/1742-5468/2014/02/P02001
external_id:
arxiv:
- '1403.4516'
intvolume: ' 2014'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1403.4516
month: '02'
oa: 1
oa_version: Submitted Version
publication: Journal of Statistical Mechanics Theory and Experiment
publication_identifier:
issn:
- '17425468'
publication_status: published
publisher: IOP Publishing
publist_id: '4729'
quality_controlled: '1'
status: public
title: Deterministic and stochastic aspects of the transition to turbulence
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2014
year: '2014'
...