---
_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'
...
---
_id: '2233'
abstract:
- lang: eng
text: ' A discounted-sum automaton (NDA) is a nondeterministic finite automaton
with edge weights, valuing a run by the discounted sum of visited edge weights.
More precisely, the weight in the i-th position of the run is divided by λi, where
the discount factor λ is a fixed rational number greater than 1. The value of
a word is the minimal value of the automaton runs on it. Discounted summation
is a common and useful measuring scheme, especially for infinite sequences, reflecting
the assumption that earlier weights are more important than later weights. Unfortunately,
determinization of NDAs, which is often essential in formal verification, is,
in general, not possible. We provide positive news, showing that every NDA with
an integral discount factor is determinizable. We complete the picture by proving
that the integers characterize exactly the discount factors that guarantee determinizability:
for every nonintegral rational discount factor λ, there is a nondeterminizable
λ-NDA. We also prove that the class of NDAs with integral discount factors enjoys
closure under the algebraic operations min, max, addition, and subtraction, which
is not the case for general NDAs nor for deterministic NDAs. For general NDAs,
we look into approximate determinization, which is always possible as the influence
of a word''s suffix decays. We show that the naive approach, of unfolding the
automaton computations up to a sufficient level, is doubly exponential in the
discount factor. We provide an alternative construction for approximate determinization,
which is singly exponential in the discount factor, in the precision, and in the
number of states. We also prove matching lower bounds, showing that the exponential
dependency on each of these three parameters cannot be avoided. All our results
hold equally for automata over finite words and for automata over infinite words. '
author:
- first_name: Udi
full_name: Boker, Udi
last_name: Boker
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: Boker U, Henzinger TA. Exact and approximate determinization of discounted-sum
automata. Logical Methods in Computer Science. 2014;10(1). doi:10.2168/LMCS-10(1:10)2014
apa: Boker, U., & Henzinger, T. A. (2014). Exact and approximate determinization
of discounted-sum automata. Logical Methods in Computer Science. International
Federation of Computational Logic. https://doi.org/10.2168/LMCS-10(1:10)2014
chicago: Boker, Udi, and Thomas A Henzinger. “Exact and Approximate Determinization
of Discounted-Sum Automata.” Logical Methods in Computer Science. International
Federation of Computational Logic, 2014. https://doi.org/10.2168/LMCS-10(1:10)2014.
ieee: U. Boker and T. A. Henzinger, “Exact and approximate determinization of discounted-sum
automata,” Logical Methods in Computer Science, vol. 10, no. 1. International
Federation of Computational Logic, 2014.
ista: Boker U, Henzinger TA. 2014. Exact and approximate determinization of discounted-sum
automata. Logical Methods in Computer Science. 10(1).
mla: Boker, Udi, and Thomas A. Henzinger. “Exact and Approximate Determinization
of Discounted-Sum Automata.” Logical Methods in Computer Science, vol.
10, no. 1, International Federation of Computational Logic, 2014, doi:10.2168/LMCS-10(1:10)2014.
short: U. Boker, T.A. Henzinger, Logical Methods in Computer Science 10 (2014).
date_created: 2018-12-11T11:56:28Z
date_published: 2014-02-13T00:00:00Z
date_updated: 2021-01-12T06:56:11Z
day: '13'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.2168/LMCS-10(1:10)2014
ec_funded: 1
file:
- access_level: open_access
checksum: 9f6ea2e2d8d4a32ff0becc29d835bbf8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:45Z
date_updated: 2020-07-14T12:45:34Z
file_id: '4643'
file_name: IST-2015-389-v1+1_1401.3957.pdf
file_size: 550936
relation: main_file
file_date_updated: 2020-07-14T12:45:34Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication: Logical Methods in Computer Science
publication_identifier:
issn:
- '18605974'
publication_status: published
publisher: International Federation of Computational Logic
publist_id: '4728'
pubrep_id: '389'
quality_controlled: '1'
scopus_import: 1
status: public
title: Exact and approximate determinization of discounted-sum automata
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2014'
...
---
_id: '2234'
abstract:
- lang: eng
text: We study Markov decision processes (MDPs) with multiple limit-average (or
mean-payoff) functions. We consider two different objectives, namely, expectation
and satisfaction objectives. Given an MDP with κ limit-average functions, in the
expectation objective the goal is to maximize the expected limit-average value,
and in the satisfaction objective the goal is to maximize the probability of runs
such that the limit-average value stays above a given vector. We show that under
the expectation objective, in contrast to the case of one limit-average function,
both randomization and memory are necessary for strategies even for ε-approximation,
and that finite-memory randomized strategies are sufficient for achieving Pareto
optimal values. Under the satisfaction objective, in contrast to the case of one
limit-average function, infinite memory is necessary for strategies achieving
a specific value (i.e. randomized finite-memory strategies are not sufficient),
whereas memoryless randomized strategies are sufficient for ε-approximation, for
all ε > 0. We further prove that the decision problems for both expectation
and satisfaction objectives can be solved in polynomial time and the trade-off
curve (Pareto curve) can be ε-approximated in time polynomial in the size of the
MDP and 1/ε, and exponential in the number of limit-average functions, for all
ε > 0. Our analysis also reveals flaws in previous work for MDPs with multiple
mean-payoff functions under the expectation objective, corrects the flaws, and
allows us to obtain improved results.
author:
- first_name: Tomáš
full_name: Brázdil, Tomáš
last_name: Brázdil
- first_name: Václav
full_name: Brožek, Václav
last_name: Brožek
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Vojtěch
full_name: Forejt, Vojtěch
last_name: Forejt
- first_name: Antonín
full_name: Kučera, Antonín
last_name: Kučera
citation:
ama: Brázdil T, Brožek V, Chatterjee K, Forejt V, Kučera A. Markov decision processes
with multiple long-run average objectives. Logical Methods in Computer Science.
2014;10(1). doi:10.2168/LMCS-10(1:13)2014
apa: Brázdil, T., Brožek, V., Chatterjee, K., Forejt, V., & Kučera, A. (2014).
Markov decision processes with multiple long-run average objectives. Logical
Methods in Computer Science. International Federation of Computational Logic.
https://doi.org/10.2168/LMCS-10(1:13)2014
chicago: Brázdil, Tomáš, Václav Brožek, Krishnendu Chatterjee, Vojtěch Forejt, and
Antonín Kučera. “Markov Decision Processes with Multiple Long-Run Average Objectives.”
Logical Methods in Computer Science. International Federation of Computational
Logic, 2014. https://doi.org/10.2168/LMCS-10(1:13)2014.
ieee: T. Brázdil, V. Brožek, K. Chatterjee, V. Forejt, and A. Kučera, “Markov decision
processes with multiple long-run average objectives,” Logical Methods in Computer
Science, vol. 10, no. 1. International Federation of Computational Logic,
2014.
ista: Brázdil T, Brožek V, Chatterjee K, Forejt V, Kučera A. 2014. Markov decision
processes with multiple long-run average objectives. Logical Methods in Computer
Science. 10(1).
mla: Brázdil, Tomáš, et al. “Markov Decision Processes with Multiple Long-Run Average
Objectives.” Logical Methods in Computer Science, vol. 10, no. 1, International
Federation of Computational Logic, 2014, doi:10.2168/LMCS-10(1:13)2014.
short: T. Brázdil, V. Brožek, K. Chatterjee, V. Forejt, A. Kučera, Logical Methods
in Computer Science 10 (2014).
date_created: 2018-12-11T11:56:29Z
date_published: 2014-02-14T00:00:00Z
date_updated: 2021-01-12T06:56:11Z
day: '14'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.2168/LMCS-10(1:13)2014
ec_funded: 1
file:
- access_level: open_access
checksum: 803edcc2d8c1acfba44a9ec43a5eb9f0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:57Z
date_updated: 2020-07-14T12:45:34Z
file_id: '4656'
file_name: IST-2016-428-v1+1_1104.3489.pdf
file_size: 375388
relation: main_file
file_date_updated: 2020-07-14T12:45:34Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://repository.ist.ac.at/id/eprint/428
month: '02'
oa: 1
oa_version: Published Version
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: Logical Methods in Computer Science
publication_identifier:
issn:
- '18605974'
publication_status: published
publisher: International Federation of Computational Logic
publist_id: '4727'
pubrep_id: '428'
quality_controlled: '1'
scopus_import: 1
status: public
title: Markov decision processes with multiple long-run average objectives
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: 10
year: '2014'
...
---
_id: '2235'
abstract:
- lang: eng
text: Emerging infectious diseases (EIDs) pose a risk to human welfare, both directly
and indirectly, by affecting managed livestock and wildlife that provide valuable
resources and ecosystem services, such as the pollination of crops. Honeybees
(Apis mellifera), the prevailing managed insect crop pollinator, suffer from a
range of emerging and exotic high-impact pathogens, and population maintenance
requires active management by beekeepers to control them. Wild pollinators such
as bumblebees (Bombus spp.) are in global decline, one cause of which may be pathogen
spillover from managed pollinators like honeybees or commercial colonies of bumblebees.
Here we use a combination of infection experiments and landscape-scale field data
to show that honeybee EIDs are indeed widespread infectious agents within the
pollinator assemblage. The prevalence of deformed wing virus (DWV) and the exotic
parasite Nosema ceranae in honeybees and bumblebees is linked; as honeybees have
higher DWV prevalence, and sympatric bumblebees and honeybees are infected by
the same DWV strains, Apis is the likely source of at least one major EID in wild
pollinators. Lessons learned from vertebrates highlight the need for increased
pathogen control in managed bee species to maintain wild pollinators, as declines
in native pollinators may be caused by interspecies pathogen transmission originating
from managed pollinators.
author:
- first_name: Matthias
full_name: Fürst, Matthias
id: 393B1196-F248-11E8-B48F-1D18A9856A87
last_name: Fürst
orcid: 0000-0002-3712-925X
- first_name: Dino
full_name: Mcmahon, Dino
last_name: Mcmahon
- first_name: Juliet
full_name: Osborne, Juliet
last_name: Osborne
- first_name: Robert
full_name: Paxton, Robert
last_name: Paxton
- first_name: Mark
full_name: Brown, Mark
last_name: Brown
citation:
ama: Fürst M, Mcmahon D, Osborne J, Paxton R, Brown M. Disease associations between
honeybees and bumblebees as a threat to wild pollinators. Nature. 2014;506(7488):364-366.
doi:10.1038/nature12977
apa: Fürst, M., Mcmahon, D., Osborne, J., Paxton, R., & Brown, M. (2014). Disease
associations between honeybees and bumblebees as a threat to wild pollinators.
Nature. Nature Publishing Group. https://doi.org/10.1038/nature12977
chicago: Fürst, Matthias, Dino Mcmahon, Juliet Osborne, Robert Paxton, and Mark
Brown. “Disease Associations between Honeybees and Bumblebees as a Threat to Wild
Pollinators.” Nature. Nature Publishing Group, 2014. https://doi.org/10.1038/nature12977.
ieee: M. Fürst, D. Mcmahon, J. Osborne, R. Paxton, and M. Brown, “Disease associations
between honeybees and bumblebees as a threat to wild pollinators,” Nature,
vol. 506, no. 7488. Nature Publishing Group, pp. 364–366, 2014.
ista: Fürst M, Mcmahon D, Osborne J, Paxton R, Brown M. 2014. Disease associations
between honeybees and bumblebees as a threat to wild pollinators. Nature. 506(7488),
364–366.
mla: Fürst, Matthias, et al. “Disease Associations between Honeybees and Bumblebees
as a Threat to Wild Pollinators.” Nature, vol. 506, no. 7488, Nature Publishing
Group, 2014, pp. 364–66, doi:10.1038/nature12977.
short: M. Fürst, D. Mcmahon, J. Osborne, R. Paxton, M. Brown, Nature 506 (2014)
364–366.
date_created: 2018-12-11T11:56:29Z
date_published: 2014-02-20T00:00:00Z
date_updated: 2021-01-12T06:56:11Z
day: '20'
department:
- _id: SyCr
doi: 10.1038/nature12977
intvolume: ' 506'
issue: '7488'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3985068/
month: '02'
oa: 1
oa_version: Submitted Version
page: 364 - 366
publication: Nature
publication_identifier:
issn:
- '00280836'
publication_status: published
publisher: Nature Publishing Group
publist_id: '4726'
quality_controlled: '1'
scopus_import: 1
status: public
title: Disease associations between honeybees and bumblebees as a threat to wild pollinators
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 506
year: '2014'
...
---
_id: '2236'
abstract:
- lang: eng
text: Consider a joint distribution (X,A) on a set. We show that for any family
of distinguishers, there exists a simulator such that 1 no function in can distinguish
(X,A) from (X,h(X)) with advantage ε, 2 h is only O(2 3ℓ ε -2) times less efficient
than the functions in. For the most interesting settings of the parameters (in
particular, the cryptographic case where X has superlogarithmic min-entropy, ε
> 0 is negligible and consists of circuits of polynomial size), we can make
the simulator h deterministic. As an illustrative application of our theorem,
we give a new security proof for the leakage-resilient stream-cipher from Eurocrypt'09.
Our proof is simpler and quantitatively much better than the original proof using
the dense model theorem, giving meaningful security guarantees if instantiated
with a standard blockcipher like AES. Subsequent to this work, Chung, Lui and
Pass gave an interactive variant of our main theorem, and used it to investigate
weak notions of Zero-Knowledge. Vadhan and Zheng give a more constructive version
of our theorem using their new uniform min-max theorem.
alternative_title:
- LNCS
author:
- first_name: Dimitar
full_name: Jetchev, Dimitar
last_name: Jetchev
- 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: 'Jetchev D, Pietrzak KZ. How to fake auxiliary input. In: Lindell Y, ed. Vol
8349. Springer; 2014:566-590. doi:10.1007/978-3-642-54242-8_24'
apa: 'Jetchev, D., & Pietrzak, K. Z. (2014). How to fake auxiliary input. In
Y. Lindell (Ed.) (Vol. 8349, pp. 566–590). Presented at the TCC: Theory of Cryptography
Conference, San Diego, USA: Springer. https://doi.org/10.1007/978-3-642-54242-8_24'
chicago: Jetchev, Dimitar, and Krzysztof Z Pietrzak. “How to Fake Auxiliary Input.”
edited by Yehuda Lindell, 8349:566–90. Springer, 2014. https://doi.org/10.1007/978-3-642-54242-8_24.
ieee: 'D. Jetchev and K. Z. Pietrzak, “How to fake auxiliary input,” presented at
the TCC: Theory of Cryptography Conference, San Diego, USA, 2014, vol. 8349, pp.
566–590.'
ista: 'Jetchev D, Pietrzak KZ. 2014. How to fake auxiliary input. TCC: Theory of
Cryptography Conference, LNCS, vol. 8349, 566–590.'
mla: Jetchev, Dimitar, and Krzysztof Z. Pietrzak. How to Fake Auxiliary Input.
Edited by Yehuda Lindell, vol. 8349, Springer, 2014, pp. 566–90, doi:10.1007/978-3-642-54242-8_24.
short: D. Jetchev, K.Z. Pietrzak, in:, Y. Lindell (Ed.), Springer, 2014, pp. 566–590.
conference:
end_date: 2014-02-26
location: San Diego, USA
name: 'TCC: Theory of Cryptography Conference'
start_date: 2014-02-24
date_created: 2018-12-11T11:56:29Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2021-01-12T06:56:12Z
day: '01'
ddc:
- '004'
department:
- _id: KrPi
doi: 10.1007/978-3-642-54242-8_24
ec_funded: 1
editor:
- first_name: Yehuda
full_name: Lindell, Yehuda
last_name: Lindell
file:
- access_level: open_access
checksum: 42960325c29dcd8d832edadcc3ce0045
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:21Z
date_updated: 2020-07-14T12:45:34Z
file_id: '5275'
file_name: IST-2016-681-v1+1_869_1_.pdf
file_size: 313528
relation: main_file
file_date_updated: 2020-07-14T12:45:34Z
has_accepted_license: '1'
intvolume: ' 8349'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://repository.ist.ac.at/id/eprint/681
month: '02'
oa: 1
oa_version: Submitted Version
page: 566 - 590
project:
- _id: 258C570E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '259668'
name: Provable Security for Physical Cryptography
publication_identifier:
isbn:
- 978-364254241-1
publication_status: published
publisher: Springer
publist_id: '4725'
pubrep_id: '681'
quality_controlled: '1'
status: public
title: How to fake auxiliary input
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 8349
year: '2014'
...
---
_id: '2246'
abstract:
- lang: eng
text: 'Muller games are played by two players moving a token along a graph; the
winner is determined by the set of vertices that occur infinitely often. The central
algorithmic problem is to compute the winning regions for the players. Different
classes and representations of Muller games lead to problems of varying computational
complexity. One such class are parity games; these are of particular significance
in computational complexity, as they remain one of the few combinatorial problems
known to be in NP ∩ co-NP but not known to be in P. We show that winning regions
for a Muller game can be determined from the alternating structure of its traps.
To every Muller game we then associate a natural number that we call its trap
depth; this parameter measures how complicated the trap structure is. We present
algorithms for parity games that run in polynomial time for graphs of bounded
trap depth, and in general run in time exponential in the trap depth. '
author:
- first_name: Andrey
full_name: Grinshpun, Andrey
last_name: Grinshpun
- first_name: Pakawat
full_name: Phalitnonkiat, Pakawat
last_name: Phalitnonkiat
- first_name: Sasha
full_name: Rubin, Sasha
id: 2EC51194-F248-11E8-B48F-1D18A9856A87
last_name: Rubin
- first_name: Andrei
full_name: Tarfulea, Andrei
last_name: Tarfulea
citation:
ama: Grinshpun A, Phalitnonkiat P, Rubin S, Tarfulea A. Alternating traps in Muller
and parity games. Theoretical Computer Science. 2014;521:73-91. doi:10.1016/j.tcs.2013.11.032
apa: Grinshpun, A., Phalitnonkiat, P., Rubin, S., & Tarfulea, A. (2014). Alternating
traps in Muller and parity games. Theoretical Computer Science. Elsevier.
https://doi.org/10.1016/j.tcs.2013.11.032
chicago: Grinshpun, Andrey, Pakawat Phalitnonkiat, Sasha Rubin, and Andrei Tarfulea.
“Alternating Traps in Muller and Parity Games.” Theoretical Computer Science.
Elsevier, 2014. https://doi.org/10.1016/j.tcs.2013.11.032.
ieee: A. Grinshpun, P. Phalitnonkiat, S. Rubin, and A. Tarfulea, “Alternating traps
in Muller and parity games,” Theoretical Computer Science, vol. 521. Elsevier,
pp. 73–91, 2014.
ista: Grinshpun A, Phalitnonkiat P, Rubin S, Tarfulea A. 2014. Alternating traps
in Muller and parity games. Theoretical Computer Science. 521, 73–91.
mla: Grinshpun, Andrey, et al. “Alternating Traps in Muller and Parity Games.” Theoretical
Computer Science, vol. 521, Elsevier, 2014, pp. 73–91, doi:10.1016/j.tcs.2013.11.032.
short: A. Grinshpun, P. Phalitnonkiat, S. Rubin, A. Tarfulea, Theoretical Computer
Science 521 (2014) 73–91.
date_created: 2018-12-11T11:56:33Z
date_published: 2014-02-13T00:00:00Z
date_updated: 2021-01-12T06:56:16Z
day: '13'
department:
- _id: KrCh
doi: 10.1016/j.tcs.2013.11.032
intvolume: ' 521'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1303.3777
month: '02'
oa: 1
oa_version: Submitted Version
page: 73 - 91
publication: Theoretical Computer Science
publication_identifier:
issn:
- '03043975'
publication_status: published
publisher: Elsevier
publist_id: '4703'
quality_controlled: '1'
scopus_import: 1
status: public
title: Alternating traps in Muller and parity games
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 521
year: '2014'
...
---
_id: '2249'
abstract:
- lang: eng
text: The unfolded protein response (UPR) is a signaling network triggered by overload
of protein-folding demand in the endoplasmic reticulum (ER), a condition termed
ER stress. The UPR is critical for growth and development; nonetheless, connections
between the UPR and other cellular regulatory processes remain largely unknown.
Here, we identify a link between the UPR and the phytohormone auxin, a master
regulator of plant physiology. We show that ER stress triggers down-regulation
of auxin receptors and transporters in Arabidopsis thaliana. We also demonstrate
that an Arabidopsis mutant of a conserved ER stress sensor IRE1 exhibits defects
in the auxin response and levels. These data not only support that the plant IRE1
is required for auxin homeostasis, they also reveal a species-specific feature
of IRE1 in multicellular eukaryotes. Furthermore, by establishing that UPR activation
is reduced in mutants of ER-localized auxin transporters, including PIN5, we define
a long-neglected biological significance of ER-based auxin regulation. We further
examine the functional relationship of IRE1 and PIN5 by showing that an ire1 pin5
triple mutant enhances defects of UPR activation and auxin homeostasis in ire1
or pin5. Our results imply that the plant UPR has evolved a hormone-dependent
strategy for coordinating ER function with physiological processes.
author:
- first_name: Yani
full_name: Chen, Yani
last_name: Chen
- first_name: Kyaw
full_name: Aung, Kyaw
last_name: Aung
- first_name: Jakub
full_name: Rolčík, Jakub
last_name: Rolčík
- first_name: Kathryn
full_name: Walicki, Kathryn
last_name: Walicki
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Federica
full_name: Brandizzí, Federica
last_name: Brandizzí
citation:
ama: Chen Y, Aung K, Rolčík J, Walicki K, Friml J, Brandizzí F. Inter-regulation
of the unfolded protein response and auxin signaling. Plant Journal. 2014;77(1):97-107.
doi:10.1111/tpj.12373
apa: Chen, Y., Aung, K., Rolčík, J., Walicki, K., Friml, J., & Brandizzí, F.
(2014). Inter-regulation of the unfolded protein response and auxin signaling.
Plant Journal. Wiley-Blackwell. https://doi.org/10.1111/tpj.12373
chicago: Chen, Yani, Kyaw Aung, Jakub Rolčík, Kathryn Walicki, Jiří Friml, and Federica
Brandizzí. “Inter-Regulation of the Unfolded Protein Response and Auxin Signaling.”
Plant Journal. Wiley-Blackwell, 2014. https://doi.org/10.1111/tpj.12373.
ieee: Y. Chen, K. Aung, J. Rolčík, K. Walicki, J. Friml, and F. Brandizzí, “Inter-regulation
of the unfolded protein response and auxin signaling,” Plant Journal, vol.
77, no. 1. Wiley-Blackwell, pp. 97–107, 2014.
ista: Chen Y, Aung K, Rolčík J, Walicki K, Friml J, Brandizzí F. 2014. Inter-regulation
of the unfolded protein response and auxin signaling. Plant Journal. 77(1), 97–107.
mla: Chen, Yani, et al. “Inter-Regulation of the Unfolded Protein Response and Auxin
Signaling.” Plant Journal, vol. 77, no. 1, Wiley-Blackwell, 2014, pp. 97–107,
doi:10.1111/tpj.12373.
short: Y. Chen, K. Aung, J. Rolčík, K. Walicki, J. Friml, F. Brandizzí, Plant Journal
77 (2014) 97–107.
date_created: 2018-12-11T11:56:34Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:56:17Z
day: '01'
department:
- _id: JiFr
doi: 10.1111/tpj.12373
intvolume: ' 77'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3981873/
month: '01'
oa: 1
oa_version: Submitted Version
page: 97 - 107
publication: Plant Journal
publication_identifier:
issn:
- '09607412'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4699'
quality_controlled: '1'
scopus_import: 1
status: public
title: Inter-regulation of the unfolded protein response and auxin signaling
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 77
year: '2014'
...
---
_id: '2250'
abstract:
- lang: eng
text: The genome sequences of new viruses often contain many "orphan"
or "taxon-specific" proteins apparently lacking homologs. However, because
viral proteins evolve very fast, commonly used sequence similarity detection methods
such as BLAST may overlook homologs. We analyzed a data set of proteins from RNA
viruses characterized as "genus specific" by BLAST. More powerful methods
developed recently, such as HHblits or HHpred (available through web-based, user-friendly
interfaces), could detect distant homologs of a quarter of these proteins, suggesting
that these methods should be used to annotate viral genomes. In-depth manual analyses
of a subset of the remaining sequences, guided by contextual information such
as taxonomy, gene order, or domain cooccurrence, identified distant homologs of
another third. Thus, a combination of powerful automated methods and manual analyses
can uncover distant homologs of many proteins thought to be orphans. We expect
these methodological results to be also applicable to cellular organisms, since
they generally evolve much more slowly than RNA viruses. As an application, we
reanalyzed the genome of a bee pathogen, Chronic bee paralysis virus (CBPV). We
could identify homologs of most of its proteins thought to be orphans; in each
case, identifying homologs provided functional clues. We discovered that CBPV
encodes a domain homologous to the Alphavirus methyltransferase-guanylyltransferase;
a putative membrane protein, SP24, with homologs in unrelated insect viruses and
insect-transmitted plant viruses having different morphologies (cileviruses, higreviruses,
blunerviruses, negeviruses); and a putative virion glycoprotein, ORF2, also found
in negeviruses. SP24 and ORF2 are probably major structural components of the
virionsd.
author:
- first_name: Durga
full_name: Kuchibhatla, Durga
last_name: Kuchibhatla
- first_name: Westley
full_name: Sherman, Westley
last_name: Sherman
- first_name: Betty
full_name: Chung, Betty
last_name: Chung
- first_name: Shelley
full_name: Cook, Shelley
last_name: Cook
- first_name: Georg
full_name: Schneider, Georg
id: 329095A0-F248-11E8-B48F-1D18A9856A87
last_name: Schneider
- first_name: Birgit
full_name: Eisenhaber, Birgit
last_name: Eisenhaber
- first_name: David
full_name: Karlin, David
last_name: Karlin
citation:
ama: Kuchibhatla D, Sherman W, Chung B, et al. Powerful sequence similarity search
methods and in-depth manual analyses can identify remote homologs in many apparently
“orphan” viral proteins. Journal of Virology. 2014;88(1):10-20. doi:10.1128/JVI.02595-13
apa: Kuchibhatla, D., Sherman, W., Chung, B., Cook, S., Schneider, G., Eisenhaber,
B., & Karlin, D. (2014). Powerful sequence similarity search methods and in-depth
manual analyses can identify remote homologs in many apparently “orphan” viral
proteins. Journal of Virology. ASM. https://doi.org/10.1128/JVI.02595-13
chicago: Kuchibhatla, Durga, Westley Sherman, Betty Chung, Shelley Cook, Georg Schneider,
Birgit Eisenhaber, and David Karlin. “Powerful Sequence Similarity Search Methods
and In-Depth Manual Analyses Can Identify Remote Homologs in Many Apparently ‘Orphan’
Viral Proteins.” Journal of Virology. ASM, 2014. https://doi.org/10.1128/JVI.02595-13.
ieee: D. Kuchibhatla et al., “Powerful sequence similarity search methods
and in-depth manual analyses can identify remote homologs in many apparently ‘orphan’
viral proteins,” Journal of Virology, vol. 88, no. 1. ASM, pp. 10–20, 2014.
ista: Kuchibhatla D, Sherman W, Chung B, Cook S, Schneider G, Eisenhaber B, Karlin
D. 2014. Powerful sequence similarity search methods and in-depth manual analyses
can identify remote homologs in many apparently ‘orphan’ viral proteins. Journal
of Virology. 88(1), 10–20.
mla: Kuchibhatla, Durga, et al. “Powerful Sequence Similarity Search Methods and
In-Depth Manual Analyses Can Identify Remote Homologs in Many Apparently ‘Orphan’
Viral Proteins.” Journal of Virology, vol. 88, no. 1, ASM, 2014, pp. 10–20,
doi:10.1128/JVI.02595-13.
short: D. Kuchibhatla, W. Sherman, B. Chung, S. Cook, G. Schneider, B. Eisenhaber,
D. Karlin, Journal of Virology 88 (2014) 10–20.
date_created: 2018-12-11T11:56:34Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:56:17Z
day: '01'
ddc:
- '570'
department:
- _id: MD
doi: 10.1128/JVI.02595-13
file:
- access_level: open_access
checksum: 2c121b5e884992dfec5605bdf4e659da
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:43Z
date_updated: 2020-07-14T12:45:34Z
file_id: '5029'
file_name: IST-2016-417-v1+1_J._Virol.-2014-Kuchibhatla-10-20.pdf
file_size: 825756
relation: main_file
file_date_updated: 2020-07-14T12:45:34Z
has_accepted_license: '1'
intvolume: ' 88'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 10 - 20
publication: Journal of Virology
publication_identifier:
issn:
- 0022538X
publication_status: published
publisher: ASM
publist_id: '4698'
pubrep_id: '417'
quality_controlled: '1'
scopus_import: 1
status: public
title: Powerful sequence similarity search methods and in-depth manual analyses can
identify remote homologs in many apparently "orphan" viral proteins
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: 88
year: '2014'
...
---
_id: '2251'
abstract:
- lang: eng
text: 'Sharp wave/ripple (SWR, 150–250 Hz) hippocampal events have long been postulated
to be involved in memory consolidation. However, more recent work has investigated
SWRs that occur during active waking behaviour: findings that suggest that SWRs
may also play a role in cell assembly strengthening or spatial working memory.
Do such theories of SWR function apply to animal learning? This review discusses
how general theories linking SWRs to memory-related function may explain circuit
mechanisms related to rodent spatial learning and to the associated stabilization
of new cognitive maps.'
acknowledgement: CC BY 3.0
article_number: '20120528'
article_processing_charge: No
author:
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
- first_name: David
full_name: Dupret, David
last_name: Dupret
citation:
ama: Csicsvari JL, Dupret D. Sharp wave/ripple network oscillations and learning-associated
hippocampal maps. Philosophical Transactions of the Royal Society of London
Series B, Biological Sciences. 2014;369(1635). doi:10.1098/rstb.2012.0528
apa: Csicsvari, J. L., & Dupret, D. (2014). Sharp wave/ripple network oscillations
and learning-associated hippocampal maps. Philosophical Transactions of the
Royal Society of London. Series B, Biological Sciences. Royal Society, The.
https://doi.org/10.1098/rstb.2012.0528
chicago: Csicsvari, Jozsef L, and David Dupret. “Sharp Wave/Ripple Network Oscillations
and Learning-Associated Hippocampal Maps.” Philosophical Transactions of the
Royal Society of London. Series B, Biological Sciences. Royal Society, The,
2014. https://doi.org/10.1098/rstb.2012.0528.
ieee: J. L. Csicsvari and D. Dupret, “Sharp wave/ripple network oscillations and
learning-associated hippocampal maps,” Philosophical Transactions of the Royal
Society of London. Series B, Biological Sciences, vol. 369, no. 1635. Royal
Society, The, 2014.
ista: Csicsvari JL, Dupret D. 2014. Sharp wave/ripple network oscillations and learning-associated
hippocampal maps. Philosophical Transactions of the Royal Society of London. Series
B, Biological Sciences. 369(1635), 20120528.
mla: Csicsvari, Jozsef L., and David Dupret. “Sharp Wave/Ripple Network Oscillations
and Learning-Associated Hippocampal Maps.” Philosophical Transactions of the
Royal Society of London. Series B, Biological Sciences, vol. 369, no. 1635,
20120528, Royal Society, The, 2014, doi:10.1098/rstb.2012.0528.
short: J.L. Csicsvari, D. Dupret, Philosophical Transactions of the Royal Society
of London. Series B, Biological Sciences 369 (2014).
date_created: 2018-12-11T11:56:34Z
date_published: 2014-02-05T00:00:00Z
date_updated: 2021-01-12T06:56:18Z
day: '05'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1098/rstb.2012.0528
external_id:
pmid:
- '24366138'
file:
- access_level: open_access
checksum: 51beb33de71c9c19e0c205a20d206f9a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:24Z
date_updated: 2020-07-14T12:45:34Z
file_id: '5006'
file_name: IST-2016-527-v1+1_20120528.full.pdf
file_size: 771896
relation: main_file
file_date_updated: 2020-07-14T12:45:34Z
has_accepted_license: '1'
intvolume: ' 369'
issue: '1635'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_identifier:
issn:
- '09628436'
publication_status: published
publisher: Royal Society, The
publist_id: '4697'
pubrep_id: '527'
quality_controlled: '1'
scopus_import: 1
status: public
title: Sharp wave/ripple network oscillations and learning-associated hippocampal
maps
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 369
year: '2014'
...
---
_id: '2253'
abstract:
- lang: eng
text: Plant growth is achieved predominantly by cellular elongation, which is thought
to be controlled on several levels by apoplastic auxin. Auxin export into the
apoplast is achieved by plasma membrane efflux catalysts of the PIN-FORMED (PIN)
and ATP-binding cassette protein subfamily B/phosphor- glycoprotein (ABCB/PGP)
classes; the latter were shown to depend on interaction with the FKBP42, TWISTED
DWARF1 (TWD1). Here by using a transgenic approach in combination with phenotypical,
biochemical and cell biological analyses we demonstrate the importance of a putative
C-terminal in-plane membrane anchor of TWD1 in the regulation of ABCB-mediated
auxin transport. In contrast with dwarfed twd1 loss-of-function alleles, TWD1
gain-of-function lines that lack a putative in-plane membrane anchor (HA-TWD1-Ct)
show hypermorphic plant architecture, characterized by enhanced stem length and
leaf surface but reduced shoot branching. Greater hypocotyl length is the result
of enhanced cell elongation that correlates with reduced polar auxin transport
capacity for HA-TWD1-Ct. As a consequence, HA-TWD1-Ct displays higher hypocotyl
auxin accumulation, which is shown to result in elevated auxin-induced cell elongation
rates. Our data highlight the importance of C-terminal membrane anchoring for
TWD1 action, which is required for specific regulation of ABCB-mediated auxin
transport. These data support a model in which TWD1 controls lateral ABCB1-mediated
export into the apoplast, which is required for auxin-mediated cell elongation.
article_processing_charge: No
article_type: original
author:
- first_name: Aurélien
full_name: Bailly, Aurélien
last_name: Bailly
- first_name: Bangjun
full_name: Wang, Bangjun
last_name: Wang
- first_name: Marta
full_name: Zwiewka, Marta
last_name: Zwiewka
- first_name: Stephan
full_name: Pollmann, Stephan
last_name: Pollmann
- first_name: Daniel
full_name: Schenck, Daniel
last_name: Schenck
- first_name: Hartwig
full_name: Lüthen, Hartwig
last_name: Lüthen
- first_name: Alexander
full_name: Schulz, Alexander
last_name: Schulz
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Markus
full_name: Geisler, Markus
last_name: Geisler
citation:
ama: Bailly A, Wang B, Zwiewka M, et al. Expression of TWISTED DWARF1 lacking its
in-plane membrane anchor leads to increased cell elongation and hypermorphic growth.
Plant Journal. 2014;77(1):108-118. doi:10.1111/tpj.12369
apa: Bailly, A., Wang, B., Zwiewka, M., Pollmann, S., Schenck, D., Lüthen, H., …
Geisler, M. (2014). Expression of TWISTED DWARF1 lacking its in-plane membrane
anchor leads to increased cell elongation and hypermorphic growth. Plant Journal.
Wiley-Blackwell. https://doi.org/10.1111/tpj.12369
chicago: Bailly, Aurélien, Bangjun Wang, Marta Zwiewka, Stephan Pollmann, Daniel
Schenck, Hartwig Lüthen, Alexander Schulz, Jiří Friml, and Markus Geisler. “Expression
of TWISTED DWARF1 Lacking Its In-Plane Membrane Anchor Leads to Increased Cell
Elongation and Hypermorphic Growth.” Plant Journal. Wiley-Blackwell, 2014.
https://doi.org/10.1111/tpj.12369.
ieee: A. Bailly et al., “Expression of TWISTED DWARF1 lacking its in-plane
membrane anchor leads to increased cell elongation and hypermorphic growth,” Plant
Journal, vol. 77, no. 1. Wiley-Blackwell, pp. 108–118, 2014.
ista: Bailly A, Wang B, Zwiewka M, Pollmann S, Schenck D, Lüthen H, Schulz A, Friml
J, Geisler M. 2014. Expression of TWISTED DWARF1 lacking its in-plane membrane
anchor leads to increased cell elongation and hypermorphic growth. Plant Journal.
77(1), 108–118.
mla: Bailly, Aurélien, et al. “Expression of TWISTED DWARF1 Lacking Its In-Plane
Membrane Anchor Leads to Increased Cell Elongation and Hypermorphic Growth.” Plant
Journal, vol. 77, no. 1, Wiley-Blackwell, 2014, pp. 108–18, doi:10.1111/tpj.12369.
short: A. Bailly, B. Wang, M. Zwiewka, S. Pollmann, D. Schenck, H. Lüthen, A. Schulz,
J. Friml, M. Geisler, Plant Journal 77 (2014) 108–118.
date_created: 2018-12-11T11:56:35Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:56:18Z
day: '01'
department:
- _id: JiFr
doi: 10.1111/tpj.12369
intvolume: ' 77'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/tpj.12369
month: '01'
oa: 1
oa_version: Published Version
page: 108 - 118
project:
- _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 Journal
publication_identifier:
issn:
- '09607412'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4694'
quality_controlled: '1'
scopus_import: 1
status: public
title: Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to
increased cell elongation and hypermorphic growth
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 77
year: '2014'
...
---
_id: '2254'
abstract:
- lang: eng
text: Theta-gamma network oscillations are thought to represent key reference signals
for information processing in neuronal ensembles, but the underlying synaptic
mechanisms remain unclear. To address this question, we performed whole-cell (WC)
patch-clamp recordings from mature hippocampal granule cells (GCs) in vivo in
the dentate gyrus of anesthetized and awake rats. GCs in vivo fired action potentials
at low frequency, consistent with sparse coding in the dentate gyrus. GCs were
exposed to barrages of fast AMPAR-mediated excitatory postsynaptic currents (EPSCs),
primarily relayed from the entorhinal cortex, and inhibitory postsynaptic currents
(IPSCs), presumably generated by local interneurons. EPSCs exhibited coherence
with the field potential predominantly in the theta frequency band, whereas IPSCs
showed coherence primarily in the gamma range. Action potentials in GCs were phase
locked to network oscillations. Thus, theta-gamma-modulated synaptic currents
may provide a framework for sparse temporal coding of information in the dentate
gyrus.
author:
- first_name: Alejandro
full_name: Pernia-Andrade, Alejandro
id: 36963E98-F248-11E8-B48F-1D18A9856A87
last_name: Pernia-Andrade
- 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: Pernia-Andrade A, Jonas PM. Theta-gamma-modulated synaptic currents in hippocampal
granule cells in vivo define a mechanism for network oscillations. Neuron.
2014;81(1):140-152. doi:10.1016/j.neuron.2013.09.046
apa: Pernia-Andrade, A., & Jonas, P. M. (2014). Theta-gamma-modulated synaptic
currents in hippocampal granule cells in vivo define a mechanism for network oscillations.
Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2013.09.046
chicago: Pernia-Andrade, Alejandro, and Peter M Jonas. “Theta-Gamma-Modulated Synaptic
Currents in Hippocampal Granule Cells in Vivo Define a Mechanism for Network Oscillations.”
Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2013.09.046.
ieee: A. Pernia-Andrade and P. M. Jonas, “Theta-gamma-modulated synaptic currents
in hippocampal granule cells in vivo define a mechanism for network oscillations,”
Neuron, vol. 81, no. 1. Elsevier, pp. 140–152, 2014.
ista: Pernia-Andrade A, Jonas PM. 2014. Theta-gamma-modulated synaptic currents
in hippocampal granule cells in vivo define a mechanism for network oscillations.
Neuron. 81(1), 140–152.
mla: Pernia-Andrade, Alejandro, and Peter M. Jonas. “Theta-Gamma-Modulated Synaptic
Currents in Hippocampal Granule Cells in Vivo Define a Mechanism for Network Oscillations.”
Neuron, vol. 81, no. 1, Elsevier, 2014, pp. 140–52, doi:10.1016/j.neuron.2013.09.046.
short: A. Pernia-Andrade, P.M. Jonas, Neuron 81 (2014) 140–152.
date_created: 2018-12-11T11:56:35Z
date_published: 2014-01-08T00:00:00Z
date_updated: 2021-01-12T06:56:19Z
day: '08'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1016/j.neuron.2013.09.046
ec_funded: 1
file:
- access_level: open_access
checksum: 438547cfcd9045a22f065f2019f07849
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:48Z
date_updated: 2020-07-14T12:45:35Z
file_id: '4773'
file_name: IST-2016-422-v1+1_1-s2.0-S0896627313009227-main.pdf
file_size: 4373072
relation: main_file
file_date_updated: 2020-07-14T12:45:35Z
has_accepted_license: '1'
intvolume: ' 81'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 140 - 152
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: Neuron
publication_identifier:
issn:
- '08966273'
publication_status: published
publisher: Elsevier
publist_id: '4692'
pubrep_id: '422'
quality_controlled: '1'
scopus_import: 1
status: public
title: Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo
define a mechanism for network oscillations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 81
year: '2014'
...
---
_id: '2255'
abstract:
- lang: eng
text: Motivated by applications in biology, we present an algorithm for estimating
the length of tube-like shapes in 3-dimensional Euclidean space. In a first step,
we combine the tube formula of Weyl with integral geometric methods to obtain
an integral representation of the length, which we approximate using a variant
of the Koksma-Hlawka Theorem. In a second step, we use tools from computational
topology to decrease the dependence on small perturbations of the shape. We present
computational experiments that shed light on the stability and the convergence
rate of our algorithm.
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Florian
full_name: Pausinger, Florian
id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87
last_name: Pausinger
orcid: 0000-0002-8379-3768
citation:
ama: Edelsbrunner H, Pausinger F. Stable length estimates of tube-like shapes. Journal
of Mathematical Imaging and Vision. 2014;50(1):164-177. doi:10.1007/s10851-013-0468-x
apa: Edelsbrunner, H., & Pausinger, F. (2014). Stable length estimates of tube-like
shapes. Journal of Mathematical Imaging and Vision. Springer. https://doi.org/10.1007/s10851-013-0468-x
chicago: Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates
of Tube-like Shapes.” Journal of Mathematical Imaging and Vision. Springer,
2014. https://doi.org/10.1007/s10851-013-0468-x.
ieee: H. Edelsbrunner and F. Pausinger, “Stable length estimates of tube-like shapes,”
Journal of Mathematical Imaging and Vision, vol. 50, no. 1. Springer, pp.
164–177, 2014.
ista: Edelsbrunner H, Pausinger F. 2014. Stable length estimates of tube-like shapes.
Journal of Mathematical Imaging and Vision. 50(1), 164–177.
mla: Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like
Shapes.” Journal of Mathematical Imaging and Vision, vol. 50, no. 1, Springer,
2014, pp. 164–77, doi:10.1007/s10851-013-0468-x.
short: H. Edelsbrunner, F. Pausinger, Journal of Mathematical Imaging and Vision
50 (2014) 164–177.
date_created: 2018-12-11T11:56:36Z
date_published: 2014-09-01T00:00:00Z
date_updated: 2023-09-07T11:41:25Z
day: '01'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1007/s10851-013-0468-x
ec_funded: 1
file:
- access_level: open_access
checksum: 2f93f3e63a38a85cd4404d7953913b14
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:18Z
date_updated: 2020-07-14T12:45:35Z
file_id: '5204'
file_name: IST-2016-549-v1+1_2014-J-06-LengthEstimate.pdf
file_size: 3941391
relation: main_file
file_date_updated: 2020-07-14T12:45:35Z
has_accepted_license: '1'
intvolume: ' 50'
issue: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 164 - 177
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Journal of Mathematical Imaging and Vision
publication_identifier:
issn:
- '09249907'
publication_status: published
publisher: Springer
publist_id: '4691'
pubrep_id: '549'
quality_controlled: '1'
related_material:
record:
- id: '2843'
relation: earlier_version
status: public
- id: '1399'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Stable length estimates of tube-like shapes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2014'
...
---
_id: '2257'
abstract:
- lang: eng
text: 'Maximum entropy models are the least structured probability distributions
that exactly reproduce a chosen set of statistics measured in an interacting network.
Here we use this principle to construct probabilistic models which describe the
correlated spiking activity of populations of up to 120 neurons in the salamander
retina as it responds to natural movies. Already in groups as small as 10 neurons,
interactions between spikes can no longer be regarded as small perturbations in
an otherwise independent system; for 40 or more neurons pairwise interactions
need to be supplemented by a global interaction that controls the distribution
of synchrony in the population. Here we show that such “K-pairwise” models—being
systematic extensions of the previously used pairwise Ising models—provide an
excellent account of the data. We explore the properties of the neural vocabulary
by: 1) estimating its entropy, which constrains the population''s capacity to
represent visual information; 2) classifying activity patterns into a small set
of metastable collective modes; 3) showing that the neural codeword ensembles
are extremely inhomogenous; 4) demonstrating that the state of individual neurons
is highly predictable from the rest of the population, allowing the capacity for
error correction.'
acknowledgement: "\r\n\r\n\r\n\r\nThis work was funded by NSF grant IIS-0613435, NSF
grant PHY-0957573, NSF grant CCF-0939370, NIH grant R01 EY14196, NIH grant P50 GM071508,
the Fannie and John Hertz Foundation, the Swartz Foundation, the WM Keck Foundation,
ANR Optima and the French State program “Investissements d'Avenir” [LIFESENSES:
ANR-10-LABX-65], and the Austrian Research Foundation FWF P25651."
article_number: e1003408
author:
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Dario
full_name: Amodei, Dario
last_name: Amodei
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
- first_name: William
full_name: Bialek, William
last_name: Bialek
- first_name: Michael
full_name: Berry, Michael
last_name: Berry
citation:
ama: Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry M. Searching for
collective behavior in a large network of sensory neurons. PLoS Computational
Biology. 2014;10(1). doi:10.1371/journal.pcbi.1003408
apa: Tkačik, G., Marre, O., Amodei, D., Schneidman, E., Bialek, W., & Berry,
M. (2014). Searching for collective behavior in a large network of sensory neurons.
PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1003408
chicago: Tkačik, Gašper, Olivier Marre, Dario Amodei, Elad Schneidman, William Bialek,
and Michael Berry. “Searching for Collective Behavior in a Large Network of Sensory
Neurons.” PLoS Computational Biology. Public Library of Science, 2014.
https://doi.org/10.1371/journal.pcbi.1003408.
ieee: G. Tkačik, O. Marre, D. Amodei, E. Schneidman, W. Bialek, and M. Berry, “Searching
for collective behavior in a large network of sensory neurons,” PLoS Computational
Biology, vol. 10, no. 1. Public Library of Science, 2014.
ista: Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry M. 2014. Searching
for collective behavior in a large network of sensory neurons. PLoS Computational
Biology. 10(1), e1003408.
mla: Tkačik, Gašper, et al. “Searching for Collective Behavior in a Large Network
of Sensory Neurons.” PLoS Computational Biology, vol. 10, no. 1, e1003408,
Public Library of Science, 2014, doi:10.1371/journal.pcbi.1003408.
short: G. Tkačik, O. Marre, D. Amodei, E. Schneidman, W. Bialek, M. Berry, PLoS
Computational Biology 10 (2014).
date_created: 2018-12-11T11:56:36Z
date_published: 2014-01-02T00:00:00Z
date_updated: 2024-02-21T13:46:14Z
day: '02'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1003408
file:
- access_level: open_access
checksum: c720222c5e924a4acb17f23b9381a6ca
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:46Z
date_updated: 2020-07-14T12:45:35Z
file_id: '4965'
file_name: IST-2016-436-v1+1_journal.pcbi.1003408.pdf
file_size: 2194790
relation: main_file
file_date_updated: 2020-07-14T12:45:35Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://repository.ist.ac.at/id/eprint/436
month: '01'
oa: 1
oa_version: Published Version
publication: PLoS Computational Biology
publication_identifier:
issn:
- 1553734X
publication_status: published
publisher: Public Library of Science
publist_id: '4689'
pubrep_id: '436'
quality_controlled: '1'
related_material:
record:
- id: '5562'
relation: popular_science
status: public
scopus_import: 1
status: public
title: Searching for collective behavior in a large network of sensory neurons
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: 10
year: '2014'
...
---
_id: '2261'
abstract:
- lang: eng
text: To reveal the full potential of human pluripotent stem cells, new methods
for rapid, site-specific genomic engineering are needed. Here, we describe a system
for precise genetic modification of human embryonic stem cells (ESCs) and induced
pluripotent stem cells (iPSCs). We identified a novel human locus, H11, located
in a safe, intergenic, transcriptionally active region of chromosome 22, as the
recipient site, to provide robust, ubiquitous expression of inserted genes. Recipient
cell lines were established by site-specific placement of a ‘landing pad’ cassette
carrying attP sites for phiC31 and Bxb1 integrases at the H11 locus by spontaneous
or TALEN-assisted homologous recombination. Dual integrase cassette exchange (DICE)
mediated by phiC31 and Bxb1 integrases was used to insert genes of interest flanked
by phiC31 and Bxb1 attB sites at the H11 locus, replacing the landing pad. This
system provided complete control over content, direction and copy number of inserted
genes, with a specificity of 100%. A series of genes, including mCherry and various
combinations of the neural transcription factors LMX1a, FOXA2 and OTX2, were inserted
in recipient cell lines derived from H9 ESC, as well as iPSC lines derived from
a Parkinson’s disease patient and a normal sibling control. The DICE system offers
rapid, efficient and precise gene insertion in ESC and iPSC and is particularly
well suited for repeated modifications of the same locus.
acknowledgement: "California Institute for Regenerative Medicine [RT2-01880 and TR2-01756].
Funding for open access charge: California Institute for Regenerative Medicine [RT2-01880
and TR2-01756]\r\nCC BY 3,0"
article_number: e34
author:
- first_name: Fangfang
full_name: Zhu, Fangfang
last_name: Zhu
- first_name: Matthew
full_name: Gamboa, Matthew
last_name: Gamboa
- first_name: Alfonso
full_name: Farruggio, Alfonso
last_name: Farruggio
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Bosiljka
full_name: Tasic, Bosiljka
last_name: Tasic
- first_name: Birgitt
full_name: Schüle, Birgitt
last_name: Schüle
- first_name: Yanru
full_name: Chen Tsai, Yanru
last_name: Chen Tsai
- first_name: Michele
full_name: Calos, Michele
last_name: Calos
citation:
ama: Zhu F, Gamboa M, Farruggio A, et al. DICE, an efficient system for iterative
genomic editing in human pluripotent stem cells. Nucleic Acids Research.
2014;42(5). doi:10.1093/nar/gkt1290
apa: Zhu, F., Gamboa, M., Farruggio, A., Hippenmeyer, S., Tasic, B., Schüle, B.,
… Calos, M. (2014). DICE, an efficient system for iterative genomic editing in
human pluripotent stem cells. Nucleic Acids Research. Oxford University
Press. https://doi.org/10.1093/nar/gkt1290
chicago: Zhu, Fangfang, Matthew Gamboa, Alfonso Farruggio, Simon Hippenmeyer, Bosiljka
Tasic, Birgitt Schüle, Yanru Chen Tsai, and Michele Calos. “DICE, an Efficient
System for Iterative Genomic Editing in Human Pluripotent Stem Cells.” Nucleic
Acids Research. Oxford University Press, 2014. https://doi.org/10.1093/nar/gkt1290.
ieee: F. Zhu et al., “DICE, an efficient system for iterative genomic editing
in human pluripotent stem cells,” Nucleic Acids Research, vol. 42, no.
5. Oxford University Press, 2014.
ista: Zhu F, Gamboa M, Farruggio A, Hippenmeyer S, Tasic B, Schüle B, Chen Tsai
Y, Calos M. 2014. DICE, an efficient system for iterative genomic editing in human
pluripotent stem cells. Nucleic Acids Research. 42(5), e34.
mla: Zhu, Fangfang, et al. “DICE, an Efficient System for Iterative Genomic Editing
in Human Pluripotent Stem Cells.” Nucleic Acids Research, vol. 42, no.
5, e34, Oxford University Press, 2014, doi:10.1093/nar/gkt1290.
short: F. Zhu, M. Gamboa, A. Farruggio, S. Hippenmeyer, B. Tasic, B. Schüle, Y.
Chen Tsai, M. Calos, Nucleic Acids Research 42 (2014).
date_created: 2018-12-11T11:56:38Z
date_published: 2014-03-05T00:00:00Z
date_updated: 2021-01-12T06:56:22Z
day: '05'
ddc:
- '571'
- '610'
department:
- _id: SiHi
doi: 10.1093/nar/gkt1290
file:
- access_level: open_access
checksum: e9268f5f96a820f04d7ebbf85927c3cb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:15Z
date_updated: 2020-07-14T12:45:35Z
file_id: '4738'
file_name: IST-2018-961-v1+1_2014_Hippenmeyer_DICE.pdf
file_size: 11044478
relation: main_file
file_date_updated: 2020-07-14T12:45:35Z
has_accepted_license: '1'
intvolume: ' 42'
issue: '5'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Preprint
publication: Nucleic Acids Research
publication_status: published
publisher: Oxford University Press
publist_id: '4684'
pubrep_id: '961'
quality_controlled: '1'
scopus_import: 1
status: public
title: DICE, an efficient system for iterative genomic editing in human pluripotent
stem cells
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: 42
year: '2014'
...
---
_id: '2275'
abstract:
- lang: eng
text: "Energies with high-order non-submodular interactions have been shown to be
very useful in vision due to their high modeling power. Optimization of such energies,
however, is generally NP-hard. A naive approach that works for small problem instances
is exhaustive search, that is, enumeration of all possible labelings of the underlying
graph. We propose a general minimization approach for large graphs based on enumeration
of labelings of certain small patches. \r\nThis partial enumeration technique
reduces complex high-order energy formulations to pairwise Constraint Satisfaction
Problems with unary costs (uCSP), which can be efficiently solved using standard
methods like TRW-S. Our approach outperforms a number of existing state-of-the-art
algorithms on well known difficult problems (e.g. curvature regularization, stereo,
deconvolution); it gives near global minimum and better speed. \r\nOur main application
of interest is curvature regularization. In the context of segmentation, our partial
enumeration technique allows to evaluate curvature directly on small patches using
a novel integral geometry approach.\r\n"
author:
- first_name: Carl
full_name: Olsson, Carl
last_name: Olsson
- first_name: Johannes
full_name: Ulen, Johannes
last_name: Ulen
- first_name: Yuri
full_name: Boykov, Yuri
last_name: Boykov
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Olsson C, Ulen J, Boykov Y, Kolmogorov V. Partial enumeration and curvature
regularization. In: IEEE; 2014:2936-2943. doi:10.1109/ICCV.2013.365'
apa: 'Olsson, C., Ulen, J., Boykov, Y., & Kolmogorov, V. (2014). Partial enumeration
and curvature regularization (pp. 2936–2943). Presented at the ICCV: International
Conference on Computer Vision, Sydney, Australia: IEEE. https://doi.org/10.1109/ICCV.2013.365'
chicago: Olsson, Carl, Johannes Ulen, Yuri Boykov, and Vladimir Kolmogorov. “Partial
Enumeration and Curvature Regularization,” 2936–43. IEEE, 2014. https://doi.org/10.1109/ICCV.2013.365.
ieee: 'C. Olsson, J. Ulen, Y. Boykov, and V. Kolmogorov, “Partial enumeration and
curvature regularization,” presented at the ICCV: International Conference on
Computer Vision, Sydney, Australia, 2014, pp. 2936–2943.'
ista: 'Olsson C, Ulen J, Boykov Y, Kolmogorov V. 2014. Partial enumeration and curvature
regularization. ICCV: International Conference on Computer Vision, 2936–2943.'
mla: Olsson, Carl, et al. Partial Enumeration and Curvature Regularization.
IEEE, 2014, pp. 2936–43, doi:10.1109/ICCV.2013.365.
short: C. Olsson, J. Ulen, Y. Boykov, V. Kolmogorov, in:, IEEE, 2014, pp. 2936–2943.
conference:
end_date: 2013-12-08
location: Sydney, Australia
name: 'ICCV: International Conference on Computer Vision'
start_date: 2013-12-01
date_created: 2018-12-11T11:56:42Z
date_published: 2014-03-03T00:00:00Z
date_updated: 2021-01-12T06:56:28Z
day: '03'
ddc:
- '000'
department:
- _id: VlKo
doi: 10.1109/ICCV.2013.365
file:
- access_level: open_access
checksum: 4a74b5c92d6dcd2348c2c10ec8dd18bf
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:30Z
date_updated: 2020-07-14T12:45:36Z
file_id: '4754'
file_name: IST-2016-566-v1+1_iccv13_part_enumeration.pdf
file_size: 378601
relation: main_file
file_date_updated: 2020-07-14T12:45:36Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 2936 - 2943
publication_status: published
publisher: IEEE
publist_id: '4669'
pubrep_id: '566'
quality_controlled: '1'
scopus_import: 1
status: public
title: Partial enumeration and curvature regularization
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '2281'
abstract:
- lang: eng
text: We consider two-dimensional Bose-Einstein condensates with attractive interaction,
described by the Gross-Pitaevskii functional. Minimizers of this functional exist
only if the interaction strength a satisfies {Mathematical expression}, where
Q is the unique positive radial solution of {Mathematical expression} in {Mathematical
expression}. We present a detailed analysis of the behavior of minimizers as a
approaches a*, where all the mass concentrates at a global minimum of the trapping
potential.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Yujin
full_name: Guo, Yujin
last_name: Guo
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Guo Y, Seiringer R. On the mass concentration for Bose-Einstein condensates
with attractive interactions. Letters in Mathematical Physics. 2014;104(2):141-156.
doi:10.1007/s11005-013-0667-9
apa: Guo, Y., & Seiringer, R. (2014). On the mass concentration for Bose-Einstein
condensates with attractive interactions. Letters in Mathematical Physics.
Springer. https://doi.org/10.1007/s11005-013-0667-9
chicago: Guo, Yujin, and Robert Seiringer. “On the Mass Concentration for Bose-Einstein
Condensates with Attractive Interactions.” Letters in Mathematical Physics.
Springer, 2014. https://doi.org/10.1007/s11005-013-0667-9.
ieee: Y. Guo and R. Seiringer, “On the mass concentration for Bose-Einstein condensates
with attractive interactions,” Letters in Mathematical Physics, vol. 104,
no. 2. Springer, pp. 141–156, 2014.
ista: Guo Y, Seiringer R. 2014. On the mass concentration for Bose-Einstein condensates
with attractive interactions. Letters in Mathematical Physics. 104(2), 141–156.
mla: Guo, Yujin, and Robert Seiringer. “On the Mass Concentration for Bose-Einstein
Condensates with Attractive Interactions.” Letters in Mathematical Physics,
vol. 104, no. 2, Springer, 2014, pp. 141–56, doi:10.1007/s11005-013-0667-9.
short: Y. Guo, R. Seiringer, Letters in Mathematical Physics 104 (2014) 141–156.
date_created: 2018-12-11T11:56:44Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2024-02-14T12:19:42Z
day: '01'
department:
- _id: RoSe
doi: 10.1007/s11005-013-0667-9
external_id:
arxiv:
- '1301.5682'
intvolume: ' 104'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1301.5682
month: '02'
oa: 1
oa_version: Preprint
page: 141 - 156
publication: Letters in Mathematical Physics
publication_status: published
publisher: Springer
publist_id: '4653'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the mass concentration for Bose-Einstein condensates with attractive interactions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 104
year: '2014'
...
---
_id: '2285'
abstract:
- lang: eng
text: GABAergic inhibitory interneurons control fundamental aspects of neuronal
network function. Their functional roles are assumed to be defined by the identity
of their input synapses, the architecture of their dendritic tree, the passive
and active membrane properties and finally the nature of their postsynaptic targets.
Indeed, interneurons display a high degree of morphological and physiological
heterogeneity. However, whether their morphological and physiological characteristics
are correlated and whether interneuron diversity can be described by a continuum
of GABAergic cell types or by distinct classes has remained unclear. Here we perform
a detailed morphological and physiological characterization of GABAergic cells
in the dentate gyrus, the input region of the hippocampus. To achieve an unbiased
and efficient sampling and classification we used knock-in mice expressing the
enhanced green fluorescent protein (eGFP) in glutamate decarboxylase 67 (GAD67)-positive
neurons and performed cluster analysis. We identified five interneuron classes,
each of them characterized by a distinct set of anatomical and physiological parameters.
Cross-correlation analysis further revealed a direct relation between morphological
and physiological properties indicating that dentate gyrus interneurons fall into
functionally distinct classes which may differentially control neuronal network
activity.
acknowledgement: 'Funded by Deutsche Forschungsgemeinschaft. Grant Numbers: SFB 505,
SFB 780, BA1582/2-1 Excellence Initiative of the German Research Foundation (Spemann
Graduate School). Grant Number: GSC-4 Lichtenberg Professorship-Award (VW-Foundation);
Schram-Foundation; Excellence Initiative Brain Links-Brain Tools. The authors thank
Drs. Jonas-Frederic Sauer and Claudio Elgueta for critically reading the manuscript.
They also thank Karin Winterhalter, Margit Northemann and Ulrich Nöller for technical
assistance.'
author:
- first_name: Jonas
full_name: Hosp, Jonas
last_name: Hosp
- first_name: Michael
full_name: Strüber, Michael
last_name: Strüber
- first_name: Yuchio
full_name: Yanagawa, Yuchio
last_name: Yanagawa
- first_name: Kunihiko
full_name: Obata, Kunihiko
last_name: Obata
- first_name: Imre
full_name: Vida, Imre
last_name: Vida
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Marlene
full_name: Bartos, Marlene
last_name: Bartos
citation:
ama: Hosp J, Strüber M, Yanagawa Y, et al. Morpho-physiological criteria divide
dentate gyrus interneurons into classes. Hippocampus. 2014;23(2):189-203.
doi:10.1002/hipo.22214
apa: Hosp, J., Strüber, M., Yanagawa, Y., Obata, K., Vida, I., Jonas, P. M., &
Bartos, M. (2014). Morpho-physiological criteria divide dentate gyrus interneurons
into classes. Hippocampus. Wiley-Blackwell. https://doi.org/10.1002/hipo.22214
chicago: Hosp, Jonas, Michael Strüber, Yuchio Yanagawa, Kunihiko Obata, Imre Vida,
Peter M Jonas, and Marlene Bartos. “Morpho-Physiological Criteria Divide Dentate
Gyrus Interneurons into Classes.” Hippocampus. Wiley-Blackwell, 2014. https://doi.org/10.1002/hipo.22214.
ieee: J. Hosp et al., “Morpho-physiological criteria divide dentate gyrus
interneurons into classes,” Hippocampus, vol. 23, no. 2. Wiley-Blackwell,
pp. 189–203, 2014.
ista: Hosp J, Strüber M, Yanagawa Y, Obata K, Vida I, Jonas PM, Bartos M. 2014.
Morpho-physiological criteria divide dentate gyrus interneurons into classes.
Hippocampus. 23(2), 189–203.
mla: Hosp, Jonas, et al. “Morpho-Physiological Criteria Divide Dentate Gyrus Interneurons
into Classes.” Hippocampus, vol. 23, no. 2, Wiley-Blackwell, 2014, pp.
189–203, doi:10.1002/hipo.22214.
short: J. Hosp, M. Strüber, Y. Yanagawa, K. Obata, I. Vida, P.M. Jonas, M. Bartos,
Hippocampus 23 (2014) 189–203.
date_created: 2018-12-11T11:56:46Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2021-01-12T06:56:32Z
day: '01'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1002/hipo.22214
file:
- access_level: open_access
checksum: ff6bc75a79dbc985a2e31b79253e6444
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:54Z
date_updated: 2020-07-14T12:45:37Z
file_id: '5178'
file_name: IST-2016-461-v1+1_Hosp_et_al-2014-Hippocampus.pdf
file_size: 801589
relation: main_file
file_date_updated: 2020-07-14T12:45:37Z
has_accepted_license: '1'
intvolume: ' 23'
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 189 - 203
publication: Hippocampus
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4646'
pubrep_id: '461'
quality_controlled: '1'
scopus_import: 1
status: public
title: Morpho-physiological criteria divide dentate gyrus interneurons into classes
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: 3FFCCD3A-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2014'
...
---
_id: '2407'
abstract:
- lang: eng
text: 'Two definitions of the effective mass of a particle interacting with a quantum
field, such as a polaron, are considered and shown to be equal in models similar
to the Fröhlich polaron model. These are: 1. the mass defined by the low momentum
energy E(P)≈E(0)+P2/2 M of the translation invariant system constrained to have
momentum P and 2. the mass M of a simple particle in an arbitrary slowly varying
external potential, V, described by the nonrelativistic Schrödinger equation,
whose ground state energy equals that of the combined particle/field system in
a bound state in the same V.'
author:
- first_name: Élliott
full_name: Lieb, Élliott
last_name: Lieb
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Lieb É, Seiringer R. Equivalence of two definitions of the effective mass of
a polaron. Journal of Statistical Physics. 2014;154(1-2):51-57. doi:10.1007/s10955-013-0791-z
apa: Lieb, É., & Seiringer, R. (2014). Equivalence of two definitions of the
effective mass of a polaron. Journal of Statistical Physics. Springer.
https://doi.org/10.1007/s10955-013-0791-z
chicago: Lieb, Élliott, and Robert Seiringer. “Equivalence of Two Definitions of
the Effective Mass of a Polaron.” Journal of Statistical Physics. Springer,
2014. https://doi.org/10.1007/s10955-013-0791-z.
ieee: É. Lieb and R. Seiringer, “Equivalence of two definitions of the effective
mass of a polaron,” Journal of Statistical Physics, vol. 154, no. 1–2.
Springer, pp. 51–57, 2014.
ista: Lieb É, Seiringer R. 2014. Equivalence of two definitions of the effective
mass of a polaron. Journal of Statistical Physics. 154(1–2), 51–57.
mla: Lieb, Élliott, and Robert Seiringer. “Equivalence of Two Definitions of the
Effective Mass of a Polaron.” Journal of Statistical Physics, vol. 154,
no. 1–2, Springer, 2014, pp. 51–57, doi:10.1007/s10955-013-0791-z.
short: É. Lieb, R. Seiringer, Journal of Statistical Physics 154 (2014) 51–57.
date_created: 2018-12-11T11:57:29Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:57:18Z
day: '01'
doi: 10.1007/s10955-013-0791-z
extern: '1'
intvolume: ' 154'
issue: 1-2
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1304.1780
month: '01'
oa: 1
oa_version: Submitted Version
page: 51 - 57
project:
- _id: 26450934-B435-11E9-9278-68D0E5697425
name: NSERC Postdoctoral fellowship
publication: Journal of Statistical Physics
publication_status: published
publisher: Springer
publist_id: '4519'
quality_controlled: '1'
status: public
title: Equivalence of two definitions of the effective mass of a polaron
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 154
year: '2014'
...
---
_id: '6739'
abstract:
- lang: eng
text: 'We explore the relationship between polar and RM codes and we describe a
coding scheme which improves upon the performance of the standard polar code at
practical block lengths. Our starting point is the experimental observation that
RM codes have a smaller error probability than polar codes under MAP decoding.
This motivates us to introduce a family of codes that “interpolates” between RM
and polar codes, call this family C inter = {C α : α ∈ [0, 1j}, where C α|α=1
is the original polar code, and C α|α=0 is an RM code. Based on numerical observations,
we remark that the error probability under MAP decoding is an increasing function
of α. MAP decoding has in general exponential complexity, but empirically the
performance of polar codes at finite block lengths is boosted by moving along
the family Cinter even under low-complexity decoding schemes such as, for instance,
belief propagation or successive cancellation list decoder. We demonstrate the
performance gain via numerical simulations for transmission over the erasure channel
as well as the Gaussian channel.'
arxiv: 1
author:
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
- first_name: Hamed
full_name: Hassani, Hamed
last_name: Hassani
- first_name: Rudiger
full_name: Urbanke, Rudiger
last_name: Urbanke
citation:
ama: 'Mondelli M, Hassani H, Urbanke R. From polar to Reed-Muller codes: A technique
to improve the finite-length performance. IEEE Transactions on Communications.
2014;62(9):3084-3091. doi:10.1109/tcomm.2014.2345069'
apa: 'Mondelli, M., Hassani, H., & Urbanke, R. (2014). From polar to Reed-Muller
codes: A technique to improve the finite-length performance. IEEE Transactions
on Communications. IEEE. https://doi.org/10.1109/tcomm.2014.2345069'
chicago: 'Mondelli, Marco, Hamed Hassani, and Rudiger Urbanke. “From Polar to Reed-Muller
Codes: A Technique to Improve the Finite-Length Performance.” IEEE Transactions
on Communications. IEEE, 2014. https://doi.org/10.1109/tcomm.2014.2345069.'
ieee: 'M. Mondelli, H. Hassani, and R. Urbanke, “From polar to Reed-Muller codes:
A technique to improve the finite-length performance,” IEEE Transactions on
Communications, vol. 62, no. 9. IEEE, pp. 3084–3091, 2014.'
ista: 'Mondelli M, Hassani H, Urbanke R. 2014. From polar to Reed-Muller codes:
A technique to improve the finite-length performance. IEEE Transactions on Communications.
62(9), 3084–3091.'
mla: 'Mondelli, Marco, et al. “From Polar to Reed-Muller Codes: A Technique to Improve
the Finite-Length Performance.” IEEE Transactions on Communications, vol.
62, no. 9, IEEE, 2014, pp. 3084–91, doi:10.1109/tcomm.2014.2345069.'
short: M. Mondelli, H. Hassani, R. Urbanke, IEEE Transactions on Communications
62 (2014) 3084–3091.
date_created: 2019-07-31T07:20:21Z
date_published: 2014-09-01T00:00:00Z
date_updated: 2021-01-12T08:08:46Z
day: '01'
doi: 10.1109/tcomm.2014.2345069
extern: '1'
external_id:
arxiv:
- '1401.3127'
intvolume: ' 62'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1401.3127
month: '09'
oa: 1
oa_version: Preprint
page: 3084-3091
publication: IEEE Transactions on Communications
publication_identifier:
issn:
- 0090-6778
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: 'From polar to Reed-Muller codes: A technique to improve the finite-length
performance'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 62
year: '2014'
...