---
_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.
article_processing_charge: No
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.
corr_author: '1'
date_created: 2018-12-11T11:56:27Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2025-09-29T11:24:38Z
day: '01'
department:
- _id: PeJo
doi: 10.1126/science.1244811
ec_funded: 1
external_id:
isi:
- '000330724000044'
fulldoi: https://doi.org/10.1126/science.1244811
intvolume: ' 343'
isi: 1
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:
- 0036-8075
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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'
article_processing_charge: No
author:
- first_name: José
full_name: Guzmán, José
id: 30CC5506-F248-11E8-B48F-1D18A9856A87
last_name: Guzmán
orcid: 0000-0003-2209-5242
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: 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: 2025-09-29T11:24:02Z
day: '21'
ddc:
- '570'
department:
- _id: ScienComp
- _id: PeJo
doi: 10.3389/fninf.2014.00016
external_id:
isi:
- '000348105900001'
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
fulldoi: https://doi.org/10.3389/fninf.2014.00016
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: FEB
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: Frontiers in Neuroinformatics
publication_identifier:
issn:
- 1662-5196
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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.
article_processing_charge: No
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.
corr_author: '1'
date_created: 2018-12-11T11:56:28Z
date_published: 2014-03-04T00:00:00Z
date_updated: 2025-09-29T11:23:30Z
day: '04'
department:
- _id: GaTk
doi: 10.1016/j.bpj.2014.01.014
external_id:
isi:
- '000332501300022'
pmid:
- '24606943'
fulldoi: https://doi.org/10.1016/j.bpj.2014.01.014
intvolume: ' 106'
isi: 1
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:
- 0006-3495
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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).
corr_author: '1'
date_created: 2018-12-11T11:56:28Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2025-09-29T11:22:37Z
day: '01'
department:
- _id: BjHo
doi: 10.1088/1742-5468/2014/02/P02001
external_id:
arxiv:
- '1403.4516'
isi:
- '000332098100001'
fulldoi: https://doi.org/10.1088/1742-5468/2014/02/P02001
intvolume: ' 2014'
isi: 1
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:
- 1742-5468
publication_status: published
publisher: IOP Publishing
publist_id: '4729'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Deterministic and stochastic aspects of the transition to turbulence
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 2014
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.
article_processing_charge: No
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.
corr_author: '1'
date_created: 2018-12-11T11:56:29Z
date_published: 2014-02-20T00:00:00Z
date_updated: 2025-09-29T11:21:06Z
day: '20'
department:
- _id: SyCr
doi: 10.1038/nature12977
external_id:
isi:
- '000331477800040'
fulldoi: https://doi.org/10.1038/nature12977
intvolume: ' 506'
isi: 1
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:
- 0028-0836
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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
article_processing_charge: No
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
corr_author: '1'
date_created: 2018-12-11T11:56:29Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2025-06-11T08:02:25Z
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
fulldoi: https://doi.org/10.1007/978-3-642-54242-8_24
has_accepted_license: '1'
intvolume: ' 8349'
language:
- iso: eng
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'
scopus_import: '1'
status: public
title: How to fake auxiliary input
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8349
year: '2014'
...
---
_id: '2239'
abstract:
- lang: eng
text: The analysis of the energy consumption of software is an important goal for
quantitative formal methods. Current methods, using weighted transition systems
or energy games, model the energy source as an ideal resource whose status is
characterized by one number, namely the amount of remaining energy. Real batteries,
however, exhibit behaviors that can deviate substantially from an ideal energy
resource. Based on a discretization of a standard continuous battery model, we
introduce battery transition systems. In this model, a battery is viewed as consisting
of two parts-the available-charge tank and the bound-charge tank. Any charge or
discharge is applied to the available-charge tank. Over time, the energy from
each tank diffuses to the other tank. Battery transition systems are infinite
state systems that, being not well-structured, fall into no decidable class that
is known to us. Nonetheless, we are able to prove that the !-regular modelchecking
problem is decidable for battery transition systems. We also present a case study
on the verification of control programs for energy-constrained semi-autonomous
robots.
author:
- first_name: Udi
full_name: Boker, Udi
id: 31E297B6-F248-11E8-B48F-1D18A9856A87
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
- first_name: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
citation:
ama: 'Boker U, Henzinger TA, Radhakrishna A. Battery transition systems. In: Vol
49. ACM; 2014:595-606. doi:10.1145/2535838.2535875'
apa: 'Boker, U., Henzinger, T. A., & Radhakrishna, A. (2014). Battery transition
systems (Vol. 49, pp. 595–606). Presented at the POPL: Principles of Programming
Languages, San Diego, USA: ACM. https://doi.org/10.1145/2535838.2535875'
chicago: Boker, Udi, Thomas A Henzinger, and Arjun Radhakrishna. “Battery Transition
Systems,” 49:595–606. ACM, 2014. https://doi.org/10.1145/2535838.2535875.
ieee: 'U. Boker, T. A. Henzinger, and A. Radhakrishna, “Battery transition systems,”
presented at the POPL: Principles of Programming Languages, San Diego, USA, 2014,
vol. 49, no. 1, pp. 595–606.'
ista: 'Boker U, Henzinger TA, Radhakrishna A. 2014. Battery transition systems.
POPL: Principles of Programming Languages vol. 49, 595–606.'
mla: Boker, Udi, et al. Battery Transition Systems. Vol. 49, no. 1, ACM,
2014, pp. 595–606, doi:10.1145/2535838.2535875.
short: U. Boker, T.A. Henzinger, A. Radhakrishna, in:, ACM, 2014, pp. 595–606.
conference:
end_date: 2014-01-24
location: San Diego, USA
name: 'POPL: Principles of Programming Languages'
start_date: 2014-01-22
date_created: 2018-12-11T11:56:30Z
date_published: 2014-01-13T00:00:00Z
date_updated: 2021-01-12T06:56:13Z
day: '13'
department:
- _id: ToHe
doi: 10.1145/2535838.2535875
ec_funded: 1
fulldoi: https://doi.org/10.1145/2535838.2535875
intvolume: ' 49'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 595 - 606
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_identifier:
isbn:
- 978-145032544-8
publication_status: published
publisher: ACM
publist_id: '4722'
quality_controlled: '1'
scopus_import: 1
status: public
title: Battery transition systems
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 49
year: '2014'
...
---
_id: '2240'
abstract:
- lang: eng
text: Clathrin-mediated endocytosis is the major mechanism for eukaryotic plasma
membrane-based proteome turn-over. In plants, clathrin-mediated endocytosis is
essential for physiology and development, but the identification and organization
of the machinery operating this process remains largely obscure. Here, we identified
an eight-core-component protein complex, the TPLATE complex, essential for plant
growth via its role as major adaptor module for clathrin-mediated endocytosis.
This complex consists of evolutionarily unique proteins that associate closely
with core endocytic elements. The TPLATE complex is recruited as dynamic foci
at the plasma membrane preceding recruitment of adaptor protein complex 2, clathrin,
and dynamin-related proteins. Reduced function of different complex components
severely impaired internalization of assorted endocytic cargoes, demonstrating
its pivotal role in clathrin-mediated endocytosis. Taken together, the TPLATE
complex is an early endocytic module representing a unique evolutionary plant
adaptation of the canonical eukaryotic pathway for clathrin-mediated endocytosis.
article_processing_charge: No
author:
- first_name: Astrid
full_name: Gadeyne, Astrid
last_name: Gadeyne
- first_name: Clara
full_name: Sánchez Rodríguez, Clara
last_name: Sánchez Rodríguez
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Simone
full_name: Di Rubbo, Simone
last_name: Di Rubbo
- first_name: Henrik
full_name: Zauber, Henrik
last_name: Zauber
- first_name: Kevin
full_name: Vanneste, Kevin
last_name: Vanneste
- first_name: Jelle
full_name: Van Leene, Jelle
last_name: Van Leene
- first_name: Nancy
full_name: De Winne, Nancy
last_name: De Winne
- first_name: Dominique
full_name: Eeckhout, Dominique
last_name: Eeckhout
- first_name: Geert
full_name: Persiau, Geert
last_name: Persiau
- first_name: Eveline
full_name: Van De Slijke, Eveline
last_name: Van De Slijke
- first_name: Bernard
full_name: Cannoot, Bernard
last_name: Cannoot
- first_name: Leen
full_name: Vercruysse, Leen
last_name: Vercruysse
- first_name: Jonathan
full_name: Mayers, Jonathan
last_name: Mayers
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Urszula
full_name: Kania, Urszula
id: 4AE5C486-F248-11E8-B48F-1D18A9856A87
last_name: Kania
- first_name: Matthias
full_name: Ehrlich, Matthias
last_name: Ehrlich
- first_name: Alois
full_name: Schweighofer, Alois
last_name: Schweighofer
- first_name: Tijs
full_name: Ketelaar, Tijs
last_name: Ketelaar
- first_name: Steven
full_name: Maere, Steven
last_name: Maere
- first_name: Sebastian
full_name: Bednarek, Sebastian
last_name: Bednarek
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Kris
full_name: Gevaert, Kris
last_name: Gevaert
- first_name: Erwin
full_name: Witters, Erwin
last_name: Witters
- first_name: Eugenia
full_name: Russinova, Eugenia
last_name: Russinova
- first_name: Staffan
full_name: Persson, Staffan
last_name: Persson
- first_name: Geert
full_name: De Jaeger, Geert
last_name: De Jaeger
- first_name: Daniël
full_name: Van Damme, Daniël
last_name: Van Damme
citation:
ama: Gadeyne A, Sánchez Rodríguez C, Vanneste S, et al. The TPLATE adaptor complex
drives clathrin-mediated endocytosis in plants. Cell. 2014;156(4):691-704.
doi:10.1016/j.cell.2014.01.039
apa: Gadeyne, A., Sánchez Rodríguez, C., Vanneste, S., Di Rubbo, S., Zauber, H.,
Vanneste, K., … Van Damme, D. (2014). The TPLATE adaptor complex drives clathrin-mediated
endocytosis in plants. Cell. Cell Press. https://doi.org/10.1016/j.cell.2014.01.039
chicago: Gadeyne, Astrid, Clara Sánchez Rodríguez, Steffen Vanneste, Simone Di Rubbo,
Henrik Zauber, Kevin Vanneste, Jelle Van Leene, et al. “The TPLATE Adaptor Complex
Drives Clathrin-Mediated Endocytosis in Plants.” Cell. Cell Press, 2014.
https://doi.org/10.1016/j.cell.2014.01.039.
ieee: A. Gadeyne et al., “The TPLATE adaptor complex drives clathrin-mediated
endocytosis in plants,” Cell, vol. 156, no. 4. Cell Press, pp. 691–704,
2014.
ista: Gadeyne A, Sánchez Rodríguez C, Vanneste S, Di Rubbo S, Zauber H, Vanneste
K, Van Leene J, De Winne N, Eeckhout D, Persiau G, Van De Slijke E, Cannoot B,
Vercruysse L, Mayers J, Adamowski M, Kania U, Ehrlich M, Schweighofer A, Ketelaar
T, Maere S, Bednarek S, Friml J, Gevaert K, Witters E, Russinova E, Persson S,
De Jaeger G, Van Damme D. 2014. The TPLATE adaptor complex drives clathrin-mediated
endocytosis in plants. Cell. 156(4), 691–704.
mla: Gadeyne, Astrid, et al. “The TPLATE Adaptor Complex Drives Clathrin-Mediated
Endocytosis in Plants.” Cell, vol. 156, no. 4, Cell Press, 2014, pp. 691–704,
doi:10.1016/j.cell.2014.01.039.
short: A. Gadeyne, C. Sánchez Rodríguez, S. Vanneste, S. Di Rubbo, H. Zauber, K.
Vanneste, J. Van Leene, N. De Winne, D. Eeckhout, G. Persiau, E. Van De Slijke,
B. Cannoot, L. Vercruysse, J. Mayers, M. Adamowski, U. Kania, M. Ehrlich, A. Schweighofer,
T. Ketelaar, S. Maere, S. Bednarek, J. Friml, K. Gevaert, E. Witters, E. Russinova,
S. Persson, G. De Jaeger, D. Van Damme, Cell 156 (2014) 691–704.
date_created: 2018-12-11T11:56:31Z
date_published: 2014-02-13T00:00:00Z
date_updated: 2025-09-29T11:20:21Z
day: '13'
department:
- _id: JiFr
doi: 10.1016/j.cell.2014.01.039
external_id:
isi:
- '000331379800009'
fulldoi: https://doi.org/10.1016/j.cell.2014.01.039
intvolume: ' 156'
isi: 1
issue: '4'
language:
- iso: eng
month: '02'
oa_version: None
page: 691 - 704
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Cell Press
publist_id: '4721'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 156
year: '2014'
...
---
_id: '2241'
abstract:
- lang: eng
text: 'The brain demands high-energy supply and obstruction of blood flow causes
rapid deterioration of the healthiness of brain cells. Two major events occur
upon ischemia: acidosis and liberation of excess glutamate, which leads to excitotoxicity.
However, cellular source of glutamate and its release mechanism upon ischemia
remained unknown. Here we show a causal relationship between glial acidosis and
neuronal excitotoxicity. As the major cation that flows through channelrhodopsin-2
(ChR2) is proton, this could be regarded as an optogenetic tool for instant intracellular
acidification. Optical activation of ChR2 expressed in glial cells led to glial
acidification and to release of glutamate. On the other hand, glial alkalization
via optogenetic activation of a proton pump, archaerhodopsin (ArchT), led to cessation
of glutamate release and to the relief of ischemic brain damage in vivo. Our results
suggest that controlling glial pH may be an effective therapeutic strategy for
intervention of ischemic brain damage.'
article_processing_charge: No
author:
- first_name: Kaoru
full_name: Beppu, Kaoru
last_name: Beppu
- first_name: Takuya
full_name: Sasaki, Takuya
last_name: Sasaki
- first_name: Kenji
full_name: Tanaka, Kenji
last_name: Tanaka
- first_name: Akihiro
full_name: Yamanaka, Akihiro
last_name: Yamanaka
- first_name: Yugo
full_name: Fukazawa, Yugo
last_name: Fukazawa
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Ko
full_name: Matsui, Ko
last_name: Matsui
citation:
ama: Beppu K, Sasaki T, Tanaka K, et al. Optogenetic countering of glial acidosis
suppresses glial glutamate release and ischemic brain damage. Neuron. 2014;81(2):314-320.
doi:10.1016/j.neuron.2013.11.011
apa: Beppu, K., Sasaki, T., Tanaka, K., Yamanaka, A., Fukazawa, Y., Shigemoto, R.,
& Matsui, K. (2014). Optogenetic countering of glial acidosis suppresses glial
glutamate release and ischemic brain damage. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2013.11.011
chicago: Beppu, Kaoru, Takuya Sasaki, Kenji Tanaka, Akihiro Yamanaka, Yugo Fukazawa,
Ryuichi Shigemoto, and Ko Matsui. “Optogenetic Countering of Glial Acidosis Suppresses
Glial Glutamate Release and Ischemic Brain Damage.” Neuron. Elsevier, 2014.
https://doi.org/10.1016/j.neuron.2013.11.011.
ieee: K. Beppu et al., “Optogenetic countering of glial acidosis suppresses
glial glutamate release and ischemic brain damage,” Neuron, vol. 81, no.
2. Elsevier, pp. 314–320, 2014.
ista: Beppu K, Sasaki T, Tanaka K, Yamanaka A, Fukazawa Y, Shigemoto R, Matsui K.
2014. Optogenetic countering of glial acidosis suppresses glial glutamate release
and ischemic brain damage. Neuron. 81(2), 314–320.
mla: Beppu, Kaoru, et al. “Optogenetic Countering of Glial Acidosis Suppresses Glial
Glutamate Release and Ischemic Brain Damage.” Neuron, vol. 81, no. 2, Elsevier,
2014, pp. 314–20, doi:10.1016/j.neuron.2013.11.011.
short: K. Beppu, T. Sasaki, K. Tanaka, A. Yamanaka, Y. Fukazawa, R. Shigemoto, K.
Matsui, Neuron 81 (2014) 314–320.
date_created: 2018-12-11T11:56:31Z
date_published: 2014-01-22T00:00:00Z
date_updated: 2026-04-16T10:07:56Z
day: '22'
department:
- _id: RySh
doi: 10.1016/j.neuron.2013.11.011
external_id:
isi:
- '000330420700010'
fulldoi: https://doi.org/10.1016/j.neuron.2013.11.011
intvolume: ' 81'
isi: 1
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 314 - 320
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
publist_id: '4715'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optogenetic countering of glial acidosis suppresses glial glutamate release
and ischemic brain damage
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 81
year: '2014'
...
---
_id: '2242'
abstract:
- lang: eng
text: MicroRNAs (miRNAs) are small RNAs that play important regulatory roles in
many cellular pathways. MiRNAs associate with members of the Argonaute protein
family and bind to partially complementary sequences on mRNAs and induce translational
repression or mRNA decay. Using deep sequencing and Northern blotting, we characterized
miRNA expression in wild type and miR-155-deficient dendritic cells (DCs) and
macrophages. Analysis of different stimuli (LPS, LDL, eLDL, oxLDL) reveals a direct
influence of miR-155 on the expression levels of other miRNAs. For example, miR-455
is negatively regulated in miR-155-deficient cells possibly due to inhibition
of the transcription factor C/EBPbeta by miR-155. Based on our comprehensive data
sets, we propose a model of hierarchical miRNA expression dominated by miR-155
in DCs and macrophages.
article_processing_charge: No
author:
- first_name: Anne
full_name: Dueck, Anne
last_name: Dueck
- first_name: Alexander
full_name: Eichner, Alexander
id: 4DFA52AE-F248-11E8-B48F-1D18A9856A87
last_name: Eichner
- 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: Gunter
full_name: Meister, Gunter
last_name: Meister
citation:
ama: Dueck A, Eichner A, Sixt MK, Meister G. A miR-155-dependent microRNA hierarchy
in dendritic cell maturation and macrophage activation. FEBS Letters. 2014;588(4):632-640.
doi:10.1016/j.febslet.2014.01.009
apa: Dueck, A., Eichner, A., Sixt, M. K., & Meister, G. (2014). A miR-155-dependent
microRNA hierarchy in dendritic cell maturation and macrophage activation. FEBS
Letters. Elsevier. https://doi.org/10.1016/j.febslet.2014.01.009
chicago: Dueck, Anne, Alexander Eichner, Michael K Sixt, and Gunter Meister. “A
MiR-155-Dependent MicroRNA Hierarchy in Dendritic Cell Maturation and Macrophage
Activation.” FEBS Letters. Elsevier, 2014. https://doi.org/10.1016/j.febslet.2014.01.009.
ieee: A. Dueck, A. Eichner, M. K. Sixt, and G. Meister, “A miR-155-dependent microRNA
hierarchy in dendritic cell maturation and macrophage activation,” FEBS Letters,
vol. 588, no. 4. Elsevier, pp. 632–640, 2014.
ista: Dueck A, Eichner A, Sixt MK, Meister G. 2014. A miR-155-dependent microRNA
hierarchy in dendritic cell maturation and macrophage activation. FEBS Letters.
588(4), 632–640.
mla: Dueck, Anne, et al. “A MiR-155-Dependent MicroRNA Hierarchy in Dendritic Cell
Maturation and Macrophage Activation.” FEBS Letters, vol. 588, no. 4, Elsevier,
2014, pp. 632–40, doi:10.1016/j.febslet.2014.01.009.
short: A. Dueck, A. Eichner, M.K. Sixt, G. Meister, FEBS Letters 588 (2014) 632–640.
date_created: 2018-12-11T11:56:31Z
date_published: 2014-02-14T00:00:00Z
date_updated: 2025-09-29T11:19:23Z
day: '14'
department:
- _id: MiSi
doi: 10.1016/j.febslet.2014.01.009
external_id:
isi:
- '000331115700016'
fulldoi: https://doi.org/10.1016/j.febslet.2014.01.009
intvolume: ' 588'
isi: 1
issue: '4'
language:
- iso: eng
month: '02'
oa_version: None
page: 632 - 640
publication: FEBS Letters
publication_identifier:
issn:
- 0014-5793
publication_status: published
publisher: Elsevier
publist_id: '4714'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A miR-155-dependent microRNA hierarchy in dendritic cell maturation and macrophage
activation
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 588
year: '2014'
...
---
_id: '2245'
abstract:
- lang: eng
text: 'Exogenous application of biologically important molecules for plant growth
promotion and/or regulation is very common both in plant research and horticulture.
Plant hormones such as auxins and cytokinins are classes of compounds which are
often applied exogenously. Nevertheless, plants possess a well-established machinery
to regulate the active pool of exogenously applied compounds by converting them
to metabolites and conjugates. Consequently, it is often very useful to know the
in vivo status of applied compounds to connect them with some of the regulatory
events in plant developmental processes. The in vivo status of applied compounds
can be measured by incubating plants with radiolabeled compounds, followed by
extraction, purification, and HPLC metabolic profiling of plant extracts. Recently
we have used this method to characterize the intracellularly localized PIN protein,
PIN5. Here we explain the method in detail, with a focus on general application. '
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Sibu
full_name: Simon, Sibu
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Petr
full_name: Skůpa, Petr
last_name: Skůpa
- first_name: Petre
full_name: Dobrev, Petre
last_name: Dobrev
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Simon S, Skůpa P, Dobrev P, Petrášek J, Zažímalová E, Friml J. Analyzing the
in vivo status of exogenously applied auxins: A HPLC-based method to characterize
the intracellularly localized auxin transporters. In: Hicks G, Robert S, eds.
Plant Chemical Genomics. Vol 1056. Methods in Molecular Biology. Springer;
2014:255-264. doi:10.1007/978-1-62703-592-7_23'
apa: 'Simon, S., Skůpa, P., Dobrev, P., Petrášek, J., Zažímalová, E., & Friml,
J. (2014). Analyzing the in vivo status of exogenously applied auxins: A HPLC-based
method to characterize the intracellularly localized auxin transporters. In G.
Hicks & S. Robert (Eds.), Plant Chemical Genomics (Vol. 1056, pp. 255–264).
Springer. https://doi.org/10.1007/978-1-62703-592-7_23'
chicago: 'Simon, Sibu, Petr Skůpa, Petre Dobrev, Jan Petrášek, Eva Zažímalová, and
Jiří Friml. “Analyzing the in Vivo Status of Exogenously Applied Auxins: A HPLC-Based
Method to Characterize the Intracellularly Localized Auxin Transporters.” In Plant
Chemical Genomics, edited by Glenn Hicks and Stéphanie Robert, 1056:255–64.
Methods in Molecular Biology. Springer, 2014. https://doi.org/10.1007/978-1-62703-592-7_23.'
ieee: 'S. Simon, P. Skůpa, P. Dobrev, J. Petrášek, E. Zažímalová, and J. Friml,
“Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method
to characterize the intracellularly localized auxin transporters,” in Plant
Chemical Genomics, vol. 1056, G. Hicks and S. Robert, Eds. Springer, 2014,
pp. 255–264.'
ista: 'Simon S, Skůpa P, Dobrev P, Petrášek J, Zažímalová E, Friml J. 2014.Analyzing
the in vivo status of exogenously applied auxins: A HPLC-based method to characterize
the intracellularly localized auxin transporters. In: Plant Chemical Genomics.
Methods in Molecular Biology, vol. 1056, 255–264.'
mla: 'Simon, Sibu, et al. “Analyzing the in Vivo Status of Exogenously Applied Auxins:
A HPLC-Based Method to Characterize the Intracellularly Localized Auxin Transporters.”
Plant Chemical Genomics, edited by Glenn Hicks and Stéphanie Robert, vol.
1056, Springer, 2014, pp. 255–64, doi:10.1007/978-1-62703-592-7_23.'
short: S. Simon, P. Skůpa, P. Dobrev, J. Petrášek, E. Zažímalová, J. Friml, in:,
G. Hicks, S. Robert (Eds.), Plant Chemical Genomics, Springer, 2014, pp. 255–264.
date_created: 2018-12-11T11:56:32Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2025-07-10T11:52:16Z
day: '01'
department:
- _id: JiFr
doi: 10.1007/978-1-62703-592-7_23
editor:
- first_name: Glenn
full_name: Hicks, Glenn
last_name: Hicks
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
fulldoi: https://doi.org/10.1007/978-1-62703-592-7_23
intvolume: ' 1056'
language:
- iso: eng
month: '01'
oa_version: None
page: 255 - 264
publication: Plant Chemical Genomics
publication_identifier:
issn:
- 1064-3745
publication_status: published
publisher: Springer
publist_id: '4704'
quality_controlled: '1'
scopus_import: '1'
series_title: Methods in Molecular Biology
status: public
title: 'Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method
to characterize the intracellularly localized auxin transporters'
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1056
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. '
article_processing_charge: No
arxiv: 1
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.
corr_author: '1'
date_created: 2018-12-11T11:56:33Z
date_published: 2014-02-13T00:00:00Z
date_updated: 2026-04-16T10:08:15Z
day: '13'
department:
- _id: KrCh
doi: 10.1016/j.tcs.2013.11.032
external_id:
arxiv:
- '1303.3777'
isi:
- '000331433100007'
fulldoi: https://doi.org/10.1016/j.tcs.2013.11.032
intvolume: ' 521'
isi: 1
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:
- 0304-3975
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 521
year: '2014'
...
---
_id: '2248'
abstract:
- lang: eng
text: 'Avian forelimb digit homology remains one of the standard themes in comparative
biology and EvoDevo research. In order to resolve the apparent contradictions
between embryological and paleontological evidence a variety of hypotheses have
been presented in recent years. The proposals range from excluding birds from
the dinosaur clade, to assignments of homology by different criteria, or even
assuming a hexadactyl tetrapod limb ground state. At present two approaches prevail:
the frame shift hypothesis and the pyramid reduction hypothesis. While the former
postulates a homeotic shift of digit identities, the latter argues for a gradual
bilateral reduction of phalanges and digits. Here we present a new model that
integrates elements from both hypotheses with the existing experimental and fossil
evidence. We start from the main feature common to both earlier concepts, the
initiating ontogenetic event: reduction and loss of the anterior-most digit. It
is proposed that a concerted mechanism of molecular regulation and developmental
mechanics is capable of shifting the boundaries of hoxD expression in embryonic
forelimb buds as well as changing the digit phenotypes. Based on a distinction
between positional (topological) and compositional (phenotypic) homology criteria,
we argue that the identity of the avian digits is II, III, IV, despite a partially
altered phenotype. Finally, we introduce an alternative digit reduction scheme
that reconciles the current fossil evidence with the presented molecular-morphogenetic
model. Our approach identifies specific experiments that allow to test whether
gene expression can be shifted and digit phenotypes can be altered by induced
digit loss or digit gain.'
article_processing_charge: No
author:
- first_name: Daniel
full_name: Capek, Daniel
id: 31C42484-F248-11E8-B48F-1D18A9856A87
last_name: Capek
orcid: 0000-0001-5199-9940
- first_name: Brian
full_name: Metscher, Brian
last_name: Metscher
- first_name: Gerd
full_name: Müller, Gerd
last_name: Müller
citation:
ama: 'Capek D, Metscher B, Müller G. Thumbs down: A molecular-morphogenetic approach
to avian digit homology. Journal of Experimental Zoology Part B: Molecular
and Developmental Evolution. 2014;322(1):1-12. doi:10.1002/jez.b.22545'
apa: 'Capek, D., Metscher, B., & Müller, G. (2014). Thumbs down: A molecular-morphogenetic
approach to avian digit homology. Journal of Experimental Zoology Part B: Molecular
and Developmental Evolution. Wiley-Blackwell. https://doi.org/10.1002/jez.b.22545'
chicago: 'Capek, Daniel, Brian Metscher, and Gerd Müller. “Thumbs down: A Molecular-Morphogenetic
Approach to Avian Digit Homology.” Journal of Experimental Zoology Part B:
Molecular and Developmental Evolution. Wiley-Blackwell, 2014. https://doi.org/10.1002/jez.b.22545.'
ieee: 'D. Capek, B. Metscher, and G. Müller, “Thumbs down: A molecular-morphogenetic
approach to avian digit homology,” Journal of Experimental Zoology Part B:
Molecular and Developmental Evolution, vol. 322, no. 1. Wiley-Blackwell, pp.
1–12, 2014.'
ista: 'Capek D, Metscher B, Müller G. 2014. Thumbs down: A molecular-morphogenetic
approach to avian digit homology. Journal of Experimental Zoology Part B: Molecular
and Developmental Evolution. 322(1), 1–12.'
mla: 'Capek, Daniel, et al. “Thumbs down: A Molecular-Morphogenetic Approach to
Avian Digit Homology.” Journal of Experimental Zoology Part B: Molecular and
Developmental Evolution, vol. 322, no. 1, Wiley-Blackwell, 2014, pp. 1–12,
doi:10.1002/jez.b.22545.'
short: 'D. Capek, B. Metscher, G. Müller, Journal of Experimental Zoology Part B:
Molecular and Developmental Evolution 322 (2014) 1–12.'
date_created: 2018-12-11T11:56:33Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2025-09-29T11:18:02Z
day: '01'
department:
- _id: CaHe
doi: 10.1002/jez.b.22545
external_id:
isi:
- '000335377400001'
fulldoi: https://doi.org/10.1002/jez.b.22545
intvolume: ' 322'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 1 - 12
publication: 'Journal of Experimental Zoology Part B: Molecular and Developmental
Evolution'
publication_identifier:
issn:
- 1552-5007
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4701'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Thumbs down: A molecular-morphogenetic approach to avian digit homology'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 322
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.
article_processing_charge: No
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: 2026-04-16T10:08:30Z
day: '01'
department:
- _id: JiFr
doi: 10.1111/tpj.12373
external_id:
isi:
- '000328661300008'
fulldoi: https://doi.org/10.1111/tpj.12373
intvolume: ' 77'
isi: 1
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:
- 0960-7412
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 77
year: '2014'
...
---
_id: '2252'
abstract:
- lang: eng
text: The pattern of inheritance and mechanism of sex determination can have important
evolutionary consequences. We studied probabilistic sex determination in the ciliate
Tetrahymena thermophila, which was previously shown to cause evolution of skewed
sex ratios. We find that the genetic background alters the sex determination patterns
of mat alleles in heterozygotes and that allelic interaction can differentially
influence the expression probability of the 7 sexes. We quantify the dominance
relationships between several mat alleles and find that A-type alleles, which
specify sex I, are indeed recessive to B-type alleles, which are unable to specify
that sex. Our results provide additional support for the presence of modifier
loci and raise implications for the dynamics of sex ratios in populations of T.
thermophila.
article_processing_charge: No
author:
- first_name: Sujal
full_name: Phadke, Sujal
last_name: Phadke
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Tuan
full_name: Pham, Tuan
last_name: Pham
- first_name: Stephanie
full_name: Pham, Stephanie
last_name: Pham
- first_name: Rebecca
full_name: Zufall, Rebecca
last_name: Zufall
citation:
ama: Phadke S, Paixao T, Pham T, Pham S, Zufall R. Genetic background alters dominance
relationships between mat alleles in the ciliate Tetrahymena Thermophila. Journal
of Heredity. 2014;105(1):130-135. doi:10.1093/jhered/est063
apa: Phadke, S., Paixao, T., Pham, T., Pham, S., & Zufall, R. (2014). Genetic
background alters dominance relationships between mat alleles in the ciliate Tetrahymena
Thermophila. Journal of Heredity. Oxford University Press. https://doi.org/10.1093/jhered/est063
chicago: Phadke, Sujal, Tiago Paixao, Tuan Pham, Stephanie Pham, and Rebecca Zufall.
“Genetic Background Alters Dominance Relationships between Mat Alleles in the
Ciliate Tetrahymena Thermophila.” Journal of Heredity. Oxford University
Press, 2014. https://doi.org/10.1093/jhered/est063.
ieee: S. Phadke, T. Paixao, T. Pham, S. Pham, and R. Zufall, “Genetic background
alters dominance relationships between mat alleles in the ciliate Tetrahymena
Thermophila,” Journal of Heredity, vol. 105, no. 1. Oxford University Press,
pp. 130–135, 2014.
ista: Phadke S, Paixao T, Pham T, Pham S, Zufall R. 2014. Genetic background alters
dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila.
Journal of Heredity. 105(1), 130–135.
mla: Phadke, Sujal, et al. “Genetic Background Alters Dominance Relationships between
Mat Alleles in the Ciliate Tetrahymena Thermophila.” Journal of Heredity,
vol. 105, no. 1, Oxford University Press, 2014, pp. 130–35, doi:10.1093/jhered/est063.
short: S. Phadke, T. Paixao, T. Pham, S. Pham, R. Zufall, Journal of Heredity 105
(2014) 130–135.
corr_author: '1'
date_created: 2018-12-11T11:56:35Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2025-09-29T11:16:03Z
day: '01'
department:
- _id: NiBa
doi: 10.1093/jhered/est063
external_id:
isi:
- '000328427800013'
fulldoi: https://doi.org/10.1093/jhered/est063
intvolume: ' 105'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 130 - 135
publication: Journal of Heredity
publication_identifier:
issn:
- 0022-1503
publication_status: published
publisher: Oxford University Press
publist_id: '4695'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetic background alters dominance relationships between mat alleles in the
ciliate Tetrahymena Thermophila
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 105
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: 2026-06-18T18:33:25Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1111/tpj.12369
external_id:
isi:
- '000328661300009'
fulldoi: https://doi.org/10.1111/tpj.12369
intvolume: ' 77'
isi: 1
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:
- 0960-7412
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.
article_processing_charge: No
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.
corr_author: '1'
date_created: 2018-12-11T11:56:35Z
date_published: 2014-01-08T00:00:00Z
date_updated: 2026-04-16T10:08:53Z
day: '08'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1016/j.neuron.2013.09.046
ec_funded: 1
external_id:
isi:
- '000329559000015'
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
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intvolume: ' 81'
isi: 1
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:
- 0896-6273
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 81
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: 'This 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
article_processing_charge: No
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).
corr_author: '1'
date_created: 2018-12-11T11:56:36Z
date_published: 2014-01-02T00:00:00Z
date_updated: 2025-09-29T11:14:06Z
day: '02'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1003408
external_id:
isi:
- '000337948500010'
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
fulldoi: https://doi.org/10.1371/journal.pcbi.1003408
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
publication: PLoS Computational Biology
publication_identifier:
issn:
- 1553-734X
publication_status: published
publisher: Public Library of Science
publist_id: '4689'
pubrep_id: '436'
quality_controlled: '1'
related_material:
record:
- id: '5562'
relation: research_data
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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
article_processing_charge: No
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: 2025-09-29T11:13:18Z
day: '05'
ddc:
- '571'
- '610'
department:
- _id: SiHi
doi: 10.1093/nar/gkt1290
external_id:
isi:
- '000333093600005'
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
fulldoi: https://doi.org/10.1093/nar/gkt1290
has_accepted_license: '1'
intvolume: ' 42'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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"
article_processing_charge: No
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: 2025-09-29T14:28:16Z
day: '03'
ddc:
- '000'
department:
- _id: VlKo
doi: 10.1109/ICCV.2013.365
external_id:
isi:
- '000351830500367'
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
fulldoi: https://doi.org/10.1109/ICCV.2013.365
has_accepted_license: '1'
isi: 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2014'
...