---
_id: '2226'
abstract:
- lang: eng
text: Coriolis force effects on shear flows are important in geophysical and astrophysical
contexts. We report a study on the linear stability and the transient energy growth
of the plane Couette flow with system rotation perpendicular to the shear direction.
External rotation causes linear instability. At small rotation rates, the onset
of linear instability scales inversely with the rotation rate and the optimal
transient growth in the linearly stable region is slightly enhanced ∼Re2. The
corresponding optimal initial perturbations are characterized by roll structures
inclined in the streamwise direction and are twisted under external rotation.
At large rotation rates, the transient growth is significantly inhibited and hence
linear stability analysis is a reliable indicator for instability.
article_number: '013001'
author:
- first_name: Liang
full_name: Shi, Liang
last_name: Shi
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
- first_name: Andreas
full_name: Tilgner, Andreas
last_name: Tilgner
citation:
ama: Shi L, Hof B, Tilgner A. Transient growth of Ekman-Couette flow. Physical
Review E Statistical Nonlinear and Soft Matter Physics. 2014;89(1). doi:10.1103/PhysRevE.89.013001
apa: Shi, L., Hof, B., & Tilgner, A. (2014). Transient growth of Ekman-Couette
flow. Physical Review E Statistical Nonlinear and Soft Matter Physics.
American Institute of Physics. https://doi.org/10.1103/PhysRevE.89.013001
chicago: Shi, Liang, Björn Hof, and Andreas Tilgner. “Transient Growth of Ekman-Couette
Flow.” Physical Review E Statistical Nonlinear and Soft Matter Physics.
American Institute of Physics, 2014. https://doi.org/10.1103/PhysRevE.89.013001.
ieee: L. Shi, B. Hof, and A. Tilgner, “Transient growth of Ekman-Couette flow,”
Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89,
no. 1. American Institute of Physics, 2014.
ista: Shi L, Hof B, Tilgner A. 2014. Transient growth of Ekman-Couette flow. Physical
Review E Statistical Nonlinear and Soft Matter Physics. 89(1), 013001.
mla: Shi, Liang, et al. “Transient Growth of Ekman-Couette Flow.” Physical Review
E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 1, 013001, American
Institute of Physics, 2014, doi:10.1103/PhysRevE.89.013001.
short: L. Shi, B. Hof, A. Tilgner, Physical Review E Statistical Nonlinear and Soft
Matter Physics 89 (2014).
date_created: 2018-12-11T11:56:26Z
date_published: 2014-01-06T00:00:00Z
date_updated: 2021-01-12T06:56:08Z
day: '06'
department:
- _id: BjHo
doi: 10.1103/PhysRevE.89.013001
intvolume: ' 89'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1312.5095
month: '01'
oa: 1
oa_version: Submitted Version
project:
- _id: 25BDE9A4-B435-11E9-9278-68D0E5697425
grant_number: SFB-TR3-TP10B
name: Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_identifier:
issn:
- '15393755'
publication_status: published
publisher: American Institute of Physics
publist_id: '4737'
quality_controlled: '1'
scopus_import: 1
status: public
title: Transient growth of Ekman-Couette flow
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 89
year: '2014'
...
---
_id: '2227'
abstract:
- lang: eng
text: The Balkan Peninsula, characterized by high rates of endemism, is recognised
as one of the most diverse and species-rich areas of Europe. However, little is
known about the origin of Balkan endemics. The present study addresses the phylogenetic
position of the Balkan endemic Ranunculus wettsteinii, as well as its taxonomic
status and relationship with the widespread R. parnassiifolius, based on nuclear
DNA (internal transcribed spacer, ITS) and plastid regions (rpl32-trnL, rps16-trnQ,
trnK-matK and ycf6-psbM). Maximum parsimony and Bayesian inference analyses revealed
a well-supported clade formed by accessions of R. wettsteinii. Furthermore, our
phylogenetic and network analyses supported previous hypotheses of a likely allopolyploid
origin for R. wettsteinii between R. montenegrinus and R. parnassiifolius, with
the latter as the maternal parent.
article_processing_charge: No
author:
- first_name: Eduardo
full_name: Cires Rodriguez, Eduardo
id: 2AD56A7A-F248-11E8-B48F-1D18A9856A87
last_name: Cires Rodriguez
- first_name: Matthias
full_name: Baltisberger, Matthias
last_name: Baltisberger
- first_name: Candela
full_name: Cuesta, Candela
id: 33A3C818-F248-11E8-B48F-1D18A9856A87
last_name: Cuesta
orcid: 0000-0003-1923-2410
- first_name: Pablo
full_name: Vargas, Pablo
last_name: Vargas
- first_name: José
full_name: Prieto, José
last_name: Prieto
citation:
ama: Cires Rodriguez E, Baltisberger M, Cuesta C, Vargas P, Prieto J. Allopolyploid
origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from
nuclear and plastid DNA sequences. Organisms Diversity and Evolution. 2014;14(1):1-10.
doi:10.1007/s13127-013-0150-6
apa: Cires Rodriguez, E., Baltisberger, M., Cuesta, C., Vargas, P., & Prieto,
J. (2014). Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae)
inferred from nuclear and plastid DNA sequences. Organisms Diversity and Evolution.
Springer. https://doi.org/10.1007/s13127-013-0150-6
chicago: Cires Rodriguez, Eduardo, Matthias Baltisberger, Candela Cuesta, Pablo
Vargas, and José Prieto. “Allopolyploid Origin of the Balkan Endemic Ranunculus
Wettsteinii (Ranunculaceae) Inferred from Nuclear and Plastid DNA Sequences.”
Organisms Diversity and Evolution. Springer, 2014. https://doi.org/10.1007/s13127-013-0150-6.
ieee: E. Cires Rodriguez, M. Baltisberger, C. Cuesta, P. Vargas, and J. Prieto,
“Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae)
inferred from nuclear and plastid DNA sequences,” Organisms Diversity and Evolution,
vol. 14, no. 1. Springer, pp. 1–10, 2014.
ista: Cires Rodriguez E, Baltisberger M, Cuesta C, Vargas P, Prieto J. 2014. Allopolyploid
origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from
nuclear and plastid DNA sequences. Organisms Diversity and Evolution. 14(1), 1–10.
mla: Cires Rodriguez, Eduardo, et al. “Allopolyploid Origin of the Balkan Endemic
Ranunculus Wettsteinii (Ranunculaceae) Inferred from Nuclear and Plastid DNA Sequences.”
Organisms Diversity and Evolution, vol. 14, no. 1, Springer, 2014, pp.
1–10, doi:10.1007/s13127-013-0150-6.
short: E. Cires Rodriguez, M. Baltisberger, C. Cuesta, P. Vargas, J. Prieto, Organisms
Diversity and Evolution 14 (2014) 1–10.
date_created: 2018-12-11T11:56:26Z
date_published: 2014-03-01T00:00:00Z
date_updated: 2022-08-25T14:42:46Z
day: '01'
department:
- _id: JiFr
- _id: EvBe
doi: 10.1007/s13127-013-0150-6
intvolume: ' 14'
issue: '1'
language:
- iso: eng
month: '03'
oa_version: None
page: 1 - 10
publication: Organisms Diversity and Evolution
publication_identifier:
issn:
- '14396092'
publication_status: published
publisher: Springer
publist_id: '4734'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae)
inferred from nuclear and plastid DNA sequences
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2014'
...
---
_id: '2228'
abstract:
- lang: eng
text: Fast-spiking, parvalbumin-expressing GABAergic interneurons, a large proportion
of which are basket cells (BCs), have a key role in feedforward and feedback inhibition,
gamma oscillations and complex information processing. For these functions, fast
propagation of action potentials (APs) from the soma to the presynaptic terminals
is important. However, the functional properties of interneuron axons remain elusive.
We examined interneuron axons by confocally targeted subcellular patch-clamp recording
in rat hippocampal slices. APs were initiated in the proximal axon ∼20 μm from
the soma and propagated to the distal axon with high reliability and speed. Subcellular
mapping revealed a stepwise increase of Na^+ conductance density from the soma
to the proximal axon, followed by a further gradual increase in the distal axon.
Active cable modeling and experiments with partial channel block revealed that
low axonal Na^+ conductance density was sufficient for reliability, but high Na^+
density was necessary for both speed of propagation and fast-spiking AP phenotype.
Our results suggest that a supercritical density of Na^+ channels compensates
for the morphological properties of interneuron axons (small segmental diameter,
extensive branching and high bouton density), ensuring fast AP propagation and
high-frequency repetitive firing.
author:
- first_name: Hua
full_name: Hu, Hua
id: 4AC0145C-F248-11E8-B48F-1D18A9856A87
last_name: Hu
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Hu H, Jonas PM. A supercritical density of Na^+ channels ensures fast signaling
in GABAergic interneuron axons. Nature Neuroscience. 2014;17(5):686-693.
doi:10.1038/nn.3678
apa: Hu, H., & Jonas, P. M. (2014). A supercritical density of Na^+ channels
ensures fast signaling in GABAergic interneuron axons. Nature Neuroscience.
Nature Publishing Group. https://doi.org/10.1038/nn.3678
chicago: Hu, Hua, and Peter M Jonas. “A Supercritical Density of Na^+ Channels Ensures
Fast Signaling in GABAergic Interneuron Axons.” Nature Neuroscience. Nature
Publishing Group, 2014. https://doi.org/10.1038/nn.3678.
ieee: H. Hu and P. M. Jonas, “A supercritical density of Na^+ channels ensures fast
signaling in GABAergic interneuron axons,” Nature Neuroscience, vol. 17,
no. 5. Nature Publishing Group, pp. 686–693, 2014.
ista: Hu H, Jonas PM. 2014. A supercritical density of Na^+ channels ensures fast
signaling in GABAergic interneuron axons. Nature Neuroscience. 17(5), 686–693.
mla: Hu, Hua, and Peter M. Jonas. “A Supercritical Density of Na^+ Channels Ensures
Fast Signaling in GABAergic Interneuron Axons.” Nature Neuroscience, vol.
17, no. 5, Nature Publishing Group, 2014, pp. 686–93, doi:10.1038/nn.3678.
short: H. Hu, P.M. Jonas, Nature Neuroscience 17 (2014) 686–693.
date_created: 2018-12-11T11:56:26Z
date_published: 2014-03-23T00:00:00Z
date_updated: 2021-01-12T06:56:08Z
day: '23'
department:
- _id: PeJo
doi: 10.1038/nn.3678
ec_funded: 1
intvolume: ' 17'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286295/
month: '03'
oa: 1
oa_version: Submitted Version
page: 686-693
project:
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
- _id: 25C26B1E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P24909-B24
name: Mechanisms of transmitter release at GABAergic synapses
publication: Nature Neuroscience
publication_identifier:
issn:
- '10976256'
publication_status: published
publisher: Nature Publishing Group
publist_id: '4733'
quality_controlled: '1'
scopus_import: 1
status: public
title: A supercritical density of Na^+ channels ensures fast signaling in GABAergic
interneuron axons
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2014'
...
---
_id: '2229'
abstract:
- lang: eng
text: The distance between Ca^2+ channels and release sensors determines the speed
and efficacy of synaptic transmission. Tight "nanodomain" channel-sensor
coupling initiates transmitter release at synapses in the mature brain, whereas
loose "microdomain" coupling appears restricted to early developmental
stages. To probe the coupling configuration at a plastic synapse in the mature
central nervous system, we performed paired recordings between mossy fiber terminals
and CA3 pyramidal neurons in rat hippocampus. Millimolar concentrations of both
the fast Ca^2+ chelator BAPTA [1,2-bis(2-aminophenoxy)ethane- N,N, N′,N′-tetraacetic
acid] and the slow chelator EGTA efficiently suppressed transmitter release, indicating
loose coupling between Ca^2+ channels and release sensors. Loose coupling enabled
the control of initial release probability by fast endogenous Ca^2+ buffers and
the generation of facilitation by buffer saturation. Thus, loose coupling provides
the molecular framework for presynaptic plasticity.
author:
- first_name: Nicholas
full_name: Vyleta, Nicholas
id: 36C4978E-F248-11E8-B48F-1D18A9856A87
last_name: Vyleta
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Vyleta N, Jonas PM. Loose coupling between Ca^2+ channels and release sensors
at a plastic hippocampal synapse. Science. 2014;343(6171):665-670. doi:10.1126/science.1244811
apa: Vyleta, N., & Jonas, P. M. (2014). Loose coupling between Ca^2+ channels
and release sensors at a plastic hippocampal synapse. Science. American
Association for the Advancement of Science. https://doi.org/10.1126/science.1244811
chicago: Vyleta, Nicholas, and Peter M Jonas. “Loose Coupling between Ca^2+ Channels
and Release Sensors at a Plastic Hippocampal Synapse.” Science. American
Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1244811.
ieee: N. Vyleta and P. M. Jonas, “Loose coupling between Ca^2+ channels and release
sensors at a plastic hippocampal synapse,” Science, vol. 343, no. 6171.
American Association for the Advancement of Science, pp. 665–670, 2014.
ista: Vyleta N, Jonas PM. 2014. Loose coupling between Ca^2+ channels and release
sensors at a plastic hippocampal synapse. Science. 343(6171), 665–670.
mla: Vyleta, Nicholas, and Peter M. Jonas. “Loose Coupling between Ca^2+ Channels
and Release Sensors at a Plastic Hippocampal Synapse.” Science, vol. 343,
no. 6171, American Association for the Advancement of Science, 2014, pp. 665–70,
doi:10.1126/science.1244811.
short: N. Vyleta, P.M. Jonas, Science 343 (2014) 665–670.
date_created: 2018-12-11T11:56:27Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2021-01-12T06:56:09Z
day: '01'
department:
- _id: PeJo
doi: 10.1126/science.1244811
ec_funded: 1
intvolume: ' 343'
issue: '6171'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617475/
month: '02'
oa: 1
oa_version: Submitted Version
page: 665 - 670
project:
- _id: 25C26B1E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P24909-B24
name: Mechanisms of transmitter release at GABAergic synapses
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
publication: Science
publication_identifier:
issn:
- '00368075'
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '4732'
quality_controlled: '1'
scopus_import: 1
status: public
title: Loose coupling between Ca^2+ channels and release sensors at a plastic hippocampal
synapse
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 343
year: '2014'
...
---
_id: '2230'
abstract:
- lang: eng
text: Intracellular electrophysiological recordings provide crucial insights into
elementary neuronal signals such as action potentials and synaptic currents. Analyzing
and interpreting these signals is essential for a quantitative understanding of
neuronal information processing, and requires both fast data visualization and
ready access to complex analysis routines. To achieve this goal, we have developed
Stimfit, a free software package for cellular neurophysiology with a Python scripting
interface and a built-in Python shell. The program supports most standard file
formats for cellular neurophysiology and other biomedical signals through the
Biosig library. To quantify and interpret the activity of single neurons and communication
between neurons, the program includes algorithms to characterize the kinetics
of presynaptic action potentials and postsynaptic currents, estimate latencies
between pre- and postsynaptic events, and detect spontaneously occurring events.
We validate and benchmark these algorithms, give estimation errors, and provide
sample use cases, showing that Stimfit represents an efficient, accessible and
extensible way to accurately analyze and interpret neuronal signals.
article_number: '16'
author:
- first_name: José
full_name: Guzmán, José
id: 30CC5506-F248-11E8-B48F-1D18A9856A87
last_name: Guzmán
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Christoph
full_name: Schmidt Hieber, Christoph
last_name: Schmidt Hieber
citation:
ama: 'Guzmán J, Schlögl A, Schmidt Hieber C. Stimfit: Quantifying electrophysiological
data with Python. Frontiers in Neuroinformatics. 2014;8(FEB). doi:10.3389/fninf.2014.00016'
apa: 'Guzmán, J., Schlögl, A., & Schmidt Hieber, C. (2014). Stimfit: Quantifying
electrophysiological data with Python. Frontiers in Neuroinformatics. Frontiers
Research Foundation. https://doi.org/10.3389/fninf.2014.00016'
chicago: 'Guzmán, José, Alois Schlögl, and Christoph Schmidt Hieber. “Stimfit: Quantifying
Electrophysiological Data with Python.” Frontiers in Neuroinformatics.
Frontiers Research Foundation, 2014. https://doi.org/10.3389/fninf.2014.00016.'
ieee: 'J. Guzmán, A. Schlögl, and C. Schmidt Hieber, “Stimfit: Quantifying electrophysiological
data with Python,” Frontiers in Neuroinformatics, vol. 8, no. FEB. Frontiers
Research Foundation, 2014.'
ista: 'Guzmán J, Schlögl A, Schmidt Hieber C. 2014. Stimfit: Quantifying electrophysiological
data with Python. Frontiers in Neuroinformatics. 8(FEB), 16.'
mla: 'Guzmán, José, et al. “Stimfit: Quantifying Electrophysiological Data with
Python.” Frontiers in Neuroinformatics, vol. 8, no. FEB, 16, Frontiers
Research Foundation, 2014, doi:10.3389/fninf.2014.00016.'
short: J. Guzmán, A. Schlögl, C. Schmidt Hieber, Frontiers in Neuroinformatics 8
(2014).
date_created: 2018-12-11T11:56:27Z
date_published: 2014-02-21T00:00:00Z
date_updated: 2021-01-12T06:56:09Z
day: '21'
ddc:
- '570'
department:
- _id: ScienComp
- _id: PeJo
doi: 10.3389/fninf.2014.00016
file:
- access_level: open_access
checksum: eeca00bba7232ff7d27db83321f6ea30
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:17Z
date_updated: 2020-07-14T12:45:34Z
file_id: '4935'
file_name: IST-2016-425-v1+1_fninf-08-00016.pdf
file_size: 2883372
relation: main_file
file_date_updated: 2020-07-14T12:45:34Z
has_accepted_license: '1'
intvolume: ' 8'
issue: FEB
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: Frontiers in Neuroinformatics
publication_identifier:
issn:
- '16625196'
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '4731'
pubrep_id: '425'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Stimfit: Quantifying electrophysiological data with Python'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2014'
...
---
_id: '2231'
abstract:
- lang: eng
text: Based on the measurements of noise in gene expression performed during the
past decade, it has become customary to think of gene regulation in terms of a
two-state model, where the promoter of a gene can stochastically switch between
an ON and an OFF state. As experiments are becoming increasingly precise and the
deviations from the two-state model start to be observable, we ask about the experimental
signatures of complex multistate promoters, as well as the functional consequences
of this additional complexity. In detail, we i), extend the calculations for noise
in gene expression to promoters described by state transition diagrams with multiple
states, ii), systematically compute the experimentally accessible noise characteristics
for these complex promoters, and iii), use information theory to evaluate the
channel capacities of complex promoter architectures and compare them with the
baseline provided by the two-state model. We find that adding internal states
to the promoter generically decreases channel capacity, except in certain cases,
three of which (cooperativity, dual-role regulation, promoter cycling) we analyze
in detail.
author:
- first_name: Georg
full_name: Rieckh, Georg
id: 34DA8BD6-F248-11E8-B48F-1D18A9856A87
last_name: Rieckh
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Rieckh G, Tkačik G. Noise and information transmission in promoters with multiple
internal states. Biophysical Journal. 2014;106(5):1194-1204. doi:10.1016/j.bpj.2014.01.014
apa: Rieckh, G., & Tkačik, G. (2014). Noise and information transmission in
promoters with multiple internal states. Biophysical Journal. Biophysical
Society. https://doi.org/10.1016/j.bpj.2014.01.014
chicago: Rieckh, Georg, and Gašper Tkačik. “Noise and Information Transmission in
Promoters with Multiple Internal States.” Biophysical Journal. Biophysical
Society, 2014. https://doi.org/10.1016/j.bpj.2014.01.014.
ieee: G. Rieckh and G. Tkačik, “Noise and information transmission in promoters
with multiple internal states,” Biophysical Journal, vol. 106, no. 5. Biophysical
Society, pp. 1194–1204, 2014.
ista: Rieckh G, Tkačik G. 2014. Noise and information transmission in promoters
with multiple internal states. Biophysical Journal. 106(5), 1194–1204.
mla: Rieckh, Georg, and Gašper Tkačik. “Noise and Information Transmission in Promoters
with Multiple Internal States.” Biophysical Journal, vol. 106, no. 5, Biophysical
Society, 2014, pp. 1194–204, doi:10.1016/j.bpj.2014.01.014.
short: G. Rieckh, G. Tkačik, Biophysical Journal 106 (2014) 1194–1204.
date_created: 2018-12-11T11:56:28Z
date_published: 2014-03-04T00:00:00Z
date_updated: 2021-01-12T06:56:10Z
day: '04'
department:
- _id: GaTk
doi: 10.1016/j.bpj.2014.01.014
external_id:
pmid:
- '24606943'
intvolume: ' 106'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4026790/
month: '03'
oa: 1
oa_version: Submitted Version
page: 1194 - 1204
pmid: 1
publication: Biophysical Journal
publication_identifier:
issn:
- '00063495'
publication_status: published
publisher: Biophysical Society
publist_id: '4730'
quality_controlled: '1'
scopus_import: 1
status: public
title: Noise and information transmission in promoters with multiple internal states
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 106
year: '2014'
...
---
_id: '2232'
abstract:
- lang: eng
text: The purpose of this contribution is to summarize and discuss recent advances
regarding the onset of turbulence in shear flows. The absence of a clear-cut instability
mechanism, the spatio-temporal intermittent character and extremely long lived
transients are some of the major difficulties encountered in these flows and have
hindered progress towards understanding the transition process. We will show for
the case of pipe flow that concepts from nonlinear dynamics and statistical physics
can help to explain the onset of turbulence. In particular, the turbulent structures
(puffs) observed close to onset are spatially localized chaotic transients and
their lifetimes increase super-exponentially with Reynolds number. At the same
time fluctuations of individual turbulent puffs can (although very rarely) lead
to the nucleation of new puffs. The competition between these two stochastic processes
gives rise to a non-equilibrium phase transition where turbulence changes from
a super-transient to a sustained state.
article_number: P02001
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Baofang
full_name: Song, Baofang
id: a79e57f5-e8a5-11ec-9dc9-83fb8c81cf72
last_name: Song
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Song B, Hof B. Deterministic and stochastic aspects of the transition to turbulence.
Journal of Statistical Mechanics Theory and Experiment. 2014;2014(2). doi:10.1088/1742-5468/2014/02/P02001
apa: Song, B., & Hof, B. (2014). Deterministic and stochastic aspects of the
transition to turbulence. Journal of Statistical Mechanics Theory and Experiment.
IOP Publishing. https://doi.org/10.1088/1742-5468/2014/02/P02001
chicago: Song, Baofang, and Björn Hof. “Deterministic and Stochastic Aspects of
the Transition to Turbulence.” Journal of Statistical Mechanics Theory and
Experiment. IOP Publishing, 2014. https://doi.org/10.1088/1742-5468/2014/02/P02001.
ieee: B. Song and B. Hof, “Deterministic and stochastic aspects of the transition
to turbulence,” Journal of Statistical Mechanics Theory and Experiment,
vol. 2014, no. 2. IOP Publishing, 2014.
ista: Song B, Hof B. 2014. Deterministic and stochastic aspects of the transition
to turbulence. Journal of Statistical Mechanics Theory and Experiment. 2014(2),
P02001.
mla: Song, Baofang, and Björn Hof. “Deterministic and Stochastic Aspects of the
Transition to Turbulence.” Journal of Statistical Mechanics Theory and Experiment,
vol. 2014, no. 2, P02001, IOP Publishing, 2014, doi:10.1088/1742-5468/2014/02/P02001.
short: B. Song, B. Hof, Journal of Statistical Mechanics Theory and Experiment 2014
(2014).
date_created: 2018-12-11T11:56:28Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2022-06-10T10:13:15Z
day: '01'
department:
- _id: BjHo
doi: 10.1088/1742-5468/2014/02/P02001
external_id:
arxiv:
- '1403.4516'
intvolume: ' 2014'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1403.4516
month: '02'
oa: 1
oa_version: Submitted Version
publication: Journal of Statistical Mechanics Theory and Experiment
publication_identifier:
issn:
- '17425468'
publication_status: published
publisher: IOP Publishing
publist_id: '4729'
quality_controlled: '1'
status: public
title: Deterministic and stochastic aspects of the transition to turbulence
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2014
year: '2014'
...
---
_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: '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
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.
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: 2021-01-12T06:56:13Z
day: '13'
department:
- _id: JiFr
doi: 10.1016/j.cell.2014.01.039
intvolume: ' 156'
issue: '4'
language:
- iso: eng
month: '02'
oa_version: None
page: 691 - 704
publication: Cell
publication_identifier:
issn:
- '00928674'
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
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.'
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: 2021-01-12T06:56:14Z
day: '22'
department:
- _id: RySh
doi: 10.1016/j.neuron.2013.11.011
intvolume: ' 81'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 314 - 320
publication: Neuron
publication_identifier:
issn:
- '08966273'
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
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.
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: 2021-01-12T06:56:14Z
day: '14'
department:
- _id: MiSi
doi: 10.1016/j.febslet.2014.01.009
intvolume: ' 588'
issue: '4'
language:
- iso: eng
month: '02'
oa_version: None
page: 632 - 640
publication: FEBS Letters
publication_identifier:
issn:
- '00145793'
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
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
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: 2021-01-12T06:56:15Z
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
intvolume: ' 1056'
language:
- iso: eng
month: '01'
oa_version: None
page: 255 - 264
publication: Plant Chemical Genomics
publication_identifier:
issn:
- '10643745'
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: 4435EBFC-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. '
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: '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.'
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: 2021-01-12T06:56:16Z
day: '01'
department:
- _id: CaHe
doi: 10.1002/jez.b.22545
intvolume: ' 322'
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:
- '15525007'
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
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.
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'
...