---
_id: '3813'
abstract:
- lang: eng
text: Hyperpolarization-activated channels (Ih or HCN channels) are widely expressed
in principal neurons in the central nervous system. However, Ih in inhibitory
GABAergic interneurons is less well characterized. We examined the functional
properties of Ih in fast-spiking basket cells (BCs) of the dentate gyrus, using
hippocampal slices from 17- to 21-day-old rats. Bath application of the Ih channel
blocker ZD 7288 at a concentration of 30 microm induced a hyperpolarization of
5.7 +/- 1.5 mV, an increase in input resistance and a correlated increase in apparent
membrane time constant. ZD 7288 blocked a hyperpolarization-activated current
in a concentration-dependent manner (IC50, 1.4 microm). The effects of ZD 7288
were mimicked by external Cs+. The reversal potential of Ih was -27.4 mV, corresponding
to a Na+ to K+ permeability ratio (PNa/PK) of 0.36. The midpoint potential of
the activation curve of Ih was -83.9 mV, and the activation time constant at -120
mV was 190 ms. Single-cell expression analysis using reverse transcription followed
by quantitative polymerase chain reaction revealed that BCs coexpress HCN1 and
HCN2 subunit mRNA, suggesting the formation of heteromeric HCN1/2 channels. ZD
7288 increased the current threshold for evoking antidromic action potentials
by extracellular stimulation, consistent with the expression of Ih in BC axons.
Finally, ZD 7288 decreased the frequency of miniature inhibitory postsynaptic
currents (mIPSCs) in hippocampal granule cells, the main target cells of BCs,
to 70 +/- 4% of the control value. In contrast, the amplitude of mIPSCs was unchanged,
consistent with the presence of Ih in inhibitory terminals. In conclusion, our
results suggest that Ih channels are expressed in the somatodendritic region,
axon and presynaptic elements of fast-spiking BCs in the hippocampus.
author:
- first_name: Yexica
full_name: Aponte, Yexica
last_name: Aponte
- first_name: Cheng
full_name: Lien, Cheng-Chang
last_name: Lien
- first_name: Ellen
full_name: Reisinger, Ellen
last_name: Reisinger
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Aponte Y, Lien C, Reisinger E, Jonas PM. Hyperpolarization-activated cation
channels in fast-spiking interneurons of rat hippocampus. Journal of Physiology.
2006;574(Pt 1):229-243. doi:10.1113/jphysiol.2005.104042
apa: Aponte, Y., Lien, C., Reisinger, E., & Jonas, P. M. (2006). Hyperpolarization-activated
cation channels in fast-spiking interneurons of rat hippocampus. Journal of
Physiology. Wiley-Blackwell. https://doi.org/10.1113/jphysiol.2005.104042
chicago: Aponte, Yexica, Cheng Lien, Ellen Reisinger, and Peter M Jonas. “Hyperpolarization-Activated
Cation Channels in Fast-Spiking Interneurons of Rat Hippocampus.” Journal of
Physiology. Wiley-Blackwell, 2006. https://doi.org/10.1113/jphysiol.2005.104042.
ieee: Y. Aponte, C. Lien, E. Reisinger, and P. M. Jonas, “Hyperpolarization-activated
cation channels in fast-spiking interneurons of rat hippocampus,” Journal of
Physiology, vol. 574, no. Pt 1. Wiley-Blackwell, pp. 229–43, 2006.
ista: Aponte Y, Lien C, Reisinger E, Jonas PM. 2006. Hyperpolarization-activated
cation channels in fast-spiking interneurons of rat hippocampus. Journal of Physiology.
574(Pt 1), 229–43.
mla: Aponte, Yexica, et al. “Hyperpolarization-Activated Cation Channels in Fast-Spiking
Interneurons of Rat Hippocampus.” Journal of Physiology, vol. 574, no.
Pt 1, Wiley-Blackwell, 2006, pp. 229–43, doi:10.1113/jphysiol.2005.104042.
short: Y. Aponte, C. Lien, E. Reisinger, P.M. Jonas, Journal of Physiology 574 (2006)
229–43.
date_created: 2018-12-11T12:05:19Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:23Z
day: '01'
doi: 10.1113/jphysiol.2005.104042
extern: 1
intvolume: ' 574'
issue: Pt 1
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1817792/
month: '01'
oa: 1
page: 229 - 43
publication: Journal of Physiology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2397'
quality_controlled: 0
status: public
title: Hyperpolarization-activated cation channels in fast-spiking interneurons of
rat hippocampus
type: journal_article
volume: 574
year: '2006'
...
---
_id: '3814'
abstract:
- lang: eng
text: The axon terminals (mossy fibers) of hippocampal dentate granule cells form
characteristic synaptic connections with large spines or excrescences of both
hilar mossy cells and CA3 pyramidal neurons. Interneurons of the hilar region
and area CA3 are also prominent targets of mossy fibers. The tracing of biocytin-filled
mossy fibers and immunolabeling of target cells with interneuron markers has revealed
that the majority of mossy fiber synapses project to gamma aminobutyric acid (GABA)-ergic
inhibitory interneurons rather than to excitatory principal cells, although the
functional implications of these quantitative differences are unclear. Following
a brief description of the "classical" mossy fiber synapse on excrescences
of CA3 pyramidal cells, the present review focuses on the contacts formed between
granule cells and GABAergic interneurons, both normally and after synaptic reorganization.
In response to deafferentation of mossy cell target cells, which include both
granule cells and interneurons, mossy fibers "sprout" new axon collaterals
that form a band of supragranular mossy fibers in the inner molecular layer of
the dentate gyrus. Although most newly formed recurrent mossy fibers establish
synapses with granule cells, there is an apparently convergent input of new mossy
fibers onto GABA-immunoreactive interneuron dendrites that traverse the inner
molecular layer. These mossy fiber-interneuron synapses in the dentate gyrus are
observed in chronically epileptic rats and may be the structural correlate of
the granule cell hyperinhibition observed in these animals in vivo. Together,
the findings reviewed here establish mossy fiber synapses as an important component
of inhibitory circuits in the hippocampus.
author:
- first_name: Michael
full_name: Frotscher, Michael
last_name: Frotscher
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Robert
full_name: Sloviter, Robert S
last_name: Sloviter
citation:
ama: Frotscher M, Jonas PM, Sloviter R. Synapses formed by normal and abnormal hippocampal
mossy fibers (Review). Cell and Tissue Research. 2006;326(2):361-367. doi:10.1007/s00441-006-0269-2
apa: Frotscher, M., Jonas, P. M., & Sloviter, R. (2006). Synapses formed by
normal and abnormal hippocampal mossy fibers (Review). Cell and Tissue Research.
Springer. https://doi.org/10.1007/s00441-006-0269-2
chicago: Frotscher, Michael, Peter M Jonas, and Robert Sloviter. “Synapses Formed
by Normal and Abnormal Hippocampal Mossy Fibers (Review).” Cell and Tissue
Research. Springer, 2006. https://doi.org/10.1007/s00441-006-0269-2.
ieee: M. Frotscher, P. M. Jonas, and R. Sloviter, “Synapses formed by normal and
abnormal hippocampal mossy fibers (Review),” Cell and Tissue Research,
vol. 326, no. 2. Springer, pp. 361–7, 2006.
ista: Frotscher M, Jonas PM, Sloviter R. 2006. Synapses formed by normal and abnormal
hippocampal mossy fibers (Review). Cell and Tissue Research. 326(2), 361–7.
mla: Frotscher, Michael, et al. “Synapses Formed by Normal and Abnormal Hippocampal
Mossy Fibers (Review).” Cell and Tissue Research, vol. 326, no. 2, Springer,
2006, pp. 361–67, doi:10.1007/s00441-006-0269-2.
short: M. Frotscher, P.M. Jonas, R. Sloviter, Cell and Tissue Research 326 (2006)
361–7.
date_created: 2018-12-11T12:05:19Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2019-04-26T07:22:35Z
day: '01'
doi: 10.1007/s00441-006-0269-2
extern: 1
intvolume: ' 326'
issue: '2'
month: '01'
page: 361 - 7
publication: Cell and Tissue Research
publication_status: published
publisher: Springer
publist_id: '2395'
quality_controlled: 0
status: public
title: Synapses formed by normal and abnormal hippocampal mossy fibers (Review)
type: review
volume: 326
year: '2006'
...
---
_id: '3815'
abstract:
- lang: eng
text: It is widely accepted that the hippocampus plays a major role in learning
and memory. The mossy fiber synapse between granule cells in the dentate gyrus
and pyramidal neurons in the CA3 region is a key component of the hippocampal
trisynaptic circuit. Recent work, partially based on direct presynaptic patch-clamp
recordings from hippocampal mossy fiber boutons, sheds light on the mechanisms
of synaptic transmission and plasticity at mossy fiber synapses. A high Na(+)
channel density in mossy fiber boutons leads to a large amplitude of the presynaptic
action potential. Together with the fast gating of presynaptic Ca(2+) channels,
this generates a large and brief presynaptic Ca(2+) influx, which can trigger
transmitter release with high efficiency and temporal precision. The large number
of release sites, the large size of the releasable pool of vesicles, and the huge
extent of presynaptic plasticity confer unique strength to this synapse, suggesting
a large impact onto the CA3 pyramidal cell network under specific behavioral conditions.
The characteristic properties of the hippocampal mossy fiber synapse may be important
for pattern separation and information storage in the dentate gyrus-CA3 cell network.
author:
- first_name: Josef
full_name: Bischofberger, Josef
last_name: Bischofberger
- first_name: Dominique
full_name: Engel, Dominique
last_name: Engel
- first_name: Michael
full_name: Frotscher, Michael
last_name: Frotscher
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: 'Bischofberger J, Engel D, Frotscher M, Jonas PM. Timing and efficacy of transmitter
release at mossy fiber synapses in the hippocampal network. Pflugers Archiv :
European Journal of Physiology. 2006;453(3):361-372. doi:10.1007/s00424-006-0093-2'
apa: 'Bischofberger, J., Engel, D., Frotscher, M., & Jonas, P. M. (2006). Timing
and efficacy of transmitter release at mossy fiber synapses in the hippocampal
network. Pflugers Archiv : European Journal of Physiology. Springer. https://doi.org/10.1007/s00424-006-0093-2'
chicago: 'Bischofberger, Josef, Dominique Engel, Michael Frotscher, and Peter M
Jonas. “Timing and Efficacy of Transmitter Release at Mossy Fiber Synapses in
the Hippocampal Network.” Pflugers Archiv : European Journal of Physiology.
Springer, 2006. https://doi.org/10.1007/s00424-006-0093-2.'
ieee: 'J. Bischofberger, D. Engel, M. Frotscher, and P. M. Jonas, “Timing and efficacy
of transmitter release at mossy fiber synapses in the hippocampal network,” Pflugers
Archiv : European Journal of Physiology, vol. 453, no. 3. Springer, pp. 361–72,
2006.'
ista: 'Bischofberger J, Engel D, Frotscher M, Jonas PM. 2006. Timing and efficacy
of transmitter release at mossy fiber synapses in the hippocampal network. Pflugers
Archiv : European Journal of Physiology. 453(3), 361–72.'
mla: 'Bischofberger, Josef, et al. “Timing and Efficacy of Transmitter Release at
Mossy Fiber Synapses in the Hippocampal Network.” Pflugers Archiv : European
Journal of Physiology, vol. 453, no. 3, Springer, 2006, pp. 361–72, doi:10.1007/s00424-006-0093-2.'
short: 'J. Bischofberger, D. Engel, M. Frotscher, P.M. Jonas, Pflugers Archiv :
European Journal of Physiology 453 (2006) 361–72.'
date_created: 2018-12-11T12:05:19Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:24Z
day: '01'
doi: 10.1007/s00424-006-0093-2
extern: 1
intvolume: ' 453'
issue: '3'
month: '01'
page: 361 - 72
publication: 'Pflugers Archiv : European Journal of Physiology'
publication_status: published
publisher: Springer
publist_id: '2396'
quality_controlled: 0
status: public
title: Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal
network
type: journal_article
volume: 453
year: '2006'
...
---
_id: '3817'
author:
- first_name: Michael
full_name: Frotscher, Michael
last_name: Frotscher
- first_name: Eckart
full_name: Gundelfinger, Eckart
last_name: Gundelfinger
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Erwin
full_name: Neher, Erwin
last_name: Neher
- first_name: Peter
full_name: Seeburg, Peter
last_name: Seeburg
citation:
ama: Frotscher M, Gundelfinger E, Jonas PM, Neher E, Seeburg P. The most important
recent advances in synapse research from my point of view--and what remains to
be done. Cell and Tissue Research. 2006;326(2):203-204. doi:10.1007/s00441-006-0325-y
apa: Frotscher, M., Gundelfinger, E., Jonas, P. M., Neher, E., & Seeburg, P.
(2006). The most important recent advances in synapse research from my point of
view--and what remains to be done. Cell and Tissue Research. Springer.
https://doi.org/10.1007/s00441-006-0325-y
chicago: Frotscher, Michael, Eckart Gundelfinger, Peter M Jonas, Erwin Neher, and
Peter Seeburg. “The Most Important Recent Advances in Synapse Research from My
Point of View--and What Remains to Be Done.” Cell and Tissue Research.
Springer, 2006. https://doi.org/10.1007/s00441-006-0325-y.
ieee: M. Frotscher, E. Gundelfinger, P. M. Jonas, E. Neher, and P. Seeburg, “The
most important recent advances in synapse research from my point of view--and
what remains to be done,” Cell and Tissue Research, vol. 326, no. 2. Springer,
pp. 203–4, 2006.
ista: Frotscher M, Gundelfinger E, Jonas PM, Neher E, Seeburg P. 2006. The most
important recent advances in synapse research from my point of view--and what
remains to be done. Cell and Tissue Research. 326(2), 203–4.
mla: Frotscher, Michael, et al. “The Most Important Recent Advances in Synapse Research
from My Point of View--and What Remains to Be Done.” Cell and Tissue Research,
vol. 326, no. 2, Springer, 2006, pp. 203–04, doi:10.1007/s00441-006-0325-y.
short: M. Frotscher, E. Gundelfinger, P.M. Jonas, E. Neher, P. Seeburg, Cell and
Tissue Research 326 (2006) 203–4.
date_created: 2018-12-11T12:05:20Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:24Z
day: '01'
doi: 10.1007/s00441-006-0325-y
extern: 1
intvolume: ' 326'
issue: '2'
month: '01'
page: 203 - 4
publication: Cell and Tissue Research
publication_status: published
publisher: Springer
publist_id: '2394'
quality_controlled: 0
status: public
title: The most important recent advances in synapse research from my point of view--and
what remains to be done
type: journal_article
volume: 326
year: '2006'
...
---
_id: '3818'
abstract:
- lang: eng
text: Rigorous analysis of synaptic transmission in the central nervous system requires
access to presynaptic terminals. However, cortical terminals have been largely
inaccessible to presynaptic patch-clamp recording, due to their small size. Using
improved patch-clamp techniques in brain slices, we recorded from mossy fiber
terminals in the CA3 region of the hippocampus, which have a diameter of 2-5 microm.
The major steps of improvement were the enhanced visibility provided by high-numerical
aperture objectives and infrared illumination, the development of vibratomes with
minimal vertical blade vibrations and the use of sucrose-based solutions for storage
and cutting. Based on these improvements, we describe a protocol that allows us
to routinely record from hippocampal mossy fiber boutons. Presynaptic recordings
can be obtained in slices from both rats and mice. Presynaptic recordings can
be also obtained in slices from transgenic mice in which terminals are labeled
with enhanced green fluorescent protein.
author:
- first_name: Josef
full_name: Bischofberger, Josef
last_name: Bischofberger
- first_name: Dominique
full_name: Engel, Dominique
last_name: Engel
- first_name: Liyi
full_name: Li, Liyi
last_name: Li
- first_name: Jörg
full_name: Geiger, Jörg R
last_name: Geiger
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Bischofberger J, Engel D, Li L, Geiger J, Jonas PM. Patch-clamp recording from
mossy fiber terminals in hippocampal slices. Nature Protocols. 2006;1(4):2075-2081.
doi:10.1038/nprot.2006.312
apa: Bischofberger, J., Engel, D., Li, L., Geiger, J., & Jonas, P. M. (2006).
Patch-clamp recording from mossy fiber terminals in hippocampal slices. Nature
Protocols. Nature Publishing Group. https://doi.org/10.1038/nprot.2006.312
chicago: Bischofberger, Josef, Dominique Engel, Liyi Li, Jörg Geiger, and Peter
M Jonas. “Patch-Clamp Recording from Mossy Fiber Terminals in Hippocampal Slices.”
Nature Protocols. Nature Publishing Group, 2006. https://doi.org/10.1038/nprot.2006.312 .
ieee: J. Bischofberger, D. Engel, L. Li, J. Geiger, and P. M. Jonas, “Patch-clamp
recording from mossy fiber terminals in hippocampal slices,” Nature Protocols,
vol. 1, no. 4. Nature Publishing Group, pp. 2075–81, 2006.
ista: Bischofberger J, Engel D, Li L, Geiger J, Jonas PM. 2006. Patch-clamp recording
from mossy fiber terminals in hippocampal slices. Nature Protocols. 1(4), 2075–81.
mla: Bischofberger, Josef, et al. “Patch-Clamp Recording from Mossy Fiber Terminals
in Hippocampal Slices.” Nature Protocols, vol. 1, no. 4, Nature Publishing
Group, 2006, pp. 2075–81, doi:10.1038/nprot.2006.312 .
short: J. Bischofberger, D. Engel, L. Li, J. Geiger, P.M. Jonas, Nature Protocols
1 (2006) 2075–81.
date_created: 2018-12-11T12:05:20Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:25Z
day: '01'
doi: '10.1038/nprot.2006.312 '
extern: 1
intvolume: ' 1'
issue: '4'
month: '01'
page: 2075 - 81
publication: Nature Protocols
publication_status: published
publisher: Nature Publishing Group
publist_id: '2392'
quality_controlled: 0
status: public
title: Patch-clamp recording from mossy fiber terminals in hippocampal slices
type: journal_article
volume: 1
year: '2006'
...
---
_id: '3888'
abstract:
- lang: eng
text: A stochastic graph game is played by two players on a game graph with probabilistic
transitions. We consider stochastic graph games with omega-regular winning conditions
specified as Rabin or Streett objectives. These games are NP-complete and coNP-complete,
respectively. The value of the game for a player at a state s given an objective
Phi is the maximal probability with which the player can guarantee the satisfaction
of Phi from s. We present a strategy-improvement algorithm to compute values in
stochastic Rabin games, where an improvement step involves solving Markov decision
processes (MDPs) and nonstochastic Rabin games. The algorithm also computes values
for stochastic Streett games but does not directly yield an optimal strategy for
Streett objectives. We then show how to obtain an optimal strategy for Streett
objectives by solving certain nonstochastic Streett games.
acknowledgement: This research was supported in part by the NSF grants CCR-0225610
and CCR-0234690, and by the SNSF under the Indo-Swiss Joint Research Programme.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Chatterjee K, Henzinger TA. Strategy improvement for stochastic Rabin and
Streett games. In: Vol 4137. Schloss Dagstuhl - Leibniz-Zentrum für Informatik;
2006:375-389. doi:10.1007/11817949_25'
apa: 'Chatterjee, K., & Henzinger, T. A. (2006). Strategy improvement for stochastic
Rabin and Streett games (Vol. 4137, pp. 375–389). Presented at the CONCUR: Concurrency
Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/11817949_25'
chicago: Chatterjee, Krishnendu, and Thomas A Henzinger. “Strategy Improvement for
Stochastic Rabin and Streett Games,” 4137:375–89. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2006. https://doi.org/10.1007/11817949_25.
ieee: 'K. Chatterjee and T. A. Henzinger, “Strategy improvement for stochastic Rabin
and Streett games,” presented at the CONCUR: Concurrency Theory, 2006, vol. 4137,
pp. 375–389.'
ista: 'Chatterjee K, Henzinger TA. 2006. Strategy improvement for stochastic Rabin
and Streett games. CONCUR: Concurrency Theory, LNCS, vol. 4137, 375–389.'
mla: Chatterjee, Krishnendu, and Thomas A. Henzinger. Strategy Improvement for
Stochastic Rabin and Streett Games. Vol. 4137, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2006, pp. 375–89, doi:10.1007/11817949_25.
short: K. Chatterjee, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2006, pp. 375–389.
conference:
name: 'CONCUR: Concurrency Theory'
date_created: 2018-12-11T12:05:43Z
date_published: 2006-08-10T00:00:00Z
date_updated: 2021-01-12T07:52:58Z
day: '10'
doi: 10.1007/11817949_25
extern: 1
intvolume: ' 4137'
month: '08'
page: 375 - 389
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '2278'
quality_controlled: 0
status: public
title: Strategy improvement for stochastic Rabin and Streett games
type: conference
volume: 4137
year: '2006'
...
---
_id: '3889'
abstract:
- lang: eng
text: We study observation-based strategies for two-player turn-based games on graphs
with omega-regular objectives. An observation-based strategy relies on imperfect
information about the history of a play, namely, on the past sequence of observations.
Such games occur in the synthesis of a controller that does not see the private
state of the plant. Our main results are twofold. First, we give a fixed-point
algorithm for computing the set of states from which a player can win with a deterministic
observation-based strategy for any omega-regular objective. The fixed point is
computed in the lattice of antichains of state sets. This algorithm has the advantages
of being directed by the objective and of avoiding an explicit subset construction
on the game graph. Second, we give an algorithm for computing the set of states
from which a player can win with probability 1 with a randomized observation-based
strategy for a Buchi objective. This set is of interest because in the absence
of perfect information, randomized strategies are more powerful than deterministic
ones. We show that our algorithms are optimal by proving matching lower bounds.
acknowledgement: This research was supported in part by the NSF grants CCR-0225610
and CCR-0234690, by the SNSF under the Indo-Swiss Joint Research Programme, and
by the FRFC project “Centre Fédéré en Vérification” funded by the FNRS under grant
2.4530.02.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jean
full_name: Raskin, Jean-François
last_name: Raskin
citation:
ama: 'Chatterjee K, Doyen L, Henzinger TA, Raskin J. Algorithms for omega-regular
games with imperfect information. In: Vol 4207. Springer; 2006:287-302. doi:10.1007/11874683_19'
apa: 'Chatterjee, K., Doyen, L., Henzinger, T. A., & Raskin, J. (2006). Algorithms
for omega-regular games with imperfect information (Vol. 4207, pp. 287–302). Presented
at the CSL: Computer Science Logic, Springer. https://doi.org/10.1007/11874683_19'
chicago: Chatterjee, Krishnendu, Laurent Doyen, Thomas A Henzinger, and Jean Raskin.
“Algorithms for Omega-Regular Games with Imperfect Information,” 4207:287–302.
Springer, 2006. https://doi.org/10.1007/11874683_19.
ieee: 'K. Chatterjee, L. Doyen, T. A. Henzinger, and J. Raskin, “Algorithms for
omega-regular games with imperfect information,” presented at the CSL: Computer
Science Logic, 2006, vol. 4207, pp. 287–302.'
ista: 'Chatterjee K, Doyen L, Henzinger TA, Raskin J. 2006. Algorithms for omega-regular
games with imperfect information. CSL: Computer Science Logic, LNCS, vol. 4207,
287–302.'
mla: Chatterjee, Krishnendu, et al. Algorithms for Omega-Regular Games with Imperfect
Information. Vol. 4207, Springer, 2006, pp. 287–302, doi:10.1007/11874683_19.
short: K. Chatterjee, L. Doyen, T.A. Henzinger, J. Raskin, in:, Springer, 2006,
pp. 287–302.
conference:
name: 'CSL: Computer Science Logic'
date_created: 2018-12-11T12:05:43Z
date_published: 2006-11-13T00:00:00Z
date_updated: 2021-01-12T07:52:59Z
day: '13'
doi: 10.1007/11874683_19
extern: 1
intvolume: ' 4207'
month: '11'
page: 287 - 302
publication_status: published
publisher: Springer
publist_id: '2276'
quality_controlled: 0
status: public
title: Algorithms for omega-regular games with imperfect information
type: conference
volume: 4207
year: '2006'
...
---
_id: '3890'
abstract:
- lang: eng
text: We consider two-player infinite games played on graphs. The games are concurrent,
in that at each state the players choose their moves simultaneously and independently,
and stochastic, in that the moves determine a probability distribution for the
successor state. The value of a game is the maximal probability with which a player
can guarantee the satisfaction of her objective. We show that the values of concurrent
games with w-regular objectives expressed as parity conditions can be decided
in NP boolean AND coNP. This result substantially improves the best known previous
bound of 3EXPTIME. It also shows that the full class of concurrent parity games
is no harder than the special case of turn-based stochastic reachability games,
for which NP boolean AND coNP is the best known bound. While the previous, more
restricted NP boolean AND coNP results for graph games relied on the existence
of particularly simple (pure memoryless) optimal strategies, in concurrent games
with parity objectives optimal strategies may not exist, and epsilon-optimal strategies
(which achieve the value of the game within a parameter epsilon > 0) require
in general both randomization and infinite memory. Hence our proof must rely on
a more detailed analysis of strategies and, in addition to the main result, yields
two results that are interesting on their own. First, we show that there exist
epsilon-optimal strategies that in the limit coincide with memoryless strategies;
this parallels the celebrated result of Mertens-Neyman for concurrent games with
limit-average objectives. Second, we complete the characterization of the memory
requirements for epsilon-optimal strategies for concurrent games with parity conditions,
by showing that memoryless strategies suffice for epsilon-optimality for coBachi
conditions.
acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327
and the NSF ITR grant CCR-0225610.
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Luca
full_name: de Alfaro, Luca
last_name: De Alfaro
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Chatterjee K, De Alfaro L, Henzinger TA. The complexity of quantitative concurrent
parity games. In: SIAM; 2006:678-687. doi:10.1145/1109557.1109631'
apa: 'Chatterjee, K., De Alfaro, L., & Henzinger, T. A. (2006). The complexity
of quantitative concurrent parity games (pp. 678–687). Presented at the SODA:
Symposium on Discrete Algorithms, SIAM. https://doi.org/10.1145/1109557.1109631'
chicago: Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “The Complexity
of Quantitative Concurrent Parity Games,” 678–87. SIAM, 2006. https://doi.org/10.1145/1109557.1109631.
ieee: 'K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “The complexity of quantitative
concurrent parity games,” presented at the SODA: Symposium on Discrete Algorithms,
2006, pp. 678–687.'
ista: 'Chatterjee K, De Alfaro L, Henzinger TA. 2006. The complexity of quantitative
concurrent parity games. SODA: Symposium on Discrete Algorithms, 678–687.'
mla: Chatterjee, Krishnendu, et al. The Complexity of Quantitative Concurrent
Parity Games. SIAM, 2006, pp. 678–87, doi:10.1145/1109557.1109631.
short: K. Chatterjee, L. De Alfaro, T.A. Henzinger, in:, SIAM, 2006, pp. 678–687.
conference:
name: 'SODA: Symposium on Discrete Algorithms'
date_created: 2018-12-11T12:05:43Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:59Z
day: '01'
doi: 10.1145/1109557.1109631
extern: 1
month: '01'
page: 678 - 687
publication_status: published
publisher: SIAM
publist_id: '2273'
quality_controlled: 0
status: public
title: The complexity of quantitative concurrent parity games
type: conference
year: '2006'
...
---
_id: '3891'
abstract:
- lang: eng
text: 'We study infinite stochastic games played by two-players over a finite state
space, with objectives specified by sets of infinite traces. The games are concurrent
(players make moves simultaneously and independently), stochastic (the next state
is determined by a probability distribution that depends on the current state
and chosen moves of the players) and infinite (proceeds for infinite number of
rounds). The analysis of concurrent stochastic games can be classified into: quantitative
analysis, analyzing the optimum value of the game; and qualitative analysis, analyzing
the set of states with optimum value 1. We consider concurrent games with tail
objectives, i.e., objectives that are independent of the finite-prefix of traces,
and show that the class of tail objectives are strictly richer than the omega-regular
objectives. We develop new proof techniques to extend several properties of concurrent
games with omega-regular objectives to concurrent games with tail objectives.
We prove the positive limit-one property for tail objectives, that states for
all concurrent games if the optimum value for a player is positive for a tail
objective Phi at some state, then there is a state where the optimum value is
1 for Phi, for the player. We also show that the optimum values of zero-sum (strictly
conflicting objectives) games with tail objectives can be related to equilibrium
values of nonzero-sum (not strictly conflicting objectives) games with simpler
reachability objectives. A consequence of our analysis presents a polynomial time
reduction of the quantitative analysis of tail objectives to the qualitative analysis
for the sub-class of one-player stochastic games (Markov decision processes).'
alternative_title:
- 'LNCS '
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Chatterjee K. Concurrent games with tail objectives. In: Vol 4207. Springer;
2006:256-270. doi:10.1007/11874683_17'
apa: 'Chatterjee, K. (2006). Concurrent games with tail objectives (Vol. 4207, pp.
256–270). Presented at the CSL: Computer Science Logic, Springer. https://doi.org/10.1007/11874683_17'
chicago: Chatterjee, Krishnendu. “Concurrent Games with Tail Objectives,” 4207:256–70.
Springer, 2006. https://doi.org/10.1007/11874683_17.
ieee: 'K. Chatterjee, “Concurrent games with tail objectives,” presented at the
CSL: Computer Science Logic, 2006, vol. 4207, pp. 256–270.'
ista: 'Chatterjee K. 2006. Concurrent games with tail objectives. CSL: Computer
Science Logic, LNCS , vol. 4207, 256–270.'
mla: Chatterjee, Krishnendu. Concurrent Games with Tail Objectives. Vol.
4207, Springer, 2006, pp. 256–70, doi:10.1007/11874683_17.
short: K. Chatterjee, in:, Springer, 2006, pp. 256–270.
conference:
name: 'CSL: Computer Science Logic'
date_created: 2018-12-11T12:05:44Z
date_published: 2006-09-28T00:00:00Z
date_updated: 2021-01-12T07:53:00Z
day: '28'
doi: 10.1007/11874683_17
extern: 1
intvolume: ' 4207'
month: '09'
page: 256 - 270
publication_status: published
publisher: Springer
publist_id: '2272'
quality_controlled: 0
status: public
title: Concurrent games with tail objectives
type: conference
volume: 4207
year: '2006'
...
---
_id: '3908'
abstract:
- lang: eng
text: 'It is commonly believed that both the average length and the frequency of
microsatellites correlate with genome size. We have estimated the frequency and
the average length for 69 perfect dinucleotide microsatellites in an insect with
an exceptionally large genome: Chorthippus biguttulus (Orthoptera, Acrididae).
Dinucleotide microsatellites are not more frequent in C. biguttulus, but repeat
arrays are 1.4 to 2 times longer than in other insect species. The average repeat
number in C. biguttulus lies in the range of higher vertebrates. Natural populations
are highly variable. At least 30 alleles per locus were found and the expected
heterozygosity is above 0.95 at all three loci studied. In contrast, the observed
heterozygosity is much lower (≤0.51), which could be caused by long null alleles.'
author:
- first_name: Jana
full_name: Ustinova, Jana
last_name: Ustinova
- first_name: Roland
full_name: Achmann, Roland
last_name: Achmann
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Frieder
full_name: Mayer, Frieder
last_name: Mayer
citation:
ama: 'Ustinova J, Achmann R, Cremer S, Mayer F. Long repeats in a huge gemome: microsatellite
loci in the grasshopper Chorthippus biguttulus. Journal of Molecular Evolution.
2006;62(2):158-167. doi:10.1007/s00239-005-0022-6'
apa: 'Ustinova, J., Achmann, R., Cremer, S., & Mayer, F. (2006). Long repeats
in a huge gemome: microsatellite loci in the grasshopper Chorthippus biguttulus.
Journal of Molecular Evolution. Springer. https://doi.org/10.1007/s00239-005-0022-6'
chicago: 'Ustinova, Jana, Roland Achmann, Sylvia Cremer, and Frieder Mayer. “Long
Repeats in a Huge Gemome: Microsatellite Loci in the Grasshopper Chorthippus Biguttulus.”
Journal of Molecular Evolution. Springer, 2006. https://doi.org/10.1007/s00239-005-0022-6.'
ieee: 'J. Ustinova, R. Achmann, S. Cremer, and F. Mayer, “Long repeats in a huge
gemome: microsatellite loci in the grasshopper Chorthippus biguttulus,” Journal
of Molecular Evolution, vol. 62, no. 2. Springer, pp. 158–167, 2006.'
ista: 'Ustinova J, Achmann R, Cremer S, Mayer F. 2006. Long repeats in a huge gemome:
microsatellite loci in the grasshopper Chorthippus biguttulus. Journal of Molecular
Evolution. 62(2), 158–167.'
mla: 'Ustinova, Jana, et al. “Long Repeats in a Huge Gemome: Microsatellite Loci
in the Grasshopper Chorthippus Biguttulus.” Journal of Molecular Evolution,
vol. 62, no. 2, Springer, 2006, pp. 158–67, doi:10.1007/s00239-005-0022-6.'
short: J. Ustinova, R. Achmann, S. Cremer, F. Mayer, Journal of Molecular Evolution
62 (2006) 158–167.
date_created: 2018-12-11T12:05:49Z
date_published: 2006-02-01T00:00:00Z
date_updated: 2021-01-12T07:53:07Z
day: '01'
doi: 10.1007/s00239-005-0022-6
extern: '1'
intvolume: ' 62'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 158 - 167
publication: Journal of Molecular Evolution
publication_status: published
publisher: Springer
publist_id: '2242'
status: public
title: 'Long repeats in a huge gemome: microsatellite loci in the grasshopper Chorthippus
biguttulus'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 62
year: '2006'
...
---
_id: '3912'
abstract:
- lang: eng
text: Invasive species often dramatically change native species communities by directly
and indirectly out-competing native species. We studied the direct interference
abilities of the invasive garden ant, Lasius neglectus VAN LOON, BOOMSMA &
ANDRÁSFALVY, 1990, by performing one-to-one aggression tests of L. neglectus workers
towards three native Lasius ant species that occur at the edge of a L. neglectus
supercolony in Seva, Spain. Our results show that L. neglectus is highly aggressive
against all three native Lasius species tested (L. grandis FOREL, 1909, L. emarginatus
(OLIVIER, 1792), and L. cinereus SEIFERT, 1992), expressed as a higher attack
rate of L. neglectus and behavioural dominance throughout the aggressive encounters.
Attacks of L. neglectus were performed fastest and most frequent against L. grandis,
and also the highest antennation frequencies were observed in encounters between
these two species. This could be due to the largest difference in body size, or
due to a greater overlap in ecological niche between L. neglectus and L. grandis
compared to the other two native species. There was only weak support for L. neglectus
workers from the periphery of the supercolony to be more aggressive relative to
workers from the centre, even though the former encounter native ant species on
a daily basis at the edge of the supercolony.
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Suzanne
full_name: Lommen, Suzanne
last_name: Lommen
- first_name: Klaus
full_name: Petersen, Klaus
last_name: Petersen
- first_name: Jes
full_name: Pedersen, Jes
last_name: Pedersen
citation:
ama: 'Cremer S, Ugelvig LV, Lommen S, Petersen K, Pedersen J. Attack of the invasive
garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae)
against native Lasius species in Spain. Myrmecological News. 2006;9:13-19.'
apa: 'Cremer, S., Ugelvig, L. V., Lommen, S., Petersen, K., & Pedersen, J. (2006).
Attack of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera:
Formicidae) against native Lasius species in Spain. Myrmecological News.
Österreichische Gesellschaft für Entomofaunistik.'
chicago: 'Cremer, Sylvia, Line V Ugelvig, Suzanne Lommen, Klaus Petersen, and Jes
Pedersen. “Attack of the Invasive Garden Ant: Aggression Behaviour of Lasius Neglectus
(Hymenoptera: Formicidae) against Native Lasius Species in Spain.” Myrmecological
News. Österreichische Gesellschaft für Entomofaunistik, 2006.'
ieee: 'S. Cremer, L. V. Ugelvig, S. Lommen, K. Petersen, and J. Pedersen, “Attack
of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera:
Formicidae) against native Lasius species in Spain,” Myrmecological News,
vol. 9. Österreichische Gesellschaft für Entomofaunistik, pp. 13–19, 2006.'
ista: 'Cremer S, Ugelvig LV, Lommen S, Petersen K, Pedersen J. 2006. Attack of the
invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae)
against native Lasius species in Spain. Myrmecological News. 9, 13–19.'
mla: 'Cremer, Sylvia, et al. “Attack of the Invasive Garden Ant: Aggression Behaviour
of Lasius Neglectus (Hymenoptera: Formicidae) against Native Lasius Species in
Spain.” Myrmecological News, vol. 9, Österreichische Gesellschaft für Entomofaunistik,
2006, pp. 13–19.'
short: S. Cremer, L.V. Ugelvig, S. Lommen, K. Petersen, J. Pedersen, Myrmecological
News 9 (2006) 13–19.
date_created: 2018-12-11T12:05:51Z
date_published: 2006-12-01T00:00:00Z
date_updated: 2021-01-12T07:53:09Z
day: '01'
extern: '1'
intvolume: ' 9'
language:
- iso: eng
month: '12'
oa_version: None
page: 13 - 19
publication: Myrmecological News
publication_status: published
publisher: Österreichische Gesellschaft für Entomofaunistik
publist_id: '2239'
status: public
title: 'Attack of the invasive garden ant: aggression behaviour of Lasius neglectus
(Hymenoptera: Formicidae) against native Lasius species in Spain'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2006'
...
---
_id: '3913'
abstract:
- lang: eng
text: Many invasive ant species, such as the Argentine ant or the red imported fire
ant, have huge colonies with thousands of mass-foraging workers, which quickly
monopolise resources and therefore represent a considerable threat to the native
ant fauna. Cardiocondyla obscurior and several other species of this myrmicine
genus have similarly been transferred throughout the tropics by human activities.
However, because their colonies are tiny and workers forage solitarily, Cardiocondyla
are often not recognized as successful invaders. Here, we document that the life
history of Cardiocondyla closely resembles that of the more conspicuous tramp
species, with polygyny, intranidal mating, budding, worker sterility, low genetic
variability, and possibly also unicoloniality. Given that introduced Cardiocondyla
may locally reach a very high population density, the effects of these stealthy
invaders on the native arthropod fauna should receive more attention.
author:
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Norbert
full_name: Eckl, Norbert
last_name: Eckl
- first_name: Alexandra
full_name: Schrempf, Alexandra
last_name: Schrempf
citation:
ama: 'Heinze J, Cremer S, Eckl N, Schrempf A. Stealthy invaders: the biology of
Cardiocondyla tramp ants. Insectes Sociaux. 2006;53(1):1-7. doi:10.1007/s00040-005-0847-4'
apa: 'Heinze, J., Cremer, S., Eckl, N., & Schrempf, A. (2006). Stealthy invaders:
the biology of Cardiocondyla tramp ants. Insectes Sociaux. Springer. https://doi.org/10.1007/s00040-005-0847-4'
chicago: 'Heinze, Jürgen, Sylvia Cremer, Norbert Eckl, and Alexandra Schrempf. “Stealthy
Invaders: The Biology of Cardiocondyla Tramp Ants.” Insectes Sociaux. Springer,
2006. https://doi.org/10.1007/s00040-005-0847-4.'
ieee: 'J. Heinze, S. Cremer, N. Eckl, and A. Schrempf, “Stealthy invaders: the biology
of Cardiocondyla tramp ants,” Insectes Sociaux, vol. 53, no. 1. Springer,
pp. 1–7, 2006.'
ista: 'Heinze J, Cremer S, Eckl N, Schrempf A. 2006. Stealthy invaders: the biology
of Cardiocondyla tramp ants. Insectes Sociaux. 53(1), 1–7.'
mla: 'Heinze, Jürgen, et al. “Stealthy Invaders: The Biology of Cardiocondyla Tramp
Ants.” Insectes Sociaux, vol. 53, no. 1, Springer, 2006, pp. 1–7, doi:10.1007/s00040-005-0847-4.'
short: J. Heinze, S. Cremer, N. Eckl, A. Schrempf, Insectes Sociaux 53 (2006) 1–7.
date_created: 2018-12-11T12:05:51Z
date_published: 2006-02-01T00:00:00Z
date_updated: 2021-01-12T07:53:09Z
day: '01'
doi: 10.1007/s00040-005-0847-4
extern: '1'
intvolume: ' 53'
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 1 - 7
publication: Insectes Sociaux
publication_status: published
publisher: Springer
publist_id: '2240'
status: public
title: 'Stealthy invaders: the biology of Cardiocondyla tramp ants'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 53
year: '2006'
...
---
_id: '3914'
abstract:
- lang: eng
text: We compare the performances of established means of character selection for
discriminant analysis in species distinction with a combination procedure for
finding the optimal character combination (minimum classification error, minimum
number of required characters), using morphometric data sets from the ant genera
Cardiocondyla, Lasius and Tetramorium. The established methods are empirical character
selection as well as forward selection, backward elimination and stepwise selection
of discriminant analysis. The combination procedure is clearly superior to the
established methods of character selection, and is widely applicable.
author:
- first_name: Karl
full_name: Moder, Karl
last_name: Moder
- first_name: Birgit
full_name: Schlick Steiner, Birgit
last_name: Schlick Steiner
- first_name: Florian
full_name: Steiner, Florian
last_name: Steiner
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Erhard
full_name: Christian, Erhard
last_name: Christian
- first_name: Bernhard
full_name: Seifert, Bernhard
last_name: Seifert
citation:
ama: 'Moder K, Schlick Steiner B, Steiner F, Cremer S, Christian E, Seifert B. Optimal
species distinction by discriminant analysis: comparing established methods of
character selection with a combination procedure using ant morphometrics as a
case study. Journal of Zoological Systematics and Evolutionary Research.
2006;45(1):82-87. doi:10.1111/j.1439-0469.2006.00372.x'
apa: 'Moder, K., Schlick Steiner, B., Steiner, F., Cremer, S., Christian, E., &
Seifert, B. (2006). Optimal species distinction by discriminant analysis: comparing
established methods of character selection with a combination procedure using
ant morphometrics as a case study. Journal of Zoological Systematics and Evolutionary
Research. Wiley-Blackwell. https://doi.org/10.1111/j.1439-0469.2006.00372.x'
chicago: 'Moder, Karl, Birgit Schlick Steiner, Florian Steiner, Sylvia Cremer, Erhard
Christian, and Bernhard Seifert. “Optimal Species Distinction by Discriminant
Analysis: Comparing Established Methods of Character Selection with a Combination
Procedure Using Ant Morphometrics as a Case Study.” Journal of Zoological Systematics
and Evolutionary Research. Wiley-Blackwell, 2006. https://doi.org/10.1111/j.1439-0469.2006.00372.x.'
ieee: 'K. Moder, B. Schlick Steiner, F. Steiner, S. Cremer, E. Christian, and B.
Seifert, “Optimal species distinction by discriminant analysis: comparing established
methods of character selection with a combination procedure using ant morphometrics
as a case study,” Journal of Zoological Systematics and Evolutionary Research,
vol. 45, no. 1. Wiley-Blackwell, pp. 82–87, 2006.'
ista: 'Moder K, Schlick Steiner B, Steiner F, Cremer S, Christian E, Seifert B.
2006. Optimal species distinction by discriminant analysis: comparing established
methods of character selection with a combination procedure using ant morphometrics
as a case study. Journal of Zoological Systematics and Evolutionary Research.
45(1), 82–87.'
mla: 'Moder, Karl, et al. “Optimal Species Distinction by Discriminant Analysis:
Comparing Established Methods of Character Selection with a Combination Procedure
Using Ant Morphometrics as a Case Study.” Journal of Zoological Systematics
and Evolutionary Research, vol. 45, no. 1, Wiley-Blackwell, 2006, pp. 82–87,
doi:10.1111/j.1439-0469.2006.00372.x.'
short: K. Moder, B. Schlick Steiner, F. Steiner, S. Cremer, E. Christian, B. Seifert,
Journal of Zoological Systematics and Evolutionary Research 45 (2006) 82–87.
date_created: 2018-12-11T12:05:52Z
date_published: 2006-08-29T00:00:00Z
date_updated: 2021-01-12T07:53:10Z
day: '29'
doi: 10.1111/j.1439-0469.2006.00372.x
extern: '1'
intvolume: ' 45'
issue: '1'
language:
- iso: eng
month: '08'
oa_version: None
page: 82 - 87
publication: Journal of Zoological Systematics and Evolutionary Research
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2241'
status: public
title: 'Optimal species distinction by discriminant analysis: comparing established
methods of character selection with a combination procedure using ant morphometrics
as a case study'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2006'
...
---
_id: '3932'
abstract:
- lang: eng
text: 'OBJECTIVES: The EGFR is expressed in malignant ovarian tumor tissue, and
tissue content of EGFR has been directly associated with poor prognosis in patients
with ovarian cancer. The uPA system plays a role in pericellular proteolysis,
cell migration, invasion, and is over-expressed in ovarian cancer. This study
explored the effects of EGF on uPAR expression in the ovarian cancer cell line
OVCAR-3. METHODS: We used OVCAR-3 cells and the following methods: cell migration
assay, time-lapse video microscopy, real-time PCR, assays for cellular binding
of 125I-uPA and cellular degradation of 125I-uPA:PAI-1 complex, biosynthetic labeling
using 35S-methionin, Western blot, Northern blot, and ELISAs for uPA, PAI-1, and
uPAR. RESULTS: EGF up-regulates both protein and mRNA not only for uPAR, but also
for the ligand uPA and its inhibitor PAI-1. Cell surface uPAR, in control as well
as EGF-stimulated cells, is present only in the intact, not the cleaved, form.
Ligand binding experiments showed an increase of endogenously occupied uPAR, whereas
non-occupied receptor sites were not increased. In addition, EGF treatment resulted
in decreased degradation of radiolabeled uPA:PAI-1 complex. This suggests decreased
internalization of uPAR, since the complex is internalized together with uPAR.
Like EGF, colchicine, which inhibits endocytosis, increased cell surface expression
of uPAR. In addition, we found an immediate increase of uPAR after exposing the
cells to EGF and this was accompanied by a transient increase of cell migration.
The increase of cell surface uPAR in response to EGF is accompanied by increased
release of the soluble form of uPAR (suPAR) to the medium as well as by increased
cell migration. Both uPAR and suPAR increased in cells treated with the endocytosis
inhibitor colchicine even though cell migration was inhibited, suggesting that
the mechanism of uPAR shedding is not related to cell migration. CONCLUSION: Increased
cell surface uPAR in response to EGF stimulation results from mobilization of
uPAR from detergent-resistant domains, increased expression of uPAR mRNA, and
decreased internalization and degradation of uPAR. Both the anti-uPAR antibody
R3, which inhibits binding of uPA, and the EGFR phosphorylation inhibitor Iressa
inhibited cell migration in response to uPA as well as to EGF, suggesting that
EGFR and uPAR are engaged in the same multiprotein assembly on the cell surface.'
author:
- first_name: Emir
full_name: Henic, Emir
last_name: Henic
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Stefan
full_name: Hansson, Stefan
last_name: Hansson
- first_name: Gunilla
full_name: Høyer-Hansen, Gunilla
last_name: Høyer Hansen
- first_name: Bertil
full_name: Casslén, Bertil
last_name: Casslén
citation:
ama: Henic E, Sixt MK, Hansson S, Høyer Hansen G, Casslén B. EGF-stimulated migration
in ovarian cancer cells is associated with decreased internalization, increased
surface expression, and increased shedding of the urokinase plasminogen activator
receptor. Gynecologic Oncology. 2006;101(1):28-39. doi:10.1016/j.ygyno.2005.09.038
apa: Henic, E., Sixt, M. K., Hansson, S., Høyer Hansen, G., & Casslén, B. (2006).
EGF-stimulated migration in ovarian cancer cells is associated with decreased
internalization, increased surface expression, and increased shedding of the urokinase
plasminogen activator receptor. Gynecologic Oncology. Elsevier. https://doi.org/10.1016/j.ygyno.2005.09.038
chicago: Henic, Emir, Michael K Sixt, Stefan Hansson, Gunilla Høyer Hansen, and
Bertil Casslén. “EGF-Stimulated Migration in Ovarian Cancer Cells Is Associated
with Decreased Internalization, Increased Surface Expression, and Increased Shedding
of the Urokinase Plasminogen Activator Receptor.” Gynecologic Oncology.
Elsevier, 2006. https://doi.org/10.1016/j.ygyno.2005.09.038.
ieee: E. Henic, M. K. Sixt, S. Hansson, G. Høyer Hansen, and B. Casslén, “EGF-stimulated
migration in ovarian cancer cells is associated with decreased internalization,
increased surface expression, and increased shedding of the urokinase plasminogen
activator receptor,” Gynecologic Oncology, vol. 101, no. 1. Elsevier, pp.
28–39, 2006.
ista: Henic E, Sixt MK, Hansson S, Høyer Hansen G, Casslén B. 2006. EGF-stimulated
migration in ovarian cancer cells is associated with decreased internalization,
increased surface expression, and increased shedding of the urokinase plasminogen
activator receptor. Gynecologic Oncology. 101(1), 28–39.
mla: Henic, Emir, et al. “EGF-Stimulated Migration in Ovarian Cancer Cells Is Associated
with Decreased Internalization, Increased Surface Expression, and Increased Shedding
of the Urokinase Plasminogen Activator Receptor.” Gynecologic Oncology,
vol. 101, no. 1, Elsevier, 2006, pp. 28–39, doi:10.1016/j.ygyno.2005.09.038.
short: E. Henic, M.K. Sixt, S. Hansson, G. Høyer Hansen, B. Casslén, Gynecologic
Oncology 101 (2006) 28–39.
date_created: 2018-12-11T12:05:57Z
date_published: 2006-04-01T00:00:00Z
date_updated: 2021-01-12T07:53:17Z
day: '01'
doi: 10.1016/j.ygyno.2005.09.038
extern: 1
intvolume: ' 101'
issue: '1'
month: '04'
page: 28 - 39
publication: Gynecologic Oncology
publication_status: published
publisher: Elsevier
publist_id: '2194'
quality_controlled: 0
status: public
title: EGF-stimulated migration in ovarian cancer cells is associated with decreased
internalization, increased surface expression, and increased shedding of the urokinase
plasminogen activator receptor
type: journal_article
volume: 101
year: '2006'
...
---
_id: '3934'
abstract:
- lang: eng
text: T cells develop in the thymus in a highly specialized cellular and extracellular
microenvironment. The basement membrane molecule, laminin-5 (LN-5), is predominantly
found in the medulla of the human thymic lobules. Using high-resolution light
microscopy, we show here that LN-5 is localized in a bi-membranous conduit-like
structure, together with other typical basement membrane components including
collagen type IV, nidogen and perlecan. Other interstitial matrix components,
such as fibrillin-1 or -2, tenascin-C or fibrillar collagen types, were also associated
with these structures. Three-dimensional (3D) confocal microscopy suggested a
tubular structure, whereas immunoelectron and transmission electron microscopy
showed that the core of these tubes contained fibrillar collagens enwrapped by
the LN-5-containing membrane. These medullary conduits are surrounded by thymic
epithelial cells, which in vitro were found to bind LN-5, but also fibrillin and
tenascin-C. Dendritic cells were also detected in close vicinity to the conduits.
Both of these stromal cell types express major histocompatibility complex (MHC)
class II molecules capable of antigen presentation. The conduits are connected
to blood vessels but, with an average diameter of 2 mum, they are too small to
transport cells. However, evidence is provided that smaller molecules such as
a 10 kDa dextran, but not large molecules (>500 kDa), can be transported in
the conduits. These results clearly demonstrate that a conduit system, which is
also known from secondary lymphatic organs such as lymph nodes and spleen, is
present in the medulla of the human thymus, and that it might serve to transport
small blood-borne molecules or chemokines to defined locations within the medulla.
author:
- first_name: Mihaela
full_name: Drumea-Mirancea, Mihaela
last_name: Drumea Mirancea
- first_name: Johannes
full_name: Wessels, Johannes T
last_name: Wessels
- first_name: Claudia
full_name: Müller, Claudia A
last_name: Müller
- first_name: Mike
full_name: Essl, Mike
last_name: Essl
- first_name: Johannes
full_name: Eble, Johannes A
last_name: Eble
- first_name: Eva
full_name: Tolosa, Eva
last_name: Tolosa
- first_name: Manuel
full_name: Koch, Manuel
last_name: Koch
- first_name: Dieter
full_name: Reinhardt, Dieter P
last_name: Reinhardt
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Lydia
full_name: Sorokin, Lydia
last_name: Sorokin
- first_name: York
full_name: Stierhof, York-Dieter
last_name: Stierhof
- first_name: Heinz
full_name: Schwarz, Heinz
last_name: Schwarz
- first_name: Gerd
full_name: Klein, Gerd
last_name: Klein
citation:
ama: 'Drumea Mirancea M, Wessels J, Müller C, et al. Characterization of a conduit
system containing laminin-5 in the human thymus: a potential transport system
for small molecules. Journal of Cell Science. 2006;119(Pt 7):1396-1405.
doi:10.1242/jcs.02840'
apa: 'Drumea Mirancea, M., Wessels, J., Müller, C., Essl, M., Eble, J., Tolosa,
E., … Klein, G. (2006). Characterization of a conduit system containing laminin-5
in the human thymus: a potential transport system for small molecules. Journal
of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.02840'
chicago: 'Drumea Mirancea, Mihaela, Johannes Wessels, Claudia Müller, Mike Essl,
Johannes Eble, Eva Tolosa, Manuel Koch, et al. “Characterization of a Conduit
System Containing Laminin-5 in the Human Thymus: A Potential Transport System
for Small Molecules.” Journal of Cell Science. Company of Biologists, 2006.
https://doi.org/10.1242/jcs.02840.'
ieee: 'M. Drumea Mirancea et al., “Characterization of a conduit system containing
laminin-5 in the human thymus: a potential transport system for small molecules,”
Journal of Cell Science, vol. 119, no. Pt 7. Company of Biologists, pp.
1396–1405, 2006.'
ista: 'Drumea Mirancea M, Wessels J, Müller C, Essl M, Eble J, Tolosa E, Koch M,
Reinhardt D, Sixt MK, Sorokin L, Stierhof Y, Schwarz H, Klein G. 2006. Characterization
of a conduit system containing laminin-5 in the human thymus: a potential transport
system for small molecules. Journal of Cell Science. 119(Pt 7), 1396–1405.'
mla: 'Drumea Mirancea, Mihaela, et al. “Characterization of a Conduit System Containing
Laminin-5 in the Human Thymus: A Potential Transport System for Small Molecules.”
Journal of Cell Science, vol. 119, no. Pt 7, Company of Biologists, 2006,
pp. 1396–405, doi:10.1242/jcs.02840.'
short: M. Drumea Mirancea, J. Wessels, C. Müller, M. Essl, J. Eble, E. Tolosa, M.
Koch, D. Reinhardt, M.K. Sixt, L. Sorokin, Y. Stierhof, H. Schwarz, G. Klein,
Journal of Cell Science 119 (2006) 1396–1405.
date_created: 2018-12-11T12:05:58Z
date_published: 2006-04-01T00:00:00Z
date_updated: 2021-01-12T07:53:18Z
day: '01'
doi: 10.1242/jcs.02840
extern: 1
intvolume: ' 119'
issue: Pt 7
month: '04'
page: 1396 - 1405
publication: Journal of Cell Science
publication_status: published
publisher: Company of Biologists
publist_id: '2192'
quality_controlled: 0
status: public
title: 'Characterization of a conduit system containing laminin-5 in the human thymus:
a potential transport system for small molecules'
type: journal_article
volume: 119
year: '2006'
...
---
_id: '3935'
abstract:
- lang: eng
text: Integrins regulate cell behavior through the assembly of multiprotein complexes
at the site of cell adhesion. Parvins are components of such a multiprotein complex.
They consist of three members (alpha-, beta-, and gamma-parvin), form a functional
complex with integrin-linked kinase (ILK) and PINCH, and link integrins to the
actin cytoskeleton. Whereas alpha- and beta-parvins are widely expressed, gamma-parvin
has been reported to be expressed in hematopoietic organs. In the present study,
we report the expression pattern of the parvins in hematopoietic cells and the
phenotypic analysis of gamma-parvin-deficient mice. Whereas alpha-parvin is not
expressed in hematopoietic cells, beta-parvin is only found in myeloid cells and
gamma-parvin is present in both cells of the myeloid and lymphoid lineages, where
it binds ILK. Surprisingly, loss of gamma-parvin expression had no effect on blood
cell differentiation, proliferation, and survival and no consequence for the T-cell-dependent
antibody response and lymphocyte and dendritic cell migration. These data indicate
that despite the high expression of gamma-parvin in hematopoietic cells it must
play a more subtle role for blood cell homeostasis.
author:
- first_name: Haiyan
full_name: Chu, Haiyan
last_name: Chu
- first_name: Ingo
full_name: Thievessen, Ingo
last_name: Thievessen
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Tim
full_name: Lämmermann, Tim
last_name: Lämmermann
- first_name: Ari
full_name: Waisman, Ari
last_name: Waisman
- first_name: Attila
full_name: Braun, Attila
last_name: Braun
- first_name: Angelika
full_name: Noegel, Angelika A
last_name: Noegel
- first_name: Reinhard
full_name: Fässler, Reinhard
last_name: Fässler
citation:
ama: Chu H, Thievessen I, Sixt MK, et al. γ-Parvin is dispensable for hematopoiesis,
leukocyte trafficking, and T-cell-dependent antibody response. Molecular and
Cellular Biology. 2006;26(5):1817-1825. doi:10.1128/MCB.26.5.1817-1825.2006
apa: Chu, H., Thievessen, I., Sixt, M. K., Lämmermann, T., Waisman, A., Braun, A.,
… Fässler, R. (2006). γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking,
and T-cell-dependent antibody response. Molecular and Cellular Biology.
American Society for Microbiology. https://doi.org/10.1128/MCB.26.5.1817-1825.2006
chicago: Chu, Haiyan, Ingo Thievessen, Michael K Sixt, Tim Lämmermann, Ari Waisman,
Attila Braun, Angelika Noegel, and Reinhard Fässler. “γ-Parvin Is Dispensable
for Hematopoiesis, Leukocyte Trafficking, and T-Cell-Dependent Antibody Response.”
Molecular and Cellular Biology. American Society for Microbiology, 2006.
https://doi.org/10.1128/MCB.26.5.1817-1825.2006.
ieee: H. Chu et al., “γ-Parvin is dispensable for hematopoiesis, leukocyte
trafficking, and T-cell-dependent antibody response,” Molecular and Cellular
Biology, vol. 26, no. 5. American Society for Microbiology, pp. 1817–1825,
2006.
ista: Chu H, Thievessen I, Sixt MK, Lämmermann T, Waisman A, Braun A, Noegel A,
Fässler R. 2006. γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking,
and T-cell-dependent antibody response. Molecular and Cellular Biology. 26(5),
1817–1825.
mla: Chu, Haiyan, et al. “γ-Parvin Is Dispensable for Hematopoiesis, Leukocyte Trafficking,
and T-Cell-Dependent Antibody Response.” Molecular and Cellular Biology,
vol. 26, no. 5, American Society for Microbiology, 2006, pp. 1817–25, doi:10.1128/MCB.26.5.1817-1825.2006.
short: H. Chu, I. Thievessen, M.K. Sixt, T. Lämmermann, A. Waisman, A. Braun, A.
Noegel, R. Fässler, Molecular and Cellular Biology 26 (2006) 1817–1825.
date_created: 2018-12-11T12:05:58Z
date_published: 2006-03-01T00:00:00Z
date_updated: 2021-01-12T07:53:18Z
day: '01'
doi: 10.1128/MCB.26.5.1817-1825.2006
extern: 1
intvolume: ' 26'
issue: '5'
month: '03'
page: 1817 - 1825
publication: Molecular and Cellular Biology
publication_status: published
publisher: American Society for Microbiology
publist_id: '2193'
quality_controlled: 0
status: public
title: γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent
antibody response
type: journal_article
volume: 26
year: '2006'
...
---
_id: '3936'
abstract:
- lang: eng
text: At least eight of the twelve known members of the beta1 integrin family are
expressed on hematopoietic cells. Among these, the VCAM-1 receptor alpha4beta1
has received most attention as a main factor mediating firm adhesion to the endothelium
during blood cell extravasation. Therapeutic trials are ongoing into the use of
antibodies and small molecule inhibitors to target this interaction and hence
obtain anti-inflammatory effects. However, extravasation is only one possible
process that is mediated by beta1 integrins and there is evidence that they also
mediate leukocyte retention and positioning in the tissue, lymphocyte activation
and possibly migration within the interstitium. Genetic mouse models where integrins
are selectively deleted on blood cells have been used to investigate these functions
and further studies will be invaluable to critically evaluate therapeutic trials.
author:
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Martina
full_name: Bauer, Martina
last_name: Bauer
- first_name: Tim
full_name: Lämmermann, Tim
last_name: Lämmermann
- first_name: Reinhard
full_name: Fässler, Reinhard
last_name: Fässler
citation:
ama: 'Sixt MK, Bauer M, Lämmermann T, Fässler R. β1 integrins: zip codes and signaling
relay for blood cells. Current Opinion in Cell Biology. 2006;18(5):482-490.
doi:10.1016/j.ceb.2006.08.007'
apa: 'Sixt, M. K., Bauer, M., Lämmermann, T., & Fässler, R. (2006). β1 integrins:
zip codes and signaling relay for blood cells. Current Opinion in Cell Biology.
Elsevier. https://doi.org/10.1016/j.ceb.2006.08.007'
chicago: 'Sixt, Michael K, Martina Bauer, Tim Lämmermann, and Reinhard Fässler.
“Β1 Integrins: Zip Codes and Signaling Relay for Blood Cells.” Current Opinion
in Cell Biology. Elsevier, 2006. https://doi.org/10.1016/j.ceb.2006.08.007.'
ieee: 'M. K. Sixt, M. Bauer, T. Lämmermann, and R. Fässler, “β1 integrins: zip codes
and signaling relay for blood cells,” Current Opinion in Cell Biology,
vol. 18, no. 5. Elsevier, pp. 482–490, 2006.'
ista: 'Sixt MK, Bauer M, Lämmermann T, Fässler R. 2006. β1 integrins: zip codes
and signaling relay for blood cells. Current Opinion in Cell Biology. 18(5), 482–490.'
mla: 'Sixt, Michael K., et al. “Β1 Integrins: Zip Codes and Signaling Relay for
Blood Cells.” Current Opinion in Cell Biology, vol. 18, no. 5, Elsevier,
2006, pp. 482–90, doi:10.1016/j.ceb.2006.08.007.'
short: M.K. Sixt, M. Bauer, T. Lämmermann, R. Fässler, Current Opinion in Cell Biology
18 (2006) 482–490.
date_created: 2018-12-11T12:05:59Z
date_published: 2006-10-01T00:00:00Z
date_updated: 2021-01-12T07:53:19Z
day: '01'
doi: 10.1016/j.ceb.2006.08.007
extern: 1
intvolume: ' 18'
issue: '5'
month: '10'
page: 482 - 490
publication: Current Opinion in Cell Biology
publication_status: published
publisher: Elsevier
publist_id: '2191'
quality_controlled: 0
status: public
title: 'β1 integrins: zip codes and signaling relay for blood cells'
type: journal_article
volume: 18
year: '2006'
...
---
_id: '3978'
abstract:
- lang: eng
text: Evaluating the quality of experimentally determined protein structural models
is an essential step toward identifying potential errors and guiding further structural
refinement. Herein, we report the use of proton local density as a sensitive measure
to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256
high-resolution crystal structures with protons added and optimized, we show that
the local density of different proton types display distinct distributions. These
distributions can be characterized by statistical moments and are used to establish
local density Z-scores for evaluating both global and local packing for individual
protons. Analysis of 546 crystal structures at various resolutions shows that
the local density Z-scores increase as the structural resolution decreases and
correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733)
generated by all atom contact analysis. Local density Z-scores for NMR structures
exhibit a significantly wider range of values than for X-ray structures and demonstrate
a combination of potentially problematic inflation and compression. Water-refined
NMR structures show improved packing quality. Our analysis of a high-quality structural
ensemble of ubiquitin refined against order parameters shows proton density distributions
that correlate nearly perfectly with our standards derived from crystal structures,
further validating our approach. We present an automated analysis and visualization
tool for proton packing to evaluate the quality of NMR structures.
author:
- first_name: Yih
full_name: Ban, Yih-En Andrew
last_name: Ban
- first_name: Johannes
full_name: Rudolph, Johannes
last_name: Rudolph
- first_name: Pei
full_name: Zhou, Pei
last_name: Zhou
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Ban Y, Rudolph J, Zhou P, Edelsbrunner H. Evaluating the quality of NMR structures
by local density of protons. Proteins: Structure, Function and Bioinformatics.
2006;62(4):852-864. doi:10.1002/prot.20811'
apa: 'Ban, Y., Rudolph, J., Zhou, P., & Edelsbrunner, H. (2006). Evaluating
the quality of NMR structures by local density of protons. Proteins: Structure,
Function and Bioinformatics. Wiley-Blackwell. https://doi.org/10.1002/prot.20811'
chicago: 'Ban, Yih, Johannes Rudolph, Pei Zhou, and Herbert Edelsbrunner. “Evaluating
the Quality of NMR Structures by Local Density of Protons.” Proteins: Structure,
Function and Bioinformatics. Wiley-Blackwell, 2006. https://doi.org/10.1002/prot.20811.'
ieee: 'Y. Ban, J. Rudolph, P. Zhou, and H. Edelsbrunner, “Evaluating the quality
of NMR structures by local density of protons,” Proteins: Structure, Function
and Bioinformatics, vol. 62, no. 4. Wiley-Blackwell, pp. 852–864, 2006.'
ista: 'Ban Y, Rudolph J, Zhou P, Edelsbrunner H. 2006. Evaluating the quality of
NMR structures by local density of protons. Proteins: Structure, Function and
Bioinformatics. 62(4), 852–864.'
mla: 'Ban, Yih, et al. “Evaluating the Quality of NMR Structures by Local Density
of Protons.” Proteins: Structure, Function and Bioinformatics, vol. 62,
no. 4, Wiley-Blackwell, 2006, pp. 852–64, doi:10.1002/prot.20811.'
short: 'Y. Ban, J. Rudolph, P. Zhou, H. Edelsbrunner, Proteins: Structure, Function
and Bioinformatics 62 (2006) 852–864.'
date_created: 2018-12-11T12:06:14Z
date_published: 2006-03-01T00:00:00Z
date_updated: 2021-01-12T07:53:36Z
day: '01'
doi: 10.1002/prot.20811
extern: 1
intvolume: ' 62'
issue: '4'
month: '03'
page: 852 - 864
publication: 'Proteins: Structure, Function and Bioinformatics'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2146'
quality_controlled: 0
status: public
title: Evaluating the quality of NMR structures by local density of protons
type: journal_article
volume: 62
year: '2006'
...
---
_id: '3979'
abstract:
- lang: eng
text: Protein-protein interactions, which form the basis for most cellular processes,
result in the formation of protein interfaces. Believing that the local shape
of proteins is crucial, we take a geometric approach and present a definition
of an interface surface formed by two or more proteins as a subset of their Voronoi
diagram. The definition deals with the difficult and important problem of specifying
interface boundaries by invoking methods used in the alpha shape representation
of molecules, the discrete flow on Delaunay simplices to define pockets and reconstruct
surfaces, and the assessment of the importance of topological features. We present
an algorithm to construct the surface and define a hierarchy that distinguishes
core and peripheral regions. This hierarchy is shown to have correlation with
hot-spots in protein-protein interactions. Finally, we study the geometric and
topological properties of interface surfaces and show their high degree of contortion.
author:
- first_name: Yih
full_name: Ban, Yih-En Andrew
last_name: Ban
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Johannes
full_name: Rudolph, Johannes
last_name: Rudolph
citation:
ama: Ban Y, Edelsbrunner H, Rudolph J. Interface surfaces for protein-protein complexes.
Journal of the ACM. 2006;53(3):361-378. doi:10.1145/1147954.1147957
apa: Ban, Y., Edelsbrunner, H., & Rudolph, J. (2006). Interface surfaces for
protein-protein complexes. Journal of the ACM. ACM. https://doi.org/10.1145/1147954.1147957
chicago: Ban, Yih, Herbert Edelsbrunner, and Johannes Rudolph. “Interface Surfaces
for Protein-Protein Complexes.” Journal of the ACM. ACM, 2006. https://doi.org/10.1145/1147954.1147957.
ieee: Y. Ban, H. Edelsbrunner, and J. Rudolph, “Interface surfaces for protein-protein
complexes,” Journal of the ACM, vol. 53, no. 3. ACM, pp. 361–378, 2006.
ista: Ban Y, Edelsbrunner H, Rudolph J. 2006. Interface surfaces for protein-protein
complexes. Journal of the ACM. 53(3), 361–378.
mla: Ban, Yih, et al. “Interface Surfaces for Protein-Protein Complexes.” Journal
of the ACM, vol. 53, no. 3, ACM, 2006, pp. 361–78, doi:10.1145/1147954.1147957.
short: Y. Ban, H. Edelsbrunner, J. Rudolph, Journal of the ACM 53 (2006) 361–378.
date_created: 2018-12-11T12:06:14Z
date_published: 2006-05-01T00:00:00Z
date_updated: 2021-01-12T07:53:37Z
day: '01'
doi: 10.1145/1147954.1147957
extern: 1
intvolume: ' 53'
issue: '3'
month: '05'
page: 361 - 378
publication: Journal of the ACM
publication_status: published
publisher: ACM
publist_id: '2147'
quality_controlled: 0
status: public
title: Interface surfaces for protein-protein complexes
type: journal_article
volume: 53
year: '2006'
...
---
_id: '3980'
abstract:
- lang: eng
text: Given a smoothly embedded 2-manifold in R-3, we define the elevation of a
point as the height difference to a canonically defined second point on the same
manifold. Our definition is invariant under rigid motions and can be used to define
features such as lines of discontinuous or continuous but non-smooth elevation.
We give an algorithm for finding points of locally maximum elevation, which we
suggest mark cavities and protrusions and are useful in matching shapes as for
example in protein docking.
author:
- first_name: Pankaj
full_name: Agarwal, Pankaj K
last_name: Agarwal
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: John
full_name: Harer, John
last_name: Harer
- first_name: Yusu
full_name: Wang, Yusu
last_name: Wang
citation:
ama: Agarwal P, Edelsbrunner H, Harer J, Wang Y. Extreme elevation on a 2-manifold.
Discrete & Computational Geometry. 2006;36(4):553-572. doi:10.1007/s00454-006-1265-8
apa: Agarwal, P., Edelsbrunner, H., Harer, J., & Wang, Y. (2006). Extreme elevation
on a 2-manifold. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-006-1265-8
chicago: Agarwal, Pankaj, Herbert Edelsbrunner, John Harer, and Yusu Wang. “Extreme
Elevation on a 2-Manifold.” Discrete & Computational Geometry. Springer,
2006. https://doi.org/10.1007/s00454-006-1265-8.
ieee: P. Agarwal, H. Edelsbrunner, J. Harer, and Y. Wang, “Extreme elevation on
a 2-manifold,” Discrete & Computational Geometry, vol. 36, no. 4. Springer,
pp. 553–572, 2006.
ista: Agarwal P, Edelsbrunner H, Harer J, Wang Y. 2006. Extreme elevation on a 2-manifold.
Discrete & Computational Geometry. 36(4), 553–572.
mla: Agarwal, Pankaj, et al. “Extreme Elevation on a 2-Manifold.” Discrete &
Computational Geometry, vol. 36, no. 4, Springer, 2006, pp. 553–72, doi:10.1007/s00454-006-1265-8.
short: P. Agarwal, H. Edelsbrunner, J. Harer, Y. Wang, Discrete & Computational
Geometry 36 (2006) 553–572.
date_created: 2018-12-11T12:06:15Z
date_published: 2006-12-01T00:00:00Z
date_updated: 2021-01-12T07:53:38Z
day: '01'
doi: 10.1007/s00454-006-1265-8
extern: 1
intvolume: ' 36'
issue: '4'
month: '12'
page: 553 - 572
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '2148'
quality_controlled: 0
status: public
title: Extreme elevation on a 2-manifold
type: journal_article
volume: 36
year: '2006'
...