---
_id: '3178'
abstract:
- lang: eng
text: Minimum cut/maximum flow algorithms on graphs have emerged as an increasingly
useful tool for exactor approximate energy minimization in low-level vision. The
combinatorial optimization literature provides many min-cut/max-flow algorithms
with different polynomial time complexity. Their practical efficiency, however,
has to date been studied mainly outside the scope of computer vision. The goal
of this paper is to provide an experimental comparison of the efficiency of min-cut/max
flow algorithms for applications in vision. We compare the running times of several
standard algorithms, as well as a new algorithm that we have recently developed.
The algorithms we study include both Goldberg-Tarjan style "push -relabel"
methods and algorithms based on Ford-Fulkerson style "augmenting paths."
We benchmark these algorithms on a number of typical graphs in the contexts of
image restoration, stereo, and segmentation. In many cases, our new algorithm
works several times faster than any of the other methods, making near real-time
performance possible. An implementation of our max-flow/min-cut algorithm is available
upon request for research purposes.
author:
- first_name: Yuri
full_name: Boykov, Yuri
last_name: Boykov
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: Boykov Y, Kolmogorov V. An experimental comparison of min-cut/max-flow algorithms
for energy minimization in vision. IEEE Transactions on Pattern Analysis and
Machine Intelligence. 2004;26(9):1124-1137. doi:10.1109/TPAMI.2004.60
apa: Boykov, Y., & Kolmogorov, V. (2004). An experimental comparison of min-cut/max-flow
algorithms for energy minimization in vision. IEEE Transactions on Pattern
Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2004.60
chicago: Boykov, Yuri, and Vladimir Kolmogorov. “An Experimental Comparison of Min-Cut/Max-Flow
Algorithms for Energy Minimization in Vision.” IEEE Transactions on Pattern
Analysis and Machine Intelligence. IEEE, 2004. https://doi.org/10.1109/TPAMI.2004.60.
ieee: Y. Boykov and V. Kolmogorov, “An experimental comparison of min-cut/max-flow
algorithms for energy minimization in vision,” IEEE Transactions on Pattern
Analysis and Machine Intelligence, vol. 26, no. 9. IEEE, pp. 1124–1137, 2004.
ista: Boykov Y, Kolmogorov V. 2004. An experimental comparison of min-cut/max-flow
algorithms for energy minimization in vision. IEEE Transactions on Pattern Analysis
and Machine Intelligence. 26(9), 1124–1137.
mla: Boykov, Yuri, and Vladimir Kolmogorov. “An Experimental Comparison of Min-Cut/Max-Flow
Algorithms for Energy Minimization in Vision.” IEEE Transactions on Pattern
Analysis and Machine Intelligence, vol. 26, no. 9, IEEE, 2004, pp. 1124–37,
doi:10.1109/TPAMI.2004.60.
short: Y. Boykov, V. Kolmogorov, IEEE Transactions on Pattern Analysis and Machine
Intelligence 26 (2004) 1124–1137.
date_created: 2018-12-11T12:01:51Z
date_published: 2004-09-01T00:00:00Z
date_updated: 2021-01-12T07:41:36Z
day: '01'
doi: 10.1109/TPAMI.2004.60
extern: 1
intvolume: ' 26'
issue: '9'
month: '09'
page: 1124 - 1137
publication: IEEE Transactions on Pattern Analysis and Machine Intelligence
publication_status: published
publisher: IEEE
publist_id: '3507'
quality_controlled: 0
status: public
title: An experimental comparison of min-cut/max-flow algorithms for energy minimization
in vision
type: journal_article
volume: 26
year: '2004'
...
---
_id: '3179'
abstract:
- lang: eng
text: The problem of efficient, interactive foreground/background segmentation in
still images is of great practical importance in image editing. Classical image
segmentation tools use either texture (colour) information, e.g. Magic Wand, or
edge (contrast) information, e.g. Intelligent Scissors. Recently, an approach
based on optimization by graph-cut has been developed which successfully combines
both types of information. In this paper we extend the graph-cut approach in three
respects. First, we have developed a more powerful, iterative version of the optimisation.
Secondly, the power of the iterative algorithm is used to simplify substantially
the user interaction needed for a given quality of result. Thirdly, a robust algorithm
for "border matting" has been developed to estimate simultaneously the
alpha-matte around an object boundary and the colours of foreground pixels. We
show that for moderately difficult examples the proposed method outperforms competitive
tools.
author:
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Andrew
full_name: Blake, Andrew
last_name: Blake
citation:
ama: 'Rother C, Kolmogorov V, Blake A. "GrabCut" - Interactive
foreground extraction using iterated graph cuts . In: Vol 23. ACM; 2004:309-314.
doi:10.1145/1015706.1015720'
apa: 'Rother, C., Kolmogorov, V., & Blake, A. (2004). "GrabCut"
- Interactive foreground extraction using iterated graph cuts (Vol. 23, pp. 309–314).
Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive
Techniques, ACM. https://doi.org/10.1145/1015706.1015720'
chicago: Rother, Carsten, Vladimir Kolmogorov, and Andrew Blake. “"GrabCut"
- Interactive Foreground Extraction Using Iterated Graph Cuts ,” 23:309–14. ACM,
2004. https://doi.org/10.1145/1015706.1015720.
ieee: 'C. Rother, V. Kolmogorov, and A. Blake, “"GrabCut" - Interactive
foreground extraction using iterated graph cuts ,” presented at the SIGGRAPH:
Special Interest Group on Computer Graphics and Interactive Techniques, 2004,
vol. 23, no. 3, pp. 309–314.'
ista: 'Rother C, Kolmogorov V, Blake A. 2004. "GrabCut" - Interactive
foreground extraction using iterated graph cuts . SIGGRAPH: Special Interest Group
on Computer Graphics and Interactive Techniques vol. 23, 309–314.'
mla: Rother, Carsten, et al. "GrabCut" - Interactive Foreground
Extraction Using Iterated Graph Cuts . Vol. 23, no. 3, ACM, 2004, pp. 309–14,
doi:10.1145/1015706.1015720.
short: C. Rother, V. Kolmogorov, A. Blake, in:, ACM, 2004, pp. 309–314.
conference:
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
date_created: 2018-12-11T12:01:51Z
date_published: 2004-08-01T00:00:00Z
date_updated: 2021-01-12T07:41:36Z
day: '01'
doi: 10.1145/1015706.1015720
extern: 1
intvolume: ' 23'
issue: '3'
main_file_link:
- open_access: '0'
url: http://research.microsoft.com/pubs/67890/siggraph04-grabcut.pdf
month: '08'
page: 309 - 314
publication_status: published
publisher: ACM
publist_id: '3505'
quality_controlled: 0
status: public
title: '"GrabCut" - Interactive foreground extraction using iterated graph
cuts '
type: conference
volume: 23
year: '2004'
...
---
_id: '3208'
abstract:
- lang: eng
text: |-
A new technique for proving the adaptive indistinguishability of two systems, each composed of some component systems, is presented, using only the fact that corresponding component systems are non-adaptively indistinguishable. The main tool is the definition of a special monotone condition for a random system F, relative to another random system G, whose probability of occurring for a given distinguisher D is closely related to the distinguishing advantage ε of D for F and G, namely it is lower and upper bounded by ε and (1+ln1), respectively.
A concrete instantiation of this result shows that the cascade of two random permutations (with the second one inverted) is indistinguishable from a uniform random permutation by adaptive distinguishers which may query the system from both sides, assuming the components’ security only against non-adaptive one-sided distinguishers.
As applications we provide some results in various fields as almost k-wise independent probability spaces, decorrelation theory and computational indistinguishability (i.e., pseudo-randomness).
alternative_title:
- LNCS
author:
- first_name: Ueli
full_name: Maurer, Ueli M
last_name: Maurer
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Maurer U, Pietrzak KZ. Composition of random systems: When two weak make one
strong. In: Vol 2951. Springer; 2004:410-427. doi:10.1007/978-3-540-24638-1_23'
apa: 'Maurer, U., & Pietrzak, K. Z. (2004). Composition of random systems: When
two weak make one strong (Vol. 2951, pp. 410–427). Presented at the TCC: Theory
of Cryptography Conference, Springer. https://doi.org/10.1007/978-3-540-24638-1_23'
chicago: 'Maurer, Ueli, and Krzysztof Z Pietrzak. “Composition of Random Systems:
When Two Weak Make One Strong,” 2951:410–27. Springer, 2004. https://doi.org/10.1007/978-3-540-24638-1_23.'
ieee: 'U. Maurer and K. Z. Pietrzak, “Composition of random systems: When two weak
make one strong,” presented at the TCC: Theory of Cryptography Conference, 2004,
vol. 2951, pp. 410–427.'
ista: 'Maurer U, Pietrzak KZ. 2004. Composition of random systems: When two weak
make one strong. TCC: Theory of Cryptography Conference, LNCS, vol. 2951, 410–427.'
mla: 'Maurer, Ueli, and Krzysztof Z. Pietrzak. Composition of Random Systems:
When Two Weak Make One Strong. Vol. 2951, Springer, 2004, pp. 410–27, doi:10.1007/978-3-540-24638-1_23.'
short: U. Maurer, K.Z. Pietrzak, in:, Springer, 2004, pp. 410–427.
conference:
name: 'TCC: Theory of Cryptography Conference'
date_created: 2018-12-11T12:02:01Z
date_published: 2004-03-19T00:00:00Z
date_updated: 2021-01-12T07:41:48Z
day: '19'
doi: 10.1007/978-3-540-24638-1_23
extern: 1
intvolume: ' 2951'
month: '03'
page: 410 - 427
publication_status: published
publisher: Springer
publist_id: '3471'
quality_controlled: 0
status: public
title: 'Composition of random systems: When two weak make one strong'
type: conference
volume: 2951
year: '2004'
...
---
_id: '3419'
abstract:
- lang: eng
text: The folding and stability of transmembrane proteins is a fundamental and unsolved
biological problem. Here, single bacteriorhodopsin molecules were mechanically
unfolded from native purple membranes using atomic force microscopy and force
spectroscopy. The energy landscape of individual transmembrane α helices and polypeptide
loops was mapped by monitoring the pulling speed dependence of the unfolding forces
and applying Monte Carlo simulations. Single helices formed independently stable
units stabilized by a single potential barrier. Mechanical unfolding of the helices
was triggered by 3.9–7.7 Å extension, while natural unfolding rates were of the
order of 10−3 s−1. Besides acting as individually stable units, helices associated
pairwise, establishing a collective potential barrier. The unfolding pathways
of individual proteins reflect distinct pulling speed-dependent unfolding routes
in their energy landscapes. These observations support the two-stage model of
membrane protein folding in which α helices insert into the membrane as stable
units and then assemble into the functional protein.
author:
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Jens
full_name: Struckmeier, Jens
last_name: Struckmeier
- first_name: Maurice
full_name: Hubain, Maurice
last_name: Hubain
- first_name: Max
full_name: Kessler, Max
last_name: Kessler
- first_name: Alexej
full_name: Kedrov, Alexej
last_name: Kedrov
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: Janovjak HL, Struckmeier J, Hubain M, Kessler M, Kedrov A, Mueller D. Probing
the energy landscape of the membrane protein bacteriorhodopsin. Structure.
2004;12(5):871-879. doi:10.1016/j.str.2004.03.016
apa: Janovjak, H. L., Struckmeier, J., Hubain, M., Kessler, M., Kedrov, A., &
Mueller, D. (2004). Probing the energy landscape of the membrane protein bacteriorhodopsin.
Structure. Cell Press. https://doi.org/10.1016/j.str.2004.03.016
chicago: Janovjak, Harald L, Jens Struckmeier, Maurice Hubain, Max Kessler, Alexej
Kedrov, and Daniel Mueller. “Probing the Energy Landscape of the Membrane Protein
Bacteriorhodopsin.” Structure. Cell Press, 2004. https://doi.org/10.1016/j.str.2004.03.016.
ieee: H. L. Janovjak, J. Struckmeier, M. Hubain, M. Kessler, A. Kedrov, and D. Mueller,
“Probing the energy landscape of the membrane protein bacteriorhodopsin,” Structure,
vol. 12, no. 5. Cell Press, pp. 871–879, 2004.
ista: Janovjak HL, Struckmeier J, Hubain M, Kessler M, Kedrov A, Mueller D. 2004.
Probing the energy landscape of the membrane protein bacteriorhodopsin. Structure.
12(5), 871–879.
mla: Janovjak, Harald L., et al. “Probing the Energy Landscape of the Membrane Protein
Bacteriorhodopsin.” Structure, vol. 12, no. 5, Cell Press, 2004, pp. 871–79,
doi:10.1016/j.str.2004.03.016.
short: H.L. Janovjak, J. Struckmeier, M. Hubain, M. Kessler, A. Kedrov, D. Mueller,
Structure 12 (2004) 871–879.
date_created: 2018-12-11T12:03:14Z
date_published: 2004-05-01T00:00:00Z
date_updated: 2021-01-12T07:43:20Z
day: '01'
doi: 10.1016/j.str.2004.03.016
extern: 1
intvolume: ' 12'
issue: '5'
month: '05'
page: 871 - 879
publication: Structure
publication_status: published
publisher: Cell Press
publist_id: '2982'
quality_controlled: 0
status: public
title: Probing the energy landscape of the membrane protein bacteriorhodopsin
type: journal_article
volume: 12
year: '2004'
...
---
_id: '3420'
abstract:
- lang: eng
text: Single-molecule force-spectroscopy was employed to unfold and refold single
sodium-proton antiporters (NhaA) of Escherichia coli from membrane patches. Although
transmembrane α-helices and extracellular polypeptide loops exhibited sufficient
stability to individually establish potential barriers against unfolding, two
helices predominantly unfolded pairwise, thereby acting as one structural unit.
Many of the potential barriers were detected unfolding NhaA either from the C-terminal
or the N-terminal end. It was found that some molecular interactions stabilizing
secondary structural elements were directional, while others were not. Additionally,
some interactions appeared to occur between the secondary structural elements.
After unfolding ten of the 12 helices, the extracted polypeptide was allowed to
refold back into the membrane. After five seconds, the refolded polypeptide established
all secondary structure elements of the native protein. One helical pair showed
a characteristic spring like “snap in” into its folded conformation, while the
refolding process of other helices was not detected in particular. Additionally,
individual helices required characteristic periods of time to fold. Correlating
these results with the primary structure of NhaA allowed us to obtain the first
insights into how potential barriers establish and determine the folding kinetics
of the secondary structure elements.
author:
- first_name: Alexej
full_name: Kedrov, Alexej
last_name: Kedrov
- first_name: Christine
full_name: Ziegler, Christine
last_name: Ziegler
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Werner
full_name: Kühlbrandt, Werner
last_name: Kühlbrandt
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: Kedrov A, Ziegler C, Janovjak HL, Kühlbrandt W, Mueller D. Controlled unfolding
and refolding of a single sodium/proton antiporter using atomic force microscopy.
Journal of Molecular Biology. 2004;340(5):1143-1152. doi:10.1016/j.jmb.2004.05.026
apa: Kedrov, A., Ziegler, C., Janovjak, H. L., Kühlbrandt, W., & Mueller, D.
(2004). Controlled unfolding and refolding of a single sodium/proton antiporter
using atomic force microscopy. Journal of Molecular Biology. Elsevier.
https://doi.org/10.1016/j.jmb.2004.05.026
chicago: Kedrov, Alexej, Christine Ziegler, Harald L Janovjak, Werner Kühlbrandt,
and Daniel Mueller. “Controlled Unfolding and Refolding of a Single Sodium/Proton
Antiporter Using Atomic Force Microscopy.” Journal of Molecular Biology.
Elsevier, 2004. https://doi.org/10.1016/j.jmb.2004.05.026.
ieee: A. Kedrov, C. Ziegler, H. L. Janovjak, W. Kühlbrandt, and D. Mueller, “Controlled
unfolding and refolding of a single sodium/proton antiporter using atomic force
microscopy,” Journal of Molecular Biology, vol. 340, no. 5. Elsevier, pp.
1143–1152, 2004.
ista: Kedrov A, Ziegler C, Janovjak HL, Kühlbrandt W, Mueller D. 2004. Controlled
unfolding and refolding of a single sodium/proton antiporter using atomic force
microscopy. Journal of Molecular Biology. 340(5), 1143–1152.
mla: Kedrov, Alexej, et al. “Controlled Unfolding and Refolding of a Single Sodium/Proton
Antiporter Using Atomic Force Microscopy.” Journal of Molecular Biology,
vol. 340, no. 5, Elsevier, 2004, pp. 1143–52, doi:10.1016/j.jmb.2004.05.026.
short: A. Kedrov, C. Ziegler, H.L. Janovjak, W. Kühlbrandt, D. Mueller, Journal
of Molecular Biology 340 (2004) 1143–1152.
date_created: 2018-12-11T12:03:14Z
date_published: 2004-07-23T00:00:00Z
date_updated: 2021-01-12T07:43:21Z
day: '23'
doi: 10.1016/j.jmb.2004.05.026
extern: 1
intvolume: ' 340'
issue: '5'
month: '07'
page: 1143 - 1152
publication: Journal of Molecular Biology
publication_status: published
publisher: Elsevier
publist_id: '2981'
quality_controlled: 0
status: public
title: Controlled unfolding and refolding of a single sodium/proton antiporter using
atomic force microscopy
type: journal_article
volume: 340
year: '2004'
...
---
_id: '3574'
author:
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Edelsbrunner H. Biological applications of computational topology. In: Handbook
of Discrete and Computational Geometry. CRC Press; 2004:1395-1412.'
apa: Edelsbrunner, H. (2004). Biological applications of computational topology.
In Handbook of Discrete and Computational Geometry (pp. 1395–1412). CRC
Press.
chicago: Edelsbrunner, Herbert. “Biological Applications of Computational Topology.”
In Handbook of Discrete and Computational Geometry, 1395–1412. CRC Press,
2004.
ieee: H. Edelsbrunner, “Biological applications of computational topology,” in Handbook
of Discrete and Computational Geometry, CRC Press, 2004, pp. 1395–1412.
ista: 'Edelsbrunner H. 2004.Biological applications of computational topology. In:
Handbook of Discrete and Computational Geometry. , 1395–1412.'
mla: Edelsbrunner, Herbert. “Biological Applications of Computational Topology.”
Handbook of Discrete and Computational Geometry, CRC Press, 2004, pp. 1395–412.
short: H. Edelsbrunner, in:, Handbook of Discrete and Computational Geometry, CRC
Press, 2004, pp. 1395–1412.
date_created: 2018-12-11T12:04:02Z
date_published: 2004-04-15T00:00:00Z
date_updated: 2021-01-12T07:44:24Z
day: '15'
extern: 1
main_file_link:
- open_access: '0'
url: http://www.cs.duke.edu/~edels/Papers/2004-B-01-BiologicalApplicationsTopology.pdf
month: '04'
page: 1395 - 1412
publication: Handbook of Discrete and Computational Geometry
publication_status: published
publisher: CRC Press
publist_id: '2811'
quality_controlled: 0
status: public
title: Biological applications of computational topology
type: book_chapter
year: '2004'
...
---
_id: '3575'
abstract:
- lang: eng
text: The Jacobi set of two Morse functions defined on a common - manifold is the
set of critical points of the restrictions of one func- tion to the level sets
of the other function. Equivalently, it is the set of points where the gradients
of the functions are parallel. For a generic pair of Morse functions, the Jacobi
set is a smoothly embed- ded 1-manifold. We give a polynomial-time algorithm that
com- putes the piecewise linear analog of the Jacobi set for functions specified
at the vertices of a triangulation, and we generalize all results to more than
two but at most Morse functions.
alternative_title:
- London Mathematical Society Lecture Note
author:
- 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
citation:
ama: 'Edelsbrunner H, Harer J. Jacobi sets of multiple Morse functions. In: Foundations
of Computational Mathematics. Vol 312. Springer; 2004:37-57. doi:10.1017/CBO9781139106962.003'
apa: Edelsbrunner, H., & Harer, J. (2004). Jacobi sets of multiple Morse functions.
In Foundations of Computational Mathematics (Vol. 312, pp. 37–57). Springer.
https://doi.org/10.1017/CBO9781139106962.003
chicago: Edelsbrunner, Herbert, and John Harer. “Jacobi Sets of Multiple Morse Functions.”
In Foundations of Computational Mathematics, 312:37–57. Springer, 2004.
https://doi.org/10.1017/CBO9781139106962.003.
ieee: H. Edelsbrunner and J. Harer, “Jacobi sets of multiple Morse functions,” in
Foundations of Computational Mathematics, vol. 312, Springer, 2004, pp.
37–57.
ista: 'Edelsbrunner H, Harer J. 2004.Jacobi sets of multiple Morse functions. In:
Foundations of Computational Mathematics. London Mathematical Society Lecture
Note, vol. 312, 37–57.'
mla: Edelsbrunner, Herbert, and John Harer. “Jacobi Sets of Multiple Morse Functions.”
Foundations of Computational Mathematics, vol. 312, Springer, 2004, pp.
37–57, doi:10.1017/CBO9781139106962.003.
short: H. Edelsbrunner, J. Harer, in:, Foundations of Computational Mathematics,
Springer, 2004, pp. 37–57.
date_created: 2018-12-11T12:04:02Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:44:24Z
day: '01'
doi: 10.1017/CBO9781139106962.003
extern: 1
intvolume: ' 312'
month: '01'
page: 37 - 57
publication: Foundations of Computational Mathematics
publication_status: published
publisher: Springer
publist_id: '2810'
quality_controlled: 0
status: public
title: Jacobi sets of multiple Morse functions
type: book_chapter
volume: 312
year: '2004'
...
---
_id: '3587'
alternative_title:
- Molecular Aspects of Fish and Marine Biology
article_processing_charge: No
author:
- first_name: Florian
full_name: Ulrich, Florian
last_name: Ulrich
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: 'Ulrich F, Heisenberg C-PJ. Gastrulation in zebrafish. In: Korzh V, Gong Z,
eds. Fish Development and Genetics : The Zebrafish and Medaka Models. Vol
2. World Scientific Publishing; 2004:39-86.'
apa: 'Ulrich, F., & Heisenberg, C.-P. J. (2004). Gastrulation in zebrafish.
In V. Korzh & Z. Gong (Eds.), Fish development and genetics : the zebrafish
and medaka models (Vol. 2, pp. 39–86). World Scientific Publishing.'
chicago: 'Ulrich, Florian, and Carl-Philipp J Heisenberg. “Gastrulation in Zebrafish.”
In Fish Development and Genetics : The Zebrafish and Medaka Models, edited
by Vladimir Korzh and Zhiyuan Gong, 2:39–86. World Scientific Publishing, 2004.'
ieee: 'F. Ulrich and C.-P. J. Heisenberg, “Gastrulation in zebrafish,” in Fish
development and genetics : the zebrafish and medaka models, vol. 2, V. Korzh
and Z. Gong, Eds. World Scientific Publishing, 2004, pp. 39–86.'
ista: 'Ulrich F, Heisenberg C-PJ. 2004.Gastrulation in zebrafish. In: Fish development
and genetics : the zebrafish and medaka models. Molecular Aspects of Fish and
Marine Biology, vol. 2, 39–86.'
mla: 'Ulrich, Florian, and Carl-Philipp J. Heisenberg. “Gastrulation in Zebrafish.”
Fish Development and Genetics : The Zebrafish and Medaka Models, edited
by Vladimir Korzh and Zhiyuan Gong, vol. 2, World Scientific Publishing, 2004,
pp. 39–86.'
short: 'F. Ulrich, C.-P.J. Heisenberg, in:, V. Korzh, Z. Gong (Eds.), Fish Development
and Genetics : The Zebrafish and Medaka Models, World Scientific Publishing, 2004,
pp. 39–86.'
date_created: 2018-12-11T12:04:06Z
date_published: 2004-11-01T00:00:00Z
date_updated: 2021-01-12T07:44:29Z
day: '01'
editor:
- first_name: Vladimir
full_name: Korzh, Vladimir
last_name: Korzh
- first_name: Zhiyuan
full_name: Gong, Zhiyuan
last_name: Gong
extern: '1'
intvolume: ' 2'
language:
- iso: eng
month: '11'
oa_version: None
page: 39 - 86
publication: 'Fish development and genetics : the zebrafish and medaka models'
publication_status: published
publisher: World Scientific Publishing
publist_id: '2796'
status: public
title: Gastrulation in zebrafish
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2004'
...
---
_id: '3595'
abstract:
- lang: eng
text: Genome sizes vary enormously. This variation in DNA content correlates with
effective population size, suggesting that deleterious additions to the genome
can accumulate in small populations. On this view, the increased complexity of
biological functions associated with large genomes partly reflects evolutionary
degeneration.
author:
- first_name: Brian
full_name: Charlesworth, Brian
last_name: Charlesworth
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Charlesworth B, Barton NH. Genome size: Does bigger mean worse? Current
Biology. 2004;14(6):R233-R235. doi:10.1016/j.cub.2004.02.054'
apa: 'Charlesworth, B., & Barton, N. H. (2004). Genome size: Does bigger mean
worse? Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2004.02.054'
chicago: 'Charlesworth, Brian, and Nicholas H Barton. “Genome Size: Does Bigger
Mean Worse?” Current Biology. Cell Press, 2004. https://doi.org/10.1016/j.cub.2004.02.054.'
ieee: 'B. Charlesworth and N. H. Barton, “Genome size: Does bigger mean worse?,”
Current Biology, vol. 14, no. 6. Cell Press, pp. R233–R235, 2004.'
ista: 'Charlesworth B, Barton NH. 2004. Genome size: Does bigger mean worse? Current
Biology. 14(6), R233–R235.'
mla: 'Charlesworth, Brian, and Nicholas H. Barton. “Genome Size: Does Bigger Mean
Worse?” Current Biology, vol. 14, no. 6, Cell Press, 2004, pp. R233–35,
doi:10.1016/j.cub.2004.02.054.'
short: B. Charlesworth, N.H. Barton, Current Biology 14 (2004) R233–R235.
date_created: 2018-12-11T12:04:09Z
date_published: 2004-03-01T00:00:00Z
date_updated: 2019-04-26T07:22:31Z
day: '01'
doi: 10.1016/j.cub.2004.02.054
extern: 1
intvolume: ' 14'
issue: '6'
month: '03'
page: R233 - R235
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '2788'
quality_controlled: 0
status: public
title: 'Genome size: Does bigger mean worse?'
type: review
volume: 14
year: '2004'
...
---
_id: '3614'
abstract:
- lang: eng
text: 'We analyze the changes in the mean and variance components of a quantitative
trait caused by changes in allele frequencies, concentrating on the effects of
genetic drift. We use a general representation of epistasis and dominance that
allows an arbitrary relation between genotype and phenotype for any number of
diallelic loci. We assume initial and final Hardy-Weinberg and linkage equilibrium
in our analyses of drift-induced changes. Random drift generates transient linkage
disequilibria that cause correlations between allele frequency fluctuations at
different loci. However, we show that these have negligible effects, at least
for interactions among small numbers of loci. Our analyses are based on diffusion
approximations that summarize the effects of drift in terms of F, the inbreeding
coefficient, interpreted as the expected proportional decrease in heterozygosity
at each locus. For haploids, the variance of the trait mean after a population
bottleneck is var(Δz̄) =inline imagewhere n is the number of loci contributing
to the trait variance, VA(1)=VA is the additive genetic variance, and VA(k) is
the kth-order additive epistatic variance. The expected additive genetic variance
after the bottleneck, denoted (V*A), is closely related to var(Δz̄);
(V*A) (1 –F)inline imageThus, epistasis inflates the expected additive variance
above VA(1 –F), the expectation under additivity. For haploids (and diploids without
dominance), the expected value of every variance component is inflated by the
existence of higher order interactions (e.g., third-order epistasis inflates (V*AA)).
This is not true in general with diploidy, because dominance alone can reduce
(V*A) below VA(1 –F) (e.g., when dominant alleles are rare). Without dominance,
diploidy produces simple expressions: var(Δz̄)=inline image=1 (2F)
kVA(k) and (V*A) = (1 –F)inline imagek(2F)k-1VA(k) With dominance (and even without
epistasis), var(Δz̄)and (V*A) no longer depend solely on the variance
components in the base population. For small F, the expected additive variance
simplifies to (V*A)(1 –F) VA+ 4FVAA+2FVD+2FCAD, where CAD is a sum of two terms
describing covariances between additive effects and dominance and additive × dominance
interactions. Whether population bottlenecks lead to expected increases in additive
variance depends primarily on the ratio of nonadditive to additive genetic variance
in the base population, but dominance precludes simple predictions based solely
on variance components. We illustrate these results using a model in which genotypic
values are drawn at random, allowing extreme and erratic epistatic interactions.
Although our analyses clarify the conditions under which drift is expected to
increase VA, we question the evolutionary importance of such increases.'
author:
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
citation:
ama: Barton NH, Turelli M. Effects of allele frequency changes on variance components
under a general model of epistasis. Evolution; International Journal of Organic
Evolution. 2004;58(10):2111-2132. doi:10.1111/j.0014-3820.2004.tb01591.x
apa: Barton, N. H., & Turelli, M. (2004). Effects of allele frequency changes
on variance components under a general model of epistasis. Evolution; International
Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.0014-3820.2004.tb01591.x
chicago: Barton, Nicholas H, and Michael Turelli. “Effects of Allele Frequency Changes
on Variance Components under a General Model of Epistasis.” Evolution; International
Journal of Organic Evolution. Wiley-Blackwell, 2004. https://doi.org/10.1111/j.0014-3820.2004.tb01591.x.
ieee: N. H. Barton and M. Turelli, “Effects of allele frequency changes on variance
components under a general model of epistasis,” Evolution; International Journal
of Organic Evolution, vol. 58, no. 10. Wiley-Blackwell, pp. 2111–2132, 2004.
ista: Barton NH, Turelli M. 2004. Effects of allele frequency changes on variance
components under a general model of epistasis. Evolution; International Journal
of Organic Evolution. 58(10), 2111–2132.
mla: Barton, Nicholas H., and Michael Turelli. “Effects of Allele Frequency Changes
on Variance Components under a General Model of Epistasis.” Evolution; International
Journal of Organic Evolution, vol. 58, no. 10, Wiley-Blackwell, 2004, pp.
2111–32, doi:10.1111/j.0014-3820.2004.tb01591.x.
short: N.H. Barton, M. Turelli, Evolution; International Journal of Organic Evolution
58 (2004) 2111–2132.
date_created: 2018-12-11T12:04:15Z
date_published: 2004-10-01T00:00:00Z
date_updated: 2021-01-12T07:44:40Z
day: '01'
doi: 10.1111/j.0014-3820.2004.tb01591.x
extern: 1
intvolume: ' 58'
issue: '10'
month: '10'
page: 2111 - 2132
publication: Evolution; International Journal of Organic Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2769'
quality_controlled: 0
status: public
title: Effects of allele frequency changes on variance components under a general
model of epistasis
type: journal_article
volume: 58
year: '2004'
...
---
_id: '3615'
abstract:
- lang: eng
text: 'We investigate three alternative selection-based scenarios proposed to maintain
polygenic variation: pleiotropic balancing selection, G x E interactions (with
spatial or temporal variation in allelic effects), and sex-dependent allelic effects.
Each analysis assumes an additive polygenic trait with n diallelic loci under
stabilizing selection. We allow loci to have different effects and consider equilibria
at which the population mean departs from the stabilizing-selection optimum. Under
weak selection, each model produces essentially identical, approximate allele-frequency
dynamics. Variation is maintained under pleiotropic balancing selection only at
loci for which the strength of balancing selection exceeds the effective strength
of stabilizing selection. In addition, for all models, polymorphism requires that
the population mean be close enough to the optimum that directional selection
does not overwhelm balancing selection. This balance allows many simultaneously
stable equilibria, and we explore their properties numerically. Both spatial and
temporal G x E can maintain variation at loci for which the coefficient of variation
(across environments) of the effect of a substitution exceeds a critical value
greater than one. The critical value depends on the correlation between substitution
effects at different loci. For large positive correlations (e.g., ρ2ij > 3/4),
even extreme fluctuations in allelic effects cannot maintain variation. Surprisingly,
this constraint on correlations implies that sex-dependent allelic effects cannot
maintain polygenic variation. We present numerical results that support our analytical
approximations and discuss our results in connection to relevant data and alternative
variance-maintaining mechanisms.'
author:
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Turelli M, Barton NH. Polygenic variation maintained by balancing selection:
pleiotropy, sex-dependent allelic effects and GxE interactions. Genetics.
2004;166(2):1053-1079. doi:10.1534/genetics.166.2.1053'
apa: 'Turelli, M., & Barton, N. H. (2004). Polygenic variation maintained by
balancing selection: pleiotropy, sex-dependent allelic effects and GxE interactions.
Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.166.2.1053'
chicago: 'Turelli, Michael, and Nicholas H Barton. “Polygenic Variation Maintained
by Balancing Selection: Pleiotropy, Sex-Dependent Allelic Effects and GxE Interactions.”
Genetics. Genetics Society of America, 2004. https://doi.org/10.1534/genetics.166.2.1053.'
ieee: 'M. Turelli and N. H. Barton, “Polygenic variation maintained by balancing
selection: pleiotropy, sex-dependent allelic effects and GxE interactions,” Genetics,
vol. 166, no. 2. Genetics Society of America, pp. 1053–1079, 2004.'
ista: 'Turelli M, Barton NH. 2004. Polygenic variation maintained by balancing selection:
pleiotropy, sex-dependent allelic effects and GxE interactions. Genetics. 166(2),
1053–1079.'
mla: 'Turelli, Michael, and Nicholas H. Barton. “Polygenic Variation Maintained
by Balancing Selection: Pleiotropy, Sex-Dependent Allelic Effects and GxE Interactions.”
Genetics, vol. 166, no. 2, Genetics Society of America, 2004, pp. 1053–79,
doi:10.1534/genetics.166.2.1053.'
short: M. Turelli, N.H. Barton, Genetics 166 (2004) 1053–1079.
date_created: 2018-12-11T12:04:15Z
date_published: 2004-02-01T00:00:00Z
date_updated: 2021-01-12T07:44:41Z
day: '01'
doi: 10.1534/genetics.166.2.1053
extern: 1
intvolume: ' 166'
issue: '2'
month: '02'
page: 1053 - 1079
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '2768'
quality_controlled: 0
status: public
title: 'Polygenic variation maintained by balancing selection: pleiotropy, sex-dependent
allelic effects and GxE interactions'
type: journal_article
volume: 166
year: '2004'
...
---
_id: '3616'
author:
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Speciation: Why, how, where and when? Current Biology. 2004;14(15):R603-R604.
doi:10.1016/j.cub.2004.07.037'
apa: 'Barton, N. H. (2004). Speciation: Why, how, where and when? Current Biology.
Cell Press. https://doi.org/10.1016/j.cub.2004.07.037'
chicago: 'Barton, Nicholas H. “Speciation: Why, How, Where and When?” Current
Biology. Cell Press, 2004. https://doi.org/10.1016/j.cub.2004.07.037.'
ieee: 'N. H. Barton, “Speciation: Why, how, where and when?,” Current Biology,
vol. 14, no. 15. Cell Press, pp. R603–R604, 2004.'
ista: 'Barton NH. 2004. Speciation: Why, how, where and when? Current Biology. 14(15),
R603–R604.'
mla: 'Barton, Nicholas H. “Speciation: Why, How, Where and When?” Current Biology,
vol. 14, no. 15, Cell Press, 2004, pp. R603–04, doi:10.1016/j.cub.2004.07.037.'
short: N.H. Barton, Current Biology 14 (2004) R603–R604.
date_created: 2018-12-11T12:04:16Z
date_published: 2004-08-10T00:00:00Z
date_updated: 2019-04-26T07:22:31Z
day: '10'
doi: 10.1016/j.cub.2004.07.037
extern: 1
intvolume: ' 14'
issue: '15'
month: '08'
page: R603 - R604
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '2767'
quality_controlled: 0
status: public
title: 'Speciation: Why, how, where and when?'
type: review
volume: 14
year: '2004'
...
---
_id: '3617'
abstract:
- lang: eng
text: 'The coalescent process can describe the effects of selection at linked loci
only if selection is so strong that genotype frequencies evolve deterministically.
Here, we develop methods proposed by Kaplan, Darden, and Hudson to find the effects
of weak selection. We show that the overall effect is given by an extension to
Price''s equation: the change in properties such as moments of coalescence times
is equal to the covariance between those properties and the fitness of the sample
of genes. The distribution of coalescence times differs substantially between
allelic classes, even in the absence of selection. However, the average coalescence
time between randomly chosen genes is insensitive to the current allele frequency
and is affected significantly by purifying selection only if deleterious mutations
are common and selection is strong (i.e., the product of population size and selection
coefficient, Ns > 3). Balancing selection increases mean coalescence times,
but the effect becomes large only when mutation rates between allelic classes
are low and when selection is extremely strong. Our analysis supports previous
simulations that show that selection has surprisingly little effect on genealogies.
Moreover, small fluctuations in allele frequency due to random drift can greatly
reduce any such effects. This will make it difficult to detect the action of selection
from neutral variation alone.'
author:
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison
full_name: Etheridge, Alison M
last_name: Etheridge
citation:
ama: Barton NH, Etheridge A. The effect of selection on genealogies. Genetics.
2004;166(2):1115-1131. doi:10.1534/genetics.166.2.1115
apa: Barton, N. H., & Etheridge, A. (2004). The effect of selection on genealogies.
Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.166.2.1115
chicago: Barton, Nicholas H, and Alison Etheridge. “The Effect of Selection on Genealogies.”
Genetics. Genetics Society of America, 2004. https://doi.org/10.1534/genetics.166.2.1115.
ieee: N. H. Barton and A. Etheridge, “The effect of selection on genealogies,” Genetics,
vol. 166, no. 2. Genetics Society of America, pp. 1115–1131, 2004.
ista: Barton NH, Etheridge A. 2004. The effect of selection on genealogies. Genetics.
166(2), 1115–1131.
mla: Barton, Nicholas H., and Alison Etheridge. “The Effect of Selection on Genealogies.”
Genetics, vol. 166, no. 2, Genetics Society of America, 2004, pp. 1115–31,
doi:10.1534/genetics.166.2.1115.
short: N.H. Barton, A. Etheridge, Genetics 166 (2004) 1115–1131.
date_created: 2018-12-11T12:04:16Z
date_published: 2004-02-01T00:00:00Z
date_updated: 2021-01-12T07:44:41Z
day: '01'
doi: 10.1534/genetics.166.2.1115
extern: 1
intvolume: ' 166'
issue: '2'
month: '02'
page: 1115 - 1131
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '2766'
quality_controlled: 0
status: public
title: The effect of selection on genealogies
type: journal_article
volume: 166
year: '2004'
...
---
_id: '3688'
abstract:
- lang: eng
text: Capturing images of documents using handheld digital cameras has a variety
of applications in academia, research, knowledge management, retail, and office
settings. The ultimate goal of such systems is to achieve image quality comparable
to that currently achieved with flatbed scanners even for curved, warped, or curled
pages. This can be achieved by high-accuracy 3D modeling of the page surface,
followed by a "flattening" of the surface. A number of previous systems
have either assumed only perspective distortions, or used techniques like structured
lighting, shading, or side-imaging for obtaining 3D shape. This paper describes
a system for handheld camera-based document capture using general purpose stereo
vision methods followed by a new document dewarping technique. Examples of shape
modeling and dewarping of book images is shown.
author:
- first_name: Adrian
full_name: Ulges, Adrian
last_name: Ulges
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Thomas
full_name: Breuel,Thomas M
last_name: Breuel
citation:
ama: 'Ulges A, Lampert C, Breuel T. Document capture using stereo vision. In: ACM;
2004:198-200. doi:10.1145/1030397.1030434'
apa: 'Ulges, A., Lampert, C., & Breuel, T. (2004). Document capture using stereo
vision (pp. 198–200). Presented at the DocEng: ACM Symposium on Document Engineering,
ACM. https://doi.org/10.1145/1030397.1030434'
chicago: Ulges, Adrian, Christoph Lampert, and Thomas Breuel. “Document Capture
Using Stereo Vision,” 198–200. ACM, 2004. https://doi.org/10.1145/1030397.1030434.
ieee: 'A. Ulges, C. Lampert, and T. Breuel, “Document capture using stereo vision,”
presented at the DocEng: ACM Symposium on Document Engineering, 2004, pp. 198–200.'
ista: 'Ulges A, Lampert C, Breuel T. 2004. Document capture using stereo vision.
DocEng: ACM Symposium on Document Engineering, 198–200.'
mla: Ulges, Adrian, et al. Document Capture Using Stereo Vision. ACM, 2004,
pp. 198–200, doi:10.1145/1030397.1030434.
short: A. Ulges, C. Lampert, T. Breuel, in:, ACM, 2004, pp. 198–200.
conference:
name: 'DocEng: ACM Symposium on Document Engineering'
date_created: 2018-12-11T12:04:38Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:48:58Z
day: '01'
doi: 10.1145/1030397.1030434
extern: 1
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/~chl/papers/ulges-doceng2004.pdf
month: '01'
page: 198 - 200
publication_status: published
publisher: ACM
publist_id: '2679'
quality_controlled: 0
status: public
title: Document capture using stereo vision
type: conference
year: '2004'
...
---
_id: '3805'
abstract:
- lang: eng
text: The operation of neuronal networks crucially depends on a fast time course
of signaling in inhibitory interneurons. Synapses that excite interneurons generate
fast currents, owing to the expression of glutamate receptors of specific subunit
composition. Interneurons generate brief action potentials in response to transient
synaptic activation and discharge repetitively at very high frequencies during
sustained stimulation. The ability to generate short-duration action potentials
at high frequencies depends on the expression of specific voltage-gated K+ channels.
Factors facilitating fast action potential initiation following synaptic excitation
include depolarized interneuron resting potential, subthreshold conductances and
active dendrites. Finally, GABA release at interneuron output synapses is rapid
and highly synchronized, leading to a faster inhibition in postsynaptic interneurons
than in principal cells. Thus, the expression of distinct transmitter receptors
and voltage-gated ion channels ensures that interneurons operate with high speed
and temporal precision.
author:
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Josef
full_name: Bischofberger, Josef
last_name: Bischofberger
- first_name: Desdemona
full_name: Fricker, Desdemona
last_name: Fricker
- first_name: Richard
full_name: Miles, Richard
last_name: Miles
citation:
ama: 'Jonas PM, Bischofberger J, Fricker D, Miles R. Interneuron Diversity series:
Fast in, fast out--temporal and spatial signal processing in hippocampal interneurons.
Trends in Neurosciences. 2004;27(1):30-40. doi:doi:10.1016/j.tins.2003.10.010'
apa: 'Jonas, P. M., Bischofberger, J., Fricker, D., & Miles, R. (2004). Interneuron
Diversity series: Fast in, fast out--temporal and spatial signal processing in
hippocampal interneurons. Trends in Neurosciences. Elsevier. https://doi.org/doi:10.1016/j.tins.2003.10.010'
chicago: 'Jonas, Peter M, Josef Bischofberger, Desdemona Fricker, and Richard Miles.
“Interneuron Diversity Series: Fast in, Fast out--Temporal and Spatial Signal
Processing in Hippocampal Interneurons.” Trends in Neurosciences. Elsevier,
2004. https://doi.org/doi:10.1016/j.tins.2003.10.010.'
ieee: 'P. M. Jonas, J. Bischofberger, D. Fricker, and R. Miles, “Interneuron Diversity
series: Fast in, fast out--temporal and spatial signal processing in hippocampal
interneurons,” Trends in Neurosciences, vol. 27, no. 1. Elsevier, pp. 30–40,
2004.'
ista: 'Jonas PM, Bischofberger J, Fricker D, Miles R. 2004. Interneuron Diversity
series: Fast in, fast out--temporal and spatial signal processing in hippocampal
interneurons. Trends in Neurosciences. 27(1), 30–40.'
mla: 'Jonas, Peter M., et al. “Interneuron Diversity Series: Fast in, Fast out--Temporal
and Spatial Signal Processing in Hippocampal Interneurons.” Trends in Neurosciences,
vol. 27, no. 1, Elsevier, 2004, pp. 30–40, doi:doi:10.1016/j.tins.2003.10.010.'
short: P.M. Jonas, J. Bischofberger, D. Fricker, R. Miles, Trends in Neurosciences
27 (2004) 30–40.
date_created: 2018-12-11T12:05:16Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:19Z
day: '01'
doi: doi:10.1016/j.tins.2003.10.010
extern: 1
intvolume: ' 27'
issue: '1'
month: '01'
page: 30 - 40
publication: Trends in Neurosciences
publication_status: published
publisher: Elsevier
publist_id: '2404'
quality_controlled: 0
status: public
title: 'Interneuron Diversity series: Fast in, fast out--temporal and spatial signal
processing in hippocampal interneurons'
type: journal_article
volume: 27
year: '2004'
...
---
_id: '3807'
abstract:
- lang: eng
text: The time course of Mg(2+) block and unblock of NMDA receptors (NMDARs) determines
the extent they are activated by depolarization. Here, we directly measure the
rate of NMDAR channel opening in response to depolarizations at different times
after brief (1 ms) and sustained (4.6 s) applications of glutamate to nucleated
patches from neocortical pyramidal neurons. The kinetics of Mg(2+) unblock were
found to be non-instantaneous and complex, consisting of a prominent fast component
(time constant approximately 100 micros) and slower components (time constants
4 and approximately 300 ms), the relative amplitudes of which depended on the
timing of the depolarizing pulse. Fitting a kinetic model to these data indicated
that Mg(2+) not only blocks the NMDAR channel, but reduces both the open probability
and affinity for glutamate, while enhancing desensitization. These effects slow
the rate of NMDAR channel opening in response to depolarization in a time-dependent
manner such that the slower components of Mg(2+) unblock are enhanced during depolarizations
at later times after glutamate application. One physiological consequence of this
is that brief depolarizations occurring earlier in time after glutamate application
are better able to open NMDAR channels. This finding has important implications
for spike-timing-dependent synaptic plasticity (STDP), where the precise (millisecond)
timing of action potentials relative to synaptic inputs determines the magnitude
and sign of changes in synaptic strength. Indeed, we find that STDP timing curves
of NMDAR channel activation elicited by realistic dendritic action potential waveforms
are narrower than expected assuming instantaneous Mg(2+) unblock, indicating that
slow Mg(2+) unblock of NMDAR channels makes the STDP timing window more precise.
author:
- first_name: Bjorn
full_name: Kampa, Bjorn M
last_name: Kampa
- first_name: John
full_name: Clements, John
last_name: Clements
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Greg
full_name: Stuart, Greg J
last_name: Stuart
citation:
ama: 'Kampa B, Clements J, Jonas PM, Stuart G. Kinetics of Mg(2+) unblock of NMDA
receptors: implications for spike-timing dependent synaptic plasticity. Journal
of Physiology. 2004;556(Pt 2):337-345. doi:10.1113/jphysiol.2003.058842 '
apa: 'Kampa, B., Clements, J., Jonas, P. M., & Stuart, G. (2004). Kinetics of
Mg(2+) unblock of NMDA receptors: implications for spike-timing dependent synaptic
plasticity. Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/jphysiol.2003.058842 '
chicago: 'Kampa, Bjorn, John Clements, Peter M Jonas, and Greg Stuart. “Kinetics
of Mg(2+) Unblock of NMDA Receptors: Implications for Spike-Timing Dependent Synaptic
Plasticity.” Journal of Physiology. Wiley-Blackwell, 2004. https://doi.org/10.1113/jphysiol.2003.058842 .'
ieee: 'B. Kampa, J. Clements, P. M. Jonas, and G. Stuart, “Kinetics of Mg(2+) unblock
of NMDA receptors: implications for spike-timing dependent synaptic plasticity,”
Journal of Physiology, vol. 556, no. Pt 2. Wiley-Blackwell, pp. 337–45,
2004.'
ista: 'Kampa B, Clements J, Jonas PM, Stuart G. 2004. Kinetics of Mg(2+) unblock
of NMDA receptors: implications for spike-timing dependent synaptic plasticity.
Journal of Physiology. 556(Pt 2), 337–45.'
mla: 'Kampa, Bjorn, et al. “Kinetics of Mg(2+) Unblock of NMDA Receptors: Implications
for Spike-Timing Dependent Synaptic Plasticity.” Journal of Physiology,
vol. 556, no. Pt 2, Wiley-Blackwell, 2004, pp. 337–45, doi:10.1113/jphysiol.2003.058842 .'
short: B. Kampa, J. Clements, P.M. Jonas, G. Stuart, Journal of Physiology 556 (2004)
337–45.
date_created: 2018-12-11T12:05:17Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:20Z
day: '01'
doi: '10.1113/jphysiol.2003.058842 '
extern: 1
intvolume: ' 556'
issue: Pt 2
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664940/
month: '01'
oa: 1
page: 337 - 45
publication: Journal of Physiology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2403'
quality_controlled: 0
status: public
title: 'Kinetics of Mg(2+) unblock of NMDA receptors: implications for spike-timing
dependent synaptic plasticity'
type: journal_article
volume: 556
year: '2004'
...
---
_id: '3809'
abstract:
- lang: eng
text: Neural stem cells in various regions of the vertebrate brain continuously
generate neurons throughout life. In the mammalian hippocampus, a region important
for spatial and episodic memory, thousands of new granule cells are produced per
day, with the exact number depending on environmental conditions and physical
exercise. The survival of these neurons is improved by learning and conversely
learning may be promoted by neurogenesis. Although it has been suggested that
newly generated neurons may have specific properties to facilitate learning, the
cellular and synaptic mechanisms of plasticity in these neurons are largely unknown.
Here we show that young granule cells in the adult hippocampus differ substantially
from mature granule cells in both active and passive membrane properties. In young
neurons, T-type Ca2+ channels can generate isolated Ca2+ spikes and boost fast
Na+ action potentials, contributing to the induction of synaptic plasticity. Associative
long-term potentiation can be induced more easily in young neurons than in mature
neurons under identical conditions. Thus, newly generated neurons express unique
mechanisms to facilitate synaptic plasticity, which may be important for the formation
of new memories.
author:
- first_name: Christoph
full_name: Schmidt-Hieber, Christoph
last_name: Schmidt Hieber
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Josef
full_name: Bischofberger, Josef
last_name: Bischofberger
citation:
ama: Schmidt Hieber C, Jonas PM, Bischofberger J. Enhanced synaptic plasticity in
newly generated granule cells of the adult hippocampus. Nature. 2004;429(6988):184-187.
doi:10.1038/nature02553
apa: Schmidt Hieber, C., Jonas, P. M., & Bischofberger, J. (2004). Enhanced
synaptic plasticity in newly generated granule cells of the adult hippocampus.
Nature. Nature Publishing Group. https://doi.org/10.1038/nature02553
chicago: Schmidt Hieber, Christoph, Peter M Jonas, and Josef Bischofberger. “Enhanced
Synaptic Plasticity in Newly Generated Granule Cells of the Adult Hippocampus.”
Nature. Nature Publishing Group, 2004. https://doi.org/10.1038/nature02553.
ieee: C. Schmidt Hieber, P. M. Jonas, and J. Bischofberger, “Enhanced synaptic plasticity
in newly generated granule cells of the adult hippocampus,” Nature, vol.
429, no. 6988. Nature Publishing Group, pp. 184–7, 2004.
ista: Schmidt Hieber C, Jonas PM, Bischofberger J. 2004. Enhanced synaptic plasticity
in newly generated granule cells of the adult hippocampus. Nature. 429(6988),
184–7.
mla: Schmidt Hieber, Christoph, et al. “Enhanced Synaptic Plasticity in Newly Generated
Granule Cells of the Adult Hippocampus.” Nature, vol. 429, no. 6988, Nature
Publishing Group, 2004, pp. 184–87, doi:10.1038/nature02553.
short: C. Schmidt Hieber, P.M. Jonas, J. Bischofberger, Nature 429 (2004) 184–7.
date_created: 2018-12-11T12:05:17Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:21Z
day: '01'
doi: 10.1038/nature02553
extern: 1
intvolume: ' 429'
issue: '6988'
month: '01'
page: 184 - 7
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '2401'
quality_controlled: 0
status: public
title: Enhanced synaptic plasticity in newly generated granule cells of the adult
hippocampus
type: journal_article
volume: 429
year: '2004'
...
---
_id: '3810'
abstract:
- lang: eng
text: Voltage-gated potassium (Kv) channels control action potential repolarization,
interspike membrane potential, and action potential frequency in excitable cells.
It is thought that the combinatorial association between distinct alpha and beta
subunits determines whether Kv channels function as non-inactivating delayed rectifiers
or as rapidly inactivating A-type channels. We show that membrane lipids can convert
A-type channels into delayed rectifiers and vice versa. Phosphoinositides remove
N-type inactivation from A-type channels by immobilizing the inactivation domains.
Conversely, arachidonic acid and its amide anandamide endow delayed rectifiers
with rapid voltage-dependent inactivation. The bidirectional control of Kv channel
gating by lipids may provide a mechanism for the dynamic regulation of electrical
signaling in the nervous system.
author:
- first_name: Dominik
full_name: Oliver, Dominik
last_name: Oliver
- first_name: Cheng
full_name: Lien, Cheng-Chang
last_name: Lien
- first_name: Malle
full_name: Soom, Malle
last_name: Soom
- first_name: Thomas
full_name: Baukrowitz, Thomas
last_name: Baukrowitz
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Bernd
full_name: Fakler, Bernd
last_name: Fakler
citation:
ama: Oliver D, Lien C, Soom M, Baukrowitz T, Jonas PM, Fakler B. Functional conversion
between A-type and delayed rectifier K+ channels by membrane lipids. Science.
2004;304(5668):265-270. doi:10.1126/science.1094113
apa: Oliver, D., Lien, C., Soom, M., Baukrowitz, T., Jonas, P. M., & Fakler,
B. (2004). Functional conversion between A-type and delayed rectifier K+ channels
by membrane lipids. Science. American Association for the Advancement of
Science. https://doi.org/10.1126/science.1094113
chicago: Oliver, Dominik, Cheng Lien, Malle Soom, Thomas Baukrowitz, Peter M Jonas,
and Bernd Fakler. “Functional Conversion between A-Type and Delayed Rectifier
K+ Channels by Membrane Lipids.” Science. American Association for the
Advancement of Science, 2004. https://doi.org/10.1126/science.1094113.
ieee: D. Oliver, C. Lien, M. Soom, T. Baukrowitz, P. M. Jonas, and B. Fakler, “Functional
conversion between A-type and delayed rectifier K+ channels by membrane lipids,”
Science, vol. 304, no. 5668. American Association for the Advancement of
Science, pp. 265–70, 2004.
ista: Oliver D, Lien C, Soom M, Baukrowitz T, Jonas PM, Fakler B. 2004. Functional
conversion between A-type and delayed rectifier K+ channels by membrane lipids.
Science. 304(5668), 265–70.
mla: Oliver, Dominik, et al. “Functional Conversion between A-Type and Delayed Rectifier
K+ Channels by Membrane Lipids.” Science, vol. 304, no. 5668, American
Association for the Advancement of Science, 2004, pp. 265–70, doi:10.1126/science.1094113.
short: D. Oliver, C. Lien, M. Soom, T. Baukrowitz, P.M. Jonas, B. Fakler, Science
304 (2004) 265–70.
date_created: 2018-12-11T12:05:18Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:22Z
day: '01'
doi: 10.1126/science.1094113
extern: 1
intvolume: ' 304'
issue: '5668'
month: '01'
page: 265 - 70
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '2402'
quality_controlled: 0
status: public
title: Functional conversion between A-type and delayed rectifier K+ channels by membrane
lipids
type: journal_article
volume: 304
year: '2004'
...
---
_id: '3894'
abstract:
- lang: eng
text: We study infinite stochastic games played by n-players on a finite graph with
goals given by sets of infinite traces. The games are stochastic (each player
simultaneously and independently chooses an action at each round, and the next
state is determined by a probability distribution depending on the current state
and the chosen actions), infinite (the game continues for an infinite number of
rounds), nonzero sum (the players' goals are not necessarily conflicting), and
undiscounted. We show that if each player has a reachability objective, that is,
if the goal for each player i is to visit some subset R-i of the states, then
there exists an epsilon-Nash equilibrium in memoryless strategies, for every epsilon
> 0. However, exact Nash equilibria need not exist. We study the complexity
of finding such Nash equilibria, and show that the payoff of some epsilon-Nash
equilibrium in memoryless strategies can be epsilon-approximated in NP. We study
the important subclass of n-player turn-based probabilistic games, where at each
state at most one player has a nontrivial choice of moves. For turn-based probabilistic
games, we show the existence of epsilon-Nash equilibria in pure strategies for
games where the objective of player i is a Borel set B-i of infinite traces. However,
exact Nash equilibria may not exist. For the special case of omega-regular objectives,
we show exact Nash equilibria exist, and can be computed in NP when the omega-regular
objectives are expressed as parity objectives.
acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327,
ONR grant N00014-02-1-0671, NSF grants CCR-9988172 and CCR-0225610
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: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
- first_name: Marcin
full_name: Jurdziński, Marcin
last_name: Jurdziński
citation:
ama: 'Chatterjee K, Majumdar R, Jurdziński M. On Nash equilibria in stochastic games.
In: Vol 3210. Springer; 2004:26-40. doi:10.1007/978-3-540-30124-0_6'
apa: 'Chatterjee, K., Majumdar, R., & Jurdziński, M. (2004). On Nash equilibria
in stochastic games (Vol. 3210, pp. 26–40). Presented at the CSL: Computer Science
Logic, Springer. https://doi.org/10.1007/978-3-540-30124-0_6'
chicago: Chatterjee, Krishnendu, Ritankar Majumdar, and Marcin Jurdziński. “On Nash
Equilibria in Stochastic Games,” 3210:26–40. Springer, 2004. https://doi.org/10.1007/978-3-540-30124-0_6.
ieee: 'K. Chatterjee, R. Majumdar, and M. Jurdziński, “On Nash equilibria in stochastic
games,” presented at the CSL: Computer Science Logic, 2004, vol. 3210, pp. 26–40.'
ista: 'Chatterjee K, Majumdar R, Jurdziński M. 2004. On Nash equilibria in stochastic
games. CSL: Computer Science Logic, LNCS , vol. 3210, 26–40.'
mla: Chatterjee, Krishnendu, et al. On Nash Equilibria in Stochastic Games.
Vol. 3210, Springer, 2004, pp. 26–40, doi:10.1007/978-3-540-30124-0_6.
short: K. Chatterjee, R. Majumdar, M. Jurdziński, in:, Springer, 2004, pp. 26–40.
conference:
name: 'CSL: Computer Science Logic'
date_created: 2018-12-11T12:05:45Z
date_published: 2004-09-09T00:00:00Z
date_updated: 2021-01-12T07:53:01Z
day: '09'
doi: 10.1007/978-3-540-30124-0_6
extern: 1
intvolume: ' 3210'
month: '09'
page: 26 - 40
publication_status: published
publisher: Springer
publist_id: '2264'
quality_controlled: 0
status: public
title: On Nash equilibria in stochastic games
type: conference
volume: 3210
year: '2004'
...
---
_id: '3895'
abstract:
- lang: eng
text: 'In 2-player non-zero-sum games, Nash equilibria capture the options for rational
behavior if each player attempts to maximize her payoff. In contrast to classical
game theory, we consider lexicographic objectives: first, each player tries to
maximize her own payoff, and then, the player tries to minimize the opponent''s
payoff. Such objectives arise naturally in the verification of systems with multiple
components. There, instead of proving that each component satisfies its specification
no matter how the other components behave, it often suffices to prove that each
component satisfies its specification provided that the other components satisfy
their specifications. We say that a Nash equilibrium is secure if it is an equilibrium
with respect to the lexicographic objectives of both players. We prove that in
graph games with Borel objectives, which include the games that arise in verification,
there may be several Nash equilibria, but there is always a unique maximal payoff
profile of secure equilibria. We show how this equilibrium can be computed in
the case of omega-regular objectives, and we characterize the memory requirements
of strategies that achieve the equilibrium.'
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
- first_name: Marcin
full_name: Jurdziński, Marcin
last_name: Jurdziński
citation:
ama: 'Chatterjee K, Henzinger TA, Jurdziński M. Games with secure equilibria. In:
IEEE; 2004:160-169. doi:10.1109/LICS.2004.1319610'
apa: 'Chatterjee, K., Henzinger, T. A., & Jurdziński, M. (2004). Games with
secure equilibria (pp. 160–169). Presented at the LICS: Logic in Computer Science,
IEEE. https://doi.org/10.1109/LICS.2004.1319610'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Marcin Jurdziński. “Games
with Secure Equilibria,” 160–69. IEEE, 2004. https://doi.org/10.1109/LICS.2004.1319610.
ieee: 'K. Chatterjee, T. A. Henzinger, and M. Jurdziński, “Games with secure equilibria,”
presented at the LICS: Logic in Computer Science, 2004, pp. 160–169.'
ista: 'Chatterjee K, Henzinger TA, Jurdziński M. 2004. Games with secure equilibria.
LICS: Logic in Computer Science, 160–169.'
mla: Chatterjee, Krishnendu, et al. Games with Secure Equilibria. IEEE, 2004,
pp. 160–69, doi:10.1109/LICS.2004.1319610.
short: K. Chatterjee, T.A. Henzinger, M. Jurdziński, in:, IEEE, 2004, pp. 160–169.
conference:
name: 'LICS: Logic in Computer Science'
date_created: 2018-12-11T12:05:45Z
date_published: 2004-08-09T00:00:00Z
date_updated: 2021-01-12T07:53:01Z
day: '09'
doi: 10.1109/LICS.2004.1319610
extern: 1
month: '08'
page: 160 - 169
publication_status: published
publisher: IEEE
publist_id: '2262'
quality_controlled: 0
status: public
title: Games with secure equilibria
type: conference
year: '2004'
...