---
_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: '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: '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'
...
---
_id: '3931'
abstract:
- lang: eng
text: Hyaluronan is an unsulfated glycosaminoglycan (GAG) that is ubiquitously expressed
in the extracellular matrix (ECM) of all vertebrates, where hyaluronan rich matrices
constitute a particular permissive environment for the development of complex
biological structures and also for tumor progression. Because of its conserved
structure and ubiquitous expression, antibodies for its histochemical detection
cannot be produced. We have engineered a fusion protein, neurocan-GFP, and expressed
it as a secreted molecule in mammalian cells. Neurocan-GFP fusion protein specifically
binds to hyaluronan and directly visualizes hyaluronan on tissue sections, revealing
a very detailed picture of hyaluronan distribution. The fluorescent fusion protein
can be used in combination with antibodies and nuclear markers for double or triple
staining. In addition, it is suitable to visualize hyaluronan on living cells
by time-lapse video microscopy. The successful production and application of the
neurocan-GFP fusion protein opens up new perspectives for using GFP fusion proteins
as detection tools in histological and cytological studies complementing conventional
antibody and biotin/avidin techniques.
author:
- first_name: Hui
full_name: Zhang, Hui
last_name: Zhang
- first_name: Stephan
full_name: Baader, Stephan L
last_name: Baader
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Joachim
full_name: Kappler, Joachim
last_name: Kappler
- first_name: Uwe
full_name: Rauch, Uwe
last_name: Rauch
citation:
ama: 'Zhang H, Baader S, Sixt MK, Kappler J, Rauch U. Neurocan-GFP fusion protein:
a new approach to detect hyaluronan on tissue sections and living cells. Journal
of Histochemistry and Cytochemistry. 2004;52(7):915-922. doi:10.1369/jhc.3A6221.2004'
apa: 'Zhang, H., Baader, S., Sixt, M. K., Kappler, J., & Rauch, U. (2004). Neurocan-GFP
fusion protein: a new approach to detect hyaluronan on tissue sections and living
cells. Journal of Histochemistry and Cytochemistry. Histochemical Society.
https://doi.org/10.1369/jhc.3A6221.2004'
chicago: 'Zhang, Hui, Stephan Baader, Michael K Sixt, Joachim Kappler, and Uwe Rauch.
“Neurocan-GFP Fusion Protein: A New Approach to Detect Hyaluronan on Tissue Sections
and Living Cells.” Journal of Histochemistry and Cytochemistry. Histochemical
Society, 2004. https://doi.org/10.1369/jhc.3A6221.2004.'
ieee: 'H. Zhang, S. Baader, M. K. Sixt, J. Kappler, and U. Rauch, “Neurocan-GFP
fusion protein: a new approach to detect hyaluronan on tissue sections and living
cells,” Journal of Histochemistry and Cytochemistry, vol. 52, no. 7. Histochemical
Society, pp. 915–922, 2004.'
ista: 'Zhang H, Baader S, Sixt MK, Kappler J, Rauch U. 2004. Neurocan-GFP fusion
protein: a new approach to detect hyaluronan on tissue sections and living cells.
Journal of Histochemistry and Cytochemistry. 52(7), 915–922.'
mla: 'Zhang, Hui, et al. “Neurocan-GFP Fusion Protein: A New Approach to Detect
Hyaluronan on Tissue Sections and Living Cells.” Journal of Histochemistry
and Cytochemistry, vol. 52, no. 7, Histochemical Society, 2004, pp. 915–22,
doi:10.1369/jhc.3A6221.2004.'
short: H. Zhang, S. Baader, M.K. Sixt, J. Kappler, U. Rauch, Journal of Histochemistry
and Cytochemistry 52 (2004) 915–922.
date_created: 2018-12-11T12:05:57Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:53:17Z
day: '01'
doi: 10.1369/jhc.3A6221.2004
extern: 1
intvolume: ' 52'
issue: '7'
month: '01'
page: 915 - 922
publication: Journal of Histochemistry and Cytochemistry
publication_status: published
publisher: Histochemical Society
publist_id: '2196'
quality_controlled: 0
status: public
title: 'Neurocan-GFP fusion protein: a new approach to detect hyaluronan on tissue
sections and living cells'
type: journal_article
volume: 52
year: '2004'
...
---
_id: '3929'
abstract:
- lang: eng
text: The Nef protein of human and simian immunodeficiency virus (HIV/SIV) is believed
to interfere with T cell activation signals by forming a signaling complex at
the plasma membrane. Composition and function of the complex are not fully understood.
Here we report that Nef recruits the Polycomb Group (PcG) protein Eed, so far
known as a nuclear factor and repressor of transcription, to the membrane of cells.
The Nef-induced translocation of Eed led to a potent stimulation of Tat-dependent
HIV transcription, implying that Eed removal from the nucleus is required for
optimal Tat function. Similar to Nef action, activation of integrin receptors
recruited Eed to the plasma membrane, also leading to enhanced Tat/Nef-mediated
transcription. Our results suggest a link between membrane-associated activation
processes and transcriptional derepression and demonstrate how HIV exploits this
mechanism.
author:
- first_name: Vanessa
full_name: Witte, Vanessa
last_name: Witte
- first_name: Bernd
full_name: Laffert, Bernd
last_name: Laffert
- first_name: Olaf
full_name: Rosorius, Olaf
last_name: Rosorius
- first_name: Peter
full_name: Lischka, Peter
last_name: Lischka
- first_name: Katja
full_name: Blume, Katja
last_name: Blume
- first_name: Gunther
full_name: Galler, Gunther
last_name: Galler
- first_name: Andrea
full_name: Stilper, Andrea
last_name: Stilper
- first_name: Dieter
full_name: Willbold, Dieter
last_name: Willbold
- first_name: Paola
full_name: D'Aloja, Paola
last_name: D'Aloja
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Johanna
full_name: Kolanus, Johanna
last_name: Kolanus
- first_name: Melanie
full_name: Ott, Melanie
last_name: Ott
- first_name: Waldemar
full_name: Kolanus, Waldemar
last_name: Kolanus
- first_name: Gerold
full_name: Schuler, Gerold
last_name: Schuler
- first_name: Andreas
full_name: Baur, Andreas S
last_name: Baur
citation:
ama: Witte V, Laffert B, Rosorius O, et al. HIV-1 Nef mimics an integrin receptor
signal that recruits the polycomb group protein Eed to the plasma membrane. Molecular
Cell. 2004;13(2):179-190. doi:10.1016/S1097-2765(04)00004-8
apa: Witte, V., Laffert, B., Rosorius, O., Lischka, P., Blume, K., Galler, G., …
Baur, A. (2004). HIV-1 Nef mimics an integrin receptor signal that recruits the
polycomb group protein Eed to the plasma membrane. Molecular Cell. Cell
Press. https://doi.org/10.1016/S1097-2765(04)00004-8
chicago: Witte, Vanessa, Bernd Laffert, Olaf Rosorius, Peter Lischka, Katja Blume,
Gunther Galler, Andrea Stilper, et al. “HIV-1 Nef Mimics an Integrin Receptor
Signal That Recruits the Polycomb Group Protein Eed to the Plasma Membrane.” Molecular
Cell. Cell Press, 2004. https://doi.org/10.1016/S1097-2765(04)00004-8.
ieee: V. Witte et al., “HIV-1 Nef mimics an integrin receptor signal that
recruits the polycomb group protein Eed to the plasma membrane,” Molecular
Cell, vol. 13, no. 2. Cell Press, pp. 179–190, 2004.
ista: Witte V, Laffert B, Rosorius O, Lischka P, Blume K, Galler G, Stilper A, Willbold
D, D’Aloja P, Sixt MK, Kolanus J, Ott M, Kolanus W, Schuler G, Baur A. 2004. HIV-1
Nef mimics an integrin receptor signal that recruits the polycomb group protein
Eed to the plasma membrane. Molecular Cell. 13(2), 179–190.
mla: Witte, Vanessa, et al. “HIV-1 Nef Mimics an Integrin Receptor Signal That Recruits
the Polycomb Group Protein Eed to the Plasma Membrane.” Molecular Cell,
vol. 13, no. 2, Cell Press, 2004, pp. 179–90, doi:10.1016/S1097-2765(04)00004-8.
short: V. Witte, B. Laffert, O. Rosorius, P. Lischka, K. Blume, G. Galler, A. Stilper,
D. Willbold, P. D’Aloja, M.K. Sixt, J. Kolanus, M. Ott, W. Kolanus, G. Schuler,
A. Baur, Molecular Cell 13 (2004) 179–190.
date_created: 2018-12-11T12:05:56Z
date_published: 2004-01-30T00:00:00Z
date_updated: 2021-01-12T07:53:16Z
day: '30'
doi: 10.1016/S1097-2765(04)00004-8
extern: 1
intvolume: ' 13'
issue: '2'
month: '01'
page: 179 - 190
publication: Molecular Cell
publication_status: published
publisher: Cell Press
publist_id: '2197'
quality_controlled: 0
status: public
title: HIV-1 Nef mimics an integrin receptor signal that recruits the polycomb group
protein Eed to the plasma membrane
type: journal_article
volume: 13
year: '2004'
...
---
_id: '3990'
abstract:
- lang: eng
text: The writhing number measures the global geometry of a closed space curve or
knot. We show that this measure is related to the average winding number of its
Gauss map. Using this relationship, we give an algorithm for computing the writhing
number for a polygonal knot with n edges in time roughly proportional to n(1.6).
We also implement a different, simple algorithm and provide experimental evidence
for its practical efficiency.
acknowledgement: Partially supported by NSF under grants CCR-00-86013, EIA-9972879
and NSF under grant CCR-97-12088.
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: Yusu
full_name: Wang, Yusu
last_name: Wang
citation:
ama: Agarwal P, Edelsbrunner H, Wang Y. Computing the writhing number of a polygonal
knot. Discrete & Computational Geometry. 2004;32(1):37-53. doi:10.1007/s00454-004-2864-x
apa: Agarwal, P., Edelsbrunner, H., & Wang, Y. (2004). Computing the writhing
number of a polygonal knot. Discrete & Computational Geometry. Springer.
https://doi.org/10.1007/s00454-004-2864-x
chicago: Agarwal, Pankaj, Herbert Edelsbrunner, and Yusu Wang. “Computing the Writhing
Number of a Polygonal Knot.” Discrete & Computational Geometry. Springer,
2004. https://doi.org/10.1007/s00454-004-2864-x.
ieee: P. Agarwal, H. Edelsbrunner, and Y. Wang, “Computing the writhing number of
a polygonal knot,” Discrete & Computational Geometry, vol. 32, no.
1. Springer, pp. 37–53, 2004.
ista: Agarwal P, Edelsbrunner H, Wang Y. 2004. Computing the writhing number of
a polygonal knot. Discrete & Computational Geometry. 32(1), 37–53.
mla: Agarwal, Pankaj, et al. “Computing the Writhing Number of a Polygonal Knot.”
Discrete & Computational Geometry, vol. 32, no. 1, Springer, 2004,
pp. 37–53, doi:10.1007/s00454-004-2864-x.
short: P. Agarwal, H. Edelsbrunner, Y. Wang, Discrete & Computational Geometry
32 (2004) 37–53.
date_created: 2018-12-11T12:06:18Z
date_published: 2004-05-01T00:00:00Z
date_updated: 2021-01-12T07:53:42Z
day: '01'
doi: 10.1007/s00454-004-2864-x
extern: 1
intvolume: ' 32'
issue: '1'
month: '05'
page: 37 - 53
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '2138'
quality_controlled: 0
status: public
title: Computing the writhing number of a polygonal knot
type: journal_article
volume: 32
year: '2004'
...
---
_id: '4224'
abstract:
- lang: eng
text: Developing cells acquire positional information by reading the graded distribution
of morphogens. In Drosophila, the Dpp morphogen forms a long-range concentration
gradient by spreading from a restricted source in the developing wing. It has
been assumed that Dpp spreads by extracellular diffusion. Under this assumption,
the main role of endocytosis in gradient formation is to downregulate receptors
at the cell surface. These surface receptors bind to the ligand and thereby interfere
with its long-range movement. Recent experiments indicate that Dpp spreading is
mediated by Dynamin-dependent endocytosis in the target tissue, suggesting that
extracellular diffusion alone cannot account for Dpp dispersal. Here, we perform
a theoretical study of a model for morphogen spreading based on extracellular
diffusion, which takes into account receptor binding and trafficking. We compare
profiles of ligand and surface receptors obtained in this model with experimental
data. To this end, we monitored directly the pool of surface receptors and extracellular
Dpp with specific antibodies. We conclude that current models considering pure
extracellular diffusion cannot explain the observed role of endocytosis during
Dpp long-range movement.
article_processing_charge: No
author:
- first_name: Karsten
full_name: Kruse, Karsten
last_name: Kruse
- first_name: Periklis
full_name: Pantazis, Periklis
last_name: Pantazis
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
- first_name: Frank
full_name: Julicher, Frank
last_name: Julicher
- first_name: Marcos
full_name: Gonzalez Gaitan, Marcos
last_name: Gonzalez Gaitan
citation:
ama: 'Kruse K, Pantazis P, Bollenbach MT, Julicher F, Gonzalez Gaitan M. Dpp gradient
formation by dynamin-dependent endocytosis: receptor trafficking and the diffusion
model. Development. 2004;131(19):4843-4856. doi:10.1242/dev.01335'
apa: 'Kruse, K., Pantazis, P., Bollenbach, M. T., Julicher, F., & Gonzalez Gaitan,
M. (2004). Dpp gradient formation by dynamin-dependent endocytosis: receptor trafficking
and the diffusion model. Development. Company of Biologists. https://doi.org/10.1242/dev.01335'
chicago: 'Kruse, Karsten, Periklis Pantazis, Mark Tobias Bollenbach, Frank Julicher,
and Marcos Gonzalez Gaitan. “Dpp Gradient Formation by Dynamin-Dependent Endocytosis:
Receptor Trafficking and the Diffusion Model.” Development. Company of
Biologists, 2004. https://doi.org/10.1242/dev.01335.'
ieee: 'K. Kruse, P. Pantazis, M. T. Bollenbach, F. Julicher, and M. Gonzalez Gaitan,
“Dpp gradient formation by dynamin-dependent endocytosis: receptor trafficking
and the diffusion model,” Development, vol. 131, no. 19. Company of Biologists,
pp. 4843–4856, 2004.'
ista: 'Kruse K, Pantazis P, Bollenbach MT, Julicher F, Gonzalez Gaitan M. 2004.
Dpp gradient formation by dynamin-dependent endocytosis: receptor trafficking
and the diffusion model. Development. 131(19), 4843–4856.'
mla: 'Kruse, Karsten, et al. “Dpp Gradient Formation by Dynamin-Dependent Endocytosis:
Receptor Trafficking and the Diffusion Model.” Development, vol. 131, no.
19, Company of Biologists, 2004, pp. 4843–56, doi:10.1242/dev.01335.'
short: K. Kruse, P. Pantazis, M.T. Bollenbach, F. Julicher, M. Gonzalez Gaitan,
Development 131 (2004) 4843–4856.
date_created: 2018-12-11T12:07:41Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:55:26Z
day: '01'
doi: 10.1242/dev.01335
extern: '1'
intvolume: ' 131'
issue: '19'
language:
- iso: eng
month: '01'
oa_version: None
page: 4843 - 4856
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '1893'
status: public
title: 'Dpp gradient formation by dynamin-dependent endocytosis: receptor trafficking
and the diffusion model'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 131
year: '2004'
...
---
_id: '4239'
alternative_title:
- Cellular Origin, Life in Extreme Habitats and Astrobiology
author:
- first_name: Harold
full_name: Harold Vladar
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: Vladar
orcid: 0000-0002-5985-7653
- first_name: Roberto
full_name: 'Cipriani, Roberto '
last_name: Cipriani
- first_name: Benjamin
full_name: Scharifker, Benjamin
last_name: Scharifker
- first_name: Jose
full_name: Bubis, Jose
last_name: Bubis
citation:
ama: 'de Vladar H, Cipriani R, Scharifker B, Bubis J. A Mechanism for the Prebiotic
Emergence of Proteins. In: Seckbach J, Chela Flores J, Owen T, Raulin F, eds.
Life in the Universe From the Miller Experiment to the Search for Life on Other
Worlds. Vol 7. Springer; 2004:83-87. doi:3807'
apa: de Vladar, H., Cipriani, R., Scharifker, B., & Bubis, J. (2004). A Mechanism
for the Prebiotic Emergence of Proteins. In J. Seckbach, J. Chela Flores, T. Owen,
& F. Raulin (Eds.), Life in the Universe From the Miller Experiment to
the Search for Life on Other Worlds (Vol. 7, pp. 83–87). Springer. https://doi.org/3807
chicago: Vladar, Harold de, Roberto Cipriani, Benjamin Scharifker, and Jose Bubis.
“A Mechanism for the Prebiotic Emergence of Proteins.” In Life in the Universe
From the Miller Experiment to the Search for Life on Other Worlds, edited
by J. Seckbach, J. Chela Flores, T. Owen, and F. Raulin, 7:83–87. Springer, 2004.
https://doi.org/3807.
ieee: H. de Vladar, R. Cipriani, B. Scharifker, and J. Bubis, “A Mechanism for the
Prebiotic Emergence of Proteins,” in Life in the Universe From the Miller Experiment
to the Search for Life on Other Worlds, vol. 7, J. Seckbach, J. Chela Flores,
T. Owen, and F. Raulin, Eds. Springer, 2004, pp. 83–87.
ista: 'de Vladar H, Cipriani R, Scharifker B, Bubis J. 2004.A Mechanism for the
Prebiotic Emergence of Proteins. In: Life in the Universe From the Miller Experiment
to the Search for Life on Other Worlds. Cellular Origin, Life in Extreme Habitats
and Astrobiology, vol. 7, 83–87.'
mla: de Vladar, Harold, et al. “A Mechanism for the Prebiotic Emergence of Proteins.”
Life in the Universe From the Miller Experiment to the Search for Life on Other
Worlds, edited by J. Seckbach et al., vol. 7, Springer, 2004, pp. 83–87, doi:3807.
short: H. de Vladar, R. Cipriani, B. Scharifker, J. Bubis, in:, J. Seckbach, J.
Chela Flores, T. Owen, F. Raulin (Eds.), Life in the Universe From the Miller
Experiment to the Search for Life on Other Worlds, Springer, 2004, pp. 83–87.
date_created: 2018-12-11T12:07:47Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:55:32Z
day: '01'
doi: '3807'
editor:
- first_name: J.
full_name: Seckbach,J.
last_name: Seckbach
- first_name: J.
full_name: Chela-Flores,J.
last_name: Chela Flores
- first_name: T.
full_name: Owen,T.
last_name: Owen
- first_name: F.
full_name: Raulin,F.
last_name: Raulin
extern: 1
intvolume: ' 7'
month: '01'
page: 83 - 87
publication: Life in the Universe From the Miller Experiment to the Search for Life
on Other Worlds
publication_status: published
publisher: Springer
publist_id: '1875'
quality_controlled: 0
status: public
title: A Mechanism for the Prebiotic Emergence of Proteins
type: book_chapter
volume: 7
year: '2004'
...
---
_id: '4253'
abstract:
- lang: eng
text: We consider a single genetic locus which carries two alleles, labelled P and
Q. This locus experiences selection and mutation. It is linked to a second neutral
locus with recombination rate r. If r = 0, this reduces to the study of a single
selected locus. Assuming a Moran model for the population dynamics, we pass to
a diffusion approximation and, assuming that the allele frequencies at the selected
locus have reached stationarity, establish the joint generating function for the
genealogy of a sample from the population and the frequency of the P allele. In
essence this is the joint generating function for a coalescent and the random
background in which it evolves. We use this to characterize, for the diffusion
approximation, the probability of identity in state at the neutral locus of a
sample of two individuals (whose type at the selected locus is known) as solutions
to a system of ordinary differential equations. The only subtlety is to find the
boundary conditions for this system. Finally, numerical examples are presented
that illustrate the accuracy and predictions of the diffusion approximation. In
particular, a comparison is made between this approach and one in which the frequencies
at the selected locus are estimated by their value in the absence of fluctuations
and a classical structured coalescent model is used.
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
- first_name: Anja
full_name: Sturm, Anja K
last_name: Sturm
citation:
ama: Barton NH, Etheridge A, Sturm A. Coalescence in a Random Background. Annals
of Applied Probability. 2004;14(2):754-785.
apa: Barton, N. H., Etheridge, A., & Sturm, A. (2004). Coalescence in a Random
Background. Annals of Applied Probability. Institute of Mathematical Statistics.
chicago: Barton, Nicholas H, Alison Etheridge, and Anja Sturm. “Coalescence in a
Random Background.” Annals of Applied Probability. Institute of Mathematical
Statistics, 2004.
ieee: N. H. Barton, A. Etheridge, and A. Sturm, “Coalescence in a Random Background,”
Annals of Applied Probability, vol. 14, no. 2. Institute of Mathematical
Statistics, pp. 754–785, 2004.
ista: Barton NH, Etheridge A, Sturm A. 2004. Coalescence in a Random Background.
Annals of Applied Probability. 14(2), 754–785.
mla: Barton, Nicholas H., et al. “Coalescence in a Random Background.” Annals
of Applied Probability, vol. 14, no. 2, Institute of Mathematical Statistics,
2004, pp. 754–85.
short: N.H. Barton, A. Etheridge, A. Sturm, Annals of Applied Probability 14 (2004)
754–785.
date_created: 2018-12-11T12:07:52Z
date_published: 2004-05-01T00:00:00Z
date_updated: 2021-01-12T07:55:38Z
day: '01'
extern: 1
intvolume: ' 14'
issue: '2'
main_file_link:
- open_access: '0'
url: http://www.jstor.org/stable/4140427
month: '05'
page: 754 - 785
publication: Annals of Applied Probability
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '1842'
quality_controlled: 0
status: public
title: Coalescence in a Random Background
type: journal_article
volume: 14
year: '2004'
...
---
_id: '3142'
abstract:
- lang: eng
text: Assembly of neuronal circuits is controlled by the sequential acquisition
of neuronal subpopulation-specific identities at progressive developmental steps.
Whereas neuronal features involved in initial phases of differentiation are already
established at cell-cycle exit, recent findings, based mainly on work in the peripheral
nervous system, suggest that the timely integration of signals encountered en
route to targets and from the target region itself is essential to control late
steps in connectivity. As neurons project towards their targets they require target-derived
signals to establish mature axonal projections and acquire neuronal traits such
as the expression of distinct combinations of neurotransmitters. Recent evidence
presented in this review shows that this principle, of a signaling interplay between
target-derived signals and neuronal cell bodies, is often mediated through transcriptional
events and is evolutionarily conserved.
author:
- first_name: Simon
full_name: Simon Hippenmeyer
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Ina
full_name: Kramer, Ina
last_name: Kramer
- first_name: Silvia
full_name: Arber, Silvia
last_name: Arber
citation:
ama: 'Hippenmeyer S, Kramer I, Arber S. Control of neuronal phenotype: What targets
tell the cell bodies. Trends in Neurosciences. 2004;27(8):482-488. doi:10.1016/j.tins.2004.05.012'
apa: 'Hippenmeyer, S., Kramer, I., & Arber, S. (2004). Control of neuronal phenotype:
What targets tell the cell bodies. Trends in Neurosciences. Elsevier. https://doi.org/10.1016/j.tins.2004.05.012'
chicago: 'Hippenmeyer, Simon, Ina Kramer, and Silvia Arber. “Control of Neuronal
Phenotype: What Targets Tell the Cell Bodies.” Trends in Neurosciences.
Elsevier, 2004. https://doi.org/10.1016/j.tins.2004.05.012.'
ieee: 'S. Hippenmeyer, I. Kramer, and S. Arber, “Control of neuronal phenotype:
What targets tell the cell bodies,” Trends in Neurosciences, vol. 27, no.
8. Elsevier, pp. 482–488, 2004.'
ista: 'Hippenmeyer S, Kramer I, Arber S. 2004. Control of neuronal phenotype: What
targets tell the cell bodies. Trends in Neurosciences. 27(8), 482–488.'
mla: 'Hippenmeyer, Simon, et al. “Control of Neuronal Phenotype: What Targets Tell
the Cell Bodies.” Trends in Neurosciences, vol. 27, no. 8, Elsevier, 2004,
pp. 482–88, doi:10.1016/j.tins.2004.05.012.'
short: S. Hippenmeyer, I. Kramer, S. Arber, Trends in Neurosciences 27 (2004) 482–488.
date_created: 2018-12-11T12:01:38Z
date_published: 2004-08-01T00:00:00Z
date_updated: 2019-04-26T07:22:25Z
day: '01'
doi: 10.1016/j.tins.2004.05.012
extern: 1
intvolume: ' 27'
issue: '8'
month: '08'
page: 482 - 488
publication: Trends in Neurosciences
publication_status: published
publisher: Elsevier
publist_id: '3555'
quality_controlled: 0
status: public
title: 'Control of neuronal phenotype: What targets tell the cell bodies'
type: review
volume: 27
year: '2004'
...
---
_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: '3173'
abstract:
- lang: eng
text: In the last few years, several new algorithms based on graph cuts have been
developed to solve energy minimization problems in computer vision. Each of these
techniques constructs a graph such that the minimum cut on the graph also minimizes
the energy. Yet, because these graph constructions are complex and highly specific
to a particular energy function, graph cuts have seen limited application to date.
In this paper, we give a characterization of the energy functions that can be
minimized by graph cuts. Our results are restricted to functions of binary variables.
However, our work generalizes many previous constructions and is easily applicable
to vision problems that involve large numbers of labels, such as stereo, motion,
image restoration, and scene reconstruction. We give a precise characterization
of what energy functions can be minimized using graph cuts, among the energy functions
that can be written as a sum of terms containing three or fewer binary variables.
We also provide a general-purpose construction to minimize such an energy function.
Finally, we give a necessary condition for any energy function of binary variables
to be minimized by graph cuts. Researchers who are considering the use of graph
cuts to optimize a particular energy function can use our results to determine
if this is possible and then follow our construction to create the appropriate
graph. A software implementation is freely available.
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Ramin
full_name: Zabih, Ramin
last_name: Zabih
citation:
ama: Kolmogorov V, Zabih R. What energy functions can be minimized via graph cuts?
. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2004;26(2):147-159.
doi:10.1109/TPAMI.2004.1262177
apa: Kolmogorov, V., & Zabih, R. (2004). What energy functions can be minimized
via graph cuts? . IEEE Transactions on Pattern Analysis and Machine Intelligence.
IEEE. https://doi.org/10.1109/TPAMI.2004.1262177
chicago: Kolmogorov, Vladimir, and Ramin Zabih. “What Energy Functions Can Be Minimized
via Graph Cuts? .” IEEE Transactions on Pattern Analysis and Machine Intelligence.
IEEE, 2004. https://doi.org/10.1109/TPAMI.2004.1262177.
ieee: V. Kolmogorov and R. Zabih, “What energy functions can be minimized via graph
cuts? ,” IEEE Transactions on Pattern Analysis and Machine Intelligence,
vol. 26, no. 2. IEEE, pp. 147–159, 2004.
ista: Kolmogorov V, Zabih R. 2004. What energy functions can be minimized via graph
cuts? . IEEE Transactions on Pattern Analysis and Machine Intelligence. 26(2),
147–159.
mla: Kolmogorov, Vladimir, and Ramin Zabih. “What Energy Functions Can Be Minimized
via Graph Cuts? .” IEEE Transactions on Pattern Analysis and Machine Intelligence,
vol. 26, no. 2, IEEE, 2004, pp. 147–59, doi:10.1109/TPAMI.2004.1262177.
short: V. Kolmogorov, R. Zabih, IEEE Transactions on Pattern Analysis and Machine
Intelligence 26 (2004) 147–159.
date_created: 2018-12-11T12:01:49Z
date_published: 2004-02-01T00:00:00Z
date_updated: 2021-01-12T07:41:34Z
day: '01'
doi: 10.1109/TPAMI.2004.1262177
extern: 1
intvolume: ' 26'
issue: '2'
month: '02'
page: 147 - 159
publication: IEEE Transactions on Pattern Analysis and Machine Intelligence
publication_status: published
publisher: IEEE
publist_id: '3509'
quality_controlled: 0
status: public
title: 'What energy functions can be minimized via graph cuts? '
type: journal_article
volume: 26
year: '2004'
...
---
_id: '3172'
abstract:
- lang: eng
text: The simultaneous multiple volume (SMV) approach in navigator-gated MRI allows
the use of the whole motion range or the entire scan time for the reconstruction
of final images by simultaneously acquiring different image volumes at different
motion states. The motion tolerance range for each volume is kept small, thus
SMV substantially increases the scan efficiency of navigator methods while maintaining
the effectiveness of motion suppression. This article reports a general implementation
of the SMV approach using a multiprocessor scheduling algorithm. Each motion state
is regarded as a processor and each volume is regarded as a job. An efficient
scheduling that completes all jobs in minimal time is maintained even when the
motion pattern changes. Initial experiments demonstrated that SMV significantly
increased the scan efficiency of navigatorgated MRI.
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Thành
full_name: Nguyen, Thành D
last_name: Nguyen
- first_name: Anthony
full_name: Nuval, Anthony
last_name: Nuval
- first_name: Pascal
full_name: Spincemaille, Pascal
last_name: Spincemaille
- first_name: Martin
full_name: Prince, Martin R
last_name: Prince
- first_name: Ramin
full_name: Zabih, Ramin
last_name: Zabih
- first_name: Yusu
full_name: Wang, Yusu
last_name: Wang
citation:
ama: Kolmogorov V, Nguyen T, Nuval A, et al. Multiprocessor scheduling implementation
of the simultaneous multiple volume SMV navigator method. Magnetic Resonance
in Medicine. 2004;52(2):362-367. doi:10.1002/mrm.20162
apa: Kolmogorov, V., Nguyen, T., Nuval, A., Spincemaille, P., Prince, M., Zabih,
R., & Wang, Y. (2004). Multiprocessor scheduling implementation of the simultaneous
multiple volume SMV navigator method. Magnetic Resonance in Medicine. Wiley-Blackwell.
https://doi.org/10.1002/mrm.20162
chicago: Kolmogorov, Vladimir, Thành Nguyen, Anthony Nuval, Pascal Spincemaille,
Martin Prince, Ramin Zabih, and Yusu Wang. “Multiprocessor Scheduling Implementation
of the Simultaneous Multiple Volume SMV Navigator Method.” Magnetic Resonance
in Medicine. Wiley-Blackwell, 2004. https://doi.org/10.1002/mrm.20162.
ieee: V. Kolmogorov et al., “Multiprocessor scheduling implementation of
the simultaneous multiple volume SMV navigator method,” Magnetic Resonance
in Medicine, vol. 52, no. 2. Wiley-Blackwell, pp. 362–367, 2004.
ista: Kolmogorov V, Nguyen T, Nuval A, Spincemaille P, Prince M, Zabih R, Wang Y.
2004. Multiprocessor scheduling implementation of the simultaneous multiple volume
SMV navigator method. Magnetic Resonance in Medicine. 52(2), 362–367.
mla: Kolmogorov, Vladimir, et al. “Multiprocessor Scheduling Implementation of the
Simultaneous Multiple Volume SMV Navigator Method.” Magnetic Resonance in Medicine,
vol. 52, no. 2, Wiley-Blackwell, 2004, pp. 362–67, doi:10.1002/mrm.20162.
short: V. Kolmogorov, T. Nguyen, A. Nuval, P. Spincemaille, M. Prince, R. Zabih,
Y. Wang, Magnetic Resonance in Medicine 52 (2004) 362–367.
date_created: 2018-12-11T12:01:48Z
date_published: 2004-08-01T00:00:00Z
date_updated: 2021-01-12T07:41:34Z
day: '01'
doi: 10.1002/mrm.20162
extern: 1
intvolume: ' 52'
issue: '2'
month: '08'
page: 362 - 367
publication: Magnetic Resonance in Medicine
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3508'
quality_controlled: 0
status: public
title: Multiprocessor scheduling implementation of the simultaneous multiple volume
SMV navigator method
type: journal_article
volume: 52
year: '2004'
...
---
_id: '3177'
abstract:
- lang: eng
text: Feature space clustering is a popular approach to image segmentation, in which
a feature vector of local properties (such as intensity, texture or motion) is
computed at each pixel. The feature space is then clustered, and each pixel is
labeled with the cluster that contains its feature vector. A major limitation
of this approach is that feature space clusters generally lack spatial coherence
(i.e., they do not correspond to a compact grouping of pixels). In this paper,
we propose a segmentation algorithm that operates simultaneously in feature space
and in image space. We define an energy function over both a set of clusters and
a labeling of pixels with clusters. In our framework, a pixel is labeled with
a single cluster (rather than, for example, a distribution over clusters). Our
energy function penalizes clusters that are a poor fit to the data in feature
space, and also penalizes clusters whose pixels lack spatial coherence. The energy
function can be efficiently minimized using graph cuts. Our algorithm can incorporate
both parametric and non-parametric clustering methods. It can be applied to many
optimization-based clustering methods, including k-means and k-medians, and can
handle models which are very close in feature space. Preliminary results are presented
on segmenting real and synthetic images, using both parametric and non-parametric
clustering.
author:
- first_name: Ramin
full_name: Zabih, Ramin
last_name: Zabih
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Zabih R, Kolmogorov V. Spatially coherent clustering using graph cuts. In:
Vol 2. IEEE; 2004:437-444. doi:10.1109/CVPR.2004.1315196'
apa: 'Zabih, R., & Kolmogorov, V. (2004). Spatially coherent clustering using
graph cuts (Vol. 2, pp. 437–444). Presented at the CVPR: Computer Vision and Pattern
Recognition, IEEE. https://doi.org/10.1109/CVPR.2004.1315196'
chicago: Zabih, Ramin, and Vladimir Kolmogorov. “Spatially Coherent Clustering Using
Graph Cuts,” 2:437–44. IEEE, 2004. https://doi.org/10.1109/CVPR.2004.1315196.
ieee: 'R. Zabih and V. Kolmogorov, “Spatially coherent clustering using graph cuts,”
presented at the CVPR: Computer Vision and Pattern Recognition, 2004, vol. 2,
pp. 437–444.'
ista: 'Zabih R, Kolmogorov V. 2004. Spatially coherent clustering using graph cuts.
CVPR: Computer Vision and Pattern Recognition vol. 2, 437–444.'
mla: Zabih, Ramin, and Vladimir Kolmogorov. Spatially Coherent Clustering Using
Graph Cuts. Vol. 2, IEEE, 2004, pp. 437–44, doi:10.1109/CVPR.2004.1315196.
short: R. Zabih, V. Kolmogorov, in:, IEEE, 2004, pp. 437–444.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:01:50Z
date_published: 2004-06-01T00:00:00Z
date_updated: 2021-01-12T07:41:36Z
day: '01'
doi: 10.1109/CVPR.2004.1315196
extern: 1
intvolume: ' 2'
month: '06'
page: 437 - 444
publication_status: published
publisher: IEEE
publist_id: '3506'
quality_controlled: 0
status: public
title: Spatially coherent clustering using graph cuts
type: conference
volume: 2
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: '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: '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: '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'
...