---
_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'
...
---
_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: '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: '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: '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: '3918'
abstract:
- lang: eng
text: Wingless (ergatoid) males of the tramp ant Cardiocondyla minutior attack and
kill their young ergatoid rivals and thus attempt to monopolize mating with female
sexuals reared in the colony. Because of the different strength of local mate
competition in colonies with one or several reproductive queens, we expected the
production of new ergatoid males to vary with queen number. Sex ratios were mostly
female-biased, but in contrast to the sympatric species C. obscurior (Cremer and
Heinze, 2002) neither the percentage of ergatoid males nor of female sexuals among
the first 20 sexuals produced varied considerably with queen number. As in C.
obscurior, experimental colony fragmentation led to the production of winged males,
whereas in unfragmented control colonies only ergatoid males eclosed.
author:
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
- first_name: A.
full_name: Böttcher, A.
last_name: Böttcher
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: Heinze J, Böttcher A, Cremer S. Production of winged and wingless males in
the ant, Cardiocondyla minutior. Insectes Sociaux. 2004;51(3):275-278.
doi:10.1007/s00040-004-0740-6
apa: Heinze, J., Böttcher, A., & Cremer, S. (2004). Production of winged and
wingless males in the ant, Cardiocondyla minutior. Insectes Sociaux. Springer.
https://doi.org/10.1007/s00040-004-0740-6
chicago: Heinze, Jürgen, A. Böttcher, and Sylvia Cremer. “Production of Winged and
Wingless Males in the Ant, Cardiocondyla Minutior.” Insectes Sociaux. Springer,
2004. https://doi.org/10.1007/s00040-004-0740-6.
ieee: J. Heinze, A. Böttcher, and S. Cremer, “Production of winged and wingless
males in the ant, Cardiocondyla minutior,” Insectes Sociaux, vol. 51, no.
3. Springer, pp. 275–278, 2004.
ista: Heinze J, Böttcher A, Cremer S. 2004. Production of winged and wingless males
in the ant, Cardiocondyla minutior. Insectes Sociaux. 51(3), 275–278.
mla: Heinze, Jürgen, et al. “Production of Winged and Wingless Males in the Ant,
Cardiocondyla Minutior.” Insectes Sociaux, vol. 51, no. 3, Springer, 2004,
pp. 275–78, doi:10.1007/s00040-004-0740-6.
short: J. Heinze, A. Böttcher, S. Cremer, Insectes Sociaux 51 (2004) 275–278.
date_created: 2018-12-11T12:05:53Z
date_published: 2004-08-19T00:00:00Z
date_updated: 2021-01-12T07:53:11Z
day: '19'
doi: 10.1007/s00040-004-0740-6
extern: '1'
intvolume: ' 51'
issue: '3'
language:
- iso: eng
month: '08'
oa_version: None
page: 275 - 278
publication: Insectes Sociaux
publication_status: published
publisher: Springer
publist_id: '2236'
status: public
title: Production of winged and wingless males in the ant, Cardiocondyla minutior
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 51
year: '2004'
...
---
_id: '3988'
abstract:
- lang: eng
text: We give an algorithm that locally improves the fit between two proteins modeled
as space-filling diagrams. The algorithm defines the fit in purely geometric terms
and improves by applying a rigid motion to one of the two proteins. Our implementation
of the algorithm takes between three and ten seconds and converges with high likelihood
to the correct docked configuration, provided it starts at a position away from
the correct one by at most 18 degrees of rotation and at most 3.0Angstrom of translation.
The speed and convergence radius make this an attractive algorithm to use in combination
with a coarse sampling of the six-dimensional space of rigid motions.
acknowledgement: Supported by NSF under grant CCR-00-86013, BGT Postdoc Program from
Duke University and NIH under grant R01 GM61822-01.
alternative_title:
- LNCS
author:
- first_name: Vicky
full_name: Choi, Vicky
last_name: Choi
- 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: Johannes
full_name: Rudolph, Johannes
last_name: Rudolph
citation:
ama: 'Choi V, Agarwal P, Edelsbrunner H, Rudolph J. Local search heuristic for rigid
protein docking. In: Vol 3240. Springer; 2004:218-229. doi:10.1007/978-3-540-30219-3_19'
apa: 'Choi, V., Agarwal, P., Edelsbrunner, H., & Rudolph, J. (2004). Local search
heuristic for rigid protein docking (Vol. 3240, pp. 218–229). Presented at the
WABI: 4th International Workshop on Algorithms in Bioinformatics, Springer. https://doi.org/10.1007/978-3-540-30219-3_19'
chicago: Choi, Vicky, Pankaj Agarwal, Herbert Edelsbrunner, and Johannes Rudolph.
“Local Search Heuristic for Rigid Protein Docking,” 3240:218–29. Springer, 2004.
https://doi.org/10.1007/978-3-540-30219-3_19.
ieee: 'V. Choi, P. Agarwal, H. Edelsbrunner, and J. Rudolph, “Local search heuristic
for rigid protein docking,” presented at the WABI: 4th International Workshop
on Algorithms in Bioinformatics, 2004, vol. 3240, pp. 218–229.'
ista: 'Choi V, Agarwal P, Edelsbrunner H, Rudolph J. 2004. Local search heuristic
for rigid protein docking. WABI: 4th International Workshop on Algorithms in Bioinformatics,
LNCS, vol. 3240, 218–229.'
mla: Choi, Vicky, et al. Local Search Heuristic for Rigid Protein Docking.
Vol. 3240, Springer, 2004, pp. 218–29, doi:10.1007/978-3-540-30219-3_19.
short: V. Choi, P. Agarwal, H. Edelsbrunner, J. Rudolph, in:, Springer, 2004, pp.
218–229.
conference:
name: 'WABI: 4th International Workshop on Algorithms in Bioinformatics'
date_created: 2018-12-11T12:06:17Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:53:41Z
day: '01'
doi: 10.1007/978-3-540-30219-3_19
extern: 1
intvolume: ' 3240'
month: '01'
page: 218 - 229
publication_status: published
publisher: Springer
publist_id: '2136'
quality_controlled: 0
status: public
title: Local search heuristic for rigid protein docking
type: conference
volume: 3240
year: '2004'
...
---
_id: '3986'
abstract:
- lang: eng
text: The motion of a biomolecule greatly depends on the engulfing solution, which
is mostly water. Instead of representing individual water molecules, it is desirable
to develop implicit solvent models that nevertheless accurately represent the
contribution of the solvent interaction to the motion. In such models, hydrophobicity
is expressed as a weighted sum of atomic surface areas. The derivatives of these
weighted areas contribute to the force that drives the motion. In this paper we
give formulas for the weighted and unweighted area derivatives of a molecule modeled
as a space-filling diagram made up of balls in motion. Other than the radii and
the centers of the balls, the formulas are given in terms of the sizes of circular
arcs of the boundary and edges of the power diagram. We also give inclusion-exclusion
formulas for these sizes.
acknowledgement: Partially supported by NSF under grant CCR-00-86013 and NSF under
grant CCR-97-12088.
author:
- first_name: Robert
full_name: Bryant, Robert
last_name: Bryant
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Patrice
full_name: Koehl, Patrice
last_name: Koehl
- first_name: Michael
full_name: Levitt, Michael
last_name: Levitt
citation:
ama: Bryant R, Edelsbrunner H, Koehl P, Levitt M. The area derivative of a space-filling
diagram. Discrete & Computational Geometry. 2004;32(3):293-308. doi:10.1007/s00454-004-1099-1
apa: Bryant, R., Edelsbrunner, H., Koehl, P., & Levitt, M. (2004). The area
derivative of a space-filling diagram. Discrete & Computational Geometry.
Springer. https://doi.org/10.1007/s00454-004-1099-1
chicago: Bryant, Robert, Herbert Edelsbrunner, Patrice Koehl, and Michael Levitt.
“The Area Derivative of a Space-Filling Diagram.” Discrete & Computational
Geometry. Springer, 2004. https://doi.org/10.1007/s00454-004-1099-1.
ieee: R. Bryant, H. Edelsbrunner, P. Koehl, and M. Levitt, “The area derivative
of a space-filling diagram,” Discrete & Computational Geometry, vol.
32, no. 3. Springer, pp. 293–308, 2004.
ista: Bryant R, Edelsbrunner H, Koehl P, Levitt M. 2004. The area derivative of
a space-filling diagram. Discrete & Computational Geometry. 32(3), 293–308.
mla: Bryant, Robert, et al. “The Area Derivative of a Space-Filling Diagram.” Discrete
& Computational Geometry, vol. 32, no. 3, Springer, 2004, pp. 293–308,
doi:10.1007/s00454-004-1099-1.
short: R. Bryant, H. Edelsbrunner, P. Koehl, M. Levitt, Discrete & Computational
Geometry 32 (2004) 293–308.
date_created: 2018-12-11T12:06:17Z
date_published: 2004-09-01T00:00:00Z
date_updated: 2021-01-12T07:53:40Z
day: '01'
doi: 10.1007/s00454-004-1099-1
extern: 1
intvolume: ' 32'
issue: '3'
month: '09'
page: 293 - 308
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '2141'
quality_controlled: 0
status: public
title: The area derivative of a space-filling diagram
type: journal_article
volume: 32
year: '2004'
...
---
_id: '3984'
abstract:
- lang: eng
text: We combine topological and geometric methods to construct a multiresolution
representation for a function over a two-dimensional domain. In a preprocessing
stage, we create the Morse-Smale complex of the function and progressively simplify
its topology by cancelling pairs of critical points. Based on a simple notion
of dependency among these cancellations, we construct a hierarchical data structure
supporting traversal and reconstruction operations similarly to traditional geometry-based
representations. We use this data structure to extract topologically valid approximations
that satisfy error bounds provided at runtime.
author:
- first_name: Peer
full_name: Bremer, Peer-Timo
last_name: Bremer
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Bernd
full_name: Hamann, Bernd
last_name: Hamann
- first_name: Valerio
full_name: Pascucci, Valerio
last_name: Pascucci
citation:
ama: Bremer P, Edelsbrunner H, Hamann B, Pascucci V. A topological hierarchy for
functions on triangulated surfaces. IEEE Transactions on Visualization and
Computer Graphics. 2004;10(4):385-396. doi:10.1109/TVCG.2004.3
apa: Bremer, P., Edelsbrunner, H., Hamann, B., & Pascucci, V. (2004). A topological
hierarchy for functions on triangulated surfaces. IEEE Transactions on Visualization
and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2004.3
chicago: Bremer, Peer, Herbert Edelsbrunner, Bernd Hamann, and Valerio Pascucci.
“A Topological Hierarchy for Functions on Triangulated Surfaces.” IEEE Transactions
on Visualization and Computer Graphics. IEEE, 2004. https://doi.org/10.1109/TVCG.2004.3.
ieee: P. Bremer, H. Edelsbrunner, B. Hamann, and V. Pascucci, “A topological hierarchy
for functions on triangulated surfaces,” IEEE Transactions on Visualization
and Computer Graphics, vol. 10, no. 4. IEEE, pp. 385–396, 2004.
ista: Bremer P, Edelsbrunner H, Hamann B, Pascucci V. 2004. A topological hierarchy
for functions on triangulated surfaces. IEEE Transactions on Visualization and
Computer Graphics. 10(4), 385–396.
mla: Bremer, Peer, et al. “A Topological Hierarchy for Functions on Triangulated
Surfaces.” IEEE Transactions on Visualization and Computer Graphics, vol.
10, no. 4, IEEE, 2004, pp. 385–96, doi:10.1109/TVCG.2004.3.
short: P. Bremer, H. Edelsbrunner, B. Hamann, V. Pascucci, IEEE Transactions on
Visualization and Computer Graphics 10 (2004) 385–396.
date_created: 2018-12-11T12:06:16Z
date_published: 2004-07-01T00:00:00Z
date_updated: 2021-01-12T07:53:39Z
day: '01'
doi: 10.1109/TVCG.2004.3
extern: 1
intvolume: ' 10'
issue: '4'
month: '07'
page: 385 - 396
publication: IEEE Transactions on Visualization and Computer Graphics
publication_status: published
publisher: IEEE
publist_id: '2139'
quality_controlled: 0
status: public
title: A topological hierarchy for functions on triangulated surfaces
type: journal_article
volume: 10
year: '2004'
...
---
_id: '3987'
abstract:
- lang: eng
text: 'We consider scientific data sets that describe density functions over three-dimensional
geometric domains. Such data sets are often large and coarsened representations
are needed for visualization and analysis. Assuming a tetrahedral mesh representation,
we construct such representations with a simplification algorithm that combines
three goals: the approximation of the function, the preservation of the mesh topology,
and the improvement of the mesh quality. The third goal is achieved with a novel
extension of the well-known quadric error metric. We perform a number of computational
experiments to understand the effect of mesh quality improvement on the density
map approximation. In addition, we study the effect of geometric simplification
on the topological features of the function by monitoring its critical points.'
author:
- first_name: Vijay
full_name: Natarajan, Vijay
last_name: Natarajan
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: Natarajan V, Edelsbrunner H. Simplification of three-dimensional density maps.
IEEE Transactions on Visualization and Computer Graphics. 2004;10(5):587-597.
doi:10.1109/TVCG.2004.32
apa: Natarajan, V., & Edelsbrunner, H. (2004). Simplification of three-dimensional
density maps. IEEE Transactions on Visualization and Computer Graphics.
IEEE. https://doi.org/10.1109/TVCG.2004.32
chicago: Natarajan, Vijay, and Herbert Edelsbrunner. “Simplification of Three-Dimensional
Density Maps.” IEEE Transactions on Visualization and Computer Graphics.
IEEE, 2004. https://doi.org/10.1109/TVCG.2004.32.
ieee: V. Natarajan and H. Edelsbrunner, “Simplification of three-dimensional density
maps,” IEEE Transactions on Visualization and Computer Graphics, vol. 10,
no. 5. IEEE, pp. 587–597, 2004.
ista: Natarajan V, Edelsbrunner H. 2004. Simplification of three-dimensional density
maps. IEEE Transactions on Visualization and Computer Graphics. 10(5), 587–597.
mla: Natarajan, Vijay, and Herbert Edelsbrunner. “Simplification of Three-Dimensional
Density Maps.” IEEE Transactions on Visualization and Computer Graphics,
vol. 10, no. 5, IEEE, 2004, pp. 587–97, doi:10.1109/TVCG.2004.32.
short: V. Natarajan, H. Edelsbrunner, IEEE Transactions on Visualization and Computer
Graphics 10 (2004) 587–597.
date_created: 2018-12-11T12:06:17Z
date_published: 2004-07-12T00:00:00Z
date_updated: 2021-01-12T07:53:40Z
day: '12'
doi: 10.1109/TVCG.2004.32
extern: 1
intvolume: ' 10'
issue: '5'
month: '07'
page: 587 - 597
publication: IEEE Transactions on Visualization and Computer Graphics
publication_status: published
publisher: IEEE
publist_id: '2142'
quality_controlled: 0
status: public
title: Simplification of three-dimensional density maps
type: journal_article
volume: 10
year: '2004'
...
---
_id: '3985'
abstract:
- lang: eng
text: Given a Morse function f over a 2-manifold with or without boundary, the Reeb
graph is obtained by contracting the connected components of the level sets to
points. We prove tight upper and lower bounds on the number of loops in the Reeb
graph that depend on the genus, the number of boundary components, and whether
or not the 2-manifold is orientable. We also give an algorithm that constructs
the Reeb graph in time O(n log n), where n is the number of edges in the triangulation
used to represent the 2-manifold and the Morse function.
acknowledgement: Partially supported by NSF under Grants EIA-99-72879 and CCR-00-86013.
author:
- first_name: Kree
full_name: Cole-McLaughlin, Kree
last_name: Cole Mclaughlin
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: John
full_name: Harer, John
last_name: Harer
- first_name: Vijay
full_name: Natarajan, Vijay
last_name: Natarajan
- first_name: Valerio
full_name: Pascucci, Valerio
last_name: Pascucci
citation:
ama: Cole Mclaughlin K, Edelsbrunner H, Harer J, Natarajan V, Pascucci V. Loops
in Reeb graphs of 2-manifolds. Discrete & Computational Geometry. 2004;32(2):231-244.
doi:10.1007/s00454-004-1122-6
apa: Cole Mclaughlin, K., Edelsbrunner, H., Harer, J., Natarajan, V., & Pascucci,
V. (2004). Loops in Reeb graphs of 2-manifolds. Discrete & Computational
Geometry. Springer. https://doi.org/10.1007/s00454-004-1122-6
chicago: Cole Mclaughlin, Kree, Herbert Edelsbrunner, John Harer, Vijay Natarajan,
and Valerio Pascucci. “Loops in Reeb Graphs of 2-Manifolds.” Discrete &
Computational Geometry. Springer, 2004. https://doi.org/10.1007/s00454-004-1122-6.
ieee: K. Cole Mclaughlin, H. Edelsbrunner, J. Harer, V. Natarajan, and V. Pascucci,
“Loops in Reeb graphs of 2-manifolds,” Discrete & Computational Geometry,
vol. 32, no. 2. Springer, pp. 231–244, 2004.
ista: Cole Mclaughlin K, Edelsbrunner H, Harer J, Natarajan V, Pascucci V. 2004.
Loops in Reeb graphs of 2-manifolds. Discrete & Computational Geometry. 32(2),
231–244.
mla: Cole Mclaughlin, Kree, et al. “Loops in Reeb Graphs of 2-Manifolds.” Discrete
& Computational Geometry, vol. 32, no. 2, Springer, 2004, pp. 231–44,
doi:10.1007/s00454-004-1122-6.
short: K. Cole Mclaughlin, H. Edelsbrunner, J. Harer, V. Natarajan, V. Pascucci,
Discrete & Computational Geometry 32 (2004) 231–244.
date_created: 2018-12-11T12:06:16Z
date_published: 2004-07-01T00:00:00Z
date_updated: 2021-01-12T07:53:39Z
day: '01'
doi: 10.1007/s00454-004-1122-6
extern: 1
intvolume: ' 32'
issue: '2'
month: '07'
page: 231 - 244
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '2140'
quality_controlled: 0
status: public
title: Loops in Reeb graphs of 2-manifolds
type: journal_article
volume: 32
year: '2004'
...
---
_id: '3989'
abstract:
- lang: eng
text: We introduce local and global comparison measures for a collection of k less
than or equal to d real-valued smooth functions on a common d-dimensional Riemannian
manifold. For k = d = 2 we relate the measures to the set of critical points of
one function restricted to the level sets of the other. The definition of the
measures extends to piecewise linear functions for which they ace easy to compute.
The computation of the measures forms the centerpiece of a software tool which
we use to study scientific datasets.
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
- first_name: Vijay
full_name: Natarajan, Vijay
last_name: Natarajan
- first_name: Valerio
full_name: Pascucci, Valerio
last_name: Pascucci
citation:
ama: 'Edelsbrunner H, Harer J, Natarajan V, Pascucci V. Local and global comparison
of continuous functions. In: IEEE; 2004:275-280. doi:10.1109/VISUAL.2004.68'
apa: 'Edelsbrunner, H., Harer, J., Natarajan, V., & Pascucci, V. (2004). Local
and global comparison of continuous functions (pp. 275–280). Presented at the
VIS: IEEE Visualization, IEEE. https://doi.org/10.1109/VISUAL.2004.68'
chicago: Edelsbrunner, Herbert, John Harer, Vijay Natarajan, and Valerio Pascucci.
“Local and Global Comparison of Continuous Functions,” 275–80. IEEE, 2004. https://doi.org/10.1109/VISUAL.2004.68.
ieee: 'H. Edelsbrunner, J. Harer, V. Natarajan, and V. Pascucci, “Local and global
comparison of continuous functions,” presented at the VIS: IEEE Visualization,
2004, pp. 275–280.'
ista: 'Edelsbrunner H, Harer J, Natarajan V, Pascucci V. 2004. Local and global
comparison of continuous functions. VIS: IEEE Visualization, 275–280.'
mla: Edelsbrunner, Herbert, et al. Local and Global Comparison of Continuous
Functions. IEEE, 2004, pp. 275–80, doi:10.1109/VISUAL.2004.68.
short: H. Edelsbrunner, J. Harer, V. Natarajan, V. Pascucci, in:, IEEE, 2004, pp.
275–280.
conference:
name: 'VIS: IEEE Visualization'
date_created: 2018-12-11T12:06:18Z
date_published: 2004-10-01T00:00:00Z
date_updated: 2021-01-12T07:53:41Z
day: '01'
doi: 10.1109/VISUAL.2004.68
extern: 1
month: '10'
page: 275 - 280
publication_status: published
publisher: IEEE
publist_id: '2137'
quality_controlled: 0
status: public
title: Local and global comparison of continuous functions
type: conference
year: '2004'
...
---
_id: '4172'
abstract:
- lang: eng
text: 'During vertebrate gastrulation, a relatively limited number of blastodermal
cells undergoes a stereotypical set of cellular movements that leads to formation
of the three germ layers: ectoderm, mesoderm and endoderm. Gastrulation, therefore,
provides a unique developmental system in which to study cell movements in vivo
in a fairly simple cellular context. Recent advances have been made in elucidating
the cellular and molecular mechanisms that underlie cell movements during zebrafish
gastrulation. These findings can be compared with observations made in other model
systems to identify potential general mechanisms of cell migration during development.'
article_processing_charge: No
author:
- first_name: Juan
full_name: Montero, Juan
last_name: Montero
- 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: 'Montero J, Heisenberg C-PJ. Gastrulation dynamics: cells move into focus.
Trends in Cell Biology. 2004;14(11):620-627. doi:10.1016/j.tcb.2004.09.008'
apa: 'Montero, J., & Heisenberg, C.-P. J. (2004). Gastrulation dynamics: cells
move into focus. Trends in Cell Biology. Cell Press. https://doi.org/10.1016/j.tcb.2004.09.008'
chicago: 'Montero, Juan, and Carl-Philipp J Heisenberg. “Gastrulation Dynamics:
Cells Move into Focus.” Trends in Cell Biology. Cell Press, 2004. https://doi.org/10.1016/j.tcb.2004.09.008.'
ieee: 'J. Montero and C.-P. J. Heisenberg, “Gastrulation dynamics: cells move into
focus,” Trends in Cell Biology, vol. 14, no. 11. Cell Press, pp. 620–627,
2004.'
ista: 'Montero J, Heisenberg C-PJ. 2004. Gastrulation dynamics: cells move into
focus. Trends in Cell Biology. 14(11), 620–627.'
mla: 'Montero, Juan, and Carl-Philipp J. Heisenberg. “Gastrulation Dynamics: Cells
Move into Focus.” Trends in Cell Biology, vol. 14, no. 11, Cell Press,
2004, pp. 620–27, doi:10.1016/j.tcb.2004.09.008.'
short: J. Montero, C.-P.J. Heisenberg, Trends in Cell Biology 14 (2004) 620–627.
date_created: 2018-12-11T12:07:23Z
date_published: 2004-11-01T00:00:00Z
date_updated: 2021-01-12T07:55:02Z
day: '01'
doi: 10.1016/j.tcb.2004.09.008
extern: '1'
intvolume: ' 14'
issue: '11'
language:
- iso: eng
month: '11'
oa_version: None
page: 620 - 627
publication: Trends in Cell Biology
publication_status: published
publisher: Cell Press
publist_id: '1948'
status: public
title: 'Gastrulation dynamics: cells move into focus'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2004'
...
---
_id: '4238'
abstract:
- lang: eng
text: The dynamical basis of tumoral growth has been controversial. Many models
have been proposed to explain cancer development. The descriptions employ exponential,
potential, logistic or Gompertzian growth laws. Some of these models are concerned
with the interaction between cancer and the immunological, system. Among other
properties, these models are concerned with the microscopic behavior of tumors
and the emergence of cancer. We propose a modification of a previous model by
Stepanova, which describes the specific immunological response against cancer.
The modification consists of the substitution of a Gompertian law for the exponential
rate used for tumoral growth. This modification is motivated by the numerous works
confirming that Gompertz's equation correctly describes solid tumor growth. The
modified model predicts that near zero, tumors always tend to grow. Immunological
contraposition never suffices to induce a complete regression of the tumor. Instead,
a stable microscopic equilibrium between cancer and immunological activity can
be attained. In other words, our model predicts that the theory of immune surveillance
is plausible. A macroscopic equilibrium in which the system develops cancer is
also possible. In this case, immunological activity is depleted. This is consistent
with the phenomena of cancer tolerance. Both equilibrium points can coexist or
can exist without the other. In all cases the fixed point at zero tumor size is
unstable. Since immunity cannot induce a complete tumor regression, a therapy
is required. We include constant-dose therapies and show that they are insufficient.
Final levels of immunocompetent cells and tumoral cells are finite, thus post-treatment
regrowth of the tumor is certain. We also evaluate late-intensification therapies
which are successful. They induce an asymptotic regression to zero tumor size.
Immune response is also suppressed by the therapy, and thus plays a negligible
role in the remission. We conclude that treatment evaluation should be successful
without taking into account immunological effects. (C) 2003 Elsevier Ltd. All
rights reserved.
article_processing_charge: No
author:
- first_name: Harold
full_name: de Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: de Vladar
orcid: 0000-0002-5985-7653
- first_name: J.
full_name: González, J.
last_name: González
citation:
ama: de Vladar H, González J. Dynamic response of cancer under the influence of
immunological activity and therapy. Journal of Theoretical Biology. 2004;227(3):335-348.
doi:3801
apa: de Vladar, H., & González, J. (2004). Dynamic response of cancer under
the influence of immunological activity and therapy. Journal of Theoretical
Biology. Elsevier. https://doi.org/3801
chicago: Vladar, Harold de, and J. González. “Dynamic Response of Cancer under the
Influence of Immunological Activity and Therapy.” Journal of Theoretical Biology.
Elsevier, 2004. https://doi.org/3801.
ieee: H. de Vladar and J. González, “Dynamic response of cancer under the influence
of immunological activity and therapy,” Journal of Theoretical Biology,
vol. 227, no. 3. Elsevier, pp. 335–348, 2004.
ista: de Vladar H, González J. 2004. Dynamic response of cancer under the influence
of immunological activity and therapy. Journal of Theoretical Biology. 227(3),
335–348.
mla: de Vladar, Harold, and J. González. “Dynamic Response of Cancer under the Influence
of Immunological Activity and Therapy.” Journal of Theoretical Biology,
vol. 227, no. 3, Elsevier, 2004, pp. 335–48, doi:3801.
short: H. de Vladar, J. González, Journal of Theoretical Biology 227 (2004) 335–348.
date_created: 2018-12-11T12:07:46Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:55:31Z
day: '01'
doi: '3801'
extern: '1'
intvolume: ' 227'
issue: '3'
language:
- iso: eng
month: '01'
oa_version: None
page: 335 - 348
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '1876'
status: public
title: Dynamic response of cancer under the influence of immunological activity and
therapy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 227
year: '2004'
...
---
_id: '4230'
alternative_title:
- Cellular Origin and 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: Hanslmeier A, Kempe S, Seckbach J, eds. Life in
the Universe From the Miller Experiment to the Search for Life on Other Worlds.
Springer; 2004:83-87.'
apa: de Vladar, H., Cipriani, R., Scharifker, B., & Bubis, J. (2004). A mechanism
for the prebiotic emergence of proteins. In A. Hanslmeier, S. Kempe, & J.
Seckbach (Eds.), Life in the Universe From the Miller Experiment to the Search
for Life on Other Worlds (pp. 83–87). Springer.
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 A. Hanslmeier, S. Kempe, and J. Seckbach, 83–87. Springer, 2004.
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, A. Hanslmeier, S. Kempe, and J. Seckbach,
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 and Life in Extreme Habitats
and Astrobiology, , 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 A. Hanslmeier et al., Springer, 2004, pp. 83–87.
short: H. de Vladar, R. Cipriani, B. Scharifker, J. Bubis, in:, A. Hanslmeier, S.
Kempe, J. Seckbach (Eds.), Life in the Universe From the Miller Experiment to
the Search for Life on Other Worlds, Springer, 2004, pp. 83–87.
date_created: 2018-12-11T12:07:44Z
date_published: 2004-12-31T00:00:00Z
date_updated: 2021-01-12T07:55:28Z
day: '31'
editor:
- first_name: A.
full_name: Hanslmeier,A.
last_name: Hanslmeier
- first_name: S.
full_name: Kempe,S.
last_name: Kempe
- first_name: J.
full_name: Seckbach,J.
last_name: Seckbach
extern: 1
month: '12'
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: '1884'
quality_controlled: 0
status: public
title: A mechanism for the prebiotic emergence of proteins
type: book_chapter
year: '2004'
...
---
_id: '4236'
article_processing_charge: No
author:
- first_name: Harold
full_name: de Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: de Vladar
orcid: 0000-0002-5985-7653
citation:
ama: de Vladar H. Métodos no lineales y sus aplicaciones en dinámicas aleatorias
de poblaciones celulares. 2004. doi:3810
apa: de Vladar, H. (2004). Métodos no lineales y sus aplicaciones en dinámicas
aleatorias de poblaciones celulares. Centro de estudios avazados, IVIC. https://doi.org/3810
chicago: Vladar, Harold de. “Métodos No Lineales y Sus Aplicaciones En Dinámicas
Aleatorias de Poblaciones Celulares.” Centro de estudios avazados, IVIC, 2004.
https://doi.org/3810.
ieee: H. de Vladar, “Métodos no lineales y sus aplicaciones en dinámicas aleatorias
de poblaciones celulares,” Centro de estudios avazados, IVIC, 2004.
ista: de Vladar H. 2004. Métodos no lineales y sus aplicaciones en dinámicas aleatorias
de poblaciones celulares. Centro de estudios avazados, IVIC.
mla: de Vladar, Harold. Métodos No Lineales y Sus Aplicaciones En Dinámicas Aleatorias
de Poblaciones Celulares. Centro de estudios avazados, IVIC, 2004, doi:3810.
short: H. de Vladar, Métodos No Lineales y Sus Aplicaciones En Dinámicas Aleatorias
de Poblaciones Celulares, Centro de estudios avazados, IVIC, 2004.
date_created: 2018-12-11T12:07:46Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:55:30Z
day: '01'
doi: '3810'
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
publication_status: published
publisher: Centro de estudios avazados, IVIC
publist_id: '1877'
status: public
title: Métodos no lineales y sus aplicaciones en dinámicas aleatorias de poblaciones
celulares
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2004'
...
---
_id: '4372'
alternative_title:
- LNCS
author:
- first_name: Oded
full_name: Maler, Oded
last_name: Maler
- first_name: Dejan
full_name: Dejan Nickovic
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
citation:
ama: 'Maler O, Nickovic D. Monitoring Temporal Properties of Continuous Signals.
In: Springer; 2004:152-166. doi:1572'
apa: 'Maler, O., & Nickovic, D. (2004). Monitoring Temporal Properties of Continuous
Signals (pp. 152–166). Presented at the FORMATS: Formal Modeling and Analysis
of Timed Systems, Springer. https://doi.org/1572'
chicago: Maler, Oded, and Dejan Nickovic. “Monitoring Temporal Properties of Continuous
Signals,” 152–66. Springer, 2004. https://doi.org/1572.
ieee: 'O. Maler and D. Nickovic, “Monitoring Temporal Properties of Continuous Signals,”
presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, 2004,
pp. 152–166.'
ista: 'Maler O, Nickovic D. 2004. Monitoring Temporal Properties of Continuous Signals.
FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, , 152–166.'
mla: Maler, Oded, and Dejan Nickovic. Monitoring Temporal Properties of Continuous
Signals. Springer, 2004, pp. 152–66, doi:1572.
short: O. Maler, D. Nickovic, in:, Springer, 2004, pp. 152–166.
conference:
name: 'FORMATS: Formal Modeling and Analysis of Timed Systems'
date_created: 2018-12-11T12:08:31Z
date_published: 2004-12-14T00:00:00Z
date_updated: 2021-01-12T07:56:29Z
day: '14'
doi: '1572'
extern: 1
month: '12'
page: 152 - 166
publication_status: published
publisher: Springer
publist_id: '1088'
quality_controlled: 0
status: public
title: Monitoring Temporal Properties of Continuous Signals
type: conference
year: '2004'
...
---
_id: '4424'
abstract:
- lang: eng
text: "The enormous cost and ubiquity of software errors necessitates the need for
techniques and tools that can precisely analyze large systems and prove that they
meet given specifications, or if they don't, return counterexample behaviors showing
how the system fails. Recent advances in model checking, decision procedures,
program analysis and type systems, and a shift of focus to partial specifications
common to several systems (e.g., memory safety and race freedom) have resulted
in several practical verification methods. However, these methods are either precise
or they are scalable, depending on whether they track the values of variables
or only a fixed small set of dataflow facts (e.g., types), and are usually insufficient
for precisely verifying large programs.\r\n\r\nWe describe a new technique called
Lazy Abstraction (LA) which achieves both precision and scalability by localizing
the use of precise information. LA automatically builds, explores and refines
a single abstract model of the program in a way that different parts of the model
exhibit different degrees of precision, namely just enough to verify the desired
property. The algorithm automatically mines the information required by partitioning
mechanical proofs of unsatisfiability of spurious counterexamples into Craig Interpolants.
For multithreaded systems, we give a new technique based on analyzing the behavior
of a single thread executing in a context which is an abstraction of the other
(arbitrarily many) threads. We define novel context models and show how to automatically
infer them and analyze the full system (thread + context) using LA.\r\n\r\nLA
is implemented in BLAST. We have run BLAST on Windows and Linux Device Drivers
to verify API conformance properties, and have used it to find (or guarantee the
absence of) data races in multithreaded Networked Embedded Systems (NESC) applications.
BLAST is able to prove the absence of races in several cases where earlier methods,
which depend on lock-based synchronization, fail."
article_processing_charge: No
author:
- first_name: Ranjit
full_name: Jhala, Ranjit
last_name: Jhala
citation:
ama: Jhala R. Program verification by lazy abstraction. 2004:1-165.
apa: Jhala, R. (2004). Program verification by lazy abstraction. University
of California, Berkeley.
chicago: Jhala, Ranjit. “Program Verification by Lazy Abstraction.” University of
California, Berkeley, 2004.
ieee: R. Jhala, “Program verification by lazy abstraction,” University of California,
Berkeley, 2004.
ista: Jhala R. 2004. Program verification by lazy abstraction. University of California,
Berkeley.
mla: Jhala, Ranjit. Program Verification by Lazy Abstraction. University
of California, Berkeley, 2004, pp. 1–165.
short: R. Jhala, Program Verification by Lazy Abstraction, University of California,
Berkeley, 2004.
date_created: 2018-12-11T12:08:47Z
date_published: 2004-12-01T00:00:00Z
date_updated: 2021-01-12T07:56:52Z
day: '01'
extern: '1'
language:
- iso: eng
month: '12'
oa_version: None
page: 1 - 165
publication_status: published
publisher: University of California, Berkeley
publist_id: '307'
status: public
supervisor:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
title: Program verification by lazy abstraction
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2004'
...
---
_id: '4445'
abstract:
- lang: eng
text: We present a type system for E code, which is an assembly language that manages
the release, interaction, and termination of real-time tasks. E code specifies
a deadline for each task, and the type system ensures that the deadlines are path-insensitive.
We show that typed E programs allow, for given worst-case execution times of tasks,
a simple schedulability analysis. Moreover, the real-time programming language
Giotto can be compiled into typed E~code. This shows that typed E~code identifies
an easily schedulable yet expressive class of real-time programs. We have extended
the Giotto compiler to generate typed E code, and enabled the run-time system
for E code to perform a type and schedulability check before executing the code.
acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327
and by the NSF grants CCR- 0208875 and CCR-0225610.
author:
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Christoph
full_name: Kirsch, Christoph M
last_name: Kirsch
citation:
ama: 'Henzinger TA, Kirsch C. A typed assembly language for real-time programs.
In: ACM; 2004:104-113. doi:10.1145/1017753.1017774'
apa: 'Henzinger, T. A., & Kirsch, C. (2004). A typed assembly language for real-time
programs (pp. 104–113). Presented at the EMSOFT: Embedded Software , ACM. https://doi.org/10.1145/1017753.1017774'
chicago: Henzinger, Thomas A, and Christoph Kirsch. “A Typed Assembly Language for
Real-Time Programs,” 104–13. ACM, 2004. https://doi.org/10.1145/1017753.1017774.
ieee: 'T. A. Henzinger and C. Kirsch, “A typed assembly language for real-time programs,”
presented at the EMSOFT: Embedded Software , 2004, pp. 104–113.'
ista: 'Henzinger TA, Kirsch C. 2004. A typed assembly language for real-time programs.
EMSOFT: Embedded Software , 104–113.'
mla: Henzinger, Thomas A., and Christoph Kirsch. A Typed Assembly Language for
Real-Time Programs. ACM, 2004, pp. 104–13, doi:10.1145/1017753.1017774.
short: T.A. Henzinger, C. Kirsch, in:, ACM, 2004, pp. 104–113.
conference:
name: 'EMSOFT: Embedded Software '
date_created: 2018-12-11T12:08:53Z
date_published: 2004-09-01T00:00:00Z
date_updated: 2021-01-12T07:57:01Z
day: '01'
doi: 10.1145/1017753.1017774
extern: 1
month: '09'
page: 104 - 113
publication_status: published
publisher: ACM
publist_id: '285'
quality_controlled: 0
status: public
title: A typed assembly language for real-time programs
type: conference
year: '2004'
...
---
_id: '4458'
abstract:
- lang: eng
text: 'The success of model checking for large programs depends crucially on the
ability to efficiently construct parsimonious abstractions. A predicate abstraction
is parsimonious if at each control location, it specifies only relationships between
current values of variables, and only those which are required for proving correctness.
Previous methods for automatically refining predicate abstractions until sufficient
precision is obtained do not systematically construct parsimonious abstractions:
predicates usually contain symbolic variables, and are added heuristically and
often uniformly to many or all control locations at once. We use Craig interpolation
to efficiently construct, from a given abstract error trace which cannot be concretized,
a parsominous abstraction that removes the trace. At each location of the trace,
we infer the relevant predicates as an interpolant between the two formulas that
define the past and the future segment of the trace. Each interpolant is a relationship
between current values of program variables, and is relevant only at that particular
program location. It can be found by a linear scan of the proof of infeasibility
of the trace.We develop our method for programs with arithmetic and pointer expressions,
and call-by-value function calls. For function calls, Craig interpolation offers
a systematic way of generating relevant predicates that contain only the local
variables of the function and the values of the formal parameters when the function
was called. We have extended our model checker Blast with predicate discovery
by Craig interpolation, and applied it successfully to C programs with more than
130,000 lines of code, which was not possible with approaches that build less
parsimonious abstractions.'
author:
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ranjit
full_name: Jhala, Ranjit
last_name: Jhala
- first_name: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
- first_name: Kenneth
full_name: McMillan, Kenneth L
last_name: Mcmillan
citation:
ama: 'Henzinger TA, Jhala R, Majumdar R, Mcmillan K. Abstractions from proofs. In:
ACM; 2004:232-244. doi:10.1145/964001.964021'
apa: 'Henzinger, T. A., Jhala, R., Majumdar, R., & Mcmillan, K. (2004). Abstractions
from proofs (pp. 232–244). Presented at the POPL: Principles of Programming Languages,
ACM. https://doi.org/10.1145/964001.964021'
chicago: Henzinger, Thomas A, Ranjit Jhala, Ritankar Majumdar, and Kenneth Mcmillan.
“Abstractions from Proofs,” 232–44. ACM, 2004. https://doi.org/10.1145/964001.964021.
ieee: 'T. A. Henzinger, R. Jhala, R. Majumdar, and K. Mcmillan, “Abstractions from
proofs,” presented at the POPL: Principles of Programming Languages, 2004, pp.
232–244.'
ista: 'Henzinger TA, Jhala R, Majumdar R, Mcmillan K. 2004. Abstractions from proofs.
POPL: Principles of Programming Languages, 232–244.'
mla: Henzinger, Thomas A., et al. Abstractions from Proofs. ACM, 2004, pp.
232–44, doi:10.1145/964001.964021.
short: T.A. Henzinger, R. Jhala, R. Majumdar, K. Mcmillan, in:, ACM, 2004, pp. 232–244.
conference:
name: 'POPL: Principles of Programming Languages'
date_created: 2018-12-11T12:08:57Z
date_published: 2004-04-01T00:00:00Z
date_updated: 2021-01-12T07:57:06Z
day: '01'
doi: 10.1145/964001.964021
extern: 1
month: '04'
page: 232 - 244
publication_status: published
publisher: ACM
publist_id: '270'
quality_controlled: 0
status: public
title: Abstractions from proofs
type: conference
year: '2004'
...
---
_id: '4461'
abstract:
- lang: eng
text: One of the central axioms of extreme programming is the disciplined use of
regression testing during stepwise software development. Due to recent progress
in software model checking, it has become possible to supplement this process
with automatic checks for behavioral safety properties of programs, such as conformance
with locking idioms and other programming protocols and patterns. For efficiency
reasons, all checks must be incremental, i.e., they must reuse partial results
from previous checks in order to avoid all unnecessary repetition of expensive
verification tasks. We show that the lazy-abstraction algorithm, and its implementation
in Blast, can be extended to support the fully automatic and incremental checking
of temporal safety properties during software development.
acknowledgement: 'This work was supported in part by the NSF grants CCR-9988172, CCR-0085949,
and CCR-0234690, the ONR grant N00014-02-1-0671, the DARPA grant F33615-00-C-1693,
and the MARCO grant 98-DT-660. '
alternative_title:
- LNCS
author:
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ranjit
full_name: Jhala, Ranjit
last_name: Jhala
- first_name: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
- first_name: Marco
full_name: Sanvido, Marco A
last_name: Sanvido
citation:
ama: 'Henzinger TA, Jhala R, Majumdar R, Sanvido M. Extreme model checking. In:
Verification: Theory and Practice. Vol 2772. Springer; 2004:332-358. doi:10.1007/978-3-540-39910-0_16'
apa: 'Henzinger, T. A., Jhala, R., Majumdar, R., & Sanvido, M. (2004). Extreme
model checking. In Verification: Theory and Practice (Vol. 2772, pp. 332–358).
Springer. https://doi.org/10.1007/978-3-540-39910-0_16'
chicago: 'Henzinger, Thomas A, Ranjit Jhala, Ritankar Majumdar, and Marco Sanvido.
“Extreme Model Checking.” In Verification: Theory and Practice, 2772:332–58.
Springer, 2004. https://doi.org/10.1007/978-3-540-39910-0_16.'
ieee: 'T. A. Henzinger, R. Jhala, R. Majumdar, and M. Sanvido, “Extreme model checking,”
in Verification: Theory and Practice, vol. 2772, Springer, 2004, pp. 332–358.'
ista: 'Henzinger TA, Jhala R, Majumdar R, Sanvido M. 2004.Extreme model checking.
In: Verification: Theory and Practice. LNCS, vol. 2772, 332–358.'
mla: 'Henzinger, Thomas A., et al. “Extreme Model Checking.” Verification: Theory
and Practice, vol. 2772, Springer, 2004, pp. 332–58, doi:10.1007/978-3-540-39910-0_16.'
short: 'T.A. Henzinger, R. Jhala, R. Majumdar, M. Sanvido, in:, Verification: Theory
and Practice, Springer, 2004, pp. 332–358.'
date_created: 2018-12-11T12:08:58Z
date_published: 2004-02-24T00:00:00Z
date_updated: 2021-01-12T07:57:08Z
day: '24'
doi: 10.1007/978-3-540-39910-0_16
extern: 1
intvolume: ' 2772'
month: '02'
page: 332 - 358
publication: 'Verification: Theory and Practice'
publication_status: published
publisher: Springer
publist_id: '269'
quality_controlled: 0
status: public
title: Extreme model checking
type: book_chapter
volume: 2772
year: '2004'
...
---
_id: '4459'
abstract:
- lang: eng
text: Software model checking has been successful for sequential programs, where
predicate abstraction offers suitable models, and counterexample-guided abstraction
refinement permits the automatic inference of models. When checking concurrent
programs, we need to abstract threads as well as the contexts in which they execute.
Stateless context models, such as predicates on global variables, prove insufficient
for showing the absence of race conditions in many examples. We therefore use
richer context models, which combine (1) predicates for abstracting data state,
(2) control flow quotients for abstracting control state, and (3) counters for
abstracting an unbounded number of threads. We infer suitable context models automatically
by a combination of counterexample-guided abstraction refinement, bisimulation
minimization, circular assume-guarantee reasoning, and parametric reasoning about
an unbounded number of threads. This algorithm, called CIRC, has been implemented
in BLAST and succeeds in checking many examples of NESC code for data races. In
particular, BLAST proves the absence of races in several cases where previous
race checkers give false positives.
author:
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ranjit
full_name: Jhala, Ranjit
last_name: Jhala
- first_name: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
citation:
ama: 'Henzinger TA, Jhala R, Majumdar R. Race checking by context inference. In:
ACM; 2004:1-13. doi:10.1145/996841.996844'
apa: 'Henzinger, T. A., Jhala, R., & Majumdar, R. (2004). Race checking by context
inference (pp. 1–13). Presented at the PLDI: Programming Languages Design and
Implementation, ACM. https://doi.org/10.1145/996841.996844'
chicago: Henzinger, Thomas A, Ranjit Jhala, and Ritankar Majumdar. “Race Checking
by Context Inference,” 1–13. ACM, 2004. https://doi.org/10.1145/996841.996844.
ieee: 'T. A. Henzinger, R. Jhala, and R. Majumdar, “Race checking by context inference,”
presented at the PLDI: Programming Languages Design and Implementation, 2004,
pp. 1–13.'
ista: 'Henzinger TA, Jhala R, Majumdar R. 2004. Race checking by context inference.
PLDI: Programming Languages Design and Implementation, 1–13.'
mla: Henzinger, Thomas A., et al. Race Checking by Context Inference. ACM,
2004, pp. 1–13, doi:10.1145/996841.996844.
short: T.A. Henzinger, R. Jhala, R. Majumdar, in:, ACM, 2004, pp. 1–13.
conference:
name: 'PLDI: Programming Languages Design and Implementation'
date_created: 2018-12-11T12:08:57Z
date_published: 2004-06-01T00:00:00Z
date_updated: 2021-01-12T07:57:07Z
day: '01'
doi: 10.1145/996841.996844
extern: 1
month: '06'
page: 1 - 13
publication_status: published
publisher: ACM
publist_id: '271'
quality_controlled: 0
status: public
title: Race checking by context inference
type: conference
year: '2004'
...
---
_id: '4525'
abstract:
- lang: eng
text: 'We present a new high-level programming language, called xGiotto, for programming
applications with hard real-time constraints. Like its predecessor, xGiotto is
based on the LET (logical execution time) assumption: the programmer specifies
when the outputs of a task become available, and the compiler checks if the specification
can be implemented on a given platform. However, while the predecessor language
xGiotto was purely time-triggered, xGiotto accommodates also asynchronous events.
Indeed, through a mechanism called event scoping, events are the main structuring
principle of the new language. The xGiotto compiler and run-time system implement
event scoping through a tree-based event filter. The compiler also checks programs
for determinism (absence of race conditions).'
acknowledgement: This research is supported by the AFOSR MURI grant F49620-00-1-0327,
the DARPA SEC grant F33615-C-98-3614, the MARCO GSRC grant 98-DT-660, and the NSF
grants CCR-0208875 and CCR-0225610.
alternative_title:
- LNCS
author:
- first_name: Arkadeb
full_name: Ghosal, Arkadeb
last_name: Ghosal
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Christoph
full_name: Kirsch, Christoph M
last_name: Kirsch
- first_name: Marco
full_name: Sanvido, Marco A
last_name: Sanvido
citation:
ama: 'Ghosal A, Henzinger TA, Kirsch C, Sanvido M. Event-driven programming with
logical execution times. In: Vol 2993. Springer; 2004:167-170. doi:10.1007/978-3-540-24743-2_24'
apa: 'Ghosal, A., Henzinger, T. A., Kirsch, C., & Sanvido, M. (2004). Event-driven
programming with logical execution times (Vol. 2993, pp. 167–170). Presented at
the HSCC: Hybrid Systems - Computation and Control, Springer. https://doi.org/10.1007/978-3-540-24743-2_24'
chicago: Ghosal, Arkadeb, Thomas A Henzinger, Christoph Kirsch, and Marco Sanvido.
“Event-Driven Programming with Logical Execution Times,” 2993:167–70. Springer,
2004. https://doi.org/10.1007/978-3-540-24743-2_24.
ieee: 'A. Ghosal, T. A. Henzinger, C. Kirsch, and M. Sanvido, “Event-driven programming
with logical execution times,” presented at the HSCC: Hybrid Systems - Computation
and Control, 2004, vol. 2993, pp. 167–170.'
ista: 'Ghosal A, Henzinger TA, Kirsch C, Sanvido M. 2004. Event-driven programming
with logical execution times. HSCC: Hybrid Systems - Computation and Control,
LNCS, vol. 2993, 167–170.'
mla: Ghosal, Arkadeb, et al. Event-Driven Programming with Logical Execution
Times. Vol. 2993, Springer, 2004, pp. 167–70, doi:10.1007/978-3-540-24743-2_24.
short: A. Ghosal, T.A. Henzinger, C. Kirsch, M. Sanvido, in:, Springer, 2004, pp.
167–170.
conference:
name: 'HSCC: Hybrid Systems - Computation and Control'
date_created: 2018-12-11T12:09:18Z
date_published: 2004-03-12T00:00:00Z
date_updated: 2021-01-12T07:59:26Z
day: '12'
doi: 10.1007/978-3-540-24743-2_24
extern: 1
intvolume: ' 2993'
month: '03'
page: 167 - 170
publication_status: published
publisher: Springer
publist_id: '200'
quality_controlled: 0
status: public
title: Event-driven programming with logical execution times
type: conference
volume: 2993
year: '2004'
...
---
_id: '4555'
abstract:
- lang: eng
text: Strategies in repeated games can be classified as to whether or not they use
memory and/or randomization. We consider Markov decision processes and 2-player
graph games, both of the deterministic and probabilistic varieties. We characterize
when memory and/or randomization are required for winning with respect to various
classes of w-regular objectives, noting particularly when the use of memory can
be traded for the use of randomization. In particular, we show that Markov decision
processes allow randomized memoryless optimal strategies for all M?ller objectives.
Furthermore, we show that 2-player probabilistic graph games allow randomized
memoryless strategies for winning with probability 1 those M?ller objectives which
are upward-closed. Upward-closure means that if a set α of infinitely repeating
vertices is winning, then all supersets of α are also winning.
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Luca
full_name: de Alfaro, Luca
last_name: De Alfaro
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Chatterjee K, De Alfaro L, Henzinger TA. Trading memory for randomness. In:
IEEE; 2004:206-217. doi:10.1109/QEST.2004.10051'
apa: 'Chatterjee, K., De Alfaro, L., & Henzinger, T. A. (2004). Trading memory
for randomness (pp. 206–217). Presented at the QEST: Quantitative Evaluation of
Systems, IEEE. https://doi.org/10.1109/QEST.2004.10051'
chicago: Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “Trading
Memory for Randomness,” 206–17. IEEE, 2004. https://doi.org/10.1109/QEST.2004.10051.
ieee: 'K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “Trading memory for randomness,”
presented at the QEST: Quantitative Evaluation of Systems, 2004, pp. 206–217.'
ista: 'Chatterjee K, De Alfaro L, Henzinger TA. 2004. Trading memory for randomness.
QEST: Quantitative Evaluation of Systems, 206–217.'
mla: Chatterjee, Krishnendu, et al. Trading Memory for Randomness. IEEE,
2004, pp. 206–17, doi:10.1109/QEST.2004.10051.
short: K. Chatterjee, L. De Alfaro, T.A. Henzinger, in:, IEEE, 2004, pp. 206–217.
conference:
name: 'QEST: Quantitative Evaluation of Systems'
date_created: 2018-12-11T12:09:27Z
date_published: 2004-09-30T00:00:00Z
date_updated: 2021-01-12T07:59:40Z
day: '30'
doi: 10.1109/QEST.2004.10051
extern: 1
month: '09'
page: 206 - 217
publication_status: published
publisher: IEEE
publist_id: '155'
quality_controlled: 0
status: public
title: Trading memory for randomness
type: conference
year: '2004'
...
---
_id: '4558'
abstract:
- lang: eng
text: We study perfect-information stochastic parity games. These are two-player
nonterminating games which are played on a graph with turn-based probabilistic
transitions. A play results in an infinite path and the conflicting goals of the
two players are ω-regular path properties, formalized as parity winning conditions.
The qualitative solution of such a game amounts to computing the set of vertices
from which a player has a strategy to win with probability 1 (or with positive
probability). The quantitative solution amounts to computing the value of the
game in every vertex, i.e., the highest probability with which a player can guarantee
satisfaction of his own objective in a play that starts from the vertex.For the
important special case of one-player stochastic parity games (parity Markov decision
processes) we give polynomial-time algorithms both for the qualitative and the
quantitative solution. The running time of the qualitative solution is O(d · m3/2)
for graphs with m edges and d priorities. The quantitative solution is based on
a linear-programming formulation.For the two-player case, we establish the existence
of optimal pure memoryless strategies. This has several important ramifications.
First, it implies that the values of the games are rational. This is in contrast
to the concurrent stochastic parity games of de Alfaro et al.; there, values are
in general algebraic numbers, optimal strategies do not exist, and ε-optimal strategies
have to be mixed and with infinite memory. Second, the existence of optimal pure
memoryless strategies together with the polynomial-time solution forone-player
case implies that the quantitative two-player stochastic parity game problem is
in NP ∩ co-NP. This generalizes a result of Condon for stochastic games with reachability
objectives. It also constitutes an exponential improvement over the best previous
algorithm, which is based on a doubly exponential procedure of de Alfaro and Majumdar
for concurrent stochastic parity games and provides only ε-approximations of the
values.
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Marcin
full_name: Jurdziński, Marcin
last_name: Jurdziński
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Chatterjee K, Jurdziński M, Henzinger TA. Quantitative stochastic parity games.
In: SIAM; 2004:121-130.'
apa: 'Chatterjee, K., Jurdziński, M., & Henzinger, T. A. (2004). Quantitative
stochastic parity games (pp. 121–130). Presented at the SODA: Symposium on Discrete
Algorithms, SIAM.'
chicago: Chatterjee, Krishnendu, Marcin Jurdziński, and Thomas A Henzinger. “Quantitative
Stochastic Parity Games,” 121–30. SIAM, 2004.
ieee: 'K. Chatterjee, M. Jurdziński, and T. A. Henzinger, “Quantitative stochastic
parity games,” presented at the SODA: Symposium on Discrete Algorithms, 2004,
pp. 121–130.'
ista: 'Chatterjee K, Jurdziński M, Henzinger TA. 2004. Quantitative stochastic parity
games. SODA: Symposium on Discrete Algorithms, 121–130.'
mla: Chatterjee, Krishnendu, et al. Quantitative Stochastic Parity Games.
SIAM, 2004, pp. 121–30.
short: K. Chatterjee, M. Jurdziński, T.A. Henzinger, in:, SIAM, 2004, pp. 121–130.
conference:
name: 'SODA: Symposium on Discrete Algorithms'
date_created: 2018-12-11T12:09:28Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T07:59:41Z
day: '01'
extern: 1
month: '01'
page: 121 - 130
publication_status: published
publisher: SIAM
publist_id: '153'
quality_controlled: 0
status: public
title: Quantitative stochastic parity games
type: conference
year: '2004'
...
---
_id: '4556'
abstract:
- lang: eng
text: We study the problem of determining stack boundedness and the exact maximum
stack size for three classes of interrupt-driven programs. Interrupt-driven programs
are used in many real-time applications that require responsive interrupt handling.
In order to ensure responsiveness, programmers often enable interrupt processing
in the body of lower-priority interrupt handlers. In such programs a programming
error can allow interrupt handlers to be interrupted in a cyclic fashion to lead
to an unbounded stack, causing the system to crash. For a restricted class of
interrupt-driven programs, we show that there is a polynomial-time procedure to
check stack boundedness, while determining the exact maximum stack size is PSPACE-complete.
For a larger class of programs, the two problems are both PSPACE-complete, and
for the largest class of programs we consider, the two problems are PSPACE-hard
and can be solved in exponential time. While the complexities are high, our algorithms
are exponential only in the number of handlers, and polynomial in the size of
the program.
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Di
full_name: Ma, Di
last_name: Ma
- first_name: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
- first_name: Tian
full_name: Zhao, Tian
last_name: Zhao
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jens
full_name: Palsberg, Jens
last_name: Palsberg
citation:
ama: Chatterjee K, Ma D, Majumdar R, Zhao T, Henzinger TA, Palsberg J. Stack size
analysis for interrupt-driven programs. Information and Computation. 2004;194(2):144-174.
doi:10.1016/j.ic.2004.06.001
apa: Chatterjee, K., Ma, D., Majumdar, R., Zhao, T., Henzinger, T. A., & Palsberg,
J. (2004). Stack size analysis for interrupt-driven programs. Information and
Computation. Elsevier. https://doi.org/10.1016/j.ic.2004.06.001
chicago: Chatterjee, Krishnendu, Di Ma, Ritankar Majumdar, Tian Zhao, Thomas A Henzinger,
and Jens Palsberg. “Stack Size Analysis for Interrupt-Driven Programs.” Information
and Computation. Elsevier, 2004. https://doi.org/10.1016/j.ic.2004.06.001.
ieee: K. Chatterjee, D. Ma, R. Majumdar, T. Zhao, T. A. Henzinger, and J. Palsberg,
“Stack size analysis for interrupt-driven programs,” Information and Computation,
vol. 194, no. 2. Elsevier, pp. 144–174, 2004.
ista: Chatterjee K, Ma D, Majumdar R, Zhao T, Henzinger TA, Palsberg J. 2004. Stack
size analysis for interrupt-driven programs. Information and Computation. 194(2),
144–174.
mla: Chatterjee, Krishnendu, et al. “Stack Size Analysis for Interrupt-Driven Programs.”
Information and Computation, vol. 194, no. 2, Elsevier, 2004, pp. 144–74,
doi:10.1016/j.ic.2004.06.001.
short: K. Chatterjee, D. Ma, R. Majumdar, T. Zhao, T.A. Henzinger, J. Palsberg,
Information and Computation 194 (2004) 144–174.
date_created: 2018-12-11T12:09:28Z
date_published: 2004-08-11T00:00:00Z
date_updated: 2021-01-12T07:59:40Z
day: '11'
doi: 10.1016/j.ic.2004.06.001
extern: 1
intvolume: ' 194'
issue: '2'
month: '08'
page: 144 - 174
publication: Information and Computation
publication_status: published
publisher: Elsevier
publist_id: '156'
quality_controlled: 0
status: public
title: Stack size analysis for interrupt-driven programs
type: journal_article
volume: 194
year: '2004'
...
---
_id: '4578'
abstract:
- lang: eng
text: 'BLAST is an automatic verification tool for checking temporal safety properties
of C programs. Blast is based on lazy predicate abstraction driven by interpolation-based
predicate discovery. In this paper, we present the Blast specification language.
The language specifies program properties at two levels of precision. At the lower
level, monitor automata are used to specify temporal safety properties of program
executions (traces). At the higher level, relational reachability queries over
program locations are used to combine lower-level trace properties. The two-level
specification language can be used to break down a verification task into several
independent calls of the model-checking engine. In this way, each call to the
model checker may have to analyze only part of the program, or part of the specification,
and may thus succeed in a reduction of the number of predicates needed for the
analysis. In addition, the two-level specification language provides a means for
structuring and maintaining specifications. '
acknowledgement: This research was supported in part by the NSF grants CCR-0085949,
CCR-0234690, and ITR-0326577.
alternative_title:
- LNCS
author:
- first_name: Dirk
full_name: Beyer, Dirk
last_name: Beyer
- first_name: Adam
full_name: Chlipala, Adam J
last_name: Chlipala
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ranjit
full_name: Jhala, Ranjit
last_name: Jhala
- first_name: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
citation:
ama: 'Beyer D, Chlipala A, Henzinger TA, Jhala R, Majumdar R. The BLAST query language
for software verification. In: Vol 3148. Springer; 2004:2-18. doi:10.1007/978-3-540-27864-1_2'
apa: 'Beyer, D., Chlipala, A., Henzinger, T. A., Jhala, R., & Majumdar, R. (2004).
The BLAST query language for software verification (Vol. 3148, pp. 2–18). Presented
at the SAS: Static Analysis Symposium, Springer. https://doi.org/10.1007/978-3-540-27864-1_2'
chicago: Beyer, Dirk, Adam Chlipala, Thomas A Henzinger, Ranjit Jhala, and Ritankar
Majumdar. “The BLAST Query Language for Software Verification,” 3148:2–18. Springer,
2004. https://doi.org/10.1007/978-3-540-27864-1_2.
ieee: 'D. Beyer, A. Chlipala, T. A. Henzinger, R. Jhala, and R. Majumdar, “The BLAST
query language for software verification,” presented at the SAS: Static Analysis
Symposium, 2004, vol. 3148, pp. 2–18.'
ista: 'Beyer D, Chlipala A, Henzinger TA, Jhala R, Majumdar R. 2004. The BLAST query
language for software verification. SAS: Static Analysis Symposium, LNCS, vol.
3148, 2–18.'
mla: Beyer, Dirk, et al. The BLAST Query Language for Software Verification.
Vol. 3148, Springer, 2004, pp. 2–18, doi:10.1007/978-3-540-27864-1_2.
short: D. Beyer, A. Chlipala, T.A. Henzinger, R. Jhala, R. Majumdar, in:, Springer,
2004, pp. 2–18.
conference:
name: 'SAS: Static Analysis Symposium'
date_created: 2018-12-11T12:09:34Z
date_published: 2004-08-17T00:00:00Z
date_updated: 2021-01-12T07:59:50Z
day: '17'
doi: 10.1007/978-3-540-27864-1_2
extern: 1
intvolume: ' 3148'
month: '08'
page: 2 - 18
publication_status: published
publisher: Springer
publist_id: '130'
quality_controlled: 0
status: public
title: The BLAST query language for software verification
type: conference
volume: 3148
year: '2004'
...
---
_id: '4577'
abstract:
- lang: eng
text: While model checking has been successful in uncovering subtle bugs in code,
its adoption in software engineering practice has been hampered by the absence
of a simple interface to the programmer in an integrated development environment.
We describe an integration of the software model checker BLAST into the Eclipse
development environment. We provide a verification interface for practical solutions
for some typical program analysis problems - assertion checking, reachability
analysis, dead code analysis, and test generation - directly on the source code.
The analysis is completely automatic, and assumes no knowledge of model checking
or formal notation. Moreover, the interface supports incremental program verification
to support incremental design and evolution of code.
acknowledgement: This research was supported in part by the NSF grants CCR-0085949,
CCR-0234690, and ITR-0326577.
author:
- first_name: Dirk
full_name: Beyer, Dirk
last_name: Beyer
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ranjit
full_name: Jhala, Ranjit
last_name: Jhala
- first_name: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
citation:
ama: 'Beyer D, Henzinger TA, Jhala R, Majumdar R. An eclipse plug-in for model checking.
In: IEEE; 2004:251-255. doi:10.1109/WPC.2004.1311069 '
apa: 'Beyer, D., Henzinger, T. A., Jhala, R., & Majumdar, R. (2004). An eclipse
plug-in for model checking (pp. 251–255). Presented at the IWPC: Program Comprehension,
IEEE. https://doi.org/10.1109/WPC.2004.1311069
'
chicago: Beyer, Dirk, Thomas A Henzinger, Ranjit Jhala, and Ritankar Majumdar. “An
Eclipse Plug-in for Model Checking,” 251–55. IEEE, 2004. https://doi.org/10.1109/WPC.2004.1311069 .
ieee: 'D. Beyer, T. A. Henzinger, R. Jhala, and R. Majumdar, “An eclipse plug-in
for model checking,” presented at the IWPC: Program Comprehension, 2004, pp. 251–255.'
ista: 'Beyer D, Henzinger TA, Jhala R, Majumdar R. 2004. An eclipse plug-in for
model checking. IWPC: Program Comprehension, 251–255.'
mla: Beyer, Dirk, et al. An Eclipse Plug-in for Model Checking. IEEE, 2004,
pp. 251–55, doi:10.1109/WPC.2004.1311069
.
short: D. Beyer, T.A. Henzinger, R. Jhala, R. Majumdar, in:, IEEE, 2004, pp. 251–255.
conference:
name: 'IWPC: Program Comprehension'
date_created: 2018-12-11T12:09:34Z
date_published: 2004-07-12T00:00:00Z
date_updated: 2021-01-12T07:59:50Z
day: '12'
doi: '10.1109/WPC.2004.1311069 '
extern: 1
month: '07'
page: 251 - 255
publication_status: published
publisher: IEEE
publist_id: '129'
quality_controlled: 0
status: public
title: An eclipse plug-in for model checking
type: conference
year: '2004'
...