--- _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' ...