--- _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' ...