[{"date_updated":"2021-01-12T07:44:05Z","day":"01","abstract":[{"lang":"eng","text":"Gamma frequency oscillations (30-100 Hz) have been suggested to underlie various cognitive and motor functions. Here, we examine the generation of gamma oscillation currents in the hippocampus, using two-dimensional, 96-site silicon probes. Two gamma generators were identified, one in the dentate gyrus and another in the CA3-CA1 regions. The coupling strength between the two oscillators varied during both theta and nontheta states. Both pyramidal cells and interneurons were phase-locked to gamma waves. Anatomical connectivity, rather than physical distance, determined the coupling strength of the oscillating neurons. CA3 pyramidal neurons discharged CA3 and CA1 interneurons at latencies indicative of monosynaptic connections. Intrahippocampal gamma oscillation emerges in the CA3 recurrent system, which entrains the CA1 region via its interneurons."}],"month":"01","type":"journal_article","author":[{"full_name":"Jozsef Csicsvari","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","last_name":"Csicsvari"},{"full_name":"Jamieson, Brian G","last_name":"Jamieson","first_name":"Brian"},{"full_name":"Wise, Kensall D","first_name":"Kensall","last_name":"Wise"},{"last_name":"Buzsáki","first_name":"György","full_name":"Buzsáki, György"}],"page":"311 - 322","date_created":"2018-12-11T12:03:48Z","publist_id":"2857","title":"Mechanisms of gamma oscillations in the hippocampus of the behaving rat","volume":37,"year":"2003","publisher":"Elsevier","publication":"Neuron","_id":"3528","publication_status":"published","quality_controlled":0,"doi":"10.1016/S0896-6273(02)01169-8","date_published":"2003-01-01T00:00:00Z","status":"public","citation":{"mla":"Csicsvari, Jozsef L., et al. “Mechanisms of Gamma Oscillations in the Hippocampus of the Behaving Rat.” <i>Neuron</i>, vol. 37, no. 2, Elsevier, 2003, pp. 311–22, doi:<a href=\"https://doi.org/10.1016/S0896-6273(02)01169-8\">10.1016/S0896-6273(02)01169-8</a>.","ista":"Csicsvari JL, Jamieson B, Wise K, Buzsáki G. 2003. Mechanisms of gamma oscillations in the hippocampus of the behaving rat. Neuron. 37(2), 311–322.","apa":"Csicsvari, J. L., Jamieson, B., Wise, K., &#38; Buzsáki, G. (2003). Mechanisms of gamma oscillations in the hippocampus of the behaving rat. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/S0896-6273(02)01169-8\">https://doi.org/10.1016/S0896-6273(02)01169-8</a>","ama":"Csicsvari JL, Jamieson B, Wise K, Buzsáki G. Mechanisms of gamma oscillations in the hippocampus of the behaving rat. <i>Neuron</i>. 2003;37(2):311-322. doi:<a href=\"https://doi.org/10.1016/S0896-6273(02)01169-8\">10.1016/S0896-6273(02)01169-8</a>","short":"J.L. Csicsvari, B. Jamieson, K. Wise, G. Buzsáki, Neuron 37 (2003) 311–322.","ieee":"J. L. Csicsvari, B. Jamieson, K. Wise, and G. Buzsáki, “Mechanisms of gamma oscillations in the hippocampus of the behaving rat,” <i>Neuron</i>, vol. 37, no. 2. Elsevier, pp. 311–322, 2003.","chicago":"Csicsvari, Jozsef L, Brian Jamieson, Kensall Wise, and György Buzsáki. “Mechanisms of Gamma Oscillations in the Hippocampus of the Behaving Rat.” <i>Neuron</i>. Elsevier, 2003. <a href=\"https://doi.org/10.1016/S0896-6273(02)01169-8\">https://doi.org/10.1016/S0896-6273(02)01169-8</a>."},"issue":"2","extern":1,"intvolume":"        37"},{"publication_status":"published","quality_controlled":0,"doi":"10.1152/jn.00116.2003","date_published":"2003-08-01T00:00:00Z","status":"public","citation":{"ama":"Csicsvari JL, Henze D, Jamieson B, et al. Massively parallel recording of unit and local field potentials with silicon-based electrodes. <i>Journal of Neurophysiology</i>. 2003;90(2):1314-1323. doi:<a href=\"https://doi.org/10.1152/jn.00116.2003\">10.1152/jn.00116.2003</a>","mla":"Csicsvari, Jozsef L., et al. “Massively Parallel Recording of Unit and Local Field Potentials with Silicon-Based Electrodes.” <i>Journal of Neurophysiology</i>, vol. 90, no. 2, American Physiological Society, 2003, pp. 1314–23, doi:<a href=\"https://doi.org/10.1152/jn.00116.2003\">10.1152/jn.00116.2003</a>.","ista":"Csicsvari JL, Henze D, Jamieson B, Harris K, Sirota A, Bartho P, Wise K, Buzsáki G. 2003. Massively parallel recording of unit and local field potentials with silicon-based electrodes. Journal of Neurophysiology. 90(2), 1314–1323.","apa":"Csicsvari, J. L., Henze, D., Jamieson, B., Harris, K., Sirota, A., Bartho, P., … Buzsáki, G. (2003). Massively parallel recording of unit and local field potentials with silicon-based electrodes. <i>Journal of Neurophysiology</i>. American Physiological Society. <a href=\"https://doi.org/10.1152/jn.00116.2003\">https://doi.org/10.1152/jn.00116.2003</a>","ieee":"J. L. Csicsvari <i>et al.</i>, “Massively parallel recording of unit and local field potentials with silicon-based electrodes,” <i>Journal of Neurophysiology</i>, vol. 90, no. 2. American Physiological Society, pp. 1314–1323, 2003.","chicago":"Csicsvari, Jozsef L, Darrell Henze, Brian Jamieson, Kenneth Harris, Anton Sirota, Peter Bartho, Kensall Wise, and György Buzsáki. “Massively Parallel Recording of Unit and Local Field Potentials with Silicon-Based Electrodes.” <i>Journal of Neurophysiology</i>. American Physiological Society, 2003. <a href=\"https://doi.org/10.1152/jn.00116.2003\">https://doi.org/10.1152/jn.00116.2003</a>.","short":"J.L. Csicsvari, D. Henze, B. Jamieson, K. Harris, A. Sirota, P. Bartho, K. Wise, G. Buzsáki, Journal of Neurophysiology 90 (2003) 1314–1323."},"issue":"2","intvolume":"        90","extern":1,"abstract":[{"text":"Parallel recording of neuronal activity in the behaving animal is a prerequisite for our understanding of neuronal representation and storage of information. Here we describe the development of micro-machined silicon microelectrode arrays for unit and local field recordings. The two-dimensional probes with 96 or 64 recording sites provided high-density recording of unit and field activity with minimal tissue displacement or damage. The on-chip active circuit eliminated movement and other artifacts and greatly reduced the weight of the headgear. The precise geometry of the recording tips allowed for the estimation of the spatial location of the recorded neurons and for high-resolution estimation of extracellular current source density. Action potentials could be simultaneously recorded from the soma and dendrites of the same neurons. Silicon technology is a promising approach for high-density, high-resolution sampling of neuronal activity in both basic research and prosthetic devices.","lang":"eng"}],"date_updated":"2021-01-12T07:44:05Z","day":"01","month":"08","type":"journal_article","author":[{"last_name":"Csicsvari","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","full_name":"Jozsef Csicsvari"},{"full_name":"Henze, Darrell A","last_name":"Henze","first_name":"Darrell"},{"last_name":"Jamieson","first_name":"Brian","full_name":"Jamieson, Brian G"},{"full_name":"Harris, Kenneth D","last_name":"Harris","first_name":"Kenneth"},{"full_name":"Sirota, Anton M","first_name":"Anton","last_name":"Sirota"},{"last_name":"Bartho","first_name":"Peter","full_name":"Bartho, Peter"},{"last_name":"Wise","first_name":"Kensall","full_name":"Wise, Kensall D"},{"full_name":"Buzsáki, György","last_name":"Buzsáki","first_name":"György"}],"page":"1314 - 1323","publist_id":"2856","date_created":"2018-12-11T12:03:48Z","volume":90,"title":"Massively parallel recording of unit and local field potentials with silicon-based electrodes","year":"2003","publisher":"American Physiological Society","publication":"Journal of Neurophysiology","_id":"3529"},{"date_created":"2018-12-11T12:03:50Z","publist_id":"2849","volume":116,"title":"Hippocampal network patterns of activity in the mouse","day":"15","date_updated":"2021-01-12T07:44:09Z","abstract":[{"text":"Genetic engineering of the mouse brain allows investigators to address novel hypotheses in vivo. Because of the paucity of information on the network patterns of the mouse hippocampus, we investigated the electrical patterns in the behaving animal using multisite silicon probes and wire tetrodes. Theta (6-9 Hz) and gamma (40-100 Hz) oscillations were present during exploration and rapid eye movement sleep. Gamma power and theta power were comodulated and gamma power varied as a function of the theta cycle. Pyramidal cells and putative interneurons were phase-locked to theta oscillations. During immobility, consummatory behaviors and slow-wave sleep, sharp waves were present in cornu ammonis region CA1 of the hippocampus stratum radiatum associated with 140-200-Hz “ripples” in the pyramidal cell layer and population burst of CA1 neurons. In the hilus, large-amplitude “dentate spikes” occurred in association with increased discharge of hilar neurons. The amplitude of field patterns was larger in the mouse than in the rat, likely reflecting the higher neuron density in a smaller brain. We suggest that the main hippocampal network patterns are mediated by similar pathways and mechanisms in mouse and rat. ","lang":"eng"}],"month":"01","type":"journal_article","page":"201 - 211","author":[{"full_name":"Buzsáki, György","last_name":"Buzsáki","first_name":"György"},{"first_name":"Derek","last_name":"Buhl","full_name":"Buhl, Derek L"},{"full_name":"Harris, Kenneth D","first_name":"Kenneth","last_name":"Harris"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","full_name":"Jozsef Csicsvari","first_name":"Jozsef L","last_name":"Csicsvari"},{"last_name":"Czéh","first_name":"Boldizsár","full_name":"Czéh, Boldizsár"},{"last_name":"Morozov","first_name":"Alexei","full_name":"Morozov, Alexei"}],"publication":"Neuroscience","_id":"3536","year":"2003","publisher":"Elsevier","quality_controlled":0,"date_published":"2003-01-15T00:00:00Z","doi":"10.1016/S0306-4522(02)00669-3","publication_status":"published","citation":{"ama":"Buzsáki G, Buhl D, Harris K, Csicsvari JL, Czéh B, Morozov A. Hippocampal network patterns of activity in the mouse. <i>Neuroscience</i>. 2003;116(1):201-211. doi:<a href=\"https://doi.org/10.1016/S0306-4522(02)00669-3\">10.1016/S0306-4522(02)00669-3</a>","mla":"Buzsáki, György, et al. “Hippocampal Network Patterns of Activity in the Mouse.” <i>Neuroscience</i>, vol. 116, no. 1, Elsevier, 2003, pp. 201–11, doi:<a href=\"https://doi.org/10.1016/S0306-4522(02)00669-3\">10.1016/S0306-4522(02)00669-3</a>.","ista":"Buzsáki G, Buhl D, Harris K, Csicsvari JL, Czéh B, Morozov A. 2003. Hippocampal network patterns of activity in the mouse. Neuroscience. 116(1), 201–211.","apa":"Buzsáki, G., Buhl, D., Harris, K., Csicsvari, J. L., Czéh, B., &#38; Morozov, A. (2003). Hippocampal network patterns of activity in the mouse. <i>Neuroscience</i>. Elsevier. <a href=\"https://doi.org/10.1016/S0306-4522(02)00669-3\">https://doi.org/10.1016/S0306-4522(02)00669-3</a>","ieee":"G. Buzsáki, D. Buhl, K. Harris, J. L. Csicsvari, B. Czéh, and A. Morozov, “Hippocampal network patterns of activity in the mouse,” <i>Neuroscience</i>, vol. 116, no. 1. Elsevier, pp. 201–211, 2003.","chicago":"Buzsáki, György, Derek Buhl, Kenneth Harris, Jozsef L Csicsvari, Boldizsár Czéh, and Alexei Morozov. “Hippocampal Network Patterns of Activity in the Mouse.” <i>Neuroscience</i>. Elsevier, 2003. <a href=\"https://doi.org/10.1016/S0306-4522(02)00669-3\">https://doi.org/10.1016/S0306-4522(02)00669-3</a>.","short":"G. Buzsáki, D. Buhl, K. Harris, J.L. Csicsvari, B. Czéh, A. Morozov, Neuroscience 116 (2003) 201–211."},"issue":"1","extern":1,"intvolume":"       116","status":"public"},{"title":"Communication between neocortex and hippocampus during sleep in rodents","volume":100,"publist_id":"2841","date_created":"2018-12-11T12:03:53Z","page":"2065 - 2069","author":[{"full_name":"Sirota, Anton M","last_name":"Sirota","first_name":"Anton"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","full_name":"Jozsef Csicsvari","last_name":"Csicsvari","first_name":"Jozsef L"},{"last_name":"Buhl","first_name":"Derek","full_name":"Buhl, Derek L"},{"full_name":"Buzsáki, György","first_name":"György","last_name":"Buzsáki"}],"type":"journal_article","month":"02","abstract":[{"lang":"eng","text":"Both neocortical and hippocampal networks organize the firing patterns of their neurons by prominent oscillations during sleep, but the functional role of these rhythms is not well understood. Here, we show a robust correlation of neuronal discharges between the somatosensory cortex and hippocampus on both slow and fine time scales in the mouse and rat. Neuronal bursts in deep cortical layers, associated with sleep spindles and delta waves/slow rhythm, effectively triggered hippocampal discharges related to fast (ripple) oscillations. We hypothesize that oscillation-mediated temporal links coordinate specific information transfer between neocortical and hippocampal cell assemblies. Such a neocortical-hippocampal interplay may be important for memory consolidation."}],"day":"18","date_updated":"2021-01-12T07:44:12Z","_id":"3543","publication":"PNAS","publisher":"National Academy of Sciences","year":"2003","date_published":"2003-02-18T00:00:00Z","doi":"10.1073/pnas.0437938100","quality_controlled":0,"publication_status":"published","intvolume":"       100","extern":1,"issue":"4","citation":{"ama":"Sirota A, Csicsvari JL, Buhl D, Buzsáki G. Communication between neocortex and hippocampus during sleep in rodents. <i>PNAS</i>. 2003;100(4):2065-2069. doi:<a href=\"https://doi.org/10.1073/pnas.0437938100\">10.1073/pnas.0437938100</a>","apa":"Sirota, A., Csicsvari, J. L., Buhl, D., &#38; Buzsáki, G. (2003). Communication between neocortex and hippocampus during sleep in rodents. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0437938100\">https://doi.org/10.1073/pnas.0437938100</a>","mla":"Sirota, Anton, et al. “Communication between Neocortex and Hippocampus during Sleep in Rodents.” <i>PNAS</i>, vol. 100, no. 4, National Academy of Sciences, 2003, pp. 2065–69, doi:<a href=\"https://doi.org/10.1073/pnas.0437938100\">10.1073/pnas.0437938100</a>.","ista":"Sirota A, Csicsvari JL, Buhl D, Buzsáki G. 2003. Communication between neocortex and hippocampus during sleep in rodents. PNAS. 100(4), 2065–2069.","chicago":"Sirota, Anton, Jozsef L Csicsvari, Derek Buhl, and György Buzsáki. “Communication between Neocortex and Hippocampus during Sleep in Rodents.” <i>PNAS</i>. National Academy of Sciences, 2003. <a href=\"https://doi.org/10.1073/pnas.0437938100\">https://doi.org/10.1073/pnas.0437938100</a>.","ieee":"A. Sirota, J. L. Csicsvari, D. Buhl, and G. Buzsáki, “Communication between neocortex and hippocampus during sleep in rodents,” <i>PNAS</i>, vol. 100, no. 4. National Academy of Sciences, pp. 2065–2069, 2003.","short":"A. Sirota, J.L. Csicsvari, D. Buhl, G. Buzsáki, PNAS 100 (2003) 2065–2069."},"status":"public"},{"title":"Morse-Smale complexes for piecewise linear 3-manifolds","date_created":"2018-12-11T12:03:57Z","publist_id":"2829","author":[{"first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Herbert Edelsbrunner","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"John","last_name":"Harer","full_name":"Harer, John"},{"last_name":"Natarajan","first_name":"Vijay","full_name":"Natarajan, Vijay"},{"full_name":"Pascucci, Valerio","first_name":"Valerio","last_name":"Pascucci"}],"page":"361 - 370","date_updated":"2021-01-12T07:44:17Z","abstract":[{"lang":"eng","text":"We define the Morse-Smale complex of a Morse function over a 3-manifold as the overlay of the descending and as- cending manifolds of all critical points. In the generic case, its 3-dimensional cells are shaped like crystals and are sepa- rated by quadrangular faces. In this paper, we give a combi- natorial algorithm for constructing such complexes for piece- wise linear data."}],"day":"01","month":"06","type":"conference","_id":"3556","publisher":"ACM","year":"2003","date_published":"2003-06-01T00:00:00Z","doi":"10.1145/777792.777846","main_file_link":[{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.14.9592","open_access":"0"}],"quality_controlled":0,"publication_status":"published","extern":1,"conference":{"name":"SCG: Symposium on Computational Geometry"},"citation":{"ieee":"H. Edelsbrunner, J. Harer, V. Natarajan, and V. Pascucci, “Morse-Smale complexes for piecewise linear 3-manifolds,” presented at the SCG: Symposium on Computational Geometry, 2003, pp. 361–370.","chicago":"Edelsbrunner, Herbert, John Harer, Vijay Natarajan, and Valerio Pascucci. “Morse-Smale Complexes for Piecewise Linear 3-Manifolds,” 361–70. ACM, 2003. <a href=\"https://doi.org/10.1145/777792.777846\">https://doi.org/10.1145/777792.777846</a>.","short":"H. Edelsbrunner, J. Harer, V. Natarajan, V. Pascucci, in:, ACM, 2003, pp. 361–370.","ama":"Edelsbrunner H, Harer J, Natarajan V, Pascucci V. Morse-Smale complexes for piecewise linear 3-manifolds. In: ACM; 2003:361-370. doi:<a href=\"https://doi.org/10.1145/777792.777846\">10.1145/777792.777846</a>","ista":"Edelsbrunner H, Harer J, Natarajan V, Pascucci V. 2003. Morse-Smale complexes for piecewise linear 3-manifolds. SCG: Symposium on Computational Geometry, 361–370.","mla":"Edelsbrunner, Herbert, et al. <i>Morse-Smale Complexes for Piecewise Linear 3-Manifolds</i>. ACM, 2003, pp. 361–70, doi:<a href=\"https://doi.org/10.1145/777792.777846\">10.1145/777792.777846</a>.","apa":"Edelsbrunner, H., Harer, J., Natarajan, V., &#38; Pascucci, V. (2003). Morse-Smale complexes for piecewise linear 3-manifolds (pp. 361–370). Presented at the SCG: Symposium on Computational Geometry, ACM. <a href=\"https://doi.org/10.1145/777792.777846\">https://doi.org/10.1145/777792.777846</a>"},"status":"public"},{"date_created":"2018-12-11T12:04:02Z","publist_id":"2812","title":"Surface reconstruction by wrapping finite sets in space","day":"23","abstract":[{"text":"Given a finite point set in R, the surface reconstruction problem asks for a surface that passes through many but not necessarily all points. We describe an unambigu- ous definition of such a surface in geometric and topological terms, and sketch a fast algorithm for constructing it. Our solution overcomes past limitations to special point distributions and heuristic design decisions.","lang":"eng"}],"date_updated":"2021-01-12T07:44:24Z","type":"book_chapter","month":"06","author":[{"last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Herbert Edelsbrunner","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"page":"379 - 404","publication":"Discrete & Computational Geometry","_id":"3573","year":"2003","publisher":"Springer","main_file_link":[{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.129.3633","open_access":"0"}],"quality_controlled":0,"doi":"10.1007/978-3-642-55566-4_17","date_published":"2003-06-23T00:00:00Z","publication_status":"published","citation":{"ama":"Edelsbrunner H. Surface reconstruction by wrapping finite sets in space. In: <i>Discrete &#38; Computational Geometry</i>. Springer; 2003:379-404. doi:<a href=\"https://doi.org/10.1007/978-3-642-55566-4_17\">10.1007/978-3-642-55566-4_17</a>","apa":"Edelsbrunner, H. (2003). Surface reconstruction by wrapping finite sets in space. In <i>Discrete &#38; Computational Geometry</i> (pp. 379–404). Springer. <a href=\"https://doi.org/10.1007/978-3-642-55566-4_17\">https://doi.org/10.1007/978-3-642-55566-4_17</a>","mla":"Edelsbrunner, Herbert. “Surface Reconstruction by Wrapping Finite Sets in Space.” <i>Discrete &#38; Computational Geometry</i>, Springer, 2003, pp. 379–404, doi:<a href=\"https://doi.org/10.1007/978-3-642-55566-4_17\">10.1007/978-3-642-55566-4_17</a>.","ista":"Edelsbrunner H. 2003.Surface reconstruction by wrapping finite sets in space. In: Discrete &#38; Computational Geometry. , 379–404.","chicago":"Edelsbrunner, Herbert. “Surface Reconstruction by Wrapping Finite Sets in Space.” In <i>Discrete &#38; Computational Geometry</i>, 379–404. Springer, 2003. <a href=\"https://doi.org/10.1007/978-3-642-55566-4_17\">https://doi.org/10.1007/978-3-642-55566-4_17</a>.","ieee":"H. Edelsbrunner, “Surface reconstruction by wrapping finite sets in space,” in <i>Discrete &#38; Computational Geometry</i>, Springer, 2003, pp. 379–404.","short":"H. Edelsbrunner, in:, Discrete &#38; Computational Geometry, Springer, 2003, pp. 379–404."},"extern":1,"status":"public"},{"status":"public","extern":"1","intvolume":"         5","citation":{"ieee":"H. Edelsbrunner and A. Zomorodian, “Computing linking numbers of a filtration,” <i>Homology, Homotopy and Applications</i>, vol. 5, no. 2. International Press, pp. 19–37, 2003.","chicago":"Edelsbrunner, Herbert, and Afra Zomorodian. “Computing Linking Numbers of a Filtration.” <i>Homology, Homotopy and Applications</i>. International Press, 2003.","short":"H. Edelsbrunner, A. Zomorodian, Homology, Homotopy and Applications 5 (2003) 19–37.","ama":"Edelsbrunner H, Zomorodian A. Computing linking numbers of a filtration. <i>Homology, Homotopy and Applications</i>. 2003;5(2):19-37.","mla":"Edelsbrunner, Herbert, and Afra Zomorodian. “Computing Linking Numbers of a Filtration.” <i>Homology, Homotopy and Applications</i>, vol. 5, no. 2, International Press, 2003, pp. 19–37.","ista":"Edelsbrunner H, Zomorodian A. 2003. Computing linking numbers of a filtration. Homology, Homotopy and Applications. 5(2), 19–37.","apa":"Edelsbrunner, H., &#38; Zomorodian, A. (2003). Computing linking numbers of a filtration. <i>Homology, Homotopy and Applications</i>. International Press."},"language":[{"iso":"eng"}],"issue":"2","publication_status":"published","date_published":"2003-04-22T00:00:00Z","main_file_link":[{"url":"http://projecteuclid.org/euclid.hha/1088453320"}],"quality_controlled":"1","publisher":"International Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2003","publication":"Homology, Homotopy and Applications","_id":"3584","page":"19 - 37","author":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"},{"full_name":"Zomorodian, Afra","last_name":"Zomorodian","first_name":"Afra"}],"abstract":[{"text":"We develop fast algorithms for computing the linking number of a simplicial complex within a filtration.We give experimental results in applying our work toward the detection of non-trivial tangling in biomolecules, modeled as alpha complexes.","lang":"eng"}],"day":"22","date_updated":"2021-01-12T07:44:28Z","oa_version":"None","type":"journal_article","month":"04","title":"Computing linking numbers of a filtration","volume":5,"date_created":"2018-12-11T12:04:05Z","publist_id":"2801"},{"doi":"10.1023/A:1023217515688","date_published":"2003-02-01T00:00:00Z","quality_controlled":0,"publication_status":"published","extern":1,"intvolume":"        30","issue":"2","citation":{"apa":"Chatterjee, K., Dasgupta, P., &#38; Chakrabarti, P. (2003). A branching time temporal framework for quantitative reasoning. <i>Journal of Automated Reasoning</i>. Springer. <a href=\"https://doi.org/10.1023/A:1023217515688\">https://doi.org/10.1023/A:1023217515688</a>","mla":"Chatterjee, Krishnendu, et al. “A Branching Time Temporal Framework for Quantitative Reasoning.” <i>Journal of Automated Reasoning</i>, vol. 30, no. 2, Springer, 2003, pp. 205–32, doi:<a href=\"https://doi.org/10.1023/A:1023217515688\">10.1023/A:1023217515688</a>.","ista":"Chatterjee K, Dasgupta P, Chakrabarti P. 2003. A branching time temporal framework for quantitative reasoning. Journal of Automated Reasoning. 30(2), 205–232.","ama":"Chatterjee K, Dasgupta P, Chakrabarti P. A branching time temporal framework for quantitative reasoning. <i>Journal of Automated Reasoning</i>. 2003;30(2):205-232. doi:<a href=\"https://doi.org/10.1023/A:1023217515688\">10.1023/A:1023217515688</a>","short":"K. Chatterjee, P. Dasgupta, P. Chakrabarti, Journal of Automated Reasoning 30 (2003) 205–232.","chicago":"Chatterjee, Krishnendu, Pallab Dasgupta, and Partha Chakrabarti. “A Branching Time Temporal Framework for Quantitative Reasoning.” <i>Journal of Automated Reasoning</i>. Springer, 2003. <a href=\"https://doi.org/10.1023/A:1023217515688\">https://doi.org/10.1023/A:1023217515688</a>.","ieee":"K. Chatterjee, P. Dasgupta, and P. Chakrabarti, “A branching time temporal framework for quantitative reasoning,” <i>Journal of Automated Reasoning</i>, vol. 30, no. 2. Springer, pp. 205–232, 2003."},"status":"public","title":"A branching time temporal framework for quantitative reasoning","volume":30,"date_created":"2018-12-11T12:04:08Z","publist_id":"2790","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Krishnendu Chatterjee"},{"last_name":"Dasgupta","first_name":"Pallab","full_name":"Dasgupta, Pallab"},{"last_name":"Chakrabarti","first_name":"Partha","full_name":"Chakrabarti, Partha P"}],"page":"205 - 232","month":"02","type":"journal_article","date_updated":"2021-01-12T07:44:31Z","abstract":[{"text":"Temporal logics such as Computation Tree Logic (CTL) and Linear Temporal Logic (LTL) have become popular for specifying temporal properties over a wide variety of planning and verification problems. In this paper we work towards building a generalized framework for automated reasoning based on temporal logics. We present a powerful extension of CTL with first-order quantification over the set of reachable states for reasoning about extremal properties of weighted labeled transition systems in general. The proposed logic, which we call Weighted Quantified Computation Tree Logic (WQCTL), captures the essential elements common to the domain of planning and verification problems and can thereby be used as an effective specification language in both domains. We show that in spite of the rich, expressive power of the logic, we are able to evaluate WQCTL formulas in time polynomial in the size of the state space times the length of the formula. Wepresent experimental results on the WQCTL verifier.","lang":"eng"}],"day":"01","_id":"3593","publication":"Journal of Automated Reasoning","publisher":"Springer","year":"2003"},{"type":"journal_article","month":"07","abstract":[{"lang":"eng","text":"There are several analyses in evolutionary ecology which assume that a family of offspring has come from only two parents. Here, we present a simple test for detecting when a batch involves two or more subfamilies. It is based on the fact that the mixing of families generates associations amongst unlinked marker loci. We also present simulations illustrating the power of our method for varying numbers of loci, alleles per locus and genotyped individuals."}],"date_updated":"2021-01-12T07:44:42Z","day":"01","author":[{"last_name":"Vines","first_name":"Timothy","full_name":"Vines, Timothy H"},{"full_name":"Nicholas Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"}],"page":"1999 - 2002","publist_id":"2765","date_created":"2018-12-11T12:04:16Z","volume":12,"title":"A new approach to detecting mixed families","year":"2003","publisher":"Wiley-Blackwell","_id":"3618","publication":"Molecular Ecology","publication_status":"published","quality_controlled":0,"doi":"10.1046/j.1365-294X.2003.01867.x","date_published":"2003-07-01T00:00:00Z","status":"public","issue":"7","citation":{"short":"T. Vines, N.H. Barton, Molecular Ecology 12 (2003) 1999–2002.","ieee":"T. Vines and N. H. Barton, “A new approach to detecting mixed families,” <i>Molecular Ecology</i>, vol. 12, no. 7. Wiley-Blackwell, pp. 1999–2002, 2003.","chicago":"Vines, Timothy, and Nicholas H Barton. “A New Approach to Detecting Mixed Families.” <i>Molecular Ecology</i>. Wiley-Blackwell, 2003. <a href=\"https://doi.org/10.1046/j.1365-294X.2003.01867.x\">https://doi.org/10.1046/j.1365-294X.2003.01867.x</a>.","mla":"Vines, Timothy, and Nicholas H. Barton. “A New Approach to Detecting Mixed Families.” <i>Molecular Ecology</i>, vol. 12, no. 7, Wiley-Blackwell, 2003, pp. 1999–2002, doi:<a href=\"https://doi.org/10.1046/j.1365-294X.2003.01867.x\">10.1046/j.1365-294X.2003.01867.x</a>.","ista":"Vines T, Barton NH. 2003. A new approach to detecting mixed families. Molecular Ecology. 12(7), 1999–2002.","apa":"Vines, T., &#38; Barton, N. H. (2003). A new approach to detecting mixed families. <i>Molecular Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1046/j.1365-294X.2003.01867.x\">https://doi.org/10.1046/j.1365-294X.2003.01867.x</a>","ama":"Vines T, Barton NH. A new approach to detecting mixed families. <i>Molecular Ecology</i>. 2003;12(7):1999-2002. doi:<a href=\"https://doi.org/10.1046/j.1365-294X.2003.01867.x\">10.1046/j.1365-294X.2003.01867.x</a>"},"intvolume":"        12","extern":1},{"publication_status":"published","date_published":"2003-12-01T00:00:00Z","doi":"10.1016/S0040-5809(03)00098-4","quality_controlled":0,"status":"public","extern":1,"intvolume":"        64","issue":"4","citation":{"apa":"Baird, S., Barton, N. H., &#38; Etheridge, A. (2003). The distribution of surviving blocks of an ancestral genome. <i>Theoretical Population Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/S0040-5809(03)00098-4\">https://doi.org/10.1016/S0040-5809(03)00098-4</a>","ista":"Baird S, Barton NH, Etheridge A. 2003. The distribution of surviving blocks of an ancestral genome. Theoretical Population Biology. 64(4), 451–471.","mla":"Baird, Stuart, et al. “The Distribution of Surviving Blocks of an Ancestral Genome.” <i>Theoretical Population Biology</i>, vol. 64, no. 4, Academic Press, 2003, pp. 451–71, doi:<a href=\"https://doi.org/10.1016/S0040-5809(03)00098-4\">10.1016/S0040-5809(03)00098-4</a>.","ama":"Baird S, Barton NH, Etheridge A. The distribution of surviving blocks of an ancestral genome. <i>Theoretical Population Biology</i>. 2003;64(4):451-471. doi:<a href=\"https://doi.org/10.1016/S0040-5809(03)00098-4\">10.1016/S0040-5809(03)00098-4</a>","short":"S. Baird, N.H. Barton, A. Etheridge, Theoretical Population Biology 64 (2003) 451–471.","chicago":"Baird, Stuart, Nicholas H Barton, and Alison Etheridge. “The Distribution of Surviving Blocks of an Ancestral Genome.” <i>Theoretical Population Biology</i>. Academic Press, 2003. <a href=\"https://doi.org/10.1016/S0040-5809(03)00098-4\">https://doi.org/10.1016/S0040-5809(03)00098-4</a>.","ieee":"S. Baird, N. H. Barton, and A. Etheridge, “The distribution of surviving blocks of an ancestral genome,” <i>Theoretical Population Biology</i>, vol. 64, no. 4. Academic Press, pp. 451–471, 2003."},"author":[{"full_name":"Baird, Stuart J","first_name":"Stuart","last_name":"Baird"},{"full_name":"Nicholas Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"},{"last_name":"Etheridge","first_name":"Alison","full_name":"Etheridge, Alison M"}],"page":"451 - 471","month":"12","type":"journal_article","date_updated":"2021-01-12T07:44:42Z","abstract":[{"text":"What is the chance that some part of a stretch of genome will survive? In a population of constant size, and with no selection, the probability of survival of some part of a stretch of map length y&lt;1 approaches View the MathML source for View the MathML source. Thus, the whole genome is certain to be lost, but the rate of loss is extremely slow. This solution extends to give the whole distribution of surviving block sizes as a function of time. We show that the expected number of blocks at time t is 1+yt and give expressions for the moments of the number of blocks and the total amount of genome that survives for a given time. The solution is based on a branching process and assumes complete interference between crossovers, so that each descendant carries only a single block of ancestral material. We consider cases where most individuals carry multiple blocks, either because there are multiple crossovers in a long genetic map, or because enough time has passed that most individuals in the population are related to each other. For species such as ours, which have a long genetic map, the genome of any individual which leaves descendants (∼80% of the population for a Poisson offspring number with mean two) is likely to persist for an extremely long time, in the form of a few short blocks of genome.","lang":"eng"}],"day":"01","title":"The distribution of surviving blocks of an ancestral genome","volume":64,"date_created":"2018-12-11T12:04:17Z","publist_id":"2764","publisher":"Academic Press","year":"2003","_id":"3619","publication":"Theoretical Population Biology"},{"citation":{"short":"B. Nürnberger, S. Hofman, B. Förg Brey, G. Praetzel, A. Maclean, J. Szymura, C. Abbott, N.H. Barton, Heredity 91 (2003) 136–142.","chicago":"Nürnberger, Beate, Sebastian Hofman, Bqruni Förg Brey, Gabriele Praetzel, Alan Maclean, Jacek Szymura, Catherine Abbott, and Nicholas H Barton. “A Linkage Map for the Hybridising Toads Bombina Bombina and B. Variegata (Anura: Discoglossidae).” <i>Heredity</i>. Nature Publishing Group, 2003. <a href=\"https://doi.org/10.1038/sj.hdy.6800291\">https://doi.org/10.1038/sj.hdy.6800291</a>.","ieee":"B. Nürnberger <i>et al.</i>, “A linkage map for the hybridising toads Bombina bombina and B. variegata (Anura: Discoglossidae),” <i>Heredity</i>, vol. 91, no. 2. Nature Publishing Group, pp. 136–142, 2003.","apa":"Nürnberger, B., Hofman, S., Förg Brey, B., Praetzel, G., Maclean, A., Szymura, J., … Barton, N. H. (2003). A linkage map for the hybridising toads Bombina bombina and B. variegata (Anura: Discoglossidae). <i>Heredity</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/sj.hdy.6800291\">https://doi.org/10.1038/sj.hdy.6800291</a>","mla":"Nürnberger, Beate, et al. “A Linkage Map for the Hybridising Toads Bombina Bombina and B. Variegata (Anura: Discoglossidae).” <i>Heredity</i>, vol. 91, no. 2, Nature Publishing Group, 2003, pp. 136–42, doi:<a href=\"https://doi.org/10.1038/sj.hdy.6800291\">10.1038/sj.hdy.6800291</a>.","ista":"Nürnberger B, Hofman S, Förg Brey B, Praetzel G, Maclean A, Szymura J, Abbott C, Barton NH. 2003. A linkage map for the hybridising toads Bombina bombina and B. variegata (Anura: Discoglossidae). Heredity. 91(2), 136–142.","ama":"Nürnberger B, Hofman S, Förg Brey B, et al. A linkage map for the hybridising toads Bombina bombina and B. variegata (Anura: Discoglossidae). <i>Heredity</i>. 2003;91(2):136-142. doi:<a href=\"https://doi.org/10.1038/sj.hdy.6800291\">10.1038/sj.hdy.6800291</a>"},"issue":"2","intvolume":"        91","extern":1,"status":"public","quality_controlled":0,"date_published":"2003-08-01T00:00:00Z","doi":"10.1038/sj.hdy.6800291","publication_status":"published","publication":"Heredity","_id":"3620","year":"2003","publisher":"Nature Publishing Group","publist_id":"2763","date_created":"2018-12-11T12:04:17Z","volume":91,"title":"A linkage map for the hybridising toads Bombina bombina and B. variegata (Anura: Discoglossidae)","day":"01","date_updated":"2021-01-12T07:44:43Z","abstract":[{"lang":"eng","text":"Stable hybrid zones in which ecologically divergent taxa give rise to a range of recombinants are natural laboratories in which the genetic basis of adaptation and reproductive isolation can be unraveled. One such hybrid zone is formed by the fire-bellied toads Bombina bombina and B. variegata (Anura: Discoglossidae). Adaptations to permanent and ephemeral breeding habitats, respectively, have shaped numerous phenotypic differences between the taxa. All of these are, in principle, candidates for a genetic dissection via QTL mapping. We present here a linkage map of 28 codominant and 10 dominant markers in the Bombina genome. In an F2 cross, markers that were mainly microsatellites, SSCPs or allozymes were mapped to 20 linkage groups. Among the 40 isolated CA microsatellites, we noted a preponderance of compound and frequently interleaved CA-TA repeats as well as a striking polarity at the 5′ end of the repeats."}],"type":"journal_article","month":"08","page":"136 - 142","author":[{"full_name":"Nürnberger, Beate","last_name":"Nürnberger","first_name":"Beate"},{"full_name":"Hofman, Sebastian","last_name":"Hofman","first_name":"Sebastian"},{"full_name":"Förg-Brey, Bqruni","first_name":"Bqruni","last_name":"Förg Brey"},{"first_name":"Gabriele","last_name":"Praetzel","full_name":"Praetzel, Gabriele"},{"first_name":"Alan","last_name":"Maclean","full_name":"Maclean, Alan W"},{"first_name":"Jacek","last_name":"Szymura","full_name":"Szymura, Jacek M"},{"first_name":"Catherine","last_name":"Abbott","full_name":"Abbott, Catherine M"},{"last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Nicholas Barton"}]},{"status":"public","intvolume":"       356","extern":1,"citation":{"ama":"Lampert C. The Neumann operator in strictly pseudoconvex domains with weighted Bergman metric . <i>Bonner Mathematische Schriften</i>. 2003;356:1-165.","apa":"Lampert, C. (2003). <i>The Neumann operator in strictly pseudoconvex domains with weighted Bergman metric </i>. <i>Bonner Mathematische Schriften</i>. Universität Bonn, Fachbibliothek Mathematik.","mla":"Lampert, Christoph. “The Neumann Operator in Strictly Pseudoconvex Domains with Weighted Bergman Metric .” <i>Bonner Mathematische Schriften</i>, vol. 356, Universität Bonn, Fachbibliothek Mathematik, 2003, pp. 1–165.","ista":"Lampert C. 2003. The Neumann operator in strictly pseudoconvex domains with weighted Bergman metric . Universität Bonn, Fachbibliothek Mathematik.","chicago":"Lampert, Christoph. “The Neumann Operator in Strictly Pseudoconvex Domains with Weighted Bergman Metric .” <i>Bonner Mathematische Schriften</i>. Universität Bonn, Fachbibliothek Mathematik, 2003.","ieee":"C. Lampert, “The Neumann operator in strictly pseudoconvex domains with weighted Bergman metric ,” Universität Bonn, Fachbibliothek Mathematik, 2003.","short":"C. Lampert, The Neumann Operator in Strictly Pseudoconvex Domains with Weighted Bergman Metric , Universität Bonn, Fachbibliothek Mathematik, 2003."},"publication_status":"published","date_published":"2003-03-31T00:00:00Z","main_file_link":[{"url":"http://pub.ist.ac.at/~chl/papers/lampert-phd2003.pdf","open_access":"0"}],"quality_controlled":0,"publisher":"Universität Bonn, Fachbibliothek Mathematik","year":"2003","publication":"Bonner Mathematische Schriften","_id":"3678","page":"1 - 165","author":[{"first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Christoph Lampert"}],"date_updated":"2021-01-12T07:45:05Z","day":"31","type":"dissertation","month":"03","volume":356,"title":"The Neumann operator in strictly pseudoconvex domains with weighted Bergman metric ","publist_id":"2704","date_created":"2018-12-11T12:04:34Z"},{"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC204492/","open_access":"1"}],"quality_controlled":0,"doi":"10.1093/emboj/cdg509","date_published":"2003-01-01T00:00:00Z","publication_status":"published","oa":1,"citation":{"chicago":"Janovjak, Harald L, Max Kessler, Dieter Oesterhelt, Hermann Gaub, and Daniel Mueller. “Unfolding Pathways of Native Bacteriorhodopsin Depend on Temperature.” <i>EMBO Journal</i>. Wiley-Blackwell, 2003. <a href=\"https://doi.org/10.1093/emboj/cdg509\">https://doi.org/10.1093/emboj/cdg509</a>.","ieee":"H. L. Janovjak, M. Kessler, D. Oesterhelt, H. Gaub, and D. Mueller, “Unfolding pathways of native bacteriorhodopsin depend on temperature,” <i>EMBO Journal</i>, vol. 22, no. 19. Wiley-Blackwell, pp. 5220–5229, 2003.","short":"H.L. Janovjak, M. Kessler, D. Oesterhelt, H. Gaub, D. Mueller, EMBO Journal 22 (2003) 5220–5229.","ama":"Janovjak HL, Kessler M, Oesterhelt D, Gaub H, Mueller D. Unfolding pathways of native bacteriorhodopsin depend on temperature. <i>EMBO Journal</i>. 2003;22(19):5220-5229. doi:<a href=\"https://doi.org/10.1093/emboj/cdg509\">10.1093/emboj/cdg509</a>","apa":"Janovjak, H. L., Kessler, M., Oesterhelt, D., Gaub, H., &#38; Mueller, D. (2003). Unfolding pathways of native bacteriorhodopsin depend on temperature. <i>EMBO Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1093/emboj/cdg509\">https://doi.org/10.1093/emboj/cdg509</a>","mla":"Janovjak, Harald L., et al. “Unfolding Pathways of Native Bacteriorhodopsin Depend on Temperature.” <i>EMBO Journal</i>, vol. 22, no. 19, Wiley-Blackwell, 2003, pp. 5220–29, doi:<a href=\"https://doi.org/10.1093/emboj/cdg509\">10.1093/emboj/cdg509</a>.","ista":"Janovjak HL, Kessler M, Oesterhelt D, Gaub H, Mueller D. 2003. Unfolding pathways of native bacteriorhodopsin depend on temperature. EMBO Journal. 22(19), 5220–5229."},"issue":"19","intvolume":"        22","extern":1,"status":"public","publist_id":"2506","date_created":"2018-12-11T12:04:50Z","title":"Unfolding pathways of native bacteriorhodopsin depend on temperature","volume":22,"date_updated":"2021-01-12T07:51:45Z","day":"01","abstract":[{"lang":"eng","text":"The combination of high-resolution atomic force microscopy (AFM) imaging and single-molecule force-spectroscopy was employed to unfold single bacteriorhodopsins (BR) from native purple membrane patches at various physiologically relevant temperatures. The unfolding spectra reveal detailed insight into the stability of individual structural elements of BR against mechanical unfolding. Intermittent states in the unfolding process are associated with the stepwise unfolding of alpha-helices, whereas other states are associated with the unfolding of polypeptide loops connecting the alpha-helices. It was found that the unfolding forces of the secondary structures considerably decreased upon increasing the temperature from 8 to 52°C. Associated with this effect, the probability of individual unfolding pathways of BR was significantly influenced by the temperature. At lower temperatures, transmembrane alpha-helices and extracellular polypeptide loops exhibited sufficient stability to individually establish potential barriers against unfolding, whereas they predominantly unfolded collectively at elevated temperatures. This suggests that increasing the temperature decreases the mechanical stability of secondary structural elements and changes molecular interactions between secondary structures, thereby forcing them to act as grouped structures."}],"month":"01","type":"journal_article","author":[{"first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Harald Janovjak"},{"last_name":"Kessler","first_name":"Max","full_name":"Kessler, Max"},{"first_name":"Dieter","last_name":"Oesterhelt","full_name":"Oesterhelt, Dieter"},{"first_name":"Hermann","last_name":"Gaub","full_name":"Gaub, Hermann"},{"full_name":"Mueller, Daniel J","last_name":"Mueller","first_name":"Daniel"}],"page":"5220 - 5229","publication":"EMBO Journal","_id":"3725","year":"2003","publisher":"Wiley-Blackwell"},{"quality_controlled":0,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2172934/?tool=pubmed","open_access":"1"}],"date_published":"2003-01-12T00:00:00Z","doi":"10.1083/jcb.200301125","publication_status":"published","oa":1,"issue":"3","citation":{"ama":"Vilar J, Guet CC, Leibler S. Modeling network dynamics: the lac operon, a case study. <i>Journal of Cell Biology</i>. 2003;161(3):471-476. doi:<a href=\"https://doi.org/10.1083/jcb.200301125\">10.1083/jcb.200301125</a>","mla":"Vilar, Jose, et al. “Modeling Network Dynamics: The Lac Operon, a Case Study.” <i>Journal of Cell Biology</i>, vol. 161, no. 3, Rockefeller University Press, 2003, pp. 471–76, doi:<a href=\"https://doi.org/10.1083/jcb.200301125\">10.1083/jcb.200301125</a>.","ista":"Vilar J, Guet CC, Leibler S. 2003. Modeling network dynamics: the lac operon, a case study. Journal of Cell Biology. 161(3), 471–476.","apa":"Vilar, J., Guet, C. C., &#38; Leibler, S. (2003). Modeling network dynamics: the lac operon, a case study. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.200301125\">https://doi.org/10.1083/jcb.200301125</a>","ieee":"J. Vilar, C. C. Guet, and S. Leibler, “Modeling network dynamics: the lac operon, a case study,” <i>Journal of Cell Biology</i>, vol. 161, no. 3. Rockefeller University Press, pp. 471–476, 2003.","chicago":"Vilar, Jose, Calin C Guet, and Stanislas Leibler. “Modeling Network Dynamics: The Lac Operon, a Case Study.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2003. <a href=\"https://doi.org/10.1083/jcb.200301125\">https://doi.org/10.1083/jcb.200301125</a>.","short":"J. Vilar, C.C. Guet, S. Leibler, Journal of Cell Biology 161 (2003) 471–476."},"intvolume":"       161","extern":1,"status":"public","date_created":"2018-12-11T12:04:58Z","publist_id":"2475","volume":161,"title":"Modeling network dynamics: the lac operon, a case study","type":"journal_article","month":"01","abstract":[{"lang":"eng","text":"We use the lac operon in Escherichia coli as a prototype system to illustrate the current state, applicability, and limitations of modeling the dynamics of cellular networks. We integrate three different levels of description (molecular, cellular, and that of cell population) into a single model, which seems to capture many experimental aspects of the system."}],"date_updated":"2021-01-12T07:51:57Z","day":"12","author":[{"first_name":"Jose","last_name":"Vilar","full_name":"Vilar,Jose M"},{"first_name":"Calin C","last_name":"Guet","full_name":"Calin Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"},{"full_name":"Leibler, Stanislas","first_name":"Stanislas","last_name":"Leibler"}],"page":"471 - 476","_id":"3752","publication":"Journal of Cell Biology","year":"2003","publisher":"Rockefeller University Press"},{"status":"public","language":[{"iso":"eng"}],"citation":{"short":"W. Bauer, M. Kleine Berkenbusch, M.T. Bollenbach, Revista Mexicana De Fisica 49 (2003) 1–6.","ieee":"W. Bauer, M. Kleine Berkenbusch, and M. T. Bollenbach, “Breaking atomic nuclei into little pieces: evidence for a phase transition,” <i>Revista Mexicana De Fisica</i>, vol. 49, no. 4. Sociedad Mexicana de Física, pp. 1–6, 2003.","chicago":"Bauer, Wolfgang, Marco Kleine Berkenbusch, and Mark Tobias Bollenbach. “Breaking Atomic Nuclei into Little Pieces: Evidence for a Phase Transition.” <i>Revista Mexicana De Fisica</i>. Sociedad Mexicana de Física, 2003.","ista":"Bauer W, Kleine Berkenbusch M, Bollenbach MT. 2003. Breaking atomic nuclei into little pieces: evidence for a phase transition. Revista Mexicana De Fisica. 49(4), 1–6.","mla":"Bauer, Wolfgang, et al. “Breaking Atomic Nuclei into Little Pieces: Evidence for a Phase Transition.” <i>Revista Mexicana De Fisica</i>, vol. 49, no. 4, Sociedad Mexicana de Física, 2003, pp. 1–6.","apa":"Bauer, W., Kleine Berkenbusch, M., &#38; Bollenbach, M. T. (2003). Breaking atomic nuclei into little pieces: evidence for a phase transition. <i>Revista Mexicana De Fisica</i>. Sociedad Mexicana de Física.","ama":"Bauer W, Kleine Berkenbusch M, Bollenbach MT. Breaking atomic nuclei into little pieces: evidence for a phase transition. <i>Revista Mexicana De Fisica</i>. 2003;49(4):1-6."},"issue":"4","extern":"1","intvolume":"        49","publication_status":"published","date_published":"2003-01-01T00:00:00Z","year":"2003","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Sociedad Mexicana de Física","article_processing_charge":"No","publication":"Revista Mexicana De Fisica","_id":"3797","day":"01","date_updated":"2021-01-12T07:52:16Z","type":"journal_article","oa_version":"None","month":"01","author":[{"last_name":"Bauer","first_name":"Wolfgang","full_name":"Bauer, Wolfgang"},{"full_name":"Kleine Berkenbusch, Marco","first_name":"Marco","last_name":"Kleine Berkenbusch"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias","last_name":"Bollenbach"}],"page":"1 - 6","date_created":"2018-12-11T12:05:13Z","publist_id":"2413","title":"Breaking atomic nuclei into little pieces: evidence for a phase transition","volume":49},{"status":"public","citation":{"ieee":"C. Lien and P. M. Jonas, “Kv3 potassium conductance is necessary and kinetically optimized for high-frequency action potential generation in hippocampal interneurons,” <i>Journal of Neuroscience</i>, vol. 23, no. 6. Society for Neuroscience, pp. 2058–68, 2003.","chicago":"Lien, Cheng, and Peter M Jonas. “Kv3 Potassium Conductance Is Necessary and Kinetically Optimized for High-Frequency Action Potential Generation in Hippocampal Interneurons.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2003.","short":"C. Lien, P.M. Jonas, Journal of Neuroscience 23 (2003) 2058–68.","ama":"Lien C, Jonas PM. Kv3 potassium conductance is necessary and kinetically optimized for high-frequency action potential generation in hippocampal interneurons. <i>Journal of Neuroscience</i>. 2003;23(6):2058-2068.","ista":"Lien C, Jonas PM. 2003. Kv3 potassium conductance is necessary and kinetically optimized for high-frequency action potential generation in hippocampal interneurons. Journal of Neuroscience. 23(6), 2058–68.","mla":"Lien, Cheng, and Peter M. Jonas. “Kv3 Potassium Conductance Is Necessary and Kinetically Optimized for High-Frequency Action Potential Generation in Hippocampal Interneurons.” <i>Journal of Neuroscience</i>, vol. 23, no. 6, Society for Neuroscience, 2003, pp. 2058–68.","apa":"Lien, C., &#38; Jonas, P. M. (2003). Kv3 potassium conductance is necessary and kinetically optimized for high-frequency action potential generation in hippocampal interneurons. <i>Journal of Neuroscience</i>. Society for Neuroscience."},"issue":"6","extern":1,"intvolume":"        23","publication_status":"published","quality_controlled":0,"date_published":"2003-01-01T00:00:00Z","year":"2003","publisher":"Society for Neuroscience","publication":"Journal of Neuroscience","_id":"3804","day":"01","date_updated":"2021-01-12T07:52:19Z","abstract":[{"text":"Kv3 channels are thought to be essential for the fast-spiking (FS) phenotype in GABAergic interneurons, but how these channels confer the ability to generate action potentials (APs) at high frequency is unknown. To address this question, we developed a fast dynamic-clamp system (approximately 50 kHz) that allowed us to add a Kv3 model conductance to CA1 oriens alveus (OA) interneurons in hippocampal slices. Selective pharmacological block of Kv3 channels by 0.3 mm 4-aminopyridine or 1 mm tetraethylammonium ions led to a marked broadening of APs during trains of short stimuli and a reduction in AP frequency during 1 sec stimuli. The addition of artificial Kv3 conductance restored the original AP pattern. Subtraction of Kv3 conductance by dynamic clamp mimicked the effects of the blockers. Application of artificial Kv3 conductance also led to FS in OA interneurons after complete K+ channel block and even induced FS in hippocampal pyramidal neurons in the absence of blockers. Adding artificial Kv3 conductance with altered deactivation kinetics revealed a nonmonotonic relationship between mean AP frequency and deactivation rate, with a maximum slightly above the original value. Insertion of artificial Kv3 conductance with either lowered activation threshold or inactivation also led to a reduction in the mean AP frequency. However, the mechanisms were distinct. Shifting the activation threshold induced adaptation, whereas adding inactivation caused frequency-dependent AP broadening. In conclusion, Kv3 channels are necessary for the FS phenotype of OA interneurons, and several of their gating properties appear to be optimized for high-frequency repetitive activity.","lang":"eng"}],"type":"journal_article","month":"01","page":"2058 - 68","author":[{"first_name":"Cheng","last_name":"Lien","full_name":"Lien, Cheng-Chang"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Peter Jonas","first_name":"Peter M","last_name":"Jonas"}],"date_created":"2018-12-11T12:05:16Z","publist_id":"2406","volume":23,"title":"Kv3 potassium conductance is necessary and kinetically optimized for high-frequency action potential generation in hippocampal interneurons"},{"publication":"PNAS","_id":"3806","publisher":"National Academy of Sciences","year":"2003","title":"A large pool of releasable vesicles in a cortical glutamatergic synapse","volume":100,"publist_id":"2405","date_created":"2018-12-11T12:05:16Z","author":[{"full_name":"Hallermann, Stefan","first_name":"Stefan","last_name":"Hallermann"},{"full_name":"Pawlu, Christian","last_name":"Pawlu","first_name":"Christian"},{"full_name":"Peter Jonas","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M"},{"full_name":"Heckmann, Manfred","last_name":"Heckmann","first_name":"Manfred"}],"page":"8975 - 80","date_updated":"2021-01-12T07:52:20Z","day":"01","abstract":[{"lang":"eng","text":"To probe exocytosis at a cortical glutamatergic synapse, we made capacitance measurements in whole-cell recorded hippocampal mossy fiber terminals. Evaluation of different methods by using a morphology-based equivalent electrical model revealed that quantitative capacitance measurements are possible in this presynaptic structure. Voltage pulses leading to presynaptic Ca2+ inflow evoked large capacitance signals that showed saturation with increasing pulse duration. The mean peak capacitance increase was 100 fF, corresponding to a pool of approximately 1,400 releasable vesicles. Thus hippocampal mossy fiber synapses have a vesicular &quot;maxipool.&quot; Large pool size and rapid vesicle recycling may underlie the uniquely large extent of activity-dependent plasticity in this synapse."}],"type":"journal_article","month":"01","extern":1,"intvolume":"       100","citation":{"ama":"Hallermann S, Pawlu C, Jonas PM, Heckmann M. A large pool of releasable vesicles in a cortical glutamatergic synapse. <i>PNAS</i>. 2003;100(15):8975-8980. doi:<a href=\"https://doi.org/10.1073/pnas.1432836100\">10.1073/pnas.1432836100</a>","mla":"Hallermann, Stefan, et al. “A Large Pool of Releasable Vesicles in a Cortical Glutamatergic Synapse.” <i>PNAS</i>, vol. 100, no. 15, National Academy of Sciences, 2003, pp. 8975–80, doi:<a href=\"https://doi.org/10.1073/pnas.1432836100\">10.1073/pnas.1432836100</a>.","ista":"Hallermann S, Pawlu C, Jonas PM, Heckmann M. 2003. A large pool of releasable vesicles in a cortical glutamatergic synapse. PNAS. 100(15), 8975–80.","apa":"Hallermann, S., Pawlu, C., Jonas, P. M., &#38; Heckmann, M. (2003). A large pool of releasable vesicles in a cortical glutamatergic synapse. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1432836100\">https://doi.org/10.1073/pnas.1432836100</a>","ieee":"S. Hallermann, C. Pawlu, P. M. Jonas, and M. Heckmann, “A large pool of releasable vesicles in a cortical glutamatergic synapse,” <i>PNAS</i>, vol. 100, no. 15. National Academy of Sciences, pp. 8975–80, 2003.","chicago":"Hallermann, Stefan, Christian Pawlu, Peter M Jonas, and Manfred Heckmann. “A Large Pool of Releasable Vesicles in a Cortical Glutamatergic Synapse.” <i>PNAS</i>. National Academy of Sciences, 2003. <a href=\"https://doi.org/10.1073/pnas.1432836100\">https://doi.org/10.1073/pnas.1432836100</a>.","short":"S. Hallermann, C. Pawlu, P.M. Jonas, M. Heckmann, PNAS 100 (2003) 8975–80."},"issue":"15","status":"public","doi":"10.1073/pnas.1432836100","date_published":"2003-01-01T00:00:00Z","quality_controlled":0,"publication_status":"published"},{"alternative_title":["LNCS"],"status":"public","conference":{"name":"CSL: Computer Science Logic"},"intvolume":"      2803","extern":1,"citation":{"chicago":"Chatterjee, Krishnendu, Marcin Jurdziński, and Thomas A Henzinger. “Simple Stochastic Parity Games,” 2803:100–113. Springer, 2003. <a href=\"https://doi.org/10.1007/978-3-540-45220-1_11\">https://doi.org/10.1007/978-3-540-45220-1_11</a>.","ieee":"K. Chatterjee, M. Jurdziński, and T. A. Henzinger, “Simple stochastic parity games,” presented at the CSL: Computer Science Logic, 2003, vol. 2803, pp. 100–113.","short":"K. Chatterjee, M. Jurdziński, T.A. Henzinger, in:, Springer, 2003, pp. 100–113.","ama":"Chatterjee K, Jurdziński M, Henzinger TA. Simple stochastic parity games. In: Vol 2803. Springer; 2003:100-113. doi:<a href=\"https://doi.org/10.1007/978-3-540-45220-1_11\">10.1007/978-3-540-45220-1_11</a>","apa":"Chatterjee, K., Jurdziński, M., &#38; Henzinger, T. A. (2003). Simple stochastic parity games (Vol. 2803, pp. 100–113). Presented at the CSL: Computer Science Logic, Springer. <a href=\"https://doi.org/10.1007/978-3-540-45220-1_11\">https://doi.org/10.1007/978-3-540-45220-1_11</a>","mla":"Chatterjee, Krishnendu, et al. <i>Simple Stochastic Parity Games</i>. Vol. 2803, Springer, 2003, pp. 100–13, doi:<a href=\"https://doi.org/10.1007/978-3-540-45220-1_11\">10.1007/978-3-540-45220-1_11</a>.","ista":"Chatterjee K, Jurdziński M, Henzinger TA. 2003. Simple stochastic parity games. CSL: Computer Science Logic, LNCS, vol. 2803, 100–113."},"publication_status":"published","date_published":"2003-08-18T00:00:00Z","doi":"10.1007/978-3-540-45220-1_11","quality_controlled":0,"acknowledgement":"This research was supported in part by the DARPA grant F33615-C-98-3614, the ONR grant N00014-02-1-0671, the NSF grants CCR-9988172 and CCR-0225610, and the Polish KBN grant 7-T11C-027-20.","publisher":"Springer","year":"2003","_id":"3897","page":"100 - 113","author":[{"full_name":"Krishnendu Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"first_name":"Marcin","last_name":"Jurdziński","full_name":"Jurdziński, Marcin"},{"last_name":"Henzinger","first_name":"Thomas A","full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"month":"08","type":"conference","abstract":[{"lang":"eng","text":"Many verification, planning, and control problems can be modeled as games played on state-transition graphs by one or two players whose conflicting goals are to form a path in the graph. The focus here is on simple stochastic parity games, that is, two-player games with turn-based probabilistic transitions and omega-regular objectives formalized as parity (Rabin chain) winning conditions. An efficient translation from simple stochastic parity games to nonstochastic parity games is given. As many algorithms are known for solving the latter, the translation yields efficient algorithms for computing the states of a simple stochastic parity game from which a player can win with probability 1. An important special case of simple stochastic parity games are the Markov decision processes with Buchi objectives. For this special case a first provably subquadratic algorithm is given for computing the states from which the single player has a strategy to achieve a Buchi objective with probability 1. For game graphs with m edges the algorithm works in time O(mrootm). Interestingly, a similar technique sheds light on the question of the computational complexity of solving simple Buchi games and yields the first provably subquadratic algorithm, with a running time of O(n(2)/log n) for game graphs with n vertices and O(n) edges."}],"day":"18","date_updated":"2021-01-12T07:53:02Z","volume":2803,"title":"Simple stochastic parity games","date_created":"2018-12-11T12:05:46Z","publist_id":"2259"},{"year":"2003","acknowledgement":"Jens Palsberg, Di Ma, and Tian Zhao were supported by the NSF ITR award 0112628. Thomas A. Henzinger, Krishnendu Chatterjee, and Rupak Majumdar were supported by the AFOSR grant F49620-00-1-0327, the DARPA grants F33615-C-98-3614 and F33615-00-C-1693, the MARCO grant 98-DT-660, and the NSF grants CCR-0208875 and CCR-0085949.","publisher":"Springer","_id":"3898","month":"05","type":"conference","day":"28","date_updated":"2021-01-12T07:53:02Z","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 axe 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 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."}],"page":"109 - 126","author":[{"full_name":"Krishnendu Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Ma","first_name":"Di","full_name":"Ma, Di"},{"full_name":"Majumdar, Ritankar S","first_name":"Ritankar","last_name":"Majumdar"},{"first_name":"Tian","last_name":"Zhao","full_name":"Zhao, Tian"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Palsberg, Jens","last_name":"Palsberg","first_name":"Jens"}],"date_created":"2018-12-11T12:05:46Z","publist_id":"2260","title":"Stack size analysis for interrupt-driven programs","volume":2694,"status":"public","alternative_title":["LNCS"],"citation":{"short":"K. Chatterjee, D. Ma, R. Majumdar, T. Zhao, T.A. Henzinger, J. Palsberg, in:, Springer, 2003, pp. 109–126.","ieee":"K. Chatterjee, D. Ma, R. Majumdar, T. Zhao, T. A. Henzinger, and J. Palsberg, “Stack size analysis for interrupt-driven programs,” presented at the SAS: Static Analysis Symposium, 2003, vol. 2694, pp. 109–126.","chicago":"Chatterjee, Krishnendu, Di Ma, Ritankar Majumdar, Tian Zhao, Thomas A Henzinger, and Jens Palsberg. “Stack Size Analysis for Interrupt-Driven Programs,” 2694:109–26. Springer, 2003. <a href=\"https://doi.org/10.1007/3-540-44898-5_7\">https://doi.org/10.1007/3-540-44898-5_7</a>.","mla":"Chatterjee, Krishnendu, et al. <i>Stack Size Analysis for Interrupt-Driven Programs</i>. Vol. 2694, Springer, 2003, pp. 109–26, doi:<a href=\"https://doi.org/10.1007/3-540-44898-5_7\">10.1007/3-540-44898-5_7</a>.","ista":"Chatterjee K, Ma D, Majumdar R, Zhao T, Henzinger TA, Palsberg J. 2003. Stack size analysis for interrupt-driven programs. SAS: Static Analysis Symposium, LNCS, vol. 2694, 109–126.","apa":"Chatterjee, K., Ma, D., Majumdar, R., Zhao, T., Henzinger, T. A., &#38; Palsberg, J. (2003). Stack size analysis for interrupt-driven programs (Vol. 2694, pp. 109–126). Presented at the SAS: Static Analysis Symposium, Springer. <a href=\"https://doi.org/10.1007/3-540-44898-5_7\">https://doi.org/10.1007/3-540-44898-5_7</a>","ama":"Chatterjee K, Ma D, Majumdar R, Zhao T, Henzinger TA, Palsberg J. Stack size analysis for interrupt-driven programs. In: Vol 2694. Springer; 2003:109-126. doi:<a href=\"https://doi.org/10.1007/3-540-44898-5_7\">10.1007/3-540-44898-5_7</a>"},"conference":{"name":"SAS: Static Analysis Symposium"},"extern":1,"intvolume":"      2694","publication_status":"published","quality_controlled":0,"doi":"10.1007/3-540-44898-5_7","date_published":"2003-05-28T00:00:00Z"},{"publication_status":"published","date_published":"2003-01-01T00:00:00Z","status":"public","citation":{"ieee":"S. Cremer and J. Heinze, “Zwischen Hochzeitsflug und Brudermord: reproduktive Taktiken bei Ameisenmännchen,” <i>Blick in die Wissenschaft</i>, vol. 12, no. 15. Schnell und Steiner, pp. 32–36, 2003.","chicago":"Cremer, Sylvia, and Jürgen Heinze. “Zwischen Hochzeitsflug Und Brudermord: Reproduktive Taktiken Bei Ameisenmännchen.” <i>Blick in Die Wissenschaft</i>. Schnell und Steiner, 2003.","short":"S. Cremer, J. Heinze, Blick in Die Wissenschaft 12 (2003) 32–36.","ama":"Cremer S, Heinze J. Zwischen Hochzeitsflug und Brudermord: reproduktive Taktiken bei Ameisenmännchen. <i>Blick in die Wissenschaft</i>. 2003;12(15):32-36.","mla":"Cremer, Sylvia, and Jürgen Heinze. “Zwischen Hochzeitsflug Und Brudermord: Reproduktive Taktiken Bei Ameisenmännchen.” <i>Blick in Die Wissenschaft</i>, vol. 12, no. 15, Schnell und Steiner, 2003, pp. 32–36.","ista":"Cremer S, Heinze J. 2003. Zwischen Hochzeitsflug und Brudermord: reproduktive Taktiken bei Ameisenmännchen. Blick in die Wissenschaft. 12(15), 32–36.","apa":"Cremer, S., &#38; Heinze, J. (2003). Zwischen Hochzeitsflug und Brudermord: reproduktive Taktiken bei Ameisenmännchen. <i>Blick in Die Wissenschaft</i>. Schnell und Steiner."},"language":[{"iso":"eng"}],"issue":"15","intvolume":"        12","extern":"1","date_updated":"2021-01-12T07:53:11Z","day":"01","abstract":[{"lang":"eng","text":"Male dimorphism is not genetically determined, but is induced by environmental conditions particularly decreasing temperature and density."}],"month":"01","oa_version":"None","type":"journal_article","page":"32 - 36","author":[{"first_name":"Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia"},{"last_name":"Heinze","first_name":"Jürgen","full_name":"Heinze, Jürgen"}],"publist_id":"2235","date_created":"2018-12-11T12:05:53Z","title":"Zwischen Hochzeitsflug und Brudermord: reproduktive Taktiken bei Ameisenmännchen","volume":12,"year":"2003","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Schnell und Steiner","publication":"Blick in die Wissenschaft","_id":"3917"}]