--- _id: '2628' abstract: - lang: eng text: We aimed to estimate the number of AMPA receptors (AMPARs) bound by the quantal transmitter packet, their single-channel conductance and their density in the postsynaptic membrane at cerebellar Purkinje cell synapses. The synaptic and extrasynaptic AMPARs were examined in Purkinje cells in 2- to 4-day-old rats, when they receive synaptic inputs solely from climbing fibres (CFs). Evoked CF EPSCs and whole-cell AMPA currents displayed roughly linear current-voltage relationships, consistent with the presence of GluR2 subunits in synaptic and extrasynaptic AMPARs. The mean quantal size, estimated from the miniature EPSCs (MEPSCs), was ∼300 pS. Peak-scaled non-stationary fluctuation analysis of spontaneous EPSCs and MEPSCs gave a weighted-mean synaptic channel conductance of ∼5 pS (∼7 pS when corrected for filtering). By applying non-stationary fluctuation analysis to extrasynaptic currents activated by brief glutamate pulses (5 mM), we also obtained a small single-channel conductance estimate for extrasynaptic AMPARs (∼11 pS). This approach allowed us to obtain a maximum open probability (Po,max) value for the extrasynaptic receptors (Po,max = 0.72). Directly resolved extrasynaptic channel openings in the continued presence of glutamate exhibited clear multiple-conductance levels. The mean area of the postsynaptic density (PSD) of these synapses was 0.074 μm2, measured by reconstructing electron-microscopic (EM) serial sections. Postembedding immunogold labelling by anti-GluR2/3 antibody revealed that AMPARs are localised in PSDs. From these data and by simulating error factors, we estimate that at least 66 AMPARs are bound by a quantal transmitter packet at CF-Purkinje cell synapses, and the receptors are packed at a minimum density of ∼900 μm-2 in the postsynaptic membrane. author: - first_name: Akiko full_name: Momiyama, Akiko last_name: Momiyama - first_name: Rachel full_name: Silver, Rachel A last_name: Silver - first_name: Michael full_name: Häusser, Michael A last_name: Häusser - first_name: Takuya full_name: Notomi, Takuya last_name: Notomi - first_name: Yue full_name: Wu, Yue last_name: Wu - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Stuart full_name: Cull-Candy, Stuart G last_name: Cull Candy citation: ama: Momiyama A, Silver R, Häusser M, et al. The density of AMPA receptors activated by a transmitter quantum at the climbing fibre - Purkinje cell synapse in immature rats. Journal of Physiology. 2003;549(1):75-92. doi:10.1113/jphysiol.2002.033472 apa: Momiyama, A., Silver, R., Häusser, M., Notomi, T., Wu, Y., Shigemoto, R., & Cull Candy, S. (2003). The density of AMPA receptors activated by a transmitter quantum at the climbing fibre - Purkinje cell synapse in immature rats. Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/jphysiol.2002.033472 chicago: Momiyama, Akiko, Rachel Silver, Michael Häusser, Takuya Notomi, Yue Wu, Ryuichi Shigemoto, and Stuart Cull Candy. “The Density of AMPA Receptors Activated by a Transmitter Quantum at the Climbing Fibre - Purkinje Cell Synapse in Immature Rats.” Journal of Physiology. Wiley-Blackwell, 2003. https://doi.org/10.1113/jphysiol.2002.033472. ieee: A. Momiyama et al., “The density of AMPA receptors activated by a transmitter quantum at the climbing fibre - Purkinje cell synapse in immature rats,” Journal of Physiology, vol. 549, no. 1. Wiley-Blackwell, pp. 75–92, 2003. ista: Momiyama A, Silver R, Häusser M, Notomi T, Wu Y, Shigemoto R, Cull Candy S. 2003. The density of AMPA receptors activated by a transmitter quantum at the climbing fibre - Purkinje cell synapse in immature rats. Journal of Physiology. 549(1), 75–92. mla: Momiyama, Akiko, et al. “The Density of AMPA Receptors Activated by a Transmitter Quantum at the Climbing Fibre - Purkinje Cell Synapse in Immature Rats.” Journal of Physiology, vol. 549, no. 1, Wiley-Blackwell, 2003, pp. 75–92, doi:10.1113/jphysiol.2002.033472. short: A. Momiyama, R. Silver, M. Häusser, T. Notomi, Y. Wu, R. Shigemoto, S. Cull Candy, Journal of Physiology 549 (2003) 75–92. date_created: 2018-12-11T11:58:45Z date_published: 2003-05-15T00:00:00Z date_updated: 2021-01-12T06:58:40Z day: '15' doi: 10.1113/jphysiol.2002.033472 extern: 1 intvolume: ' 549' issue: '1' month: '05' page: 75 - 92 publication: Journal of Physiology publication_status: published publisher: Wiley-Blackwell publist_id: '4270' quality_controlled: 0 status: public title: The density of AMPA receptors activated by a transmitter quantum at the climbing fibre - Purkinje cell synapse in immature rats type: journal_article volume: 549 year: '2003' ... --- _id: '2631' abstract: - lang: eng text: Cyclic ADP-ribose (cADP-ribose) is a putative second messenger or modulator. However, the role of cADP-ribose in the downstream signals of the metabotropic glutamate receptors (mGluRs) is unclear. Here, we show that glutamate stimulates ADP-ribosyl cyclase activity in rat or mouse crude membranes of retina via group III mGluRs or in superior cervical ganglion via group I mGluRs. The retina of mGluR6-deficient mice showed no increase in the ADP-ribosyl cyclase level in response to glutamate. GTP enhanced the initial rate of basal and glutamate-stimulated cyclase activity. GTP-γ-S also stimulated basal activity. To determine whether the coupling mode of mGluRs to ADP-ribosyl cyclase is a feature common to individual cloned mGluRs, we expressed each mGluR subtype in NG108-15 neuroblastoma x glioma hybrid cells. The glutamate-induced stimulation of the cyclase occurs preferentially in NG108-15 cells over-expressing mGluRs1, 3, 5, and 6. Cells expressing mGluR2 or mGluRs4 and 7 exhibit inhibition or no coupling, respectively. Glutamate-induced activation or inhibition of the cyclase activity was eliminated after pre-treatment with cholera or pertussis toxin, respectively. Thus, the subtype-specific coupling of mGluRs to ADP-ribosyl cyclase via G proteins suggests that some glutamate-evoked neuronal functions are mediated by cADP-ribose. author: - first_name: Haruhiro full_name: Higashida, Haruhiro last_name: Higashida - first_name: Jia full_name: Zhang, Jia-Sheng last_name: Zhang - first_name: Sumiko full_name: Mochida, Sumiko last_name: Mochida - first_name: Xiao full_name: Chen, Xiao-Liang last_name: Chen - first_name: Yeonsook full_name: Shin, Yeonsook last_name: Shin - first_name: Mami full_name: Noda, Mami last_name: Noda - first_name: Kazi full_name: Hossain, Kazi Z last_name: Hossain - first_name: Naoto full_name: Hoshi, Naoto last_name: Hoshi - first_name: Minako full_name: Hashii, Minako last_name: Hashii - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Shigetada full_name: Nakanishi, Shigetada last_name: Nakanishi - first_name: Yutaka full_name: Fukuda, Yutaka last_name: Fukuda - first_name: Shigeru full_name: Yokoyama, Shigeru last_name: Yokoyama citation: ama: Higashida H, Zhang J, Mochida S, et al. Subtype-specific coupling with ADP-ribosyl cyclase of metabotropic glutamate receptors in retina, cervical superior ganglion and NG108-15 cells. Journal of Neurochemistry. 2003;85(5):1148-1158. doi:10.1046/j.1471-4159.2003.01751.x apa: Higashida, H., Zhang, J., Mochida, S., Chen, X., Shin, Y., Noda, M., … Yokoyama, S. (2003). Subtype-specific coupling with ADP-ribosyl cyclase of metabotropic glutamate receptors in retina, cervical superior ganglion and NG108-15 cells. Journal of Neurochemistry. Wiley-Blackwell. https://doi.org/10.1046/j.1471-4159.2003.01751.x chicago: Higashida, Haruhiro, Jia Zhang, Sumiko Mochida, Xiao Chen, Yeonsook Shin, Mami Noda, Kazi Hossain, et al. “Subtype-Specific Coupling with ADP-Ribosyl Cyclase of Metabotropic Glutamate Receptors in Retina, Cervical Superior Ganglion and NG108-15 Cells.” Journal of Neurochemistry. Wiley-Blackwell, 2003. https://doi.org/10.1046/j.1471-4159.2003.01751.x. ieee: H. Higashida et al., “Subtype-specific coupling with ADP-ribosyl cyclase of metabotropic glutamate receptors in retina, cervical superior ganglion and NG108-15 cells,” Journal of Neurochemistry, vol. 85, no. 5. Wiley-Blackwell, pp. 1148–1158, 2003. ista: Higashida H, Zhang J, Mochida S, Chen X, Shin Y, Noda M, Hossain K, Hoshi N, Hashii M, Shigemoto R, Nakanishi S, Fukuda Y, Yokoyama S. 2003. Subtype-specific coupling with ADP-ribosyl cyclase of metabotropic glutamate receptors in retina, cervical superior ganglion and NG108-15 cells. Journal of Neurochemistry. 85(5), 1148–1158. mla: Higashida, Haruhiro, et al. “Subtype-Specific Coupling with ADP-Ribosyl Cyclase of Metabotropic Glutamate Receptors in Retina, Cervical Superior Ganglion and NG108-15 Cells.” Journal of Neurochemistry, vol. 85, no. 5, Wiley-Blackwell, 2003, pp. 1148–58, doi:10.1046/j.1471-4159.2003.01751.x. short: H. Higashida, J. Zhang, S. Mochida, X. Chen, Y. Shin, M. Noda, K. Hossain, N. Hoshi, M. Hashii, R. Shigemoto, S. Nakanishi, Y. Fukuda, S. Yokoyama, Journal of Neurochemistry 85 (2003) 1148–1158. date_created: 2018-12-11T11:58:46Z date_published: 2003-06-01T00:00:00Z date_updated: 2021-01-12T06:58:42Z day: '01' doi: 10.1046/j.1471-4159.2003.01751.x extern: 1 intvolume: ' 85' issue: '5' month: '06' page: 1148 - 1158 publication: Journal of Neurochemistry publication_status: published publisher: Wiley-Blackwell publist_id: '4268' quality_controlled: 0 status: public title: Subtype-specific coupling with ADP-ribosyl cyclase of metabotropic glutamate receptors in retina, cervical superior ganglion and NG108-15 cells type: journal_article volume: 85 year: '2003' ... --- _id: '2633' abstract: - lang: eng text: The modulation of calcium channels by metabotropic glutamate receptors (mGluRs) is a key event in the fine-tuning of neurotransmitter release. Here we report that, in cerebrocortical nerve terminals of adult rats, the inhibition of glutamate release is mediated by mGluR7. In this preparation, the major component of glutamate release is supported by P/Q-type Ca2+ channels (72.7%). However, mGluR7 selectively reduced the release component that is associated with N-type Ca2+ channels (29.9%). Inhibition of P/Q channels by mGluR7 is not masked by the higher efficiency of these channels in driving glutamate release when compared with N-type channels. Thus, activation of mGluR7 failed to reduce the release associated with P/Q channels when the extracellular calcium concentration, ([Ca2+]o), was reduced from 1.3 to 0.5 mM. Through Ca2+ imaging, we show that Ca2+ channels are distributed in a heterogeneous manner in individual nerve terminals. Indeed, in this preparation, nerve terminals were observed that contain N-type (31.1%; conotoxin GVIA-sensitive) or P/Q-type (64.3%; agatoxin IVA-sensitive) channels or that were insensitive to these two toxins (4.6%). Interestingly, the great majority of the responses to L-AP4 (95.4%) were observed in nerve terminals containing N-type channels. This specific co-localization of mGluR7 and N-type Ca2+-channels could explain the failure of the receptor to inhibit the P/Q channel-associated release component and also reveal the existence of specific targeting mechanisms to localize the two proteins in the same nerve terminal subset. author: - first_name: Carmelo full_name: Millán, Carmelo last_name: Millán - first_name: Enrique full_name: Castro, Enrique G last_name: Castro - first_name: Magdalena full_name: Torres, Magdalena last_name: Torres - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: José full_name: Sánchez-Prieto, José last_name: Sánchez Prieto citation: ama: Millán C, Castro E, Torres M, Shigemoto R, Sánchez Prieto J. Co-expression of metabotropic glutamate receptor 7 and N-type Ca2+ channels in single cerebrocortical nerve terminals of adult rats. Journal of Biological Chemistry. 2003;278(26):23955-23962. doi:10.1074/jbc.M211471200 apa: Millán, C., Castro, E., Torres, M., Shigemoto, R., & Sánchez Prieto, J. (2003). Co-expression of metabotropic glutamate receptor 7 and N-type Ca2+ channels in single cerebrocortical nerve terminals of adult rats. Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M211471200 chicago: Millán, Carmelo, Enrique Castro, Magdalena Torres, Ryuichi Shigemoto, and José Sánchez Prieto. “Co-Expression of Metabotropic Glutamate Receptor 7 and N-Type Ca2+ Channels in Single Cerebrocortical Nerve Terminals of Adult Rats.” Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology, 2003. https://doi.org/10.1074/jbc.M211471200. ieee: C. Millán, E. Castro, M. Torres, R. Shigemoto, and J. Sánchez Prieto, “Co-expression of metabotropic glutamate receptor 7 and N-type Ca2+ channels in single cerebrocortical nerve terminals of adult rats,” Journal of Biological Chemistry, vol. 278, no. 26. American Society for Biochemistry and Molecular Biology, pp. 23955–23962, 2003. ista: Millán C, Castro E, Torres M, Shigemoto R, Sánchez Prieto J. 2003. Co-expression of metabotropic glutamate receptor 7 and N-type Ca2+ channels in single cerebrocortical nerve terminals of adult rats. Journal of Biological Chemistry. 278(26), 23955–23962. mla: Millán, Carmelo, et al. “Co-Expression of Metabotropic Glutamate Receptor 7 and N-Type Ca2+ Channels in Single Cerebrocortical Nerve Terminals of Adult Rats.” Journal of Biological Chemistry, vol. 278, no. 26, American Society for Biochemistry and Molecular Biology, 2003, pp. 23955–62, doi:10.1074/jbc.M211471200. short: C. Millán, E. Castro, M. Torres, R. Shigemoto, J. Sánchez Prieto, Journal of Biological Chemistry 278 (2003) 23955–23962. date_created: 2018-12-11T11:58:47Z date_published: 2003-07-27T00:00:00Z date_updated: 2021-01-12T06:58:42Z day: '27' doi: 10.1074/jbc.M211471200 extern: 1 intvolume: ' 278' issue: '26' month: '07' page: 23955 - 23962 publication: Journal of Biological Chemistry publication_status: published publisher: American Society for Biochemistry and Molecular Biology publist_id: '4265' quality_controlled: 0 status: public title: Co-expression of metabotropic glutamate receptor 7 and N-type Ca2+ channels in single cerebrocortical nerve terminals of adult rats type: journal_article volume: 278 year: '2003' ... --- _id: '2632' abstract: - lang: eng text: In many brain regions, hyperpolarization-activated cationic currents (Ih) are involved in the generation of rhythmic activities, but the role of Ih in olfactory oscillations remains unclear. Knowledge of the cellular and subcellular distributions of hyperpolarization-activated and cyclic nucleotide-gated channel (HCN) subunits is necessary for understanding the role of Ih in olfactory network activities. Using light microscopic immunocytochemistry, we demonstrate strong HCN1 labelling of the glomerular layer and moderate staining of granule cell, internal and external plexiform layers of the rat main olfactory bulb. In the glomerular layer, among many unlabelled neurons, two distinct subpopulations of juxtaglomerular cells are labelled. Approximately 10% of the juxtaglomerular cells strongly express HCN1. These small diameter cells are immunoreactive for GABA and comprise a subpopulation of periglomerular cells. An additional subset of juxtaglomerular cells (≈ 1%) expresses low levels of HCN1. They are large in diameter, GABA immunonegative but immunopositive for vesicular glutamate transporter 2, characterizing them as external tufted cells. Quantitative immunogold localization revealed that the somatic plasma membranes of periglomerular cells contain approximately four times more HCN1 labelling than those of external tufted cells. Unlike in cortical pyramidal cells, immunogold density for HCN1 does not significantly differ in somatic and dendritic plasma membranes of external tufted cells, indicating that post-synaptic potentials arriving at proximal and distal dendrites are modulated by the same density of I h. Our results demonstrate a cell type-dependent expression of HCN1 in the olfactory bulb and predict a differential contribution of distinct juxtaglomerular cell types to network oscillations. author: - first_name: Noémi full_name: Holderith, Noémi B last_name: Holderith - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Zoltán full_name: Nusser, Zoltán last_name: Nusser citation: ama: Holderith N, Shigemoto R, Nusser Z. Cell type-dependent expression of HCN1 in the main olfactory bulb. European Journal of Neuroscience. 2003;18(2):344-354. doi:10.1046/j.1460-9568.2003.02756.x apa: Holderith, N., Shigemoto, R., & Nusser, Z. (2003). Cell type-dependent expression of HCN1 in the main olfactory bulb. European Journal of Neuroscience. Wiley-Blackwell. https://doi.org/10.1046/j.1460-9568.2003.02756.x chicago: Holderith, Noémi, Ryuichi Shigemoto, and Zoltán Nusser. “Cell Type-Dependent Expression of HCN1 in the Main Olfactory Bulb.” European Journal of Neuroscience. Wiley-Blackwell, 2003. https://doi.org/10.1046/j.1460-9568.2003.02756.x. ieee: N. Holderith, R. Shigemoto, and Z. Nusser, “Cell type-dependent expression of HCN1 in the main olfactory bulb,” European Journal of Neuroscience, vol. 18, no. 2. Wiley-Blackwell, pp. 344–354, 2003. ista: Holderith N, Shigemoto R, Nusser Z. 2003. Cell type-dependent expression of HCN1 in the main olfactory bulb. European Journal of Neuroscience. 18(2), 344–354. mla: Holderith, Noémi, et al. “Cell Type-Dependent Expression of HCN1 in the Main Olfactory Bulb.” European Journal of Neuroscience, vol. 18, no. 2, Wiley-Blackwell, 2003, pp. 344–54, doi:10.1046/j.1460-9568.2003.02756.x. short: N. Holderith, R. Shigemoto, Z. Nusser, European Journal of Neuroscience 18 (2003) 344–354. date_created: 2018-12-11T11:58:47Z date_published: 2003-07-01T00:00:00Z date_updated: 2021-01-12T06:58:42Z day: '01' doi: 10.1046/j.1460-9568.2003.02756.x extern: 1 intvolume: ' 18' issue: '2' month: '07' page: 344 - 354 publication: European Journal of Neuroscience publication_status: published publisher: Wiley-Blackwell publist_id: '4266' quality_controlled: 0 status: public title: Cell type-dependent expression of HCN1 in the main olfactory bulb type: journal_article volume: 18 year: '2003' ... --- _id: '2635' abstract: - lang: eng text: Metabotropic GABAB receptors mediate slow inhibitory effects presynaptically and postsynaptically. Using preembedding immunohistochemical methods combined with quantitative analysis of GABAB receptor subunit immunoreactivity, this study provides a detailed description of the cellular and subcellular localization of GABAB1a/b and GABA B2 in the rat hippocampus. At the light microscopic level, an overlapping distribution of GABAB1a/b and GABAB2 was revealed in the dendritic layers of the hippocampus. In addition, expression of the GABAB1a/b subunit was found in somata of CA1 pyramidal cells and of a subset of GABAergic interneurons. At the electron microscopic level, immunoreactivity for both subunits was observed on presynaptic and, more abundantly, on postsynaptic elements. Presynaptically, subunits were mainly detected in the extrasynaptic membrane and occasionally over the presynaptic membrane specialization of putative glutamatergic and, to a lesser extent, GABAergic axon terminals. Postsynaptically, the majority of GABAB receptor subunits were localized to the extrasynaptic plasma membrane of spines and dendritic shafts of principal cells and shafts of interneuron dendrites. Quantitative analysis revealed enrichment of GABAB1a/b around putative glutamatergic synapses on spines and an even distribution on dendritic shafts of pyramidal cells contacted by GABAergic boutons. The association of GABAB receptors with glutamatergic synapses at both presynaptic and postsynaptic sides indicates their intimate involvement in the modulation of glutamatergic neurotransmission. The dominant extrasynaptic localization of GABAB receptor subunits suggests that their activation is dependent on spillover of GABA requiring simultaneous activity of populations of GABAergic cells as it occurs during population oscillations or epileptic seizures. author: - first_name: Ákos full_name: Kulik, Ákos last_name: Kulik - first_name: Imre full_name: Vida, Imre last_name: Vida - first_name: Rafael full_name: Luján, Rafael last_name: Luján - first_name: Carola full_name: Haas, Carola A last_name: Haas - first_name: Guillermina full_name: López-Bendito, Guillermina last_name: López Bendito - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Michael full_name: Frotscher, Michael last_name: Frotscher citation: ama: Kulik Á, Vida I, Luján R, et al. Subcellular Localization of Metabotropic GABAB Receptor Subunits GABAB1a/b and GABAB2 in the Rat Hippocampus. Journal of Neuroscience. 2003;23(35):11026-11035. apa: Kulik, Á., Vida, I., Luján, R., Haas, C., López Bendito, G., Shigemoto, R., & Frotscher, M. (2003). Subcellular Localization of Metabotropic GABAB Receptor Subunits GABAB1a/b and GABAB2 in the Rat Hippocampus. Journal of Neuroscience. Society for Neuroscience. chicago: Kulik, Ákos, Imre Vida, Rafael Luján, Carola Haas, Guillermina López Bendito, Ryuichi Shigemoto, and Michael Frotscher. “Subcellular Localization of Metabotropic GABAB Receptor Subunits GABAB1a/b and GABAB2 in the Rat Hippocampus.” Journal of Neuroscience. Society for Neuroscience, 2003. ieee: Á. Kulik et al., “Subcellular Localization of Metabotropic GABAB Receptor Subunits GABAB1a/b and GABAB2 in the Rat Hippocampus,” Journal of Neuroscience, vol. 23, no. 35. Society for Neuroscience, pp. 11026–11035, 2003. ista: Kulik Á, Vida I, Luján R, Haas C, López Bendito G, Shigemoto R, Frotscher M. 2003. Subcellular Localization of Metabotropic GABAB Receptor Subunits GABAB1a/b and GABAB2 in the Rat Hippocampus. Journal of Neuroscience. 23(35), 11026–11035. mla: Kulik, Ákos, et al. “Subcellular Localization of Metabotropic GABAB Receptor Subunits GABAB1a/b and GABAB2 in the Rat Hippocampus.” Journal of Neuroscience, vol. 23, no. 35, Society for Neuroscience, 2003, pp. 11026–35. short: Á. Kulik, I. Vida, R. Luján, C. Haas, G. López Bendito, R. Shigemoto, M. Frotscher, Journal of Neuroscience 23 (2003) 11026–11035. date_created: 2018-12-11T11:58:47Z date_published: 2003-12-03T00:00:00Z date_updated: 2021-01-12T06:58:43Z day: '03' extern: 1 intvolume: ' 23' issue: '35' month: '12' page: 11026 - 11035 publication: Journal of Neuroscience publication_status: published publisher: Society for Neuroscience publist_id: '4263' quality_controlled: 0 status: public title: Subcellular Localization of Metabotropic GABAB Receptor Subunits GABAB1a/b and GABAB2 in the Rat Hippocampus type: journal_article volume: 23 year: '2003' ... --- _id: '2634' abstract: - lang: eng text: To better understand the role of neurotransmitter receptors in neuronal differentiation and maturation a detailed knowledge of their identity, location and function in the plasma membrane of specific neuronal populations during development is required. Combining pre-embedding immunocytochemistry with cell tracking in embryonic brain slice cultures we show that virtually all neurons (∼98%) migrating through the lower intermediate zone (LIZ) on their way from the medial ganglionic eminence to the cerebral cortex, express GABA BR1. Blockade of GABABRs with a specific antagonist, CGP52432, resulted in a concentration-dependent accumulation of these tangentially migrating neurons in the ventricular/subventricular zones (VZ/SVZ) of the cortex and fewer cells were observed in the cortical plate/marginal zone (CP/MZ) and LIZ. Moreover, they had significantly shorter leading processes compared with similar migrating cells in control slices. Electrophysiological recording in LIZ and CP cells revealed no direct effect of either CGP52432 or the GABABR agonist, baclofen, on resting membrane properties suggesting that the effect of CGP52432 on migration might be mediated through a metabotropic action or the regulation of release of factors controlling migration. These results suggest that GABABRs have an important modulatory role in the migration of cortical interneurons. author: - first_name: Guillermina full_name: López-Bendito, Guillermina last_name: López Bendito - first_name: Rafael full_name: Luján, Rafael last_name: Luján - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Paul full_name: Ganter, Paul last_name: Ganter - first_name: Ole full_name: Paulsen, Ole last_name: Paulsen - first_name: Zoltán full_name: Molnár, Zoltán last_name: Molnár citation: ama: López Bendito G, Luján R, Shigemoto R, Ganter P, Paulsen O, Molnár Z. Blockade of GABAB receptors alters the tangential migration of cortical neurons. Cerebral Cortex. 2003;13(9):932-942. doi:10.1093/cercor/13.9.932 apa: López Bendito, G., Luján, R., Shigemoto, R., Ganter, P., Paulsen, O., & Molnár, Z. (2003). Blockade of GABAB receptors alters the tangential migration of cortical neurons. Cerebral Cortex. Oxford University Press. https://doi.org/10.1093/cercor/13.9.932 chicago: López Bendito, Guillermina, Rafael Luján, Ryuichi Shigemoto, Paul Ganter, Ole Paulsen, and Zoltán Molnár. “Blockade of GABAB Receptors Alters the Tangential Migration of Cortical Neurons.” Cerebral Cortex. Oxford University Press, 2003. https://doi.org/10.1093/cercor/13.9.932. ieee: G. López Bendito, R. Luján, R. Shigemoto, P. Ganter, O. Paulsen, and Z. Molnár, “Blockade of GABAB receptors alters the tangential migration of cortical neurons,” Cerebral Cortex, vol. 13, no. 9. Oxford University Press, pp. 932–942, 2003. ista: López Bendito G, Luján R, Shigemoto R, Ganter P, Paulsen O, Molnár Z. 2003. Blockade of GABAB receptors alters the tangential migration of cortical neurons. Cerebral Cortex. 13(9), 932–942. mla: López Bendito, Guillermina, et al. “Blockade of GABAB Receptors Alters the Tangential Migration of Cortical Neurons.” Cerebral Cortex, vol. 13, no. 9, Oxford University Press, 2003, pp. 932–42, doi:10.1093/cercor/13.9.932. short: G. López Bendito, R. Luján, R. Shigemoto, P. Ganter, O. Paulsen, Z. Molnár, Cerebral Cortex 13 (2003) 932–942. date_created: 2018-12-11T11:58:47Z date_published: 2003-09-01T00:00:00Z date_updated: 2021-01-12T06:58:43Z day: '01' doi: 10.1093/cercor/13.9.932 extern: 1 intvolume: ' 13' issue: '9' month: '09' page: 932 - 942 publication: Cerebral Cortex publication_status: published publisher: Oxford University Press publist_id: '4264' quality_controlled: 0 status: public title: Blockade of GABAB receptors alters the tangential migration of cortical neurons type: journal_article volume: 13 year: '2003' ... --- _id: '2630' abstract: - lang: eng text: Taste-metabotropic glutamate receptor 4 (taste-mGluR4) and the heteromers of T1R1 and T1R3 are candidate receptors involved in the sense of umami (monosodium glutamate) taste. Although the expression of group III mGluRs (taste-mGluR4) has been demonstrated in taste tissues, no mention has been made of the expression of group I mGluRs (mGluR1 and mGluR5) in taste tissues. We examined the expression of mGluR1 and mGluR5 in rat gustatory tissues by using reverse transcription-polymerase chain reaction (RT-PCR), in situ hybridization, immunohistochemistry and immunoelectron microscopy. RT-PCR assay showed that mGluR1α and mGluR1β mRNAs were expressed in circumvallate papillae, but mGluR5 mRNA was not expressed. The positive signals of mGluR1 mRNA were detected only in circumvallate taste buds by in situ hybridization analysis. In cryosections of fungiform, foliate and circumvallate papillae, the antibody against mGluRla gave intense labeling on the taste hairs in all taste pores examined. In the developing taste buds, the positive signals of mGluR1α in taste hairs gradually increased with the increase in number of taste bud cells. These results show that, in addition to taste-mGluR4 and the heteromer of T1R1 and T1R3, mGluR1α may function as a receptor for glutamate (umami) taste sensation. author: - first_name: Takashi full_name: Toyono, Takashi last_name: Toyono - first_name: Yuji full_name: Seta, Yuji last_name: Seta - first_name: Shinji full_name: Kataoka, Shinji last_name: Kataoka - first_name: Shintaro full_name: Kawano, Shintaro last_name: Kawano - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Kuniaki full_name: Toyoshima, Kuniaki last_name: Toyoshima citation: ama: Toyono T, Seta Y, Kataoka S, Kawano S, Shigemoto R, Toyoshima K. Expression of metabotropic glutamate receptor group I in rat gustatory papillae. Cell and Tissue Research. 2003;313(1):29-35. doi:10.1007/s00441-003-0740-2 apa: Toyono, T., Seta, Y., Kataoka, S., Kawano, S., Shigemoto, R., & Toyoshima, K. (2003). Expression of metabotropic glutamate receptor group I in rat gustatory papillae. Cell and Tissue Research. Springer. https://doi.org/10.1007/s00441-003-0740-2 chicago: Toyono, Takashi, Yuji Seta, Shinji Kataoka, Shintaro Kawano, Ryuichi Shigemoto, and Kuniaki Toyoshima. “Expression of Metabotropic Glutamate Receptor Group I in Rat Gustatory Papillae.” Cell and Tissue Research. Springer, 2003. https://doi.org/10.1007/s00441-003-0740-2. ieee: T. Toyono, Y. Seta, S. Kataoka, S. Kawano, R. Shigemoto, and K. Toyoshima, “Expression of metabotropic glutamate receptor group I in rat gustatory papillae,” Cell and Tissue Research, vol. 313, no. 1. Springer, pp. 29–35, 2003. ista: Toyono T, Seta Y, Kataoka S, Kawano S, Shigemoto R, Toyoshima K. 2003. Expression of metabotropic glutamate receptor group I in rat gustatory papillae. Cell and Tissue Research. 313(1), 29–35. mla: Toyono, Takashi, et al. “Expression of Metabotropic Glutamate Receptor Group I in Rat Gustatory Papillae.” Cell and Tissue Research, vol. 313, no. 1, Springer, 2003, pp. 29–35, doi:10.1007/s00441-003-0740-2. short: T. Toyono, Y. Seta, S. Kataoka, S. Kawano, R. Shigemoto, K. Toyoshima, Cell and Tissue Research 313 (2003) 29–35. date_created: 2018-12-11T11:58:46Z date_published: 2003-07-01T00:00:00Z date_updated: 2021-01-12T06:58:41Z day: '01' doi: 10.1007/s00441-003-0740-2 extern: 1 intvolume: ' 313' issue: '1' month: '07' page: 29 - 35 publication: Cell and Tissue Research publication_status: published publisher: Springer publist_id: '4267' quality_controlled: 0 status: public title: Expression of metabotropic glutamate receptor group I in rat gustatory papillae type: journal_article volume: 313 year: '2003' ... --- _id: '2637' abstract: - lang: eng text: While the cholinergic depletion in Alzheimer's disease (AD) has been known for some time, a definitive involvement of other neurotransmitter systems has been somewhat more elusive. Our study demonstrates a clear involvement of both glutamatergic and, to a lesser extent, GABAergic neurons in an early onset transgenic mouse model of AD-like amyloid pathology. Immunohistochemical staining and subsequent quantification has revealed a statistically significant increased density of glutamatergic and GABAergic presynaptic boutons in both the plaque free and plaque adjacent cortical neuropile areas of transgenic mice as compared to non-transgenic controls. Furthermore, amyloid plaque size was shown to have a statistically significant effect on the relative area occupied by dystrophic glutamatergic neurites in the peri-plaque neuropile. These findings support our hypothesis that the amyloid pathology progresses in a time and neurotransmitter specific manner, first in the cholinergic system which appears to be most vulnerable, followed by the glutamatergic presynaptic boutons and finally the somewhat more resilient GABAergic terminals. author: - first_name: Karen full_name: Bell, Karen F last_name: Bell - first_name: G J full_name: De Kort, G J last_name: De Kort - first_name: S full_name: Steggerda, S last_name: Steggerda - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Alfredo full_name: Ribeiro-da-Silva, Alfredo last_name: Ribeiro Da Silva - first_name: Augusto full_name: Cuello, Augusto C last_name: Cuello citation: ama: Bell K, De Kort GJ, Steggerda S, Shigemoto R, Ribeiro Da Silva A, Cuello A. Structural involvement of the glutamatergic presynaptic boutons in a transgenic mouse model expressing early onset amyloid pathology. Neuroscience Letters. 2003;353(2):143-147. doi:10.1016/j.neulet.2003.09.027 apa: Bell, K., De Kort, G. J., Steggerda, S., Shigemoto, R., Ribeiro Da Silva, A., & Cuello, A. (2003). Structural involvement of the glutamatergic presynaptic boutons in a transgenic mouse model expressing early onset amyloid pathology. Neuroscience Letters. Elsevier. https://doi.org/10.1016/j.neulet.2003.09.027 chicago: Bell, Karen, G J De Kort, S Steggerda, Ryuichi Shigemoto, Alfredo Ribeiro Da Silva, and Augusto Cuello. “Structural Involvement of the Glutamatergic Presynaptic Boutons in a Transgenic Mouse Model Expressing Early Onset Amyloid Pathology.” Neuroscience Letters. Elsevier, 2003. https://doi.org/10.1016/j.neulet.2003.09.027. ieee: K. Bell, G. J. De Kort, S. Steggerda, R. Shigemoto, A. Ribeiro Da Silva, and A. Cuello, “Structural involvement of the glutamatergic presynaptic boutons in a transgenic mouse model expressing early onset amyloid pathology,” Neuroscience Letters, vol. 353, no. 2. Elsevier, pp. 143–147, 2003. ista: Bell K, De Kort GJ, Steggerda S, Shigemoto R, Ribeiro Da Silva A, Cuello A. 2003. Structural involvement of the glutamatergic presynaptic boutons in a transgenic mouse model expressing early onset amyloid pathology. Neuroscience Letters. 353(2), 143–147. mla: Bell, Karen, et al. “Structural Involvement of the Glutamatergic Presynaptic Boutons in a Transgenic Mouse Model Expressing Early Onset Amyloid Pathology.” Neuroscience Letters, vol. 353, no. 2, Elsevier, 2003, pp. 143–47, doi:10.1016/j.neulet.2003.09.027. short: K. Bell, G.J. De Kort, S. Steggerda, R. Shigemoto, A. Ribeiro Da Silva, A. Cuello, Neuroscience Letters 353 (2003) 143–147. date_created: 2018-12-11T11:58:48Z date_published: 2003-12-19T00:00:00Z date_updated: 2021-01-12T06:58:44Z day: '19' doi: 10.1016/j.neulet.2003.09.027 extern: 1 intvolume: ' 353' issue: '2' month: '12' page: 143 - 147 publication: Neuroscience Letters publication_status: published publisher: Elsevier publist_id: '4262' quality_controlled: 0 status: public title: Structural involvement of the glutamatergic presynaptic boutons in a transgenic mouse model expressing early onset amyloid pathology type: journal_article volume: 353 year: '2003' ... --- _id: '2784' abstract: - lang: eng text: We report the results of an experimental study of magnetohydrodynamic damping of sidewall convection in a rectangular enclosure filled with gallium. In particular we investigate the suppression of convection when a steady magnetic field is applied separately in each of the three principal directions of the flow. The strongest damping of the steady flow is found for a vertical magnetic field, which is in agreement with theory. However, we observe that the application of a field transverse to the flow provides greater damping than a longitudinal one, which seems to contradict available theory. We provide a possible resolution of this apparent dichotomy in terms of the length scale of the experiment. author: - first_name: Björn full_name: Björn Hof id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 - first_name: Anne full_name: Juel, Anne last_name: Juel - first_name: Tom full_name: Mullin, Tom P last_name: Mullin citation: ama: Hof B, Juel A, Mullin T. Magnetohydrodynamic damping of convective flows in molten gallium. Journal of Fluid Mechanics. 2003;482:163-179. doi:10.1017/S0022112003004014 apa: Hof, B., Juel, A., & Mullin, T. (2003). Magnetohydrodynamic damping of convective flows in molten gallium. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/S0022112003004014 chicago: Hof, Björn, Anne Juel, and Tom Mullin. “Magnetohydrodynamic Damping of Convective Flows in Molten Gallium.” Journal of Fluid Mechanics. Cambridge University Press, 2003. https://doi.org/10.1017/S0022112003004014. ieee: B. Hof, A. Juel, and T. Mullin, “Magnetohydrodynamic damping of convective flows in molten gallium,” Journal of Fluid Mechanics, vol. 482. Cambridge University Press, pp. 163–179, 2003. ista: Hof B, Juel A, Mullin T. 2003. Magnetohydrodynamic damping of convective flows in molten gallium. Journal of Fluid Mechanics. 482, 163–179. mla: Hof, Björn, et al. “Magnetohydrodynamic Damping of Convective Flows in Molten Gallium.” Journal of Fluid Mechanics, vol. 482, Cambridge University Press, 2003, pp. 163–79, doi:10.1017/S0022112003004014. short: B. Hof, A. Juel, T. Mullin, Journal of Fluid Mechanics 482 (2003) 163–179. date_created: 2018-12-11T11:59:35Z date_published: 2003-05-13T00:00:00Z date_updated: 2021-01-12T06:59:42Z day: '13' doi: 10.1017/S0022112003004014 extern: 1 intvolume: ' 482' month: '05' page: 163 - 179 publication: Journal of Fluid Mechanics publication_status: published publisher: Cambridge University Press publist_id: '4105' quality_controlled: 0 status: public title: Magnetohydrodynamic damping of convective flows in molten gallium type: journal_article volume: 482 year: '2003' ... --- _id: '2785' abstract: - lang: eng text: Experimental evidence for the scaling of the finite amplitude of perturbation theory required to promote transition in Poiseuille flow was found. The exponent is -1 and was uncovered using considerable care in the design and execution of the experiment. Interestingly, this exponent was also found in experiments on transition in boundary layers. author: - first_name: Björn full_name: Björn Hof id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 - first_name: Anne full_name: Juel, Anne last_name: Juel - first_name: Tom full_name: Mullin, Tom P last_name: Mullin citation: ama: Hof B, Juel A, Mullin T. Scaling of the turbulence transition threshold in a pipe. Physical Review Letters. 2003;91(24):244502/1-244502/4. doi:10.1103/PhysRevLett.91.244502 apa: Hof, B., Juel, A., & Mullin, T. (2003). Scaling of the turbulence transition threshold in a pipe. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.91.244502 chicago: Hof, Björn, Anne Juel, and Tom Mullin. “Scaling of the Turbulence Transition Threshold in a Pipe.” Physical Review Letters. American Physical Society, 2003. https://doi.org/10.1103/PhysRevLett.91.244502. ieee: B. Hof, A. Juel, and T. Mullin, “Scaling of the turbulence transition threshold in a pipe,” Physical Review Letters, vol. 91, no. 24. American Physical Society, p. 244502/1-244502/4, 2003. ista: Hof B, Juel A, Mullin T. 2003. Scaling of the turbulence transition threshold in a pipe. Physical Review Letters. 91(24), 244502/1-244502/4. mla: Hof, Björn, et al. “Scaling of the Turbulence Transition Threshold in a Pipe.” Physical Review Letters, vol. 91, no. 24, American Physical Society, 2003, p. 244502/1-244502/4, doi:10.1103/PhysRevLett.91.244502. short: B. Hof, A. Juel, T. Mullin, Physical Review Letters 91 (2003) 244502/1-244502/4. date_created: 2018-12-11T11:59:35Z date_published: 2003-12-12T00:00:00Z date_updated: 2021-01-12T06:59:42Z day: '12' doi: 10.1103/PhysRevLett.91.244502 extern: 1 intvolume: ' 91' issue: '24' month: '12' page: 244502/1 - 244502/4 publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '4104' quality_controlled: 0 status: public title: Scaling of the turbulence transition threshold in a pipe type: journal_article volume: 91 year: '2003' ... --- _id: '2990' abstract: - lang: eng text: Plant growth is marked by its adaptability to continuous changes in environment. A regulated, differential distribution of auxin underlies many adaptation processes including organogenesis, meristem patterning and tropisms. In executing its multiple roles, auxin displays some characteristics of both a hormone and a morphogen. Studies on auxin transport, as well as tracing the intracellular movement of its molecular components, have suggested a possible scenario to explain how growth plasticity is conferred at the cellular and molecular level. The plant perceives stimuli and changes the subcellular position of auxin-transport components accordingly. These changes modulate auxin fluxes, and the newly established auxin distribution triggers the corresponding developmental response. author: - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Friml J. Auxin transport - Shaping the plant. Current Opinion in Plant Biology. 2003;6(1):7-12. doi:10.1016/S1369526602000031 apa: Friml, J. (2003). Auxin transport - Shaping the plant. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/S1369526602000031 chicago: Friml, Jiří. “Auxin Transport - Shaping the Plant.” Current Opinion in Plant Biology. Elsevier, 2003. https://doi.org/10.1016/S1369526602000031. ieee: J. Friml, “Auxin transport - Shaping the plant,” Current Opinion in Plant Biology, vol. 6, no. 1. Elsevier, pp. 7–12, 2003. ista: Friml J. 2003. Auxin transport - Shaping the plant. Current Opinion in Plant Biology. 6(1), 7–12. mla: Friml, Jiří. “Auxin Transport - Shaping the Plant.” Current Opinion in Plant Biology, vol. 6, no. 1, Elsevier, 2003, pp. 7–12, doi:10.1016/S1369526602000031. short: J. Friml, Current Opinion in Plant Biology 6 (2003) 7–12. date_created: 2018-12-11T12:00:43Z date_published: 2003-02-01T00:00:00Z date_updated: 2021-01-12T07:40:17Z day: '01' doi: 10.1016/S1369526602000031 extern: '1' intvolume: ' 6' issue: '1' language: - iso: eng month: '02' oa_version: None page: 7 - 12 publication: Current Opinion in Plant Biology publication_status: published publisher: Elsevier publist_id: '3711' quality_controlled: '1' status: public title: Auxin transport - Shaping the plant type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2003' ... --- _id: '2992' abstract: - lang: eng text: Plants have many polarized cell types, but relatively little is known about the mechanisms that establish polarity. The orc mutant was identified originally by defects in root patterning, and positional cloning revealed that the affected gene encodes STEROL METHYLTRANSFERASE1, which is required for the appropriate synthesis and composition of major membrane sterols. smt1orc mutants displayed several conspicuous cell polarity defects. Columella root cap cells revealed perturbed polar positioning of different organelles, and in the smt1orc root epidermis, polar initiation of root hairs was more randomized. Polar auxin transport and expression of the auxin reporter DR5-β-glucuronidase were aberrant in smt1orc. Patterning defects in smt1orc resembled those observed in mutants of the PIN gene family of putative auxin efflux transporters. Consistently, the membrane localization of the PIN1 and PIN3 proteins was disturbed in smt1orc, whereas polar positioning of the influx carrier AUX1 appeared normal. Our results suggest that balanced sterol composition is a major requirement for cell polarity and auxin efflux in Arabidopsis. author: - first_name: Viola full_name: Willemsen, Viola last_name: Willemsen - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Markus full_name: Grebe, Markus last_name: Grebe - first_name: Albert full_name: Van Den Toorn, Albert last_name: Van Den Toorn - first_name: Klaus full_name: Palme, Klaus last_name: Palme - first_name: Ben full_name: Scheres, Ben last_name: Scheres citation: ama: Willemsen V, Friml J, Grebe M, Van Den Toorn A, Palme K, Scheres B. Cell polarity and PIN protein positioning in Arabidopsis require STEROL METHYLTRANSFERASE1 function. Plant Cell. 2003;15(3):612-625. doi:10.1105/tpc.008433 apa: Willemsen, V., Friml, J., Grebe, M., Van Den Toorn, A., Palme, K., & Scheres, B. (2003). Cell polarity and PIN protein positioning in Arabidopsis require STEROL METHYLTRANSFERASE1 function. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.008433 chicago: Willemsen, Viola, Jiří Friml, Markus Grebe, Albert Van Den Toorn, Klaus Palme, and Ben Scheres. “Cell Polarity and PIN Protein Positioning in Arabidopsis Require STEROL METHYLTRANSFERASE1 Function.” Plant Cell. American Society of Plant Biologists, 2003. https://doi.org/10.1105/tpc.008433. ieee: V. Willemsen, J. Friml, M. Grebe, A. Van Den Toorn, K. Palme, and B. Scheres, “Cell polarity and PIN protein positioning in Arabidopsis require STEROL METHYLTRANSFERASE1 function,” Plant Cell, vol. 15, no. 3. American Society of Plant Biologists, pp. 612–625, 2003. ista: Willemsen V, Friml J, Grebe M, Van Den Toorn A, Palme K, Scheres B. 2003. Cell polarity and PIN protein positioning in Arabidopsis require STEROL METHYLTRANSFERASE1 function. Plant Cell. 15(3), 612–625. mla: Willemsen, Viola, et al. “Cell Polarity and PIN Protein Positioning in Arabidopsis Require STEROL METHYLTRANSFERASE1 Function.” Plant Cell, vol. 15, no. 3, American Society of Plant Biologists, 2003, pp. 612–25, doi:10.1105/tpc.008433. short: V. Willemsen, J. Friml, M. Grebe, A. Van Den Toorn, K. Palme, B. Scheres, Plant Cell 15 (2003) 612–625. date_created: 2018-12-11T12:00:44Z date_published: 2003-03-01T00:00:00Z date_updated: 2021-01-12T07:40:18Z day: '01' doi: 10.1105/tpc.008433 extern: 1 intvolume: ' 15' issue: '3' month: '03' page: 612 - 625 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '3710' quality_controlled: 0 status: public title: Cell polarity and PIN protein positioning in Arabidopsis require STEROL METHYLTRANSFERASE1 function type: journal_article volume: 15 year: '2003' ... --- _id: '2996' abstract: - lang: eng text: | Plants, compared to animals, exhibit an amazing adaptability and plasticity in their development. This is largely dependent on the ability of plants to form new organs, such as lateral roots, leaves, and flowers during postembryonic development. Organ primordia develop from founder cell populations into organs by coordinated cell division and differentiation. Here, we show that organ formation in Arabidopsis involves dynamic gradients of the signaling molecule auxin with maxima at the primordia tips. These gradients are mediated by cellular efflux requiring asymmetrically localized PIN proteins, which represent a functionally redundant network for auxin distribution in both aerial and underground organs. PIN1 polar localization undergoes a dynamic rearrangement, which correlates with establishment of auxin gradients and primordium development. Our results suggest that PIN-dependent, local auxin gradients represent a common module for formation of all plant organs, regardless of their mature morphology or developmental origin. author: - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Marta full_name: Michniewicz, Marta last_name: Michniewicz - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Thomas full_name: Teichmann, Thomas last_name: Teichmann - first_name: Daniela full_name: Seifertová, Daniela last_name: Seifertová - first_name: Gerd full_name: Jürgens, Gerd last_name: Jürgens - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Benková E, Michniewicz M, Sauer M, et al. Local, efflux-dependent auxin gradients as a common module for plant organ formation. Cell. 2003;115(5):591-602. doi:10.1016/S0092-8674(03)00924-3 apa: Benková, E., Michniewicz, M., Sauer, M., Teichmann, T., Seifertová, D., Jürgens, G., & Friml, J. (2003). Local, efflux-dependent auxin gradients as a common module for plant organ formation. Cell. Cell Press. https://doi.org/10.1016/S0092-8674(03)00924-3 chicago: Benková, Eva, Marta Michniewicz, Michael Sauer, Thomas Teichmann, Daniela Seifertová, Gerd Jürgens, and Jiří Friml. “Local, Efflux-Dependent Auxin Gradients as a Common Module for Plant Organ Formation.” Cell. Cell Press, 2003. https://doi.org/10.1016/S0092-8674(03)00924-3. ieee: E. Benková et al., “Local, efflux-dependent auxin gradients as a common module for plant organ formation,” Cell, vol. 115, no. 5. Cell Press, pp. 591–602, 2003. ista: Benková E, Michniewicz M, Sauer M, Teichmann T, Seifertová D, Jürgens G, Friml J. 2003. Local, efflux-dependent auxin gradients as a common module for plant organ formation. Cell. 115(5), 591–602. mla: Benková, Eva, et al. “Local, Efflux-Dependent Auxin Gradients as a Common Module for Plant Organ Formation.” Cell, vol. 115, no. 5, Cell Press, 2003, pp. 591–602, doi:10.1016/S0092-8674(03)00924-3. short: E. Benková, M. Michniewicz, M. Sauer, T. Teichmann, D. Seifertová, G. Jürgens, J. Friml, Cell 115 (2003) 591–602. date_created: 2018-12-11T12:00:46Z date_published: 2003-11-26T00:00:00Z date_updated: 2021-01-12T07:40:19Z day: '26' doi: 10.1016/S0092-8674(03)00924-3 extern: 1 intvolume: ' 115' issue: '5' month: '11' page: 591 - 602 publication: Cell publication_status: published publisher: Cell Press publist_id: '3706' quality_controlled: 0 status: public title: Local, efflux-dependent auxin gradients as a common module for plant organ formation type: journal_article volume: 115 year: '2003' ... --- _id: '2995' abstract: - lang: eng text: | Axis formation occurs in plants, as in animals, during early embryogenesis. However, the underlying mechanism is not known. Here we show that the first manifestation of the apical-basal axis in plants, the asymmetric division of the zygote, produces a basal cell that transports and an apical cell that responds to the signalling molecule auxin. This apical-basal auxin activity gradient triggers the specification of apical embryo structures and is actively maintained by a novel component of auxin efflux, PIN7, which is located apically in the basal cell. Later, the developmentally regulated reversal of PIN7 and onset of PIN1 polar localization reorganize the auxin gradient for specification of the basal root pole. An analysis of pin quadruple mutants identifies PIN-dependent transport as an essential part of the mechanism for embryo axis formation. Our results indicate how the establishment of cell polarity, polar auxin efflux and local auxin response result in apical-basal axis formation of the embryo, and thus determine the axiality of the adult plant. author: - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Anne full_name: Vieten, Anne last_name: Vieten - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers - first_name: Heinz full_name: Schwarz, Heinz last_name: Schwarz - first_name: Thorsten full_name: Hamann, Thorsten last_name: Hamann - first_name: Remko full_name: Offringa, Remko last_name: Offringa - first_name: Gerd full_name: Jürgens, Gerd last_name: Jürgens citation: ama: Friml J, Vieten A, Sauer M, et al. Efflux dependent auxin gradients establish the apical basal axis of Arabidopsis. Nature. 2003;426(6963):147-153. doi:10.1038/nature02085 apa: Friml, J., Vieten, A., Sauer, M., Weijers, D., Schwarz, H., Hamann, T., … Jürgens, G. (2003). Efflux dependent auxin gradients establish the apical basal axis of Arabidopsis. Nature. Nature Publishing Group. https://doi.org/10.1038/nature02085 chicago: Friml, Jiří, Anne Vieten, Michael Sauer, Dolf Weijers, Heinz Schwarz, Thorsten Hamann, Remko Offringa, and Gerd Jürgens. “Efflux Dependent Auxin Gradients Establish the Apical Basal Axis of Arabidopsis.” Nature. Nature Publishing Group, 2003. https://doi.org/10.1038/nature02085. ieee: J. Friml et al., “Efflux dependent auxin gradients establish the apical basal axis of Arabidopsis,” Nature, vol. 426, no. 6963. Nature Publishing Group, pp. 147–153, 2003. ista: Friml J, Vieten A, Sauer M, Weijers D, Schwarz H, Hamann T, Offringa R, Jürgens G. 2003. Efflux dependent auxin gradients establish the apical basal axis of Arabidopsis. Nature. 426(6963), 147–153. mla: Friml, Jiří, et al. “Efflux Dependent Auxin Gradients Establish the Apical Basal Axis of Arabidopsis.” Nature, vol. 426, no. 6963, Nature Publishing Group, 2003, pp. 147–53, doi:10.1038/nature02085. short: J. Friml, A. Vieten, M. Sauer, D. Weijers, H. Schwarz, T. Hamann, R. Offringa, G. Jürgens, Nature 426 (2003) 147–153. date_created: 2018-12-11T12:00:45Z date_published: 2003-11-13T00:00:00Z date_updated: 2021-01-12T07:40:19Z day: '13' doi: 10.1038/nature02085 extern: 1 intvolume: ' 426' issue: '6963' month: '11' page: 147 - 153 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '3708' quality_controlled: 0 status: public title: Efflux dependent auxin gradients establish the apical basal axis of Arabidopsis type: journal_article volume: 426 year: '2003' ... --- _id: '2994' abstract: - lang: eng text: The regular arrangement of leaves around a plant's stem, called phyllotaxis, has for centuries attracted the attention of philosophers, mathematicians and natural scientists; however, to date, studies of phyllotaxis have been largely theoretical. Leaves and flowers are formed from the shoot apical meristem, triggered by the plant hormone auxin. Auxin is transported through plant tissues by specific cellular influx and efflux carrier proteins. Here we show that proteins involved in auxin transport regulate phyllotaxis. Our data indicate that auxin is transported upwards into the meristem through the epidermis and the outermost meristem cell layer. Existing leaf primordia act as sinks, redistributing auxin and creating its heterogeneous distribution in the meristem. Auxin accumulation occurs only at certain minimal distances from existing primordia, defining the position of future primordia. This model for phyllotaxis accounts for its reiterative nature, as well as its regularity and stability. author: - first_name: Didier full_name: Reinhardt, Didier last_name: Reinhardt - first_name: Eva full_name: Pesce, Eva-Rachele last_name: Pesce - first_name: Pia full_name: Stieger, Pia last_name: Stieger - first_name: Therese full_name: Mandel, Therese last_name: Mandel - first_name: Kurt full_name: Baltensperger, Kurt last_name: Baltensperger - first_name: Malcolm full_name: Bennett, Malcolm last_name: Bennett - first_name: Jan full_name: Traas, Jan last_name: Traas - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Cris full_name: Kuhlemeier, Cris last_name: Kuhlemeier citation: ama: Reinhardt D, Pesce E, Stieger P, et al. Regulation of phyllotaxis by polar auxin transport. Nature. 2003;426(6964):255-260. doi:10.1038/nature02081 apa: Reinhardt, D., Pesce, E., Stieger, P., Mandel, T., Baltensperger, K., Bennett, M., … Kuhlemeier, C. (2003). Regulation of phyllotaxis by polar auxin transport. Nature. Nature Publishing Group. https://doi.org/10.1038/nature02081 chicago: Reinhardt, Didier, Eva Pesce, Pia Stieger, Therese Mandel, Kurt Baltensperger, Malcolm Bennett, Jan Traas, Jiří Friml, and Cris Kuhlemeier. “Regulation of Phyllotaxis by Polar Auxin Transport.” Nature. Nature Publishing Group, 2003. https://doi.org/10.1038/nature02081. ieee: D. Reinhardt et al., “Regulation of phyllotaxis by polar auxin transport,” Nature, vol. 426, no. 6964. Nature Publishing Group, pp. 255–260, 2003. ista: Reinhardt D, Pesce E, Stieger P, Mandel T, Baltensperger K, Bennett M, Traas J, Friml J, Kuhlemeier C. 2003. Regulation of phyllotaxis by polar auxin transport. Nature. 426(6964), 255–260. mla: Reinhardt, Didier, et al. “Regulation of Phyllotaxis by Polar Auxin Transport.” Nature, vol. 426, no. 6964, Nature Publishing Group, 2003, pp. 255–60, doi:10.1038/nature02081. short: D. Reinhardt, E. Pesce, P. Stieger, T. Mandel, K. Baltensperger, M. Bennett, J. Traas, J. Friml, C. Kuhlemeier, Nature 426 (2003) 255–260. date_created: 2018-12-11T12:00:45Z date_published: 2003-11-20T00:00:00Z date_updated: 2021-01-12T07:40:18Z day: '20' doi: 10.1038/nature02081 extern: 1 intvolume: ' 426' issue: '6964' month: '11' page: 255 - 260 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '3707' quality_controlled: 0 status: public title: Regulation of phyllotaxis by polar auxin transport type: journal_article volume: 426 year: '2003' ... --- _id: '2993' abstract: - lang: eng text: Plant biology is currently experiencing a growing demand for easy and reliable mRNA and protein localisation techniques. Here, we present novel whole mount in situ hybridisation and immunolocalisation protocols, suitable to localise mRNAs and proteins in Arabidopsis seedlings. We demonstrate that these methods can be used in different organs of Arabidopsis seedlings as well as in other plant species. In order to achieve better reproducibility and higher throughput, we modified these protocols for automation to be performed by a liquid handling robot. In addition, we show that other procedures such as reporter enzyme assays and tissue clearing can be similarly automated. We present examples of application of our protocols including mRNA localisation and proteins and epitope tag (co)localisations which demonstrate that these methods provide reliable and versatile tools for expression, localisation and anatomical studies in plants. author: - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Ulrike full_name: Mayer, Ulrike last_name: Mayer - first_name: Klaus full_name: Palme, Klaus last_name: Palme - first_name: Gerhard full_name: Muster, Gerhard last_name: Muster citation: ama: Friml J, Benková E, Mayer U, Palme K, Muster G. Automated whole mount localisation techniques for plant seedlings. Plant Journal. 2003;34(1):115-124. doi:10.1046/j.1365-313X.2003.01705.x apa: Friml, J., Benková, E., Mayer, U., Palme, K., & Muster, G. (2003). Automated whole mount localisation techniques for plant seedlings. Plant Journal. Wiley-Blackwell. https://doi.org/10.1046/j.1365-313X.2003.01705.x chicago: Friml, Jiří, Eva Benková, Ulrike Mayer, Klaus Palme, and Gerhard Muster. “Automated Whole Mount Localisation Techniques for Plant Seedlings.” Plant Journal. Wiley-Blackwell, 2003. https://doi.org/10.1046/j.1365-313X.2003.01705.x. ieee: J. Friml, E. Benková, U. Mayer, K. Palme, and G. Muster, “Automated whole mount localisation techniques for plant seedlings,” Plant Journal, vol. 34, no. 1. Wiley-Blackwell, pp. 115–124, 2003. ista: Friml J, Benková E, Mayer U, Palme K, Muster G. 2003. Automated whole mount localisation techniques for plant seedlings. Plant Journal. 34(1), 115–124. mla: Friml, Jiří, et al. “Automated Whole Mount Localisation Techniques for Plant Seedlings.” Plant Journal, vol. 34, no. 1, Wiley-Blackwell, 2003, pp. 115–24, doi:10.1046/j.1365-313X.2003.01705.x. short: J. Friml, E. Benková, U. Mayer, K. Palme, G. Muster, Plant Journal 34 (2003) 115–124. date_created: 2018-12-11T12:00:44Z date_published: 2003-04-01T00:00:00Z date_updated: 2021-01-12T07:40:18Z day: '01' doi: 10.1046/j.1365-313X.2003.01705.x extern: 1 intvolume: ' 34' issue: '1' month: '04' page: 115 - 124 publication: Plant Journal publication_status: published publisher: Wiley-Blackwell publist_id: '3709' quality_controlled: 0 status: public title: Automated whole mount localisation techniques for plant seedlings type: journal_article volume: 34 year: '2003' ... --- _id: '3151' abstract: - lang: eng text: Biosynthesis of most peptide hormones and neuropeptides requires proteolytic excision of the active peptide from inactive proprotein precursors, an activity carried out by subtilisin-like proprotein convertases (SPCs) in constitutive or regulated secretory pathways. The Drosophila amontillado (amon) gene encodes a homolog of the mammalian PC2 protein, an SPC that functions in the regulated secretory pathway in neuroendocrine tissues. We have identified amon mutants by isolating ethylmethanesulfonate (EMS)-induced lethal and visible mutations that define two complementation groups in the amon interval at 97D1 of the third chromosome. DNA sequencing identified the amon complementation group and the DNA sequence change for each of the nine amon alleles isolated. amon mutants display partial embryonic lethality, are defective in larval growth, and arrest during the first to second instar larval molt. Mutant larvae can be rescued by heat-shock-induced expression of the amon protein. Rescued larvae arrest at the subsequent larval molt, suggesting that amon is also required for the second to third instar larval molt. Our data indicate that the amon proprotein convertase is required during embryogenesis and larval development in Drosophila and support the hypothesis that AMON acts to proteolytically process peptide hormones that regulate hatching, larval growth, and larval ecdysis. author: - first_name: Lowell full_name: Rayburn, Lowell Y last_name: Rayburn - first_name: Holly full_name: Gooding, Holly C last_name: Gooding - first_name: Semil full_name: Choksi, Semil P last_name: Choksi - first_name: Dhea full_name: Maloney, Dhea last_name: Maloney - first_name: Ambrose full_name: Kidd, Ambrose R last_name: Kidd - first_name: Daria E full_name: Daria Siekhaus id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 - first_name: Michael full_name: Bender, Michael last_name: Bender citation: ama: Rayburn L, Gooding H, Choksi S, et al. Amontillado, the Drosophila homolog of the prohormone processing protease PC2, is required during embryogenesis and early larval development. Genetics. 2003;163(1):227-237. apa: Rayburn, L., Gooding, H., Choksi, S., Maloney, D., Kidd, A., Siekhaus, D. E., & Bender, M. (2003). Amontillado, the Drosophila homolog of the prohormone processing protease PC2, is required during embryogenesis and early larval development. Genetics. Genetics Society of America. chicago: Rayburn, Lowell, Holly Gooding, Semil Choksi, Dhea Maloney, Ambrose Kidd, Daria E Siekhaus, and Michael Bender. “Amontillado, the Drosophila Homolog of the Prohormone Processing Protease PC2, Is Required during Embryogenesis and Early Larval Development.” Genetics. Genetics Society of America, 2003. ieee: L. Rayburn et al., “Amontillado, the Drosophila homolog of the prohormone processing protease PC2, is required during embryogenesis and early larval development,” Genetics, vol. 163, no. 1. Genetics Society of America, pp. 227–237, 2003. ista: Rayburn L, Gooding H, Choksi S, Maloney D, Kidd A, Siekhaus DE, Bender M. 2003. Amontillado, the Drosophila homolog of the prohormone processing protease PC2, is required during embryogenesis and early larval development. Genetics. 163(1), 227–237. mla: Rayburn, Lowell, et al. “Amontillado, the Drosophila Homolog of the Prohormone Processing Protease PC2, Is Required during Embryogenesis and Early Larval Development.” Genetics, vol. 163, no. 1, Genetics Society of America, 2003, pp. 227–37. short: L. Rayburn, H. Gooding, S. Choksi, D. Maloney, A. Kidd, D.E. Siekhaus, M. Bender, Genetics 163 (2003) 227–237. date_created: 2018-12-11T12:01:41Z date_published: 2003-01-01T00:00:00Z date_updated: 2021-01-12T07:41:25Z day: '01' extern: 1 intvolume: ' 163' issue: '1' month: '01' page: 227 - 237 publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '3545' quality_controlled: 0 status: public title: Amontillado, the Drosophila homolog of the prohormone processing protease PC2, is required during embryogenesis and early larval development type: journal_article volume: 163 year: '2003' ... --- _id: '3150' abstract: - lang: eng text: Tripartite G-protein-coupled receptors (GPCRs) represent one of the largest groups of signal transducers, transmitting signals from hormones, neuropeptides, odorants, food and light. Ligand-bound receptors catalyse GDP/GTP exchange on the G-protein α-subunit (Gα), leading to α-GTP separation from the βγ subunits and pathway activation. Activating mutations in the receptors or G proteins underlie many human diseases, including some cancers, dwarfism and premature puberty. Regulators of G-protein signalling (RGS proteins) are known to modulate the level and duration of ligand-induced signalling by accelerating the intrinsic GTPase activity of the Gα subunit, and thus reformation of the inactive GDP-bound Gα. Here we find that even in the absence of receptor, mutation of the RGS family member Sst2 (refs 6-9) permits spontaneous activation of the G-protein-coupled mating pathway in Saccharomyces cerevisiae at levels normally seen only in the presence of ligand. Our work demonstrates the occurence of spontaneous tripartite G-protein signalling in vivo and identifies a requirement for RGS proteins in preventing such receptor-independent activation. author: - first_name: Daria E full_name: Daria Siekhaus id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 - first_name: David full_name: Drubin, David G last_name: Drubin citation: ama: Siekhaus DE, Drubin D. Spontaneous receptor-independent heterotrimeric G-protein signalling in an RGS mutant. Nature Cell Biology. 2003;5(3):231-235. doi:10.1038/ncb941 apa: Siekhaus, D. E., & Drubin, D. (2003). Spontaneous receptor-independent heterotrimeric G-protein signalling in an RGS mutant. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb941 chicago: Siekhaus, Daria E, and David Drubin. “Spontaneous Receptor-Independent Heterotrimeric G-Protein Signalling in an RGS Mutant.” Nature Cell Biology. Nature Publishing Group, 2003. https://doi.org/10.1038/ncb941. ieee: D. E. Siekhaus and D. Drubin, “Spontaneous receptor-independent heterotrimeric G-protein signalling in an RGS mutant,” Nature Cell Biology, vol. 5, no. 3. Nature Publishing Group, pp. 231–235, 2003. ista: Siekhaus DE, Drubin D. 2003. Spontaneous receptor-independent heterotrimeric G-protein signalling in an RGS mutant. Nature Cell Biology. 5(3), 231–235. mla: Siekhaus, Daria E., and David Drubin. “Spontaneous Receptor-Independent Heterotrimeric G-Protein Signalling in an RGS Mutant.” Nature Cell Biology, vol. 5, no. 3, Nature Publishing Group, 2003, pp. 231–35, doi:10.1038/ncb941. short: D.E. Siekhaus, D. Drubin, Nature Cell Biology 5 (2003) 231–235. date_created: 2018-12-11T12:01:41Z date_published: 2003-03-01T00:00:00Z date_updated: 2021-01-12T07:41:24Z day: '01' doi: 10.1038/ncb941 extern: 1 intvolume: ' 5' issue: '3' month: '03' page: 231 - 235 publication: Nature Cell Biology publication_status: published publisher: Nature Publishing Group publist_id: '3544' quality_controlled: 0 status: public title: Spontaneous receptor-independent heterotrimeric G-protein signalling in an RGS mutant type: journal_article volume: 5 year: '2003' ... --- _id: '3209' abstract: - lang: eng text: We show that the fixed alphabet shortest common supersequence (SCS) and the fixed alphabet longest common subsequence (LCS) problems parameterized in the number of strings are W[1]-hard. Unless W[1]=FPT, this rules out the existence of algorithms with time complexity of O(f(k)nα) for those problems. Here n is the size of the problem instance, α is constant, k is the number of strings and f is any function of k. The fixed alphabet version of the LCS problem is of particular interest considering the importance of sequence comparison (e.g. multiple sequence alignment) in the fixed length alphabet world of DNA and protein sequences. author: - first_name: Krzysztof Z full_name: Krzysztof Pietrzak id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: Pietrzak KZ. On the parameterized complexity of the fixed alphabet shortest common supersequence and longest common subsequence problems. Journal of Computer and System Sciences. 2003;67(4):757-771. doi:10.1016/S0022-0000(03)00078-3 apa: Pietrzak, K. Z. (2003). On the parameterized complexity of the fixed alphabet shortest common supersequence and longest common subsequence problems. Journal of Computer and System Sciences. Elsevier. https://doi.org/10.1016/S0022-0000(03)00078-3 chicago: Pietrzak, Krzysztof Z. “On the Parameterized Complexity of the Fixed Alphabet Shortest Common Supersequence and Longest Common Subsequence Problems.” Journal of Computer and System Sciences. Elsevier, 2003. https://doi.org/10.1016/S0022-0000(03)00078-3. ieee: K. Z. Pietrzak, “On the parameterized complexity of the fixed alphabet shortest common supersequence and longest common subsequence problems,” Journal of Computer and System Sciences, vol. 67, no. 4. Elsevier, pp. 757–771, 2003. ista: Pietrzak KZ. 2003. On the parameterized complexity of the fixed alphabet shortest common supersequence and longest common subsequence problems. Journal of Computer and System Sciences. 67(4), 757–771. mla: Pietrzak, Krzysztof Z. “On the Parameterized Complexity of the Fixed Alphabet Shortest Common Supersequence and Longest Common Subsequence Problems.” Journal of Computer and System Sciences, vol. 67, no. 4, Elsevier, 2003, pp. 757–71, doi:10.1016/S0022-0000(03)00078-3. short: K.Z. Pietrzak, Journal of Computer and System Sciences 67 (2003) 757–771. date_created: 2018-12-11T12:02:01Z date_published: 2003-12-01T00:00:00Z date_updated: 2021-01-12T07:41:49Z day: '01' doi: 10.1016/S0022-0000(03)00078-3 extern: 1 intvolume: ' 67' issue: '4' month: '12' page: 757 - 771 publication: Journal of Computer and System Sciences publication_status: published publisher: Elsevier publist_id: '3472' quality_controlled: 0 status: public title: On the parameterized complexity of the fixed alphabet shortest common supersequence and longest common subsequence problems type: journal_article volume: 67 year: '2003' ... --- _id: '3210' abstract: - lang: eng text: 'Luby and Rackoff showed how to construct a (super-)pseudo-random permutation {0,1}2n→ {0,1}2n from some number r of pseudo-random functions {0,1}n → {0,1}n. Their construction, motivated by DES, consists of a cascade of r Feistel permutations. A Feistel permutation 1for a pseudo-random function f is defined as (L, R) → (R,L ⊕ f (R)), where L and R are the left and right part of the input and ⊕ denotes bitwise XOR or, in this paper, any other group operation on {0,1}n. The only non-trivial step of the security proof consists of proving that the cascade of r Feistel permutations with independent uniform random functions {0,1}n → {0,1}n, denoted Ψ2nr is indistinguishable from a uniform random permutation {0,1}2n → {0,1}2n by any computationally unbounded adaptive distinguisher making at most O(2cn) combined chosen plaintext/ciphertext queries for any c < α, where a is a security parameter. Luby and Rackoff proved α = 1/2 for r = 4. A natural problem, proposed by Pieprzyk is to improve on α for larger r. The best known result, α = 3/4 for r = 6, is due to Patarin. In this paper we prove a = 1 -O(1/r), i.e., the trivial upper bound α = 1 can be approached. The proof uses some new techniques that can be of independent interest. ' alternative_title: - LNCS author: - first_name: Ueli full_name: Maurer, Ueli M last_name: Maurer - first_name: Krzysztof Z full_name: Krzysztof Pietrzak id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Maurer U, Pietrzak KZ. The security of many round Luby Rackoff pseudo random permutations. In: Vol 2656. Springer; 2003:544-561. doi:10.1007/3-540-39200-9_34' apa: 'Maurer, U., & Pietrzak, K. Z. (2003). The security of many round Luby Rackoff pseudo random permutations (Vol. 2656, pp. 544–561). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Springer. https://doi.org/10.1007/3-540-39200-9_34' chicago: Maurer, Ueli, and Krzysztof Z Pietrzak. “The Security of Many Round Luby Rackoff Pseudo Random Permutations,” 2656:544–61. Springer, 2003. https://doi.org/10.1007/3-540-39200-9_34. ieee: 'U. Maurer and K. Z. Pietrzak, “The security of many round Luby Rackoff pseudo random permutations,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, 2003, vol. 2656, pp. 544–561.' ista: 'Maurer U, Pietrzak KZ. 2003. The security of many round Luby Rackoff pseudo random permutations. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 2656, 544–561.' mla: Maurer, Ueli, and Krzysztof Z. Pietrzak. The Security of Many Round Luby Rackoff Pseudo Random Permutations. Vol. 2656, Springer, 2003, pp. 544–61, doi:10.1007/3-540-39200-9_34. short: U. Maurer, K.Z. Pietrzak, in:, Springer, 2003, pp. 544–561. conference: name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques' date_created: 2018-12-11T12:02:02Z date_published: 2003-06-04T00:00:00Z date_updated: 2021-01-12T07:41:49Z day: '04' doi: 10.1007/3-540-39200-9_34 extern: 1 intvolume: ' 2656' month: '06' page: 544 - 561 publication_status: published publisher: Springer publist_id: '3473' quality_controlled: 0 status: public title: The security of many round Luby Rackoff pseudo random permutations type: conference volume: 2656 year: '2003' ... --- _id: '3425' alternative_title: - Nato Science Series II article_processing_charge: No author: - 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: T. full_name: Strother, T. last_name: Strother - first_name: Wolfgang full_name: Bauer, Wolfgang last_name: Bauer citation: ama: 'Bollenbach MT, Strother T, Bauer W. 3D supernova collapse calculations. In: Vol 166. Springer; 2003:277-288. doi:10.1007/978-1-4020-2705-5_21' apa: Bollenbach, M. T., Strother, T., & Bauer, W. (2003). 3D supernova collapse calculations (Vol. 166, pp. 277–288). Presented at the NATO ASI on Structure and Dynamics of Elementary Matter, Springer. https://doi.org/10.1007/978-1-4020-2705-5_21 chicago: Bollenbach, Mark Tobias, T. Strother, and Wolfgang Bauer. “3D Supernova Collapse Calculations,” 166:277–88. Springer, 2003. https://doi.org/10.1007/978-1-4020-2705-5_21. ieee: M. T. Bollenbach, T. Strother, and W. Bauer, “3D supernova collapse calculations,” presented at the NATO ASI on Structure and Dynamics of Elementary Matter, 2003, vol. 166, pp. 277–288. ista: Bollenbach MT, Strother T, Bauer W. 2003. 3D supernova collapse calculations. NATO ASI on Structure and Dynamics of Elementary Matter, Nato Science Series II, vol. 166, 277–288. mla: Bollenbach, Mark Tobias, et al. 3D Supernova Collapse Calculations. Vol. 166, Springer, 2003, pp. 277–88, doi:10.1007/978-1-4020-2705-5_21. short: M.T. Bollenbach, T. Strother, W. Bauer, in:, Springer, 2003, pp. 277–288. conference: name: NATO ASI on Structure and Dynamics of Elementary Matter date_created: 2018-12-11T12:03:16Z date_published: 2003-01-01T00:00:00Z date_updated: 2021-01-12T07:43:23Z day: '01' doi: 10.1007/978-1-4020-2705-5_21 extern: '1' intvolume: ' 166' language: - iso: eng month: '01' oa_version: None page: 277 - 288 publication_status: published publisher: Springer publist_id: '2976' status: public title: 3D supernova collapse calculations type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 166 year: '2003' ... --- _id: '3458' author: - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: Klaus full_name: Unsicker, Klaus last_name: Unsicker citation: ama: 'Jonas PM, Unsicker K. Molekulare und zelluläre Grundlagen des Nervensystems. In: Schmidt R, ed. Lehrbuch Vorklinik. Vol B. Deutscher Ärzte Verlag; 2003:3-26.' apa: Jonas, P. M., & Unsicker, K. (2003). Molekulare und zelluläre Grundlagen des Nervensystems. In R. Schmidt (Ed.), Lehrbuch Vorklinik (Vol. B, pp. 3–26). Deutscher Ärzte Verlag. chicago: Jonas, Peter M, and Klaus Unsicker. “Molekulare Und Zelluläre Grundlagen Des Nervensystems.” In Lehrbuch Vorklinik, edited by R. Schmidt, B:3–26. Deutscher Ärzte Verlag, 2003. ieee: P. M. Jonas and K. Unsicker, “Molekulare und zelluläre Grundlagen des Nervensystems.,” in Lehrbuch Vorklinik, vol. B, R. Schmidt, Ed. Deutscher Ärzte Verlag, 2003, pp. 3–26. ista: 'Jonas PM, Unsicker K. 2003.Molekulare und zelluläre Grundlagen des Nervensystems. In: Lehrbuch Vorklinik. vol. B, 3–26.' mla: Jonas, Peter M., and Klaus Unsicker. “Molekulare Und Zelluläre Grundlagen Des Nervensystems.” Lehrbuch Vorklinik, edited by R. Schmidt, vol. B, Deutscher Ärzte Verlag, 2003, pp. 3–26. short: P.M. Jonas, K. Unsicker, in:, R. Schmidt (Ed.), Lehrbuch Vorklinik, Deutscher Ärzte Verlag, 2003, pp. 3–26. date_created: 2018-12-11T12:03:26Z date_published: 2003-01-01T00:00:00Z date_updated: 2021-01-12T07:43:35Z day: '01' editor: - first_name: R. full_name: Schmidt, R. F. last_name: Schmidt extern: 1 month: '01' page: 3 - 26 publication: Lehrbuch Vorklinik publication_status: published publisher: Deutscher Ärzte Verlag publist_id: '2929' quality_controlled: 0 status: public title: Molekulare und zelluläre Grundlagen des Nervensystems. type: book_chapter volume: B year: '2003' ... --- _id: '3536' abstract: - lang: eng 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. ' author: - first_name: György full_name: Buzsáki, György last_name: Buzsáki - first_name: Derek full_name: Buhl, Derek L last_name: Buhl - first_name: Kenneth full_name: Harris, Kenneth D last_name: Harris - first_name: Jozsef L full_name: Jozsef Csicsvari id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 - first_name: Boldizsár full_name: Czéh, Boldizsár last_name: Czéh - first_name: Alexei full_name: Morozov, Alexei last_name: Morozov citation: ama: Buzsáki G, Buhl D, Harris K, Csicsvari JL, Czéh B, Morozov A. Hippocampal network patterns of activity in the mouse. Neuroscience. 2003;116(1):201-211. doi:10.1016/S0306-4522(02)00669-3 apa: Buzsáki, G., Buhl, D., Harris, K., Csicsvari, J. L., Czéh, B., & Morozov, A. (2003). Hippocampal network patterns of activity in the mouse. Neuroscience. Elsevier. https://doi.org/10.1016/S0306-4522(02)00669-3 chicago: Buzsáki, György, Derek Buhl, Kenneth Harris, Jozsef L Csicsvari, Boldizsár Czéh, and Alexei Morozov. “Hippocampal Network Patterns of Activity in the Mouse.” Neuroscience. Elsevier, 2003. https://doi.org/10.1016/S0306-4522(02)00669-3. ieee: G. Buzsáki, D. Buhl, K. Harris, J. L. Csicsvari, B. Czéh, and A. Morozov, “Hippocampal network patterns of activity in the mouse,” Neuroscience, vol. 116, no. 1. Elsevier, pp. 201–211, 2003. 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. mla: Buzsáki, György, et al. “Hippocampal Network Patterns of Activity in the Mouse.” Neuroscience, vol. 116, no. 1, Elsevier, 2003, pp. 201–11, doi:10.1016/S0306-4522(02)00669-3. short: G. Buzsáki, D. Buhl, K. Harris, J.L. Csicsvari, B. Czéh, A. Morozov, Neuroscience 116 (2003) 201–211. date_created: 2018-12-11T12:03:50Z date_published: 2003-01-15T00:00:00Z date_updated: 2021-01-12T07:44:09Z day: '15' doi: 10.1016/S0306-4522(02)00669-3 extern: 1 intvolume: ' 116' issue: '1' month: '01' page: 201 - 211 publication: Neuroscience publication_status: published publisher: Elsevier publist_id: '2849' quality_controlled: 0 status: public title: Hippocampal network patterns of activity in the mouse type: journal_article volume: 116 year: '2003' ... --- _id: '3556' 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. author: - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: John full_name: Harer, John last_name: Harer - first_name: Vijay full_name: Natarajan, Vijay last_name: Natarajan - first_name: Valerio full_name: Pascucci, Valerio last_name: Pascucci citation: ama: 'Edelsbrunner H, Harer J, Natarajan V, Pascucci V. Morse-Smale complexes for piecewise linear 3-manifolds. In: ACM; 2003:361-370. doi:10.1145/777792.777846' apa: 'Edelsbrunner, H., Harer, J., Natarajan, V., & Pascucci, V. (2003). Morse-Smale complexes for piecewise linear 3-manifolds (pp. 361–370). Presented at the SCG: Symposium on Computational Geometry, ACM. https://doi.org/10.1145/777792.777846' chicago: Edelsbrunner, Herbert, John Harer, Vijay Natarajan, and Valerio Pascucci. “Morse-Smale Complexes for Piecewise Linear 3-Manifolds,” 361–70. ACM, 2003. https://doi.org/10.1145/777792.777846. 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.' 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. Morse-Smale Complexes for Piecewise Linear 3-Manifolds. ACM, 2003, pp. 361–70, doi:10.1145/777792.777846. short: H. Edelsbrunner, J. Harer, V. Natarajan, V. Pascucci, in:, ACM, 2003, pp. 361–370. conference: name: 'SCG: Symposium on Computational Geometry' date_created: 2018-12-11T12:03:57Z date_published: 2003-06-01T00:00:00Z date_updated: 2021-01-12T07:44:17Z day: '01' doi: 10.1145/777792.777846 extern: 1 main_file_link: - open_access: '0' url: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.14.9592 month: '06' page: 361 - 370 publication_status: published publisher: ACM publist_id: '2829' quality_controlled: 0 status: public title: Morse-Smale complexes for piecewise linear 3-manifolds type: conference year: '2003' ... --- _id: '3573' abstract: - lang: eng 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. author: - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: 'Edelsbrunner H. Surface reconstruction by wrapping finite sets in space. In: Discrete & Computational Geometry. Springer; 2003:379-404. doi:10.1007/978-3-642-55566-4_17' apa: Edelsbrunner, H. (2003). Surface reconstruction by wrapping finite sets in space. In Discrete & Computational Geometry (pp. 379–404). Springer. https://doi.org/10.1007/978-3-642-55566-4_17 chicago: Edelsbrunner, Herbert. “Surface Reconstruction by Wrapping Finite Sets in Space.” In Discrete & Computational Geometry, 379–404. Springer, 2003. https://doi.org/10.1007/978-3-642-55566-4_17. ieee: H. Edelsbrunner, “Surface reconstruction by wrapping finite sets in space,” in Discrete & Computational Geometry, Springer, 2003, pp. 379–404. ista: 'Edelsbrunner H. 2003.Surface reconstruction by wrapping finite sets in space. In: Discrete & Computational Geometry. , 379–404.' mla: Edelsbrunner, Herbert. “Surface Reconstruction by Wrapping Finite Sets in Space.” Discrete & Computational Geometry, Springer, 2003, pp. 379–404, doi:10.1007/978-3-642-55566-4_17. short: H. Edelsbrunner, in:, Discrete & Computational Geometry, Springer, 2003, pp. 379–404. date_created: 2018-12-11T12:04:02Z date_published: 2003-06-23T00:00:00Z date_updated: 2021-01-12T07:44:24Z day: '23' doi: 10.1007/978-3-642-55566-4_17 extern: 1 main_file_link: - open_access: '0' url: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.129.3633 month: '06' page: 379 - 404 publication: Discrete & Computational Geometry publication_status: published publisher: Springer publist_id: '2812' quality_controlled: 0 status: public title: Surface reconstruction by wrapping finite sets in space type: book_chapter year: '2003' ... --- _id: '3584' abstract: - lang: eng 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. author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Afra full_name: Zomorodian, Afra last_name: Zomorodian citation: ama: Edelsbrunner H, Zomorodian A. Computing linking numbers of a filtration. Homology, Homotopy and Applications. 2003;5(2):19-37. apa: Edelsbrunner, H., & Zomorodian, A. (2003). Computing linking numbers of a filtration. Homology, Homotopy and Applications. International Press. chicago: Edelsbrunner, Herbert, and Afra Zomorodian. “Computing Linking Numbers of a Filtration.” Homology, Homotopy and Applications. International Press, 2003. ieee: H. Edelsbrunner and A. Zomorodian, “Computing linking numbers of a filtration,” Homology, Homotopy and Applications, vol. 5, no. 2. International Press, pp. 19–37, 2003. ista: Edelsbrunner H, Zomorodian A. 2003. Computing linking numbers of a filtration. Homology, Homotopy and Applications. 5(2), 19–37. mla: Edelsbrunner, Herbert, and Afra Zomorodian. “Computing Linking Numbers of a Filtration.” Homology, Homotopy and Applications, vol. 5, no. 2, International Press, 2003, pp. 19–37. short: H. Edelsbrunner, A. Zomorodian, Homology, Homotopy and Applications 5 (2003) 19–37. date_created: 2018-12-11T12:04:05Z date_published: 2003-04-22T00:00:00Z date_updated: 2021-01-12T07:44:28Z day: '22' extern: '1' intvolume: ' 5' issue: '2' language: - iso: eng main_file_link: - url: http://projecteuclid.org/euclid.hha/1088453320 month: '04' oa_version: None page: 19 - 37 publication: Homology, Homotopy and Applications publication_status: published publisher: International Press publist_id: '2801' quality_controlled: '1' status: public title: Computing linking numbers of a filtration type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2003' ... --- _id: '3620' 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.' author: - first_name: Beate full_name: Nürnberger, Beate last_name: Nürnberger - first_name: Sebastian full_name: Hofman, Sebastian last_name: Hofman - first_name: Bqruni full_name: Förg-Brey, Bqruni last_name: Förg Brey - first_name: Gabriele full_name: Praetzel, Gabriele last_name: Praetzel - first_name: Alan full_name: Maclean, Alan W last_name: Maclean - first_name: Jacek full_name: Szymura, Jacek M last_name: Szymura - first_name: Catherine full_name: Abbott, Catherine M last_name: Abbott - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Nürnberger B, Hofman S, Förg Brey B, et al. A linkage map for the hybridising toads Bombina bombina and B. variegata (Anura: Discoglossidae). Heredity. 2003;91(2):136-142. doi:10.1038/sj.hdy.6800291' 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). Heredity. Nature Publishing Group. https://doi.org/10.1038/sj.hdy.6800291' 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).” Heredity. Nature Publishing Group, 2003. https://doi.org/10.1038/sj.hdy.6800291.' ieee: 'B. Nürnberger et al., “A linkage map for the hybridising toads Bombina bombina and B. variegata (Anura: Discoglossidae),” Heredity, vol. 91, no. 2. Nature Publishing Group, pp. 136–142, 2003.' 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.' mla: 'Nürnberger, Beate, et al. “A Linkage Map for the Hybridising Toads Bombina Bombina and B. Variegata (Anura: Discoglossidae).” Heredity, vol. 91, no. 2, Nature Publishing Group, 2003, pp. 136–42, doi:10.1038/sj.hdy.6800291.' short: B. Nürnberger, S. Hofman, B. Förg Brey, G. Praetzel, A. Maclean, J. Szymura, C. Abbott, N.H. Barton, Heredity 91 (2003) 136–142. date_created: 2018-12-11T12:04:17Z date_published: 2003-08-01T00:00:00Z date_updated: 2021-01-12T07:44:43Z day: '01' doi: 10.1038/sj.hdy.6800291 extern: 1 intvolume: ' 91' issue: '2' month: '08' page: 136 - 142 publication: Heredity publication_status: published publisher: Nature Publishing Group publist_id: '2763' quality_controlled: 0 status: public title: 'A linkage map for the hybridising toads Bombina bombina and B. variegata (Anura: Discoglossidae)' type: journal_article volume: 91 year: '2003' ... --- _id: '3619' abstract: - lang: eng 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<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. author: - first_name: Stuart full_name: Baird, Stuart J last_name: Baird - 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 citation: ama: Baird S, Barton NH, Etheridge A. The distribution of surviving blocks of an ancestral genome. Theoretical Population Biology. 2003;64(4):451-471. doi:10.1016/S0040-5809(03)00098-4 apa: Baird, S., Barton, N. H., & Etheridge, A. (2003). The distribution of surviving blocks of an ancestral genome. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/S0040-5809(03)00098-4 chicago: Baird, Stuart, Nicholas H Barton, and Alison Etheridge. “The Distribution of Surviving Blocks of an Ancestral Genome.” Theoretical Population Biology. Academic Press, 2003. https://doi.org/10.1016/S0040-5809(03)00098-4. ieee: S. Baird, N. H. Barton, and A. Etheridge, “The distribution of surviving blocks of an ancestral genome,” Theoretical Population Biology, vol. 64, no. 4. Academic Press, pp. 451–471, 2003. 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.” Theoretical Population Biology, vol. 64, no. 4, Academic Press, 2003, pp. 451–71, doi:10.1016/S0040-5809(03)00098-4. short: S. Baird, N.H. Barton, A. Etheridge, Theoretical Population Biology 64 (2003) 451–471. date_created: 2018-12-11T12:04:17Z date_published: 2003-12-01T00:00:00Z date_updated: 2021-01-12T07:44:42Z day: '01' doi: 10.1016/S0040-5809(03)00098-4 extern: 1 intvolume: ' 64' issue: '4' month: '12' page: 451 - 471 publication: Theoretical Population Biology publication_status: published publisher: Academic Press publist_id: '2764' quality_controlled: 0 status: public title: The distribution of surviving blocks of an ancestral genome type: journal_article volume: 64 year: '2003' ... --- _id: '3618' 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. author: - first_name: Timothy full_name: Vines, Timothy H last_name: Vines - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Vines T, Barton NH. A new approach to detecting mixed families. Molecular Ecology. 2003;12(7):1999-2002. doi:10.1046/j.1365-294X.2003.01867.x apa: Vines, T., & Barton, N. H. (2003). A new approach to detecting mixed families. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1046/j.1365-294X.2003.01867.x chicago: Vines, Timothy, and Nicholas H Barton. “A New Approach to Detecting Mixed Families.” Molecular Ecology. Wiley-Blackwell, 2003. https://doi.org/10.1046/j.1365-294X.2003.01867.x. ieee: T. Vines and N. H. Barton, “A new approach to detecting mixed families,” Molecular Ecology, vol. 12, no. 7. Wiley-Blackwell, pp. 1999–2002, 2003. ista: Vines T, Barton NH. 2003. A new approach to detecting mixed families. Molecular Ecology. 12(7), 1999–2002. mla: Vines, Timothy, and Nicholas H. Barton. “A New Approach to Detecting Mixed Families.” Molecular Ecology, vol. 12, no. 7, Wiley-Blackwell, 2003, pp. 1999–2002, doi:10.1046/j.1365-294X.2003.01867.x. short: T. Vines, N.H. Barton, Molecular Ecology 12 (2003) 1999–2002. date_created: 2018-12-11T12:04:16Z date_published: 2003-07-01T00:00:00Z date_updated: 2021-01-12T07:44:42Z day: '01' doi: 10.1046/j.1365-294X.2003.01867.x extern: 1 intvolume: ' 12' issue: '7' month: '07' page: 1999 - 2002 publication: Molecular Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '2765' quality_controlled: 0 status: public title: A new approach to detecting mixed families type: journal_article volume: 12 year: '2003' ... --- _id: '3752' 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. author: - first_name: Jose full_name: Vilar,Jose M last_name: Vilar - first_name: Calin C full_name: Calin Guet id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Stanislas full_name: Leibler, Stanislas last_name: Leibler citation: ama: 'Vilar J, Guet CC, Leibler S. Modeling network dynamics: the lac operon, a case study. Journal of Cell Biology. 2003;161(3):471-476. doi:10.1083/jcb.200301125' apa: 'Vilar, J., Guet, C. C., & Leibler, S. (2003). Modeling network dynamics: the lac operon, a case study. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.200301125' chicago: 'Vilar, Jose, Calin C Guet, and Stanislas Leibler. “Modeling Network Dynamics: The Lac Operon, a Case Study.” Journal of Cell Biology. Rockefeller University Press, 2003. https://doi.org/10.1083/jcb.200301125.' ieee: 'J. Vilar, C. C. Guet, and S. Leibler, “Modeling network dynamics: the lac operon, a case study,” Journal of Cell Biology, vol. 161, no. 3. Rockefeller University Press, pp. 471–476, 2003.' 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.' mla: 'Vilar, Jose, et al. “Modeling Network Dynamics: The Lac Operon, a Case Study.” Journal of Cell Biology, vol. 161, no. 3, Rockefeller University Press, 2003, pp. 471–76, doi:10.1083/jcb.200301125.' short: J. Vilar, C.C. Guet, S. Leibler, Journal of Cell Biology 161 (2003) 471–476. date_created: 2018-12-11T12:04:58Z date_published: 2003-01-12T00:00:00Z date_updated: 2021-01-12T07:51:57Z day: '12' doi: 10.1083/jcb.200301125 extern: 1 intvolume: ' 161' issue: '3' main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2172934/?tool=pubmed month: '01' oa: 1 page: 471 - 476 publication: Journal of Cell Biology publication_status: published publisher: Rockefeller University Press publist_id: '2475' quality_controlled: 0 status: public title: 'Modeling network dynamics: the lac operon, a case study' type: journal_article volume: 161 year: '2003' ... --- _id: '3797' article_processing_charge: No author: - first_name: Wolfgang full_name: Bauer, Wolfgang last_name: Bauer - first_name: Marco full_name: Kleine Berkenbusch, Marco last_name: Kleine Berkenbusch - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: ama: 'Bauer W, Kleine Berkenbusch M, Bollenbach MT. Breaking atomic nuclei into little pieces: evidence for a phase transition. Revista Mexicana De Fisica. 2003;49(4):1-6.' apa: 'Bauer, W., Kleine Berkenbusch, M., & Bollenbach, M. T. (2003). Breaking atomic nuclei into little pieces: evidence for a phase transition. Revista Mexicana De Fisica. Sociedad Mexicana de Física.' chicago: 'Bauer, Wolfgang, Marco Kleine Berkenbusch, and Mark Tobias Bollenbach. “Breaking Atomic Nuclei into Little Pieces: Evidence for a Phase Transition.” Revista Mexicana De Fisica. Sociedad Mexicana de Física, 2003.' ieee: 'W. Bauer, M. Kleine Berkenbusch, and M. T. Bollenbach, “Breaking atomic nuclei into little pieces: evidence for a phase transition,” Revista Mexicana De Fisica, vol. 49, no. 4. Sociedad Mexicana de Física, pp. 1–6, 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.” Revista Mexicana De Fisica, vol. 49, no. 4, Sociedad Mexicana de Física, 2003, pp. 1–6.' short: W. Bauer, M. Kleine Berkenbusch, M.T. Bollenbach, Revista Mexicana De Fisica 49 (2003) 1–6. date_created: 2018-12-11T12:05:13Z date_published: 2003-01-01T00:00:00Z date_updated: 2021-01-12T07:52:16Z day: '01' extern: '1' intvolume: ' 49' issue: '4' language: - iso: eng month: '01' oa_version: None page: 1 - 6 publication: Revista Mexicana De Fisica publication_status: published publisher: Sociedad Mexicana de Física publist_id: '2413' status: public title: 'Breaking atomic nuclei into little pieces: evidence for a phase transition' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 49 year: '2003' ... --- _id: '3897' 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. 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. 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: Marcin full_name: Jurdziński, Marcin last_name: Jurdziński - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Chatterjee K, Jurdziński M, Henzinger TA. Simple stochastic parity games. In: Vol 2803. Springer; 2003:100-113. doi:10.1007/978-3-540-45220-1_11' apa: 'Chatterjee, K., Jurdziński, M., & Henzinger, T. A. (2003). Simple stochastic parity games (Vol. 2803, pp. 100–113). Presented at the CSL: Computer Science Logic, Springer. https://doi.org/10.1007/978-3-540-45220-1_11' chicago: Chatterjee, Krishnendu, Marcin Jurdziński, and Thomas A Henzinger. “Simple Stochastic Parity Games,” 2803:100–113. Springer, 2003. https://doi.org/10.1007/978-3-540-45220-1_11. 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.' ista: 'Chatterjee K, Jurdziński M, Henzinger TA. 2003. Simple stochastic parity games. CSL: Computer Science Logic, LNCS, vol. 2803, 100–113.' mla: Chatterjee, Krishnendu, et al. Simple Stochastic Parity Games. Vol. 2803, Springer, 2003, pp. 100–13, doi:10.1007/978-3-540-45220-1_11. short: K. Chatterjee, M. Jurdziński, T.A. Henzinger, in:, Springer, 2003, pp. 100–113. conference: name: 'CSL: Computer Science Logic' date_created: 2018-12-11T12:05:46Z date_published: 2003-08-18T00:00:00Z date_updated: 2021-01-12T07:53:02Z day: '18' doi: 10.1007/978-3-540-45220-1_11 extern: 1 intvolume: ' 2803' month: '08' page: 100 - 113 publication_status: published publisher: Springer publist_id: '2259' quality_controlled: 0 status: public title: Simple stochastic parity games type: conference volume: 2803 year: '2003' ... --- _id: '3898' 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. 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. 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: Di full_name: Ma, Di last_name: Ma - first_name: Ritankar full_name: Majumdar, Ritankar S last_name: Majumdar - first_name: Tian full_name: Zhao, Tian last_name: Zhao - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jens full_name: Palsberg, Jens last_name: Palsberg citation: ama: 'Chatterjee K, Ma D, Majumdar R, Zhao T, Henzinger TA, Palsberg J. Stack size analysis for interrupt-driven programs. In: Vol 2694. Springer; 2003:109-126. doi:10.1007/3-540-44898-5_7' apa: 'Chatterjee, K., Ma, D., Majumdar, R., Zhao, T., Henzinger, T. A., & Palsberg, J. (2003). Stack size analysis for interrupt-driven programs (Vol. 2694, pp. 109–126). Presented at the SAS: Static Analysis Symposium, Springer. https://doi.org/10.1007/3-540-44898-5_7' 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. https://doi.org/10.1007/3-540-44898-5_7. 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.' 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.' mla: Chatterjee, Krishnendu, et al. Stack Size Analysis for Interrupt-Driven Programs. Vol. 2694, Springer, 2003, pp. 109–26, doi:10.1007/3-540-44898-5_7. short: K. Chatterjee, D. Ma, R. Majumdar, T. Zhao, T.A. Henzinger, J. Palsberg, in:, Springer, 2003, pp. 109–126. conference: name: 'SAS: Static Analysis Symposium' date_created: 2018-12-11T12:05:46Z date_published: 2003-05-28T00:00:00Z date_updated: 2021-01-12T07:53:02Z day: '28' doi: 10.1007/3-540-44898-5_7 extern: 1 intvolume: ' 2694' month: '05' page: 109 - 126 publication_status: published publisher: Springer publist_id: '2260' quality_controlled: 0 status: public title: Stack size analysis for interrupt-driven programs type: conference volume: 2694 year: '2003' ... --- _id: '3993' abstract: - lang: eng text: We present algorithms for constructing a hierarchy of increasingly coarse Morse-Smale complexes that decompose a piecewise linear 2-manifold. While these complexes are defined only in the smooth category, we extend the construction to the piecewise linearcategory by ensuring structural integrity and simulating differentiability. We then simplify Morse-Smale complexes by canceling pairs of critical points in order of increasing persistence. acknowledgement: Partially supported by ARO under Grant DAAG55-98-1-0177, NSF under Grants CCR-97-12088, EIA-9972879 and CCR-00-86013. author: - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: John full_name: Harer, John last_name: Harer - first_name: Afra full_name: Zomorodian, Afra last_name: Zomorodian citation: ama: Edelsbrunner H, Harer J, Zomorodian A. Hierarchical Morse-Smale complexes for piecewise linear 2-manifolds. Discrete & Computational Geometry. 2003;30(1):87-107. doi:10.1007/s00454-003-2926-5 apa: Edelsbrunner, H., Harer, J., & Zomorodian, A. (2003). Hierarchical Morse-Smale complexes for piecewise linear 2-manifolds. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-003-2926-5 chicago: Edelsbrunner, Herbert, John Harer, and Afra Zomorodian. “Hierarchical Morse-Smale Complexes for Piecewise Linear 2-Manifolds.” Discrete & Computational Geometry. Springer, 2003. https://doi.org/10.1007/s00454-003-2926-5. ieee: H. Edelsbrunner, J. Harer, and A. Zomorodian, “Hierarchical Morse-Smale complexes for piecewise linear 2-manifolds,” Discrete & Computational Geometry, vol. 30, no. 1. Springer, pp. 87–107, 2003. ista: Edelsbrunner H, Harer J, Zomorodian A. 2003. Hierarchical Morse-Smale complexes for piecewise linear 2-manifolds. Discrete & Computational Geometry. 30(1), 87–107. mla: Edelsbrunner, Herbert, et al. “Hierarchical Morse-Smale Complexes for Piecewise Linear 2-Manifolds.” Discrete & Computational Geometry, vol. 30, no. 1, Springer, 2003, pp. 87–107, doi:10.1007/s00454-003-2926-5. short: H. Edelsbrunner, J. Harer, A. Zomorodian, Discrete & Computational Geometry 30 (2003) 87–107. date_created: 2018-12-11T12:06:19Z date_published: 2003-07-01T00:00:00Z date_updated: 2021-01-12T07:53:43Z day: '01' doi: 10.1007/s00454-003-2926-5 extern: 1 intvolume: ' 30' issue: '1' month: '07' page: 87 - 107 publication: Discrete & Computational Geometry publication_status: published publisher: Springer publist_id: '2134' quality_controlled: 0 status: public title: Hierarchical Morse-Smale complexes for piecewise linear 2-manifolds type: journal_article volume: 30 year: '2003' ... --- _id: '3994' abstract: - lang: eng text: The body defined by a finite collection of disks is a subset of the plane bounded by a tangent continuous curve, which we call the skin. We give analytic formulas for the area, the perimeter, the area derivative, and the perimeter derivative of the body. Given the filtrations of the Delaunay triangulation and the Voronoi diagram of the disks, all formulas can be evaluated in time proportional to the number of disks. acknowledgement: NSF under grant DMS-98-73945, ARO under grant DAAG55-98-1-0177 and by NSF under grants CCR- 97-12088, EIA-9972879, and CCR-00-86013. author: - first_name: Ho full_name: Cheng, Ho-Lun last_name: Cheng - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: 'Cheng H, Edelsbrunner H. Area, perimeter and derivatives of a skin curve. Computational Geometry: Theory and Applications. 2003;26(2):173-192. doi:10.1016/S0925-7721(02)00124-4' apa: 'Cheng, H., & Edelsbrunner, H. (2003). Area, perimeter and derivatives of a skin curve. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/S0925-7721(02)00124-4' chicago: 'Cheng, Ho, and Herbert Edelsbrunner. “Area, Perimeter and Derivatives of a Skin Curve.” Computational Geometry: Theory and Applications. Elsevier, 2003. https://doi.org/10.1016/S0925-7721(02)00124-4.' ieee: 'H. Cheng and H. Edelsbrunner, “Area, perimeter and derivatives of a skin curve,” Computational Geometry: Theory and Applications, vol. 26, no. 2. Elsevier, pp. 173–192, 2003.' ista: 'Cheng H, Edelsbrunner H. 2003. Area, perimeter and derivatives of a skin curve. Computational Geometry: Theory and Applications. 26(2), 173–192.' mla: 'Cheng, Ho, and Herbert Edelsbrunner. “Area, Perimeter and Derivatives of a Skin Curve.” Computational Geometry: Theory and Applications, vol. 26, no. 2, Elsevier, 2003, pp. 173–92, doi:10.1016/S0925-7721(02)00124-4.' short: 'H. Cheng, H. Edelsbrunner, Computational Geometry: Theory and Applications 26 (2003) 173–192.' date_created: 2018-12-11T12:06:20Z date_published: 2003-10-01T00:00:00Z date_updated: 2021-01-12T07:53:43Z day: '01' doi: 10.1016/S0925-7721(02)00124-4 extern: 1 intvolume: ' 26' issue: '2' month: '10' page: 173 - 192 publication: 'Computational Geometry: Theory and Applications' publication_status: published publisher: Elsevier publist_id: '2135' quality_controlled: 0 status: public title: Area, perimeter and derivatives of a skin curve type: journal_article volume: 26 year: '2003' ... --- _id: '3139' abstract: - lang: eng text: Significant advances have been made during the past few years in our understanding of how the spinal monosynaptic reflex develops. Transcription factors in the Neurogenin, Runt, ETS, and LIM families control sequential steps of the specification of various subtypes of dorsal root ganglia sensory neurons. The initiation of muscle spindle differentiation requires neuregulin 1, derived from Ia afferent sensory neurons, and signaling through ErbB receptors in intrafusal muscle fibers. Several retrograde signals from the periphery are important for the establishment of late connectivity in the reflex circuit. Finally, neurotrophin 3 released from muscle spindles regulates the strength of sensory-motor connections within the spinal cord postnatally. author: - first_name: Hsiao full_name: Chen, Hsiao Huei last_name: Chen - first_name: Simon full_name: Simon Hippenmeyer id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Silvia full_name: Arber, Silvia last_name: Arber - first_name: Eric full_name: Frank, Eric last_name: Frank citation: ama: Chen H, Hippenmeyer S, Arber S, Frank E. Development of the monosynaptic stretch reflex circuit. Current Opinion in Neurobiology. 2003;13(1):96-102. doi:10.1016/S0959-4388(03)00006-0 apa: Chen, H., Hippenmeyer, S., Arber, S., & Frank, E. (2003). Development of the monosynaptic stretch reflex circuit. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/S0959-4388(03)00006-0 chicago: Chen, Hsiao, Simon Hippenmeyer, Silvia Arber, and Eric Frank. “Development of the Monosynaptic Stretch Reflex Circuit.” Current Opinion in Neurobiology. Elsevier, 2003. https://doi.org/10.1016/S0959-4388(03)00006-0. ieee: H. Chen, S. Hippenmeyer, S. Arber, and E. Frank, “Development of the monosynaptic stretch reflex circuit,” Current Opinion in Neurobiology, vol. 13, no. 1. Elsevier, pp. 96–102, 2003. ista: Chen H, Hippenmeyer S, Arber S, Frank E. 2003. Development of the monosynaptic stretch reflex circuit. Current Opinion in Neurobiology. 13(1), 96–102. mla: Chen, Hsiao, et al. “Development of the Monosynaptic Stretch Reflex Circuit.” Current Opinion in Neurobiology, vol. 13, no. 1, Elsevier, 2003, pp. 96–102, doi:10.1016/S0959-4388(03)00006-0. short: H. Chen, S. Hippenmeyer, S. Arber, E. Frank, Current Opinion in Neurobiology 13 (2003) 96–102. date_created: 2018-12-11T12:01:37Z date_published: 2003-02-01T00:00:00Z date_updated: 2019-04-26T07:22:24Z day: '01' doi: 10.1016/S0959-4388(03)00006-0 extern: 1 intvolume: ' 13' issue: '1' month: '02' page: 96 - 102 publication: Current Opinion in Neurobiology publication_status: published publisher: Elsevier publist_id: '3557' quality_controlled: 0 status: public title: Development of the monosynaptic stretch reflex circuit type: review volume: 13 year: '2003' ... --- _id: '3171' abstract: - lang: eng text: 'Reconstructing a 3-D scene from more than one camera is a classical problem in computer vision. One of the major sources of difficulty is the fact that not all scene elements are visible from all cameras. In the last few years, two promising approaches have been developed 11,12 that formulate the scene reconstruction problem in terms of energy minimization, and minimize the energy using graph cuts. These energy minimization approaches treat the input images symmetrically, handle visibility constraints correctly, and allow spatial smoothness to be enforced. However, these algorithm propose different problem formulations, and handle a limited class of smoothness terms. One algorithm 11 uses a problem formulation that is restricted to two-camera stereo, and imposes smoothness between a pair of cameras. The other algorithm 12 can handle an arbitrary number of cameras, but imposes smoothness only with respect to a single camera. In this paper we give a more general energy minimization formulation for the problem, which allows a larger class of spatial smoothness constraints. We show that our formulation includes both of the previous approaches as special cases, as well as permitting new energy functions. Experimental results on real data with ground truth are also included. ' alternative_title: - LNCS 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 - first_name: Steven full_name: Gortler, Steven last_name: Gortler citation: ama: 'Kolmogorov V, Zabih R, Gortler S. Generalized multi camera scene reconstruction using graph cuts. In: Vol 2683. Springer; 2003:501-516. doi:10.1007/978-3-540-45063-4_32' apa: 'Kolmogorov, V., Zabih, R., & Gortler, S. (2003). Generalized multi camera scene reconstruction using graph cuts (Vol. 2683, pp. 501–516). Presented at the EMMCVPR: Energy Minimization Methods in Computer Vision and Pattern Recognition, Springer. https://doi.org/10.1007/978-3-540-45063-4_32' chicago: Kolmogorov, Vladimir, Ramin Zabih, and Steven Gortler. “Generalized Multi Camera Scene Reconstruction Using Graph Cuts,” 2683:501–16. Springer, 2003. https://doi.org/10.1007/978-3-540-45063-4_32. ieee: 'V. Kolmogorov, R. Zabih, and S. Gortler, “Generalized multi camera scene reconstruction using graph cuts,” presented at the EMMCVPR: Energy Minimization Methods in Computer Vision and Pattern Recognition, 2003, vol. 2683, pp. 501–516.' ista: 'Kolmogorov V, Zabih R, Gortler S. 2003. Generalized multi camera scene reconstruction using graph cuts. EMMCVPR: Energy Minimization Methods in Computer Vision and Pattern Recognition, LNCS, vol. 2683, 501–516.' mla: Kolmogorov, Vladimir, et al. Generalized Multi Camera Scene Reconstruction Using Graph Cuts. Vol. 2683, Springer, 2003, pp. 501–16, doi:10.1007/978-3-540-45063-4_32. short: V. Kolmogorov, R. Zabih, S. Gortler, in:, Springer, 2003, pp. 501–516. conference: name: 'EMMCVPR: Energy Minimization Methods in Computer Vision and Pattern Recognition' date_created: 2018-12-11T12:01:48Z date_published: 2003-06-26T00:00:00Z date_updated: 2021-01-12T07:41:34Z day: '26' doi: 10.1007/978-3-540-45063-4_32 extern: 1 intvolume: ' 2683' month: '06' page: 501 - 516 publication_status: published publisher: Springer publist_id: '3512' quality_controlled: 0 status: public title: Generalized multi camera scene reconstruction using graph cuts type: conference volume: 2683 year: '2003' ... --- _id: '3174' abstract: - lang: eng text: We address visual correspondence problems without assuming that scene points have similar intensities in different views. This situation is common, usually due to non-lambertian scenes or to differences between cameras. We use maximization of mutual information, a powerful technique for registering images that requires no a priori model of the relationship between scene intensities in different views. However, it has proven difficult to use mutual information to compute dense visual correspondence. Comparing fixed-size windows via mutual information suffers from the well-known problems of fixed windows, namely poor performance at discontinuities and in low-texture regions. In this paper, we show how to compute visual correspondence using mutual information without suffering from these problems. Using 'a simple approximation, mutual information can be incorporated into the standard energy minimization framework used in early vision. The energy can then be efficiently minimized using graph cuts, which preserve discontinuities and handle low-texture regions. The resulting algorithm combines the accurate disparity maps that come from graph cuts with the tolerance for intensity changes that comes from mutual information. author: - first_name: Junhwan full_name: Kim, Junhwan last_name: Kim - 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: 'Kim J, Kolmogorov V, Zabih R. Visual correspondence using energy minimization and mutual information. In: Vol 2. IEEE; 2003:1033-1040. doi:10.1109/ICCV.2003.1238463' apa: 'Kim, J., Kolmogorov, V., & Zabih, R. (2003). Visual correspondence using energy minimization and mutual information (Vol. 2, pp. 1033–1040). Presented at the ICCV: International Conference on Computer Vision, IEEE. https://doi.org/10.1109/ICCV.2003.1238463' chicago: Kim, Junhwan, Vladimir Kolmogorov, and Ramin Zabih. “Visual Correspondence Using Energy Minimization and Mutual Information,” 2:1033–40. IEEE, 2003. https://doi.org/10.1109/ICCV.2003.1238463. ieee: 'J. Kim, V. Kolmogorov, and R. Zabih, “Visual correspondence using energy minimization and mutual information,” presented at the ICCV: International Conference on Computer Vision, 2003, vol. 2, pp. 1033–1040.' ista: 'Kim J, Kolmogorov V, Zabih R. 2003. Visual correspondence using energy minimization and mutual information. ICCV: International Conference on Computer Vision vol. 2, 1033–1040.' mla: Kim, Junhwan, et al. Visual Correspondence Using Energy Minimization and Mutual Information. Vol. 2, IEEE, 2003, pp. 1033–40, doi:10.1109/ICCV.2003.1238463. short: J. Kim, V. Kolmogorov, R. Zabih, in:, IEEE, 2003, pp. 1033–1040. conference: name: 'ICCV: International Conference on Computer Vision' date_created: 2018-12-11T12:01:49Z date_published: 2003-09-30T00:00:00Z date_updated: 2021-01-12T07:41:35Z day: '30' doi: 10.1109/ICCV.2003.1238463 extern: 1 intvolume: ' 2' month: '09' page: 1033 - 1040 publication_status: published publisher: IEEE publist_id: '3510' quality_controlled: 0 status: public title: Visual correspondence using energy minimization and mutual information type: conference volume: 2 year: '2003' ... --- _id: '3170' abstract: - lang: eng text: Geodesic active contours and graph cuts are two standard image segmentation techniques. We introduce a new segmentation method combining some of their benefits. Our main intuition is that any cut on a graph embedded in some continuous space can be interpreted as a contour (in 2D) or a surface (in 3D). We show how to build a grid graph and set its edge weights so that the cost of cuts is arbitrarily close to the length (area) of the corresponding contours (surfaces) for any anisotropic Riemannian metric. There are two interesting consequences of this technical result. First, graph cut algorithms can be used to find globally minimum geodesic contours (minimal surfaces in 3D) under arbitrary Riemannian metric for a given set of boundary conditions. Second, we show how to minimize metrication artifacts in existing graph-cut based methods in vision. Theoretically speaking, our work provides an interesting link between several branches of mathematics -differential geometry, integral geometry, and combinatorial optimization. The main technical problem is solved using Cauchy-Crofton formula from integral geometry. 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. Computing geodesics and minimal surfaces via graph cuts. In: Vol 1. IEEE; 2003:26-33. doi:10.1109/ICCV.2003.1238310' apa: 'Boykov, Y., & Kolmogorov, V. (2003). Computing geodesics and minimal surfaces via graph cuts (Vol. 1, pp. 26–33). Presented at the ICCV: International Conference on Computer Vision, IEEE. https://doi.org/10.1109/ICCV.2003.1238310' chicago: Boykov, Yuri, and Vladimir Kolmogorov. “Computing Geodesics and Minimal Surfaces via Graph Cuts,” 1:26–33. IEEE, 2003. https://doi.org/10.1109/ICCV.2003.1238310. ieee: 'Y. Boykov and V. Kolmogorov, “Computing geodesics and minimal surfaces via graph cuts,” presented at the ICCV: International Conference on Computer Vision, 2003, vol. 1, pp. 26–33.' ista: 'Boykov Y, Kolmogorov V. 2003. Computing geodesics and minimal surfaces via graph cuts. ICCV: International Conference on Computer Vision vol. 1, 26–33.' mla: Boykov, Yuri, and Vladimir Kolmogorov. Computing Geodesics and Minimal Surfaces via Graph Cuts. Vol. 1, IEEE, 2003, pp. 26–33, doi:10.1109/ICCV.2003.1238310. short: Y. Boykov, V. Kolmogorov, in:, IEEE, 2003, pp. 26–33. conference: name: 'ICCV: International Conference on Computer Vision' date_created: 2018-12-11T12:01:48Z date_published: 2003-09-30T00:00:00Z date_updated: 2021-01-12T07:41:33Z day: '30' doi: 10.1109/ICCV.2003.1238310 extern: 1 intvolume: ' 1' month: '09' page: 26 - 33 publication_status: published publisher: IEEE publist_id: '3511' quality_controlled: 0 status: public title: Computing geodesics and minimal surfaces via graph cuts type: conference volume: 1 year: '2003' ... --- _id: '3526' abstract: - lang: eng text: Neurons can produce action potentials with high temporal precision(1). A fundamental issue is whether, and how, this capability is used in information processing. According to the `cell assembly' hypothesis, transient synchrony of anatomically distributed groups of neurons underlies processing of both external sensory input and internal cognitive mechanisms(2-4). Accordingly, neuron populations should be arranged into groups whose synchrony exceeds that predicted by common modulation by sensory input. Here we find that the spike times of hippocampal pyramidal cells can be predicted more accurately by using the spike times of simultaneously recorded neurons in addition to the animals location in space. This improvement remained when the spatial prediction was refined with a spatially dependent theta phase modulation(5-8). The time window in which spike times are best predicted from simultaneous peer activity is 10-30 ms, suggesting that cell assemblies are synchronized at this timescale. Because this temporal window matches the membrane time constant of pyramidal neurons(9), the period of the hippocampal gamma oscillation(10) and the time window for synaptic plasticity(11), we propose that cooperative activity at this timescale is optimal for information transmission and storage in cortical circuits. author: - first_name: Kenneth full_name: Harris, Kenneth D last_name: Harris - first_name: Jozsef L full_name: Jozsef Csicsvari id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 - first_name: Hajima full_name: Hirase, Hajima last_name: Hirase - first_name: George full_name: Dragoi, George last_name: Dragoi - first_name: György full_name: Buzsáki, György last_name: Buzsáki citation: ama: Harris K, Csicsvari JL, Hirase H, Dragoi G, Buzsáki G. Organization of cell assemblies in the hippocampus. Nature. 2003;424(6948):552-556. doi:0.1038/nature01834 apa: Harris, K., Csicsvari, J. L., Hirase, H., Dragoi, G., & Buzsáki, G. (2003). Organization of cell assemblies in the hippocampus. Nature. Nature Publishing Group. https://doi.org/0.1038/nature01834 chicago: Harris, Kenneth, Jozsef L Csicsvari, Hajima Hirase, George Dragoi, and György Buzsáki. “Organization of Cell Assemblies in the Hippocampus.” Nature. Nature Publishing Group, 2003. https://doi.org/0.1038/nature01834. ieee: K. Harris, J. L. Csicsvari, H. Hirase, G. Dragoi, and G. Buzsáki, “Organization of cell assemblies in the hippocampus,” Nature, vol. 424, no. 6948. Nature Publishing Group, pp. 552–556, 2003. ista: Harris K, Csicsvari JL, Hirase H, Dragoi G, Buzsáki G. 2003. Organization of cell assemblies in the hippocampus. Nature. 424(6948), 552–556. mla: Harris, Kenneth, et al. “Organization of Cell Assemblies in the Hippocampus.” Nature, vol. 424, no. 6948, Nature Publishing Group, 2003, pp. 552–56, doi:0.1038/nature01834. short: K. Harris, J.L. Csicsvari, H. Hirase, G. Dragoi, G. Buzsáki, Nature 424 (2003) 552–556. date_created: 2018-12-11T12:03:47Z date_published: 2003-07-31T00:00:00Z date_updated: 2021-01-12T07:44:04Z day: '31' doi: 0.1038/nature01834 extern: 1 intvolume: ' 424' issue: '6948' month: '07' page: 552 - 556 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '2859' quality_controlled: 0 status: public title: Organization of cell assemblies in the hippocampus type: journal_article volume: 424 year: '2003' ... --- _id: '3529' abstract: - lang: eng 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. author: - first_name: Jozsef L full_name: Jozsef Csicsvari id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 - first_name: Darrell full_name: Henze, Darrell A last_name: Henze - first_name: Brian full_name: Jamieson, Brian G last_name: Jamieson - first_name: Kenneth full_name: Harris, Kenneth D last_name: Harris - first_name: Anton full_name: Sirota, Anton M last_name: Sirota - first_name: Peter full_name: Bartho, Peter last_name: Bartho - first_name: Kensall full_name: Wise, Kensall D last_name: Wise - first_name: György full_name: Buzsáki, György last_name: Buzsáki citation: ama: Csicsvari JL, Henze D, Jamieson B, et al. Massively parallel recording of unit and local field potentials with silicon-based electrodes. Journal of Neurophysiology. 2003;90(2):1314-1323. doi:10.1152/jn.00116.2003 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. Journal of Neurophysiology. American Physiological Society. https://doi.org/10.1152/jn.00116.2003 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.” Journal of Neurophysiology. American Physiological Society, 2003. https://doi.org/10.1152/jn.00116.2003. ieee: J. L. Csicsvari et al., “Massively parallel recording of unit and local field potentials with silicon-based electrodes,” Journal of Neurophysiology, vol. 90, no. 2. American Physiological Society, pp. 1314–1323, 2003. 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. mla: Csicsvari, Jozsef L., et al. “Massively Parallel Recording of Unit and Local Field Potentials with Silicon-Based Electrodes.” Journal of Neurophysiology, vol. 90, no. 2, American Physiological Society, 2003, pp. 1314–23, doi:10.1152/jn.00116.2003. 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. date_created: 2018-12-11T12:03:48Z date_published: 2003-08-01T00:00:00Z date_updated: 2021-01-12T07:44:05Z day: '01' doi: 10.1152/jn.00116.2003 extern: 1 intvolume: ' 90' issue: '2' month: '08' page: 1314 - 1323 publication: Journal of Neurophysiology publication_status: published publisher: American Physiological Society publist_id: '2856' quality_controlled: 0 status: public title: Massively parallel recording of unit and local field potentials with silicon-based electrodes type: journal_article volume: 90 year: '2003' ... --- _id: '3528' 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. author: - first_name: Jozsef L full_name: Jozsef Csicsvari id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 - first_name: Brian full_name: Jamieson, Brian G last_name: Jamieson - first_name: Kensall full_name: Wise, Kensall D last_name: Wise - first_name: György full_name: Buzsáki, György last_name: Buzsáki citation: ama: Csicsvari JL, Jamieson B, Wise K, Buzsáki G. Mechanisms of gamma oscillations in the hippocampus of the behaving rat. Neuron. 2003;37(2):311-322. doi:10.1016/S0896-6273(02)01169-8 apa: Csicsvari, J. L., Jamieson, B., Wise, K., & Buzsáki, G. (2003). Mechanisms of gamma oscillations in the hippocampus of the behaving rat. Neuron. Elsevier. https://doi.org/10.1016/S0896-6273(02)01169-8 chicago: Csicsvari, Jozsef L, Brian Jamieson, Kensall Wise, and György Buzsáki. “Mechanisms of Gamma Oscillations in the Hippocampus of the Behaving Rat.” Neuron. Elsevier, 2003. https://doi.org/10.1016/S0896-6273(02)01169-8. ieee: J. L. Csicsvari, B. Jamieson, K. Wise, and G. Buzsáki, “Mechanisms of gamma oscillations in the hippocampus of the behaving rat,” Neuron, vol. 37, no. 2. Elsevier, pp. 311–322, 2003. 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. mla: Csicsvari, Jozsef L., et al. “Mechanisms of Gamma Oscillations in the Hippocampus of the Behaving Rat.” Neuron, vol. 37, no. 2, Elsevier, 2003, pp. 311–22, doi:10.1016/S0896-6273(02)01169-8. short: J.L. Csicsvari, B. Jamieson, K. Wise, G. Buzsáki, Neuron 37 (2003) 311–322. date_created: 2018-12-11T12:03:48Z date_published: 2003-01-01T00:00:00Z date_updated: 2021-01-12T07:44:05Z day: '01' doi: 10.1016/S0896-6273(02)01169-8 extern: 1 intvolume: ' 37' issue: '2' month: '01' page: 311 - 322 publication: Neuron publication_status: published publisher: Elsevier publist_id: '2857' quality_controlled: 0 status: public title: Mechanisms of gamma oscillations in the hippocampus of the behaving rat type: journal_article volume: 37 year: '2003' ... --- _id: '3543' 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. author: - first_name: Anton full_name: Sirota, Anton M last_name: Sirota - first_name: Jozsef L full_name: Jozsef Csicsvari id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 - first_name: Derek full_name: Buhl, Derek L last_name: Buhl - first_name: György full_name: Buzsáki, György last_name: Buzsáki citation: ama: Sirota A, Csicsvari JL, Buhl D, Buzsáki G. Communication between neocortex and hippocampus during sleep in rodents. PNAS. 2003;100(4):2065-2069. doi:10.1073/pnas.0437938100 apa: Sirota, A., Csicsvari, J. L., Buhl, D., & Buzsáki, G. (2003). Communication between neocortex and hippocampus during sleep in rodents. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0437938100 chicago: Sirota, Anton, Jozsef L Csicsvari, Derek Buhl, and György Buzsáki. “Communication between Neocortex and Hippocampus during Sleep in Rodents.” PNAS. National Academy of Sciences, 2003. https://doi.org/10.1073/pnas.0437938100. ieee: A. Sirota, J. L. Csicsvari, D. Buhl, and G. Buzsáki, “Communication between neocortex and hippocampus during sleep in rodents,” PNAS, vol. 100, no. 4. National Academy of Sciences, pp. 2065–2069, 2003. ista: Sirota A, Csicsvari JL, Buhl D, Buzsáki G. 2003. Communication between neocortex and hippocampus during sleep in rodents. PNAS. 100(4), 2065–2069. mla: Sirota, Anton, et al. “Communication between Neocortex and Hippocampus during Sleep in Rodents.” PNAS, vol. 100, no. 4, National Academy of Sciences, 2003, pp. 2065–69, doi:10.1073/pnas.0437938100. short: A. Sirota, J.L. Csicsvari, D. Buhl, G. Buzsáki, PNAS 100 (2003) 2065–2069. date_created: 2018-12-11T12:03:53Z date_published: 2003-02-18T00:00:00Z date_updated: 2021-01-12T07:44:12Z day: '18' doi: 10.1073/pnas.0437938100 extern: 1 intvolume: ' 100' issue: '4' month: '02' page: 2065 - 2069 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '2841' quality_controlled: 0 status: public title: Communication between neocortex and hippocampus during sleep in rodents type: journal_article volume: 100 year: '2003' ... --- _id: '3593' abstract: - lang: eng 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. author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Pallab full_name: Dasgupta, Pallab last_name: Dasgupta - first_name: Partha full_name: Chakrabarti, Partha P last_name: Chakrabarti citation: ama: Chatterjee K, Dasgupta P, Chakrabarti P. A branching time temporal framework for quantitative reasoning. Journal of Automated Reasoning. 2003;30(2):205-232. doi:10.1023/A:1023217515688 apa: Chatterjee, K., Dasgupta, P., & Chakrabarti, P. (2003). A branching time temporal framework for quantitative reasoning. Journal of Automated Reasoning. Springer. https://doi.org/10.1023/A:1023217515688 chicago: Chatterjee, Krishnendu, Pallab Dasgupta, and Partha Chakrabarti. “A Branching Time Temporal Framework for Quantitative Reasoning.” Journal of Automated Reasoning. Springer, 2003. https://doi.org/10.1023/A:1023217515688. ieee: K. Chatterjee, P. Dasgupta, and P. Chakrabarti, “A branching time temporal framework for quantitative reasoning,” Journal of Automated Reasoning, vol. 30, no. 2. Springer, pp. 205–232, 2003. ista: Chatterjee K, Dasgupta P, Chakrabarti P. 2003. A branching time temporal framework for quantitative reasoning. Journal of Automated Reasoning. 30(2), 205–232. mla: Chatterjee, Krishnendu, et al. “A Branching Time Temporal Framework for Quantitative Reasoning.” Journal of Automated Reasoning, vol. 30, no. 2, Springer, 2003, pp. 205–32, doi:10.1023/A:1023217515688. short: K. Chatterjee, P. Dasgupta, P. Chakrabarti, Journal of Automated Reasoning 30 (2003) 205–232. date_created: 2018-12-11T12:04:08Z date_published: 2003-02-01T00:00:00Z date_updated: 2021-01-12T07:44:31Z day: '01' doi: 10.1023/A:1023217515688 extern: 1 intvolume: ' 30' issue: '2' month: '02' page: 205 - 232 publication: Journal of Automated Reasoning publication_status: published publisher: Springer publist_id: '2790' quality_controlled: 0 status: public title: A branching time temporal framework for quantitative reasoning type: journal_article volume: 30 year: '2003' ... --- _id: '3678' author: - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: Lampert C. The Neumann operator in strictly pseudoconvex domains with weighted Bergman metric . Bonner Mathematische Schriften. 2003;356:1-165. apa: Lampert, C. (2003). The Neumann operator in strictly pseudoconvex domains with weighted Bergman metric . Bonner Mathematische Schriften. Universität Bonn, Fachbibliothek Mathematik. chicago: Lampert, Christoph. “The Neumann Operator in Strictly Pseudoconvex Domains with Weighted Bergman Metric .” Bonner Mathematische Schriften. Universität Bonn, Fachbibliothek Mathematik, 2003. ieee: C. Lampert, “The Neumann operator in strictly pseudoconvex domains with weighted Bergman metric ,” Universität Bonn, Fachbibliothek Mathematik, 2003. ista: Lampert C. 2003. The Neumann operator in strictly pseudoconvex domains with weighted Bergman metric . Universität Bonn, Fachbibliothek Mathematik. mla: Lampert, Christoph. “The Neumann Operator in Strictly Pseudoconvex Domains with Weighted Bergman Metric .” Bonner Mathematische Schriften, vol. 356, Universität Bonn, Fachbibliothek Mathematik, 2003, pp. 1–165. short: C. Lampert, The Neumann Operator in Strictly Pseudoconvex Domains with Weighted Bergman Metric , Universität Bonn, Fachbibliothek Mathematik, 2003. date_created: 2018-12-11T12:04:34Z date_published: 2003-03-31T00:00:00Z date_updated: 2021-01-12T07:45:05Z day: '31' extern: 1 intvolume: ' 356' main_file_link: - open_access: '0' url: http://pub.ist.ac.at/~chl/papers/lampert-phd2003.pdf month: '03' page: 1 - 165 publication: Bonner Mathematische Schriften publication_status: published publisher: Universität Bonn, Fachbibliothek Mathematik publist_id: '2704' quality_controlled: 0 status: public title: 'The Neumann operator in strictly pseudoconvex domains with weighted Bergman metric ' type: dissertation volume: 356 year: '2003' ... --- _id: '3725' 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. 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: Max full_name: Kessler, Max last_name: Kessler - first_name: Dieter full_name: Oesterhelt, Dieter last_name: Oesterhelt - first_name: Hermann full_name: Gaub, Hermann last_name: Gaub - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller citation: ama: Janovjak HL, Kessler M, Oesterhelt D, Gaub H, Mueller D. Unfolding pathways of native bacteriorhodopsin depend on temperature. EMBO Journal. 2003;22(19):5220-5229. doi:10.1093/emboj/cdg509 apa: Janovjak, H. L., Kessler, M., Oesterhelt, D., Gaub, H., & Mueller, D. (2003). Unfolding pathways of native bacteriorhodopsin depend on temperature. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1093/emboj/cdg509 chicago: Janovjak, Harald L, Max Kessler, Dieter Oesterhelt, Hermann Gaub, and Daniel Mueller. “Unfolding Pathways of Native Bacteriorhodopsin Depend on Temperature.” EMBO Journal. Wiley-Blackwell, 2003. https://doi.org/10.1093/emboj/cdg509. ieee: H. L. Janovjak, M. Kessler, D. Oesterhelt, H. Gaub, and D. Mueller, “Unfolding pathways of native bacteriorhodopsin depend on temperature,” EMBO Journal, vol. 22, no. 19. Wiley-Blackwell, pp. 5220–5229, 2003. 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. mla: Janovjak, Harald L., et al. “Unfolding Pathways of Native Bacteriorhodopsin Depend on Temperature.” EMBO Journal, vol. 22, no. 19, Wiley-Blackwell, 2003, pp. 5220–29, doi:10.1093/emboj/cdg509. short: H.L. Janovjak, M. Kessler, D. Oesterhelt, H. Gaub, D. Mueller, EMBO Journal 22 (2003) 5220–5229. date_created: 2018-12-11T12:04:50Z date_published: 2003-01-01T00:00:00Z date_updated: 2021-01-12T07:51:45Z day: '01' doi: 10.1093/emboj/cdg509 extern: 1 intvolume: ' 22' issue: '19' main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC204492/ month: '01' oa: 1 page: 5220 - 5229 publication: EMBO Journal publication_status: published publisher: Wiley-Blackwell publist_id: '2506' quality_controlled: 0 status: public title: Unfolding pathways of native bacteriorhodopsin depend on temperature type: journal_article volume: 22 year: '2003' ... --- _id: '3804' abstract: - lang: eng 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. author: - first_name: Cheng full_name: Lien, Cheng-Chang last_name: Lien - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Lien C, Jonas PM. Kv3 potassium conductance is necessary and kinetically optimized for high-frequency action potential generation in hippocampal interneurons. Journal of Neuroscience. 2003;23(6):2058-2068. apa: Lien, C., & Jonas, P. M. (2003). Kv3 potassium conductance is necessary and kinetically optimized for high-frequency action potential generation in hippocampal interneurons. Journal of Neuroscience. Society for Neuroscience. chicago: Lien, Cheng, and Peter M Jonas. “Kv3 Potassium Conductance Is Necessary and Kinetically Optimized for High-Frequency Action Potential Generation in Hippocampal Interneurons.” Journal of Neuroscience. Society for Neuroscience, 2003. ieee: C. Lien and P. M. Jonas, “Kv3 potassium conductance is necessary and kinetically optimized for high-frequency action potential generation in hippocampal interneurons,” Journal of Neuroscience, vol. 23, no. 6. Society for Neuroscience, pp. 2058–68, 2003. 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.” Journal of Neuroscience, vol. 23, no. 6, Society for Neuroscience, 2003, pp. 2058–68. short: C. Lien, P.M. Jonas, Journal of Neuroscience 23 (2003) 2058–68. date_created: 2018-12-11T12:05:16Z date_published: 2003-01-01T00:00:00Z date_updated: 2021-01-12T07:52:19Z day: '01' extern: 1 intvolume: ' 23' issue: '6' month: '01' page: 2058 - 68 publication: Journal of Neuroscience publication_status: published publisher: Society for Neuroscience publist_id: '2406' quality_controlled: 0 status: public title: Kv3 potassium conductance is necessary and kinetically optimized for high-frequency action potential generation in hippocampal interneurons type: journal_article volume: 23 year: '2003' ... --- _id: '3806' 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 "maxipool." Large pool size and rapid vesicle recycling may underlie the uniquely large extent of activity-dependent plasticity in this synapse. author: - first_name: Stefan full_name: Hallermann, Stefan last_name: Hallermann - first_name: Christian full_name: Pawlu, Christian last_name: Pawlu - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: Manfred full_name: Heckmann, Manfred last_name: Heckmann citation: ama: Hallermann S, Pawlu C, Jonas PM, Heckmann M. A large pool of releasable vesicles in a cortical glutamatergic synapse. PNAS. 2003;100(15):8975-8980. doi:10.1073/pnas.1432836100 apa: Hallermann, S., Pawlu, C., Jonas, P. M., & Heckmann, M. (2003). A large pool of releasable vesicles in a cortical glutamatergic synapse. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1432836100 chicago: Hallermann, Stefan, Christian Pawlu, Peter M Jonas, and Manfred Heckmann. “A Large Pool of Releasable Vesicles in a Cortical Glutamatergic Synapse.” PNAS. National Academy of Sciences, 2003. https://doi.org/10.1073/pnas.1432836100. ieee: S. Hallermann, C. Pawlu, P. M. Jonas, and M. Heckmann, “A large pool of releasable vesicles in a cortical glutamatergic synapse,” PNAS, vol. 100, no. 15. National Academy of Sciences, pp. 8975–80, 2003. 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. mla: Hallermann, Stefan, et al. “A Large Pool of Releasable Vesicles in a Cortical Glutamatergic Synapse.” PNAS, vol. 100, no. 15, National Academy of Sciences, 2003, pp. 8975–80, doi:10.1073/pnas.1432836100. short: S. Hallermann, C. Pawlu, P.M. Jonas, M. Heckmann, PNAS 100 (2003) 8975–80. date_created: 2018-12-11T12:05:16Z date_published: 2003-01-01T00:00:00Z date_updated: 2021-01-12T07:52:20Z day: '01' doi: 10.1073/pnas.1432836100 extern: 1 intvolume: ' 100' issue: '15' month: '01' page: 8975 - 80 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '2405' quality_controlled: 0 status: public title: A large pool of releasable vesicles in a cortical glutamatergic synapse type: journal_article volume: 100 year: '2003' ... --- _id: '3921' abstract: - lang: eng text: 'Unlike most social insects, many Cardiocondyla ant species have two male morphs: wingless (ergatoid) males, who remain in the natal nest, and winged males who disperse but, strangely, before leaving may also mate within the nest. Whereas ergatoid males are highly intolerant of each other and fight among themselves, they tend to tolerate their winged counterparts. This is despite the fact that these winged males, like ergatoid males, represent mating competition. Why should ergatoid males tolerate their winged rivals? We developed a mathematical model to address this question. Our model focuses on a number of factors likely toinfluence whether ergatoid males are tolerant of winged males: ergatoid male–winged male relatedness, number of virgin queens, number of winged males, and the number of ejaculates a winged male has (winged males are sperm limited, whereas ergatoid males have lifelong spermatogenesis). Surprisingly, we found that increasing the number of virgin queens favors a kill strategy, whereas an increase in the other factors favors a let-live strategy; these predictions appear true for C. obscurior and for a number of other Cardiocondyla species. Two further aspects, unequal insemination success and multiple mating in queens, were also incorporated into the model and predictions made about their effects on toleration of winged males. The model is applicable more generally in species that have dimorphic males, such as some other ants, bees, and fig wasps.' author: - first_name: Carl full_name: Anderson, Carl last_name: Anderson - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze citation: ama: 'Anderson C, Cremer S, Heinze J. Live and let die: Why fighter males of the ant Cardiocondyla kill each other but tolerate their winged rivals. Behavioral Ecology. 2003;14(1):54-62. doi:10.1093/beheco/14.1.54' apa: 'Anderson, C., Cremer, S., & Heinze, J. (2003). Live and let die: Why fighter males of the ant Cardiocondyla kill each other but tolerate their winged rivals. Behavioral Ecology. Oxford University Press. https://doi.org/10.1093/beheco/14.1.54' chicago: 'Anderson, Carl, Sylvia Cremer, and Jürgen Heinze. “Live and Let Die: Why Fighter Males of the Ant Cardiocondyla Kill Each Other but Tolerate Their Winged Rivals.” Behavioral Ecology. Oxford University Press, 2003. https://doi.org/10.1093/beheco/14.1.54.' ieee: 'C. Anderson, S. Cremer, and J. Heinze, “Live and let die: Why fighter males of the ant Cardiocondyla kill each other but tolerate their winged rivals,” Behavioral Ecology, vol. 14, no. 1. Oxford University Press, pp. 54–62, 2003.' ista: 'Anderson C, Cremer S, Heinze J. 2003. Live and let die: Why fighter males of the ant Cardiocondyla kill each other but tolerate their winged rivals. Behavioral Ecology. 14(1), 54–62.' mla: 'Anderson, Carl, et al. “Live and Let Die: Why Fighter Males of the Ant Cardiocondyla Kill Each Other but Tolerate Their Winged Rivals.” Behavioral Ecology, vol. 14, no. 1, Oxford University Press, 2003, pp. 54–62, doi:10.1093/beheco/14.1.54.' short: C. Anderson, S. Cremer, J. Heinze, Behavioral Ecology 14 (2003) 54–62. date_created: 2018-12-11T12:05:54Z date_published: 2003-01-01T00:00:00Z date_updated: 2021-01-12T07:53:13Z day: '01' doi: 10.1093/beheco/14.1.54 extern: '1' intvolume: ' 14' issue: '1' language: - iso: eng month: '01' oa_version: None page: 54 - 62 publication: Behavioral Ecology publication_status: published publisher: Oxford University Press publist_id: '2233' status: public title: 'Live and let die: Why fighter males of the ant Cardiocondyla kill each other but tolerate their winged rivals' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2003' ... --- _id: '3922' abstract: - lang: eng text: Dispersal is advantageous, but, at the same time, it implies high costs and risks. Due to these counteracting selection pressures, many species evolved dispersal polymorphisms, which, in ants, are typically restricted to the female sex (queens). Male polymorphism is presently only known from a few genera, such as Cardiocondyla, in which winged dispersing males coexist with wingless fighter males that mate exclusively inside their maternal nests. We studied the developmental mechanisms underlying these alternative male morphs and found that, first, male dimorphism is not genetically determined, but is induced by environmental conditions (decreasing temperature and density). Second, male morph is not yet fixed at the egg stage, but it differentiates during larval development. This flexible developmental pattern of male morphs allows Cardiocondyla ant colonies to react quickly to changes in their environment. Under good conditions, they invest exclusively in philopatric wingless males. But, when environmental conditions turn bad, colonies start to produce winged dispersal males, even though these males require a many times higher investment by the colony than their much smaller wingless counterparts. Cardiocondyla ants share this potential of optimal resource allocation with other colonial animals and some seed dimorphic plants. author: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze citation: ama: 'Cremer S, Heinze J. Stress grows wings: Environmental induction of winged dispersal males in Cardiocondyla ants. Current Biology. 2003;13(3):219-223. doi:10.1016/S0960-9822(03)00012-5' apa: 'Cremer, S., & Heinze, J. (2003). Stress grows wings: Environmental induction of winged dispersal males in Cardiocondyla ants. Current Biology. Cell Press. https://doi.org/10.1016/S0960-9822(03)00012-5' chicago: 'Cremer, Sylvia, and Jürgen Heinze. “Stress Grows Wings: Environmental Induction of Winged Dispersal Males in Cardiocondyla Ants.” Current Biology. Cell Press, 2003. https://doi.org/10.1016/S0960-9822(03)00012-5.' ieee: 'S. Cremer and J. Heinze, “Stress grows wings: Environmental induction of winged dispersal males in Cardiocondyla ants,” Current Biology, vol. 13, no. 3. Cell Press, pp. 219–223, 2003.' ista: 'Cremer S, Heinze J. 2003. Stress grows wings: Environmental induction of winged dispersal males in Cardiocondyla ants. Current Biology. 13(3), 219–223.' mla: 'Cremer, Sylvia, and Jürgen Heinze. “Stress Grows Wings: Environmental Induction of Winged Dispersal Males in Cardiocondyla Ants.” Current Biology, vol. 13, no. 3, Cell Press, 2003, pp. 219–23, doi:10.1016/S0960-9822(03)00012-5.' short: S. Cremer, J. Heinze, Current Biology 13 (2003) 219–223. date_created: 2018-12-11T12:05:54Z date_published: 2003-02-04T00:00:00Z date_updated: 2021-01-12T07:53:13Z day: '04' doi: 10.1016/S0960-9822(03)00012-5 extern: '1' intvolume: ' 13' issue: '3' language: - iso: eng month: '02' oa_version: None page: 219 - 223 publication: Current Biology publication_status: published publisher: Cell Press publist_id: '2234' status: public title: 'Stress grows wings: Environmental induction of winged dispersal males in Cardiocondyla ants' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2003' ... --- _id: '3917' abstract: - lang: eng text: Male dimorphism is not genetically determined, but is induced by environmental conditions particularly decreasing temperature and density. author: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze citation: ama: 'Cremer S, Heinze J. Zwischen Hochzeitsflug und Brudermord: reproduktive Taktiken bei Ameisenmännchen. Blick in die Wissenschaft. 2003;12(15):32-36.' apa: 'Cremer, S., & Heinze, J. (2003). Zwischen Hochzeitsflug und Brudermord: reproduktive Taktiken bei Ameisenmännchen. Blick in Die Wissenschaft. Schnell und Steiner.' chicago: 'Cremer, Sylvia, and Jürgen Heinze. “Zwischen Hochzeitsflug Und Brudermord: Reproduktive Taktiken Bei Ameisenmännchen.” Blick in Die Wissenschaft. Schnell und Steiner, 2003.' ieee: 'S. Cremer and J. Heinze, “Zwischen Hochzeitsflug und Brudermord: reproduktive Taktiken bei Ameisenmännchen,” Blick in die Wissenschaft, vol. 12, no. 15. Schnell und Steiner, pp. 32–36, 2003.' ista: 'Cremer S, Heinze J. 2003. Zwischen Hochzeitsflug und Brudermord: reproduktive Taktiken bei Ameisenmännchen. Blick in die Wissenschaft. 12(15), 32–36.' mla: 'Cremer, Sylvia, and Jürgen Heinze. “Zwischen Hochzeitsflug Und Brudermord: Reproduktive Taktiken Bei Ameisenmännchen.” Blick in Die Wissenschaft, vol. 12, no. 15, Schnell und Steiner, 2003, pp. 32–36.' short: S. Cremer, J. Heinze, Blick in Die Wissenschaft 12 (2003) 32–36. date_created: 2018-12-11T12:05:53Z date_published: 2003-01-01T00:00:00Z date_updated: 2021-01-12T07:53:11Z day: '01' extern: '1' intvolume: ' 12' issue: '15' language: - iso: eng month: '01' oa_version: None page: 32 - 36 publication: Blick in die Wissenschaft publication_status: published publisher: Schnell und Steiner publist_id: '2235' status: public title: 'Zwischen Hochzeitsflug und Brudermord: reproduktive Taktiken bei Ameisenmännchen' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2003' ... --- _id: '4416' abstract: - lang: eng text: "Methods for the formal specification and verification of systems are indispensible for the development of complex yet correct systems. In formal verification, the designer describes the system in a modeling language with a well-defined semantics, and this system description is analyzed against a set of correctness requirements. Model checking is an algorithmic technique to check that a system description indeed satisfies correctness requirements given as logical specifications. While successful in hardware verification, the potential for model checking for software and embedded systems has not yet been realized. This is because traditional model checking focuses on systems modeled as finite state-transition graphs. While a natural model for hardware (especially synchronous hardware), state-transition graphs often do not capture software and embedded systems at an appropriate level of granularity. This dissertation considers two orthogonal extensions to finite state-transition graphs making model checking techniques applicable to both a wider class of systems and a wider class of properties.\r\n\r\nThe first direction is an extension to infinite-state structures finitely represented using constraints and operations on constraints. Infinite state arises when we wish to model variables with unbounded range (e.g., integers), or data structures, or real time. We provide a uniform framework of symbolic region algebras to study model checking of infinite-state systems. We also provide sufficient language-independent termination conditions for symbolic model checking algorithms on infinite state systems.\r\n\r\nThe second direction supplements verification with game theoretic reasoning. Games are natural models for interactions between components. We study game theoretic behavior with winning conditions given by temporal logic objectives both in the deterministic and in the probabilistic context. For deterministic games, we provide an extremal model characterization of fixpoint algorithms that link solutions of verification problems to solutions for games. For probabilistic games we study fixpoint characterization of winning probabilities for games with omega-regular winning objectives, and construct (epsilon-)optimal winning strategies." article_processing_charge: No author: - first_name: Ritankar full_name: Majumdar, Ritankar last_name: Majumdar citation: ama: Majumdar R. Symbolic algorithms for verification and control. 2003:1-201. apa: Majumdar, R. (2003). Symbolic algorithms for verification and control. University of California, Berkeley. chicago: Majumdar, Ritankar. “Symbolic Algorithms for Verification and Control.” University of California, Berkeley, 2003. ieee: R. Majumdar, “Symbolic algorithms for verification and control,” University of California, Berkeley, 2003. ista: Majumdar R. 2003. Symbolic algorithms for verification and control. University of California, Berkeley. mla: Majumdar, Ritankar. Symbolic Algorithms for Verification and Control. University of California, Berkeley, 2003, pp. 1–201. short: R. Majumdar, Symbolic Algorithms for Verification and Control, University of California, Berkeley, 2003. date_created: 2018-12-11T12:08:44Z date_published: 2003-12-01T00:00:00Z date_updated: 2021-01-12T07:56:49Z day: '01' extern: '1' language: - iso: eng month: '12' oa_version: None page: 1 - 201 publication_status: published publisher: University of California, Berkeley publist_id: '313' status: public supervisor: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 title: Symbolic algorithms for verification and control type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2003' ... --- _id: '4425' abstract: - lang: eng text: "Giotto provides a time-triggered programmer’s model for the implementation of embedded control systems with hard real-time constraints. Giotto’s precise semantics and predictabil- ity make it suitable for safety-critical applications.\r\nGiotto is based around the idea that time-triggered task invocation together with time-triggered mode switching can form a useful programming model for real-time systems. To substantiate this claim, we describe the use of Giotto to refactor the software of a small, autonomous helicopter. The ease with which Giotto expresses the existing software provides evidence that Giotto is an appropriate programming language for control systems.\r\nSince Giotto is a real-time programming language, ensuring that Giotto programs meet their deadlines is crucial. To study precedence-constrained Giotto scheduling, we first examine single-mode, single-processor scheduling. We extend to an infinite, periodic setting the classical problem of meeting deadlines for a set of tasks with release times, deadlines, precedence constraints, and preemption. We then develop an algorithm for scheduling Giotto programs on a single processor by representing Giotto programs as instances of the extended scheduling problem.\r\nNext, we study multi-mode, single-processor Giotto scheduling. This problem is different from classical scheduling problems, since in our precedence-constrained approach, the deadlines of tasks may vary depending on the mode switching behavior of the program. We present conditional scheduling models which capture this varying-deadline behavior. We develop polynomial-time algorithms for some conditional scheduling models, and prove oth- ers to be computationally hard. We show how to represent multi-mode Giotto programs as instances of the model, resulting in an algorithm for scheduling multi-mode Giotto programs on a single processor.\r\nFinally, we show that the problem of scheduling Giotto programs for multiple net- worked processors is strongly NP-hard." article_processing_charge: No author: - first_name: Benjamin full_name: Horowitz, Benjamin last_name: Horowitz citation: ama: 'Horowitz B. Giotto: A time-triggered language for embedded programming. 2003:1-237.' apa: 'Horowitz, B. (2003). Giotto: A time-triggered language for embedded programming. University of California, Berkeley.' chicago: 'Horowitz, Benjamin. “Giotto: A Time-Triggered Language for Embedded Programming.” University of California, Berkeley, 2003.' ieee: 'B. Horowitz, “Giotto: A time-triggered language for embedded programming,” University of California, Berkeley, 2003.' ista: 'Horowitz B. 2003. Giotto: A time-triggered language for embedded programming. University of California, Berkeley.' mla: 'Horowitz, Benjamin. Giotto: A Time-Triggered Language for Embedded Programming. University of California, Berkeley, 2003, pp. 1–237.' short: 'B. Horowitz, Giotto: A Time-Triggered Language for Embedded Programming, University of California, Berkeley, 2003.' date_created: 2018-12-11T12:08:47Z date_published: 2003-10-01T00:00:00Z date_updated: 2021-01-12T07:56:53Z day: '01' extern: '1' language: - iso: eng month: '10' oa_version: None page: 1 - 237 publication_status: published publisher: University of California, Berkeley publist_id: '305' status: public supervisor: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 title: 'Giotto: A time-triggered language for embedded programming' type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2003' ... --- _id: '576' abstract: - lang: eng text: 'We study the free expansion of a pancake-shaped Bose-condensed gas, which is initially trapped under harmonic confinement and containing a vortex at its centre. In the case of a radial expansion holding the axial confinement fixed we consider various models for the interactions, depending on the thickness of the condensate relative to the value of the scattering length. We are thus able to evaluate different scattering regimes ranging from quasi-three-dimensional (Q3D) to strictly two-dimensional (2D). We find that as the system goes from Q3D to 2D the expansion rate of the condensate increases whereas that of the vortex core decreases. In the Q3D scattering regime we also examine a fully free expansion in 3D and find oscillatory behaviour for the vortex core radius: an initial fast expansion of the vortex core is followed by a slowing down. Such a nonuniform expansion rate of the vortex core implies that the timing of its observation should be chosen appropriately.' author: - first_name: Onur full_name: Onur Hosten id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X - first_name: Patrizia full_name: Vignolo, Patrizia last_name: Vignolo - first_name: Anna full_name: Minguzzi, Anna last_name: Minguzzi - first_name: Bilal full_name: Tanatar, Bilal last_name: Tanatar - first_name: Mario full_name: Tosi, Mario P last_name: Tosi citation: ama: 'Hosten O, Vignolo P, Minguzzi A, Tanatar B, Tosi M. Free expansion of two-dimensional condensates with a vortex. Journal of Physics B: Atomic, Molecular and Optical Physics. 2003;36(12):2455-2463. doi:10.1088/0953-4075/36/12/306' apa: 'Hosten, O., Vignolo, P., Minguzzi, A., Tanatar, B., & Tosi, M. (2003). Free expansion of two-dimensional condensates with a vortex. Journal of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing Ltd. https://doi.org/10.1088/0953-4075/36/12/306' chicago: 'Hosten, Onur, Patrizia Vignolo, Anna Minguzzi, Bilal Tanatar, and Mario Tosi. “Free Expansion of Two-Dimensional Condensates with a Vortex.” Journal of Physics B: Atomic, Molecular and Optical Physics. IOP Publishing Ltd., 2003. https://doi.org/10.1088/0953-4075/36/12/306.' ieee: 'O. Hosten, P. Vignolo, A. Minguzzi, B. Tanatar, and M. Tosi, “Free expansion of two-dimensional condensates with a vortex,” Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 36, no. 12. IOP Publishing Ltd., pp. 2455–2463, 2003.' ista: 'Hosten O, Vignolo P, Minguzzi A, Tanatar B, Tosi M. 2003. Free expansion of two-dimensional condensates with a vortex. Journal of Physics B: Atomic, Molecular and Optical Physics. 36(12), 2455–2463.' mla: 'Hosten, Onur, et al. “Free Expansion of Two-Dimensional Condensates with a Vortex.” Journal of Physics B: Atomic, Molecular and Optical Physics, vol. 36, no. 12, IOP Publishing Ltd., 2003, pp. 2455–63, doi:10.1088/0953-4075/36/12/306.' short: 'O. Hosten, P. Vignolo, A. Minguzzi, B. Tanatar, M. Tosi, Journal of Physics B: Atomic, Molecular and Optical Physics 36 (2003) 2455–2463.' date_created: 2018-12-11T11:47:16Z date_published: 2003-06-28T00:00:00Z date_updated: 2021-01-12T08:03:20Z day: '28' doi: 10.1088/0953-4075/36/12/306 extern: 1 intvolume: ' 36' issue: '12' month: '06' page: 2455 - 2463 publication: 'Journal of Physics B: Atomic, Molecular and Optical Physics' publication_status: published publisher: IOP Publishing Ltd. publist_id: '7239' quality_controlled: 0 status: public title: Free expansion of two-dimensional condensates with a vortex type: journal_article volume: 36 year: '2003' ... --- _id: '6156' abstract: - lang: eng text: 'Social and solitary feeding in natural Caenorhabditis elegans isolates are associated with two alleles of the orphan G-protein-coupled receptor (GPCR) NPR-1: social feeders contain NPR-1 215F, whereas solitary feeders contain NPR-1 215V. Here we identify FMRFamide-related neuropeptides (FaRPs) encoded by the flp-18 and flp-21 genes as NPR-1 ligands and show that these peptides can differentially activate the NPR-1 215F and NPR-1 215V receptors. Multicopy overexpression of flp-21 transformed wild social animals into solitary feeders. Conversely, a flp-21 deletion partially phenocopied the npr-1(null) phenotype, which is consistent with NPR-1 activation by FLP-21 in vivo but also implicates other ligands for NPR-1. Phylogenetic studies indicate that the dominant npr-1 215V allele likely arose from an ancestral npr-1 215F gene in C. elegans. Our data suggest a model in which solitary feeding evolved in an ancestral social strain of C. elegans by a gain-of-function mutation that modified the response of NPR-1 to FLP-18 and FLP-21 ligands.' author: - first_name: Candida full_name: Rogers, Candida last_name: Rogers - first_name: Vincenzina full_name: Reale, Vincenzina last_name: Reale - first_name: Kyuhyung full_name: Kim, Kyuhyung last_name: Kim - first_name: Heather full_name: Chatwin, Heather last_name: Chatwin - first_name: Chris full_name: Li, Chris last_name: Li - first_name: Peter full_name: Evans, Peter last_name: Evans - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 citation: ama: Rogers C, Reale V, Kim K, et al. Inhibition of Caenorhabditis elegans social feeding by FMRFamide-related peptide activation of NPR-1. Nature Neuroscience. 2003;6(11):1178-1185. doi:10.1038/nn1140 apa: Rogers, C., Reale, V., Kim, K., Chatwin, H., Li, C., Evans, P., & de Bono, M. (2003). Inhibition of Caenorhabditis elegans social feeding by FMRFamide-related peptide activation of NPR-1. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/nn1140 chicago: Rogers, Candida, Vincenzina Reale, Kyuhyung Kim, Heather Chatwin, Chris Li, Peter Evans, and Mario de Bono. “Inhibition of Caenorhabditis Elegans Social Feeding by FMRFamide-Related Peptide Activation of NPR-1.” Nature Neuroscience. Springer Nature, 2003. https://doi.org/10.1038/nn1140. ieee: C. Rogers et al., “Inhibition of Caenorhabditis elegans social feeding by FMRFamide-related peptide activation of NPR-1,” Nature Neuroscience, vol. 6, no. 11. Springer Nature, pp. 1178–1185, 2003. ista: Rogers C, Reale V, Kim K, Chatwin H, Li C, Evans P, de Bono M. 2003. Inhibition of Caenorhabditis elegans social feeding by FMRFamide-related peptide activation of NPR-1. Nature Neuroscience. 6(11), 1178–1185. mla: Rogers, Candida, et al. “Inhibition of Caenorhabditis Elegans Social Feeding by FMRFamide-Related Peptide Activation of NPR-1.” Nature Neuroscience, vol. 6, no. 11, Springer Nature, 2003, pp. 1178–85, doi:10.1038/nn1140. short: C. Rogers, V. Reale, K. Kim, H. Chatwin, C. Li, P. Evans, M. de Bono, Nature Neuroscience 6 (2003) 1178–1185. date_created: 2019-03-21T09:47:53Z date_published: 2003-10-12T00:00:00Z date_updated: 2021-01-12T08:06:25Z day: '12' doi: 10.1038/nn1140 extern: '1' external_id: pmid: - '14555955' intvolume: ' 6' issue: '11' language: - iso: eng month: '10' oa_version: None page: 1178-1185 pmid: 1 publication: Nature Neuroscience publication_identifier: issn: - 1097-6256 - 1546-1726 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Inhibition of Caenorhabditis elegans social feeding by FMRFamide-related peptide activation of NPR-1 type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2003' ... --- _id: '6157' abstract: - lang: eng text: In many animal species individuals aggregate to live in groups. A range of experimental approaches in different animals, including studies of social feeding in nematodes, maternal behavior in rats and sheep, and pair-bonding in voles, are providing insights into the neural bases for these behaviors. These studies are delineating multiple neural circuits and gene networks in the brain that interact in ways that are as yet poorly understood to coordinate social behavior. author: - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 citation: ama: de Bono M. Molecular approaches to aggregation behavior and social attachment. Journal of Neurobiology. 2003;54(1):78-92. doi:10.1002/neu.10162 apa: de Bono, M. (2003). Molecular approaches to aggregation behavior and social attachment. Journal of Neurobiology. Wiley. https://doi.org/10.1002/neu.10162 chicago: Bono, Mario de. “Molecular Approaches to Aggregation Behavior and Social Attachment.” Journal of Neurobiology. Wiley, 2003. https://doi.org/10.1002/neu.10162. ieee: M. de Bono, “Molecular approaches to aggregation behavior and social attachment,” Journal of Neurobiology, vol. 54, no. 1. Wiley, pp. 78–92, 2003. ista: de Bono M. 2003. Molecular approaches to aggregation behavior and social attachment. Journal of Neurobiology. 54(1), 78–92. mla: de Bono, Mario. “Molecular Approaches to Aggregation Behavior and Social Attachment.” Journal of Neurobiology, vol. 54, no. 1, Wiley, 2003, pp. 78–92, doi:10.1002/neu.10162. short: M. de Bono, Journal of Neurobiology 54 (2003) 78–92. date_created: 2019-03-21T09:52:31Z date_published: 2003-01-01T00:00:00Z date_updated: 2021-01-12T08:06:26Z day: '01' doi: 10.1002/neu.10162 extern: '1' external_id: pmid: - '12486699' intvolume: ' 54' issue: '1' language: - iso: eng month: '01' oa_version: None page: 78-92 pmid: 1 publication: Journal of Neurobiology publication_identifier: issn: - 0022-3034 - 1097-4695 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Molecular approaches to aggregation behavior and social attachment type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 54 year: '2003' ... --- _id: '847' abstract: - lang: eng text: The accumulation of genome-wide information on single nucleotide polymorphisms in humans provides an unprecedented opportunity to detect the evolutionary forces responsible for heterogeneity of the level of genetic variability across loci. Previous studies have shown that history of recombination events has produced long haplotype blocks in the human genome, which contribute to this heterogeneity. Other factors, however, such as natural selection or the heterogeneity of mutation rates across loci, may also lead to heterogeneity of genetic variability. We compared synonymous and non-synonymous variability within human genes with their divergence from murine orthologs. We separately analyzed the non-synonymous variants predicted to damage protein structure or function and the variants predicted to be functionally benign. The predictions were based on comparative sequence analysis and, in some cases, on the analysis of protein structure. A strong correlation between non-synonymous, benign variability and non-synonymous human-mouse divergence suggests that selection played an important role in shaping the pattern of variability in coding regions of human genes. However, the lack of correlation between deleterious variability and evolutionary divergence shows that a substantial proportion of the observed non-synonymous single-nucleotide polymorphisms reduces fitness and never reaches fixation. Evolutionary and medical implications of the impact of selection on human polymorphisms are discussed. acknowledgement: We are grateful to Alexey Kondrashov and Alison Wellman for the careful reading of the manuscript and providing us with their valuable comments. author: - first_name: Shamil full_name: Sunyaev, Shamil R last_name: Sunyaev - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Peer full_name: Bork, Peer last_name: Bork - first_name: Vasily full_name: Ramensky, Vasily last_name: Ramensky citation: ama: Sunyaev S, Kondrashov F, Bork P, Ramensky V. Impact of selection, mutation rate and genetic drift on human genetic variation. Human Molecular Genetics. 2003;12(24):3325-3330. doi:10.1093/hmg/ddg359 apa: Sunyaev, S., Kondrashov, F., Bork, P., & Ramensky, V. (2003). Impact of selection, mutation rate and genetic drift on human genetic variation. Human Molecular Genetics. Oxford University Press. https://doi.org/10.1093/hmg/ddg359 chicago: Sunyaev, Shamil, Fyodor Kondrashov, Peer Bork, and Vasily Ramensky. “Impact of Selection, Mutation Rate and Genetic Drift on Human Genetic Variation.” Human Molecular Genetics. Oxford University Press, 2003. https://doi.org/10.1093/hmg/ddg359. ieee: S. Sunyaev, F. Kondrashov, P. Bork, and V. Ramensky, “Impact of selection, mutation rate and genetic drift on human genetic variation,” Human Molecular Genetics, vol. 12, no. 24. Oxford University Press, pp. 3325–3330, 2003. ista: Sunyaev S, Kondrashov F, Bork P, Ramensky V. 2003. Impact of selection, mutation rate and genetic drift on human genetic variation. Human Molecular Genetics. 12(24), 3325–3330. mla: Sunyaev, Shamil, et al. “Impact of Selection, Mutation Rate and Genetic Drift on Human Genetic Variation.” Human Molecular Genetics, vol. 12, no. 24, Oxford University Press, 2003, pp. 3325–30, doi:10.1093/hmg/ddg359. short: S. Sunyaev, F. Kondrashov, P. Bork, V. Ramensky, Human Molecular Genetics 12 (2003) 3325–3330. date_created: 2018-12-11T11:48:49Z date_published: 2003-12-15T00:00:00Z date_updated: 2021-01-12T08:19:29Z day: '15' doi: 10.1093/hmg/ddg359 extern: 1 intvolume: ' 12' issue: '24' month: '12' page: 3325 - 3330 publication: Human Molecular Genetics publication_status: published publisher: Oxford University Press publist_id: '6803' quality_controlled: 0 status: public title: Impact of selection, mutation rate and genetic drift on human genetic variation type: journal_article volume: 12 year: '2003' ... --- _id: '876' abstract: - lang: eng text: Alternative splicing is thought to be a major source of functional diversity in animal proteins. We analyzed the evolutionary conservation of proteins encoded by alternatively spliced genes and predicted the ancestral state for 73 cases of alternative splicing (25 insertions and 48 deletions). The amino acid sequences of most of the inserts in proteins produced by alternative splicing are as conserved as the surrounding sequences. Thus, alternative splicing often creates novel isoforms by the insertion of new, functional protein sequences that probably originated from noncoding sequences of introns. acknowledgement: We thank Peer Bork, Mikhail Gelfand, Alexey Kondrashov, David Lipman and Shamil Sunyaev for critical reading of the manuscript and useful suggestions and the Koonin group members for helpful discussions. author: - first_name: Fyodor full_name: Fyodor Kondrashov id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Eugene full_name: Koonin, Eugene V last_name: Koonin citation: ama: 'Kondrashov F, Koonin E. Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences. Trends in Genetics. 2003;19(3):115-119. doi:10.1016/S0168-9525(02)00029-X' apa: 'Kondrashov, F., & Koonin, E. (2003). Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences. Trends in Genetics. Elsevier. https://doi.org/10.1016/S0168-9525(02)00029-X' chicago: 'Kondrashov, Fyodor, and Eugene Koonin. “Evolution of Alternative Splicing: Deletions, Insertions and Origin of Functional Parts of Proteins from Intron Sequences.” Trends in Genetics. Elsevier, 2003. https://doi.org/10.1016/S0168-9525(02)00029-X.' ieee: 'F. Kondrashov and E. Koonin, “Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences,” Trends in Genetics, vol. 19, no. 3. Elsevier, pp. 115–119, 2003.' ista: 'Kondrashov F, Koonin E. 2003. Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences. Trends in Genetics. 19(3), 115–119.' mla: 'Kondrashov, Fyodor, and Eugene Koonin. “Evolution of Alternative Splicing: Deletions, Insertions and Origin of Functional Parts of Proteins from Intron Sequences.” Trends in Genetics, vol. 19, no. 3, Elsevier, 2003, pp. 115–19, doi:10.1016/S0168-9525(02)00029-X.' short: F. Kondrashov, E. Koonin, Trends in Genetics 19 (2003) 115–119. date_created: 2018-12-11T11:48:58Z date_published: 2003-01-01T00:00:00Z date_updated: 2021-01-12T08:20:58Z day: '01' doi: 10.1016/S0168-9525(02)00029-X extern: 1 intvolume: ' 19' issue: '3' month: '01' page: 115 - 119 publication: Trends in Genetics publication_status: published publisher: Elsevier publist_id: '6776' quality_controlled: 0 status: public title: 'Evolution of alternative splicing: Deletions, insertions and origin of functional parts of proteins from intron sequences' type: journal_article volume: 19 year: '2003' ... --- _id: '9495' abstract: - lang: eng text: RNA interference is a conserved process in which double-stranded RNA is processed into 21–25 nucleotide siRNAs that trigger posttranscriptional gene silencing. In addition, plants display a phenomenon termed RNA-directed DNA methylation (RdDM) in which DNA with sequence identity to silenced RNA is de novo methylated at its cytosine residues. This methylation is not only at canonical CpG sites but also at cytosines in CpNpG and asymmetric sequence contexts. In this report, we study the role of the DRM and CMT3 DNA methyltransferase genes in the initiation and maintenance of RdDM. Neither drm nor cmt3 mutants affected the maintenance of preestablished RNA-directed CpG methylation. However, drm mutants showed a nearly complete loss of asymmetric methylation and a partial loss of CpNpG methylation. The remaining asymmetric and CpNpG methylation was dependent on the activity of CMT3, showing that DRM and CMT3 act redundantly to maintain non-CpG methylation. These DNA methyltransferases appear to act downstream of siRNAs, since drm1 drm2 cmt3 triple mutants show a lack of non-CpG methylation but elevated levels of siRNAs. Finally, we demonstrate that DRM activity is required for the initial establishment of RdDM in all sequence contexts including CpG, CpNpG, and asymmetric sites. article_processing_charge: No article_type: original author: - first_name: Xiaofeng full_name: Cao, Xiaofeng last_name: Cao - first_name: Werner full_name: Aufsatz, Werner last_name: Aufsatz - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: M.Florian full_name: Mette, M.Florian last_name: Mette - first_name: Michael S. full_name: Huang, Michael S. last_name: Huang - first_name: Marjori full_name: Matzke, Marjori last_name: Matzke - first_name: Steven E. full_name: Jacobsen, Steven E. last_name: Jacobsen citation: ama: Cao X, Aufsatz W, Zilberman D, et al. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Current Biology. 2003;13(24):2212-2217. doi:10.1016/j.cub.2003.11.052 apa: Cao, X., Aufsatz, W., Zilberman, D., Mette, M. F., Huang, M. S., Matzke, M., & Jacobsen, S. E. (2003). Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2003.11.052 chicago: Cao, Xiaofeng, Werner Aufsatz, Daniel Zilberman, M.Florian Mette, Michael S. Huang, Marjori Matzke, and Steven E. Jacobsen. “Role of the DRM and CMT3 Methyltransferases in RNA-Directed DNA Methylation.” Current Biology. Elsevier, 2003. https://doi.org/10.1016/j.cub.2003.11.052. ieee: X. Cao et al., “Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation,” Current Biology, vol. 13, no. 24. Elsevier, pp. 2212–2217, 2003. ista: Cao X, Aufsatz W, Zilberman D, Mette MF, Huang MS, Matzke M, Jacobsen SE. 2003. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Current Biology. 13(24), 2212–2217. mla: Cao, Xiaofeng, et al. “Role of the DRM and CMT3 Methyltransferases in RNA-Directed DNA Methylation.” Current Biology, vol. 13, no. 24, Elsevier, 2003, pp. 2212–17, doi:10.1016/j.cub.2003.11.052. short: X. Cao, W. Aufsatz, D. Zilberman, M.F. Mette, M.S. Huang, M. Matzke, S.E. Jacobsen, Current Biology 13 (2003) 2212–2217. date_created: 2021-06-07T10:43:02Z date_published: 2003-12-16T00:00:00Z date_updated: 2021-12-14T08:41:38Z day: '16' department: - _id: DaZi doi: 10.1016/j.cub.2003.11.052 extern: '1' external_id: pmid: - '14680640' intvolume: ' 13' issue: '24' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cub.2003.11.052 month: '12' oa: 1 oa_version: Published Version page: 2212-2217 pmid: 1 publication: Current Biology publication_identifier: eissn: - 1879-0445 issn: - 0960-9822 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 13 year: '2003' ... --- _id: '8519' article_processing_charge: No article_type: original author: - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 citation: ama: Kaloshin V. The existential Hilbert 16-th problem and an estimate for cyclicity of elementary polycycles. Inventiones mathematicae. 2003;151(3):451-512. doi:10.1007/s00222-002-0244-9 apa: Kaloshin, V. (2003). The existential Hilbert 16-th problem and an estimate for cyclicity of elementary polycycles. Inventiones Mathematicae. Springer Nature. https://doi.org/10.1007/s00222-002-0244-9 chicago: Kaloshin, Vadim. “The Existential Hilbert 16-Th Problem and an Estimate for Cyclicity of Elementary Polycycles.” Inventiones Mathematicae. Springer Nature, 2003. https://doi.org/10.1007/s00222-002-0244-9. ieee: V. Kaloshin, “The existential Hilbert 16-th problem and an estimate for cyclicity of elementary polycycles,” Inventiones mathematicae, vol. 151, no. 3. Springer Nature, pp. 451–512, 2003. ista: Kaloshin V. 2003. The existential Hilbert 16-th problem and an estimate for cyclicity of elementary polycycles. Inventiones mathematicae. 151(3), 451–512. mla: Kaloshin, Vadim. “The Existential Hilbert 16-Th Problem and an Estimate for Cyclicity of Elementary Polycycles.” Inventiones Mathematicae, vol. 151, no. 3, Springer Nature, 2003, pp. 451–512, doi:10.1007/s00222-002-0244-9. short: V. Kaloshin, Inventiones Mathematicae 151 (2003) 451–512. date_created: 2020-09-18T10:49:26Z date_published: 2003-03-01T00:00:00Z date_updated: 2021-01-12T08:19:50Z day: '01' doi: 10.1007/s00222-002-0244-9 extern: '1' intvolume: ' 151' issue: '3' keyword: - General Mathematics language: - iso: eng month: '03' oa_version: None page: 451-512 publication: Inventiones mathematicae publication_identifier: issn: - 0020-9910 - 1432-1297 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: The existential Hilbert 16-th problem and an estimate for cyclicity of elementary polycycles type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 151 year: '2003' ... --- _id: '9455' abstract: - lang: eng text: Proteins of the ARGONAUTE family are important in diverse posttranscriptional RNA-mediated gene-silencing systems as well as in transcriptional gene silencing in Drosophila and fission yeast and in programmed DNA elimination in Tetrahymena. We cloned ARGONAUTE4 (AGO4) from a screen for mutants that suppress silencing of the Arabidopsis SUPERMAN(SUP) gene. The ago4-1 mutant reactivated silentSUP alleles and decreased CpNpG and asymmetric DNA methylation as well as histone H3 lysine-9 methylation. In addition,ago4-1 blocked histone and DNA methylation and the accumulation of 25-nucleotide small interfering RNAs (siRNAs) that correspond to the retroelement AtSN1. These results suggest that AGO4 and long siRNAs direct chromatin modifications, including histone methylation and non-CpG DNA methylation. article_processing_charge: No article_type: original author: - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: ' Xiaofeng' full_name: Cao, Xiaofeng last_name: Cao - first_name: Steven E. full_name: Jacobsen, Steven E. last_name: Jacobsen citation: ama: Zilberman D, Cao Xiaofeng, Jacobsen SE. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science. 2003;299(5607):716-719. doi:10.1126/science.1079695 apa: Zilberman, D., Cao, Xiaofeng, & Jacobsen, S. E. (2003). ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1079695 chicago: Zilberman, Daniel, Xiaofeng Cao, and Steven E. Jacobsen. “ARGONAUTE4 Control of Locus-Specific SiRNA Accumulation and DNA and Histone Methylation.” Science. American Association for the Advancement of Science, 2003. https://doi.org/10.1126/science.1079695. ieee: D. Zilberman, Xiaofeng Cao, and S. E. Jacobsen, “ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation,” Science, vol. 299, no. 5607. American Association for the Advancement of Science, pp. 716–719, 2003. ista: Zilberman D, Cao Xiaofeng, Jacobsen SE. 2003. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science. 299(5607), 716–719. mla: Zilberman, Daniel, et al. “ARGONAUTE4 Control of Locus-Specific SiRNA Accumulation and DNA and Histone Methylation.” Science, vol. 299, no. 5607, American Association for the Advancement of Science, 2003, pp. 716–19, doi:10.1126/science.1079695. short: D. Zilberman, Xiaofeng Cao, S.E. Jacobsen, Science 299 (2003) 716–719. date_created: 2021-06-04T11:26:26Z date_published: 2003-01-31T00:00:00Z date_updated: 2021-12-14T08:43:30Z day: '31' department: - _id: DaZi doi: 10.1126/science.1079695 extern: '1' external_id: pmid: - '12522258' intvolume: ' 299' issue: '5607' keyword: - Multidisciplinary language: - iso: eng month: '01' oa_version: None page: 716-719 pmid: 1 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 299 year: '2003' ... --- _id: '4628' abstract: - lang: eng text: 'Discounting the future means that the value, today, of a unit payoffis 1 if the payoffo ccurs today, a if it occurs tomorrow, a 2 if it occurs the day after tomorrow, and so on, for some real-valued discount factor 0 < a < 1. Discounting (or inflation) is a key paradigm in economics and has been studied in Markov decision processes as well as game theory. We submit that discounting also has a natural place in systems engineering: for nonterminating systems, a potential bug in the far-away future is less troubling than a potential bug today. We therefore develop a systems theory with discounting. Our theory includes several basic elements: discounted versions of system properties that correspond to the ω-regular properties, fixpoint-based algorithms for checking discounted properties, and a quantitative notion of bisimilarity for capturing the difference between two states with respect to discounted properties. We present the theory in a general form that applies to probabilistic systems as well as multicomponent systems (games), but it readily specializes to classical transition systems. We show that discounting, besides its natural practical appeal, has also several mathematical benefits. First, the resulting theory is robust, in that small perturbations of a system can cause only small changes in the properties of the system. Second, the theory is computational, in that the values of discounted properties, as well as the discounted bisimilarity distance between states, can be computed to any desired degree of precision.' acknowledgement: This research was supported in part by the NSF CAREER award CCR-0132780, the DARPA grant F33615-C-98-3614, the NSF grants CCR-9988172, CCR-0234690 and CCR-0225610, and the ONR grant N00014-02-1-0671. alternative_title: - LNCS article_processing_charge: No author: - first_name: Luca full_name: De Alfaro, Luca last_name: De Alfaro - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Ritankar full_name: Majumdar, Ritankar last_name: Majumdar citation: ama: 'De Alfaro L, Henzinger TA, Majumdar R. Discounting the future in systems theory. In: Proceedings of the 30th International Colloquium on Automata, Languages and Programming. Vol 2719. Springer; 2003:1022-1037. doi:10.1007/3-540-45061-0_79' apa: 'De Alfaro, L., Henzinger, T. A., & Majumdar, R. (2003). Discounting the future in systems theory. In Proceedings of the 30th International Colloquium on Automata, Languages and Programming (Vol. 2719, pp. 1022–1037). Eindhoven, The Netherlands: Springer. https://doi.org/10.1007/3-540-45061-0_79' chicago: De Alfaro, Luca, Thomas A Henzinger, and Ritankar Majumdar. “Discounting the Future in Systems Theory.” In Proceedings of the 30th International Colloquium on Automata, Languages and Programming, 2719:1022–37. Springer, 2003. https://doi.org/10.1007/3-540-45061-0_79. ieee: L. De Alfaro, T. A. Henzinger, and R. Majumdar, “Discounting the future in systems theory,” in Proceedings of the 30th International Colloquium on Automata, Languages and Programming, Eindhoven, The Netherlands, 2003, vol. 2719, pp. 1022–1037. ista: 'De Alfaro L, Henzinger TA, Majumdar R. 2003. Discounting the future in systems theory. Proceedings of the 30th International Colloquium on Automata, Languages and Programming. ICALP: Automata, Languages and Programming, LNCS, vol. 2719, 1022–1037.' mla: De Alfaro, Luca, et al. “Discounting the Future in Systems Theory.” Proceedings of the 30th International Colloquium on Automata, Languages and Programming, vol. 2719, Springer, 2003, pp. 1022–37, doi:10.1007/3-540-45061-0_79. short: L. De Alfaro, T.A. Henzinger, R. Majumdar, in:, Proceedings of the 30th International Colloquium on Automata, Languages and Programming, Springer, 2003, pp. 1022–1037. conference: end_date: 2003-07-04 location: Eindhoven, The Netherlands name: 'ICALP: Automata, Languages and Programming' start_date: 2003-06-30 date_created: 2018-12-11T12:09:50Z date_published: 2003-06-25T00:00:00Z date_updated: 2023-07-26T13:07:31Z day: '25' doi: 10.1007/3-540-45061-0_79 extern: '1' intvolume: ' 2719' language: - iso: eng month: '06' oa_version: None page: 1022 - 1037 publication: Proceedings of the 30th International Colloquium on Automata, Languages and Programming publication_identifier: isbn: - '9783540404934' publication_status: published publisher: Springer publist_id: '77' quality_controlled: '1' scopus_import: '1' status: public title: Discounting the future in systems theory type: conference user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 2719 year: '2003' ... --- _id: '13436' abstract: - lang: eng text: Cross-metathesis reactions of α,β-unsaturated sulfones and sulfoxides in the presence of molybdenum and ruthenium pre-catalysts were tested. A selective metahesis reaction was achieved between functionalized terminal olefins and vinyl sulfones by using the ‘second generation’ ruthenium catalysts 1c–h while the highly active Schrock catalyst 1b was found to be functional group incompatible with vinyl sulfones. The cross-metathesis products were isolated in good yields with an excellent (E)-selectivity. Both the molybdenum and ruthenium-based complexes were, however, incompatible with α,β- and β,γ-unsaturated sulfoxides. article_processing_charge: No article_type: original author: - first_name: Anna full_name: Michrowska, Anna last_name: Michrowska - first_name: Michał full_name: Bieniek, Michał last_name: Bieniek - first_name: Mikhail full_name: Kim, Mikhail last_name: Kim - first_name: Rafal full_name: Klajn, Rafal id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b last_name: Klajn - first_name: Karol full_name: Grela, Karol last_name: Grela citation: ama: Michrowska A, Bieniek M, Kim M, Klajn R, Grela K. Cross-metathesis reaction of vinyl sulfones and sulfoxides. Tetrahedron. 2003;59(25):4525-4531. doi:10.1016/s0040-4020(03)00682-3 apa: Michrowska, A., Bieniek, M., Kim, M., Klajn, R., & Grela, K. (2003). Cross-metathesis reaction of vinyl sulfones and sulfoxides. Tetrahedron. Elsevier. https://doi.org/10.1016/s0040-4020(03)00682-3 chicago: Michrowska, Anna, Michał Bieniek, Mikhail Kim, Rafal Klajn, and Karol Grela. “Cross-Metathesis Reaction of Vinyl Sulfones and Sulfoxides.” Tetrahedron. Elsevier, 2003. https://doi.org/10.1016/s0040-4020(03)00682-3. ieee: A. Michrowska, M. Bieniek, M. Kim, R. Klajn, and K. Grela, “Cross-metathesis reaction of vinyl sulfones and sulfoxides,” Tetrahedron, vol. 59, no. 25. Elsevier, pp. 4525–4531, 2003. ista: Michrowska A, Bieniek M, Kim M, Klajn R, Grela K. 2003. Cross-metathesis reaction of vinyl sulfones and sulfoxides. Tetrahedron. 59(25), 4525–4531. mla: Michrowska, Anna, et al. “Cross-Metathesis Reaction of Vinyl Sulfones and Sulfoxides.” Tetrahedron, vol. 59, no. 25, Elsevier, 2003, pp. 4525–31, doi:10.1016/s0040-4020(03)00682-3. short: A. Michrowska, M. Bieniek, M. Kim, R. Klajn, K. Grela, Tetrahedron 59 (2003) 4525–4531. date_created: 2023-08-01T10:39:34Z date_published: 2003-06-16T00:00:00Z date_updated: 2023-08-08T12:44:17Z day: '16' doi: 10.1016/s0040-4020(03)00682-3 extern: '1' intvolume: ' 59' issue: '25' keyword: - Organic Chemistry - Drug Discovery - Biochemistry language: - iso: eng month: '06' oa_version: None page: 4525-4531 publication: Tetrahedron publication_identifier: eissn: - 1464-5416 issn: - 0040-4020 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Cross-metathesis reaction of vinyl sulfones and sulfoxides type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 59 year: '2003' ... --- _id: '4561' abstract: - lang: eng text: 'We present a formalism for specifying component interfaces that expose component requirements on limited resources. The formalism permits an algorithmic check if two or more components, when put together, exceed the available resources. Moreover, the formalism can be used to compute the quantity of resources necessary for satisfying the requirements of a collection of components. The formalism can be instantiated in several ways. For example, several components may draw power from the same source. Then, the formalism supports compatibility checks such as: can two components, when put together, achieve their tasks without ever exceeding the available amount of peak power? or, can they achieve their tasks by using no more than the initially available amount of energy (i.e., power accumulated over time)? The corresponding quantitative questions that our algorithms answer are the following: what is the amount of peak power needed for two components to be put together? what is the corresponding amount of initial energy? To solve these questions, we model interfaces with resource requirements as games with quantitative objectives. The games are played on state spaces where each state is labeled by a number (representing, e.g., power consumption), and a play produces an infinite path of labels. The objective may be, for example, to minimize the largest label that occurs during a play. We illustrate our approach by modeling compatibility questions for the components of robot control software, and of wireless sensor networks.' acknowledgement: This research was supported in part by the DARPA grant F33615-00-C-1693, the MARCO grant 98-DT-660, the ONR grant N00014-02-1-0671, and the NSF grants CCR-0085949, CCR-0132780, CCR-0234690, and CCR-9988172. alternative_title: - LNCS article_processing_charge: No author: - first_name: Arindam full_name: Chakrabarti, Arindam last_name: Chakrabarti - first_name: Luca full_name: De Alfaro, Luca last_name: De Alfaro - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Mariëlle full_name: Stoelinga, Mariëlle last_name: Stoelinga citation: ama: 'Chakrabarti A, De Alfaro L, Henzinger TA, Stoelinga M. Resource interfaces. In: Third International Conference on Embedded Software. Vol 2855. ACM; 2003:117-133. doi:10.1007/978-3-540-45212-6_9' apa: 'Chakrabarti, A., De Alfaro, L., Henzinger, T. A., & Stoelinga, M. (2003). Resource interfaces. In Third International Conference on Embedded Software (Vol. 2855, pp. 117–133). Philadelphia, PA, USA: ACM. https://doi.org/10.1007/978-3-540-45212-6_9' chicago: Chakrabarti, Arindam, Luca De Alfaro, Thomas A Henzinger, and Mariëlle Stoelinga. “Resource Interfaces.” In Third International Conference on Embedded Software, 2855:117–33. ACM, 2003. https://doi.org/10.1007/978-3-540-45212-6_9. ieee: A. Chakrabarti, L. De Alfaro, T. A. Henzinger, and M. Stoelinga, “Resource interfaces,” in Third International Conference on Embedded Software, Philadelphia, PA, USA, 2003, vol. 2855, pp. 117–133. ista: 'Chakrabarti A, De Alfaro L, Henzinger TA, Stoelinga M. 2003. Resource interfaces. Third International Conference on Embedded Software. EMSOFT: Embedded Software , LNCS, vol. 2855, 117–133.' mla: Chakrabarti, Arindam, et al. “Resource Interfaces.” Third International Conference on Embedded Software, vol. 2855, ACM, 2003, pp. 117–33, doi:10.1007/978-3-540-45212-6_9. short: A. Chakrabarti, L. De Alfaro, T.A. Henzinger, M. Stoelinga, in:, Third International Conference on Embedded Software, ACM, 2003, pp. 117–133. conference: end_date: 2003-10-15 location: Philadelphia, PA, USA name: 'EMSOFT: Embedded Software ' start_date: 2003-10-13 date_created: 2018-12-11T12:09:29Z date_published: 2003-09-29T00:00:00Z date_updated: 2024-01-08T10:48:11Z day: '29' doi: 10.1007/978-3-540-45212-6_9 extern: '1' intvolume: ' 2855' language: - iso: eng month: '09' oa_version: None page: 117 - 133 publication: Third International Conference on Embedded Software publication_identifier: isbn: - '9783540202233' publication_status: published publisher: ACM publist_id: '148' quality_controlled: '1' scopus_import: '1' status: public title: Resource interfaces type: conference user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 2855 year: '2003' ... --- _id: '4630' abstract: - lang: eng text: We consider concurrent two-person games played in real time, in which the players decide both which action to play, and when to play it. Such timed games differ from untimed games in two essential ways. First, players can take each other by surprise, because actions are played with delays that cannot be anticipated by the opponent. Second, a player should not be able to win the game by preventing time from diverging. We present a model of timed games that preserves the element of surprise and accounts for time divergence in a way that treats both players symmetrically and applies to all ω-regular winning conditions. We prove that the ability to take each other by surprise adds extra power to the players. For the case that the games are specified in the style of timed automata, we provide symbolic algorithms for their solution with respect to all ω-regular winning conditions. We also show that for these timed games, memory strategies are more powerful than memoryless strategies already in the case of reachability objectives. acknowledgement: Supported in part by the AFOSR MURI grant F49620-00-1-0327, the DARPA grant F33615-C-98-3614, the MARCO grant 98-DT-660, -the ONR grant N00014-02-1-0671, the NSF grants CCR-9988172, CCR-0225610, and CCR-0234690, the NSF CAREER award CCR-0132780, and the MIUR grant MEFISTO. alternative_title: - LNCS article_processing_charge: No author: - first_name: Luca full_name: De Alfaro, Luca last_name: De Alfaro - first_name: Marco full_name: Faella, Marco last_name: Faella - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Ritankar full_name: Majumdar, Ritankar last_name: Majumdar - first_name: Mariëlle full_name: Stoelinga, Mariëlle last_name: Stoelinga citation: ama: 'De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga M. The element of surprise in timed games. In: Proceedings of the 14th International Conference on Concurrency Theory. Vol 2761. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2003:144-158. doi:10.1007/978-3-540-45187-7_9' apa: 'De Alfaro, L., Faella, M., Henzinger, T. A., Majumdar, R., & Stoelinga, M. (2003). The element of surprise in timed games. In Proceedings of the 14th International Conference on Concurrency Theory (Vol. 2761, pp. 144–158). Marseille, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-540-45187-7_9' chicago: De Alfaro, Luca, Marco Faella, Thomas A Henzinger, Ritankar Majumdar, and Mariëlle Stoelinga. “The Element of Surprise in Timed Games.” In Proceedings of the 14th International Conference on Concurrency Theory, 2761:144–58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2003. https://doi.org/10.1007/978-3-540-45187-7_9. ieee: L. De Alfaro, M. Faella, T. A. Henzinger, R. Majumdar, and M. Stoelinga, “The element of surprise in timed games,” in Proceedings of the 14th International Conference on Concurrency Theory, Marseille, France, 2003, vol. 2761, pp. 144–158. ista: 'De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga M. 2003. The element of surprise in timed games. Proceedings of the 14th International Conference on Concurrency Theory. CONCUR: Concurrency Theory, LNCS, vol. 2761, 144–158.' mla: De Alfaro, Luca, et al. “The Element of Surprise in Timed Games.” Proceedings of the 14th International Conference on Concurrency Theory, vol. 2761, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2003, pp. 144–58, doi:10.1007/978-3-540-45187-7_9. short: L. De Alfaro, M. Faella, T.A. Henzinger, R. Majumdar, M. Stoelinga, in:, Proceedings of the 14th International Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2003, pp. 144–158. conference: end_date: 2003-09-05 location: Marseille, France name: 'CONCUR: Concurrency Theory' start_date: 2003-09-03 date_created: 2018-12-11T12:09:51Z date_published: 2003-08-21T00:00:00Z date_updated: 2024-01-08T10:05:30Z day: '21' doi: 10.1007/978-3-540-45187-7_9 extern: '1' intvolume: ' 2761' language: - iso: eng month: '08' oa_version: None page: 144 - 158 publication: Proceedings of the 14th International Conference on Concurrency Theory publication_identifier: isbn: - '9783540407539' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '78' quality_controlled: '1' scopus_import: '1' status: public title: The element of surprise in timed games type: conference user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 2761 year: '2003' ... --- _id: '4468' abstract: - lang: eng text: Giotto is a high-level programming language for time-triggered control applications. The authors begin with a conceptual overview of its methodology, discuss the Giotto helicopter project, and summarize available Giotto implementations. acknowledgement: We thank Niklaus Wirth and Walter Schaufelberger for their advice and support of the reengineering effort of the ETH Zurich helicopter control system using Giotto. This research was supported in part by DARPA SEC grant F33615-C-98–3614, MARCO GSRC grant 98-DT-660, and AFOSR MURI grant F49620–00-1–0327. A preliminary version of this article appeared as [1]. article_processing_charge: No article_type: original author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Christoph full_name: Kirsch, Christoph last_name: Kirsch - first_name: Marco full_name: Sanvido, Marco last_name: Sanvido - first_name: Wolfgang full_name: Pree, Wolfgang last_name: Pree citation: ama: Henzinger TA, Kirsch C, Sanvido M, Pree W. From control models to real-time code using Giotto. IEEE Control Systems Magazine. 2003;23(1):50-64. doi:10.1109/MCS.2003.1172829 apa: Henzinger, T. A., Kirsch, C., Sanvido, M., & Pree, W. (2003). From control models to real-time code using Giotto. IEEE Control Systems Magazine. IEEE. https://doi.org/10.1109/MCS.2003.1172829 chicago: Henzinger, Thomas A, Christoph Kirsch, Marco Sanvido, and Wolfgang Pree. “From Control Models to Real-Time Code Using Giotto.” IEEE Control Systems Magazine. IEEE, 2003. https://doi.org/10.1109/MCS.2003.1172829. ieee: T. A. Henzinger, C. Kirsch, M. Sanvido, and W. Pree, “From control models to real-time code using Giotto,” IEEE Control Systems Magazine, vol. 23, no. 1. IEEE, pp. 50–64, 2003. ista: Henzinger TA, Kirsch C, Sanvido M, Pree W. 2003. From control models to real-time code using Giotto. IEEE Control Systems Magazine. 23(1), 50–64. mla: Henzinger, Thomas A., et al. “From Control Models to Real-Time Code Using Giotto.” IEEE Control Systems Magazine, vol. 23, no. 1, IEEE, 2003, pp. 50–64, doi:10.1109/MCS.2003.1172829. short: T.A. Henzinger, C. Kirsch, M. Sanvido, W. Pree, IEEE Control Systems Magazine 23 (2003) 50–64. date_created: 2018-12-11T12:09:00Z date_published: 2003-01-29T00:00:00Z date_updated: 2024-01-08T10:54:53Z day: '29' doi: 10.1109/MCS.2003.1172829 extern: '1' intvolume: ' 23' issue: '1' language: - iso: eng month: '01' oa_version: None page: 50 - 64 publication: IEEE Control Systems Magazine publication_identifier: issn: - '1066-033X ' publication_status: published publisher: IEEE publist_id: '260' quality_controlled: '1' scopus_import: '1' status: public title: From control models to real-time code using Giotto type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 23 year: '2003' ... --- _id: '4465' abstract: - lang: eng text: Giotto is a principled, tool-supported design methodology for implementing embedded control systems on platforms of possibly distributed sensors, actuators, CPUs, and networks. Giotto is based on the principle that time-triggered task invocations plus time-triggered mode switches can form the abstract essence of programming real-time control systems. Giotto consists of a programming language with a formal semantics, and a retargetable compiler and runtime library. Giotto supports the automation of control system design by strictly separating platform-independent functionality and timing concerns from platform-dependent scheduling and communication issues. The time-triggered predictability of Giotto makes it particularly suitable for safety-critical applications with hard real-time constraints. We illustrate the platform independence and time-triggered execution of Giotto by coordinating a heterogeneous flock of Intel x86 robots and Lego Mindstorms robots. article_processing_charge: No author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Benjamin full_name: Horowitz, Benjamin last_name: Horowitz - first_name: Christoph full_name: Kirsch, Christoph last_name: Kirsch citation: ama: 'Henzinger TA, Horowitz B, Kirsch C. Embedded control systems development with Giotto. In: Software-Enabled Control: Information Technology for Dynamical Systems. Wiley-Blackwell; 2003:123-146. doi:10.1002/047172288X.ch8' apa: 'Henzinger, T. A., Horowitz, B., & Kirsch, C. (2003). Embedded control systems development with Giotto. In Software-Enabled Control: Information Technology for Dynamical Systems (pp. 123–146). Wiley-Blackwell. https://doi.org/10.1002/047172288X.ch8' chicago: 'Henzinger, Thomas A, Benjamin Horowitz, and Christoph Kirsch. “Embedded Control Systems Development with Giotto.” In Software-Enabled Control: Information Technology for Dynamical Systems, 123–46. Wiley-Blackwell, 2003. https://doi.org/10.1002/047172288X.ch8.' ieee: 'T. A. Henzinger, B. Horowitz, and C. Kirsch, “Embedded control systems development with Giotto,” in Software-Enabled Control: Information Technology for Dynamical Systems, Wiley-Blackwell, 2003, pp. 123–146.' ista: 'Henzinger TA, Horowitz B, Kirsch C. 2003.Embedded control systems development with Giotto. In: Software-Enabled Control: Information Technology for Dynamical Systems. , 123–146.' mla: 'Henzinger, Thomas A., et al. “Embedded Control Systems Development with Giotto.” Software-Enabled Control: Information Technology for Dynamical Systems, Wiley-Blackwell, 2003, pp. 123–46, doi:10.1002/047172288X.ch8.' short: 'T.A. Henzinger, B. Horowitz, C. Kirsch, in:, Software-Enabled Control: Information Technology for Dynamical Systems, Wiley-Blackwell, 2003, pp. 123–146.' date_created: 2018-12-11T12:08:59Z date_published: 2003-05-20T00:00:00Z date_updated: 2024-01-08T12:24:01Z day: '20' doi: 10.1002/047172288X.ch8 extern: '1' language: - iso: eng month: '05' oa_version: None page: 123 - 146 publication: 'Software-Enabled Control: Information Technology for Dynamical Systems' publication_identifier: isbn: - '9780471234364 ' publication_status: published publisher: Wiley-Blackwell publist_id: '262' quality_controlled: '1' status: public title: Embedded control systems development with Giotto type: book_chapter user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 year: '2003' ... --- _id: '4466' abstract: - lang: eng text: One source of complexity in the μ-calculus is its ability to specify an unbounded number of switches between universal (AX) and existential (EX) branching modes. We therefore study the problems of satisfiability, validity, model checking, and implication for the universal and existential fragments of the μ-calculus, in which only one branching mode is allowed. The universal fragment is rich enough to express most specifications of interest, and therefore improved algorithms are of practical importance. We show that while the satisfiability and validity problems become indeed simpler for the existential and universal fragments, this is, unfortunately, not the case for model checking and implication. We also show the corresponding results for the alternationfree fragment of the μ-calculus, where no alternations between least and greatest fixed points are allowed. Our results imply that efforts to find a polynomial-time model-checking algorithm for the μ-calculus can be replaced by efforts to find such an algorithm for the universal or existential fragment. acknowledgement: This work was supported in part by NSF grant CCR-9988172, the AFOSR MURI grant F49620-00-1-0327, and a Microsoft Research Fellowship. alternative_title: - LNCS article_processing_charge: No author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Orna full_name: Kupferman, Orna last_name: Kupferman - first_name: Ritankar full_name: Majumdar, Ritankar last_name: Majumdar citation: ama: 'Henzinger TA, Kupferman O, Majumdar R. On the universal and existential fragments of the mu-calculus. In: Proceedings of the 9th International Conference on Tools and Algorithms for the Construction and Analysis of Systems . Vol 2619. Springer; 2003:49-64. doi:10.1007/3-540-36577-X_5' apa: 'Henzinger, T. A., Kupferman, O., & Majumdar, R. (2003). On the universal and existential fragments of the mu-calculus. In Proceedings of the 9th International Conference on Tools and Algorithms for the Construction and Analysis of Systems (Vol. 2619, pp. 49–64). Warsaw, Poland: Springer. https://doi.org/10.1007/3-540-36577-X_5' chicago: Henzinger, Thomas A, Orna Kupferman, and Ritankar Majumdar. “On the Universal and Existential Fragments of the Mu-Calculus.” In Proceedings of the 9th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , 2619:49–64. Springer, 2003. https://doi.org/10.1007/3-540-36577-X_5. ieee: T. A. Henzinger, O. Kupferman, and R. Majumdar, “On the universal and existential fragments of the mu-calculus,” in Proceedings of the 9th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , Warsaw, Poland, 2003, vol. 2619, pp. 49–64. ista: 'Henzinger TA, Kupferman O, Majumdar R. 2003. On the universal and existential fragments of the mu-calculus. Proceedings of the 9th International Conference on Tools and Algorithms for the Construction and Analysis of Systems . TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 2619, 49–64.' mla: Henzinger, Thomas A., et al. “On the Universal and Existential Fragments of the Mu-Calculus.” Proceedings of the 9th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , vol. 2619, Springer, 2003, pp. 49–64, doi:10.1007/3-540-36577-X_5. short: T.A. Henzinger, O. Kupferman, R. Majumdar, in:, Proceedings of the 9th International Conference on Tools and Algorithms for the Construction and Analysis of Systems , Springer, 2003, pp. 49–64. conference: end_date: 2003-04-11 location: Warsaw, Poland name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems' start_date: 2003-04-07 date_created: 2018-12-11T12:08:59Z date_published: 2003-03-14T00:00:00Z date_updated: 2024-01-08T13:17:35Z day: '14' doi: 10.1007/3-540-36577-X_5 extern: '1' intvolume: ' 2619' language: - iso: eng month: '03' oa_version: None page: 49 - 64 publication: 'Proceedings of the 9th International Conference on Tools and Algorithms for the Construction and Analysis of Systems ' publication_identifier: isbn: - '9783540008989' publication_status: published publisher: Springer publist_id: '263' quality_controlled: '1' status: public title: On the universal and existential fragments of the mu-calculus type: conference user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 2619 year: '2003' ... --- _id: '4467' abstract: - lang: eng text: 'BLAST (the Berkeley Lazy Abstraction Software verification Tool) is a verification system for checking safety properties of C programs using automatic property-driven construction and model checking of software abstractions. Blast implements an abstract-model check-refine loop to check for reachability of a specified label in the program. The abstract model is built on the fly using predicate abstraction. This model is then checked for reachability. If there is no (abstract) path to the specified error label, Blast reports that the system is safe and produces a succinct proof. Otherwise, it checks if the path is feasible using symbolic execution of the program. If the path is feasible, Blast outputs the path as an error trace, otherwise, it uses the infeasibility of the path to refine the abstract model. Blast short-circuits the loop from abstraction to verification to refinement, integrating the three steps tightly through “lazy abstraction” [5]. This integration can offer significant advantages in performance by avoiding the repetition of work from one iteration of the loop to the next. ' acknowledgement: This work was supported in part by the NSF grants CCR-0085949 and CCR-9988172, the DARPA PCES grant F33615-00-C-1693, the MARCO GSRC grant 98-DT-660, and a Microsoft Research Fellowship. alternative_title: - LNCS article_processing_charge: No author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Ranjit full_name: Jhala, Ranjit last_name: Jhala - first_name: Ritankar full_name: Majumdar, Ritankar last_name: Majumdar - first_name: Grégoire full_name: Sutre, Grégoire last_name: Sutre citation: ama: 'Henzinger TA, Jhala R, Majumdar R, Sutre G. Software verification with BLAST. In: Proceedings of the 10th International SPIN Workshop . Vol 2648. Springer; 2003:235-239. doi:10.1007/3-540-44829-2_17' apa: 'Henzinger, T. A., Jhala, R., Majumdar, R., & Sutre, G. (2003). Software verification with BLAST. In Proceedings of the 10th International SPIN Workshop (Vol. 2648, pp. 235–239). Portland, OR, USA: Springer. https://doi.org/10.1007/3-540-44829-2_17' chicago: Henzinger, Thomas A, Ranjit Jhala, Ritankar Majumdar, and Grégoire Sutre. “Software Verification with BLAST.” In Proceedings of the 10th International SPIN Workshop , 2648:235–39. Springer, 2003. https://doi.org/10.1007/3-540-44829-2_17. ieee: T. A. Henzinger, R. Jhala, R. Majumdar, and G. Sutre, “Software verification with BLAST,” in Proceedings of the 10th International SPIN Workshop , Portland, OR, USA, 2003, vol. 2648, pp. 235–239. ista: 'Henzinger TA, Jhala R, Majumdar R, Sutre G. 2003. Software verification with BLAST. Proceedings of the 10th International SPIN Workshop . SPIN: Model Checking Software, LNCS, vol. 2648, 235–239.' mla: Henzinger, Thomas A., et al. “Software Verification with BLAST.” Proceedings of the 10th International SPIN Workshop , vol. 2648, Springer, 2003, pp. 235–39, doi:10.1007/3-540-44829-2_17. short: T.A. Henzinger, R. Jhala, R. Majumdar, G. Sutre, in:, Proceedings of the 10th International SPIN Workshop , Springer, 2003, pp. 235–239. conference: end_date: 2003-05-10 location: Portland, OR, USA name: 'SPIN: Model Checking Software' start_date: 2003-05-09 date_created: 2018-12-11T12:09:00Z date_published: 2003-04-28T00:00:00Z date_updated: 2024-01-08T14:05:29Z day: '28' doi: 10.1007/3-540-44829-2_17 extern: '1' intvolume: ' 2648' language: - iso: eng month: '04' oa_version: None page: 235 - 239 publication: 'Proceedings of the 10th International SPIN Workshop ' publication_identifier: isbn: - '9783540401179' publication_status: published publisher: Springer publist_id: '264' quality_controlled: '1' scopus_import: '1' status: public title: Software verification with BLAST type: conference user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 2648 year: '2003' ... --- _id: '4463' abstract: - lang: eng text: We present an algorithm called TAR (“Thread-modular Abstraction Refinement”) for model checking safety properties of concurrent software. The TAR algorithm uses thread-modular assume-guarantee reasoning to overcome the exponential complexity in the control state of multithreaded programs. Thread modularity means that TAR explores the state space of one thread at a time, making assumptions about how the environment can interfere. The TAR algorithm uses counterexample-guided predicate-abstraction refinement to overcome the usually infinite complexity in the data state of C programs. A successive approximation scheme automatically infers the necessary precision on data variables as well as suitable environment assumptions. The scheme is novel in that transition relations are approximated from above, while at the same time environment assumptions are approximated from below. In our software verification tool BLAST we have implemented a fully automatic race checker for multithreaded C programs which is based on the TAR algorithm. This tool has verified a wide variety of commonly used locking idioms, including locking schemes that are not amenable to existing dynamic and static race checkers such as ERASER or WARLOCK. acknowledgement: This work was supported in part by the NSF grants CCR-0085949 and CCR-0234690, the DARPA grant F33615-00-C-1693, and the MARCO grant 98-DT-660. alternative_title: - LNCS article_processing_charge: No author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Ranjit full_name: Jhala, Ranjit last_name: Jhala - first_name: Ritankar full_name: Majumdar, Ritankar last_name: Majumdar - first_name: Shaz full_name: Qadeer, Shaz last_name: Qadeer citation: ama: 'Henzinger TA, Jhala R, Majumdar R, Qadeer S. Thread-modular abstraction refinement. In: Proceedings of the 15th International Conference on Computer Aided Verification. Vol 2725. Springer; 2003:262-274. doi:10.1007/978-3-540-45069-6_27' apa: 'Henzinger, T. A., Jhala, R., Majumdar, R., & Qadeer, S. (2003). Thread-modular abstraction refinement. In Proceedings of the 15th International Conference on Computer Aided Verification (Vol. 2725, pp. 262–274). Boulder, CO, USA: Springer. https://doi.org/10.1007/978-3-540-45069-6_27' chicago: Henzinger, Thomas A, Ranjit Jhala, Ritankar Majumdar, and Shaz Qadeer. “Thread-Modular Abstraction Refinement.” In Proceedings of the 15th International Conference on Computer Aided Verification, 2725:262–74. Springer, 2003. https://doi.org/10.1007/978-3-540-45069-6_27. ieee: T. A. Henzinger, R. Jhala, R. Majumdar, and S. Qadeer, “Thread-modular abstraction refinement,” in Proceedings of the 15th International Conference on Computer Aided Verification, Boulder, CO, USA, 2003, vol. 2725, pp. 262–274. ista: 'Henzinger TA, Jhala R, Majumdar R, Qadeer S. 2003. Thread-modular abstraction refinement. Proceedings of the 15th International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 2725, 262–274.' mla: Henzinger, Thomas A., et al. “Thread-Modular Abstraction Refinement.” Proceedings of the 15th International Conference on Computer Aided Verification, vol. 2725, Springer, 2003, pp. 262–74, doi:10.1007/978-3-540-45069-6_27. short: T.A. Henzinger, R. Jhala, R. Majumdar, S. Qadeer, in:, Proceedings of the 15th International Conference on Computer Aided Verification, Springer, 2003, pp. 262–274. conference: end_date: 2003-07-12 location: Boulder, CO, USA name: 'CAV: Computer Aided Verification' start_date: 2003-07-08 date_created: 2018-12-11T12:08:59Z date_published: 2003-06-27T00:00:00Z date_updated: 2024-01-10T11:05:53Z day: '27' doi: 10.1007/978-3-540-45069-6_27 extern: '1' intvolume: ' 2725' language: - iso: eng month: '06' oa_version: None page: 262 - 274 publication: Proceedings of the 15th International Conference on Computer Aided Verification publication_identifier: isbn: - '9783540405245' publication_status: published publisher: Springer publist_id: '266' quality_controlled: '1' status: public title: Thread-modular abstraction refinement type: conference user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 2725 year: '2003' ... --- _id: '4462' abstract: - lang: eng text: 'A major hurdle in the algorithmic verification and control of systems is the need to find suitable abstract models, which omit enough details to overcome the state-explosion problem, but retain enough details to exhibit satisfaction or controllability with respect to the specification. The paradigm of counterexample-guided abstraction refinement suggests a fully automatic way of finding suitable abstract models: one starts with a coarse abstraction, attempts to verify or control the abstract model, and if this attempt fails and the abstract counterexample does not correspond to a concrete counterexample, then one uses the spurious counterexample to guide the refinement of the abstract model. We present a counterexample-guided refinement algorithm for solving ω-regular control objectives. The main difficulty is that in control, unlike in verification, counterexamples are strategies in a game between system and controller. In the case that the controller has no choices, our scheme subsumes known counterexample-guided refinement algorithms for the verification of ω-regular specifications. Our algorithm is useful in all situations where ω-regular games need to be solved, such as supervisory control, sequential and program synthesis, and modular verification. The algorithm is fully symbolic, and therefore applicable also to infinite-state systems.' acknowledgement: This research was supported in part by the DARPA SEC grant F33615-C-98-3614, the ONR grant N00014-02-1-0671, and the NSF grants CCR-9988172, CCR-0085949, and CCR-0225610. alternative_title: - LNCS article_processing_charge: No author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Ranjit full_name: Jhala, Ranjit last_name: Jhala - first_name: Ritankar full_name: Majumdar, Ritankar last_name: Majumdar citation: ama: 'Henzinger TA, Jhala R, Majumdar R. Counterexample-guided control. In: Proceedings of the 30th International Colloquium on Automata, Languages and Programming. Vol 2719. Springer; 2003:886-902. doi:10.1007/3-540-45061-0_69' apa: 'Henzinger, T. A., Jhala, R., & Majumdar, R. (2003). Counterexample-guided control. In Proceedings of the 30th International Colloquium on Automata, Languages and Programming (Vol. 2719, pp. 886–902). Eindhoven, The Netherlands: Springer. https://doi.org/10.1007/3-540-45061-0_69' chicago: Henzinger, Thomas A, Ranjit Jhala, and Ritankar Majumdar. “Counterexample-Guided Control.” In Proceedings of the 30th International Colloquium on Automata, Languages and Programming, 2719:886–902. Springer, 2003. https://doi.org/10.1007/3-540-45061-0_69. ieee: T. A. Henzinger, R. Jhala, and R. Majumdar, “Counterexample-guided control,” in Proceedings of the 30th International Colloquium on Automata, Languages and Programming, Eindhoven, The Netherlands, 2003, vol. 2719, pp. 886–902. ista: 'Henzinger TA, Jhala R, Majumdar R. 2003. Counterexample-guided control. Proceedings of the 30th International Colloquium on Automata, Languages and Programming. ICALP: Automata, Languages and Programming, LNCS, vol. 2719, 886–902.' mla: Henzinger, Thomas A., et al. “Counterexample-Guided Control.” Proceedings of the 30th International Colloquium on Automata, Languages and Programming, vol. 2719, Springer, 2003, pp. 886–902, doi:10.1007/3-540-45061-0_69. short: T.A. Henzinger, R. Jhala, R. Majumdar, in:, Proceedings of the 30th International Colloquium on Automata, Languages and Programming, Springer, 2003, pp. 886–902. conference: end_date: 2003-07-04 location: Eindhoven, The Netherlands name: 'ICALP: Automata, Languages and Programming' start_date: 2003-06-30 date_created: 2018-12-11T12:08:58Z date_published: 2003-06-25T00:00:00Z date_updated: 2024-01-10T11:19:41Z day: '25' doi: 10.1007/3-540-45061-0_69 extern: '1' intvolume: ' 2719' language: - iso: eng month: '06' oa_version: None page: 886 - 902 publication: Proceedings of the 30th International Colloquium on Automata, Languages and Programming publication_identifier: isbn: - '9783540404934' publication_status: published publisher: Springer publist_id: '265' quality_controlled: '1' scopus_import: '1' status: public title: Counterexample-guided control type: conference user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 2719 year: '2003' ... --- _id: '4464' abstract: - lang: eng text: We introduce the paradigm of schedule-carrying code (SCC). A hard real-time program can be executed on a given platform only if there exists a feasible schedule for the real-time tasks of the program. Traditionally, a scheduler determines the existence of a feasible schedule according to some scheduling strategy. With SCC, a compiler proves the existence of a feasible schedule by generating executable code that is attached to the program and represents its schedule. An SCC executable is a real-time program that carries its schedule as code, which is produced once and can be revalidated and executed with each use. We evaluate SCC both in theory and practice. In theory, we give two scenarios, of nonpreemptive and distributed scheduling for Giotto programs, where the generation of a feasible schedule is hard, while the validation of scheduling instructions that are attached to the programs is easy. In practice, we implement SCC and show that explicit scheduling instructions can reduce the scheduling overhead up to 35% and can provide an efficient, flexible, and verifiable means for compiling Giotto programs on complex architectures, such as the TTA. acknowledgement: This work was supported by the AFOSR MURI grant F49620-00-1-0327, the California MICRO grant 01-037, the DARPA grant F33615-C-98-3614, the MARCO grant 98-DT-660, and the NSF grants CCR-0208875, CCR-0085949, and CCR-0225610. alternative_title: - LNCS article_processing_charge: No author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Christoph full_name: Kirsch, Christoph last_name: Kirsch - first_name: Slobodan full_name: Matic, Slobodan last_name: Matic citation: ama: 'Henzinger TA, Kirsch C, Matic S. Schedule-carrying code. In: Proceedings of the 3rd International Conference on Embedded Software. Vol 2855. ACM; 2003:241-256. doi:10.1007/978-3-540-45212-6_16' apa: 'Henzinger, T. A., Kirsch, C., & Matic, S. (2003). Schedule-carrying code. In Proceedings of the 3rd International Conference on Embedded Software (Vol. 2855, pp. 241–256). Philadelphia, PA, USA: ACM. https://doi.org/10.1007/978-3-540-45212-6_16' chicago: Henzinger, Thomas A, Christoph Kirsch, and Slobodan Matic. “Schedule-Carrying Code.” In Proceedings of the 3rd International Conference on Embedded Software, 2855:241–56. ACM, 2003. https://doi.org/10.1007/978-3-540-45212-6_16. ieee: T. A. Henzinger, C. Kirsch, and S. Matic, “Schedule-carrying code,” in Proceedings of the 3rd International Conference on Embedded Software, Philadelphia, PA, USA, 2003, vol. 2855, pp. 241–256. ista: 'Henzinger TA, Kirsch C, Matic S. 2003. Schedule-carrying code. Proceedings of the 3rd International Conference on Embedded Software. EMSOFT: Embedded Software , LNCS, vol. 2855, 241–256.' mla: Henzinger, Thomas A., et al. “Schedule-Carrying Code.” Proceedings of the 3rd International Conference on Embedded Software, vol. 2855, ACM, 2003, pp. 241–56, doi:10.1007/978-3-540-45212-6_16. short: T.A. Henzinger, C. Kirsch, S. Matic, in:, Proceedings of the 3rd International Conference on Embedded Software, ACM, 2003, pp. 241–256. conference: end_date: 2003-10-15 location: Philadelphia, PA, USA name: 'EMSOFT: Embedded Software ' start_date: 2003-10-13 date_created: 2018-12-11T12:08:59Z date_published: 2003-09-29T00:00:00Z date_updated: 2024-01-10T11:33:57Z day: '29' doi: 10.1007/978-3-540-45212-6_16 extern: '1' intvolume: ' 2855' language: - iso: eng month: '09' oa_version: None page: 241 - 256 publication: Proceedings of the 3rd International Conference on Embedded Software publication_identifier: isbn: - '9783540202233' publication_status: published publisher: ACM publist_id: '267' quality_controlled: '1' scopus_import: '1' status: public title: Schedule-carrying code type: conference user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 2855 year: '2003' ... --- _id: '4460' abstract: - lang: eng text: "Symbolic model checking, which enables the automatic verification of large systems, proceeds by calculating expressions that represent state sets. Traditionally, symbolic model-checking tools are based on back- ward state traversal; their basic operation is the function pre, which, given a set of states, returns the set of all predecessor states. This is because specifiers usually employ formalisms with future-time modalities, which are naturally evaluated by iterating applications of pre. It has been shown experimentally that symbolic model checking can perform significantly better if it is based, instead, on forward state traversal; in this case, the basic operation is the function post, which, given a set of states, returns the set of all successor states. This is because forward state traversal can ensure that only parts of the state space that are reachable from an initial state and relevant for the satisfaction or violation of the specification are explored; that is, errors can be detected as soon as possible.\r\nIn this paper, we investigate which specifications can be checked by symbolic forward state traversal. We formulate the problems of symbolic backward and forward model checking by means of two μ-calculi. The pre-μ calculus is based on the pre operation, and the post-μ calculus is based on the post operation. These two μ-calculi induce query logics, which augment fixpoint expressions with a boolean emptiness query. Using query logics, we are able to relate and compare the symbolic backward and forward approaches. In particular, we prove that all ω-regular (linear-time) specifications can be expressed as post-μ queries, and therefore checked using symbolic forward state traversal. On the other hand, we show that there are simple branching-time specifications that cannot be checked in this way." acknowledgement: This research was supported in part by the SRC contract 99-TJ-683.003 and the NSF grant CCR-9988172. article_processing_charge: No article_type: original author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Orna full_name: Kupferman, Orna last_name: Kupferman - first_name: Shaz full_name: Qadeer, Shaz last_name: Qadeer citation: ama: Henzinger TA, Kupferman O, Qadeer S. From pre-historic to post-modern symbolic model checking. Formal Methods in System Design. 2003;23(3):303-327. doi:10.1023/A:1026228213080 apa: Henzinger, T. A., Kupferman, O., & Qadeer, S. (2003). From pre-historic to post-modern symbolic model checking. Formal Methods in System Design. Springer. https://doi.org/10.1023/A:1026228213080 chicago: Henzinger, Thomas A, Orna Kupferman, and Shaz Qadeer. “From Pre-Historic to Post-Modern Symbolic Model Checking.” Formal Methods in System Design. Springer, 2003. https://doi.org/10.1023/A:1026228213080. ieee: T. A. Henzinger, O. Kupferman, and S. Qadeer, “From pre-historic to post-modern symbolic model checking,” Formal Methods in System Design, vol. 23, no. 3. Springer, pp. 303–327, 2003. ista: Henzinger TA, Kupferman O, Qadeer S. 2003. From pre-historic to post-modern symbolic model checking. Formal Methods in System Design. 23(3), 303–327. mla: Henzinger, Thomas A., et al. “From Pre-Historic to Post-Modern Symbolic Model Checking.” Formal Methods in System Design, vol. 23, no. 3, Springer, 2003, pp. 303–27, doi:10.1023/A:1026228213080. short: T.A. Henzinger, O. Kupferman, S. Qadeer, Formal Methods in System Design 23 (2003) 303–327. date_created: 2018-12-11T12:08:58Z date_published: 2003-06-20T00:00:00Z date_updated: 2024-01-10T11:50:31Z day: '20' doi: 10.1023/A:1026228213080 extern: '1' intvolume: ' 23' issue: '3' language: - iso: eng month: '06' oa_version: None page: 303 - 327 publication: Formal Methods in System Design publication_identifier: issn: - 0925-9856 publication_status: published publisher: Springer publist_id: '268' quality_controlled: '1' scopus_import: '1' status: public title: From pre-historic to post-modern symbolic model checking type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 23 year: '2003' ... --- _id: '4469' abstract: - lang: eng text: Giotto provides an abstract programmer's model for the implementation of embedded control systems with hard real-time constraints. A typical control application consists of periodic software tasks together with a mode-switching logic for enabling and disabling tasks. Giotto specifies time-triggered sensor readings, task invocations, actuator updates, and mode switches independent of any implementation platform. Giotto can be annotated with platform constraints such as task-to-host mappings, and task and communication schedules. The annotations are directives for the Giotto compiler, but they do not alter the functionality and timing of a Giotto program. By separating the platform-independent from the platform-dependent concerns, Giotto enables a great deal of flexibility in choosing control platforms as well as a great deal of automation in the validation and synthesis of control software. The time-triggered nature of Giotto achieves timing predictability, which makes Giotto particularly suitable for safety-critical applications. acknowledgement: The authors would like to thank R. Majumdar for implementing a prototype Giotto compiler for Lego Mindstorms robots. They would like to thank D. Derevyanko and W. Williams for building the Intel x86 robots; and E. Lee and X. Liu for help with implementing Giotto as a “model of computation” in Ptolemy II [26]. Finally, they would also like to thank M. Sanvido for his suggestions on the design of the Giotto drivers; and P. Griffiths for implementing the functionality code of the electronic throttle controller. article_processing_charge: No article_type: original author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Benjamin full_name: Horowitz, Benjamin last_name: Horowitz - first_name: Christoph full_name: Kirsch, Christoph last_name: Kirsch citation: ama: 'Henzinger TA, Horowitz B, Kirsch C. Giotto: A time-triggered language for embedded programming. Proceedings of the IEEE. 2003;91(1):84-99. doi:10.1109/JPROC.2002.805825' apa: 'Henzinger, T. A., Horowitz, B., & Kirsch, C. (2003). Giotto: A time-triggered language for embedded programming. Proceedings of the IEEE. IEEE. https://doi.org/10.1109/JPROC.2002.805825' chicago: 'Henzinger, Thomas A, Benjamin Horowitz, and Christoph Kirsch. “Giotto: A Time-Triggered Language for Embedded Programming.” Proceedings of the IEEE. IEEE, 2003. https://doi.org/10.1109/JPROC.2002.805825.' ieee: 'T. A. Henzinger, B. Horowitz, and C. Kirsch, “Giotto: A time-triggered language for embedded programming,” Proceedings of the IEEE, vol. 91, no. 1. IEEE, pp. 84–99, 2003.' ista: 'Henzinger TA, Horowitz B, Kirsch C. 2003. Giotto: A time-triggered language for embedded programming. Proceedings of the IEEE. 91(1), 84–99.' mla: 'Henzinger, Thomas A., et al. “Giotto: A Time-Triggered Language for Embedded Programming.” Proceedings of the IEEE, vol. 91, no. 1, IEEE, 2003, pp. 84–99, doi:10.1109/JPROC.2002.805825.' short: T.A. Henzinger, B. Horowitz, C. Kirsch, Proceedings of the IEEE 91 (2003) 84–99. date_created: 2018-12-11T12:09:00Z date_published: 2003-01-29T00:00:00Z date_updated: 2024-01-10T11:55:18Z day: '29' doi: 10.1109/JPROC.2002.805825 extern: '1' intvolume: ' 91' issue: '1' language: - iso: eng month: '01' oa_version: None page: 84 - 99 publication: Proceedings of the IEEE publication_identifier: issn: - '0018-9219 ' publication_status: published publisher: IEEE publist_id: '261' quality_controlled: '1' scopus_import: '1' status: public title: 'Giotto: A time-triggered language for embedded programming' type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 91 year: '2003' ... --- _id: '4338' abstract: - lang: eng text: 'Mosaic hybrid zones arise when ecologically differentiated taxa hybridize across a network of habitat patches. Frequent interbreeding across a small-scale patchwork can erode species differences that might have been preserved in a clinal hybrid zone. In particular, the rapid breakdown of neutral divergence sets an upper limit to the time for which differences at marker loci can persist. We present here a case study of a mosaic hybrid zone between the fire-bellied toads Bombina bombina and B. variegata (Anura: Discoglossidae) near Apahida in Romania. In our 20 × 20 km study area, we detected no evidence of a clinal transition but found a strong association between aquatic habitat and mean allele frequencies at four molecular markers. In particular, pure populations of B. bombina in ponds appear to cause massive introgression into the surrounding B. variegata gene pool found in temporary aquatic sites. Nevertheless, the genetic structure of these hybrid populations was remarkably similar to those of a previously studied transect near Pescenica (Croatia), which had both clinal and mosaic features: estimates of heterozygote deficit and linkage disequilibrium in each country are similar. In Apahida, the observed strong linkage disequilibria should stem from an imperfect habitat preference that guides most (but not all) adults into the habitats to which they are adapted. In the absence of a clinal structure, the inferred migration rate between habitats implies that associations between selected loci and neutral markers should break down rapidly. Although plausible selection strengths can maintain differentiation at those loci adapting the toads to either permanent or temporary breeding sites, the divergence at neutral markers must be transient. The hybrid zone may be approaching a state in which the gene pools are homogenized at all but the selected loci, not dissimilar from an early stage of sympatric divergence.' acknowledgement: "We thank G. Mara and T. Galbena for enthusiastic field\r\nassistance, A. Hofmann and R. Sieglstetter for access to their\r\nunpublished data, B. Fo¨rg-Brey and G. Praetzel for help in\r\nthe lab. Helpful comments on a previous version of the man-\r\nuscript were provided by R. Ennos, J. Szymura, F. Balloux,\r\nJ. Bridle, L. Kruuk, F. Bonhomme, M. Arnold, and two anon-\r\nymous reviewers. We also thank A. Pinggera for providing\r\nthe cover illustration. This work was supported by Natural\r\nEnvironment Research Council studentships to THV and TRS\r\nand Deutsche Forschungsgemeinschaft grant Nu 51/2-1 to BN." article_processing_charge: No article_type: original author: - first_name: Timothy full_name: Vines, Timothy last_name: Vines - first_name: S C full_name: Kohler, S C last_name: Kohler - first_name: M full_name: Thiel, M last_name: Thiel - first_name: Ioan full_name: Ghira, Ioan last_name: Ghira - first_name: T R full_name: Sands, T R last_name: Sands - first_name: Catriona full_name: Maccallum, Catriona last_name: Maccallum - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Beate full_name: Nürnberger, Beate last_name: Nürnberger citation: ama: Vines T, Kohler SC, Thiel M, et al. On the maintenance of reproductive isolation in a mosaic hybrid zone between the toads Bombina bombina and B. variegata. Evolution. 2003;57(8):1876-1888. doi:10.1111/j.0014-3820.2003.tb00595.x apa: Vines, T., Kohler, S. C., Thiel, M., Ghira, I., Sands, T. R., Maccallum, C., … Nürnberger, B. (2003). On the maintenance of reproductive isolation in a mosaic hybrid zone between the toads Bombina bombina and B. variegata. Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.0014-3820.2003.tb00595.x chicago: Vines, Timothy, S C Kohler, M Thiel, Ioan Ghira, T R Sands, Catriona Maccallum, Nicholas H Barton, and Beate Nürnberger. “On the Maintenance of Reproductive Isolation in a Mosaic Hybrid Zone between the Toads Bombina Bombina and B. Variegata.” Evolution. Wiley-Blackwell, 2003. https://doi.org/10.1111/j.0014-3820.2003.tb00595.x. ieee: T. Vines et al., “On the maintenance of reproductive isolation in a mosaic hybrid zone between the toads Bombina bombina and B. variegata,” Evolution, vol. 57, no. 8. Wiley-Blackwell, pp. 1876–1888, 2003. ista: Vines T, Kohler SC, Thiel M, Ghira I, Sands TR, Maccallum C, Barton NH, Nürnberger B. 2003. On the maintenance of reproductive isolation in a mosaic hybrid zone between the toads Bombina bombina and B. variegata. Evolution. 57(8), 1876–1888. mla: Vines, Timothy, et al. “On the Maintenance of Reproductive Isolation in a Mosaic Hybrid Zone between the Toads Bombina Bombina and B. Variegata.” Evolution, vol. 57, no. 8, Wiley-Blackwell, 2003, pp. 1876–88, doi:10.1111/j.0014-3820.2003.tb00595.x. short: T. Vines, S.C. Kohler, M. Thiel, I. Ghira, T.R. Sands, C. Maccallum, N.H. Barton, B. Nürnberger, Evolution 57 (2003) 1876–1888. date_created: 2018-12-11T12:08:20Z date_published: 2003-08-01T00:00:00Z date_updated: 2024-01-23T09:16:43Z day: '01' doi: 10.1111/j.0014-3820.2003.tb00595.x extern: '1' intvolume: ' 57' issue: '8' language: - iso: eng month: '08' oa_version: None page: 1876 - 1888 publication: Evolution publication_identifier: issn: - 0014-3820 publication_status: published publisher: Wiley-Blackwell publist_id: '1692' quality_controlled: '1' scopus_import: '1' status: public title: On the maintenance of reproductive isolation in a mosaic hybrid zone between the toads Bombina bombina and B. variegata type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 57 year: '2003' ... --- _id: '4350' abstract: - lang: eng text: 'The phylogeny of Crocodylia offers an unusual twist on the usual molecules versus morphology story. The true gharial (Gavialis gangeticus) and the false gharial (Tomistoma schlegelii), as their common names imply, have appeared in all cladistic morphological analyses as distantly related species, convergent upon a similar morphology. In contrast, all previous molecular studies have shown them to be sister taxa. We present the first phylogenetic study of Crocodylia using a nuclear gene. We cloned and sequenced the c-myc proto-oncogene from Alligator mississippiensis to facilitate primer design and then sequenced an 1,100-base pair fragment that includes both coding and noncoding regions and informative indels for one species in each extant crocodylian genus and six avian outgroups. Phylogenetic analyses using parsimony, maximum likelihood, and Bayesian inference all strongly agreed on the same tree, which is identical to the tree found in previous molecular analyses: Gavialis and Tomistoma are sister taxa and together are the sister group of Crocodylidae. Kishino-Hasegawa tests rejected the morphological tree in favor of the molecular tree. We excluded long-branch attraction and variation in base composition among taxa as explanations for this topology. To explore the causes of discrepancy between molecular and morphological estimates of crocodylian phylogeny, we examined puzzling features of the morphological data using a priori partitions of the data based on anatomical regions and investigated the effects of different coding schemes for two obvious morphological similarities of the two gharials.' acknowledgement: "We thank Lou Densmore and Herb Dessauer for crocodylian tissue\r\nsamples. Dave Swofford, Jim Wilgenbusch, and Kevin de Queiroz gave\r\nus much helpful advice. Dave also allowed us to use an experimental\r\nversion of PAUP∗ with partitioned likelihood, and Jim also provided\r\nprograms to make possible partitioned model KH tests. Chris Brochu\r\nand Lou Densmore sent us preprints of their papers in press, and Chris\r\nprovided an unpublished version of his morphological data set. Allan\r\nBaker, Lou Densmore, and an anonymous reviewer provided useful\r\ncomments on the manuscript. We especially wish to acknowledge Chris\r\nBrochu’s help; although we remain in disagreement on many points,\r\nhis comments on several previous drafts have greatly improved this\r\npaper." article_processing_charge: No article_type: original author: - first_name: John full_name: Harshman, John last_name: Harshman - first_name: Christopher full_name: Huddleston, Christopher last_name: Huddleston - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 - first_name: Thomas full_name: Parsons, Thomas last_name: Parsons - first_name: Michael full_name: Braun, Michael last_name: Braun citation: ama: 'Harshman J, Huddleston C, Bollback JP, Parsons T, Braun M. True and false gharials: A nuclear gene phylogeny of crocodylia. Systematic Biology. 2003;52(3):386-402. doi:10.1080/10635150390197028' apa: 'Harshman, J., Huddleston, C., Bollback, J. P., Parsons, T., & Braun, M. (2003). True and false gharials: A nuclear gene phylogeny of crocodylia. Systematic Biology. Oxford University Press. https://doi.org/10.1080/10635150390197028' chicago: 'Harshman, John, Christopher Huddleston, Jonathan P Bollback, Thomas Parsons, and Michael Braun. “True and False Gharials: A Nuclear Gene Phylogeny of Crocodylia.” Systematic Biology. Oxford University Press, 2003. https://doi.org/10.1080/10635150390197028.' ieee: 'J. Harshman, C. Huddleston, J. P. Bollback, T. Parsons, and M. Braun, “True and false gharials: A nuclear gene phylogeny of crocodylia,” Systematic Biology, vol. 52, no. 3. Oxford University Press, pp. 386–402, 2003.' ista: 'Harshman J, Huddleston C, Bollback JP, Parsons T, Braun M. 2003. True and false gharials: A nuclear gene phylogeny of crocodylia. Systematic Biology. 52(3), 386–402.' mla: 'Harshman, John, et al. “True and False Gharials: A Nuclear Gene Phylogeny of Crocodylia.” Systematic Biology, vol. 52, no. 3, Oxford University Press, 2003, pp. 386–402, doi:10.1080/10635150390197028.' short: J. Harshman, C. Huddleston, J.P. Bollback, T. Parsons, M. Braun, Systematic Biology 52 (2003) 386–402. date_created: 2018-12-11T12:08:24Z date_published: 2003-06-01T00:00:00Z date_updated: 2024-01-23T08:53:58Z day: '01' doi: 10.1080/10635150390197028 extern: '1' external_id: pmid: - ' 12775527' intvolume: ' 52' issue: '3' language: - iso: eng month: '06' oa_version: None page: 386 - 402 pmid: 1 publication: Systematic Biology publication_identifier: issn: - '0039-7989 ' publication_status: published publisher: Oxford University Press publist_id: '1110' quality_controlled: '1' scopus_import: '1' status: public title: 'True and false gharials: A nuclear gene phylogeny of crocodylia' type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 52 year: '2003' ... --- _id: '4348' abstract: - lang: eng text: Many questions in evolutionary biology are best addressed by comparing traits in different species. Often such studies involve mapping characters on phylogenetic trees. Mapping characters on trees allows the nature, number, and timing of the transformations to be identified. The parsimony method is the only method available for mapping morphological characters on phylogenies. Although the parsimony method often makes reasonable reconstructions of the history of a character, it has a number of limitations. These limitations include the inability to consider more than a single change along a branch on a tree and the uncoupling of evolutionary time from amount of character change. We extended a method described by Nielsen (2002, Syst. Biol. 51:729-739) to the mapping of morphological characters under continuous-time Markov models and demonstrate here the utility of the method for mapping characters on trees and for identifying character correlation. acknowledgement: "We thank J. Kohn, D. Stern, and M. Hart for sending the alignments\r\nused in this study. J.P.H. was supported by NSF grants DEB-0075406\r\nand MCB-0075404. R.N. was supported by NSF grant DEB-0089487." article_processing_charge: No article_type: original author: - first_name: John full_name: Huelsenbeck, John last_name: Huelsenbeck - first_name: Rasmus full_name: Nielsen, Rasmus last_name: Nielsen - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: Huelsenbeck J, Nielsen R, Bollback JP. Stochastic mapping of morphological characters. Systematic Biology. 2003;52(2):131-158. doi:10.1080/10635150390192780 apa: Huelsenbeck, J., Nielsen, R., & Bollback, J. P. (2003). Stochastic mapping of morphological characters. Systematic Biology. Oxford University Press. https://doi.org/10.1080/10635150390192780 chicago: Huelsenbeck, John, Rasmus Nielsen, and Jonathan P Bollback. “Stochastic Mapping of Morphological Characters.” Systematic Biology. Oxford University Press, 2003. https://doi.org/10.1080/10635150390192780. ieee: J. Huelsenbeck, R. Nielsen, and J. P. Bollback, “Stochastic mapping of morphological characters,” Systematic Biology, vol. 52, no. 2. Oxford University Press, pp. 131–158, 2003. ista: Huelsenbeck J, Nielsen R, Bollback JP. 2003. Stochastic mapping of morphological characters. Systematic Biology. 52(2), 131–158. mla: Huelsenbeck, John, et al. “Stochastic Mapping of Morphological Characters.” Systematic Biology, vol. 52, no. 2, Oxford University Press, 2003, pp. 131–58, doi:10.1080/10635150390192780. short: J. Huelsenbeck, R. Nielsen, J.P. Bollback, Systematic Biology 52 (2003) 131–158. date_created: 2018-12-11T12:08:24Z date_published: 2003-04-01T00:00:00Z date_updated: 2024-01-23T09:10:59Z day: '01' doi: 10.1080/10635150390192780 extern: '1' external_id: pmid: - '12746144 ' intvolume: ' 52' issue: '2' language: - iso: eng month: '04' oa_version: None page: 131 - 158 pmid: 1 publication: Systematic Biology publication_identifier: issn: - '0039-7989 ' publication_status: published publisher: Oxford University Press publist_id: '1111' quality_controlled: '1' scopus_import: '1' status: public title: Stochastic mapping of morphological characters type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 52 year: '2003' ... --- _id: '4254' abstract: - lang: eng text: Chromosomal rearrangements can promote reproductive isolation by reducing recombination along a large section of the genome. We model the effects of the genetic barrier to gene flow caused by a chromosomal rearrangement on the rate of accumulation of postzygotic isolation genes in parapatry. We find that, if reproductive isolation is produced by the accumulation in parapatry of sets of alleles compatible within but incompatible across species, chromosomal rearrangements are far more likely to favor it than classical genetic barriers without chromosomal changes. New evidence of the role of chromosomal rearrangements in parapatric speciation suggests that postzygotic isolation is often due to the accumulation of such incompatibilities. The model makes testable qualitative predictions about the genetic signature of speciation. acknowledgement: "We thank A. Andrés, C. Bartolomé, J. Bertranpetit, F. Calafell, B. Charlesworth, D. Charlesworth, F. Depaulis, S. Gavrilets, T. Johnson, P. Keightley, M. Kirkpatrik, A. Kondrashov, H. Laayouni, X. Maside, M. Noor, D. Ortiz-Barrientos,\r\nL. Rieseberg, and T. Vines for valuable discussion and criticism. The detailed comments of B. Charlesworth, D. Charlesworth, and F. Depaulis greatly improved the original manuscript. AN is particularly grateful to X. Maside, who was a patient guide through the jungle of speciation. This work was supported by the NERC grant GR3/11635 (United Kingdom). AN is funded by the Ramón y Cajal Program (Spain)." article_processing_charge: No article_type: original author: - first_name: Arcadio full_name: Navarro, Arcadio last_name: Navarro - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Navarro A, Barton NH. Accumulating postzygotic isolation genes in parapatry: a new twist on chromosomal speciation. Evolution; International Journal of Organic Evolution. 2003;57(3):447-459. doi:10.1111/j.0014-3820.2003.tb01537.x' apa: 'Navarro, A., & Barton, N. H. (2003). Accumulating postzygotic isolation genes in parapatry: a new twist on chromosomal speciation. Evolution; International Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.0014-3820.2003.tb01537.x' chicago: 'Navarro, Arcadio, and Nicholas H Barton. “Accumulating Postzygotic Isolation Genes in Parapatry: A New Twist on Chromosomal Speciation.” Evolution; International Journal of Organic Evolution. Wiley-Blackwell, 2003. https://doi.org/10.1111/j.0014-3820.2003.tb01537.x.' ieee: 'A. Navarro and N. H. Barton, “Accumulating postzygotic isolation genes in parapatry: a new twist on chromosomal speciation,” Evolution; International Journal of Organic Evolution, vol. 57, no. 3. Wiley-Blackwell, pp. 447–459, 2003.' ista: 'Navarro A, Barton NH. 2003. Accumulating postzygotic isolation genes in parapatry: a new twist on chromosomal speciation. Evolution; International Journal of Organic Evolution. 57(3), 447–459.' mla: 'Navarro, Arcadio, and Nicholas H. Barton. “Accumulating Postzygotic Isolation Genes in Parapatry: A New Twist on Chromosomal Speciation.” Evolution; International Journal of Organic Evolution, vol. 57, no. 3, Wiley-Blackwell, 2003, pp. 447–59, doi:10.1111/j.0014-3820.2003.tb01537.x.' short: A. Navarro, N.H. Barton, Evolution; International Journal of Organic Evolution 57 (2003) 447–459. date_created: 2018-12-11T12:07:52Z date_published: 2003-03-01T00:00:00Z date_updated: 2024-01-23T10:21:57Z day: '01' doi: 10.1111/j.0014-3820.2003.tb01537.x extern: '1' external_id: pmid: - '12703935 ' intvolume: ' 57' issue: '3' language: - iso: eng month: '03' oa_version: None page: 447 - 459 pmid: 1 publication: Evolution; International Journal of Organic Evolution publication_identifier: issn: - 0014-3820 publication_status: published publisher: Wiley-Blackwell publist_id: '1840' quality_controlled: '1' scopus_import: '1' status: public title: 'Accumulating postzygotic isolation genes in parapatry: a new twist on chromosomal speciation' type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 57 year: '2003' ... --- _id: '4257' abstract: - lang: eng text: Variation within a species may be structured both geographically and by genetic background. We review the effects of such structuring on neutral variants, using a framework based on the coalescent process. Short-term effects of sex differences and age structure can be averaged out using fast timescale approximations, allowing a simple general treatment of effective population size and migration. We consider the effects of geographic structure on variation within and between local populations, first in general terms, and then for specific migration models. We discuss the close parallels between geographic structure and stable types of genetic structure caused by selection, including balancing selection and background selection. The effects of departures from stability, such as selective sweeps and population bottlenecks, are also described. Methods for distinguishing population history from the effects of ongoing gene flow are discussed. We relate the theoretical results to observed patterns of variation in natural populations. article_processing_charge: No article_type: original author: - first_name: Brian full_name: Charlesworth, Brian last_name: Charlesworth - first_name: Deborah full_name: Charlesworth, Deborah last_name: Charlesworth - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Charlesworth B, Charlesworth D, Barton NH. The effects of genetic and geographic structure on neutral variation. Annual Review of Ecology and Systematics. 2003;34:99-125. doi:10.1146/annurev.ecolsys.34.011802.132359 apa: Charlesworth, B., Charlesworth, D., & Barton, N. H. (2003). The effects of genetic and geographic structure on neutral variation. Annual Review of Ecology and Systematics. Annual Reviews. https://doi.org/10.1146/annurev.ecolsys.34.011802.132359 chicago: Charlesworth, Brian, Deborah Charlesworth, and Nicholas H Barton. “The Effects of Genetic and Geographic Structure on Neutral Variation.” Annual Review of Ecology and Systematics. Annual Reviews, 2003. https://doi.org/10.1146/annurev.ecolsys.34.011802.132359. ieee: B. Charlesworth, D. Charlesworth, and N. H. Barton, “The effects of genetic and geographic structure on neutral variation,” Annual Review of Ecology and Systematics, vol. 34. Annual Reviews, pp. 99–125, 2003. ista: Charlesworth B, Charlesworth D, Barton NH. 2003. The effects of genetic and geographic structure on neutral variation. Annual Review of Ecology and Systematics. 34, 99–125. mla: Charlesworth, Brian, et al. “The Effects of Genetic and Geographic Structure on Neutral Variation.” Annual Review of Ecology and Systematics, vol. 34, Annual Reviews, 2003, pp. 99–125, doi:10.1146/annurev.ecolsys.34.011802.132359. short: B. Charlesworth, D. Charlesworth, N.H. Barton, Annual Review of Ecology and Systematics 34 (2003) 99–125. date_created: 2018-12-11T12:07:53Z date_published: 2003-11-01T00:00:00Z date_updated: 2024-01-23T10:15:44Z day: '01' doi: 10.1146/annurev.ecolsys.34.011802.132359 extern: '1' intvolume: ' 34' language: - iso: eng month: '11' oa_version: None page: 99 - 125 publication: Annual Review of Ecology and Systematics publication_identifier: issn: - 1543-592X publication_status: published publisher: Annual Reviews publist_id: '1839' quality_controlled: '1' status: public title: The effects of genetic and geographic structure on neutral variation type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 34 year: '2003' ... --- _id: '4256' abstract: - lang: eng text: Artificial Life models may shed new light on the long-standing challenge for evolutionary biology of explaining the origins of complex organs. Real progress on this issue, however, requires Artificial Life researchers to take seriously the tools and insights from population genetics. article_processing_charge: No article_type: original author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Willem full_name: Zuidema, Willem last_name: Zuidema citation: ama: Barton NH, Zuidema W. The erratic path towards complexity. Current Biology. 2003;13(16):R649-R651. doi:10.1016/S0960-9822(03)00573-6 apa: Barton, N. H., & Zuidema, W. (2003). The erratic path towards complexity. Current Biology. Cell Press. https://doi.org/10.1016/S0960-9822(03)00573-6 chicago: Barton, Nicholas H, and Willem Zuidema. “The Erratic Path towards Complexity.” Current Biology. Cell Press, 2003. https://doi.org/10.1016/S0960-9822(03)00573-6. ieee: N. H. Barton and W. Zuidema, “The erratic path towards complexity,” Current Biology, vol. 13, no. 16. Cell Press, pp. R649–R651, 2003. ista: Barton NH, Zuidema W. 2003. The erratic path towards complexity. Current Biology. 13(16), R649–R651. mla: Barton, Nicholas H., and Willem Zuidema. “The Erratic Path towards Complexity.” Current Biology, vol. 13, no. 16, Cell Press, 2003, pp. R649–51, doi:10.1016/S0960-9822(03)00573-6. short: N.H. Barton, W. Zuidema, Current Biology 13 (2003) R649–R651. date_created: 2018-12-11T12:07:53Z date_published: 2003-08-19T00:00:00Z date_updated: 2024-01-23T09:41:33Z day: '19' doi: 10.1016/S0960-9822(03)00573-6 extern: '1' intvolume: ' 13' issue: '16' language: - iso: eng month: '08' oa_version: Published Version page: R649 - R651 publication: Current Biology publication_identifier: issn: - 0960-9822 publication_status: published publisher: Cell Press publist_id: '1838' quality_controlled: '1' scopus_import: '1' status: public title: The erratic path towards complexity type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 13 year: '2003' ... --- _id: '4255' abstract: - lang: eng text: 'Humans and their closest evolutionary relatives, the chimpanzees, differ in ∼1.24% of their genomic DNA sequences. The fraction of these changes accumulated during the speciation processes that have separated the two lineages may be of special relevance in understanding the basis of their differences. We analyzed human and chimpanzee sequence data to search for the patterns of divergence and polymorphism predicted by a theoretical model of speciation. According to the model, positively selected changes should accumulate in chromosomes that present fixed structural differences, such as inversions, between the two species. Protein evolution was more than 2.2 times faster in chromosomes that had undergone structural rearrangements compared with colinear chromosomes. Also, nucleotide variability is slightly lower in rearranged chromosomes. These patterns of divergence and polymorphism may be, at least in part, the molecular footprint of speciation events in the human and chimpanzee lineages. ' article_processing_charge: No article_type: original author: - first_name: Arcadio full_name: Navarro, Arcadio last_name: Navarro - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Navarro A, Barton NH. Chromosomal speciation and molecular divergence -- Accelerated evolution in rearranged chromosomes. Science. 2003;300(5617):321-324. doi:10.1126/science.1080600 apa: Navarro, A., & Barton, N. H. (2003). Chromosomal speciation and molecular divergence -- Accelerated evolution in rearranged chromosomes. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1080600 chicago: Navarro, Arcadio, and Nicholas H Barton. “Chromosomal Speciation and Molecular Divergence -- Accelerated Evolution in Rearranged Chromosomes.” Science. American Association for the Advancement of Science, 2003. https://doi.org/10.1126/science.1080600 . ieee: A. Navarro and N. H. Barton, “Chromosomal speciation and molecular divergence -- Accelerated evolution in rearranged chromosomes,” Science, vol. 300, no. 5617. American Association for the Advancement of Science, pp. 321–324, 2003. ista: Navarro A, Barton NH. 2003. Chromosomal speciation and molecular divergence -- Accelerated evolution in rearranged chromosomes. Science. 300(5617), 321–324. mla: Navarro, Arcadio, and Nicholas H. Barton. “Chromosomal Speciation and Molecular Divergence -- Accelerated Evolution in Rearranged Chromosomes.” Science, vol. 300, no. 5617, American Association for the Advancement of Science, 2003, pp. 321–24, doi:10.1126/science.1080600 . short: A. Navarro, N.H. Barton, Science 300 (2003) 321–324. date_created: 2018-12-11T12:07:53Z date_published: 2003-04-11T00:00:00Z date_updated: 2024-02-26T13:37:51Z day: '11' doi: '10.1126/science.1080600 ' extern: '1' external_id: pmid: - ' 12690198' intvolume: ' 300' issue: '5617' language: - iso: eng month: '04' oa_version: None page: 321 - 324 pmid: 1 publication: Science publication_identifier: issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science publist_id: '1841' quality_controlled: '1' scopus_import: '1' status: public title: Chromosomal speciation and molecular divergence -- Accelerated evolution in rearranged chromosomes type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 300 year: '2003' ... --- _id: '4146' abstract: - lang: eng text: During vertebrate gastrulation, highly coordinated cellular rearrangements lead to the formation of the three germ layers, ectoderm, mesoderm and endoderm. In zebrafish, silberblick (slb)/wnt11 regulates normal gastrulation movements by activating a signalling pathway similar to the Frizzled-signalling pathway, which establishes epithelial planar cell polarity (PCP) in Drosophila. However, the cellular mechanisms by which slb/wnt11 functions during zebrafish gastrulation are still unclear. Using high-resolution two-photon confocal imaging followed by computer-assisted reconstruction and motion analysis, we have analysed the movement and morphology of individual cells in three dimensions during the course of gastrulation. We show that in slb-mutant embryos, hypoblast cells within the forming germ ring have slower, less directed migratory movements at the onset of gastrulation. These aberrant cell movements are accompanied by defects in the orientation of cellular processes along the individual movement directions of these cells. We conclude that slb/wnt11-mediated orientation of cellular processes plays a role in facilitating and stabilising movements of hypoblast cells in the germ ring, thereby pointing at a novel function of the slb/wnt11 signalling pathway for the regulation of migratory cell movements at early stages of gastrulation. acknowledgement: 'We thank Jennifer Geiger, Mathias Köppen, Christian Dahmann and Marcos Gonzalez-Gaitan for helpful comments on earlier versions of this manuscript,Beate Kilian for technical assistance, Ugur Yalcin, Katrin Anczok and Viktor Schnabel for help with the image analysis, Vinzenz Link for programming Excel Macros and Harald Brush-Janovjak for extensive reviews of the statistics part of this work. We are grateful to Kurt Anderson and Jan Peychl for help with the confocal microscopy. P.J.H., E.V. and D.R.S. are supported by NIH grant HD-18577, The W.M Keck Foundation and the Developmental Studies Hybridoma Bank(DSHB), P.J.H. by The American Cancer Society (grant # PF-01-110-01-CSM),M.L.C. and S.W.W. by the Wellcome Trust, M.T. by an MRC Career Development Award, and F.U. and C.P.H. by an Emmy-Noether-Fellowship from the DFG.' article_processing_charge: No article_type: original author: - first_name: Florian full_name: Ulrich, Florian last_name: Ulrich - first_name: Miguel full_name: Concha, Miguel last_name: Concha - first_name: Paul full_name: Heid, Paul last_name: Heid - first_name: Ed full_name: Voss, Ed last_name: Voss - first_name: Sabine full_name: Witzel, Sabine last_name: Witzel - first_name: Henry full_name: Roehl, Henry last_name: Roehl - first_name: Masazumi full_name: Tada, Masazumi last_name: Tada - first_name: Stephen full_name: Wilson, Stephen last_name: Wilson - first_name: Richard full_name: Adams, Richard last_name: Adams - first_name: David full_name: Soll, David last_name: Soll - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Ulrich F, Concha M, Heid P, et al. Slb/Wnt11 controls hypoblast cell migration and morphogenesis at the onset of zebrafish gastrulation. Development. 2003;130(22):5375-5384. doi:10.1242/dev.00758 apa: Ulrich, F., Concha, M., Heid, P., Voss, E., Witzel, S., Roehl, H., … Heisenberg, C.-P. J. (2003). Slb/Wnt11 controls hypoblast cell migration and morphogenesis at the onset of zebrafish gastrulation. Development. Company of Biologists. https://doi.org/10.1242/dev.00758 chicago: Ulrich, Florian, Miguel Concha, Paul Heid, Ed Voss, Sabine Witzel, Henry Roehl, Masazumi Tada, et al. “Slb/Wnt11 Controls Hypoblast Cell Migration and Morphogenesis at the Onset of Zebrafish Gastrulation.” Development. Company of Biologists, 2003. https://doi.org/10.1242/dev.00758. ieee: F. Ulrich et al., “Slb/Wnt11 controls hypoblast cell migration and morphogenesis at the onset of zebrafish gastrulation,” Development, vol. 130, no. 22. Company of Biologists, pp. 5375–5384, 2003. ista: Ulrich F, Concha M, Heid P, Voss E, Witzel S, Roehl H, Tada M, Wilson S, Adams R, Soll D, Heisenberg C-PJ. 2003. Slb/Wnt11 controls hypoblast cell migration and morphogenesis at the onset of zebrafish gastrulation. Development. 130(22), 5375–5384. mla: Ulrich, Florian, et al. “Slb/Wnt11 Controls Hypoblast Cell Migration and Morphogenesis at the Onset of Zebrafish Gastrulation.” Development, vol. 130, no. 22, Company of Biologists, 2003, pp. 5375–84, doi:10.1242/dev.00758. short: F. Ulrich, M. Concha, P. Heid, E. Voss, S. Witzel, H. Roehl, M. Tada, S. Wilson, R. Adams, D. Soll, C.-P.J. Heisenberg, Development 130 (2003) 5375–5384. date_created: 2018-12-11T12:07:13Z date_published: 2003-11-15T00:00:00Z date_updated: 2024-02-27T10:14:21Z day: '15' doi: 10.1242/dev.00758 extern: '1' external_id: pmid: - ' PMC1414802' intvolume: ' 130' issue: '22' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1414802/ month: '11' oa: 1 oa_version: None page: 5375 - 5384 pmid: 1 publication: Development publication_identifier: issn: - 1011-6370 publication_status: published publisher: Company of Biologists publist_id: '1975' quality_controlled: '1' scopus_import: '1' status: public title: Slb/Wnt11 controls hypoblast cell migration and morphogenesis at the onset of zebrafish gastrulation type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 130 year: '2003' ... --- _id: '4169' abstract: - lang: eng text: 'Background: During vertebrate gastrulation, cell polarization and migration are core components in the cellular rearrangements that lead to the formation of the three germ layers, ectoderm, mesoderm, and endoderm. Previous studies have implicated the Wnt/planar cell polarity (PCP) signaling pathway in controlling cell morphology and movement during gastrulation. However, cell polarization and directed cell migration are reduced but not completely abolished in the absence of Wnt/PCP signals; this observation indicates that other signaling pathways must be involved. Results: We show that Phosphoinositide 3-Kinases (PI3Ks) are required at the onset of zebrafish gastrulation in mesendodermal cells for process formation and cell polarization. Platelet Derived Growth Factor (PDGF) functions upstream of PI3K, while Protein Kinase B (PKB), a downstream effector of PI3K activity, localizes to the leading edge of migrating mesendodermal cells. In the absence of PI3K activity, PKB localization and cell polarization are strongly reduced in mesendodermal cells and are followed by slower but still highly coordinated and directed movements of these cells. Conclusions: We have identified a novel role of a signaling pathway comprised of PDGF, PI3K, and PKB in the control of morphogenetic cell movements during gastrulation. Furthermore, our findings provide insight into the relationship between cell polarization and directed cell migration at the onset of zebrafish gastrulation.' acknowledgement: 'We would like to thank Jennifer Geiger, Juan Hurl& Hannu Mansu-koski, Florian Raible, Marino Zerial, Steve Wilson, and Kurt Anderson for critical reading of earlier versions of this manuscript. We thank Erez Raz, Bart Vanhaesebroeck, and Lukas Roth for sending us the pCS2-PH-GFP-nos, the p1IOCAAX, and the pCS2-actin-GFP constructs, respectively. We are grateful to Marino Zerial and his lab for encouraging us to start this work and providing us with the dnP13K construct and to Florian Ulrich and Franziska Friedrich for help with the confocal microscope and artwork, respectively. We thank Gunter Junghanns and Evelyn Lehmann for excellent fish care. C.-P.H. is supported by an Emmy-Noother-Fellowship from the Deutsche Forschungsgemeinschaft. ' article_processing_charge: No article_type: original author: - first_name: Juan full_name: Montero, Juan last_name: Montero - first_name: Beate full_name: Kilian, Beate last_name: Kilian - first_name: Joanne full_name: Chan, Joanne last_name: Chan - first_name: Peter full_name: Bayliss, Peter last_name: Bayliss - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Montero J, Kilian B, Chan J, Bayliss P, Heisenberg C-PJ. Phosphoinositide 3-kinase is required for process outgrowth and cell polarization of gastrulating mesendodermal cells. Current Biology. 2003;13(15):1279-1289. doi:10.1016/S0960-9822(03)00505-0 apa: Montero, J., Kilian, B., Chan, J., Bayliss, P., & Heisenberg, C.-P. J. (2003). Phosphoinositide 3-kinase is required for process outgrowth and cell polarization of gastrulating mesendodermal cells. Current Biology. Cell Press. https://doi.org/10.1016/S0960-9822(03)00505-0 chicago: Montero, Juan, Beate Kilian, Joanne Chan, Peter Bayliss, and Carl-Philipp J Heisenberg. “Phosphoinositide 3-Kinase Is Required for Process Outgrowth and Cell Polarization of Gastrulating Mesendodermal Cells.” Current Biology. Cell Press, 2003. https://doi.org/10.1016/S0960-9822(03)00505-0. ieee: J. Montero, B. Kilian, J. Chan, P. Bayliss, and C.-P. J. Heisenberg, “Phosphoinositide 3-kinase is required for process outgrowth and cell polarization of gastrulating mesendodermal cells,” Current Biology, vol. 13, no. 15. Cell Press, pp. 1279–1289, 2003. ista: Montero J, Kilian B, Chan J, Bayliss P, Heisenberg C-PJ. 2003. Phosphoinositide 3-kinase is required for process outgrowth and cell polarization of gastrulating mesendodermal cells. Current Biology. 13(15), 1279–1289. mla: Montero, Juan, et al. “Phosphoinositide 3-Kinase Is Required for Process Outgrowth and Cell Polarization of Gastrulating Mesendodermal Cells.” Current Biology, vol. 13, no. 15, Cell Press, 2003, pp. 1279–89, doi:10.1016/S0960-9822(03)00505-0. short: J. Montero, B. Kilian, J. Chan, P. Bayliss, C.-P.J. Heisenberg, Current Biology 13 (2003) 1279–1289. date_created: 2018-12-11T12:07:22Z date_published: 2003-08-05T00:00:00Z date_updated: 2024-02-27T10:03:37Z day: '05' doi: 10.1016/S0960-9822(03)00505-0 extern: '1' external_id: pmid: - ' 12906787' intvolume: ' 13' issue: '15' language: - iso: eng month: '08' oa_version: None page: 1279 - 1289 pmid: 1 publication: Current Biology publication_identifier: eissn: - 1879-0445 issn: - 0960-9822 publication_status: published publisher: Cell Press publist_id: '1950' quality_controlled: '1' scopus_import: '1' status: public title: Phosphoinositide 3-kinase is required for process outgrowth and cell polarization of gastrulating mesendodermal cells type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 13 year: '2003' ... --- _id: '4185' abstract: - lang: eng text: Wnt genes play important roles in regulating patterning and morphogenesis during vertebrate gastrulation. In zebrafish, slb/wnt11 is required for convergence and extension movements, but not cell fate specification during gastrulation. To determine if other Wnt genes functionally interact with slb/wnt11, we analysed the role of ppt/wnt5 during zebrafish gastrulation. ppt/wnt5 is maternally provided and zygotically expressed at all stages during gastrulation. The analysis of ppt mutant embryos reveals that Ppt/Wnt5 regulates cell elongation and convergent extension movements in posterior regions of the gastrula, while its function in more anterior regions is largely redundant to that of Slb/Wnt11. Frizzled-2 functions downstream of ppt/wnt5, indicating that it might act as a receptor for Ppt/Wnt5 in this process. The characterisation of the role of Ppt/Wnt5 provides insight into the functional diversity of Wnt genes in regulating vertebrate gastrulation movements. (C) 2003 Elsevier Science Ireland Ltd. All rights reserved. acknowledgement: We thank Michael Brand, Florian Raible, Gerlinde Reim, Tobias Langenberg, Jennifer Geiger and Kate Poole for helpful comments on earlier versions of this manuscript. We are grateful to Henry Roehl and Christiane Nüsslein Volhard for sending us the ppt mutant stock. M.T. was supported by a Career Development Fellowship from the MRC. B.K., H.M. and C.P.H. are supported by an Emmy Noether-Fellowship from the DFG. article_processing_charge: No article_type: original author: - first_name: Beate full_name: Kilian, Beate last_name: Kilian - first_name: Hannu full_name: Mansukoski, Hannu last_name: Mansukoski - first_name: Filipa full_name: Barbosa, Filipa last_name: Barbosa - first_name: Florian full_name: Ulrich, Florian last_name: Ulrich - first_name: Masazumi full_name: Tada, Masazumi last_name: Tada - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Kilian B, Mansukoski H, Barbosa F, Ulrich F, Tada M, Heisenberg C-PJ. The role of Ppt/Wnt5 in regulating cell shape and movement during zebrafish gastrulation. Mechanisms of Development. 2003;120(4):467-476. doi:10.1016/S0925-4773(03)00004-2 apa: Kilian, B., Mansukoski, H., Barbosa, F., Ulrich, F., Tada, M., & Heisenberg, C.-P. J. (2003). The role of Ppt/Wnt5 in regulating cell shape and movement during zebrafish gastrulation. Mechanisms of Development. Elsevier. https://doi.org/10.1016/S0925-4773(03)00004-2 chicago: Kilian, Beate, Hannu Mansukoski, Filipa Barbosa, Florian Ulrich, Masazumi Tada, and Carl-Philipp J Heisenberg. “The Role of Ppt/Wnt5 in Regulating Cell Shape and Movement during Zebrafish Gastrulation.” Mechanisms of Development. Elsevier, 2003. https://doi.org/10.1016/S0925-4773(03)00004-2. ieee: B. Kilian, H. Mansukoski, F. Barbosa, F. Ulrich, M. Tada, and C.-P. J. Heisenberg, “The role of Ppt/Wnt5 in regulating cell shape and movement during zebrafish gastrulation,” Mechanisms of Development, vol. 120, no. 4. Elsevier, pp. 467–476, 2003. ista: Kilian B, Mansukoski H, Barbosa F, Ulrich F, Tada M, Heisenberg C-PJ. 2003. The role of Ppt/Wnt5 in regulating cell shape and movement during zebrafish gastrulation. Mechanisms of Development. 120(4), 467–476. mla: Kilian, Beate, et al. “The Role of Ppt/Wnt5 in Regulating Cell Shape and Movement during Zebrafish Gastrulation.” Mechanisms of Development, vol. 120, no. 4, Elsevier, 2003, pp. 467–76, doi:10.1016/S0925-4773(03)00004-2. short: B. Kilian, H. Mansukoski, F. Barbosa, F. Ulrich, M. Tada, C.-P.J. Heisenberg, Mechanisms of Development 120 (2003) 467–476. date_created: 2018-12-11T12:07:27Z date_published: 2003-04-01T00:00:00Z date_updated: 2024-02-27T09:46:39Z day: '01' doi: 10.1016/S0925-4773(03)00004-2 extern: '1' external_id: pmid: - '12676324 ' intvolume: ' 120' issue: '4' language: - iso: eng month: '04' oa_version: None page: 467 - 476 pmid: 1 publication: Mechanisms of Development publication_identifier: issn: - 0925-4773 publication_status: published publisher: Elsevier publist_id: '1934' quality_controlled: '1' scopus_import: '1' status: public title: The role of Ppt/Wnt5 in regulating cell shape and movement during zebrafish gastrulation type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 120 year: '2003' ... --- _id: '3992' abstract: - lang: eng text: Computing the volume occupied by individual atoms in macromolecular structures has been the subject of research for several decades. This interest has grown in the recent years, because weighted volumes are widely used in implicit solvent models. Applications of the latter in molecular mechanics simulations require that the derivatives of these weighted volumes be known. In this article, we give a formula for the volume derivative of a molecule modeled as a space-filling diagram made up of balls in motion. The formula is given in terms of the weights, radii, and distances between the centers as well as the sizes of the facets of the power diagram restricted to the space-filling diagram. Special attention is given to the detection and treatment of singularities as well as discontinuities of the derivative. article_processing_charge: No article_type: original author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Patrice full_name: Koehl, Patrice last_name: Koehl citation: ama: Edelsbrunner H, Koehl P. The weighted-volume derivative of a space-filling diagram. PNAS. 2003;100(5):2203-2208. doi:10.1073/pnas.0537830100 apa: Edelsbrunner, H., & Koehl, P. (2003). The weighted-volume derivative of a space-filling diagram. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0537830100 chicago: Edelsbrunner, Herbert, and Patrice Koehl. “The Weighted-Volume Derivative of a Space-Filling Diagram.” PNAS. National Academy of Sciences, 2003. https://doi.org/10.1073/pnas.0537830100. ieee: H. Edelsbrunner and P. Koehl, “The weighted-volume derivative of a space-filling diagram,” PNAS, vol. 100, no. 5. National Academy of Sciences, pp. 2203–2208, 2003. ista: Edelsbrunner H, Koehl P. 2003. The weighted-volume derivative of a space-filling diagram. PNAS. 100(5), 2203–2208. mla: Edelsbrunner, Herbert, and Patrice Koehl. “The Weighted-Volume Derivative of a Space-Filling Diagram.” PNAS, vol. 100, no. 5, National Academy of Sciences, 2003, pp. 2203–08, doi:10.1073/pnas.0537830100. short: H. Edelsbrunner, P. Koehl, PNAS 100 (2003) 2203–2208. date_created: 2018-12-11T12:06:19Z date_published: 2003-03-04T00:00:00Z date_updated: 2024-02-27T12:31:59Z day: '04' doi: 10.1073/pnas.0537830100 extern: '1' external_id: pmid: - '12601153' intvolume: ' 100' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC151318/ month: '03' oa: 1 oa_version: Published Version page: 2203 - 2208 pmid: 1 publication: PNAS publication_identifier: issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences publist_id: '2133' quality_controlled: '1' scopus_import: '1' status: public title: The weighted-volume derivative of a space-filling diagram type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 100 year: '2003' ... --- _id: '3999' abstract: - lang: eng text: We introduce relaxed scheduling as a paradigm for mesh maintenance and demonstrate its applicability to triangulating a skin surface in R-3. acknowledgement: NSF under grant CCR-00- 86013. alternative_title: - LNCS article_processing_charge: No author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Alper full_name: Üngör, Alper last_name: Üngör citation: ama: 'Edelsbrunner H, Üngör A. Relaxed scheduling in dynamic skin triangulation. In: Proceedings of the Japanese Conference on Discrete and Computational Geometry . Vol 2866. Springer; 2003:135-151. doi:10.1007/978-3-540-44400-8_14' apa: 'Edelsbrunner, H., & Üngör, A. (2003). Relaxed scheduling in dynamic skin triangulation. In Proceedings of the Japanese Conference on Discrete and Computational Geometry (Vol. 2866, pp. 135–151). Tokyo, Japan: Springer. https://doi.org/10.1007/978-3-540-44400-8_14' chicago: Edelsbrunner, Herbert, and Alper Üngör. “Relaxed Scheduling in Dynamic Skin Triangulation.” In Proceedings of the Japanese Conference on Discrete and Computational Geometry , 2866:135–51. Springer, 2003. https://doi.org/10.1007/978-3-540-44400-8_14. ieee: H. Edelsbrunner and A. Üngör, “Relaxed scheduling in dynamic skin triangulation,” in Proceedings of the Japanese Conference on Discrete and Computational Geometry , Tokyo, Japan, 2003, vol. 2866, pp. 135–151. ista: 'Edelsbrunner H, Üngör A. 2003. Relaxed scheduling in dynamic skin triangulation. Proceedings of the Japanese Conference on Discrete and Computational Geometry . JCDCG: Japanese Conference on Discrete and Computational Geometry, LNCS, vol. 2866, 135–151.' mla: Edelsbrunner, Herbert, and Alper Üngör. “Relaxed Scheduling in Dynamic Skin Triangulation.” Proceedings of the Japanese Conference on Discrete and Computational Geometry , vol. 2866, Springer, 2003, pp. 135–51, doi:10.1007/978-3-540-44400-8_14. short: H. Edelsbrunner, A. Üngör, in:, Proceedings of the Japanese Conference on Discrete and Computational Geometry , Springer, 2003, pp. 135–151. conference: end_date: 2002-12-09 location: Tokyo, Japan name: 'JCDCG: Japanese Conference on Discrete and Computational Geometry' start_date: 2002-12-06 date_created: 2018-12-11T12:06:21Z date_published: 2003-12-16T00:00:00Z date_updated: 2024-02-27T11:07:15Z day: '16' doi: 10.1007/978-3-540-44400-8_14 extern: '1' intvolume: ' 2866' language: - iso: eng month: '12' oa_version: None page: 135 - 151 publication: 'Proceedings of the Japanese Conference on Discrete and Computational Geometry ' publication_identifier: isbn: - '9783540207764' publication_status: published publisher: Springer publist_id: '2127' quality_controlled: '1' scopus_import: '1' status: public title: Relaxed scheduling in dynamic skin triangulation type: conference user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 2866 year: '2003' ... --- _id: '3997' abstract: - lang: eng text: We combine topological and geometric methods to construct a multi-resolution data structure for functions over two-dimensional domains. Starting with the Morse-Smale complex, we construct a topological hierarchy by progressively canceling critical points in pairs. Concurrently, we create a geometric hierarchy by adapting the geometry to the changes in topology. The data structure supports mesh traversal operations similarly to traditional multi-resolution representations. acknowledgement: This work was performed under the auspices of the U. S. Department of Energy by University of California Lawrence Livermore National Laboratory under contract No. W-7405-Eng-48. H. Edelsbrunner is partially supported by the National Science Foundation (NFS) under grants EIA-99-72879 and CCR-00-86013. B. Hamann is supported by the NSF under contract ACI 9624034, through the LSSDSV program under contract ACI 9982251, and through the NPACI; the National Institute of Mental Health and the NSF under contract NIMH 2 P20 MH60975-06A2; the Lawrence Livermore National Laboratory under ASCI ASAP Level-2 Memorandum Agreement B347878 and under Memorandum Agreement B503159. article_processing_charge: No author: - first_name: Peer full_name: Bremer, Peer last_name: Bremer - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Bernd full_name: Hamann, Bernd last_name: Hamann - first_name: Valerio full_name: Pascucci, Valerio last_name: Pascucci citation: ama: 'Bremer P, Edelsbrunner H, Hamann B, Pascucci V. A multi-resolution data structure for two-dimensional Morse-Smale functions. In: Proceedings of the 14th IEEE Conference on Visualization . IEEE; 2003:139-146. doi:10.1109/VISUAL.2003.1250365' apa: 'Bremer, P., Edelsbrunner, H., Hamann, B., & Pascucci, V. (2003). A multi-resolution data structure for two-dimensional Morse-Smale functions. In Proceedings of the 14th IEEE Conference on Visualization (pp. 139–146). Seattle, WA, USA : IEEE. https://doi.org/10.1109/VISUAL.2003.1250365' chicago: Bremer, Peer, Herbert Edelsbrunner, Bernd Hamann, and Valerio Pascucci. “A Multi-Resolution Data Structure for Two-Dimensional Morse-Smale Functions.” In Proceedings of the 14th IEEE Conference on Visualization , 139–46. IEEE, 2003. https://doi.org/10.1109/VISUAL.2003.1250365. ieee: P. Bremer, H. Edelsbrunner, B. Hamann, and V. Pascucci, “A multi-resolution data structure for two-dimensional Morse-Smale functions,” in Proceedings of the 14th IEEE Conference on Visualization , Seattle, WA, USA , 2003, pp. 139–146. ista: 'Bremer P, Edelsbrunner H, Hamann B, Pascucci V. 2003. A multi-resolution data structure for two-dimensional Morse-Smale functions. Proceedings of the 14th IEEE Conference on Visualization . VIS: IEEE Visualization, 139–146.' mla: Bremer, Peer, et al. “A Multi-Resolution Data Structure for Two-Dimensional Morse-Smale Functions.” Proceedings of the 14th IEEE Conference on Visualization , IEEE, 2003, pp. 139–46, doi:10.1109/VISUAL.2003.1250365. short: P. Bremer, H. Edelsbrunner, B. Hamann, V. Pascucci, in:, Proceedings of the 14th IEEE Conference on Visualization , IEEE, 2003, pp. 139–146. conference: end_date: 2003-10-24 location: 'Seattle, WA, USA ' name: 'VIS: IEEE Visualization' start_date: 2003-10-19 date_created: 2018-12-11T12:06:21Z date_published: 2003-08-01T00:00:00Z date_updated: 2024-02-27T11:12:50Z day: '01' doi: 10.1109/VISUAL.2003.1250365 extern: '1' language: - iso: eng month: '08' oa_version: None page: 139 - 146 publication: 'Proceedings of the 14th IEEE Conference on Visualization ' publication_identifier: isbn: - '0780381203' publication_status: published publisher: IEEE publist_id: '2131' quality_controlled: '1' scopus_import: '1' status: public title: A multi-resolution data structure for two-dimensional Morse-Smale functions type: conference user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 year: '2003' ... --- _id: '4168' abstract: - lang: eng text: Recent studies show that signaling through integrin receptors is required for normal cell movements during Xenopus gastrulation. Integrins function in this process by modulating the activity of cadherin adhesion molecules within tissues undergoing convergence and extension movements. article_processing_charge: No article_type: original author: - first_name: Juan full_name: Montero, Juan last_name: Montero - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Montero J, Heisenberg C-PJ. Adhesive crosstalk in gastrulation. Developmental Cell. 2003;5(2):190-191. doi:10.1016/S1534-5807(03)00235-1 apa: Montero, J., & Heisenberg, C.-P. J. (2003). Adhesive crosstalk in gastrulation. Developmental Cell. Cell Press. https://doi.org/10.1016/S1534-5807(03)00235-1 chicago: Montero, Juan, and Carl-Philipp J Heisenberg. “Adhesive Crosstalk in Gastrulation.” Developmental Cell. Cell Press, 2003. https://doi.org/10.1016/S1534-5807(03)00235-1. ieee: J. Montero and C.-P. J. Heisenberg, “Adhesive crosstalk in gastrulation,” Developmental Cell, vol. 5, no. 2. Cell Press, pp. 190–191, 2003. ista: Montero J, Heisenberg C-PJ. 2003. Adhesive crosstalk in gastrulation. Developmental Cell. 5(2), 190–191. mla: Montero, Juan, and Carl-Philipp J. Heisenberg. “Adhesive Crosstalk in Gastrulation.” Developmental Cell, vol. 5, no. 2, Cell Press, 2003, pp. 190–91, doi:10.1016/S1534-5807(03)00235-1. short: J. Montero, C.-P.J. Heisenberg, Developmental Cell 5 (2003) 190–191. date_created: 2018-12-11T12:07:21Z date_published: 2003-08-01T00:00:00Z date_updated: 2024-02-27T09:54:53Z day: '01' doi: 10.1016/S1534-5807(03)00235-1 extern: '1' external_id: pmid: - '12919669 ' intvolume: ' 5' issue: '2' language: - iso: eng month: '08' oa_version: None page: 190 - 191 pmid: 1 publication: Developmental Cell publication_identifier: eissn: - 1878-1551 issn: - 1534-5807 publication_status: published publisher: Cell Press publist_id: '1949' quality_controlled: '1' scopus_import: '1' status: public title: Adhesive crosstalk in gastrulation type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 5 year: '2003' ... --- _id: '3991' abstract: - lang: eng text: We give analytic inclusion-exclusion formulas for the area and perimeter derivatives of a union of finitely many disks in the plane. acknowledgement: Partially supported by NSF under grant DMS-98-73945 and CCR-00-86013. alternative_title: - LNCS article_processing_charge: No author: - first_name: Ho full_name: Cheng, Ho last_name: Cheng - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: 'Cheng H, Edelsbrunner H. Area and perimeter derivatives of a union of disks. In: Computer Science in Perspective: Essays Dedicated to Thomas Ottmann. Vol 2598. Springer; 2003:88-97. doi:10.1007/3-540-36477-3_7' apa: 'Cheng, H., & Edelsbrunner, H. (2003). Area and perimeter derivatives of a union of disks. In Computer Science in Perspective: Essays Dedicated to Thomas Ottmann (Vol. 2598, pp. 88–97). Springer. https://doi.org/10.1007/3-540-36477-3_7' chicago: 'Cheng, Ho, and Herbert Edelsbrunner. “Area and Perimeter Derivatives of a Union of Disks.” In Computer Science in Perspective: Essays Dedicated to Thomas Ottmann, 2598:88–97. Springer, 2003. https://doi.org/10.1007/3-540-36477-3_7.' ieee: 'H. Cheng and H. Edelsbrunner, “Area and perimeter derivatives of a union of disks,” in Computer Science in Perspective: Essays Dedicated to Thomas Ottmann, vol. 2598, Springer, 2003, pp. 88–97.' ista: 'Cheng H, Edelsbrunner H. 2003.Area and perimeter derivatives of a union of disks. In: Computer Science in Perspective: Essays Dedicated to Thomas Ottmann. LNCS, vol. 2598, 88–97.' mla: 'Cheng, Ho, and Herbert Edelsbrunner. “Area and Perimeter Derivatives of a Union of Disks.” Computer Science in Perspective: Essays Dedicated to Thomas Ottmann, vol. 2598, Springer, 2003, pp. 88–97, doi:10.1007/3-540-36477-3_7.' short: 'H. Cheng, H. Edelsbrunner, in:, Computer Science in Perspective: Essays Dedicated to Thomas Ottmann, Springer, 2003, pp. 88–97.' date_created: 2018-12-11T12:06:18Z date_published: 2003-02-17T00:00:00Z date_updated: 2024-02-27T12:15:02Z day: '17' doi: 10.1007/3-540-36477-3_7 extern: '1' intvolume: ' 2598' language: - iso: eng month: '02' oa_version: None page: 88 - 97 publication: 'Computer Science in Perspective: Essays Dedicated to Thomas Ottmann' publication_identifier: isbn: - '9783540005797' publication_status: published publisher: Springer publist_id: '2132' quality_controlled: '1' scopus_import: '1' status: public title: Area and perimeter derivatives of a union of disks type: book_chapter user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 2598 year: '2003' ...