--- _id: '3574' author: - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: 'Edelsbrunner H. Biological applications of computational topology. In: Handbook of Discrete and Computational Geometry. CRC Press; 2004:1395-1412.' apa: Edelsbrunner, H. (2004). Biological applications of computational topology. In Handbook of Discrete and Computational Geometry (pp. 1395–1412). CRC Press. chicago: Edelsbrunner, Herbert. “Biological Applications of Computational Topology.” In Handbook of Discrete and Computational Geometry, 1395–1412. CRC Press, 2004. ieee: H. Edelsbrunner, “Biological applications of computational topology,” in Handbook of Discrete and Computational Geometry, CRC Press, 2004, pp. 1395–1412. ista: 'Edelsbrunner H. 2004.Biological applications of computational topology. In: Handbook of Discrete and Computational Geometry. , 1395–1412.' mla: Edelsbrunner, Herbert. “Biological Applications of Computational Topology.” Handbook of Discrete and Computational Geometry, CRC Press, 2004, pp. 1395–412. short: H. Edelsbrunner, in:, Handbook of Discrete and Computational Geometry, CRC Press, 2004, pp. 1395–1412. date_created: 2018-12-11T12:04:02Z date_published: 2004-04-15T00:00:00Z date_updated: 2021-01-12T07:44:24Z day: '15' extern: 1 main_file_link: - open_access: '0' url: http://www.cs.duke.edu/~edels/Papers/2004-B-01-BiologicalApplicationsTopology.pdf month: '04' page: 1395 - 1412 publication: Handbook of Discrete and Computational Geometry publication_status: published publisher: CRC Press publist_id: '2811' quality_controlled: 0 status: public title: Biological applications of computational topology type: book_chapter year: '2004' ... --- _id: '3595' abstract: - lang: eng text: Genome sizes vary enormously. This variation in DNA content correlates with effective population size, suggesting that deleterious additions to the genome can accumulate in small populations. On this view, the increased complexity of biological functions associated with large genomes partly reflects evolutionary degeneration. author: - first_name: Brian full_name: Charlesworth, Brian last_name: Charlesworth - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Charlesworth B, Barton NH. Genome size: Does bigger mean worse? Current Biology. 2004;14(6):R233-R235. doi:10.1016/j.cub.2004.02.054' apa: 'Charlesworth, B., & Barton, N. H. (2004). Genome size: Does bigger mean worse? Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2004.02.054' chicago: 'Charlesworth, Brian, and Nicholas H Barton. “Genome Size: Does Bigger Mean Worse?” Current Biology. Cell Press, 2004. https://doi.org/10.1016/j.cub.2004.02.054.' ieee: 'B. Charlesworth and N. H. Barton, “Genome size: Does bigger mean worse?,” Current Biology, vol. 14, no. 6. Cell Press, pp. R233–R235, 2004.' ista: 'Charlesworth B, Barton NH. 2004. Genome size: Does bigger mean worse? Current Biology. 14(6), R233–R235.' mla: 'Charlesworth, Brian, and Nicholas H. Barton. “Genome Size: Does Bigger Mean Worse?” Current Biology, vol. 14, no. 6, Cell Press, 2004, pp. R233–35, doi:10.1016/j.cub.2004.02.054.' short: B. Charlesworth, N.H. Barton, Current Biology 14 (2004) R233–R235. date_created: 2018-12-11T12:04:09Z date_published: 2004-03-01T00:00:00Z date_updated: 2019-04-26T07:22:31Z day: '01' doi: 10.1016/j.cub.2004.02.054 extern: 1 intvolume: ' 14' issue: '6' month: '03' page: R233 - R235 publication: Current Biology publication_status: published publisher: Cell Press publist_id: '2788' quality_controlled: 0 status: public title: 'Genome size: Does bigger mean worse?' type: review volume: 14 year: '2004' ... --- _id: '3614' abstract: - lang: eng text: 'We analyze the changes in the mean and variance components of a quantitative trait caused by changes in allele frequencies, concentrating on the effects of genetic drift. We use a general representation of epistasis and dominance that allows an arbitrary relation between genotype and phenotype for any number of diallelic loci. We assume initial and final Hardy-Weinberg and linkage equilibrium in our analyses of drift-induced changes. Random drift generates transient linkage disequilibria that cause correlations between allele frequency fluctuations at different loci. However, we show that these have negligible effects, at least for interactions among small numbers of loci. Our analyses are based on diffusion approximations that summarize the effects of drift in terms of F, the inbreeding coefficient, interpreted as the expected proportional decrease in heterozygosity at each locus. For haploids, the variance of the trait mean after a population bottleneck is var(Δz̄) =inline imagewhere n is the number of loci contributing to the trait variance, VA(1)=VA is the additive genetic variance, and VA(k) is the kth-order additive epistatic variance. The expected additive genetic variance after the bottleneck, denoted (V*A), is closely related to var(Δz̄); (V*A) (1 –F)inline imageThus, epistasis inflates the expected additive variance above VA(1 –F), the expectation under additivity. For haploids (and diploids without dominance), the expected value of every variance component is inflated by the existence of higher order interactions (e.g., third-order epistasis inflates (V*AA)). This is not true in general with diploidy, because dominance alone can reduce (V*A) below VA(1 –F) (e.g., when dominant alleles are rare). Without dominance, diploidy produces simple expressions: var(Δz̄)=inline image=1 (2F) kVA(k) and (V*A) = (1 –F)inline imagek(2F)k-1VA(k) With dominance (and even without epistasis), var(Δz̄)and (V*A) no longer depend solely on the variance components in the base population. For small F, the expected additive variance simplifies to (V*A)(1 –F) VA+ 4FVAA+2FVD+2FCAD, where CAD is a sum of two terms describing covariances between additive effects and dominance and additive × dominance interactions. Whether population bottlenecks lead to expected increases in additive variance depends primarily on the ratio of nonadditive to additive genetic variance in the base population, but dominance precludes simple predictions based solely on variance components. We illustrate these results using a model in which genotypic values are drawn at random, allowing extreme and erratic epistatic interactions. Although our analyses clarify the conditions under which drift is expected to increase VA, we question the evolutionary importance of such increases.' author: - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Michael full_name: Turelli, Michael last_name: Turelli citation: ama: Barton NH, Turelli M. Effects of allele frequency changes on variance components under a general model of epistasis. Evolution; International Journal of Organic Evolution. 2004;58(10):2111-2132. doi:10.1111/j.0014-3820.2004.tb01591.x apa: Barton, N. H., & Turelli, M. (2004). Effects of allele frequency changes on variance components under a general model of epistasis. Evolution; International Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.0014-3820.2004.tb01591.x chicago: Barton, Nicholas H, and Michael Turelli. “Effects of Allele Frequency Changes on Variance Components under a General Model of Epistasis.” Evolution; International Journal of Organic Evolution. Wiley-Blackwell, 2004. https://doi.org/10.1111/j.0014-3820.2004.tb01591.x. ieee: N. H. Barton and M. Turelli, “Effects of allele frequency changes on variance components under a general model of epistasis,” Evolution; International Journal of Organic Evolution, vol. 58, no. 10. Wiley-Blackwell, pp. 2111–2132, 2004. ista: Barton NH, Turelli M. 2004. Effects of allele frequency changes on variance components under a general model of epistasis. Evolution; International Journal of Organic Evolution. 58(10), 2111–2132. mla: Barton, Nicholas H., and Michael Turelli. “Effects of Allele Frequency Changes on Variance Components under a General Model of Epistasis.” Evolution; International Journal of Organic Evolution, vol. 58, no. 10, Wiley-Blackwell, 2004, pp. 2111–32, doi:10.1111/j.0014-3820.2004.tb01591.x. short: N.H. Barton, M. Turelli, Evolution; International Journal of Organic Evolution 58 (2004) 2111–2132. date_created: 2018-12-11T12:04:15Z date_published: 2004-10-01T00:00:00Z date_updated: 2021-01-12T07:44:40Z day: '01' doi: 10.1111/j.0014-3820.2004.tb01591.x extern: 1 intvolume: ' 58' issue: '10' month: '10' page: 2111 - 2132 publication: Evolution; International Journal of Organic Evolution publication_status: published publisher: Wiley-Blackwell publist_id: '2769' quality_controlled: 0 status: public title: Effects of allele frequency changes on variance components under a general model of epistasis type: journal_article volume: 58 year: '2004' ... --- _id: '3615' abstract: - lang: eng text: 'We investigate three alternative selection-based scenarios proposed to maintain polygenic variation: pleiotropic balancing selection, G x E interactions (with spatial or temporal variation in allelic effects), and sex-dependent allelic effects. Each analysis assumes an additive polygenic trait with n diallelic loci under stabilizing selection. We allow loci to have different effects and consider equilibria at which the population mean departs from the stabilizing-selection optimum. Under weak selection, each model produces essentially identical, approximate allele-frequency dynamics. Variation is maintained under pleiotropic balancing selection only at loci for which the strength of balancing selection exceeds the effective strength of stabilizing selection. In addition, for all models, polymorphism requires that the population mean be close enough to the optimum that directional selection does not overwhelm balancing selection. This balance allows many simultaneously stable equilibria, and we explore their properties numerically. Both spatial and temporal G x E can maintain variation at loci for which the coefficient of variation (across environments) of the effect of a substitution exceeds a critical value greater than one. The critical value depends on the correlation between substitution effects at different loci. For large positive correlations (e.g., ρ2ij > 3/4), even extreme fluctuations in allelic effects cannot maintain variation. Surprisingly, this constraint on correlations implies that sex-dependent allelic effects cannot maintain polygenic variation. We present numerical results that support our analytical approximations and discuss our results in connection to relevant data and alternative variance-maintaining mechanisms.' author: - first_name: Michael full_name: Turelli, Michael last_name: Turelli - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Turelli M, Barton NH. Polygenic variation maintained by balancing selection: pleiotropy, sex-dependent allelic effects and GxE interactions. Genetics. 2004;166(2):1053-1079. doi:10.1534/genetics.166.2.1053' apa: 'Turelli, M., & Barton, N. H. (2004). Polygenic variation maintained by balancing selection: pleiotropy, sex-dependent allelic effects and GxE interactions. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.166.2.1053' chicago: 'Turelli, Michael, and Nicholas H Barton. “Polygenic Variation Maintained by Balancing Selection: Pleiotropy, Sex-Dependent Allelic Effects and GxE Interactions.” Genetics. Genetics Society of America, 2004. https://doi.org/10.1534/genetics.166.2.1053.' ieee: 'M. Turelli and N. H. Barton, “Polygenic variation maintained by balancing selection: pleiotropy, sex-dependent allelic effects and GxE interactions,” Genetics, vol. 166, no. 2. Genetics Society of America, pp. 1053–1079, 2004.' ista: 'Turelli M, Barton NH. 2004. Polygenic variation maintained by balancing selection: pleiotropy, sex-dependent allelic effects and GxE interactions. Genetics. 166(2), 1053–1079.' mla: 'Turelli, Michael, and Nicholas H. Barton. “Polygenic Variation Maintained by Balancing Selection: Pleiotropy, Sex-Dependent Allelic Effects and GxE Interactions.” Genetics, vol. 166, no. 2, Genetics Society of America, 2004, pp. 1053–79, doi:10.1534/genetics.166.2.1053.' short: M. Turelli, N.H. Barton, Genetics 166 (2004) 1053–1079. date_created: 2018-12-11T12:04:15Z date_published: 2004-02-01T00:00:00Z date_updated: 2021-01-12T07:44:41Z day: '01' doi: 10.1534/genetics.166.2.1053 extern: 1 intvolume: ' 166' issue: '2' month: '02' page: 1053 - 1079 publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '2768' quality_controlled: 0 status: public title: 'Polygenic variation maintained by balancing selection: pleiotropy, sex-dependent allelic effects and GxE interactions' type: journal_article volume: 166 year: '2004' ... --- _id: '3807' abstract: - lang: eng text: The time course of Mg(2+) block and unblock of NMDA receptors (NMDARs) determines the extent they are activated by depolarization. Here, we directly measure the rate of NMDAR channel opening in response to depolarizations at different times after brief (1 ms) and sustained (4.6 s) applications of glutamate to nucleated patches from neocortical pyramidal neurons. The kinetics of Mg(2+) unblock were found to be non-instantaneous and complex, consisting of a prominent fast component (time constant approximately 100 micros) and slower components (time constants 4 and approximately 300 ms), the relative amplitudes of which depended on the timing of the depolarizing pulse. Fitting a kinetic model to these data indicated that Mg(2+) not only blocks the NMDAR channel, but reduces both the open probability and affinity for glutamate, while enhancing desensitization. These effects slow the rate of NMDAR channel opening in response to depolarization in a time-dependent manner such that the slower components of Mg(2+) unblock are enhanced during depolarizations at later times after glutamate application. One physiological consequence of this is that brief depolarizations occurring earlier in time after glutamate application are better able to open NMDAR channels. This finding has important implications for spike-timing-dependent synaptic plasticity (STDP), where the precise (millisecond) timing of action potentials relative to synaptic inputs determines the magnitude and sign of changes in synaptic strength. Indeed, we find that STDP timing curves of NMDAR channel activation elicited by realistic dendritic action potential waveforms are narrower than expected assuming instantaneous Mg(2+) unblock, indicating that slow Mg(2+) unblock of NMDAR channels makes the STDP timing window more precise. author: - first_name: Bjorn full_name: Kampa, Bjorn M last_name: Kampa - first_name: John full_name: Clements, John last_name: Clements - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: Greg full_name: Stuart, Greg J last_name: Stuart citation: ama: 'Kampa B, Clements J, Jonas PM, Stuart G. Kinetics of Mg(2+) unblock of NMDA receptors: implications for spike-timing dependent synaptic plasticity. Journal of Physiology. 2004;556(Pt 2):337-345. doi:10.1113/jphysiol.2003.058842 ' apa: 'Kampa, B., Clements, J., Jonas, P. M., & Stuart, G. (2004). Kinetics of Mg(2+) unblock of NMDA receptors: implications for spike-timing dependent synaptic plasticity. Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/jphysiol.2003.058842 ' chicago: 'Kampa, Bjorn, John Clements, Peter M Jonas, and Greg Stuart. “Kinetics of Mg(2+) Unblock of NMDA Receptors: Implications for Spike-Timing Dependent Synaptic Plasticity.” Journal of Physiology. Wiley-Blackwell, 2004. https://doi.org/10.1113/jphysiol.2003.058842 .' ieee: 'B. Kampa, J. Clements, P. M. Jonas, and G. Stuart, “Kinetics of Mg(2+) unblock of NMDA receptors: implications for spike-timing dependent synaptic plasticity,” Journal of Physiology, vol. 556, no. Pt 2. Wiley-Blackwell, pp. 337–45, 2004.' ista: 'Kampa B, Clements J, Jonas PM, Stuart G. 2004. Kinetics of Mg(2+) unblock of NMDA receptors: implications for spike-timing dependent synaptic plasticity. Journal of Physiology. 556(Pt 2), 337–45.' mla: 'Kampa, Bjorn, et al. “Kinetics of Mg(2+) Unblock of NMDA Receptors: Implications for Spike-Timing Dependent Synaptic Plasticity.” Journal of Physiology, vol. 556, no. Pt 2, Wiley-Blackwell, 2004, pp. 337–45, doi:10.1113/jphysiol.2003.058842 .' short: B. Kampa, J. Clements, P.M. Jonas, G. Stuart, Journal of Physiology 556 (2004) 337–45. date_created: 2018-12-11T12:05:17Z date_published: 2004-01-01T00:00:00Z date_updated: 2021-01-12T07:52:20Z day: '01' doi: '10.1113/jphysiol.2003.058842 ' extern: 1 intvolume: ' 556' issue: Pt 2 main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664940/ month: '01' oa: 1 page: 337 - 45 publication: Journal of Physiology publication_status: published publisher: Wiley-Blackwell publist_id: '2403' quality_controlled: 0 status: public title: 'Kinetics of Mg(2+) unblock of NMDA receptors: implications for spike-timing dependent synaptic plasticity' type: journal_article volume: 556 year: '2004' ... --- _id: '3809' abstract: - lang: eng text: Neural stem cells in various regions of the vertebrate brain continuously generate neurons throughout life. In the mammalian hippocampus, a region important for spatial and episodic memory, thousands of new granule cells are produced per day, with the exact number depending on environmental conditions and physical exercise. The survival of these neurons is improved by learning and conversely learning may be promoted by neurogenesis. Although it has been suggested that newly generated neurons may have specific properties to facilitate learning, the cellular and synaptic mechanisms of plasticity in these neurons are largely unknown. Here we show that young granule cells in the adult hippocampus differ substantially from mature granule cells in both active and passive membrane properties. In young neurons, T-type Ca2+ channels can generate isolated Ca2+ spikes and boost fast Na+ action potentials, contributing to the induction of synaptic plasticity. Associative long-term potentiation can be induced more easily in young neurons than in mature neurons under identical conditions. Thus, newly generated neurons express unique mechanisms to facilitate synaptic plasticity, which may be important for the formation of new memories. author: - first_name: Christoph full_name: Schmidt-Hieber, Christoph last_name: Schmidt Hieber - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: Josef full_name: Bischofberger, Josef last_name: Bischofberger citation: ama: Schmidt Hieber C, Jonas PM, Bischofberger J. Enhanced synaptic plasticity in newly generated granule cells of the adult hippocampus. Nature. 2004;429(6988):184-187. doi:10.1038/nature02553 apa: Schmidt Hieber, C., Jonas, P. M., & Bischofberger, J. (2004). Enhanced synaptic plasticity in newly generated granule cells of the adult hippocampus. Nature. Nature Publishing Group. https://doi.org/10.1038/nature02553 chicago: Schmidt Hieber, Christoph, Peter M Jonas, and Josef Bischofberger. “Enhanced Synaptic Plasticity in Newly Generated Granule Cells of the Adult Hippocampus.” Nature. Nature Publishing Group, 2004. https://doi.org/10.1038/nature02553. ieee: C. Schmidt Hieber, P. M. Jonas, and J. Bischofberger, “Enhanced synaptic plasticity in newly generated granule cells of the adult hippocampus,” Nature, vol. 429, no. 6988. Nature Publishing Group, pp. 184–7, 2004. ista: Schmidt Hieber C, Jonas PM, Bischofberger J. 2004. Enhanced synaptic plasticity in newly generated granule cells of the adult hippocampus. Nature. 429(6988), 184–7. mla: Schmidt Hieber, Christoph, et al. “Enhanced Synaptic Plasticity in Newly Generated Granule Cells of the Adult Hippocampus.” Nature, vol. 429, no. 6988, Nature Publishing Group, 2004, pp. 184–87, doi:10.1038/nature02553. short: C. Schmidt Hieber, P.M. Jonas, J. Bischofberger, Nature 429 (2004) 184–7. date_created: 2018-12-11T12:05:17Z date_published: 2004-01-01T00:00:00Z date_updated: 2021-01-12T07:52:21Z day: '01' doi: 10.1038/nature02553 extern: 1 intvolume: ' 429' issue: '6988' month: '01' page: 184 - 7 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '2401' quality_controlled: 0 status: public title: Enhanced synaptic plasticity in newly generated granule cells of the adult hippocampus type: journal_article volume: 429 year: '2004' ... --- _id: '3805' abstract: - lang: eng text: The operation of neuronal networks crucially depends on a fast time course of signaling in inhibitory interneurons. Synapses that excite interneurons generate fast currents, owing to the expression of glutamate receptors of specific subunit composition. Interneurons generate brief action potentials in response to transient synaptic activation and discharge repetitively at very high frequencies during sustained stimulation. The ability to generate short-duration action potentials at high frequencies depends on the expression of specific voltage-gated K+ channels. Factors facilitating fast action potential initiation following synaptic excitation include depolarized interneuron resting potential, subthreshold conductances and active dendrites. Finally, GABA release at interneuron output synapses is rapid and highly synchronized, leading to a faster inhibition in postsynaptic interneurons than in principal cells. Thus, the expression of distinct transmitter receptors and voltage-gated ion channels ensures that interneurons operate with high speed and temporal precision. author: - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: Josef full_name: Bischofberger, Josef last_name: Bischofberger - first_name: Desdemona full_name: Fricker, Desdemona last_name: Fricker - first_name: Richard full_name: Miles, Richard last_name: Miles citation: ama: 'Jonas PM, Bischofberger J, Fricker D, Miles R. Interneuron Diversity series: Fast in, fast out--temporal and spatial signal processing in hippocampal interneurons. Trends in Neurosciences. 2004;27(1):30-40. doi:doi:10.1016/j.tins.2003.10.010' apa: 'Jonas, P. M., Bischofberger, J., Fricker, D., & Miles, R. (2004). Interneuron Diversity series: Fast in, fast out--temporal and spatial signal processing in hippocampal interneurons. Trends in Neurosciences. Elsevier. https://doi.org/doi:10.1016/j.tins.2003.10.010' chicago: 'Jonas, Peter M, Josef Bischofberger, Desdemona Fricker, and Richard Miles. “Interneuron Diversity Series: Fast in, Fast out--Temporal and Spatial Signal Processing in Hippocampal Interneurons.” Trends in Neurosciences. Elsevier, 2004. https://doi.org/doi:10.1016/j.tins.2003.10.010.' ieee: 'P. M. Jonas, J. Bischofberger, D. Fricker, and R. Miles, “Interneuron Diversity series: Fast in, fast out--temporal and spatial signal processing in hippocampal interneurons,” Trends in Neurosciences, vol. 27, no. 1. Elsevier, pp. 30–40, 2004.' ista: 'Jonas PM, Bischofberger J, Fricker D, Miles R. 2004. Interneuron Diversity series: Fast in, fast out--temporal and spatial signal processing in hippocampal interneurons. Trends in Neurosciences. 27(1), 30–40.' mla: 'Jonas, Peter M., et al. “Interneuron Diversity Series: Fast in, Fast out--Temporal and Spatial Signal Processing in Hippocampal Interneurons.” Trends in Neurosciences, vol. 27, no. 1, Elsevier, 2004, pp. 30–40, doi:doi:10.1016/j.tins.2003.10.010.' short: P.M. Jonas, J. Bischofberger, D. Fricker, R. Miles, Trends in Neurosciences 27 (2004) 30–40. date_created: 2018-12-11T12:05:16Z date_published: 2004-01-01T00:00:00Z date_updated: 2021-01-12T07:52:19Z day: '01' doi: doi:10.1016/j.tins.2003.10.010 extern: 1 intvolume: ' 27' issue: '1' month: '01' page: 30 - 40 publication: Trends in Neurosciences publication_status: published publisher: Elsevier publist_id: '2404' quality_controlled: 0 status: public title: 'Interneuron Diversity series: Fast in, fast out--temporal and spatial signal processing in hippocampal interneurons' type: journal_article volume: 27 year: '2004' ... --- _id: '3918' abstract: - lang: eng text: Wingless (ergatoid) males of the tramp ant Cardiocondyla minutior attack and kill their young ergatoid rivals and thus attempt to monopolize mating with female sexuals reared in the colony. Because of the different strength of local mate competition in colonies with one or several reproductive queens, we expected the production of new ergatoid males to vary with queen number. Sex ratios were mostly female-biased, but in contrast to the sympatric species C. obscurior (Cremer and Heinze, 2002) neither the percentage of ergatoid males nor of female sexuals among the first 20 sexuals produced varied considerably with queen number. As in C. obscurior, experimental colony fragmentation led to the production of winged males, whereas in unfragmented control colonies only ergatoid males eclosed. author: - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze - first_name: A. full_name: Böttcher, A. last_name: Böttcher - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Heinze J, Böttcher A, Cremer S. Production of winged and wingless males in the ant, Cardiocondyla minutior. Insectes Sociaux. 2004;51(3):275-278. doi:10.1007/s00040-004-0740-6 apa: Heinze, J., Böttcher, A., & Cremer, S. (2004). Production of winged and wingless males in the ant, Cardiocondyla minutior. Insectes Sociaux. Springer. https://doi.org/10.1007/s00040-004-0740-6 chicago: Heinze, Jürgen, A. Böttcher, and Sylvia Cremer. “Production of Winged and Wingless Males in the Ant, Cardiocondyla Minutior.” Insectes Sociaux. Springer, 2004. https://doi.org/10.1007/s00040-004-0740-6. ieee: J. Heinze, A. Böttcher, and S. Cremer, “Production of winged and wingless males in the ant, Cardiocondyla minutior,” Insectes Sociaux, vol. 51, no. 3. Springer, pp. 275–278, 2004. ista: Heinze J, Böttcher A, Cremer S. 2004. Production of winged and wingless males in the ant, Cardiocondyla minutior. Insectes Sociaux. 51(3), 275–278. mla: Heinze, Jürgen, et al. “Production of Winged and Wingless Males in the Ant, Cardiocondyla Minutior.” Insectes Sociaux, vol. 51, no. 3, Springer, 2004, pp. 275–78, doi:10.1007/s00040-004-0740-6. short: J. Heinze, A. Böttcher, S. Cremer, Insectes Sociaux 51 (2004) 275–278. date_created: 2018-12-11T12:05:53Z date_published: 2004-08-19T00:00:00Z date_updated: 2021-01-12T07:53:11Z day: '19' doi: 10.1007/s00040-004-0740-6 extern: '1' intvolume: ' 51' issue: '3' language: - iso: eng month: '08' oa_version: None page: 275 - 278 publication: Insectes Sociaux publication_status: published publisher: Springer publist_id: '2236' status: public title: Production of winged and wingless males in the ant, Cardiocondyla minutior type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 51 year: '2004' ... --- _id: '3988' abstract: - lang: eng text: We give an algorithm that locally improves the fit between two proteins modeled as space-filling diagrams. The algorithm defines the fit in purely geometric terms and improves by applying a rigid motion to one of the two proteins. Our implementation of the algorithm takes between three and ten seconds and converges with high likelihood to the correct docked configuration, provided it starts at a position away from the correct one by at most 18 degrees of rotation and at most 3.0Angstrom of translation. The speed and convergence radius make this an attractive algorithm to use in combination with a coarse sampling of the six-dimensional space of rigid motions. acknowledgement: Supported by NSF under grant CCR-00-86013, BGT Postdoc Program from Duke University and NIH under grant R01 GM61822-01. alternative_title: - LNCS author: - first_name: Vicky full_name: Choi, Vicky last_name: Choi - first_name: Pankaj full_name: Agarwal, Pankaj K last_name: Agarwal - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Johannes full_name: Rudolph, Johannes last_name: Rudolph citation: ama: 'Choi V, Agarwal P, Edelsbrunner H, Rudolph J. Local search heuristic for rigid protein docking. In: Vol 3240. Springer; 2004:218-229. doi:10.1007/978-3-540-30219-3_19' apa: 'Choi, V., Agarwal, P., Edelsbrunner, H., & Rudolph, J. (2004). Local search heuristic for rigid protein docking (Vol. 3240, pp. 218–229). Presented at the WABI: 4th International Workshop on Algorithms in Bioinformatics, Springer. https://doi.org/10.1007/978-3-540-30219-3_19' chicago: Choi, Vicky, Pankaj Agarwal, Herbert Edelsbrunner, and Johannes Rudolph. “Local Search Heuristic for Rigid Protein Docking,” 3240:218–29. Springer, 2004. https://doi.org/10.1007/978-3-540-30219-3_19. ieee: 'V. Choi, P. Agarwal, H. Edelsbrunner, and J. Rudolph, “Local search heuristic for rigid protein docking,” presented at the WABI: 4th International Workshop on Algorithms in Bioinformatics, 2004, vol. 3240, pp. 218–229.' ista: 'Choi V, Agarwal P, Edelsbrunner H, Rudolph J. 2004. Local search heuristic for rigid protein docking. WABI: 4th International Workshop on Algorithms in Bioinformatics, LNCS, vol. 3240, 218–229.' mla: Choi, Vicky, et al. Local Search Heuristic for Rigid Protein Docking. Vol. 3240, Springer, 2004, pp. 218–29, doi:10.1007/978-3-540-30219-3_19. short: V. Choi, P. Agarwal, H. Edelsbrunner, J. Rudolph, in:, Springer, 2004, pp. 218–229. conference: name: 'WABI: 4th International Workshop on Algorithms in Bioinformatics' date_created: 2018-12-11T12:06:17Z date_published: 2004-01-01T00:00:00Z date_updated: 2021-01-12T07:53:41Z day: '01' doi: 10.1007/978-3-540-30219-3_19 extern: 1 intvolume: ' 3240' month: '01' page: 218 - 229 publication_status: published publisher: Springer publist_id: '2136' quality_controlled: 0 status: public title: Local search heuristic for rigid protein docking type: conference volume: 3240 year: '2004' ... --- _id: '3986' abstract: - lang: eng text: The motion of a biomolecule greatly depends on the engulfing solution, which is mostly water. Instead of representing individual water molecules, it is desirable to develop implicit solvent models that nevertheless accurately represent the contribution of the solvent interaction to the motion. In such models, hydrophobicity is expressed as a weighted sum of atomic surface areas. The derivatives of these weighted areas contribute to the force that drives the motion. In this paper we give formulas for the weighted and unweighted area derivatives of a molecule modeled as a space-filling diagram made up of balls in motion. Other than the radii and the centers of the balls, the formulas are given in terms of the sizes of circular arcs of the boundary and edges of the power diagram. We also give inclusion-exclusion formulas for these sizes. acknowledgement: Partially supported by NSF under grant CCR-00-86013 and NSF under grant CCR-97-12088. author: - first_name: Robert full_name: Bryant, Robert last_name: Bryant - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Patrice full_name: Koehl, Patrice last_name: Koehl - first_name: Michael full_name: Levitt, Michael last_name: Levitt citation: ama: Bryant R, Edelsbrunner H, Koehl P, Levitt M. The area derivative of a space-filling diagram. Discrete & Computational Geometry. 2004;32(3):293-308. doi:10.1007/s00454-004-1099-1 apa: Bryant, R., Edelsbrunner, H., Koehl, P., & Levitt, M. (2004). The area derivative of a space-filling diagram. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-004-1099-1 chicago: Bryant, Robert, Herbert Edelsbrunner, Patrice Koehl, and Michael Levitt. “The Area Derivative of a Space-Filling Diagram.” Discrete & Computational Geometry. Springer, 2004. https://doi.org/10.1007/s00454-004-1099-1. ieee: R. Bryant, H. Edelsbrunner, P. Koehl, and M. Levitt, “The area derivative of a space-filling diagram,” Discrete & Computational Geometry, vol. 32, no. 3. Springer, pp. 293–308, 2004. ista: Bryant R, Edelsbrunner H, Koehl P, Levitt M. 2004. The area derivative of a space-filling diagram. Discrete & Computational Geometry. 32(3), 293–308. mla: Bryant, Robert, et al. “The Area Derivative of a Space-Filling Diagram.” Discrete & Computational Geometry, vol. 32, no. 3, Springer, 2004, pp. 293–308, doi:10.1007/s00454-004-1099-1. short: R. Bryant, H. Edelsbrunner, P. Koehl, M. Levitt, Discrete & Computational Geometry 32 (2004) 293–308. date_created: 2018-12-11T12:06:17Z date_published: 2004-09-01T00:00:00Z date_updated: 2021-01-12T07:53:40Z day: '01' doi: 10.1007/s00454-004-1099-1 extern: 1 intvolume: ' 32' issue: '3' month: '09' page: 293 - 308 publication: Discrete & Computational Geometry publication_status: published publisher: Springer publist_id: '2141' quality_controlled: 0 status: public title: The area derivative of a space-filling diagram type: journal_article volume: 32 year: '2004' ... --- _id: '3984' abstract: - lang: eng text: We combine topological and geometric methods to construct a multiresolution representation for a function over a two-dimensional domain. In a preprocessing stage, we create the Morse-Smale complex of the function and progressively simplify its topology by cancelling pairs of critical points. Based on a simple notion of dependency among these cancellations, we construct a hierarchical data structure supporting traversal and reconstruction operations similarly to traditional geometry-based representations. We use this data structure to extract topologically valid approximations that satisfy error bounds provided at runtime. author: - first_name: Peer full_name: Bremer, Peer-Timo last_name: Bremer - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Bernd full_name: Hamann, Bernd last_name: Hamann - first_name: Valerio full_name: Pascucci, Valerio last_name: Pascucci citation: ama: Bremer P, Edelsbrunner H, Hamann B, Pascucci V. A topological hierarchy for functions on triangulated surfaces. IEEE Transactions on Visualization and Computer Graphics. 2004;10(4):385-396. doi:10.1109/TVCG.2004.3 apa: Bremer, P., Edelsbrunner, H., Hamann, B., & Pascucci, V. (2004). A topological hierarchy for functions on triangulated surfaces. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2004.3 chicago: Bremer, Peer, Herbert Edelsbrunner, Bernd Hamann, and Valerio Pascucci. “A Topological Hierarchy for Functions on Triangulated Surfaces.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2004. https://doi.org/10.1109/TVCG.2004.3. ieee: P. Bremer, H. Edelsbrunner, B. Hamann, and V. Pascucci, “A topological hierarchy for functions on triangulated surfaces,” IEEE Transactions on Visualization and Computer Graphics, vol. 10, no. 4. IEEE, pp. 385–396, 2004. ista: Bremer P, Edelsbrunner H, Hamann B, Pascucci V. 2004. A topological hierarchy for functions on triangulated surfaces. IEEE Transactions on Visualization and Computer Graphics. 10(4), 385–396. mla: Bremer, Peer, et al. “A Topological Hierarchy for Functions on Triangulated Surfaces.” IEEE Transactions on Visualization and Computer Graphics, vol. 10, no. 4, IEEE, 2004, pp. 385–96, doi:10.1109/TVCG.2004.3. short: P. Bremer, H. Edelsbrunner, B. Hamann, V. Pascucci, IEEE Transactions on Visualization and Computer Graphics 10 (2004) 385–396. date_created: 2018-12-11T12:06:16Z date_published: 2004-07-01T00:00:00Z date_updated: 2021-01-12T07:53:39Z day: '01' doi: 10.1109/TVCG.2004.3 extern: 1 intvolume: ' 10' issue: '4' month: '07' page: 385 - 396 publication: IEEE Transactions on Visualization and Computer Graphics publication_status: published publisher: IEEE publist_id: '2139' quality_controlled: 0 status: public title: A topological hierarchy for functions on triangulated surfaces type: journal_article volume: 10 year: '2004' ... --- _id: '3987' abstract: - lang: eng text: 'We consider scientific data sets that describe density functions over three-dimensional geometric domains. Such data sets are often large and coarsened representations are needed for visualization and analysis. Assuming a tetrahedral mesh representation, we construct such representations with a simplification algorithm that combines three goals: the approximation of the function, the preservation of the mesh topology, and the improvement of the mesh quality. The third goal is achieved with a novel extension of the well-known quadric error metric. We perform a number of computational experiments to understand the effect of mesh quality improvement on the density map approximation. In addition, we study the effect of geometric simplification on the topological features of the function by monitoring its critical points.' author: - first_name: Vijay full_name: Natarajan, Vijay last_name: Natarajan - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: Natarajan V, Edelsbrunner H. Simplification of three-dimensional density maps. IEEE Transactions on Visualization and Computer Graphics. 2004;10(5):587-597. doi:10.1109/TVCG.2004.32 apa: Natarajan, V., & Edelsbrunner, H. (2004). Simplification of three-dimensional density maps. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2004.32 chicago: Natarajan, Vijay, and Herbert Edelsbrunner. “Simplification of Three-Dimensional Density Maps.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2004. https://doi.org/10.1109/TVCG.2004.32. ieee: V. Natarajan and H. Edelsbrunner, “Simplification of three-dimensional density maps,” IEEE Transactions on Visualization and Computer Graphics, vol. 10, no. 5. IEEE, pp. 587–597, 2004. ista: Natarajan V, Edelsbrunner H. 2004. Simplification of three-dimensional density maps. IEEE Transactions on Visualization and Computer Graphics. 10(5), 587–597. mla: Natarajan, Vijay, and Herbert Edelsbrunner. “Simplification of Three-Dimensional Density Maps.” IEEE Transactions on Visualization and Computer Graphics, vol. 10, no. 5, IEEE, 2004, pp. 587–97, doi:10.1109/TVCG.2004.32. short: V. Natarajan, H. Edelsbrunner, IEEE Transactions on Visualization and Computer Graphics 10 (2004) 587–597. date_created: 2018-12-11T12:06:17Z date_published: 2004-07-12T00:00:00Z date_updated: 2021-01-12T07:53:40Z day: '12' doi: 10.1109/TVCG.2004.32 extern: 1 intvolume: ' 10' issue: '5' month: '07' page: 587 - 597 publication: IEEE Transactions on Visualization and Computer Graphics publication_status: published publisher: IEEE publist_id: '2142' quality_controlled: 0 status: public title: Simplification of three-dimensional density maps type: journal_article volume: 10 year: '2004' ... --- _id: '3985' abstract: - lang: eng text: Given a Morse function f over a 2-manifold with or without boundary, the Reeb graph is obtained by contracting the connected components of the level sets to points. We prove tight upper and lower bounds on the number of loops in the Reeb graph that depend on the genus, the number of boundary components, and whether or not the 2-manifold is orientable. We also give an algorithm that constructs the Reeb graph in time O(n log n), where n is the number of edges in the triangulation used to represent the 2-manifold and the Morse function. acknowledgement: Partially supported by NSF under Grants EIA-99-72879 and CCR-00-86013. author: - first_name: Kree full_name: Cole-McLaughlin, Kree last_name: Cole Mclaughlin - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: John full_name: Harer, John last_name: Harer - first_name: Vijay full_name: Natarajan, Vijay last_name: Natarajan - first_name: Valerio full_name: Pascucci, Valerio last_name: Pascucci citation: ama: Cole Mclaughlin K, Edelsbrunner H, Harer J, Natarajan V, Pascucci V. Loops in Reeb graphs of 2-manifolds. Discrete & Computational Geometry. 2004;32(2):231-244. doi:10.1007/s00454-004-1122-6 apa: Cole Mclaughlin, K., Edelsbrunner, H., Harer, J., Natarajan, V., & Pascucci, V. (2004). Loops in Reeb graphs of 2-manifolds. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-004-1122-6 chicago: Cole Mclaughlin, Kree, Herbert Edelsbrunner, John Harer, Vijay Natarajan, and Valerio Pascucci. “Loops in Reeb Graphs of 2-Manifolds.” Discrete & Computational Geometry. Springer, 2004. https://doi.org/10.1007/s00454-004-1122-6. ieee: K. Cole Mclaughlin, H. Edelsbrunner, J. Harer, V. Natarajan, and V. Pascucci, “Loops in Reeb graphs of 2-manifolds,” Discrete & Computational Geometry, vol. 32, no. 2. Springer, pp. 231–244, 2004. ista: Cole Mclaughlin K, Edelsbrunner H, Harer J, Natarajan V, Pascucci V. 2004. Loops in Reeb graphs of 2-manifolds. Discrete & Computational Geometry. 32(2), 231–244. mla: Cole Mclaughlin, Kree, et al. “Loops in Reeb Graphs of 2-Manifolds.” Discrete & Computational Geometry, vol. 32, no. 2, Springer, 2004, pp. 231–44, doi:10.1007/s00454-004-1122-6. short: K. Cole Mclaughlin, H. Edelsbrunner, J. Harer, V. Natarajan, V. Pascucci, Discrete & Computational Geometry 32 (2004) 231–244. date_created: 2018-12-11T12:06:16Z date_published: 2004-07-01T00:00:00Z date_updated: 2021-01-12T07:53:39Z day: '01' doi: 10.1007/s00454-004-1122-6 extern: 1 intvolume: ' 32' issue: '2' month: '07' page: 231 - 244 publication: Discrete & Computational Geometry publication_status: published publisher: Springer publist_id: '2140' quality_controlled: 0 status: public title: Loops in Reeb graphs of 2-manifolds type: journal_article volume: 32 year: '2004' ... --- _id: '3989' abstract: - lang: eng text: We introduce local and global comparison measures for a collection of k less than or equal to d real-valued smooth functions on a common d-dimensional Riemannian manifold. For k = d = 2 we relate the measures to the set of critical points of one function restricted to the level sets of the other. The definition of the measures extends to piecewise linear functions for which they ace easy to compute. The computation of the measures forms the centerpiece of a software tool which we use to study scientific datasets. author: - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: John full_name: Harer, John last_name: Harer - first_name: Vijay full_name: Natarajan, Vijay last_name: Natarajan - first_name: Valerio full_name: Pascucci, Valerio last_name: Pascucci citation: ama: 'Edelsbrunner H, Harer J, Natarajan V, Pascucci V. Local and global comparison of continuous functions. In: IEEE; 2004:275-280. doi:10.1109/VISUAL.2004.68' apa: 'Edelsbrunner, H., Harer, J., Natarajan, V., & Pascucci, V. (2004). Local and global comparison of continuous functions (pp. 275–280). Presented at the VIS: IEEE Visualization, IEEE. https://doi.org/10.1109/VISUAL.2004.68' chicago: Edelsbrunner, Herbert, John Harer, Vijay Natarajan, and Valerio Pascucci. “Local and Global Comparison of Continuous Functions,” 275–80. IEEE, 2004. https://doi.org/10.1109/VISUAL.2004.68. ieee: 'H. Edelsbrunner, J. Harer, V. Natarajan, and V. Pascucci, “Local and global comparison of continuous functions,” presented at the VIS: IEEE Visualization, 2004, pp. 275–280.' ista: 'Edelsbrunner H, Harer J, Natarajan V, Pascucci V. 2004. Local and global comparison of continuous functions. VIS: IEEE Visualization, 275–280.' mla: Edelsbrunner, Herbert, et al. Local and Global Comparison of Continuous Functions. IEEE, 2004, pp. 275–80, doi:10.1109/VISUAL.2004.68. short: H. Edelsbrunner, J. Harer, V. Natarajan, V. Pascucci, in:, IEEE, 2004, pp. 275–280. conference: name: 'VIS: IEEE Visualization' date_created: 2018-12-11T12:06:18Z date_published: 2004-10-01T00:00:00Z date_updated: 2021-01-12T07:53:41Z day: '01' doi: 10.1109/VISUAL.2004.68 extern: 1 month: '10' page: 275 - 280 publication_status: published publisher: IEEE publist_id: '2137' quality_controlled: 0 status: public title: Local and global comparison of continuous functions type: conference year: '2004' ... --- _id: '4172' abstract: - lang: eng text: 'During vertebrate gastrulation, a relatively limited number of blastodermal cells undergoes a stereotypical set of cellular movements that leads to formation of the three germ layers: ectoderm, mesoderm and endoderm. Gastrulation, therefore, provides a unique developmental system in which to study cell movements in vivo in a fairly simple cellular context. Recent advances have been made in elucidating the cellular and molecular mechanisms that underlie cell movements during zebrafish gastrulation. These findings can be compared with observations made in other model systems to identify potential general mechanisms of cell migration during development.' article_processing_charge: No author: - first_name: Juan full_name: Montero, Juan last_name: Montero - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: 'Montero J, Heisenberg C-PJ. Gastrulation dynamics: cells move into focus. Trends in Cell Biology. 2004;14(11):620-627. doi:10.1016/j.tcb.2004.09.008' apa: 'Montero, J., & Heisenberg, C.-P. J. (2004). Gastrulation dynamics: cells move into focus. Trends in Cell Biology. Cell Press. https://doi.org/10.1016/j.tcb.2004.09.008' chicago: 'Montero, Juan, and Carl-Philipp J Heisenberg. “Gastrulation Dynamics: Cells Move into Focus.” Trends in Cell Biology. Cell Press, 2004. https://doi.org/10.1016/j.tcb.2004.09.008.' ieee: 'J. Montero and C.-P. J. Heisenberg, “Gastrulation dynamics: cells move into focus,” Trends in Cell Biology, vol. 14, no. 11. Cell Press, pp. 620–627, 2004.' ista: 'Montero J, Heisenberg C-PJ. 2004. Gastrulation dynamics: cells move into focus. Trends in Cell Biology. 14(11), 620–627.' mla: 'Montero, Juan, and Carl-Philipp J. Heisenberg. “Gastrulation Dynamics: Cells Move into Focus.” Trends in Cell Biology, vol. 14, no. 11, Cell Press, 2004, pp. 620–27, doi:10.1016/j.tcb.2004.09.008.' short: J. Montero, C.-P.J. Heisenberg, Trends in Cell Biology 14 (2004) 620–627. date_created: 2018-12-11T12:07:23Z date_published: 2004-11-01T00:00:00Z date_updated: 2021-01-12T07:55:02Z day: '01' doi: 10.1016/j.tcb.2004.09.008 extern: '1' intvolume: ' 14' issue: '11' language: - iso: eng month: '11' oa_version: None page: 620 - 627 publication: Trends in Cell Biology publication_status: published publisher: Cell Press publist_id: '1948' status: public title: 'Gastrulation dynamics: cells move into focus' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2004' ... --- _id: '4238' abstract: - lang: eng text: The dynamical basis of tumoral growth has been controversial. Many models have been proposed to explain cancer development. The descriptions employ exponential, potential, logistic or Gompertzian growth laws. Some of these models are concerned with the interaction between cancer and the immunological, system. Among other properties, these models are concerned with the microscopic behavior of tumors and the emergence of cancer. We propose a modification of a previous model by Stepanova, which describes the specific immunological response against cancer. The modification consists of the substitution of a Gompertian law for the exponential rate used for tumoral growth. This modification is motivated by the numerous works confirming that Gompertz's equation correctly describes solid tumor growth. The modified model predicts that near zero, tumors always tend to grow. Immunological contraposition never suffices to induce a complete regression of the tumor. Instead, a stable microscopic equilibrium between cancer and immunological activity can be attained. In other words, our model predicts that the theory of immune surveillance is plausible. A macroscopic equilibrium in which the system develops cancer is also possible. In this case, immunological activity is depleted. This is consistent with the phenomena of cancer tolerance. Both equilibrium points can coexist or can exist without the other. In all cases the fixed point at zero tumor size is unstable. Since immunity cannot induce a complete tumor regression, a therapy is required. We include constant-dose therapies and show that they are insufficient. Final levels of immunocompetent cells and tumoral cells are finite, thus post-treatment regrowth of the tumor is certain. We also evaluate late-intensification therapies which are successful. They induce an asymptotic regression to zero tumor size. Immune response is also suppressed by the therapy, and thus plays a negligible role in the remission. We conclude that treatment evaluation should be successful without taking into account immunological effects. (C) 2003 Elsevier Ltd. All rights reserved. article_processing_charge: No author: - first_name: Harold full_name: de Vladar, Harold id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: de Vladar orcid: 0000-0002-5985-7653 - first_name: J. full_name: González, J. last_name: González citation: ama: de Vladar H, González J. Dynamic response of cancer under the influence of immunological activity and therapy. Journal of Theoretical Biology. 2004;227(3):335-348. doi:3801 apa: de Vladar, H., & González, J. (2004). Dynamic response of cancer under the influence of immunological activity and therapy. Journal of Theoretical Biology. Elsevier. https://doi.org/3801 chicago: Vladar, Harold de, and J. González. “Dynamic Response of Cancer under the Influence of Immunological Activity and Therapy.” Journal of Theoretical Biology. Elsevier, 2004. https://doi.org/3801. ieee: H. de Vladar and J. González, “Dynamic response of cancer under the influence of immunological activity and therapy,” Journal of Theoretical Biology, vol. 227, no. 3. Elsevier, pp. 335–348, 2004. ista: de Vladar H, González J. 2004. Dynamic response of cancer under the influence of immunological activity and therapy. Journal of Theoretical Biology. 227(3), 335–348. mla: de Vladar, Harold, and J. González. “Dynamic Response of Cancer under the Influence of Immunological Activity and Therapy.” Journal of Theoretical Biology, vol. 227, no. 3, Elsevier, 2004, pp. 335–48, doi:3801. short: H. de Vladar, J. González, Journal of Theoretical Biology 227 (2004) 335–348. date_created: 2018-12-11T12:07:46Z date_published: 2004-01-01T00:00:00Z date_updated: 2021-01-12T07:55:31Z day: '01' doi: '3801' extern: '1' intvolume: ' 227' issue: '3' language: - iso: eng month: '01' oa_version: None page: 335 - 348 publication: Journal of Theoretical Biology publication_status: published publisher: Elsevier publist_id: '1876' status: public title: Dynamic response of cancer under the influence of immunological activity and therapy type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 227 year: '2004' ... --- _id: '4230' alternative_title: - Cellular Origin and Life in Extreme Habitats and Astrobiology author: - first_name: Harold full_name: Harold Vladar id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: Vladar orcid: 0000-0002-5985-7653 - first_name: Roberto full_name: Cipriani, Roberto last_name: Cipriani - first_name: Benjamin full_name: Scharifker, Benjamin last_name: Scharifker - first_name: Jose full_name: Bubis, Jose last_name: Bubis citation: ama: 'de Vladar H, Cipriani R, Scharifker B, Bubis J. A mechanism for the prebiotic emergence of proteins. In: Hanslmeier A, Kempe S, Seckbach J, eds. Life in the Universe From the Miller Experiment to the Search for Life on Other Worlds. Springer; 2004:83-87.' apa: de Vladar, H., Cipriani, R., Scharifker, B., & Bubis, J. (2004). A mechanism for the prebiotic emergence of proteins. In A. Hanslmeier, S. Kempe, & J. Seckbach (Eds.), Life in the Universe From the Miller Experiment to the Search for Life on Other Worlds (pp. 83–87). Springer. chicago: Vladar, Harold de, Roberto Cipriani, Benjamin Scharifker, and Jose Bubis. “A Mechanism for the Prebiotic Emergence of Proteins.” In Life in the Universe From the Miller Experiment to the Search for Life on Other Worlds, edited by A. Hanslmeier, S. Kempe, and J. Seckbach, 83–87. Springer, 2004. ieee: H. de Vladar, R. Cipriani, B. Scharifker, and J. Bubis, “A mechanism for the prebiotic emergence of proteins,” in Life in the Universe From the Miller Experiment to the Search for Life on Other Worlds, A. Hanslmeier, S. Kempe, and J. Seckbach, Eds. Springer, 2004, pp. 83–87. ista: 'de Vladar H, Cipriani R, Scharifker B, Bubis J. 2004.A mechanism for the prebiotic emergence of proteins. In: Life in the Universe From the Miller Experiment to the Search for Life on Other Worlds. Cellular Origin and Life in Extreme Habitats and Astrobiology, , 83–87.' mla: de Vladar, Harold, et al. “A Mechanism for the Prebiotic Emergence of Proteins.” Life in the Universe From the Miller Experiment to the Search for Life on Other Worlds, edited by A. Hanslmeier et al., Springer, 2004, pp. 83–87. short: H. de Vladar, R. Cipriani, B. Scharifker, J. Bubis, in:, A. Hanslmeier, S. Kempe, J. Seckbach (Eds.), Life in the Universe From the Miller Experiment to the Search for Life on Other Worlds, Springer, 2004, pp. 83–87. date_created: 2018-12-11T12:07:44Z date_published: 2004-12-31T00:00:00Z date_updated: 2021-01-12T07:55:28Z day: '31' editor: - first_name: A. full_name: Hanslmeier,A. last_name: Hanslmeier - first_name: S. full_name: Kempe,S. last_name: Kempe - first_name: J. full_name: Seckbach,J. last_name: Seckbach extern: 1 month: '12' page: 83 - 87 publication: Life in the Universe From the Miller Experiment to the Search for Life on Other Worlds publication_status: published publisher: Springer publist_id: '1884' quality_controlled: 0 status: public title: A mechanism for the prebiotic emergence of proteins type: book_chapter year: '2004' ... --- _id: '4236' article_processing_charge: No author: - first_name: Harold full_name: de Vladar, Harold id: 2A181218-F248-11E8-B48F-1D18A9856A87 last_name: de Vladar orcid: 0000-0002-5985-7653 citation: ama: de Vladar H. Métodos no lineales y sus aplicaciones en dinámicas aleatorias de poblaciones celulares. 2004. doi:3810 apa: de Vladar, H. (2004). Métodos no lineales y sus aplicaciones en dinámicas aleatorias de poblaciones celulares. Centro de estudios avazados, IVIC. https://doi.org/3810 chicago: Vladar, Harold de. “Métodos No Lineales y Sus Aplicaciones En Dinámicas Aleatorias de Poblaciones Celulares.” Centro de estudios avazados, IVIC, 2004. https://doi.org/3810. ieee: H. de Vladar, “Métodos no lineales y sus aplicaciones en dinámicas aleatorias de poblaciones celulares,” Centro de estudios avazados, IVIC, 2004. ista: de Vladar H. 2004. Métodos no lineales y sus aplicaciones en dinámicas aleatorias de poblaciones celulares. Centro de estudios avazados, IVIC. mla: de Vladar, Harold. Métodos No Lineales y Sus Aplicaciones En Dinámicas Aleatorias de Poblaciones Celulares. Centro de estudios avazados, IVIC, 2004, doi:3810. short: H. de Vladar, Métodos No Lineales y Sus Aplicaciones En Dinámicas Aleatorias de Poblaciones Celulares, Centro de estudios avazados, IVIC, 2004. date_created: 2018-12-11T12:07:46Z date_published: 2004-01-01T00:00:00Z date_updated: 2021-01-12T07:55:30Z day: '01' doi: '3810' extern: '1' language: - iso: eng month: '01' oa_version: None publication_status: published publisher: Centro de estudios avazados, IVIC publist_id: '1877' status: public title: Métodos no lineales y sus aplicaciones en dinámicas aleatorias de poblaciones celulares type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2004' ... --- _id: '4372' alternative_title: - LNCS author: - first_name: Oded full_name: Maler, Oded last_name: Maler - first_name: Dejan full_name: Dejan Nickovic id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87 last_name: Nickovic citation: ama: 'Maler O, Nickovic D. Monitoring Temporal Properties of Continuous Signals. In: Springer; 2004:152-166. doi:1572' apa: 'Maler, O., & Nickovic, D. (2004). Monitoring Temporal Properties of Continuous Signals (pp. 152–166). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Springer. https://doi.org/1572' chicago: Maler, Oded, and Dejan Nickovic. “Monitoring Temporal Properties of Continuous Signals,” 152–66. Springer, 2004. https://doi.org/1572. ieee: 'O. Maler and D. Nickovic, “Monitoring Temporal Properties of Continuous Signals,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, 2004, pp. 152–166.' ista: 'Maler O, Nickovic D. 2004. Monitoring Temporal Properties of Continuous Signals. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, , 152–166.' mla: Maler, Oded, and Dejan Nickovic. Monitoring Temporal Properties of Continuous Signals. Springer, 2004, pp. 152–66, doi:1572. short: O. Maler, D. Nickovic, in:, Springer, 2004, pp. 152–166. conference: name: 'FORMATS: Formal Modeling and Analysis of Timed Systems' date_created: 2018-12-11T12:08:31Z date_published: 2004-12-14T00:00:00Z date_updated: 2021-01-12T07:56:29Z day: '14' doi: '1572' extern: 1 month: '12' page: 152 - 166 publication_status: published publisher: Springer publist_id: '1088' quality_controlled: 0 status: public title: Monitoring Temporal Properties of Continuous Signals type: conference year: '2004' ... --- _id: '4424' abstract: - lang: eng text: "The enormous cost and ubiquity of software errors necessitates the need for techniques and tools that can precisely analyze large systems and prove that they meet given specifications, or if they don't, return counterexample behaviors showing how the system fails. Recent advances in model checking, decision procedures, program analysis and type systems, and a shift of focus to partial specifications common to several systems (e.g., memory safety and race freedom) have resulted in several practical verification methods. However, these methods are either precise or they are scalable, depending on whether they track the values of variables or only a fixed small set of dataflow facts (e.g., types), and are usually insufficient for precisely verifying large programs.\r\n\r\nWe describe a new technique called Lazy Abstraction (LA) which achieves both precision and scalability by localizing the use of precise information. LA automatically builds, explores and refines a single abstract model of the program in a way that different parts of the model exhibit different degrees of precision, namely just enough to verify the desired property. The algorithm automatically mines the information required by partitioning mechanical proofs of unsatisfiability of spurious counterexamples into Craig Interpolants. For multithreaded systems, we give a new technique based on analyzing the behavior of a single thread executing in a context which is an abstraction of the other (arbitrarily many) threads. We define novel context models and show how to automatically infer them and analyze the full system (thread + context) using LA.\r\n\r\nLA is implemented in BLAST. We have run BLAST on Windows and Linux Device Drivers to verify API conformance properties, and have used it to find (or guarantee the absence of) data races in multithreaded Networked Embedded Systems (NESC) applications. BLAST is able to prove the absence of races in several cases where earlier methods, which depend on lock-based synchronization, fail." article_processing_charge: No author: - first_name: Ranjit full_name: Jhala, Ranjit last_name: Jhala citation: ama: Jhala R. Program verification by lazy abstraction. 2004:1-165. apa: Jhala, R. (2004). Program verification by lazy abstraction. University of California, Berkeley. chicago: Jhala, Ranjit. “Program Verification by Lazy Abstraction.” University of California, Berkeley, 2004. ieee: R. Jhala, “Program verification by lazy abstraction,” University of California, Berkeley, 2004. ista: Jhala R. 2004. Program verification by lazy abstraction. University of California, Berkeley. mla: Jhala, Ranjit. Program Verification by Lazy Abstraction. University of California, Berkeley, 2004, pp. 1–165. short: R. Jhala, Program Verification by Lazy Abstraction, University of California, Berkeley, 2004. date_created: 2018-12-11T12:08:47Z date_published: 2004-12-01T00:00:00Z date_updated: 2021-01-12T07:56:52Z day: '01' extern: '1' language: - iso: eng month: '12' oa_version: None page: 1 - 165 publication_status: published publisher: University of California, Berkeley publist_id: '307' status: public supervisor: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 title: Program verification by lazy abstraction type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2004' ...