[{"date_created":"2018-12-11T12:04:02Z","date_updated":"2021-01-12T07:44:24Z","author":[{"full_name":"Herbert Edelsbrunner","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"}],"publisher":"CRC Press","status":"public","title":"Biological applications of computational topology","publication_status":"published","_id":"3574","year":"2004","extern":1,"publist_id":"2811","type":"book_chapter","date_published":"2004-04-15T00:00:00Z","page":"1395 - 1412","quality_controlled":0,"citation":{"chicago":"Edelsbrunner, Herbert. “Biological Applications of Computational Topology.” In Handbook of Discrete and Computational Geometry, 1395–1412. CRC Press, 2004.","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.","ista":"Edelsbrunner H. 2004.Biological applications of computational topology. In: Handbook of Discrete and Computational Geometry. , 1395–1412.","apa":"Edelsbrunner, H. (2004). Biological applications of computational topology. In Handbook of Discrete and Computational Geometry (pp. 1395–1412). CRC Press.","ieee":"H. Edelsbrunner, “Biological applications of computational topology,” in Handbook of Discrete and Computational Geometry, CRC Press, 2004, pp. 1395–1412.","ama":"Edelsbrunner H. Biological applications of computational topology. In: Handbook of Discrete and Computational Geometry. CRC Press; 2004:1395-1412."},"main_file_link":[{"open_access":"0","url":"http://www.cs.duke.edu/~edels/Papers/2004-B-01-BiologicalApplicationsTopology.pdf"}],"publication":"Handbook of Discrete and Computational Geometry","day":"15","month":"04"},{"quality_controlled":0,"page":"R233 - R235","publication":"Current Biology","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","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.","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","ista":"Charlesworth B, Barton NH. 2004. Genome size: Does bigger mean worse? Current Biology. 14(6), R233–R235.","short":"B. Charlesworth, N.H. Barton, Current Biology 14 (2004) 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.","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."},"doi":"10.1016/j.cub.2004.02.054","date_published":"2004-03-01T00:00:00Z","month":"03","day":"01","publication_status":"published","title":"Genome size: Does bigger mean worse?","status":"public","publisher":"Cell Press","intvolume":" 14","_id":"3595","year":"2004","date_created":"2018-12-11T12:04:09Z","date_updated":"2019-04-26T07:22:31Z","volume":14,"author":[{"first_name":"Brian","last_name":"Charlesworth","full_name":"Charlesworth, Brian"},{"full_name":"Nicholas Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"type":"review","extern":1,"abstract":[{"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.","lang":"eng"}],"publist_id":"2788","issue":"6"},{"month":"10","day":"01","doi":"10.1111/j.0014-3820.2004.tb01591.x","date_published":"2004-10-01T00:00:00Z","page":"2111 - 2132","quality_controlled":0,"citation":{"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.","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.","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","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","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.","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."},"publication":"Evolution; International Journal of Organic Evolution","extern":1,"publist_id":"2769","issue":"10","abstract":[{"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.","lang":"eng"}],"type":"journal_article","volume":58,"date_updated":"2021-01-12T07:44:40Z","date_created":"2018-12-11T12:04:15Z","author":[{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Nicholas Barton"},{"last_name":"Turelli","first_name":"Michael","full_name":"Turelli, Michael"}],"publisher":"Wiley-Blackwell","intvolume":" 58","status":"public","title":"Effects of allele frequency changes on variance components under a general model of epistasis","publication_status":"published","year":"2004","_id":"3614"},{"doi":"10.1534/genetics.166.2.1053","date_published":"2004-02-01T00:00:00Z","publication":"Genetics","citation":{"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.","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.","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.","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","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.","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"},"quality_controlled":0,"page":"1053 - 1079","day":"01","month":"02","author":[{"first_name":"Michael","last_name":"Turelli","full_name":"Turelli, Michael"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Nicholas Barton"}],"date_created":"2018-12-11T12:04:15Z","date_updated":"2021-01-12T07:44:41Z","volume":166,"_id":"3615","year":"2004","title":"Polygenic variation maintained by balancing selection: pleiotropy, sex-dependent allelic effects and GxE interactions","publication_status":"published","status":"public","publisher":"Genetics Society of America","intvolume":" 166","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."}],"issue":"2","publist_id":"2768","extern":1,"type":"journal_article"},{"page":"337 - 45","quality_controlled":0,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664940/"}],"citation":{"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 ","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.","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 ","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 .","short":"B. Kampa, J. Clements, P.M. Jonas, G. Stuart, Journal of Physiology 556 (2004) 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 ."},"oa":1,"publication":"Journal of Physiology","date_published":"2004-01-01T00:00:00Z","doi":"10.1113/jphysiol.2003.058842 ","day":"01","month":"01","publisher":"Wiley-Blackwell","intvolume":" 556","status":"public","publication_status":"published","title":"Kinetics of Mg(2+) unblock of NMDA receptors: implications for spike-timing dependent synaptic plasticity","year":"2004","_id":"3807","volume":556,"date_created":"2018-12-11T12:05:17Z","date_updated":"2021-01-12T07:52:20Z","author":[{"full_name":"Kampa, Bjorn M","last_name":"Kampa","first_name":"Bjorn"},{"full_name":"Clements, John","first_name":"John","last_name":"Clements"},{"orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","full_name":"Peter Jonas"},{"full_name":"Stuart, Greg J","first_name":"Greg","last_name":"Stuart"}],"type":"journal_article","extern":1,"publist_id":"2403","issue":"Pt 2","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."}]},{"day":"01","month":"01","date_published":"2004-01-01T00:00:00Z","doi":"10.1038/nature02553","quality_controlled":0,"page":"184 - 7","publication":"Nature","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","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.","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","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.","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.","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."},"extern":1,"abstract":[{"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.","lang":"eng"}],"issue":"6988","publist_id":"2401","type":"journal_article","date_updated":"2021-01-12T07:52:21Z","date_created":"2018-12-11T12:05:17Z","volume":429,"author":[{"full_name":"Schmidt-Hieber, Christoph","first_name":"Christoph","last_name":"Schmidt Hieber"},{"last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Peter Jonas"},{"first_name":"Josef","last_name":"Bischofberger","full_name":"Bischofberger, Josef"}],"status":"public","title":"Enhanced synaptic plasticity in newly generated granule cells of the adult hippocampus","publication_status":"published","publisher":"Nature Publishing Group","intvolume":" 429","year":"2004","_id":"3809"},{"type":"journal_article","extern":1,"abstract":[{"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.","lang":"eng"}],"publist_id":"2404","issue":"1","publication_status":"published","status":"public","title":"Interneuron Diversity series: Fast in, fast out--temporal and spatial signal processing in hippocampal interneurons","publisher":"Elsevier","intvolume":" 27","year":"2004","_id":"3805","date_created":"2018-12-11T12:05:16Z","date_updated":"2021-01-12T07:52:19Z","volume":27,"author":[{"first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Peter Jonas"},{"full_name":"Bischofberger, Josef","last_name":"Bischofberger","first_name":"Josef"},{"last_name":"Fricker","first_name":"Desdemona","full_name":"Fricker, Desdemona"},{"last_name":"Miles","first_name":"Richard","full_name":"Miles, Richard"}],"month":"01","day":"01","quality_controlled":0,"page":"30 - 40","publication":"Trends in Neurosciences","citation":{"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.","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.","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","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","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.","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."},"doi":"doi:10.1016/j.tins.2003.10.010","date_published":"2004-01-01T00:00:00Z"},{"author":[{"first_name":"Jürgen","last_name":"Heinze","full_name":"Heinze, Jürgen"},{"last_name":"Böttcher","first_name":"A.","full_name":"Böttcher, A."},{"first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"volume":51,"oa_version":"None","date_created":"2018-12-11T12:05:53Z","date_updated":"2021-01-12T07:53:11Z","_id":"3918","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2004","intvolume":" 51","publisher":"Springer","title":"Production of winged and wingless males in the ant, Cardiocondyla minutior","status":"public","publication_status":"published","issue":"3","publist_id":"2236","abstract":[{"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.","lang":"eng"}],"extern":"1","type":"journal_article","doi":"10.1007/s00040-004-0740-6","date_published":"2004-08-19T00:00:00Z","language":[{"iso":"eng"}],"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","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.","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","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.","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.","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."},"publication":"Insectes Sociaux","page":"275 - 278","month":"08","day":"19"},{"alternative_title":["LNCS"],"type":"conference","extern":1,"publist_id":"2136","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."}],"intvolume":" 3240","publisher":"Springer","publication_status":"published","status":"public","title":"Local search heuristic for rigid protein docking","year":"2004","_id":"3988","acknowledgement":"Supported by NSF under grant CCR-00-86013, BGT Postdoc Program from Duke University and NIH under grant R01 GM61822-01.","volume":3240,"date_created":"2018-12-11T12:06:17Z","date_updated":"2021-01-12T07:53:41Z","author":[{"full_name":"Choi, Vicky","first_name":"Vicky","last_name":"Choi"},{"full_name":"Agarwal, Pankaj K","first_name":"Pankaj","last_name":"Agarwal"},{"full_name":"Herbert Edelsbrunner","last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rudolph, Johannes","first_name":"Johannes","last_name":"Rudolph"}],"month":"01","day":"01","page":"218 - 229","quality_controlled":0,"citation":{"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","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.","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","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.","short":"V. Choi, P. Agarwal, H. Edelsbrunner, J. Rudolph, in:, Springer, 2004, pp. 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."},"doi":"10.1007/978-3-540-30219-3_19","date_published":"2004-01-01T00:00:00Z","conference":{"name":"WABI: 4th International Workshop on Algorithms in Bioinformatics"}},{"publication_status":"published","status":"public","title":"The area derivative of a space-filling diagram","intvolume":" 32","publisher":"Springer","_id":"3986","acknowledgement":"Partially supported by NSF under grant CCR-00-86013 and NSF under grant CCR-97-12088.","year":"2004","date_created":"2018-12-11T12:06:17Z","date_updated":"2021-01-12T07:53:40Z","volume":32,"author":[{"full_name":"Bryant, Robert","last_name":"Bryant","first_name":"Robert"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Herbert Edelsbrunner"},{"full_name":"Koehl, Patrice","last_name":"Koehl","first_name":"Patrice"},{"last_name":"Levitt","first_name":"Michael","full_name":"Levitt, Michael"}],"type":"journal_article","extern":1,"abstract":[{"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.","lang":"eng"}],"issue":"3","publist_id":"2141","quality_controlled":0,"page":"293 - 308","publication":"Discrete & Computational Geometry","citation":{"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.","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.","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","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.","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","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."},"doi":"10.1007/s00454-004-1099-1","date_published":"2004-09-01T00:00:00Z","month":"09","day":"01"}]