--- _id: '4349' abstract: - lang: eng text: 'Bayesian inference is becoming a common statistical approach to phylogenetic estimation because, among other reasons, it allows for rapid analysis of large data sets with complex evolutionary models. Conveniently, Bayesian phylogenetic methods use currently available stochastic models of sequence evolution. However, as with other model-based approaches, the results of Bayesian inference are conditional on the assumed model of evolution: inadequate models (models that poorly fit the data) may result in erroneous inferences. In this article, I present a Bayesian phylogenetic method that evaluates the adequacy of evolutionary models using posterior predictive distributions. By evaluating a model''s posterior predictive performance, an adequate model can be selected for a Bayesian phylogenetic study. Although I present a single test statistic that assesses the overall (global) performance of a phylogenetic model, a variety of test statistics can be tailored to evaluate specific features (local performance) of evolutionary models to identify sources failure. The method presented here, unlike the likelihood-ratio test and parametric bootstrap, accounts for uncertainty in the phylogeny and model parameters.' acknowledgement: "This work was supported by grants from the NSF to John Huelsenbeck (MCB-0075404 and DEB0075406), to whom I am grateful for his support throughout this project. Also, I would like to express my deep thanks to Andrea Betancourt, John Huelsenbeck, Kelly Dyer, Rasmus Nielsen, and Frederick Ronquist for taking the time to read early versions of the\r\nmanuscript. Each and every one of them provided invaluable comments, that ultimately made the manuscript better. John Huelsenbeck, Bret Larget, Rasmus Nielsen, Ken Karol, and Andrea Betancourt patiently listened to me drone on about this project, and offered insightful comments that benefited this work, and for this they have my deepest gratitude. And finally, I would like to thank two anonymous reviewers who gave critical attention to the manuscript and provided valuable comments." article_processing_charge: No article_type: original author: - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: Bollback JP. Bayesian model adequacy and choice in phylogenetics. Molecular Biology and Evolution. 2002;19(7):1171-1180. doi:10.1093/oxfordjournals.molbev.a004175 apa: Bollback, J. P. (2002). Bayesian model adequacy and choice in phylogenetics. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/oxfordjournals.molbev.a004175 chicago: Bollback, Jonathan P. “Bayesian Model Adequacy and Choice in Phylogenetics.” Molecular Biology and Evolution. Oxford University Press, 2002. https://doi.org/10.1093/oxfordjournals.molbev.a004175. ieee: J. P. Bollback, “Bayesian model adequacy and choice in phylogenetics,” Molecular Biology and Evolution, vol. 19, no. 7. Oxford University Press, pp. 1171–80, 2002. ista: Bollback JP. 2002. Bayesian model adequacy and choice in phylogenetics. Molecular Biology and Evolution. 19(7), 1171–80. mla: Bollback, Jonathan P. “Bayesian Model Adequacy and Choice in Phylogenetics.” Molecular Biology and Evolution, vol. 19, no. 7, Oxford University Press, 2002, pp. 1171–80, doi:10.1093/oxfordjournals.molbev.a004175. short: J.P. Bollback, Molecular Biology and Evolution 19 (2002) 1171–80. date_created: 2018-12-11T12:08:24Z date_published: 2002-03-25T00:00:00Z date_updated: 2023-06-06T09:18:18Z day: '25' doi: 10.1093/oxfordjournals.molbev.a004175 extern: '1' external_id: pmid: - '12082136 ' intvolume: ' 19' issue: '7' language: - iso: eng month: '03' oa_version: None page: 1171 - 80 pmid: 1 publication: Molecular Biology and Evolution publication_identifier: issn: - 0737-4038 publication_status: published publisher: Oxford University Press publist_id: '1112' quality_controlled: '1' scopus_import: '1' status: public title: Bayesian model adequacy and choice in phylogenetics type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 19 year: '2002' ... --- _id: '4263' abstract: - lang: eng text: 'We introduce a general recursion for the probability of identity in state of two individuals sampled from a population subject to mutation, migration, and random drift in a two-dimensional continuum. The recursion allows for the interactions induced by density-dependent regulation of the population, which are inevitable in a continuous population. We give explicit series expansions for large neighbourhood size and for low mutation rates respectively and investigate the accuracy of the classical Malécot formula for these general models. When neighbourhood size is small, this formula does not give the identity even over large scales. However, for large neighbourhood size, it is an accurate approximation which summarises the local population structure in terms of three quantities: the effective dispersal rate, σe; the effective population density, ρe; and a local scale, κ, at which local interactions become significant. The results are illustrated by simulations.' acknowledgement: This work was supported by grants from the EPSRC (GR/L10048 and an advanced fellowship for A.M.E.) and NERC (GR3/11635) and by the Darwin Trust of Edinburgh. We thank Anja Sturm for her assistance with the project and anonymous reviewers for helpful comments. This paper is dedicated to Charlotte, A.M.E.’s daughter born during the gestation of the manuscript. article_processing_charge: No article_type: original author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Frantz full_name: Depaulis, Frantz last_name: Depaulis - first_name: Alison full_name: Etheridge, Alison last_name: Etheridge citation: ama: Barton NH, Depaulis F, Etheridge A. Neutral evolution in spatially continuous populations. Theoretical Population Biology. 2002;61(1):31-48. doi:10.1006/tpbi.2001.1557 apa: Barton, N. H., Depaulis, F., & Etheridge, A. (2002). Neutral evolution in spatially continuous populations. Theoretical Population Biology. Academic Press. https://doi.org/10.1006/tpbi.2001.1557 chicago: Barton, Nicholas H, Frantz Depaulis, and Alison Etheridge. “Neutral Evolution in Spatially Continuous Populations.” Theoretical Population Biology. Academic Press, 2002. https://doi.org/10.1006/tpbi.2001.1557. ieee: N. H. Barton, F. Depaulis, and A. Etheridge, “Neutral evolution in spatially continuous populations,” Theoretical Population Biology, vol. 61, no. 1. Academic Press, pp. 31–48, 2002. ista: Barton NH, Depaulis F, Etheridge A. 2002. Neutral evolution in spatially continuous populations. Theoretical Population Biology. 61(1), 31–48. mla: Barton, Nicholas H., et al. “Neutral Evolution in Spatially Continuous Populations.” Theoretical Population Biology, vol. 61, no. 1, Academic Press, 2002, pp. 31–48, doi:10.1006/tpbi.2001.1557. short: N.H. Barton, F. Depaulis, A. Etheridge, Theoretical Population Biology 61 (2002) 31–48. date_created: 2018-12-11T12:07:55Z date_published: 2002-02-01T00:00:00Z date_updated: 2023-06-06T09:57:49Z day: '01' doi: 10.1006/tpbi.2001.1557 extern: '1' external_id: pmid: - '11895381' intvolume: ' 61' issue: '1' language: - iso: eng month: '02' oa_version: None page: 31 - 48 pmid: 1 publication: Theoretical Population Biology publication_identifier: issn: - 0040-5809 publication_status: published publisher: Academic Press publist_id: '1830' quality_controlled: '1' scopus_import: '1' status: public title: Neutral evolution in spatially continuous populations type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 61 year: '2002' ... --- _id: '4261' abstract: - lang: eng text: Until recently, it was impracticable to identify the genes that are responsible for variation in continuous traits, or to directly observe the effects of their different alleles. Now, the abundance of genetic markers has made it possible to identify quantitative trait loci (QTL) — the regions of a chromosome or, ideally, individual sequence variants that are responsible for trait variation. What kind of QTL do we expect to find and what can our observations of QTL tell us about how organisms evolve? The key to understanding the evolutionary significance of QTL is to understand the nature of inherited variation, not in the immediate mechanistic sense of how genes influence phenotype, but, rather, to know what evolutionary forces maintain genetic variability. article_processing_charge: No article_type: original author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Peter full_name: Keightley, Peter last_name: Keightley citation: ama: Barton NH, Keightley P. Understanding quantitative genetic variation. Nature Reviews Genetics. 2002;3:11-21. doi:10.1038/nrg700 apa: Barton, N. H., & Keightley, P. (2002). Understanding quantitative genetic variation. Nature Reviews Genetics. Nature Publishing Group. https://doi.org/10.1038/nrg700 chicago: Barton, Nicholas H, and Peter Keightley. “Understanding Quantitative Genetic Variation.” Nature Reviews Genetics. Nature Publishing Group, 2002. https://doi.org/10.1038/nrg700. ieee: N. H. Barton and P. Keightley, “Understanding quantitative genetic variation,” Nature Reviews Genetics, vol. 3. Nature Publishing Group, pp. 11–21, 2002. ista: Barton NH, Keightley P. 2002. Understanding quantitative genetic variation. Nature Reviews Genetics. 3, 11–21. mla: Barton, Nicholas H., and Peter Keightley. “Understanding Quantitative Genetic Variation.” Nature Reviews Genetics, vol. 3, Nature Publishing Group, 2002, pp. 11–21, doi:10.1038/nrg700. short: N.H. Barton, P. Keightley, Nature Reviews Genetics 3 (2002) 11–21. date_created: 2018-12-11T12:07:55Z date_published: 2002-01-01T00:00:00Z date_updated: 2023-06-06T10:07:00Z day: '01' doi: 10.1038/nrg700 extern: '1' external_id: pmid: - '11823787' intvolume: ' 3' language: - iso: eng month: '01' oa_version: None page: 11 - 21 pmid: 1 publication: Nature Reviews Genetics publication_identifier: issn: - 1471-0056 publication_status: published publisher: Nature Publishing Group publist_id: '1831' quality_controlled: '1' scopus_import: '1' status: public title: Understanding quantitative genetic variation type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 3 year: '2002' ... --- _id: '4347' abstract: - lang: eng text: 'Phylogenetic trees can be rooted by a number of criteria. Here, we introduce a Bayesian method for inferring the root of a phylogenetic tree by using one of several criteria: the outgroup, molecular clock, and nonreversible model of DNA substitution. We perform simulation analyses to examine the relative ability of these three criteria to correctly identify the root of the tree. The outgroup and molecular clock criteria were best able to identify the root of the tree, whereas the nonreversible model was able to identify the root only when the substitution process was highly nonreversible. We also examined the performance of the criteria for a tree of four species for which the topology and root position are well supported. Results of the analyses of these data are consistent with the simulation results.' article_processing_charge: No article_type: original author: - first_name: John full_name: Huelsenbeck, John last_name: Huelsenbeck - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 - first_name: Amy full_name: Levine, Amy last_name: Levine citation: ama: Huelsenbeck J, Bollback JP, Levine A. Inferring the root of a phylogenetic tree. Systematic Biology. 2002;51(1):32-43. doi:10.1080/106351502753475862 apa: Huelsenbeck, J., Bollback, J. P., & Levine, A. (2002). Inferring the root of a phylogenetic tree. Systematic Biology. Oxford University Press. https://doi.org/10.1080/106351502753475862 chicago: Huelsenbeck, John, Jonathan P Bollback, and Amy Levine. “Inferring the Root of a Phylogenetic Tree.” Systematic Biology. Oxford University Press, 2002. https://doi.org/10.1080/106351502753475862. ieee: J. Huelsenbeck, J. P. Bollback, and A. Levine, “Inferring the root of a phylogenetic tree,” Systematic Biology, vol. 51, no. 1. Oxford University Press, pp. 32–43, 2002. ista: Huelsenbeck J, Bollback JP, Levine A. 2002. Inferring the root of a phylogenetic tree. Systematic Biology. 51(1), 32–43. mla: Huelsenbeck, John, et al. “Inferring the Root of a Phylogenetic Tree.” Systematic Biology, vol. 51, no. 1, Oxford University Press, 2002, pp. 32–43, doi:10.1080/106351502753475862. short: J. Huelsenbeck, J.P. Bollback, A. Levine, Systematic Biology 51 (2002) 32–43. date_created: 2018-12-11T12:08:23Z date_published: 2002-02-01T00:00:00Z date_updated: 2023-06-06T09:53:27Z day: '01' doi: 10.1080/106351502753475862 extern: '1' external_id: pmid: - '11943091' intvolume: ' 51' issue: '1' language: - iso: eng month: '02' oa_version: None page: 32 - 43 pmid: 1 publication: Systematic Biology publication_identifier: issn: - 0039-7989 publication_status: published publisher: Oxford University Press publist_id: '1113' quality_controlled: '1' scopus_import: '1' status: public title: Inferring the root of a phylogenetic tree type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 51 year: '2002' ... --- _id: '4407' abstract: - lang: eng text: 'This paper presents a complete axiomatization of two decidable propositional real-time linear temporal logics: Event Clock Logic (EventClockTL) and Metric Interval Temporal Logic with past (MetricIntervalTL). The completeness proof consists of an effective proof building procedure for EventClockTL. From this result we obtain a complete axiomatization of MetricIntervalTL by providing axioms translating MetricIntervalTL formulae into EventClockTL formulae, the two logics being equally expressive. Our proof is structured to yield axiomatizations also for interesting fragments of these logics, such as the linear temporal logic of the real numbers (TLR).' article_processing_charge: No article_type: original author: - first_name: Jean full_name: Raskin, Jean last_name: Raskin - first_name: Pierre full_name: Schobbens, Pierre last_name: Schobbens - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: Raskin J, Schobbens P, Henzinger TA. Axioms for real-time logics. Theoretical Computer Science. 2002;274(1-2):151-182. doi:10.1016/S0304-3975(00)00308-X apa: Raskin, J., Schobbens, P., & Henzinger, T. A. (2002). Axioms for real-time logics. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/S0304-3975(00)00308-X chicago: Raskin, Jean, Pierre Schobbens, and Thomas A Henzinger. “Axioms for Real-Time Logics.” Theoretical Computer Science. Elsevier, 2002. https://doi.org/10.1016/S0304-3975(00)00308-X. ieee: J. Raskin, P. Schobbens, and T. A. Henzinger, “Axioms for real-time logics,” Theoretical Computer Science, vol. 274, no. 1–2. Elsevier, pp. 151–182, 2002. ista: Raskin J, Schobbens P, Henzinger TA. 2002. Axioms for real-time logics. Theoretical Computer Science. 274(1–2), 151–182. mla: Raskin, Jean, et al. “Axioms for Real-Time Logics.” Theoretical Computer Science, vol. 274, no. 1–2, Elsevier, 2002, pp. 151–82, doi:10.1016/S0304-3975(00)00308-X. short: J. Raskin, P. Schobbens, T.A. Henzinger, Theoretical Computer Science 274 (2002) 151–182. date_created: 2018-12-11T12:08:42Z date_published: 2002-03-01T00:00:00Z date_updated: 2023-06-06T09:10:56Z day: '01' doi: 10.1016/S0304-3975(00)00308-X extern: '1' intvolume: ' 274' issue: 1-2 language: - iso: eng month: '03' oa_version: None page: 151 - 182 publication: Theoretical Computer Science publication_identifier: issn: - 0304-3975 publication_status: published publisher: Elsevier publist_id: '324' quality_controlled: '1' scopus_import: '1' status: public title: Axioms for real-time logics type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 274 year: '2002' ... --- _id: '4258' abstract: - lang: eng text: We studied the effect of multilocus balancing selection on neutral nucleotide variability at linked sites by simulating a model where diallelic polymorphisms are maintained at an arbitrary number of selected loci by means of symmetric overdominance. Different combinations of alleles define different genetic backgrounds that subdivide the population and strongly affect variability. Several multilocus fitness regimes with different degrees of epistasis and gametic disequilibrium are allowed. Analytical results based on a multilocus extension of the structured coalescent predict that the expected linked neutral diversity increases exponentially with the number of selected loci and can become extremely large. Our simulation results show that although variability increases with the number of genetic backgrounds that are maintained in the population, it is reduced by random fluctuations in the frequencies of those backgrounds and does not reach high levels even in very large populations. We also show that previous results on balancing selection in single-locus systems do not extend to the multilocus scenario in a straightforward way. Different patterns of linkage disequilibrium and of the frequency spectrum of neutral mutations are expected under different degrees of epistasis. Interestingly, the power to detect balancing selection using deviations from a neutral distribution of allele frequencies seems to be diminished under the fitness regime that leads to the largest increase of variability over the neutral case. This and other results are discussed in the light of data from the Mhc. acknowledgement: We thank P. Andolfatto, P. Awadalla, B. Charlesworth, D. Charles- Guillaudeux, T., M. Janer, G. K. S. Wong, T. Spies and D. E. Geraghty, F. Depaulis, S. Otto, J. Rozas, and three anonymous reviewers for valuable discussion and criticism. A.N. is grateful to F. Depaulis, whose comments were particularly helpful (and extremely funny), and to D. Charlesworth, whose ideas made this work readable. This work was supported by Biotechnology and Biological Sciences Research Council/Engineering and Physical Sciences Research Council. article_processing_charge: No article_type: original author: - first_name: Arcadio full_name: Navarro, Arcadio last_name: Navarro - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Navarro A, Barton NH. The effects of multilocus balancing selection on neutral variability. Genetics. 2002;161(2):849-863. doi:10.1093/genetics/161.2.849 apa: Navarro, A., & Barton, N. H. (2002). The effects of multilocus balancing selection on neutral variability. Genetics. Genetics Society of America. https://doi.org/10.1093/genetics/161.2.849 chicago: Navarro, Arcadio, and Nicholas H Barton. “The Effects of Multilocus Balancing Selection on Neutral Variability.” Genetics. Genetics Society of America, 2002. https://doi.org/10.1093/genetics/161.2.849. ieee: A. Navarro and N. H. Barton, “The effects of multilocus balancing selection on neutral variability,” Genetics, vol. 161, no. 2. Genetics Society of America, pp. 849–863, 2002. ista: Navarro A, Barton NH. 2002. The effects of multilocus balancing selection on neutral variability. Genetics. 161(2), 849–863. mla: Navarro, Arcadio, and Nicholas H. Barton. “The Effects of Multilocus Balancing Selection on Neutral Variability.” Genetics, vol. 161, no. 2, Genetics Society of America, 2002, pp. 849–63, doi:10.1093/genetics/161.2.849. short: A. Navarro, N.H. Barton, Genetics 161 (2002) 849–863. date_created: 2018-12-11T12:07:53Z date_published: 2002-06-01T00:00:00Z date_updated: 2023-06-06T12:02:32Z day: '01' doi: 10.1093/genetics/161.2.849 extern: '1' external_id: pmid: - '12072479' intvolume: ' 161' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1462137/ month: '06' oa: 1 oa_version: Published Version page: 849 - 863 pmid: 1 publication: Genetics publication_identifier: issn: - 0016-6731 publication_status: published publisher: Genetics Society of America publist_id: '1835' quality_controlled: '1' scopus_import: '1' status: public title: The effects of multilocus balancing selection on neutral variability type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 161 year: '2002' ... --- _id: '4259' abstract: - lang: eng text: 'We extend current multilocus models to describe the effects of migration, recombination, selection, and nonrandom mating on sets of genes in diploids with varied modes of inheritance, allowing us to consider the patterns of nuclear and cytonuclear associations (disequilibria) under various models of migration. We show the relationship between the multilocus notation recently presented by Kirkpatrick, Johnson, and Barton (developed from previous work by Barton and Turelli) and the cytonuclear parameterization of Asmussen, Arnold, and Avise and extend this notation to describe associations between cytoplasmic elements and multiple nuclear genes. Under models with sexual symmetry, both nuclear-nuclear and cytonuclear disequilibria are equivalent. They differ, however, in cases involving some type of sexual asymmetry, which is then reflected in the asymmetric inheritance of cytoplasmic markers. An example given is the case of different migration rates in males and females; simulations using 2, 3, 4, or 5 unlinked autosomal markers with a maternally inherited cytoplasmic marker illustrate how nuclear-nuclear and cytonuclear associations can be used to separately estimate female and male migration rates. The general framework developed here allows us to investigate conditions where associations between loci with different modes of inheritance are not equivalent and to use this nonequivalence to test for deviations from simple models of admixture. ' acknowledgement: The authors thank Toby Johnson for his helpful comments on this manuscript. This work was supported by a National Science Foundation NATO postdoctoral fellowship and National Science Foundation grants DEB-9813335 and DEB-0108242 to M.E.O.; N.H.B. gratefully acknowledges the support of the Darwin Trust of Edinburgh and the National Environmental Research Council. article_processing_charge: No article_type: original author: - first_name: Maria full_name: Orive, Maria last_name: Orive - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Orive M, Barton NH. Associations between cytoplasmic and nuclear loci in hybridizing populations. Genetics. 2002;162(3):1469-1485. doi:10.1093/genetics/162.3.1469 apa: Orive, M., & Barton, N. H. (2002). Associations between cytoplasmic and nuclear loci in hybridizing populations. Genetics. Genetics Society of America. https://doi.org/10.1093/genetics/162.3.1469 chicago: Orive, Maria, and Nicholas H Barton. “Associations between Cytoplasmic and Nuclear Loci in Hybridizing Populations.” Genetics. Genetics Society of America, 2002. https://doi.org/10.1093/genetics/162.3.1469. ieee: M. Orive and N. H. Barton, “Associations between cytoplasmic and nuclear loci in hybridizing populations,” Genetics, vol. 162, no. 3. Genetics Society of America, pp. 1469–1485, 2002. ista: Orive M, Barton NH. 2002. Associations between cytoplasmic and nuclear loci in hybridizing populations. Genetics. 162(3), 1469–1485. mla: Orive, Maria, and Nicholas H. Barton. “Associations between Cytoplasmic and Nuclear Loci in Hybridizing Populations.” Genetics, vol. 162, no. 3, Genetics Society of America, 2002, pp. 1469–85, doi:10.1093/genetics/162.3.1469. short: M. Orive, N.H. Barton, Genetics 162 (2002) 1469–1485. date_created: 2018-12-11T12:07:54Z date_published: 2002-11-01T00:00:00Z date_updated: 2023-06-06T12:19:54Z day: '01' doi: 10.1093/genetics/162.3.1469 extern: '1' external_id: pmid: - '12454089' intvolume: ' 162' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1462324/ month: '11' oa: 1 oa_version: Published Version page: 1469 - 1485 pmid: 1 publication: Genetics publication_identifier: issn: - 0016-6731 publication_status: published publisher: Genetics Society of America publist_id: '1836' quality_controlled: '1' scopus_import: '1' status: public title: Associations between cytoplasmic and nuclear loci in hybridizing populations type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 162 year: '2002' ... --- _id: '4209' abstract: - lang: eng text: We have identified widerborst (wdb), a B' regulatory subunit of PP2A, as a conserved component of planar cell polarization mechanisms in both Drosophila and in zebrafish. In Drosophila, wdb acts at two steps during planar polarization of wing epithelial cells. It is required to organize tissue polarity proteins into proximal and distal cortical domains, thus determining wing hair orientation. It is also needed to generate the polarized membrane outgrowth that becomes the wing hair. Widerborst activates the catalytic subunit of PP2A and localizes to the distal side of a planar microtubule web that lies at the level of apical cell junctions. This suggests that polarized PP2A activation along the planar microtubule web is important for planar polarization. In zebrafish, two wdb homologs are required for convergent extension during gastrulation, supporting the conjecture that Drosophila planar cell polarization and vertebrate gastrulation movements are regulated by similar mechanisms. acknowledgement: We gratefully acknowledge Bianca Habermann for assistance with bioinformatics, Jens Rietdorf and Arshad Desai for help with deconvolution, and Tadashi Uemura and Rick Fehon for providing antibodies. Arshad Desai, Christian Dahmann, Tony Hyman and Elly Tanaka provided helpful comments on the manuscript. Part of this work was performed at the EMBL in Heidelberg. article_processing_charge: No article_type: original author: - first_name: Michael full_name: Hannus, Michael last_name: Hannus - first_name: Fabian full_name: Feiguin, Fabian last_name: Feiguin - 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 - first_name: Suzanne full_name: Eaton, Suzanne last_name: Eaton citation: ama: Hannus M, Feiguin F, Heisenberg C-PJ, Eaton S. Planar cell polarization requires Widerborst, a B′ regulatory subunit of protein phosphatase 2A. Development. 2002;129(14):3493-3503. doi:10.1242/dev.129.14.3493 apa: Hannus, M., Feiguin, F., Heisenberg, C.-P. J., & Eaton, S. (2002). Planar cell polarization requires Widerborst, a B′ regulatory subunit of protein phosphatase 2A. Development. Company of Biologists. https://doi.org/10.1242/dev.129.14.3493 chicago: Hannus, Michael, Fabian Feiguin, Carl-Philipp J Heisenberg, and Suzanne Eaton. “Planar Cell Polarization Requires Widerborst, a B′ Regulatory Subunit of Protein Phosphatase 2A.” Development. Company of Biologists, 2002. https://doi.org/10.1242/dev.129.14.3493. ieee: M. Hannus, F. Feiguin, C.-P. J. Heisenberg, and S. Eaton, “Planar cell polarization requires Widerborst, a B′ regulatory subunit of protein phosphatase 2A,” Development, vol. 129, no. 14. Company of Biologists, pp. 3493–3503, 2002. ista: Hannus M, Feiguin F, Heisenberg C-PJ, Eaton S. 2002. Planar cell polarization requires Widerborst, a B′ regulatory subunit of protein phosphatase 2A. Development. 129(14), 3493–3503. mla: Hannus, Michael, et al. “Planar Cell Polarization Requires Widerborst, a B′ Regulatory Subunit of Protein Phosphatase 2A.” Development, vol. 129, no. 14, Company of Biologists, 2002, pp. 3493–503, doi:10.1242/dev.129.14.3493. short: M. Hannus, F. Feiguin, C.-P.J. Heisenberg, S. Eaton, Development 129 (2002) 3493–3503. date_created: 2018-12-11T12:07:36Z date_published: 2002-07-15T00:00:00Z date_updated: 2023-06-06T14:07:49Z day: '15' doi: 10.1242/dev.129.14.3493 extern: '1' external_id: pmid: - '12091318' intvolume: ' 129' issue: '14' language: - iso: eng month: '07' oa_version: None page: 3493 - 3503 pmid: 1 publication: Development publication_identifier: issn: - 0950-1991 publication_status: published publisher: Company of Biologists publist_id: '1909' quality_controlled: '1' scopus_import: '1' status: public title: Planar cell polarization requires Widerborst, a B′ regulatory subunit of protein phosphatase 2A type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 129 year: '2002' ... --- _id: '4207' abstract: - lang: eng text: Vertebrate homologues of the Strabismus/van Gogh (stbm/vang) gene have been implicated in patterning and morphogenesis during gastrulation. Recent work shows that stbm/vang is mutated in zebrafish trilobite mutants and that stbm/vang is required for morphogenesis but not patterning during zebrafish gastrulation. article_processing_charge: No article_type: original author: - 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: 'Heisenberg C-PJ. Wnt signalling: Refocusing on Strabismus. Current Biology. 2002;12(19):R657-R659. doi:10.1016/S0960-9822(02)01160-0' apa: 'Heisenberg, C.-P. J. (2002). Wnt signalling: Refocusing on Strabismus. Current Biology. Cell Press. https://doi.org/10.1016/S0960-9822(02)01160-0' chicago: 'Heisenberg, Carl-Philipp J. “Wnt Signalling: Refocusing on Strabismus.” Current Biology. Cell Press, 2002. https://doi.org/10.1016/S0960-9822(02)01160-0.' ieee: 'C.-P. J. Heisenberg, “Wnt signalling: Refocusing on Strabismus,” Current Biology, vol. 12, no. 19. Cell Press, pp. R657–R659, 2002.' ista: 'Heisenberg C-PJ. 2002. Wnt signalling: Refocusing on Strabismus. Current Biology. 12(19), R657–R659.' mla: 'Heisenberg, Carl-Philipp J. “Wnt Signalling: Refocusing on Strabismus.” Current Biology, vol. 12, no. 19, Cell Press, 2002, pp. R657–59, doi:10.1016/S0960-9822(02)01160-0.' short: C.-P.J. Heisenberg, Current Biology 12 (2002) R657–R659. date_created: 2018-12-11T12:07:35Z date_published: 2002-10-01T00:00:00Z date_updated: 2023-06-06T15:09:53Z day: '01' doi: 10.1016/S0960-9822(02)01160-0 extern: '1' external_id: pmid: - '12361585' intvolume: ' 12' issue: '19' language: - iso: eng month: '10' oa_version: None page: R657 - R659 pmid: 1 publication: Current Biology publication_identifier: issn: - 0960-9822 publication_status: published publisher: Cell Press publist_id: '1912' quality_controlled: '1' scopus_import: '1' status: public title: 'Wnt signalling: Refocusing on Strabismus' type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 12 year: '2002' ... --- _id: '4194' abstract: - lang: eng text: Cells at the anterior boundary of the neural plate (ANB) can induce telencephalic gene expression when transplanted to more posterior regions. Here, we identify a secreted Frizzled-related Wnt antagonist, Tic, that is expressed in ANB cells and can cell nonautonomously promote telencephalic gene expression in a concentration-dependent manner. Moreover, abrogation of Tlc function compromises telencephalic development. We also identify Wnt8b as a locally acting modulator of regional fate in the anterior neural plate and a likely target for antagonism by Tic. Finally, we show that tlc expression is regulated by signals that establish early antero-posterior and dorso-ventral ectodermal pattern. From these studies, we propose that local antagonism of Wnt activity within the anterior ectoderm is required to establish the telencephalon. acknowledgement: We thank many of our colleagues, especially Randy Moon, for providing reagents used in this study. This study was supported by the Wellcome Trust, MRC, and BBSRC to S.W.W. and C.H. S.W.W. is a Wellcome Trust Senior Research Fellow. article_processing_charge: No article_type: original author: - first_name: Corinne full_name: Houart, Corinne last_name: Houart - first_name: Luca full_name: Caneparo, Luca last_name: Caneparo - 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 - first_name: K Anukampa full_name: Barth, K Anukampa last_name: Barth - first_name: Masaya full_name: Take Uchi, Masaya last_name: Take Uchi - first_name: Stephen full_name: Wilson, Stephen last_name: Wilson citation: ama: Houart C, Caneparo L, Heisenberg C-PJ, Barth KA, Take Uchi M, Wilson S. Establishment of the telencephalon during gastrulation by local antagonism of Wnt signaling. Neuron. 2002;35(2):255-265. doi:10.1016/S0896-6273(02)00751-1 apa: Houart, C., Caneparo, L., Heisenberg, C.-P. J., Barth, K. A., Take Uchi, M., & Wilson, S. (2002). Establishment of the telencephalon during gastrulation by local antagonism of Wnt signaling. Neuron. Elsevier. https://doi.org/10.1016/S0896-6273(02)00751-1 chicago: Houart, Corinne, Luca Caneparo, Carl-Philipp J Heisenberg, K Anukampa Barth, Masaya Take Uchi, and Stephen Wilson. “Establishment of the Telencephalon during Gastrulation by Local Antagonism of Wnt Signaling.” Neuron. Elsevier, 2002. https://doi.org/10.1016/S0896-6273(02)00751-1. ieee: C. Houart, L. Caneparo, C.-P. J. Heisenberg, K. A. Barth, M. Take Uchi, and S. Wilson, “Establishment of the telencephalon during gastrulation by local antagonism of Wnt signaling,” Neuron, vol. 35, no. 2. Elsevier, pp. 255–265, 2002. ista: Houart C, Caneparo L, Heisenberg C-PJ, Barth KA, Take Uchi M, Wilson S. 2002. Establishment of the telencephalon during gastrulation by local antagonism of Wnt signaling. Neuron. 35(2), 255–265. mla: Houart, Corinne, et al. “Establishment of the Telencephalon during Gastrulation by Local Antagonism of Wnt Signaling.” Neuron, vol. 35, no. 2, Elsevier, 2002, pp. 255–65, doi:10.1016/S0896-6273(02)00751-1. short: C. Houart, L. Caneparo, C.-P.J. Heisenberg, K.A. Barth, M. Take Uchi, S. Wilson, Neuron 35 (2002) 255–265. date_created: 2018-12-11T12:07:30Z date_published: 2002-07-18T00:00:00Z date_updated: 2023-06-07T09:43:19Z day: '18' doi: 10.1016/S0896-6273(02)00751-1 extern: '1' external_id: pmid: - '12160744' intvolume: ' 35' issue: '2' language: - iso: eng month: '07' oa_version: None page: 255 - 265 pmid: 1 publication: Neuron publication_identifier: issn: - 0896-6273 publication_status: published publisher: Elsevier publist_id: '1925' quality_controlled: '1' scopus_import: '1' status: public title: Establishment of the telencephalon during gastrulation by local antagonism of Wnt signaling type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 35 year: '2002' ... --- _id: '4148' abstract: - lang: eng text: Members of the Wnt family have been implicated in a variety of developmental processes including axis formation, Patterning of the central nervous system and tissue morphogenesis. Recent studies have shown that a Wnt signalling pathway similar to that involved in the establishment of planar cell polarity in Drosophila regulates convergent extension movements during zebrafish and Xenopus gastrulation. This finding provides a good starting point to dissect the complex cell biology and genetic regulation of vertebrate gastrulation movements. acknowledgement: We would like to thank Steve Wilson for encouraging us to write this article and for critical comments on this manuscript, and Lila Solnica-Krezel for communicating results prior to publication. MT is supported by an MRC Career Development Award, MLC by a Wellcome Trust Fellowship and CPH by an Emmy–Noether–Fellowship from the DFG. article_processing_charge: No article_type: original author: - first_name: Masazumi full_name: Tada, Masazumi last_name: Tada - first_name: Miguel full_name: Concha, Miguel last_name: Concha - 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: Tada M, Concha M, Heisenberg C-PJ. Non-canonical Wnt signalling and regulation of gastrulation movements. Seminars in Cell & Developmental Biology. 2002;13(3):251-260. doi:10.1016/S1084-9521(02)00052-6 apa: Tada, M., Concha, M., & Heisenberg, C.-P. J. (2002). Non-canonical Wnt signalling and regulation of gastrulation movements. Seminars in Cell & Developmental Biology. Academic Press. https://doi.org/10.1016/S1084-9521(02)00052-6 chicago: Tada, Masazumi, Miguel Concha, and Carl-Philipp J Heisenberg. “Non-Canonical Wnt Signalling and Regulation of Gastrulation Movements.” Seminars in Cell & Developmental Biology. Academic Press, 2002. https://doi.org/10.1016/S1084-9521(02)00052-6. ieee: M. Tada, M. Concha, and C.-P. J. Heisenberg, “Non-canonical Wnt signalling and regulation of gastrulation movements,” Seminars in Cell & Developmental Biology, vol. 13, no. 3. Academic Press, pp. 251–260, 2002. ista: Tada M, Concha M, Heisenberg C-PJ. 2002. Non-canonical Wnt signalling and regulation of gastrulation movements. Seminars in Cell & Developmental Biology. 13(3), 251–260. mla: Tada, Masazumi, et al. “Non-Canonical Wnt Signalling and Regulation of Gastrulation Movements.” Seminars in Cell & Developmental Biology, vol. 13, no. 3, Academic Press, 2002, pp. 251–60, doi:10.1016/S1084-9521(02)00052-6. short: M. Tada, M. Concha, C.-P.J. Heisenberg, Seminars in Cell & Developmental Biology 13 (2002) 251–260. date_created: 2018-12-11T12:07:13Z date_published: 2002-06-01T00:00:00Z date_updated: 2023-06-07T09:50:14Z day: '01' doi: 10.1016/S1084-9521(02)00052-6 extern: '1' external_id: pmid: - '12137734' intvolume: ' 13' issue: '3' language: - iso: eng month: '06' oa_version: None page: 251 - 260 pmid: 1 publication: Seminars in Cell & Developmental Biology publication_identifier: issn: - 1084-9521 publication_status: published publisher: Academic Press publist_id: '1973' quality_controlled: '1' scopus_import: '1' status: public title: Non-canonical Wnt signalling and regulation of gastrulation movements type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 13 year: '2002' ... --- _id: '4196' abstract: - lang: eng text: During vertebrate gastrulation, large cellular rearrangements lead to the formation of the three germ layers, ectoderm, mesoderm and endoderm. Zebrafish offer many genetic and experimental advantages for studying vertebrate gastrulation movements. For instance, several mutants, including silberblick, knypek and trilobite, exhibit defects in morphogenesis during gastrulation. The identification of the genes mutated in these lines together with the analysis of the mutant phenotypes has provided new insights into the molecular and cellular mechanisms that underlie vertebrate gastrulation movements. acknowledgement: We would like to thank Miguel Concha, Will Norton, Tim Geach, Suzanne Eaton, Kimbo Kotovic, Jenny Geiger and Steve Wilson for critical comments on this manuscript, and Lila Solnica-Krezel for providing results prior to publication. C.-P.H. is supported by an Emmy-Noether-Fellowship from the DFG and M.T. by an MRC Career Development Award. article_processing_charge: No article_type: original author: - 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 - first_name: Masazumi full_name: Tada, Masazumi last_name: Tada citation: ama: 'Heisenberg C-PJ, Tada M. Zebrafish gastrulation movements: bridging cell and developmental biology. Seminars in Cell & Developmental Biology. 2002;13(6):471-479. doi:10.1016/S1084952102001003' apa: 'Heisenberg, C.-P. J., & Tada, M. (2002). Zebrafish gastrulation movements: bridging cell and developmental biology. Seminars in Cell & Developmental Biology. Academic Press. https://doi.org/10.1016/S1084952102001003' chicago: 'Heisenberg, Carl-Philipp J, and Masazumi Tada. “Zebrafish Gastrulation Movements: Bridging Cell and Developmental Biology.” Seminars in Cell & Developmental Biology. Academic Press, 2002. https://doi.org/10.1016/S1084952102001003.' ieee: 'C.-P. J. Heisenberg and M. Tada, “Zebrafish gastrulation movements: bridging cell and developmental biology,” Seminars in Cell & Developmental Biology, vol. 13, no. 6. Academic Press, pp. 471–479, 2002.' ista: 'Heisenberg C-PJ, Tada M. 2002. Zebrafish gastrulation movements: bridging cell and developmental biology. Seminars in Cell & Developmental Biology. 13(6), 471–479.' mla: 'Heisenberg, Carl-Philipp J., and Masazumi Tada. “Zebrafish Gastrulation Movements: Bridging Cell and Developmental Biology.” Seminars in Cell & Developmental Biology, vol. 13, no. 6, Academic Press, 2002, pp. 471–79, doi:10.1016/S1084952102001003.' short: C.-P.J. Heisenberg, M. Tada, Seminars in Cell & Developmental Biology 13 (2002) 471–479. date_created: 2018-12-11T12:07:31Z date_published: 2002-12-01T00:00:00Z date_updated: 2023-06-07T09:28:48Z day: '01' doi: 10.1016/S1084952102001003 extern: '1' external_id: pmid: - '12468250' intvolume: ' 13' issue: '6' language: - iso: eng month: '12' oa_version: None page: 471 - 479 pmid: 1 publication: Seminars in Cell & Developmental Biology publication_identifier: issn: - 1084-9521 publication_status: published publisher: Academic Press publist_id: '1920' quality_controlled: '1' scopus_import: '1' status: public title: 'Zebrafish gastrulation movements: bridging cell and developmental biology' type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 13 year: '2002' ... --- _id: '4199' abstract: - lang: eng text: Recent studies on vertebrate homologues of the van gogh/strabismus (vang/stbm) gene, a key player in planar cell polarity signalling in Drosophila, show that vang/stbm is involved in patterning and morphogenesis during vertebrate gastrulation where it modulates two distinct Wnt signals. article_processing_charge: No article_type: original author: - 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 - first_name: Masazumi full_name: Tada, Masazumi last_name: Tada citation: ama: 'Heisenberg C-PJ, Tada M. Wnt signalling: A moving picture emerges from van gogh. Current Biology. 2002;12(4):R126-R128. doi:10.1016/S0960-9822(02)00704-2' apa: 'Heisenberg, C.-P. J., & Tada, M. (2002). Wnt signalling: A moving picture emerges from van gogh. Current Biology. Cell Press. https://doi.org/10.1016/S0960-9822(02)00704-2' chicago: 'Heisenberg, Carl-Philipp J, and Masazumi Tada. “Wnt Signalling: A Moving Picture Emerges from van Gogh.” Current Biology. Cell Press, 2002. https://doi.org/10.1016/S0960-9822(02)00704-2.' ieee: 'C.-P. J. Heisenberg and M. Tada, “Wnt signalling: A moving picture emerges from van gogh,” Current Biology, vol. 12, no. 4. Cell Press, pp. R126–R128, 2002.' ista: 'Heisenberg C-PJ, Tada M. 2002. Wnt signalling: A moving picture emerges from van gogh. Current Biology. 12(4), R126–R128.' mla: 'Heisenberg, Carl-Philipp J., and Masazumi Tada. “Wnt Signalling: A Moving Picture Emerges from van Gogh.” Current Biology, vol. 12, no. 4, Cell Press, 2002, pp. R126–28, doi:10.1016/S0960-9822(02)00704-2.' short: C.-P.J. Heisenberg, M. Tada, Current Biology 12 (2002) R126–R128. date_created: 2018-12-11T12:07:32Z date_published: 2002-02-19T00:00:00Z date_updated: 2023-06-07T08:54:35Z day: '19' doi: 10.1016/S0960-9822(02)00704-2 extern: '1' external_id: pmid: - '11864583' intvolume: ' 12' issue: '4' language: - iso: eng month: '02' oa_version: None page: R126 - R128 pmid: 1 publication: Current Biology publication_identifier: issn: - 0960-9822 publication_status: published publisher: Cell Press publist_id: '1919' quality_controlled: '1' scopus_import: '1' status: public title: 'Wnt signalling: A moving picture emerges from van gogh' type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 12 year: '2002' ... --- _id: '4139' abstract: - lang: eng text: Pilot studies in England by Stopka and Macdonald revealed that allogrooming in the Old World wood mouse, Apodemus sylvaticus, is a commodity that males can trade for reproductive benefits with females. This study, which used a combination of field study and observations in experimental enclosures, revealed that specific experimental conditions such as group-size and sex-ratio manipulations have a significant effect on the pattern of allogrooming exchanged between individuals. Furthermore, females from the Czech population were more likely to associate with each other as revealed by the clustering of activity centers of females (i.e., as opposed to almost exclusive ranges in English populations), and also by the higher intensity of allogrooming exchanged between females (i.e., virtually lacking in the previous experiment with English mice). Therefore, geographic variation and specific social conditions seem to be important driving factors for allogrooming behavior. Together with changes in overall grooming patterns, allogrooming between males and females remained invariably asymmetrical over all four experimental groups (i.e., two conditions for each sex) in that males provided more allogrooming to females than they received from them. article_processing_charge: No article_type: original author: - first_name: Jitka full_name: Polechova, Jitka id: 3BBFB084-F248-11E8-B48F-1D18A9856A87 last_name: Polechova orcid: 0000-0003-0951-3112 - first_name: P. full_name: Stopka, P. last_name: Stopka citation: ama: Polechova J, Stopka P. Geometry of social relationships in the Old World wood mouse, Apodemus sylvaticus. Canadian Journal of Zoology. 2002;80(8):1383-1388. doi:10.1139/z02-128 apa: Polechova, J., & Stopka, P. (2002). Geometry of social relationships in the Old World wood mouse, Apodemus sylvaticus. Canadian Journal of Zoology. NRC Research Press. https://doi.org/10.1139/z02-128 chicago: Polechova, Jitka, and P. Stopka. “Geometry of Social Relationships in the Old World Wood Mouse, Apodemus Sylvaticus.” Canadian Journal of Zoology. NRC Research Press, 2002. https://doi.org/10.1139/z02-128. ieee: J. Polechova and P. Stopka, “Geometry of social relationships in the Old World wood mouse, Apodemus sylvaticus,” Canadian Journal of Zoology, vol. 80, no. 8. NRC Research Press, pp. 1383–1388, 2002. ista: Polechova J, Stopka P. 2002. Geometry of social relationships in the Old World wood mouse, Apodemus sylvaticus. Canadian Journal of Zoology. 80(8), 1383–1388. mla: Polechova, Jitka, and P. Stopka. “Geometry of Social Relationships in the Old World Wood Mouse, Apodemus Sylvaticus.” Canadian Journal of Zoology, vol. 80, no. 8, NRC Research Press, 2002, pp. 1383–88, doi:10.1139/z02-128. short: J. Polechova, P. Stopka, Canadian Journal of Zoology 80 (2002) 1383–1388. date_created: 2018-12-11T12:07:10Z date_published: 2002-01-01T00:00:00Z date_updated: 2023-06-07T12:53:35Z day: '01' doi: 10.1139/z02-128 extern: '1' intvolume: ' 80' issue: '8' language: - iso: eng month: '01' oa_version: None page: 1383 - 1388 publication: Canadian Journal of Zoology publication_identifier: issn: - 0008-4301 publication_status: published publisher: NRC Research Press publist_id: '1981' quality_controlled: '1' scopus_import: '1' status: public title: Geometry of social relationships in the Old World wood mouse, Apodemus sylvaticus type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 80 year: '2002' ... --- _id: '4003' abstract: - lang: eng text: The writhing number measures the global geometry of a closed space curve or knot. We show that this measure is related to the average winding number of its Gauss map. Using this relationship, we give an algorithm for computing the writhing number for a polygonal knot with n edges in time roughly proportional to n(1.6). We also implement a different, simple algorithm and provide experimental evidence for its practical efficiency. acknowledgement: NSF under grants CCR-00-86013 and EIA-9972879, NSF under grant CCR-97-12088. article_processing_charge: No author: - first_name: Pankaj full_name: Agarwal, Pankaj last_name: Agarwal - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Yusu full_name: Wang, Yusu last_name: Wang citation: ama: 'Agarwal P, Edelsbrunner H, Wang Y. Computing the writhing number of a polygonal knot. In: Proceedings of the 13th Annual ACM-SIAM Symposium on Discrete Algorithms. SIAM; 2002:791-799.' apa: 'Agarwal, P., Edelsbrunner, H., & Wang, Y. (2002). Computing the writhing number of a polygonal knot. In Proceedings of the 13th annual ACM-SIAM symposium on Discrete algorithms (pp. 791–799). San Francisco, CA, USA: SIAM.' chicago: Agarwal, Pankaj, Herbert Edelsbrunner, and Yusu Wang. “Computing the Writhing Number of a Polygonal Knot.” In Proceedings of the 13th Annual ACM-SIAM Symposium on Discrete Algorithms, 791–99. SIAM, 2002. ieee: P. Agarwal, H. Edelsbrunner, and Y. Wang, “Computing the writhing number of a polygonal knot,” in Proceedings of the 13th annual ACM-SIAM symposium on Discrete algorithms, San Francisco, CA, USA, 2002, pp. 791–799. ista: 'Agarwal P, Edelsbrunner H, Wang Y. 2002. Computing the writhing number of a polygonal knot. Proceedings of the 13th annual ACM-SIAM symposium on Discrete algorithms. SODA: Symposium on Discrete Algorithms, 791–799.' mla: Agarwal, Pankaj, et al. “Computing the Writhing Number of a Polygonal Knot.” Proceedings of the 13th Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2002, pp. 791–99. short: P. Agarwal, H. Edelsbrunner, Y. Wang, in:, Proceedings of the 13th Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2002, pp. 791–799. conference: end_date: 2002-01-08 location: San Francisco, CA, USA name: 'SODA: Symposium on Discrete Algorithms' start_date: 2002-01-06 date_created: 2018-12-11T12:06:23Z date_published: 2002-01-01T00:00:00Z date_updated: 2023-06-07T13:50:04Z day: '01' extern: '1' language: - iso: eng main_file_link: - url: https://dl.acm.org/doi/10.5555/545381.545485 month: '01' oa_version: None page: 791 - 799 publication: Proceedings of the 13th annual ACM-SIAM symposium on Discrete algorithms publication_identifier: isbn: - '9780898715132' publication_status: published publisher: SIAM publist_id: '2125' quality_controlled: '1' scopus_import: '1' status: public title: Computing the writhing number of a polygonal knot type: conference user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 year: '2002' ... --- _id: '3995' abstract: - lang: eng text: This article is a survey of research areas in which motion plays a pivotal role. The aim of the article is to review current approaches to modeling motion together with related data structures and algorithms, and to summarize the challenges that lie ahead in producing a more unified theory of motion representation that would be useful across several disciplines. acknowledgement: "This article is based on the report of the Workshop on Algorithmic Issues in Modeling Motion, sponsored\r\nby an NSF grant CCR-00-83-033 and an Army Research Office grant DAAD 19-00-1-0478, held on August 6\r\nand 7, 2000 at Duke University, Durham, NC." article_processing_charge: No article_type: original author: - first_name: Pankaj full_name: Agarwal, Pankaj last_name: Agarwal - first_name: Leonidas full_name: Guibas, Leonidas last_name: Guibas - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Jeff full_name: Erickson, Jeff last_name: Erickson - first_name: Michael full_name: Isard, Michael last_name: Isard - first_name: Sariel full_name: Har Peled, Sariel last_name: Har Peled - first_name: John full_name: Hershberger, John last_name: Hershberger - first_name: Christian full_name: Jensen, Christian last_name: Jensen - first_name: Lydia full_name: Kavraki, Lydia last_name: Kavraki - first_name: Patrice full_name: Koehl, Patrice last_name: Koehl - first_name: Ming full_name: Lin, Ming last_name: Lin - first_name: Dinesh full_name: Manocha, Dinesh last_name: Manocha - first_name: Dimitris full_name: Metaxas, Dimitris last_name: Metaxas - first_name: Brian full_name: Mirtich, Brian last_name: Mirtich - first_name: David full_name: Mount, David last_name: Mount - first_name: Sankara full_name: Muthukrishnan, Sankara last_name: Muthukrishnan - first_name: Dinesh full_name: Pai, Dinesh last_name: Pai - first_name: Elisha full_name: Sacks, Elisha last_name: Sacks - first_name: Jack full_name: Snoeyink, Jack last_name: Snoeyink - first_name: Subhash full_name: Suri, Subhash last_name: Suri - first_name: Ouri full_name: Wolefson, Ouri last_name: Wolefson citation: ama: Agarwal P, Guibas L, Edelsbrunner H, et al. Algorithmic issues in modeling motion. ACM Computing Surveys. 2002;34(4):550-572. doi:10.1145/592642.592647 apa: Agarwal, P., Guibas, L., Edelsbrunner, H., Erickson, J., Isard, M., Har Peled, S., … Wolefson, O. (2002). Algorithmic issues in modeling motion. ACM Computing Surveys. ACM. https://doi.org/10.1145/592642.592647 chicago: Agarwal, Pankaj, Leonidas Guibas, Herbert Edelsbrunner, Jeff Erickson, Michael Isard, Sariel Har Peled, John Hershberger, et al. “Algorithmic Issues in Modeling Motion.” ACM Computing Surveys. ACM, 2002. https://doi.org/10.1145/592642.592647. ieee: P. Agarwal et al., “Algorithmic issues in modeling motion,” ACM Computing Surveys, vol. 34, no. 4. ACM, pp. 550–572, 2002. ista: Agarwal P, Guibas L, Edelsbrunner H, Erickson J, Isard M, Har Peled S, Hershberger J, Jensen C, Kavraki L, Koehl P, Lin M, Manocha D, Metaxas D, Mirtich B, Mount D, Muthukrishnan S, Pai D, Sacks E, Snoeyink J, Suri S, Wolefson O. 2002. Algorithmic issues in modeling motion. ACM Computing Surveys. 34(4), 550–572. mla: Agarwal, Pankaj, et al. “Algorithmic Issues in Modeling Motion.” ACM Computing Surveys, vol. 34, no. 4, ACM, 2002, pp. 550–72, doi:10.1145/592642.592647. short: P. Agarwal, L. Guibas, H. Edelsbrunner, J. Erickson, M. Isard, S. Har Peled, J. Hershberger, C. Jensen, L. Kavraki, P. Koehl, M. Lin, D. Manocha, D. Metaxas, B. Mirtich, D. Mount, S. Muthukrishnan, D. Pai, E. Sacks, J. Snoeyink, S. Suri, O. Wolefson, ACM Computing Surveys 34 (2002) 550–572. date_created: 2018-12-11T12:06:20Z date_published: 2002-12-01T00:00:00Z date_updated: 2023-06-13T11:34:25Z day: '01' doi: 10.1145/592642.592647 extern: '1' intvolume: ' 34' issue: '4' language: - iso: eng month: '12' oa_version: None page: 550 - 572 publication: ACM Computing Surveys publication_identifier: issn: - 0360-0300 publication_status: published publisher: ACM publist_id: '2129' quality_controlled: '1' scopus_import: '1' status: public title: Algorithmic issues in modeling motion type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 34 year: '2002' ... --- _id: '4000' abstract: - lang: eng text: We present fast implementations of a hybrid algorithm for reporting box and cube intersections. Our algorithm initially takes a divide-and-conquer approach and switches to simpler algorithms for low numbers of boxes. We use our implementations as engines to solve problems about geometric primitives. We look at two such problems in the category of quality analysis of surface triangulations. acknowledgement: Center for Simulation of Advanced Rockets funded by the U.S. Department of Energy under Subcontract B341494, NSF under grant CCR-96-19542 and ARO under grant DAAG55-98-1-0177. article_processing_charge: No article_type: original author: - first_name: Afra full_name: Zomorodian, Afra last_name: Zomorodian - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: Zomorodian A, Edelsbrunner H. Fast software for box intersections. International Journal of Computational Geometry and Applications. 2002;12(1-2):143-172. doi:10.1142/S0218195902000785 apa: Zomorodian, A., & Edelsbrunner, H. (2002). Fast software for box intersections. International Journal of Computational Geometry and Applications. World Scientific Publishing. https://doi.org/10.1142/S0218195902000785 chicago: Zomorodian, Afra, and Herbert Edelsbrunner. “Fast Software for Box Intersections.” International Journal of Computational Geometry and Applications. World Scientific Publishing, 2002. https://doi.org/10.1142/S0218195902000785. ieee: A. Zomorodian and H. Edelsbrunner, “Fast software for box intersections,” International Journal of Computational Geometry and Applications, vol. 12, no. 1–2. World Scientific Publishing, pp. 143–172, 2002. ista: Zomorodian A, Edelsbrunner H. 2002. Fast software for box intersections. International Journal of Computational Geometry and Applications. 12(1–2), 143–172. mla: Zomorodian, Afra, and Herbert Edelsbrunner. “Fast Software for Box Intersections.” International Journal of Computational Geometry and Applications, vol. 12, no. 1–2, World Scientific Publishing, 2002, pp. 143–72, doi:10.1142/S0218195902000785. short: A. Zomorodian, H. Edelsbrunner, International Journal of Computational Geometry and Applications 12 (2002) 143–172. date_created: 2018-12-11T12:06:22Z date_published: 2002-01-01T00:00:00Z date_updated: 2023-06-13T11:20:09Z day: '01' doi: 10.1142/S0218195902000785 extern: '1' intvolume: ' 12' issue: 1-2 language: - iso: eng month: '01' oa_version: None page: 143 - 172 publication: International Journal of Computational Geometry and Applications publication_identifier: issn: - 0218-1959 publication_status: published publisher: World Scientific Publishing publist_id: '2128' quality_controlled: '1' scopus_import: '1' status: public title: Fast software for box intersections type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 12 year: '2002' ... --- _id: '3998' abstract: - lang: eng text: We present results on a two-step improvement of mesh quality in three-dimensional Delaunay triangulations. The first step refines the triangulation by inserting sinks and eliminates tetrahedra with large circumradius over shortest edge length ratio. The second step assigns weights to the vertices to eliminate slivers. Our experimental findings provide evidence for the practical effectiveness of sliver exudation. acknowledgement: NSF under grants CCR-97-12088 and DMS 98-73945, NSF under grands EIA-9972879 and CCR-00-86013 and by ARO under grant DAAG55-98-1- 0177. article_processing_charge: No article_type: original author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Damrong full_name: Guoy, Damrong last_name: Guoy citation: ama: Edelsbrunner H, Guoy D. An experimental study of sliver exudation. Engineering with Computers. 2002;18(3):229-240. doi:10.1007/s003660200020 apa: Edelsbrunner, H., & Guoy, D. (2002). An experimental study of sliver exudation. Engineering with Computers. Springer. https://doi.org/10.1007/s003660200020 chicago: Edelsbrunner, Herbert, and Damrong Guoy. “An Experimental Study of Sliver Exudation.” Engineering with Computers. Springer, 2002. https://doi.org/10.1007/s003660200020. ieee: H. Edelsbrunner and D. Guoy, “An experimental study of sliver exudation,” Engineering with Computers, vol. 18, no. 3. Springer, pp. 229–240, 2002. ista: Edelsbrunner H, Guoy D. 2002. An experimental study of sliver exudation. Engineering with Computers. 18(3), 229–240. mla: Edelsbrunner, Herbert, and Damrong Guoy. “An Experimental Study of Sliver Exudation.” Engineering with Computers, vol. 18, no. 3, Springer, 2002, pp. 229–40, doi:10.1007/s003660200020. short: H. Edelsbrunner, D. Guoy, Engineering with Computers 18 (2002) 229–240. date_created: 2018-12-11T12:06:21Z date_published: 2002-10-01T00:00:00Z date_updated: 2023-06-13T11:14:44Z day: '01' doi: 10.1007/s003660200020 extern: '1' intvolume: ' 18' issue: '3' language: - iso: eng month: '10' oa_version: None page: 229 - 240 publication: Engineering with Computers publication_identifier: issn: - 0177-0667 publication_status: published publisher: Springer publist_id: '2126' quality_controlled: '1' scopus_import: '1' status: public title: An experimental study of sliver exudation type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 18 year: '2002' ... --- _id: '3802' abstract: - lang: eng text: The presynaptic Ca2+ signal is a key determinant of transmitter release at chemical synapses. In cortical synaptic terminals, however, little is known about the kinetic properties of the presynaptic Ca2+ channels. To investigate the timing and magnitude of the presynaptic Ca2+ inflow, we performed whole-cell patch-clamp recordings from mossy fiber boutons (MFBs) in rat hippocampus. MFBs showed large high-voltage-activated Ca(2+) currents, with a maximal amplitude of approximately 100 pA at a membrane potential of 0 mV. Both activation and deactivation were fast, with time constants in the submillisecond range at a temperature of approximately 23 degrees C. An MFB action potential (AP) applied as a voltage-clamp command evoked a transient Ca2+ current with an average amplitude of approximately 170 pA and a half-duration of 580 microsec. A prepulse to +40 mV had only minimal effects on the AP-evoked Ca2+ current, indicating that presynaptic APs open the voltage-gated Ca2+ channels very effectively. On the basis of the experimental data, we developed a kinetic model with four closed states and one open state, linked by voltage-dependent rate constants. Simulations of the Ca2+ current could reproduce the experimental data, including the large amplitude and rapid time course of the current evoked by MFB APs. Furthermore, the simulations indicate that the shape of the presynaptic AP and the gating kinetics of the Ca2+ channels are tuned to produce a maximal Ca2+ influx during a minimal period of time. The precise timing and high efficacy of Ca2+ channel activation at this cortical glutamatergic synapse may be important for synchronous transmitter release and temporal information processing. acknowledgement: J.B. was supported by grants from the Deutsche Forschungsgemeinschaft (Bi 642/1-2 and SFB 505/C9). We thank Dr. U. Kraushaar, Dr. S. Hefft, and C. Schmidt-Hieber for critically reading this manuscript, F. Heyde for secretarial help, and A. Blomenkamp and K. Winterhalter for technical assistance. article_processing_charge: No article_type: original author: - first_name: Josef full_name: Bischofberger, Josef last_name: Bischofberger - first_name: Jörg full_name: Geiger, Jörg last_name: Geiger - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Bischofberger J, Geiger J, Jonas PM. Timing and efficacy of Ca(2+) channel activation in hippocampal mossy fiber boutons. Journal of Neuroscience. 2002;22(24):10593-10602. doi:10.1523/JNEUROSCI.22-24-10593.2002 apa: Bischofberger, J., Geiger, J., & Jonas, P. M. (2002). Timing and efficacy of Ca(2+) channel activation in hippocampal mossy fiber boutons. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.22-24-10593.2002 chicago: Bischofberger, Josef, Jörg Geiger, and Peter M Jonas. “Timing and Efficacy of Ca(2+) Channel Activation in Hippocampal Mossy Fiber Boutons.” Journal of Neuroscience. Society for Neuroscience, 2002. https://doi.org/10.1523/JNEUROSCI.22-24-10593.2002. ieee: J. Bischofberger, J. Geiger, and P. M. Jonas, “Timing and efficacy of Ca(2+) channel activation in hippocampal mossy fiber boutons,” Journal of Neuroscience, vol. 22, no. 24. Society for Neuroscience, pp. 10593–10602, 2002. ista: Bischofberger J, Geiger J, Jonas PM. 2002. Timing and efficacy of Ca(2+) channel activation in hippocampal mossy fiber boutons. Journal of Neuroscience. 22(24), 10593–10602. mla: Bischofberger, Josef, et al. “Timing and Efficacy of Ca(2+) Channel Activation in Hippocampal Mossy Fiber Boutons.” Journal of Neuroscience, vol. 22, no. 24, Society for Neuroscience, 2002, pp. 10593–602, doi:10.1523/JNEUROSCI.22-24-10593.2002. short: J. Bischofberger, J. Geiger, P.M. Jonas, Journal of Neuroscience 22 (2002) 10593–10602. date_created: 2018-12-11T12:05:15Z date_published: 2002-12-01T00:00:00Z date_updated: 2023-06-13T13:19:45Z day: '01' doi: 10.1523/JNEUROSCI.22-24-10593.2002 extern: '1' external_id: pmid: - '12486151' intvolume: ' 22' issue: '24' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6758411/ month: '12' oa: 1 oa_version: Published Version page: 10593 - 10602 pmid: 1 publication: Journal of Neuroscience publication_identifier: issn: - 0270-6474 publication_status: published publisher: Society for Neuroscience publist_id: '2407' quality_controlled: '1' scopus_import: '1' status: public title: Timing and efficacy of Ca(2+) channel activation in hippocampal mossy fiber boutons type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 22 year: '2002' ... --- _id: '3919' abstract: - lang: eng text: Hamilton's concept of local mate competition (LMC) is the standard model to explain female-biased sex ratios in solitary Hymenoptera. In social Hymenoptera, however, LMC has remained controversial, mainly because manipulation of sex allocation by workers in response to relatedness asymmetries is an additional powerful mechanism of female bias. Furthermore, the predominant mating systems in the social insects are thought to make LMC unlikely. Nevertheless, several species exist in which dispersal of males is limited and mating occurs in the nest. Some of these species, such as the ant Cardiocondyla obscurior, have evolved dimorphic males, with one morph being specialized for dispersal and the other for fighting with nest-mate males over access to females. Such life history, combining sociality and alternative reproductive tactics in males, provides a unique opportunity to test the power of LMC as a selective force leading to female-biased sex ratios in social Hymenoptera. We show that, in concordance with LMC predictions, an experimental increase in queen number leads to a shift in sex allocation in favour of non-dispersing males, but does not influence the proportion of disperser males. Furthermore, we can assign this change in sex allocation at the colony level to the queens and rule out worker manipulation. acknowledgement: 'We thank A. F. G. Bourke, J. J. Boomsma, S. Foitzik, M. Sixt,C. Anderson and C. Schubart for improving the manuscript, and E. Sixt for ant illustrations (figure 2). This study was funded by the DFG (Deutsche Forschungsgemeinschaft: He1623/7-2).' article_processing_charge: No article_type: original author: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze citation: ama: 'Cremer S, Heinze J. Adaptive production of fighter males: queens of the ant Cardiocondyla adjust the sex ratio under local mate competition. Proceedings of the Royal Society of London Series B Biological Sciences. 2002;269(1489):417-422. doi:10.1098/rspb.2001.1892' apa: 'Cremer, S., & Heinze, J. (2002). Adaptive production of fighter males: queens of the ant Cardiocondyla adjust the sex ratio under local mate competition. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2001.1892' chicago: 'Cremer, Sylvia, and Jürgen Heinze. “Adaptive Production of Fighter Males: Queens of the Ant Cardiocondyla Adjust the Sex Ratio under Local Mate Competition.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2002. https://doi.org/10.1098/rspb.2001.1892.' ieee: 'S. Cremer and J. Heinze, “Adaptive production of fighter males: queens of the ant Cardiocondyla adjust the sex ratio under local mate competition,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 269, no. 1489. Royal Society, The, pp. 417–422, 2002.' ista: 'Cremer S, Heinze J. 2002. Adaptive production of fighter males: queens of the ant Cardiocondyla adjust the sex ratio under local mate competition. Proceedings of the Royal Society of London Series B Biological Sciences. 269(1489), 417–422.' mla: 'Cremer, Sylvia, and Jürgen Heinze. “Adaptive Production of Fighter Males: Queens of the Ant Cardiocondyla Adjust the Sex Ratio under Local Mate Competition.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 269, no. 1489, Royal Society, The, 2002, pp. 417–22, doi:10.1098/rspb.2001.1892.' short: S. Cremer, J. Heinze, Proceedings of the Royal Society of London Series B Biological Sciences 269 (2002) 417–422. date_created: 2018-12-11T12:05:53Z date_published: 2002-02-22T00:00:00Z date_updated: 2023-06-13T11:52:17Z day: '22' doi: 10.1098/rspb.2001.1892 extern: '1' external_id: pmid: - '11886631' intvolume: ' 269' issue: '1489' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1690910/ month: '02' oa: 1 oa_version: None page: 417 - 422 pmid: 1 publication: Proceedings of the Royal Society of London Series B Biological Sciences publication_identifier: issn: - 0962-8452 publication_status: published publisher: Royal Society, The publist_id: '2231' quality_controlled: '1' scopus_import: '1' status: public title: 'Adaptive production of fighter males: queens of the ant Cardiocondyla adjust the sex ratio under local mate competition' type: journal_article user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17 volume: 269 year: '2002' ...