--- _id: '1787' abstract: - lang: eng text: When two indistinguishable single photons impinge at the two inputs of a beam splitter they coalesce into a pair of photons appearing in either one of its two outputs. This effect is due to the bosonic nature of photons and was first experimentally observed by Hong, Ou and Mandel. Here, we present the observation of the Hong-Ou-Mandel effect with two independent single-photon sources in the microwave frequency domain. We probe the indistinguishability of single photons, created with a controllable delay, in time-resolved second-order cross- and auto-correlation function measurements. Using quadrature amplitude detection we are able to resolve different photon numbers and detect coherence in and between the output arms. This scheme allows us to fully characterize the two-mode entanglement of the spatially separated beam-splitter output modes. Our experiments constitute a first step towards using two-photon interference at microwave frequencies for quantum communication and information processing. acknowledgement: This work was supported by the European Research Council (ERC) through a Starting Grant and by ETHZ. L.S. was supported by EU IP SOLID. A.B. and M.J.W. were supported by NSERC, CIFAR and the Alfred P. Sloan Foundation author: - first_name: C full_name: Lang, C last_name: Lang - first_name: Christopher full_name: Eichler, Christopher last_name: Eichler - first_name: L. full_name: Steffen, L. Kraig last_name: Steffen - first_name: Johannes M full_name: Johannes Fink id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: Matthew full_name: Woolley, Matthew J last_name: Woolley - first_name: Alexandre full_name: Blais, Alexandre last_name: Blais - first_name: Andreas full_name: Wallraff, Andreas last_name: Wallraff citation: ama: Lang C, Eichler C, Steffen L, et al. Correlations, indistinguishability and entanglement in Hong-Ou-Mandel experiments at microwave frequencies. Nature Physics. 2013;9(6):345-348. doi:10.1038/nphys2612 apa: Lang, C., Eichler, C., Steffen, L., Fink, J. M., Woolley, M., Blais, A., & Wallraff, A. (2013). Correlations, indistinguishability and entanglement in Hong-Ou-Mandel experiments at microwave frequencies. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/nphys2612 chicago: Lang, C, Christopher Eichler, L. Steffen, Johannes M Fink, Matthew Woolley, Alexandre Blais, and Andreas Wallraff. “Correlations, Indistinguishability and Entanglement in Hong-Ou-Mandel Experiments at Microwave Frequencies.” Nature Physics. Nature Publishing Group, 2013. https://doi.org/10.1038/nphys2612. ieee: C. Lang et al., “Correlations, indistinguishability and entanglement in Hong-Ou-Mandel experiments at microwave frequencies,” Nature Physics, vol. 9, no. 6. Nature Publishing Group, pp. 345–348, 2013. ista: Lang C, Eichler C, Steffen L, Fink JM, Woolley M, Blais A, Wallraff A. 2013. Correlations, indistinguishability and entanglement in Hong-Ou-Mandel experiments at microwave frequencies. Nature Physics. 9(6), 345–348. mla: Lang, C., et al. “Correlations, Indistinguishability and Entanglement in Hong-Ou-Mandel Experiments at Microwave Frequencies.” Nature Physics, vol. 9, no. 6, Nature Publishing Group, 2013, pp. 345–48, doi:10.1038/nphys2612. short: C. Lang, C. Eichler, L. Steffen, J.M. Fink, M. Woolley, A. Blais, A. Wallraff, Nature Physics 9 (2013) 345–348. date_created: 2018-12-11T11:54:00Z date_published: 2013-06-01T00:00:00Z date_updated: 2021-01-12T06:53:11Z day: '01' doi: 10.1038/nphys2612 extern: 1 intvolume: ' 9' issue: '6' month: '06' page: 345 - 348 publication: Nature Physics publication_status: published publisher: Nature Publishing Group publist_id: '5327' quality_controlled: 0 status: public title: Correlations, indistinguishability and entanglement in Hong-Ou-Mandel experiments at microwave frequencies type: journal_article volume: 9 year: '2013' ... --- _id: '1786' abstract: - lang: eng text: We report the experimental observation and a theoretical explanation of collective suppression of linewidths for multiple superconducting qubits coupled to a good cavity. This demonstrates how strong qubit-cavity coupling can significantly modify the dephasing and dissipation processes that might be expected for individual qubits, and can potentially improve coherence times in many-body circuit QED. acknowledgement: J. K. acknowledges financial support from EPSRC program “TOPNES” (EP/I031014/1) and EPSRC (EP/G004714/2) author: - first_name: Felix full_name: Nissen, Felix last_name: Nissen - first_name: Johannes M full_name: Johannes Fink id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: Jonas full_name: Mlynek, Jonas A last_name: Mlynek - first_name: Andreas full_name: Wallraff, Andreas last_name: Wallraff - first_name: Jonathan full_name: Keeling, Jonathan M last_name: Keeling citation: ama: Nissen F, Fink JM, Mlynek J, Wallraff A, Keeling J. Collective suppression of linewidths in circuit QED. Physical Review Letters. 2013;110(20). doi:10.1103/PhysRevLett.110.203602 apa: Nissen, F., Fink, J. M., Mlynek, J., Wallraff, A., & Keeling, J. (2013). Collective suppression of linewidths in circuit QED. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.110.203602 chicago: Nissen, Felix, Johannes M Fink, Jonas Mlynek, Andreas Wallraff, and Jonathan Keeling. “Collective Suppression of Linewidths in Circuit QED.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.203602. ieee: F. Nissen, J. M. Fink, J. Mlynek, A. Wallraff, and J. Keeling, “Collective suppression of linewidths in circuit QED,” Physical Review Letters, vol. 110, no. 20. American Physical Society, 2013. ista: Nissen F, Fink JM, Mlynek J, Wallraff A, Keeling J. 2013. Collective suppression of linewidths in circuit QED. Physical Review Letters. 110(20). mla: Nissen, Felix, et al. “Collective Suppression of Linewidths in Circuit QED.” Physical Review Letters, vol. 110, no. 20, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.203602. short: F. Nissen, J.M. Fink, J. Mlynek, A. Wallraff, J. Keeling, Physical Review Letters 110 (2013). date_created: 2018-12-11T11:54:00Z date_published: 2013-05-15T00:00:00Z date_updated: 2021-01-12T06:53:11Z day: '15' doi: 10.1103/PhysRevLett.110.203602 extern: 1 intvolume: ' 110' issue: '20' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1302.0665 month: '05' oa: 1 publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '5328' quality_controlled: 0 status: public title: Collective suppression of linewidths in circuit QED type: journal_article volume: 110 year: '2013' ... --- _id: '1790' abstract: - lang: eng text: In the September 12, 2013 issue of Nature, the Epi4K Consortium (. Allen etal., 2013) reported sequencing 264patient trios with epileptic encephalopathies. The Consortium focused on genes exceptionally intolerant to sequence variations and found substantial interconnections with autism and intellectual disability gene networks. author: - first_name: Gaia full_name: Gaia Novarino id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Seungtae full_name: Baek, SeungTae last_name: Baek - first_name: Joseph full_name: Gleeson, Joseph G last_name: Gleeson citation: ama: 'Novarino G, Baek S, Gleeson J. The sacred disease: The puzzling genetics of epileptic disorders. Neuron. 2013;80(1):9-11. doi:10.1016/j.neuron.2013.09.019' apa: 'Novarino, G., Baek, S., & Gleeson, J. (2013). The sacred disease: The puzzling genetics of epileptic disorders. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2013.09.019' chicago: 'Novarino, Gaia, Seungtae Baek, and Joseph Gleeson. “The Sacred Disease: The Puzzling Genetics of Epileptic Disorders.” Neuron. Elsevier, 2013. https://doi.org/10.1016/j.neuron.2013.09.019.' ieee: 'G. Novarino, S. Baek, and J. Gleeson, “The sacred disease: The puzzling genetics of epileptic disorders,” Neuron, vol. 80, no. 1. Elsevier, pp. 9–11, 2013.' ista: 'Novarino G, Baek S, Gleeson J. 2013. The sacred disease: The puzzling genetics of epileptic disorders. Neuron. 80(1), 9–11.' mla: 'Novarino, Gaia, et al. “The Sacred Disease: The Puzzling Genetics of Epileptic Disorders.” Neuron, vol. 80, no. 1, Elsevier, 2013, pp. 9–11, doi:10.1016/j.neuron.2013.09.019.' short: G. Novarino, S. Baek, J. Gleeson, Neuron 80 (2013) 9–11. date_created: 2018-12-11T11:54:01Z date_published: 2013-10-02T00:00:00Z date_updated: 2021-01-12T06:53:13Z day: '02' doi: 10.1016/j.neuron.2013.09.019 extern: 1 intvolume: ' 80' issue: '1' month: '10' page: 9 - 11 publication: Neuron publication_status: published publisher: Elsevier publist_id: '5323' quality_controlled: 0 status: public title: 'The sacred disease: The puzzling genetics of epileptic disorders' type: journal_article volume: 80 year: '2013' ... --- _id: '1977' abstract: - lang: eng text: Complex I (NADH:ubiquinone oxidoreductase) is central to cellular energy production, being the first and largest enzyme of the respiratory chain in mitochondria. It couples electron transfer from NADH to ubiquinone with proton translocation across the inner mitochondrial membrane and is involved in a wide range of human neurodegenerative disorders. Mammalian complex I is composed of 44 different subunits, whereas the 'minimal' bacterial version contains 14 highly conserved 'core' subunits. The L-shaped assembly consists of hydrophilic and membrane domains. We have determined all known atomic structures of complex I, starting from the hydrophilic domain of Thermus thermophilus enzyme (eight subunits, nine Fe-S clusters), followed by the membrane domains of the Escherichia coli (six subunits, 55 transmembrane helices) and T. thermophilus (seven subunits, 64 transmembrane helices) enzymes, and finally culminating in a recent crystal structure of the entire intact complex I from T. thermophilus (536 kDa, 16 subunits, nine Fe-S clusters, 64 transmembrane helices). The structure suggests an unusual and unique coupling mechanism via longrange conformational changes. Determination of the structure of the entire complex was possible only through this step-by-step approach, building on from smaller subcomplexes towards the entire assembly. Large membrane proteins are notoriously difficult to crystallize, and so various non-standard and sometimes counterintuitive approaches were employed in order to achieve crystal diffraction to high resolution and solve the structures. These steps, as well as the implications from the final structure, are discussed in the present review. acknowledgement: This work was funded by the Medical Research Council. author: - first_name: Leonid A full_name: Leonid Sazanov id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 - first_name: Rozbeh full_name: 'Baradaran, Rozbeh ' last_name: Baradaran - first_name: Rouslan full_name: Efremov, Rouslan G last_name: Efremov - first_name: John full_name: Berrisford, John M last_name: Berrisford - first_name: Gurdeep full_name: Minhas, Gurdeep S last_name: Minhas citation: ama: Sazanov LA, Baradaran R, Efremov R, Berrisford J, Minhas G. A long road towards the structure of respiratory complex I, a giant molecular proton pump. Biochemical Society Transactions. 2013;41(5):1265-1271. doi:10.1042/BST20130193 apa: Sazanov, L. A., Baradaran, R., Efremov, R., Berrisford, J., & Minhas, G. (2013). A long road towards the structure of respiratory complex I, a giant molecular proton pump. Biochemical Society Transactions. Portland Press. https://doi.org/10.1042/BST20130193 chicago: Sazanov, Leonid A, Rozbeh Baradaran, Rouslan Efremov, John Berrisford, and Gurdeep Minhas. “A Long Road towards the Structure of Respiratory Complex I, a Giant Molecular Proton Pump.” Biochemical Society Transactions. Portland Press, 2013. https://doi.org/10.1042/BST20130193. ieee: L. A. Sazanov, R. Baradaran, R. Efremov, J. Berrisford, and G. Minhas, “A long road towards the structure of respiratory complex I, a giant molecular proton pump,” Biochemical Society Transactions, vol. 41, no. 5. Portland Press, pp. 1265–1271, 2013. ista: Sazanov LA, Baradaran R, Efremov R, Berrisford J, Minhas G. 2013. A long road towards the structure of respiratory complex I, a giant molecular proton pump. Biochemical Society Transactions. 41(5), 1265–1271. mla: Sazanov, Leonid A., et al. “A Long Road towards the Structure of Respiratory Complex I, a Giant Molecular Proton Pump.” Biochemical Society Transactions, vol. 41, no. 5, Portland Press, 2013, pp. 1265–71, doi:10.1042/BST20130193. short: L.A. Sazanov, R. Baradaran, R. Efremov, J. Berrisford, G. Minhas, Biochemical Society Transactions 41 (2013) 1265–1271. date_created: 2018-12-11T11:55:00Z date_published: 2013-10-01T00:00:00Z date_updated: 2021-01-12T06:54:28Z day: '01' doi: 10.1042/BST20130193 extern: 1 intvolume: ' 41' issue: '5' month: '10' page: 1265 - 1271 publication: Biochemical Society Transactions publication_status: published publisher: Portland Press publist_id: '5106' quality_controlled: 0 status: public title: A long road towards the structure of respiratory complex I, a giant molecular proton pump type: journal_article volume: 41 year: '2013' ... --- _id: '1978' abstract: - lang: eng text: Complex I is the first and largest enzyme of the respiratory chain and has a central role in cellular energy production through the coupling of NADH:ubiquinone electron transfer to proton translocation. It is also implicated in many common human neurodegenerative diseases. Here, we report the first crystal structure of the entire, intact complex I (from Thermus thermophilus) at 3.3 Å resolution. The structure of the 536-kDa complex comprises 16 different subunits, with a total of 64 transmembrane helices and 9 iron-sulphur clusters. The core fold of subunit Nqo8 (ND1 in humans) is, unexpectedly, similar to a half-channel of the antiporter-like subunits. Small subunits nearby form a linked second half-channel, which completes the fourth proton-translocation pathway (present in addition to the channels in three antiporter-like subunits). The quinone-binding site is unusually long, narrow and enclosed. The quinone headgroup binds at the deep end of this chamber, near iron-sulphur cluster N2. Notably, the chamber is linked to the fourth channel by a 'funnel' of charged residues. The link continues over the entire membrane domain as a flexible central axis of charged and polar residues, and probably has a leading role in the propagation of conformational changes, aided by coupling elements. The structure suggests that a unique, out-of-the-membrane quinone-reaction chamber enables the redox energy to drive concerted long-range conformational changes in the four antiporter-like domains, resulting in translocation of four protons per cycle. acknowledgement: This work was funded by the Medical Research Council. author: - first_name: Rozbeh full_name: 'Baradaran, Rozbeh ' last_name: Baradaran - first_name: John full_name: Berrisford, John M last_name: Berrisford - first_name: Gurdeep full_name: Minhas, Gurdeep S last_name: Minhas - first_name: Leonid A full_name: Leonid Sazanov id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Baradaran R, Berrisford J, Minhas G, Sazanov LA. Crystal structure of the entire respiratory complex i. Nature. 2013;494(7438):443-448. doi:10.1038/nature11871 apa: Baradaran, R., Berrisford, J., Minhas, G., & Sazanov, L. A. (2013). Crystal structure of the entire respiratory complex i. Nature. Nature Publishing Group. https://doi.org/10.1038/nature11871 chicago: Baradaran, Rozbeh, John Berrisford, Gurdeep Minhas, and Leonid A Sazanov. “Crystal Structure of the Entire Respiratory Complex I.” Nature. Nature Publishing Group, 2013. https://doi.org/10.1038/nature11871. ieee: R. Baradaran, J. Berrisford, G. Minhas, and L. A. Sazanov, “Crystal structure of the entire respiratory complex i,” Nature, vol. 494, no. 7438. Nature Publishing Group, pp. 443–448, 2013. ista: Baradaran R, Berrisford J, Minhas G, Sazanov LA. 2013. Crystal structure of the entire respiratory complex i. Nature. 494(7438), 443–448. mla: Baradaran, Rozbeh, et al. “Crystal Structure of the Entire Respiratory Complex I.” Nature, vol. 494, no. 7438, Nature Publishing Group, 2013, pp. 443–48, doi:10.1038/nature11871. short: R. Baradaran, J. Berrisford, G. Minhas, L.A. Sazanov, Nature 494 (2013) 443–448. date_created: 2018-12-11T11:55:01Z date_published: 2013-02-28T00:00:00Z date_updated: 2021-01-12T06:54:28Z day: '28' doi: 10.1038/nature11871 extern: 1 intvolume: ' 494' issue: '7438' month: '02' page: 443 - 448 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '5107' quality_controlled: 0 status: public title: Crystal structure of the entire respiratory complex i type: journal_article volume: 494 year: '2013' ... --- _id: '1991' abstract: - lang: eng text: Although transitions of sex-determination mechanisms are frequent in species with homomorphic sex chromosomes, heteromorphic sex chromosomes are thought to represent a terminal evolutionary stage owing to chromosome-specific adaptations such as dosage compensation or an accumulation of sex-specific mutations. Here we show that an autosome of Drosophila, the dot chromosome, was ancestrally a differentiated X chromosome. We analyse the whole genome of true fruitflies (Tephritidae), flesh flies (Sarcophagidae) and soldier flies (Stratiomyidae) to show that genes located on the dot chromosome of Drosophila are X-linked in outgroup species, whereas Drosophila X-linked genes are autosomal. We date this chromosomal transition to early drosophilid evolution by sequencing the genome of other Drosophilidae. Our results reveal several puzzling aspects of Drosophila dot chromosome biology to be possible remnants of its former life as a sex chromosome, such as its minor feminizing role in sex determination or its targeting by a chromosome-specific regulatory mechanism. We also show that patterns of biased gene expression of the dot chromosome during early embryogenesis, oogenesis and spermatogenesis resemble that of the current X chromosome. Thus, although sex chromosomes are not necessarily evolutionary end points and can revert back to an autosomal inheritance, the highly specialized genome architecture of this former X chromosome suggests that severe fitness costs must be overcome for such a turnover to occur. acknowledgement: Funded by National Institutes of Health grants (R01GM076007 and R01GM093182) and a Packard Fellowship to D.B. author: - first_name: Beatriz full_name: Beatriz Vicoso id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: Doris full_name: Bachtrog, Doris last_name: Bachtrog citation: ama: Vicoso B, Bachtrog D. Reversal of an ancient sex chromosome to an autosome in Drosophila. Nature. 2013;499(7458):332-335. doi:10.1038/nature12235 apa: Vicoso, B., & Bachtrog, D. (2013). Reversal of an ancient sex chromosome to an autosome in Drosophila. Nature. Nature Publishing Group. https://doi.org/10.1038/nature12235 chicago: Vicoso, Beatriz, and Doris Bachtrog. “Reversal of an Ancient Sex Chromosome to an Autosome in Drosophila.” Nature. Nature Publishing Group, 2013. https://doi.org/10.1038/nature12235. ieee: B. Vicoso and D. Bachtrog, “Reversal of an ancient sex chromosome to an autosome in Drosophila,” Nature, vol. 499, no. 7458. Nature Publishing Group, pp. 332–335, 2013. ista: Vicoso B, Bachtrog D. 2013. Reversal of an ancient sex chromosome to an autosome in Drosophila. Nature. 499(7458), 332–335. mla: Vicoso, Beatriz, and Doris Bachtrog. “Reversal of an Ancient Sex Chromosome to an Autosome in Drosophila.” Nature, vol. 499, no. 7458, Nature Publishing Group, 2013, pp. 332–35, doi:10.1038/nature12235. short: B. Vicoso, D. Bachtrog, Nature 499 (2013) 332–335. date_created: 2018-12-11T11:55:05Z date_published: 2013-07-18T00:00:00Z date_updated: 2021-01-12T06:54:33Z day: '18' doi: 10.1038/nature12235 extern: 1 intvolume: ' 499' issue: '7458' month: '07' page: 332 - 335 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '5092' quality_controlled: 0 status: public title: Reversal of an ancient sex chromosome to an autosome in Drosophila type: journal_article volume: 499 year: '2013' ... --- _id: '1988' abstract: - lang: eng text: The rod-shaped bacterium Escherichia coli selects the cell center as site of division with the help of the proteins MinC, MinD, and MinE. This protein system collectively oscillates between the two cell poles by alternately binding to the membrane in one of the two cell halves. This dynamic behavior, which emerges from the interaction of the ATPase MinD and its activator MinE on the cell membrane, has become a paradigm for protein self-organization. Recently, it has been found that not only the binding of MinD to the membrane, but also interactions of MinE with the membrane contribute to Min-protein self-organization. Here, we show that by accounting for this finding in a computational model, we can comprehensively describe all observed Min-protein patterns in vivo and in vitro. Furthermore, by varying the system's geometry, our computations predict patterns that have not yet been reported. We confirm these predictions experimentally. author: - first_name: Mike full_name: 'Bonny, Mike ' last_name: Bonny - first_name: Elisabeth full_name: Fischer-Friedrich, Elisabeth last_name: Fischer Friedrich - first_name: Martin full_name: Martin Loose id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - first_name: Petra full_name: 'Schwille, Petra ' last_name: Schwille - first_name: Karsten full_name: Kruse, Karsten last_name: Kruse citation: ama: Bonny M, Fischer Friedrich E, Loose M, Schwille P, Kruse K. Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation. PLoS Computational Biology. 2013;9(12). doi:10.1371/journal.pcbi.1003347 apa: Bonny, M., Fischer Friedrich, E., Loose, M., Schwille, P., & Kruse, K. (2013). Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1003347 chicago: Bonny, Mike, Elisabeth Fischer Friedrich, Martin Loose, Petra Schwille, and Karsten Kruse. “Membrane Binding of MinE Allows for a Comprehensive Description of Min-Protein Pattern Formation.” PLoS Computational Biology. Public Library of Science, 2013. https://doi.org/10.1371/journal.pcbi.1003347. ieee: M. Bonny, E. Fischer Friedrich, M. Loose, P. Schwille, and K. Kruse, “Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation,” PLoS Computational Biology, vol. 9, no. 12. Public Library of Science, 2013. ista: Bonny M, Fischer Friedrich E, Loose M, Schwille P, Kruse K. 2013. Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation. PLoS Computational Biology. 9(12). mla: Bonny, Mike, et al. “Membrane Binding of MinE Allows for a Comprehensive Description of Min-Protein Pattern Formation.” PLoS Computational Biology, vol. 9, no. 12, Public Library of Science, 2013, doi:10.1371/journal.pcbi.1003347. short: M. Bonny, E. Fischer Friedrich, M. Loose, P. Schwille, K. Kruse, PLoS Computational Biology 9 (2013). date_created: 2018-12-11T11:55:04Z date_published: 2013-12-01T00:00:00Z date_updated: 2021-01-12T06:54:32Z day: '01' doi: 10.1371/journal.pcbi.1003347 extern: 1 intvolume: ' 9' issue: '12' month: '12' publication: PLoS Computational Biology publication_status: published publisher: Public Library of Science publist_id: '5095' quality_controlled: 0 status: public title: Membrane binding of MinE allows for a comprehensive description of Min-protein pattern formation type: journal_article volume: 9 year: '2013' ... --- _id: '2010' abstract: - lang: eng text: Many algorithms for inferring causality rely heavily on the faithfulness assumption. The main justification for imposing this assumption is that the set of unfaithful distributions has Lebesgue measure zero, since it can be seen as a collection of hypersurfaces in a hypercube. However, due to sampling error the faithfulness condition alone is not sufficient for statistical estimation, and strong-faithfulness has been proposed and assumed to achieve uniform or high-dimensional consistency. In contrast to the plain faithfulness assumption, the set of distributions that is not strong-faithful has nonzero Lebesgue measure and in fact, can be surprisingly large as we show in this paper. We study the strong-faithfulness condition from a geometric and combinatorial point of view and give upper and lower bounds on the Lebesgue measure of strong-faithful distributions for various classes of directed acyclic graphs. Our results imply fundamental limitations for the PC-algorithm and potentially also for other algorithms based on partial correlation testing in the Gaussian case. author: - first_name: Caroline full_name: Uhler, Caroline id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 - first_name: Garvesh full_name: Raskutti, Garvesh last_name: Raskutti - first_name: Peter full_name: Bühlmann, Peter last_name: Bühlmann - first_name: Bin full_name: Yu, Bin last_name: Yu citation: ama: Uhler C, Raskutti G, Bühlmann P, Yu B. Geometry of the faithfulness assumption in causal inference. The Annals of Statistics. 2013;41(2):436-463. doi:10.1214/12-AOS1080 apa: Uhler, C., Raskutti, G., Bühlmann, P., & Yu, B. (2013). Geometry of the faithfulness assumption in causal inference. The Annals of Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/12-AOS1080 chicago: Uhler, Caroline, Garvesh Raskutti, Peter Bühlmann, and Bin Yu. “Geometry of the Faithfulness Assumption in Causal Inference.” The Annals of Statistics. Institute of Mathematical Statistics, 2013. https://doi.org/10.1214/12-AOS1080. ieee: C. Uhler, G. Raskutti, P. Bühlmann, and B. Yu, “Geometry of the faithfulness assumption in causal inference,” The Annals of Statistics, vol. 41, no. 2. Institute of Mathematical Statistics, pp. 436–463, 2013. ista: Uhler C, Raskutti G, Bühlmann P, Yu B. 2013. Geometry of the faithfulness assumption in causal inference. The Annals of Statistics. 41(2), 436–463. mla: Uhler, Caroline, et al. “Geometry of the Faithfulness Assumption in Causal Inference.” The Annals of Statistics, vol. 41, no. 2, Institute of Mathematical Statistics, 2013, pp. 436–63, doi:10.1214/12-AOS1080. short: C. Uhler, G. Raskutti, P. Bühlmann, B. Yu, The Annals of Statistics 41 (2013) 436–463. date_created: 2018-12-11T11:55:11Z date_published: 2013-04-01T00:00:00Z date_updated: 2021-01-12T06:54:42Z day: '01' department: - _id: CaUh doi: 10.1214/12-AOS1080 external_id: arxiv: - '1207.0547' intvolume: ' 41' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: www.doi.org/10.1214/12-AOS1080 month: '04' oa: 1 oa_version: Published Version page: 436 - 463 publication: The Annals of Statistics publication_status: published publisher: Institute of Mathematical Statistics publist_id: '5066' quality_controlled: '1' scopus_import: 1 status: public title: Geometry of the faithfulness assumption in causal inference type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 41 year: '2013' ... --- _id: '2009' abstract: - lang: eng text: Traditional statistical methods for confidentiality protection of statistical databases do not scale well to deal with GWAS databases especially in terms of guarantees regarding protection from linkage to external information. The more recent concept of differential privacy, introduced by the cryptographic community, is an approach which provides a rigorous definition of privacy with meaningful privacy guarantees in the presence of arbitrary external information, although the guarantees may come at a serious price in terms of data utility. Building on such notions, we propose new methods to release aggregate GWAS data without compromising an individual’s privacy. We present methods for releasing differentially private minor allele frequencies, chi-square statistics and p-values. We compare these approaches on simulated data and on a GWAS study of canine hair length involving 685 dogs. We also propose a privacy-preserving method for finding genome-wide associations based on a differentially-private approach to penalized logistic regression. article_processing_charge: No author: - first_name: Caroline full_name: Uhler, Caroline id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 - first_name: Aleksandra full_name: Slavkovic, Aleksandra last_name: Slavkovic - first_name: Stephen full_name: Fienberg, Stephen last_name: Fienberg citation: ama: Uhler C, Slavkovic A, Fienberg S. Privacy-preserving data sharing for genome-wide association studies. Journal of Privacy and Confidentiality . 2013;5(1):137-166. doi:10.29012/jpc.v5i1.629 apa: Uhler, C., Slavkovic, A., & Fienberg, S. (2013). Privacy-preserving data sharing for genome-wide association studies. Journal of Privacy and Confidentiality . Carnegie Mellon University. https://doi.org/10.29012/jpc.v5i1.629 chicago: Uhler, Caroline, Aleksandra Slavkovic, and Stephen Fienberg. “Privacy-Preserving Data Sharing for Genome-Wide Association Studies.” Journal of Privacy and Confidentiality . Carnegie Mellon University, 2013. https://doi.org/10.29012/jpc.v5i1.629. ieee: C. Uhler, A. Slavkovic, and S. Fienberg, “Privacy-preserving data sharing for genome-wide association studies,” Journal of Privacy and Confidentiality , vol. 5, no. 1. Carnegie Mellon University, pp. 137–166, 2013. ista: Uhler C, Slavkovic A, Fienberg S. 2013. Privacy-preserving data sharing for genome-wide association studies. Journal of Privacy and Confidentiality . 5(1), 137–166. mla: Uhler, Caroline, et al. “Privacy-Preserving Data Sharing for Genome-Wide Association Studies.” Journal of Privacy and Confidentiality , vol. 5, no. 1, Carnegie Mellon University, 2013, pp. 137–66, doi:10.29012/jpc.v5i1.629. short: C. Uhler, A. Slavkovic, S. Fienberg, Journal of Privacy and Confidentiality 5 (2013) 137–166. date_created: 2018-12-11T11:55:11Z date_published: 2013-08-01T00:00:00Z date_updated: 2021-01-12T06:54:41Z day: '01' department: - _id: CaUh doi: 10.29012/jpc.v5i1.629 intvolume: ' 5' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://repository.cmu.edu/jpc/vol5/iss1/6 month: '08' oa: 1 oa_version: Published Version page: 137 - 166 publication: 'Journal of Privacy and Confidentiality ' publication_status: published publisher: Carnegie Mellon University publist_id: '5067' quality_controlled: '1' status: public title: Privacy-preserving data sharing for genome-wide association studies type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2013' ... --- _id: '2074' abstract: - lang: eng text: 'Sex chromosomes originate from autosomes. The accumulation of sexually antagonistic mutations on protosex chromosomes selects for a loss of recombination and sets in motion the evolutionary processes generating heteromorphic sex chromosomes. Recombination suppression and differentiation are generally viewed as the default path of sex chromosome evolution, and the occurrence of old, homomorphic sex chromosomes, such as those of ratite birds, has remained a mystery. Here, we analyze the genome and transcriptome of emu (Dromaius novaehollandiae) and confirm that most genes on the sex chromosome are shared between the Z and W. Surprisingly, however, levels of gene expression are generally sex-biased for all sex-linked genes relative to autosomes, including those in the pseudoautosomal region, and the male-bias increases after gonad formation. This expression bias suggests that the emu sex chromosomes have become masculinized, even in the absence of ZW differentiation. Thus, birds may have taken different evolutionary solutions to minimize the deleterious effects imposed by sexually antagonistic mutations: some lineages eliminate recombination along the protosex chromosomes to physically restrict sexually antagonistic alleles to one sex, whereas ratites evolved sex-biased expression to confine the product of a sexually antagonistic allele to the sex it benefits. This difference in conflict resolution may explain the preservation of recombining, homomorphic sex chromosomes in other lineages and illustrates the importance of sexually antagonistic mutations driving the evolution of sex chromosomes. ' author: - first_name: Beatriz full_name: Beatriz Vicoso id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: Vera full_name: Kaiser, Vera B last_name: Kaiser - first_name: Doris full_name: Bachtrog, Doris last_name: Bachtrog citation: ama: Vicoso B, Kaiser V, Bachtrog D. Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. PNAS. 2013;110(16):6453-6458. doi:10.1073/pnas.1217027110 apa: Vicoso, B., Kaiser, V., & Bachtrog, D. (2013). Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1217027110 chicago: Vicoso, Beatriz, Vera Kaiser, and Doris Bachtrog. “Sex Biased Gene Expression at Homomorphic Sex Chromosomes in Emus and Its Implication for Sex Chromosome Evolution.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1217027110. ieee: B. Vicoso, V. Kaiser, and D. Bachtrog, “Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution,” PNAS, vol. 110, no. 16. National Academy of Sciences, pp. 6453–6458, 2013. ista: Vicoso B, Kaiser V, Bachtrog D. 2013. Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution. PNAS. 110(16), 6453–6458. mla: Vicoso, Beatriz, et al. “Sex Biased Gene Expression at Homomorphic Sex Chromosomes in Emus and Its Implication for Sex Chromosome Evolution.” PNAS, vol. 110, no. 16, National Academy of Sciences, 2013, pp. 6453–58, doi:10.1073/pnas.1217027110. short: B. Vicoso, V. Kaiser, D. Bachtrog, PNAS 110 (2013) 6453–6458. date_created: 2018-12-11T11:55:33Z date_published: 2013-04-16T00:00:00Z date_updated: 2021-01-12T06:55:08Z day: '16' doi: 10.1073/pnas.1217027110 extern: 1 intvolume: ' 110' issue: '16' month: '04' page: 6453 - 6458 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '4964' quality_controlled: 0 status: public title: Sex biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution type: journal_article volume: 110 year: '2013' ... --- _id: '2076' abstract: - lang: eng text: | Snakes exhibit genetic sex determination, with female heterogametic sex chromosomes (ZZ males, ZW females). Extensive cytogenetic work has suggested that the level of sex chromosome heteromorphism varies among species, with Boidae having entirely homomorphic sex chromosomes, Viperidae having completely heteromorphic sex chromosomes, and Colubridae showing partial differentiation. Here, we take a genomic approach to compare sex chromosome differentiation in these three snake families. We identify homomorphic sex chromosomes in boas (Boidae), but completely heteromorphic sex chromosomes in both garter snakes (Colubridae) and pygmy rattlesnake (Viperidae). Detection of W-linked gametologs enables us to establish the presence of evolutionary strata on garter and pygmy rattlesnake sex chromosomes where recombination was abolished at different time points. Sequence analysis shows that all strata are shared between pygmy rattlesnake and garter snake, i.e., recombination was abolished between the sex chromosomes before the two lineages diverged. The sex-biased transmission of the Z and its hemizygosity in females can impact patterns of molecular evolution, and we show that rates of evolution for Z-linked genes are increased relative to their pseudoautosomal homologs, both at synonymous and amino acid sites (even after controlling for mutational biases). This demonstrates that mutation rates are male-biased in snakes (male-driven evolution), but also supports faster-Z evolution due to differential selective effects on the Z. Finally, we perform a transcriptome analysis in boa and pygmy rattlesnake to establish baseline levels of sex-biased expression in homomorphic sex chromosomes, and show that heteromorphic ZW chromosomes in rattlesnakes lack chromosome-wide dosage compensation. Our study provides the first full scale overview of the evolution of snake sex chromosomes at the genomic level, thus greatly expanding our knowledge of reptilian and vertebrate sex chromosomes evolution. acknowledgement: Funded by NIH grants (R01GM076007 and R01GM093182) and a Packard Fellowship to DB. author: - first_name: Beatriz full_name: Beatriz Vicoso id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: Jr full_name: Emerson, Jr J. last_name: Emerson - first_name: Yulia full_name: Zektser, Yulia last_name: Zektser - first_name: Shivani full_name: Mahajan, Shivani last_name: Mahajan - first_name: Doris full_name: Bachtrog, Doris last_name: Bachtrog citation: ama: 'Vicoso B, Emerson J, Zektser Y, Mahajan S, Bachtrog D. Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation. PLoS Biology. 2013;11(8). doi:10.1371/journal.pbio.1001643' apa: 'Vicoso, B., Emerson, J., Zektser, Y., Mahajan, S., & Bachtrog, D. (2013). Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1001643' chicago: 'Vicoso, Beatriz, Jr Emerson, Yulia Zektser, Shivani Mahajan, and Doris Bachtrog. “Comparative Sex Chromosome Genomics in Snakes: Differentiation Evolutionary Strata and Lack of Global Dosage Compensation.” PLoS Biology. Public Library of Science, 2013. https://doi.org/10.1371/journal.pbio.1001643.' ieee: 'B. Vicoso, J. Emerson, Y. Zektser, S. Mahajan, and D. Bachtrog, “Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation,” PLoS Biology, vol. 11, no. 8. Public Library of Science, 2013.' ista: 'Vicoso B, Emerson J, Zektser Y, Mahajan S, Bachtrog D. 2013. Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation. PLoS Biology. 11(8).' mla: 'Vicoso, Beatriz, et al. “Comparative Sex Chromosome Genomics in Snakes: Differentiation Evolutionary Strata and Lack of Global Dosage Compensation.” PLoS Biology, vol. 11, no. 8, Public Library of Science, 2013, doi:10.1371/journal.pbio.1001643.' short: B. Vicoso, J. Emerson, Y. Zektser, S. Mahajan, D. Bachtrog, PLoS Biology 11 (2013). date_created: 2018-12-11T11:55:34Z date_published: 2013-08-27T00:00:00Z date_updated: 2021-01-12T06:55:09Z day: '27' doi: 10.1371/journal.pbio.1001643 extern: 1 intvolume: ' 11' issue: '8' license: https://creativecommons.org/licenses/by/4.0/ month: '08' publication: PLoS Biology publication_status: published publisher: Public Library of Science publist_id: '4962' quality_controlled: 0 status: public title: 'Comparative sex chromosome genomics in snakes: Differentiation evolutionary strata and lack of global dosage compensation' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 11 year: '2013' ... --- _id: '2108' abstract: - lang: eng text: 'We present an interactive design system that allows non-expert users to create animated mechanical characters. Given an articulated character as input, the user iteratively creates an animation by sketching motion curves indicating how different parts of the character should move. For each motion curve, our framework creates an optimized mechanism that reproduces it as closely as possible. The resulting mechanisms are attached to the character and then connected to each other using gear trains, which are created in a semi-automated fashion. The mechanical assemblies generated with our system can be driven with a single input driver, such as a hand-operated crank or an electric motor, and they can be fabricated using rapid prototyping devices. We demonstrate the versatility of our approach by designing a wide range of mechanical characters, several of which we manufactured using 3D printing. While our pipeline is designed for characters driven by planar mechanisms, significant parts of it extend directly to non-planar mechanisms, allowing us to create characters with compelling 3D motions. ' author: - first_name: Stelian full_name: Coros, Stelian last_name: Coros - first_name: Bernhard full_name: Thomaszewski, Bernhard last_name: Thomaszewski - first_name: Gioacchino full_name: Noris, Gioacchino last_name: Noris - first_name: Shinjiro full_name: Sueda, Shinjiro last_name: Sueda - first_name: Moira full_name: Forberg, Moira last_name: Forberg - first_name: Robert full_name: Sumner, Robert W last_name: Sumner - first_name: Wojciech full_name: Matusik, Wojciech last_name: Matusik - first_name: Bernd full_name: Bernd Bickel id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 citation: ama: Coros S, Thomaszewski B, Noris G, et al. Computational design of mechanical characters. ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2461953 apa: Coros, S., Thomaszewski, B., Noris, G., Sueda, S., Forberg, M., Sumner, R., … Bickel, B. (2013). Computational design of mechanical characters. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2461953 chicago: Coros, Stelian, Bernhard Thomaszewski, Gioacchino Noris, Shinjiro Sueda, Moira Forberg, Robert Sumner, Wojciech Matusik, and Bernd Bickel. “Computational Design of Mechanical Characters.” ACM Transactions on Graphics. ACM, 2013. https://doi.org/10.1145/2461912.2461953. ieee: S. Coros et al., “Computational design of mechanical characters,” ACM Transactions on Graphics, vol. 32, no. 4. ACM, 2013. ista: Coros S, Thomaszewski B, Noris G, Sueda S, Forberg M, Sumner R, Matusik W, Bickel B. 2013. Computational design of mechanical characters. ACM Transactions on Graphics. 32(4). mla: Coros, Stelian, et al. “Computational Design of Mechanical Characters.” ACM Transactions on Graphics, vol. 32, no. 4, ACM, 2013, doi:10.1145/2461912.2461953. short: S. Coros, B. Thomaszewski, G. Noris, S. Sueda, M. Forberg, R. Sumner, W. Matusik, B. Bickel, ACM Transactions on Graphics 32 (2013). date_created: 2018-12-11T11:55:46Z date_published: 2013-07-01T00:00:00Z date_updated: 2021-01-12T06:55:21Z day: '01' doi: 10.1145/2461912.2461953 extern: 1 intvolume: ' 32' issue: '4' month: '07' publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '4927' quality_controlled: 0 status: public title: Computational design of mechanical characters type: journal_article volume: 32 year: '2013' ... --- _id: '2110' abstract: - lang: eng text: 'We present a method for practical physical reproduction and design of homogeneous materials with desired subsurface scattering. Our process uses a collection of different pigments that can be suspended in a clear base material. Our goal is to determine pigment concentrations that best reproduce the appearance and subsurface scattering of a given target material. In order to achieve this task we first fabricate a collection of material samples composed of known mixtures of the available pigments with the base material. We then acquire their reflectance profiles using a custom-built measurement device. We use the same device to measure the reflectance profile of a target material. Based on the database of mappings from pigment concentrations to reflectance profiles, we use an optimization process to compute the concentration of pigments to best replicate the target material appearance. We demonstrate the practicality of our method by reproducing a variety of different translucent materials. We also present a tool that allows the user to explore the range of achievable appearances for a given set of pigments. ' author: - first_name: Marios full_name: Papas, Marios last_name: Papas - first_name: Christian full_name: Regg, Christian last_name: Regg - first_name: Wojciech full_name: Jarosz, Wojciech last_name: Jarosz - first_name: Bernd full_name: Bernd Bickel id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Philip full_name: Jackson, Philip V last_name: Jackson - first_name: Wojciech full_name: Matusik, Wojciech last_name: Matusik - first_name: Steve full_name: Marschner, Steve last_name: Marschner - first_name: Markus full_name: Groß, Markus S last_name: Groß citation: ama: Papas M, Regg C, Jarosz W, et al. Fabricating translucent materials using continuous pigment mixtures. ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2461974 apa: Papas, M., Regg, C., Jarosz, W., Bickel, B., Jackson, P., Matusik, W., … Groß, M. (2013). Fabricating translucent materials using continuous pigment mixtures. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2461974 chicago: Papas, Marios, Christian Regg, Wojciech Jarosz, Bernd Bickel, Philip Jackson, Wojciech Matusik, Steve Marschner, and Markus Groß. “Fabricating Translucent Materials Using Continuous Pigment Mixtures.” ACM Transactions on Graphics. ACM, 2013. https://doi.org/10.1145/2461912.2461974. ieee: M. Papas et al., “Fabricating translucent materials using continuous pigment mixtures,” ACM Transactions on Graphics, vol. 32, no. 4. ACM, 2013. ista: Papas M, Regg C, Jarosz W, Bickel B, Jackson P, Matusik W, Marschner S, Groß M. 2013. Fabricating translucent materials using continuous pigment mixtures. ACM Transactions on Graphics. 32(4). mla: Papas, Marios, et al. “Fabricating Translucent Materials Using Continuous Pigment Mixtures.” ACM Transactions on Graphics, vol. 32, no. 4, ACM, 2013, doi:10.1145/2461912.2461974. short: M. Papas, C. Regg, W. Jarosz, B. Bickel, P. Jackson, W. Matusik, S. Marschner, M. Groß, ACM Transactions on Graphics 32 (2013). date_created: 2018-12-11T11:55:46Z date_published: 2013-07-01T00:00:00Z date_updated: 2021-01-12T06:55:22Z day: '01' doi: 10.1145/2461912.2461974 extern: 1 intvolume: ' 32' issue: '4' month: '07' publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '4925' quality_controlled: 0 status: public title: Fabricating translucent materials using continuous pigment mixtures type: journal_article volume: 32 year: '2013' ... --- _id: '2111' abstract: - lang: eng text: Animated animatronic figures are a unique way to give physical presence to a character. However, their movement and expressions are often limited due to mechanical constraints. In this paper, we propose a complete process for augmenting physical avatars using projector-based illumination, significantly increasing their expressiveness. Given an input animation, the system decomposes the motion into low-frequency motion that can be physically reproduced by the animatronic head and high-frequency details that are added using projected shading. At the core is a spatio-temporal optimization process that compresses the motion in gradient space, ensuring faithful motion replay while respecting the physical limitations of the system. We also propose a complete multi-camera and projection system, including a novel defocused projection and subsurface scattering compensation scheme. The result of our system is a highly expressive physical avatar that features facial details and motion otherwise unattainable due to physical constraints. author: - first_name: Amit full_name: Bermano, Amit H last_name: Bermano - first_name: Philipp full_name: Bruschweiler, Philipp last_name: Bruschweiler - first_name: Anselm full_name: Grundhöfer, Anselm last_name: Grundhöfer - first_name: Daisuke full_name: Iwai, Daisuke last_name: Iwai - first_name: Bernd full_name: Bernd Bickel id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Markus full_name: Groß, Markus S last_name: Groß citation: ama: Bermano A, Bruschweiler P, Grundhöfer A, Iwai D, Bickel B, Groß M. Augmenting physical avatars using projector-based illumination. ACM Transactions on Graphics. 2013;32(6). doi:10.1145/2508363.2508416 apa: Bermano, A., Bruschweiler, P., Grundhöfer, A., Iwai, D., Bickel, B., & Groß, M. (2013). Augmenting physical avatars using projector-based illumination. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2508363.2508416 chicago: Bermano, Amit, Philipp Bruschweiler, Anselm Grundhöfer, Daisuke Iwai, Bernd Bickel, and Markus Groß. “Augmenting Physical Avatars Using Projector-Based Illumination.” ACM Transactions on Graphics. ACM, 2013. https://doi.org/10.1145/2508363.2508416. ieee: A. Bermano, P. Bruschweiler, A. Grundhöfer, D. Iwai, B. Bickel, and M. Groß, “Augmenting physical avatars using projector-based illumination,” ACM Transactions on Graphics, vol. 32, no. 6. ACM, 2013. ista: Bermano A, Bruschweiler P, Grundhöfer A, Iwai D, Bickel B, Groß M. 2013. Augmenting physical avatars using projector-based illumination. ACM Transactions on Graphics. 32(6). mla: Bermano, Amit, et al. “Augmenting Physical Avatars Using Projector-Based Illumination.” ACM Transactions on Graphics, vol. 32, no. 6, ACM, 2013, doi:10.1145/2508363.2508416. short: A. Bermano, P. Bruschweiler, A. Grundhöfer, D. Iwai, B. Bickel, M. Groß, ACM Transactions on Graphics 32 (2013). date_created: 2018-12-11T11:55:47Z date_published: 2013-11-01T00:00:00Z date_updated: 2021-01-12T06:55:23Z day: '01' doi: 10.1145/2508363.2508416 extern: 1 intvolume: ' 32' issue: '6' month: '11' publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '4922' quality_controlled: 0 status: public title: Augmenting physical avatars using projector-based illumination type: journal_article volume: 32 year: '2013' ... --- _id: '2109' abstract: - lang: eng text: Most additive manufacturing technologies work by layering, i.e. slicing the shape and then generating each slice independently. This introduces an anisotropy into the process, often as different accuracies in the tangential and normal directions, but also in terms of other parameters such as build speed or tensile strength and strain. We model this as an anisotropic cubic element. Our approach then finds a compromise between modeling each part of the shape individually in the best possible direction and using one direction for the whole shape part. In particular, we compute an orthogonal basis and consider only the three basis vectors as slice normals (i.e. fabrication directions). Then we optimize a decomposition of the shape along this basis so that each part can be consistently sliced along one of the basis vectors. In simulation, we show that this approach is superior to slicing the whole shape in one direction, only. It also has clear benefits if the shape is larger than the build volume of the available equipment. author: - first_name: Kristian full_name: Hildebrand, Kristian last_name: Hildebrand - first_name: Bernd full_name: Bernd Bickel id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Marc full_name: Alexa, Marc last_name: Alexa citation: ama: Hildebrand K, Bickel B, Alexa M. Orthogonal slicing for additive manufacturing. Computers and Graphics (Pergamon). 2013;37(6):669-675. doi:10.1016/j.cag.2013.05.011 apa: Hildebrand, K., Bickel, B., & Alexa, M. (2013). Orthogonal slicing for additive manufacturing. Computers and Graphics (Pergamon). Elsevier. https://doi.org/10.1016/j.cag.2013.05.011 chicago: Hildebrand, Kristian, Bernd Bickel, and Marc Alexa. “Orthogonal Slicing for Additive Manufacturing.” Computers and Graphics (Pergamon). Elsevier, 2013. https://doi.org/10.1016/j.cag.2013.05.011. ieee: K. Hildebrand, B. Bickel, and M. Alexa, “Orthogonal slicing for additive manufacturing,” Computers and Graphics (Pergamon), vol. 37, no. 6. Elsevier, pp. 669–675, 2013. ista: Hildebrand K, Bickel B, Alexa M. 2013. Orthogonal slicing for additive manufacturing. Computers and Graphics (Pergamon). 37(6), 669–675. mla: Hildebrand, Kristian, et al. “Orthogonal Slicing for Additive Manufacturing.” Computers and Graphics (Pergamon), vol. 37, no. 6, Elsevier, 2013, pp. 669–75, doi:10.1016/j.cag.2013.05.011. short: K. Hildebrand, B. Bickel, M. Alexa, Computers and Graphics (Pergamon) 37 (2013) 669–675. date_created: 2018-12-11T11:55:46Z date_published: 2013-10-01T00:00:00Z date_updated: 2021-01-12T06:55:22Z day: '01' doi: 10.1016/j.cag.2013.05.011 extern: 1 intvolume: ' 37' issue: '6' month: '10' page: 669 - 675 publication: Computers and Graphics (Pergamon) publication_status: published publisher: Elsevier publist_id: '4924' quality_controlled: 0 status: public title: Orthogonal slicing for additive manufacturing type: journal_article volume: 37 year: '2013' ... --- _id: '2107' abstract: - lang: eng text: We present a method for fabrication-oriented design of actuated deformable characters that allows a user to automatically create physical replicas of digitally designed characters using rapid manufacturing technologies. Given a deformable character and a set of target poses as input, our method computes a small set of actuators along with their locations on the surface and optimizes the internal material distribution such that the resulting character exhibits the desired deformation behavior. We approach this problem with a dedicated algorithm that combines finite-element analysis, sparse regularization, and constrained optimization. We validate our pipeline on a set of two- and three-dimensional example characters and present results in simulation and physically-fabricated prototypes. acknowledgement: This work was partly funded by the NCCR Co-Me of the Swiss NSF author: - first_name: Mélina full_name: Skouras, Mélina last_name: Skouras - first_name: Bernhard full_name: Thomaszewski, Bernhard last_name: Thomaszewski - first_name: Stelian full_name: Coros, Stelian last_name: Coros - first_name: Bernd full_name: Bernd Bickel id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Markus full_name: Groß, Markus S last_name: Groß citation: ama: Skouras M, Thomaszewski B, Coros S, Bickel B, Groß M. Computational design of actuated deformable characters. ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2461979 apa: Skouras, M., Thomaszewski, B., Coros, S., Bickel, B., & Groß, M. (2013). Computational design of actuated deformable characters. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2461979 chicago: Skouras, Mélina, Bernhard Thomaszewski, Stelian Coros, Bernd Bickel, and Markus Groß. “Computational Design of Actuated Deformable Characters.” ACM Transactions on Graphics. ACM, 2013. https://doi.org/10.1145/2461912.2461979. ieee: M. Skouras, B. Thomaszewski, S. Coros, B. Bickel, and M. Groß, “Computational design of actuated deformable characters,” ACM Transactions on Graphics, vol. 32, no. 4. ACM, 2013. ista: Skouras M, Thomaszewski B, Coros S, Bickel B, Groß M. 2013. Computational design of actuated deformable characters. ACM Transactions on Graphics. 32(4). mla: Skouras, Mélina, et al. “Computational Design of Actuated Deformable Characters.” ACM Transactions on Graphics, vol. 32, no. 4, ACM, 2013, doi:10.1145/2461912.2461979. short: M. Skouras, B. Thomaszewski, S. Coros, B. Bickel, M. Groß, ACM Transactions on Graphics 32 (2013). date_created: 2018-12-11T11:55:45Z date_published: 2013-07-01T00:00:00Z date_updated: 2021-01-12T06:55:21Z day: '01' doi: 10.1145/2461912.2461979 extern: 1 intvolume: ' 32' issue: '4' month: '07' publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '4926' quality_controlled: 0 status: public title: Computational design of actuated deformable characters type: journal_article volume: 32 year: '2013' ... --- _id: '2112' abstract: - lang: eng text: Force-deformation measurements of cloth exhibit significant hysteresis, and many researchers have identified internal friction as the source of this effect. However, it has not been incorporated into computer animation models of cloth. In this paper, we propose a model of internal friction based on an augmented reparameterization of Dahl's model, and we show that this model provides a good match to several important features of cloth hysteresis even with a minimal set of parameters. We also propose novel parameter estimation procedures that are based on simple and inexpensive setups and need only sparse data, as opposed to the complex hardware and dense data acquisition of previous methods. Finally, we provide an algorithm for the efficient simulation of internal friction, and we demonstrate it on simulation examples that show disparate behavior with and without internal friction. acknowledgement: This work was supported in part by the European Research Council (ERC-2011-StG-280135 Animetrics) and the Spanish Ministry of Economy (TIN2012-35840). author: - first_name: Eder full_name: Miguel, Eder last_name: Miguel - first_name: Rasmus full_name: Tamstorf, Rasmus last_name: Tamstorf - first_name: Derek full_name: Bradley, Derek J last_name: Bradley - first_name: Sara full_name: Schvartzman, Sara C last_name: Schvartzman - first_name: Bernhard full_name: Thomaszewski, Bernhard last_name: Thomaszewski - first_name: Bernd full_name: Bernd Bickel id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Wojciech full_name: Matusik, Wojciech last_name: Matusik - first_name: Steve full_name: Marschner, Steve last_name: Marschner - first_name: Miguel full_name: Otaduy, Miguel A last_name: Otaduy citation: ama: Miguel E, Tamstorf R, Bradley D, et al. Modeling and estimation of internal friction in cloth. ACM Transactions on Graphics. 2013;32(6). doi:10.1145/2508363.2508389 apa: Miguel, E., Tamstorf, R., Bradley, D., Schvartzman, S., Thomaszewski, B., Bickel, B., … Otaduy, M. (2013). Modeling and estimation of internal friction in cloth. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2508363.2508389 chicago: Miguel, Eder, Rasmus Tamstorf, Derek Bradley, Sara Schvartzman, Bernhard Thomaszewski, Bernd Bickel, Wojciech Matusik, Steve Marschner, and Miguel Otaduy. “Modeling and Estimation of Internal Friction in Cloth.” ACM Transactions on Graphics. ACM, 2013. https://doi.org/10.1145/2508363.2508389 . ieee: E. Miguel et al., “Modeling and estimation of internal friction in cloth,” ACM Transactions on Graphics, vol. 32, no. 6. ACM, 2013. ista: Miguel E, Tamstorf R, Bradley D, Schvartzman S, Thomaszewski B, Bickel B, Matusik W, Marschner S, Otaduy M. 2013. Modeling and estimation of internal friction in cloth. ACM Transactions on Graphics. 32(6). mla: Miguel, Eder, et al. “Modeling and Estimation of Internal Friction in Cloth.” ACM Transactions on Graphics, vol. 32, no. 6, ACM, 2013, doi:10.1145/2508363.2508389 . short: E. Miguel, R. Tamstorf, D. Bradley, S. Schvartzman, B. Thomaszewski, B. Bickel, W. Matusik, S. Marschner, M. Otaduy, ACM Transactions on Graphics 32 (2013). date_created: 2018-12-11T11:55:47Z date_published: 2013-11-01T00:00:00Z date_updated: 2021-01-12T06:55:23Z day: '01' doi: '10.1145/2508363.2508389 ' extern: 1 intvolume: ' 32' issue: '6' month: '11' publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '4923' quality_controlled: 0 status: public title: Modeling and estimation of internal friction in cloth type: journal_article volume: 32 year: '2013' ... --- _id: '2117' abstract: - lang: eng text: We prove new upper and lower bounds for Banach space-valued stochastic integrals with respect to a compensated Poisson random measure. Our estimates apply to Banach spaces with non-trivial martingale (co)type and extend various results in the literature. We also develop a Malliavin framework to interpret Poisson stochastic integrals as vector-valued Skorohod integrals, and prove a Clark-Ocone representation formula. acknowledgement: The first and third named authors were supported by VICI subsidy 639.033.604 of the Netherlands Organisation for Scientific Research (NWO). The first and second named authors were supported by the German Research Foundation in the Collaborative Research C author: - first_name: Sjoerd full_name: Dirksen, Sjoerd last_name: Dirksen - first_name: Jan full_name: Jan Maas id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 - first_name: Jan full_name: van Neerven, Jan M last_name: Van Neerven citation: ama: Dirksen S, Maas J, Van Neerven J. Poisson stochastic integration in Banach spaces. Electronic Journal of Probability. 2013;18. doi:10.1214/EJP.v18-2945 apa: Dirksen, S., Maas, J., & Van Neerven, J. (2013). Poisson stochastic integration in Banach spaces. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/EJP.v18-2945 chicago: Dirksen, Sjoerd, Jan Maas, and Jan Van Neerven. “Poisson Stochastic Integration in Banach Spaces.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2013. https://doi.org/10.1214/EJP.v18-2945 . ieee: S. Dirksen, J. Maas, and J. Van Neerven, “Poisson stochastic integration in Banach spaces,” Electronic Journal of Probability, vol. 18. Institute of Mathematical Statistics, 2013. ista: Dirksen S, Maas J, Van Neerven J. 2013. Poisson stochastic integration in Banach spaces. Electronic Journal of Probability. 18. mla: Dirksen, Sjoerd, et al. “Poisson Stochastic Integration in Banach Spaces.” Electronic Journal of Probability, vol. 18, Institute of Mathematical Statistics, 2013, doi:10.1214/EJP.v18-2945 . short: S. Dirksen, J. Maas, J. Van Neerven, Electronic Journal of Probability 18 (2013). date_created: 2018-12-11T11:55:49Z date_published: 2013-11-18T00:00:00Z date_updated: 2021-01-12T06:55:24Z day: '18' doi: '10.1214/EJP.v18-2945 ' extern: 1 intvolume: ' 18' main_file_link: - open_access: '1' url: 'http://arxiv.org/abs/1307.7901 ' month: '11' oa: 1 publication: Electronic Journal of Probability publication_status: published publisher: Institute of Mathematical Statistics publist_id: '4917' quality_controlled: 0 status: public title: Poisson stochastic integration in Banach spaces type: journal_article volume: 18 year: '2013' ... --- _id: '2113' abstract: - lang: eng text: A new method fabricates custom surface reflectance and spatially varying bidirectional reflectance distribution functions (svBRDFs). Researchers optimize a microgeometry for a range of normal distribution functions and simulate the resulting surface's effective reflectance. Using the simulation's results, they reproduce an input svBRDF's appearance by distributing the microgeometry on the printed material's surface. This method lets people print svBRDFs on planar samples with current 3D printing technology, even with a limited set of printing materials. It extends naturally to printing svBRDFs on arbitrary shapes. author: - first_name: Olivier full_name: Rouiller, Olivier last_name: Rouiller - first_name: Bernd full_name: Bernd Bickel id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Jan full_name: Kautz, Jan last_name: Kautz - first_name: Wojciech full_name: Matusik, Wojciech last_name: Matusik - first_name: Marc full_name: Alexa, Marc last_name: Alexa citation: ama: Rouiller O, Bickel B, Kautz J, Matusik W, Alexa M. 3D printing spatially varying BRDFs. IEEE Computer Graphics and Applications. 2013;33(6):48-57. doi:10.1109/MCG.2013.82 apa: Rouiller, O., Bickel, B., Kautz, J., Matusik, W., & Alexa, M. (2013). 3D printing spatially varying BRDFs. IEEE Computer Graphics and Applications. IEEE. https://doi.org/10.1109/MCG.2013.82 chicago: Rouiller, Olivier, Bernd Bickel, Jan Kautz, Wojciech Matusik, and Marc Alexa. “3D Printing Spatially Varying BRDFs.” IEEE Computer Graphics and Applications. IEEE, 2013. https://doi.org/10.1109/MCG.2013.82 . ieee: O. Rouiller, B. Bickel, J. Kautz, W. Matusik, and M. Alexa, “3D printing spatially varying BRDFs,” IEEE Computer Graphics and Applications, vol. 33, no. 6. IEEE, pp. 48–57, 2013. ista: Rouiller O, Bickel B, Kautz J, Matusik W, Alexa M. 2013. 3D printing spatially varying BRDFs. IEEE Computer Graphics and Applications. 33(6), 48–57. mla: Rouiller, Olivier, et al. “3D Printing Spatially Varying BRDFs.” IEEE Computer Graphics and Applications, vol. 33, no. 6, IEEE, 2013, pp. 48–57, doi:10.1109/MCG.2013.82 . short: O. Rouiller, B. Bickel, J. Kautz, W. Matusik, M. Alexa, IEEE Computer Graphics and Applications 33 (2013) 48–57. date_created: 2018-12-11T11:55:47Z date_published: 2013-09-23T00:00:00Z date_updated: 2021-01-12T06:55:23Z day: '23' doi: '10.1109/MCG.2013.82 ' extern: 1 intvolume: ' 33' issue: '6' month: '09' page: 48 - 57 publication: IEEE Computer Graphics and Applications publication_status: published publisher: IEEE publist_id: '4920' quality_controlled: 0 status: public title: 3D printing spatially varying BRDFs type: journal_article volume: 33 year: '2013' ... --- _id: '2114' abstract: - lang: eng text: 3D printing is considered a disruptive technology with a potentially tremendous socioeconomic impact. The three articles in this special issue illustrate how novel computer graphics approaches are advancing such digital fabrication. author: - first_name: Bernd full_name: Bernd Bickel id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Marc full_name: Alexa, Marc last_name: Alexa citation: ama: 'Bickel B, Alexa M. Computational aspects of fabrication: Modeling, design and 3d printing. IEEE Computer Graphics and Applications. 2013;33(6):24-25. doi:10.1109/MCG.2013.89' apa: 'Bickel, B., & Alexa, M. (2013). Computational aspects of fabrication: Modeling, design and 3d printing. IEEE Computer Graphics and Applications. IEEE. https://doi.org/10.1109/MCG.2013.89' chicago: 'Bickel, Bernd, and Marc Alexa. “Computational Aspects of Fabrication: Modeling, Design and 3d Printing.” IEEE Computer Graphics and Applications. IEEE, 2013. https://doi.org/10.1109/MCG.2013.89.' ieee: 'B. Bickel and M. Alexa, “Computational aspects of fabrication: Modeling, design and 3d printing,” IEEE Computer Graphics and Applications, vol. 33, no. 6. IEEE, pp. 24–25, 2013.' ista: 'Bickel B, Alexa M. 2013. Computational aspects of fabrication: Modeling, design and 3d printing. IEEE Computer Graphics and Applications. 33(6), 24–25.' mla: 'Bickel, Bernd, and Marc Alexa. “Computational Aspects of Fabrication: Modeling, Design and 3d Printing.” IEEE Computer Graphics and Applications, vol. 33, no. 6, IEEE, 2013, pp. 24–25, doi:10.1109/MCG.2013.89.' short: B. Bickel, M. Alexa, IEEE Computer Graphics and Applications 33 (2013) 24–25. date_created: 2018-12-11T11:55:48Z date_published: 2013-12-01T00:00:00Z date_updated: 2021-01-12T06:55:24Z day: '01' doi: 10.1109/MCG.2013.89 extern: 1 intvolume: ' 33' issue: '6' month: '12' page: 24 - 25 publication: IEEE Computer Graphics and Applications publication_status: published publisher: IEEE publist_id: '4921' quality_controlled: 0 status: public title: 'Computational aspects of fabrication: Modeling, design and 3d printing' type: journal_article volume: 33 year: '2013' ... --- _id: '2129' abstract: - lang: eng text: "This paper continues the investigation of `Wasserstein-like' transportation distances for probability measures on discrete sets. We prove that the discrete transportation metrics on the d-dimensional discrete torus with mesh size 1/N converge, when N→∞, to the standard 2-Wasserstein distance W_2 on the continuous torus in the sense of Gromov-Hausdorff. This is the first convergence result for the recently developed discrete transportation metrics. The result shows the compatibility between these metrics and the well-established 2-Wasserstein metric. \n\n\n" acknowledgement: JM acknowledges support by Rubicon subsidy 680-50-0901 of the Netherlands Organisation for Scientific Research (NWO). author: - first_name: Nicola full_name: Gigli, Nicola last_name: Gigli - first_name: Jan full_name: Jan Maas id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 citation: ama: Gigli N, Maas J. Gromov-Hausdorff convergence of discrete transportation metrics. SIAM Journal on Mathematical Analysis. 2013;45(2):879-899. doi:10.1137/120886315 apa: Gigli, N., & Maas, J. (2013). Gromov-Hausdorff convergence of discrete transportation metrics. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/120886315 chicago: Gigli, Nicola, and Jan Maas. “Gromov-Hausdorff Convergence of Discrete Transportation Metrics.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics , 2013. https://doi.org/10.1137/120886315 . ieee: N. Gigli and J. Maas, “Gromov-Hausdorff convergence of discrete transportation metrics,” SIAM Journal on Mathematical Analysis, vol. 45, no. 2. Society for Industrial and Applied Mathematics , pp. 879–899, 2013. ista: Gigli N, Maas J. 2013. Gromov-Hausdorff convergence of discrete transportation metrics. SIAM Journal on Mathematical Analysis. 45(2), 879–899. mla: Gigli, Nicola, and Jan Maas. “Gromov-Hausdorff Convergence of Discrete Transportation Metrics.” SIAM Journal on Mathematical Analysis, vol. 45, no. 2, Society for Industrial and Applied Mathematics , 2013, pp. 879–99, doi:10.1137/120886315 . short: N. Gigli, J. Maas, SIAM Journal on Mathematical Analysis 45 (2013) 879–899. date_created: 2018-12-11T11:55:53Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T06:55:29Z day: '01' doi: '10.1137/120886315 ' extern: 1 intvolume: ' 45' issue: '2' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1207.6501 month: '01' oa: 1 page: 879 - 899 publication: SIAM Journal on Mathematical Analysis publication_status: published publisher: 'Society for Industrial and Applied Mathematics ' publist_id: '4904' quality_controlled: 0 status: public title: Gromov-Hausdorff convergence of discrete transportation metrics type: journal_article volume: 45 year: '2013' ... --- _id: '2139' abstract: - lang: eng text: Recently it has been shown that pairs of atoms can form metastable bonds due to non-conservative forces induced by dissipation [Lemeshko&Weimer, Nature Comm. 4, 2230 (2013)]. Here we study the dynamics of interaction-induced coherent population trapping - the process responsible for the formation of dissipatively bound molecules. We derive the effective dissipative potentials induced between ultracold atoms by laser light, and study the time evolution of the scattering states. We demonstrate that binding occurs on short timescales of ~10 microseconds, even if the initial kinetic energy of the atoms significantly exceeds the depth of the dissipative potential. Dissipatively-bound molecules with preordained bond lengths and vibrational wavefunctions can be created and detected in current experiments with ultracold atoms. acknowledgement: The work was supported by the NSF through a grant for the Institute for Theoretical Atomic, Molecular, and Optical Physics at Harvard University and Smithsonian Astrophysical Observatory author: - first_name: Mikhail full_name: Mikhail Lemeshko id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Lemeshko M. Manipulating scattering of ultracold atoms with light-induced dissipation. Frontiers Physics. 2013;1(17). doi:10.3389/fphy.2013.00017 apa: Lemeshko, M. (2013). Manipulating scattering of ultracold atoms with light-induced dissipation. Frontiers Physics. Frontiers Media. https://doi.org/10.3389/fphy.2013.00017 chicago: Lemeshko, Mikhail. “Manipulating Scattering of Ultracold Atoms with Light-Induced Dissipation.” Frontiers Physics. Frontiers Media, 2013. https://doi.org/10.3389/fphy.2013.00017. ieee: M. Lemeshko, “Manipulating scattering of ultracold atoms with light-induced dissipation,” Frontiers Physics, vol. 1, no. 17. Frontiers Media, 2013. ista: Lemeshko M. 2013. Manipulating scattering of ultracold atoms with light-induced dissipation. Frontiers Physics. 1(17). mla: Lemeshko, Mikhail. “Manipulating Scattering of Ultracold Atoms with Light-Induced Dissipation.” Frontiers Physics, vol. 1, no. 17, Frontiers Media, 2013, doi:10.3389/fphy.2013.00017. short: M. Lemeshko, Frontiers Physics 1 (2013). date_created: 2018-12-11T11:55:56Z date_published: 2013-10-07T00:00:00Z date_updated: 2021-01-12T06:55:32Z day: '07' doi: 10.3389/fphy.2013.00017 extern: 1 intvolume: ' 1' issue: '17' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1307.8129 month: '10' oa: 1 publication: Frontiers Physics publication_status: published publisher: Frontiers Media publist_id: '4885' quality_controlled: 0 status: public title: Manipulating scattering of ultracold atoms with light-induced dissipation type: journal_article volume: 1 year: '2013' ... --- _id: '2181' abstract: - lang: eng text: 'There is a trade-off between performance and correctness in implementing concurrent data structures. Better performance may be achieved at the expense of relaxing correctness, by redefining the semantics of data structures. We address such a redefinition of data structure semantics and present a systematic and formal framework for obtaining new data structures by quantitatively relaxing existing ones. We view a data structure as a sequential specification S containing all "legal" sequences over an alphabet of method calls. Relaxing the data structure corresponds to defining a distance from any sequence over the alphabet to the sequential specification: the k-relaxed sequential specification contains all sequences over the alphabet within distance k from the original specification. In contrast to other existing work, our relaxations are semantic (distance in terms of data structure states). As an instantiation of our framework, we present two simple yet generic relaxation schemes, called out-of-order and stuttering relaxation, along with several ways of computing distances. We show that the out-of-order relaxation, when further instantiated to stacks, queues, and priority queues, amounts to tolerating bounded out-of-order behavior, which cannot be captured by a purely syntactic relaxation (distance in terms of sequence manipulation, e.g. edit distance). We give concurrent implementations of relaxed data structures and demonstrate that bounded relaxations provide the means for trading correctness for performance in a controlled way. The relaxations are monotonic which further highlights the trade-off: increasing k increases the number of permitted sequences, which as we demonstrate can lead to better performance. Finally, since a relaxed stack or queue also implements a pool, we actually have new concurrent pool implementations that outperform the state-of-the-art ones.' acknowledgement: ' and an Elise Richter Fellowship (Austrian Science Fund V00125). ' author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Christoph full_name: Kirsch, Christoph last_name: Kirsch - first_name: Hannes full_name: Payer, Hannes last_name: Payer - first_name: Ali full_name: Sezgin, Ali id: 4C7638DA-F248-11E8-B48F-1D18A9856A87 last_name: Sezgin - first_name: Ana full_name: Sokolova, Ana last_name: Sokolova citation: ama: 'Henzinger TA, Kirsch C, Payer H, Sezgin A, Sokolova A. Quantitative relaxation of concurrent data structures. In: Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language. ACM; 2013:317-328. doi:10.1145/2429069.2429109' apa: 'Henzinger, T. A., Kirsch, C., Payer, H., Sezgin, A., & Sokolova, A. (2013). Quantitative relaxation of concurrent data structures. In Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language (pp. 317–328). Rome, Italy: ACM. https://doi.org/10.1145/2429069.2429109' chicago: Henzinger, Thomas A, Christoph Kirsch, Hannes Payer, Ali Sezgin, and Ana Sokolova. “Quantitative Relaxation of Concurrent Data Structures.” In Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language, 317–28. ACM, 2013. https://doi.org/10.1145/2429069.2429109. ieee: T. A. Henzinger, C. Kirsch, H. Payer, A. Sezgin, and A. Sokolova, “Quantitative relaxation of concurrent data structures,” in Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language, Rome, Italy, 2013, pp. 317–328. ista: 'Henzinger TA, Kirsch C, Payer H, Sezgin A, Sokolova A. 2013. Quantitative relaxation of concurrent data structures. Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language. POPL: Principles of Programming Languages, 317–328.' mla: Henzinger, Thomas A., et al. “Quantitative Relaxation of Concurrent Data Structures.” Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language, ACM, 2013, pp. 317–28, doi:10.1145/2429069.2429109. short: T.A. Henzinger, C. Kirsch, H. Payer, A. Sezgin, A. Sokolova, in:, Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language, ACM, 2013, pp. 317–328. conference: end_date: 2013-01-25 location: Rome, Italy name: 'POPL: Principles of Programming Languages' start_date: 2013-01-23 date_created: 2018-12-11T11:56:11Z date_published: 2013-01-01T00:00:00Z date_updated: 2023-02-21T16:06:49Z day: '01' ddc: - '000' - '004' department: - _id: ToHe doi: 10.1145/2429069.2429109 ec_funded: 1 file: - access_level: open_access checksum: adf465e70948f4e80e48057524516456 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:33Z date_updated: 2020-07-14T12:45:31Z file_id: '5086' file_name: IST-2014-198-v1+1_popl128-henzinger-clean.pdf file_size: 294689 relation: main_file file_date_updated: 2020-07-14T12:45:31Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 317 - 328 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms publication: Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language publication_identifier: isbn: - 978-1-4503-1832-7 publication_status: published publisher: ACM publist_id: '4801' pubrep_id: '198' quality_controlled: '1' related_material: record: - id: '10901' relation: later_version status: deleted scopus_import: 1 status: public title: Quantitative relaxation of concurrent data structures type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2182' abstract: - lang: eng text: We propose a general framework for abstraction with respect to quantitative properties, such as worst-case execution time, or power consumption. Our framework provides a systematic way for counter-example guided abstraction refinement for quantitative properties. The salient aspect of the framework is that it allows anytime verification, that is, verification algorithms that can be stopped at any time (for example, due to exhaustion of memory), and report approximations that improve monotonically when the algorithms are given more time. We instantiate the framework with a number of quantitative abstractions and refinement schemes, which differ in terms of how much quantitative information they keep from the original system. We introduce both state-based and trace-based quantitative abstractions, and we describe conditions that define classes of quantitative properties for which the abstractions provide over-approximations. We give algorithms for evaluating the quantitative properties on the abstract systems. We present algorithms for counter-example based refinements for quantitative properties for both state-based and segment-based abstractions. We perform a case study on worst-case execution time of executables to evaluate the anytime verification aspect and the quantitative abstractions we proposed. author: - first_name: Pavol full_name: Cerny, Pavol id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87 last_name: Cerny - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Arjun full_name: Radhakrishna, Arjun id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87 last_name: Radhakrishna citation: ama: 'Cerny P, Henzinger TA, Radhakrishna A. Quantitative abstraction refinement. In: Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language. ACM; 2013:115-128. doi:10.1145/2429069.2429085' apa: 'Cerny, P., Henzinger, T. A., & Radhakrishna, A. (2013). Quantitative abstraction refinement. In Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language (pp. 115–128). Rome, Italy: ACM. https://doi.org/10.1145/2429069.2429085' chicago: Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. “Quantitative Abstraction Refinement.” In Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language, 115–28. ACM, 2013. https://doi.org/10.1145/2429069.2429085. ieee: P. Cerny, T. A. Henzinger, and A. Radhakrishna, “Quantitative abstraction refinement,” in Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language, Rome, Italy, 2013, pp. 115–128. ista: 'Cerny P, Henzinger TA, Radhakrishna A. 2013. Quantitative abstraction refinement. Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language. POPL: Principles of Programming Languages, 115–128.' mla: Cerny, Pavol, et al. “Quantitative Abstraction Refinement.” Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language, ACM, 2013, pp. 115–28, doi:10.1145/2429069.2429085. short: P. Cerny, T.A. Henzinger, A. Radhakrishna, in:, Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language, ACM, 2013, pp. 115–128. conference: end_date: 2013-01-25 location: Rome, Italy name: 'POPL: Principles of Programming Languages' start_date: 2013-07-23 date_created: 2018-12-11T11:56:11Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T06:55:50Z day: '01' department: - _id: ToHe doi: 10.1145/2429069.2429085 ec_funded: 1 language: - iso: eng month: '01' oa_version: None page: 115 - 128 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms publication: Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language publication_status: published publisher: ACM publist_id: '4800' quality_controlled: '1' scopus_import: 1 status: public title: Quantitative abstraction refinement type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2209' abstract: - lang: eng text: "A straight skeleton is a well-known geometric structure, and several algorithms exist to construct the straight skeleton for a given polygon or planar straight-line graph. In this paper, we ask the reverse question: Given the straight skeleton (in form of a planar straight-line graph, with some rays to infinity), can we reconstruct a planar straight-line graph for which this was the straight skeleton? We show how to reduce this problem to the problem of finding a line that intersects a set of convex polygons. We can find these convex polygons and all such lines in $O(nlog n)$ time in the Real RAM computer model, where $n$ denotes the number of edges of the input graph. We also explain how our approach can be used for recognizing Voronoi diagrams of points, thereby completing a partial solution provided by Ash and Bolker in 1985.\r\n" alternative_title: - '2013 10th International Symposium on Voronoi Diagrams in Science and Engineering (ISVD 2013) ' author: - first_name: Therese full_name: Biedl, Therese last_name: Biedl - first_name: Martin full_name: Held, Martin last_name: Held - first_name: Stefan full_name: Huber, Stefan id: 4700A070-F248-11E8-B48F-1D18A9856A87 last_name: Huber orcid: 0000-0002-8871-5814 citation: ama: 'Biedl T, Held M, Huber S. Recognizing straight skeletons and Voronoi diagrams and reconstructing their input. In: IEEE; 2013:37-46. doi:10.1109/ISVD.2013.11' apa: 'Biedl, T., Held, M., & Huber, S. (2013). Recognizing straight skeletons and Voronoi diagrams and reconstructing their input (pp. 37–46). Presented at the ISVD: Voronoi Diagrams in Science and Engineering, St. Petersburg, Russia: IEEE. https://doi.org/10.1109/ISVD.2013.11' chicago: Biedl, Therese, Martin Held, and Stefan Huber. “Recognizing Straight Skeletons and Voronoi Diagrams and Reconstructing Their Input,” 37–46. IEEE, 2013. https://doi.org/10.1109/ISVD.2013.11. ieee: 'T. Biedl, M. Held, and S. Huber, “Recognizing straight skeletons and Voronoi diagrams and reconstructing their input,” presented at the ISVD: Voronoi Diagrams in Science and Engineering, St. Petersburg, Russia, 2013, pp. 37–46.' ista: 'Biedl T, Held M, Huber S. 2013. Recognizing straight skeletons and Voronoi diagrams and reconstructing their input. ISVD: Voronoi Diagrams in Science and Engineering, 2013 10th International Symposium on Voronoi Diagrams in Science and Engineering (ISVD 2013) , , 37–46.' mla: Biedl, Therese, et al. Recognizing Straight Skeletons and Voronoi Diagrams and Reconstructing Their Input. IEEE, 2013, pp. 37–46, doi:10.1109/ISVD.2013.11. short: T. Biedl, M. Held, S. Huber, in:, IEEE, 2013, pp. 37–46. conference: end_date: 2013-07-10 location: St. Petersburg, Russia name: 'ISVD: Voronoi Diagrams in Science and Engineering' start_date: 2013-07-08 date_created: 2018-12-11T11:56:20Z date_published: 2013-12-01T00:00:00Z date_updated: 2021-01-12T06:56:00Z day: '01' department: - _id: HeEd doi: 10.1109/ISVD.2013.11 language: - iso: eng month: '12' oa_version: None page: 37 - 46 publication_identifier: eisbn: - '978-0-7695-5037-4 ' publication_status: published publisher: IEEE publist_id: '4763' quality_controlled: '1' scopus_import: 1 status: public title: Recognizing straight skeletons and Voronoi diagrams and reconstructing their input type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2204' abstract: - lang: eng text: We introduce a new platform for quantum simulation of many-body systems based on nonspherical atoms or molecules with zero dipole moments but possessing a significant value of electric quadrupole moments. We consider a quadrupolar Fermi gas trapped in a 2D square optical lattice, and show that the peculiar symmetry and broad tunability of the quadrupole-quadrupole interaction results in a rich phase diagram encompassing unconventional BCS and charge density wave phases, and opens up a perspective to create a topological superfluid. Quadrupolar species, such as metastable alkaline-earth atoms and homonuclear molecules, are stable against chemical reactions and collapse and are readily available in experiment at high densities. article_processing_charge: No author: - first_name: Satyan full_name: Bhongale, Satyan last_name: Bhongale - first_name: Ludwig full_name: Mathey, Ludwig last_name: Mathey - first_name: Erhai full_name: Zhao, Erhai last_name: Zhao - first_name: Susanne full_name: Yelin, Susanne last_name: Yelin - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Bhongale S, Mathey L, Zhao E, Yelin S, Lemeshko M. Quantum phases of quadrupolar fermi gases in optical lattices. Physical Review Letters. 2013;110(15). doi:10.1103/PhysRevLett.110.155301 apa: Bhongale, S., Mathey, L., Zhao, E., Yelin, S., & Lemeshko, M. (2013). Quantum phases of quadrupolar fermi gases in optical lattices. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.110.155301 chicago: Bhongale, Satyan, Ludwig Mathey, Erhai Zhao, Susanne Yelin, and Mikhail Lemeshko. “Quantum Phases of Quadrupolar Fermi Gases in Optical Lattices.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.155301. ieee: S. Bhongale, L. Mathey, E. Zhao, S. Yelin, and M. Lemeshko, “Quantum phases of quadrupolar fermi gases in optical lattices,” Physical Review Letters, vol. 110, no. 15. American Physical Society, 2013. ista: Bhongale S, Mathey L, Zhao E, Yelin S, Lemeshko M. 2013. Quantum phases of quadrupolar fermi gases in optical lattices. Physical Review Letters. 110(15). mla: Bhongale, Satyan, et al. “Quantum Phases of Quadrupolar Fermi Gases in Optical Lattices.” Physical Review Letters, vol. 110, no. 15, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.155301. short: S. Bhongale, L. Mathey, E. Zhao, S. Yelin, M. Lemeshko, Physical Review Letters 110 (2013). date_created: 2018-12-11T11:56:18Z date_published: 2013-04-08T00:00:00Z date_updated: 2021-11-16T08:04:06Z day: '08' doi: 10.1103/PhysRevLett.110.155301 extern: '1' intvolume: ' 110' issue: '15' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1211.3317 month: '04' oa: 1 oa_version: None publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '4769' related_material: link: - relation: erratum url: https://doi.org/10.1103/PhysRevLett.111.239901 status: public title: Quantum phases of quadrupolar fermi gases in optical lattices type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 110 year: '2013' ... --- _id: '2206' abstract: - lang: eng text: Magnetic impurities embedded in inert solids can exhibit long coherence times and interact with one another via their intrinsic anisotropic dipolar interaction. We argue that, as a consequence of these properties, disordered ensembles of magnetic impurities provide an effective platform for realizing a controllable, tunable version of the dipolar quantum spin glass seen in LiHoxY1-xF4. Specifically, we propose and analyze a system composed of dysprosium atoms embedded in solid helium. We describe the phase diagram of the system and discuss the realizability and detectability of the quantum spin glass and antiglass phases. author: - first_name: Mikhail full_name: Mikhail Lemeshko id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Norman full_name: Yao, Norman Y last_name: Yao - first_name: Alexey full_name: Gorshkov, Alexey V last_name: Gorshkov - first_name: Hendrik full_name: Weimer, Hendrik last_name: Weimer - first_name: Steven full_name: Bennett, Steven D last_name: Bennett - first_name: Takamasa full_name: Momose, Takamasa last_name: Momose - first_name: Sarang full_name: Gopalakrishnan, Sarang last_name: Gopalakrishnan citation: ama: Lemeshko M, Yao N, Gorshkov A, et al. Controllable quantum spin glasses with magnetic impurities embedded in quantum solids. Physical Review B - Condensed Matter and Materials Physics. 2013;88(1). doi:10.1103/PhysRevB.88.014426 apa: Lemeshko, M., Yao, N., Gorshkov, A., Weimer, H., Bennett, S., Momose, T., & Gopalakrishnan, S. (2013). Controllable quantum spin glasses with magnetic impurities embedded in quantum solids. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.88.014426 chicago: Lemeshko, Mikhail, Norman Yao, Alexey Gorshkov, Hendrik Weimer, Steven Bennett, Takamasa Momose, and Sarang Gopalakrishnan. “Controllable Quantum Spin Glasses with Magnetic Impurities Embedded in Quantum Solids.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2013. https://doi.org/10.1103/PhysRevB.88.014426. ieee: M. Lemeshko et al., “Controllable quantum spin glasses with magnetic impurities embedded in quantum solids,” Physical Review B - Condensed Matter and Materials Physics, vol. 88, no. 1. American Physical Society, 2013. ista: Lemeshko M, Yao N, Gorshkov A, Weimer H, Bennett S, Momose T, Gopalakrishnan S. 2013. Controllable quantum spin glasses with magnetic impurities embedded in quantum solids. Physical Review B - Condensed Matter and Materials Physics. 88(1). mla: Lemeshko, Mikhail, et al. “Controllable Quantum Spin Glasses with Magnetic Impurities Embedded in Quantum Solids.” Physical Review B - Condensed Matter and Materials Physics, vol. 88, no. 1, American Physical Society, 2013, doi:10.1103/PhysRevB.88.014426. short: M. Lemeshko, N. Yao, A. Gorshkov, H. Weimer, S. Bennett, T. Momose, S. Gopalakrishnan, Physical Review B - Condensed Matter and Materials Physics 88 (2013). date_created: 2018-12-11T11:56:19Z date_published: 2013-07-24T00:00:00Z date_updated: 2021-01-12T06:55:59Z day: '24' doi: 10.1103/PhysRevB.88.014426 extern: 1 intvolume: ' 88' issue: '1' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1307.1130 month: '07' oa: 1 publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '4767' quality_controlled: 0 status: public title: Controllable quantum spin glasses with magnetic impurities embedded in quantum solids type: journal_article volume: 88 year: '2013' ... --- _id: '2205' abstract: - lang: eng text: The goal of the present article is to review the major developments that have led to the current understanding of molecule-field interactions and experimental methods for manipulating molecules with electromagnetic fields. Molecule-field interactions are at the core of several, seemingly distinct areas of molecular physics. This is reflected in the organisation of this article, which includes sections on field control of molecular beams, external field traps for cold molecules, control of molecular orientation and molecular alignment, manipulation of molecules by non-conservative forces, ultracold molecules and ultracold chemistry, controlled many-body phenomena, entanglement of molecules and dipole arrays, and stability of molecular systems in high-frequency super-intense laser fields. The article contains 852 references. acknowledgement: National Science Foundation; Natural Sciences and Engineering Research Council of Canada author: - first_name: Mikhail full_name: Mikhail Lemeshko id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Roman full_name: Krems, Roman V last_name: Krems - first_name: John full_name: Doyle, John M last_name: Doyle - first_name: Sabre full_name: Kais, Sabre last_name: Kais citation: ama: Lemeshko M, Krems R, Doyle J, Kais S. Manipulation of molecules with electromagnetic fields. Molecular Physics. 2013;111(12-13):1648-1682. doi:10.1080/00268976.2013.813595 apa: Lemeshko, M., Krems, R., Doyle, J., & Kais, S. (2013). Manipulation of molecules with electromagnetic fields. Molecular Physics. Taylor & Francis. https://doi.org/10.1080/00268976.2013.813595 chicago: Lemeshko, Mikhail, Roman Krems, John Doyle, and Sabre Kais. “Manipulation of Molecules with Electromagnetic Fields.” Molecular Physics. Taylor & Francis, 2013. https://doi.org/10.1080/00268976.2013.813595. ieee: M. Lemeshko, R. Krems, J. Doyle, and S. Kais, “Manipulation of molecules with electromagnetic fields,” Molecular Physics, vol. 111, no. 12–13. Taylor & Francis, pp. 1648–1682, 2013. ista: Lemeshko M, Krems R, Doyle J, Kais S. 2013. Manipulation of molecules with electromagnetic fields. Molecular Physics. 111(12–13), 1648–1682. mla: Lemeshko, Mikhail, et al. “Manipulation of Molecules with Electromagnetic Fields.” Molecular Physics, vol. 111, no. 12–13, Taylor & Francis, 2013, pp. 1648–82, doi:10.1080/00268976.2013.813595. short: M. Lemeshko, R. Krems, J. Doyle, S. Kais, Molecular Physics 111 (2013) 1648–1682. date_created: 2018-12-11T11:56:19Z date_published: 2013-07-01T00:00:00Z date_updated: 2020-07-14T12:45:32Z day: '01' doi: 10.1080/00268976.2013.813595 extern: 1 intvolume: ' 111' issue: 12-13 main_file_link: - open_access: '1' url: http://arxiv.org/abs/1306.0912 month: '07' oa: 1 page: 1648 - 1682 publication: Molecular Physics publication_status: published publisher: Taylor & Francis publist_id: '4768' quality_controlled: 0 status: public title: Manipulation of molecules with electromagnetic fields type: review volume: 111 year: '2013' ... --- _id: '2207' abstract: - lang: eng text: The formation of molecules and supramolecular structures results from bonding by conservative forces acting among electrons and nuclei and giving rise to equilibrium configurations defined by minima of the interaction potential. Here we show that bonding can also occur by the non-conservative forces responsible for interaction-induced coherent population trapping. The bound state arises in a dissipative process and manifests itself as a stationary state at a preordained interatomic distance. Remarkably, such a dissipative bonding is present even when the interactions among the atoms are purely repulsive. The dissipative bound states can be created and studied spectroscopically in present-day experiments with ultracold atoms or molecules and can potentially serve for cooling strongly interacting quantum gases. author: - first_name: Mikhail full_name: Mikhail Lemeshko id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Hendrik full_name: Weimer, Hendrik last_name: Weimer citation: ama: Lemeshko M, Weimer H. Dissipative binding of atoms by non-conservative forces. Nature Communications. 2013;4. doi:10.1038/ncomms3230 apa: Lemeshko, M., & Weimer, H. (2013). Dissipative binding of atoms by non-conservative forces. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms3230 chicago: Lemeshko, Mikhail, and Hendrik Weimer. “Dissipative Binding of Atoms by Non-Conservative Forces.” Nature Communications. Nature Publishing Group, 2013. https://doi.org/10.1038/ncomms3230. ieee: M. Lemeshko and H. Weimer, “Dissipative binding of atoms by non-conservative forces,” Nature Communications, vol. 4. Nature Publishing Group, 2013. ista: Lemeshko M, Weimer H. 2013. Dissipative binding of atoms by non-conservative forces. Nature Communications. 4. mla: Lemeshko, Mikhail, and Hendrik Weimer. “Dissipative Binding of Atoms by Non-Conservative Forces.” Nature Communications, vol. 4, Nature Publishing Group, 2013, doi:10.1038/ncomms3230. short: M. Lemeshko, H. Weimer, Nature Communications 4 (2013). date_created: 2018-12-11T11:56:20Z date_published: 2013-07-30T00:00:00Z date_updated: 2021-01-12T06:55:59Z day: '30' doi: 10.1038/ncomms3230 extern: 1 intvolume: ' 4' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1211.4035 month: '07' oa: 1 publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '4766' quality_controlled: 0 status: public title: Dissipative binding of atoms by non-conservative forces type: journal_article volume: 4 year: '2013' ... --- _id: '2210' abstract: - lang: eng text: 'A straight skeleton is a well-known geometric structure, and several algorithms exist to construct the straight skeleton for a given polygon. In this paper, we ask the reverse question: Given the straight skeleton (in form of a tree with a drawing in the plane, but with the exact position of the leaves unspecified), can we reconstruct the polygon? We show that in most cases there exists at most one polygon; in the remaining case there is an infinite number of polygons determined by one angle that can range in an interval. We can find this (set of) polygon(s) in linear time in the Real RAM computer model.' author: - first_name: Therese full_name: Biedl, Therese last_name: Biedl - first_name: Martin full_name: Held, Martin last_name: Held - first_name: Stefan full_name: Huber, Stefan id: 4700A070-F248-11E8-B48F-1D18A9856A87 last_name: Huber orcid: 0000-0002-8871-5814 citation: ama: 'Biedl T, Held M, Huber S. Reconstructing polygons from embedded straight skeletons. In: 29th European Workshop on Computational Geometry. TU Braunschweig; 2013:95-98.' apa: 'Biedl, T., Held, M., & Huber, S. (2013). Reconstructing polygons from embedded straight skeletons. In 29th European Workshop on Computational Geometry (pp. 95–98). Braunschweig, Germany: TU Braunschweig.' chicago: Biedl, Therese, Martin Held, and Stefan Huber. “Reconstructing Polygons from Embedded Straight Skeletons.” In 29th European Workshop on Computational Geometry, 95–98. TU Braunschweig, 2013. ieee: T. Biedl, M. Held, and S. Huber, “Reconstructing polygons from embedded straight skeletons,” in 29th European Workshop on Computational Geometry, Braunschweig, Germany, 2013, pp. 95–98. ista: 'Biedl T, Held M, Huber S. 2013. Reconstructing polygons from embedded straight skeletons. 29th European Workshop on Computational Geometry. EuroCG: European Workshop on Computational Geometry, 95–98.' mla: Biedl, Therese, et al. “Reconstructing Polygons from Embedded Straight Skeletons.” 29th European Workshop on Computational Geometry, TU Braunschweig, 2013, pp. 95–98. short: T. Biedl, M. Held, S. Huber, in:, 29th European Workshop on Computational Geometry, TU Braunschweig, 2013, pp. 95–98. conference: end_date: 2013-03-20 location: Braunschweig, Germany name: 'EuroCG: European Workshop on Computational Geometry' start_date: 2013-03-17 date_created: 2018-12-11T11:56:21Z date_published: 2013-03-01T00:00:00Z date_updated: 2021-01-12T06:56:00Z day: '01' department: - _id: HeEd language: - iso: eng main_file_link: - open_access: '1' url: http://www.ibr.cs.tu-bs.de/alg/eurocg13/booklet_eurocg13.pdf month: '03' oa: 1 oa_version: Submitted Version page: 95 - 98 publication: 29th European Workshop on Computational Geometry publication_status: published publisher: TU Braunschweig publist_id: '4762' status: public title: Reconstructing polygons from embedded straight skeletons type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2237' abstract: - lang: eng text: We describe new extensions of the Vampire theorem prover for computing tree interpolants. These extensions generalize Craig interpolation in Vampire, and can also be used to derive sequence interpolants. We evaluated our implementation on a large number of examples over the theory of linear integer arithmetic and integer-indexed arrays, with and without quantifiers. When compared to other methods, our experiments show that some examples could only be solved by our implementation. alternative_title: - LNCS article_processing_charge: No author: - first_name: Régis full_name: Blanc, Régis last_name: Blanc - first_name: Ashutosh full_name: Gupta, Ashutosh id: 335E5684-F248-11E8-B48F-1D18A9856A87 last_name: Gupta - first_name: Laura full_name: Kovács, Laura last_name: Kovács - first_name: Bernhard full_name: Kragl, Bernhard id: 320FC952-F248-11E8-B48F-1D18A9856A87 last_name: Kragl orcid: 0000-0001-7745-9117 citation: ama: Blanc R, Gupta A, Kovács L, Kragl B. Tree interpolation in Vampire. 2013;8312:173-181. doi:10.1007/978-3-642-45221-5_13 apa: 'Blanc, R., Gupta, A., Kovács, L., & Kragl, B. (2013). Tree interpolation in Vampire. Presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Stellenbosch, South Africa: Springer. https://doi.org/10.1007/978-3-642-45221-5_13' chicago: Blanc, Régis, Ashutosh Gupta, Laura Kovács, and Bernhard Kragl. “Tree Interpolation in Vampire.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-45221-5_13. ieee: R. Blanc, A. Gupta, L. Kovács, and B. Kragl, “Tree interpolation in Vampire,” vol. 8312. Springer, pp. 173–181, 2013. ista: Blanc R, Gupta A, Kovács L, Kragl B. 2013. Tree interpolation in Vampire. 8312, 173–181. mla: Blanc, Régis, et al. Tree Interpolation in Vampire. Vol. 8312, Springer, 2013, pp. 173–81, doi:10.1007/978-3-642-45221-5_13. short: R. Blanc, A. Gupta, L. Kovács, B. Kragl, 8312 (2013) 173–181. conference: end_date: 2013-12-19 location: Stellenbosch, South Africa name: 'LPAR: Logic for Programming, Artificial Intelligence, and Reasoning' start_date: 2013-12-14 date_created: 2018-12-11T11:56:29Z date_published: 2013-01-14T00:00:00Z date_updated: 2020-08-11T10:09:42Z day: '14' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-642-45221-5_13 file: - access_level: open_access checksum: 9cebaafca032e6769d273f393305c705 content_type: application/pdf creator: dernst date_created: 2020-05-15T11:10:40Z date_updated: 2020-07-14T12:45:34Z file_id: '7858' file_name: 2013_LPAR_Blanc.pdf file_size: 279206 relation: main_file file_date_updated: 2020-07-14T12:45:34Z has_accepted_license: '1' intvolume: ' 8312' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 173 - 181 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: Springer publist_id: '4724' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Tree interpolation in Vampire type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8312 year: '2013' ... --- _id: '2238' abstract: - lang: eng text: "We study the problem of achieving a given value in Markov decision processes (MDPs) with several independent discounted reward objectives. We consider a generalised version of discounted reward objectives, in which the amount of discounting depends on the states visited and on the objective. This definition extends the usual definition of discounted reward, and allows to capture the systems in which the value of different commodities diminish at different and variable rates.\r\n\r\nWe establish results for two prominent subclasses of the problem, namely state-discount models where the discount factors are only dependent on the state of the MDP (and independent of the objective), and reward-discount models where they are only dependent on the objective (but not on the state of the MDP). For the state-discount models we use a straightforward reduction to expected total reward and show that the problem whether a value is achievable can be solved in polynomial time. For the reward-discount model we show that memory and randomisation of the strategies are required, but nevertheless that the problem is decidable and it is sufficient to consider strategies which after a certain number of steps behave in a memoryless way.\r\n\r\nFor the general case, we show that when restricted to graphs (i.e. MDPs with no randomisation), pure strategies and discount factors of the form 1/n where n is an integer, the problem is in PSPACE and finite memory suffices for achieving a given value. We also show that when the discount factors are not of the form 1/n, the memory required by a strategy can be infinite.\r\n" alternative_title: - LNCS author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Vojtěch full_name: Forejt, Vojtěch last_name: Forejt - first_name: Dominik full_name: Wojtczak, Dominik last_name: Wojtczak citation: ama: Chatterjee K, Forejt V, Wojtczak D. Multi-objective discounted reward verification in graphs and MDPs. 2013;8312:228-242. doi:10.1007/978-3-642-45221-5_17 apa: 'Chatterjee, K., Forejt, V., & Wojtczak, D. (2013). Multi-objective discounted reward verification in graphs and MDPs. Presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Stellenbosch, South Africa: Springer. https://doi.org/10.1007/978-3-642-45221-5_17' chicago: Chatterjee, Krishnendu, Vojtěch Forejt, and Dominik Wojtczak. “Multi-Objective Discounted Reward Verification in Graphs and MDPs.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-45221-5_17. ieee: K. Chatterjee, V. Forejt, and D. Wojtczak, “Multi-objective discounted reward verification in graphs and MDPs,” vol. 8312. Springer, pp. 228–242, 2013. ista: Chatterjee K, Forejt V, Wojtczak D. 2013. Multi-objective discounted reward verification in graphs and MDPs. 8312, 228–242. mla: Chatterjee, Krishnendu, et al. Multi-Objective Discounted Reward Verification in Graphs and MDPs. Vol. 8312, Springer, 2013, pp. 228–42, doi:10.1007/978-3-642-45221-5_17. short: K. Chatterjee, V. Forejt, D. Wojtczak, 8312 (2013) 228–242. conference: end_date: 2013-12-19 location: Stellenbosch, South Africa name: 'LPAR: Logic for Programming, Artificial Intelligence, and Reasoning' start_date: 2013-12-14 date_created: 2018-12-11T11:56:30Z date_published: 2013-12-01T00:00:00Z date_updated: 2020-08-11T10:09:42Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-642-45221-5_17 ec_funded: 1 intvolume: ' 8312' language: - iso: eng month: '12' oa_version: None page: 228 - 242 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication_status: published publisher: Springer publist_id: '4723' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Multi-objective discounted reward verification in graphs and MDPs type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8312 year: '2013' ... --- _id: '2243' abstract: - lang: eng text: We show that modal logic over universally first-order definable classes of transitive frames is decidable. More precisely, let K be an arbitrary class of transitive Kripke frames definable by a universal first-order sentence. We show that the global and finite global satisfiability problems of modal logic over K are decidable in NP, regardless of choice of K. We also show that the local satisfiability and the finite local satisfiability problems of modal logic over K are decidable in NEXPTIME. alternative_title: - LIPIcs author: - first_name: Jakub full_name: Michaliszyn, Jakub last_name: Michaliszyn - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop citation: ama: Michaliszyn J, Otop J. Elementary modal logics over transitive structures. 2013;23:563-577. doi:10.4230/LIPIcs.CSL.2013.563 apa: 'Michaliszyn, J., & Otop, J. (2013). Elementary modal logics over transitive structures. Presented at the CSL: Computer Science Logic, Torino, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CSL.2013.563' chicago: Michaliszyn, Jakub, and Jan Otop. “Elementary Modal Logics over Transitive Structures.” Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013. https://doi.org/10.4230/LIPIcs.CSL.2013.563. ieee: J. Michaliszyn and J. Otop, “Elementary modal logics over transitive structures,” vol. 23. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp. 563–577, 2013. ista: Michaliszyn J, Otop J. 2013. Elementary modal logics over transitive structures. 23, 563–577. mla: Michaliszyn, Jakub, and Jan Otop. Elementary Modal Logics over Transitive Structures. Vol. 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 563–77, doi:10.4230/LIPIcs.CSL.2013.563. short: J. Michaliszyn, J. Otop, 23 (2013) 563–577. conference: end_date: 2013-09-05 location: Torino, Italy name: 'CSL: Computer Science Logic' start_date: 2013-09-02 date_created: 2018-12-11T11:56:32Z date_published: 2013-09-01T00:00:00Z date_updated: 2020-08-11T10:09:42Z day: '01' ddc: - '000' - '004' department: - _id: ToHe doi: 10.4230/LIPIcs.CSL.2013.563 ec_funded: 1 file: - access_level: open_access checksum: e0732e73a8b1e39483df7717d53e3e35 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:11Z date_updated: 2020-07-14T12:45:34Z file_id: '4929' file_name: IST-2016-136-v1+2_39.pdf file_size: 454915 relation: main_file file_date_updated: 2020-07-14T12:45:34Z has_accepted_license: '1' intvolume: ' 23' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 563 - 577 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '4708' pubrep_id: '136' quality_controlled: '1' scopus_import: 1 series_title: Leibniz International Proceedings in Informatics status: public title: Elementary modal logics over transitive structures tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2013' ... --- _id: '2244' abstract: - lang: eng text: 'We consider two systems (α1,...,αm) and (β1,...,βn) of curves drawn on a compact two-dimensional surface ℳ with boundary. Each αi and each βj is either an arc meeting the boundary of ℳ at its two endpoints, or a closed curve. The αi are pairwise disjoint except for possibly sharing endpoints, and similarly for the βj. We want to "untangle" the βj from the αi by a self-homeomorphism of ℳ; more precisely, we seek an homeomorphism φ: ℳ → ℳ fixing the boundary of ℳ pointwise such that the total number of crossings of the αi with the φ(βj) is as small as possible. This problem is motivated by an application in the algorithmic theory of embeddings and 3-manifolds. We prove that if ℳ is planar, i.e., a sphere with h ≥ 0 boundary components ("holes"), then O(mn) crossings can be achieved (independently of h), which is asymptotically tight, as an easy lower bound shows. In general, for an arbitrary (orientable or nonorientable) surface ℳ with h holes and of (orientable or nonorientable) genus g ≥ 0, we obtain an O((m + n)4) upper bound, again independent of h and g. ' acknowledgement: We would like to thank the authors of [GHR13] for mak- ing a draft of their paper available to us, and, in particular, T. Huynh for an e-mail correspondence. alternative_title: - LNCS author: - first_name: Jiří full_name: Matoušek, Jiří last_name: Matoušek - first_name: Eric full_name: Sedgwick, Eric last_name: Sedgwick - first_name: Martin full_name: Tancer, Martin id: 38AC689C-F248-11E8-B48F-1D18A9856A87 last_name: Tancer orcid: 0000-0002-1191-6714 - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: Matoušek J, Sedgwick E, Tancer M, Wagner U. Untangling two systems of noncrossing curves. 2013;8242:472-483. doi:10.1007/978-3-319-03841-4_41 apa: 'Matoušek, J., Sedgwick, E., Tancer, M., & Wagner, U. (2013). Untangling two systems of noncrossing curves. Presented at the GD: Graph Drawing and Network Visualization, Bordeaux, France: Springer. https://doi.org/10.1007/978-3-319-03841-4_41' chicago: Matoušek, Jiří, Eric Sedgwick, Martin Tancer, and Uli Wagner. “Untangling Two Systems of Noncrossing Curves.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-319-03841-4_41. ieee: J. Matoušek, E. Sedgwick, M. Tancer, and U. Wagner, “Untangling two systems of noncrossing curves,” vol. 8242. Springer, pp. 472–483, 2013. ista: Matoušek J, Sedgwick E, Tancer M, Wagner U. 2013. Untangling two systems of noncrossing curves. 8242, 472–483. mla: Matoušek, Jiří, et al. Untangling Two Systems of Noncrossing Curves. Vol. 8242, Springer, 2013, pp. 472–83, doi:10.1007/978-3-319-03841-4_41. short: J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, 8242 (2013) 472–483. conference: end_date: 2013-09-25 location: Bordeaux, France name: 'GD: Graph Drawing and Network Visualization' start_date: 2013-09-23 date_created: 2018-12-11T11:56:32Z date_published: 2013-09-01T00:00:00Z date_updated: 2023-02-21T17:03:07Z day: '01' department: - _id: UlWa doi: 10.1007/978-3-319-03841-4_41 external_id: arxiv: - '1302.6475' intvolume: ' 8242' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1302.6475 month: '09' oa: 1 oa_version: Preprint page: 472 - 483 project: - _id: 25FA3206-B435-11E9-9278-68D0E5697425 grant_number: PP00P2_138948 name: 'Embeddings in Higher Dimensions: Algorithms and Combinatorics' publication_status: published publisher: Springer publist_id: '4707' quality_controlled: '1' related_material: record: - id: '1411' relation: later_version status: public scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Untangling two systems of noncrossing curves type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8242 year: '2013' ... --- _id: '2259' abstract: - lang: eng text: "The learning with rounding (LWR) problem, introduced by Banerjee, Peikert and Rosen at EUROCRYPT ’12, is a variant of learning with errors (LWE), where one replaces random errors with deterministic rounding. The LWR problem was shown to be as hard as LWE for a setting of parameters where the modulus and modulus-to-error ratio are super-polynomial. In this work we resolve the main open problem and give a new reduction that works for a larger range of parameters, allowing for a polynomial modulus and modulus-to-error ratio. In particular, a smaller modulus gives us greater efficiency, and a smaller modulus-to-error ratio gives us greater security, which now follows from the worst-case hardness of GapSVP with polynomial (rather than super-polynomial) approximation factors.\r\n\r\nAs a tool in the reduction, we show that there is a “lossy mode” for the LWR problem, in which LWR samples only reveal partial information about the secret. This property gives us several interesting new applications, including a proof that LWR remains secure with weakly random secrets of sufficient min-entropy, and very simple constructions of deterministic encryption, lossy trapdoor functions and reusable extractors.\r\n\r\nOur approach is inspired by a technique of Goldwasser et al. from ICS ’10, which implicitly showed the existence of a “lossy mode” for LWE. By refining this technique, we also improve on the parameters of that work to only requiring a polynomial (instead of super-polynomial) modulus and modulus-to-error ratio.\r\n" alternative_title: - LNCS author: - first_name: Joel F full_name: Alwen, Joel F id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87 last_name: Alwen - first_name: Stephan full_name: Krenn, Stephan id: 329FCCF0-F248-11E8-B48F-1D18A9856A87 last_name: Krenn orcid: 0000-0003-2835-9093 - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Daniel full_name: Wichs, Daniel last_name: Wichs citation: ama: 'Alwen JF, Krenn S, Pietrzak KZ, Wichs D. Learning with rounding, revisited: New reduction properties and applications. 2013;8042(1):57-74. doi:10.1007/978-3-642-40041-4_4' apa: 'Alwen, J. F., Krenn, S., Pietrzak, K. Z., & Wichs, D. (2013). Learning with rounding, revisited: New reduction properties and applications. Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-642-40041-4_4' chicago: 'Alwen, Joel F, Stephan Krenn, Krzysztof Z Pietrzak, and Daniel Wichs. “Learning with Rounding, Revisited: New Reduction Properties and Applications.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-40041-4_4.' ieee: 'J. F. Alwen, S. Krenn, K. Z. Pietrzak, and D. Wichs, “Learning with rounding, revisited: New reduction properties and applications,” vol. 8042, no. 1. Springer, pp. 57–74, 2013.' ista: 'Alwen JF, Krenn S, Pietrzak KZ, Wichs D. 2013. Learning with rounding, revisited: New reduction properties and applications. 8042(1), 57–74.' mla: 'Alwen, Joel F., et al. Learning with Rounding, Revisited: New Reduction Properties and Applications. Vol. 8042, no. 1, Springer, 2013, pp. 57–74, doi:10.1007/978-3-642-40041-4_4.' short: J.F. Alwen, S. Krenn, K.Z. Pietrzak, D. Wichs, 8042 (2013) 57–74. conference: end_date: 2013-08-22 location: Santa Barbara, CA, United States name: 'CRYPTO: International Cryptology Conference' start_date: 2013-08-18 date_created: 2018-12-11T11:56:37Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T06:56:21Z day: '01' ddc: - '000' - '004' department: - _id: KrPi doi: 10.1007/978-3-642-40041-4_4 ec_funded: 1 file: - access_level: open_access checksum: 16d428408a806b8e49eecc607deab115 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:55Z date_updated: 2020-07-14T12:45:35Z file_id: '4912' file_name: IST-2016-684-v1+1_098.pdf file_size: 587898 relation: main_file file_date_updated: 2020-07-14T12:45:35Z has_accepted_license: '1' intvolume: ' 8042' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 57 - 74 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '4687' pubrep_id: '684' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: 'Learning with rounding, revisited: New reduction properties and applications' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8042 year: '2013' ... --- _id: '2258' abstract: - lang: eng text: "In a digital signature scheme with message recovery, rather than transmitting the message m and its signature σ, a single enhanced signature τ is transmitted. The verifier is able to recover m from τ and at the same time verify its authenticity. The two most important parameters of such a scheme are its security and overhead |τ| − |m|. A simple argument shows that for any scheme with “n bits security” |τ| − |m| ≥ n, i.e., the overhead is lower bounded by the security parameter n. Currently, the best known constructions in the random oracle model are far from this lower bound requiring an overhead of n + logq h , where q h is the number of queries to the random oracle. In this paper we give a construction which basically matches the n bit lower bound. We propose a simple digital signature scheme with n + o(logq h ) bits overhead, where q h denotes the number of random oracle queries.\r\n\r\nOur construction works in two steps. First, we propose a signature scheme with message recovery having optimal overhead in a new ideal model, the random invertible function model. Second, we show that a four-round Feistel network with random oracles as round functions is tightly “public-indifferentiable” from a random invertible function. At the core of our indifferentiability proof is an almost tight upper bound for the expected number of edges of the densest “small” subgraph of a random Cayley graph, which may be of independent interest.\r\n" alternative_title: - LNCS author: - first_name: Eike full_name: Kiltz, Eike last_name: Kiltz - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Mario full_name: Szegedy, Mario last_name: Szegedy citation: ama: Kiltz E, Pietrzak KZ, Szegedy M. Digital signatures with minimal overhead from indifferentiable random invertible functions. 2013;8042:571-588. doi:10.1007/978-3-642-40041-4_31 apa: 'Kiltz, E., Pietrzak, K. Z., & Szegedy, M. (2013). Digital signatures with minimal overhead from indifferentiable random invertible functions. Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-642-40041-4_31' chicago: Kiltz, Eike, Krzysztof Z Pietrzak, and Mario Szegedy. “Digital Signatures with Minimal Overhead from Indifferentiable Random Invertible Functions.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-40041-4_31. ieee: E. Kiltz, K. Z. Pietrzak, and M. Szegedy, “Digital signatures with minimal overhead from indifferentiable random invertible functions,” vol. 8042. Springer, pp. 571–588, 2013. ista: Kiltz E, Pietrzak KZ, Szegedy M. 2013. Digital signatures with minimal overhead from indifferentiable random invertible functions. 8042, 571–588. mla: Kiltz, Eike, et al. Digital Signatures with Minimal Overhead from Indifferentiable Random Invertible Functions. Vol. 8042, Springer, 2013, pp. 571–88, doi:10.1007/978-3-642-40041-4_31. short: E. Kiltz, K.Z. Pietrzak, M. Szegedy, 8042 (2013) 571–588. conference: end_date: 2013-08-22 location: Santa Barbara, CA, United States name: 'CRYPTO: International Cryptology Conference' start_date: 2013-08-18 date_created: 2018-12-11T11:56:37Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T06:56:21Z day: '01' ddc: - '000' - '004' department: - _id: KrPi doi: 10.1007/978-3-642-40041-4_31 ec_funded: 1 file: - access_level: open_access checksum: 18a3f602cb41de184dc0e16a0e907633 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:20Z date_updated: 2020-07-14T12:45:35Z file_id: '4744' file_name: IST-2016-685-v1+1_658.pdf file_size: 493175 relation: main_file file_date_updated: 2020-07-14T12:45:35Z has_accepted_license: '1' intvolume: ' 8042' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 571 - 588 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '4688' pubrep_id: '685' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Digital signatures with minimal overhead from indifferentiable random invertible functions type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8042 year: '2013' ... --- _id: '2256' abstract: - lang: eng text: Linked (Open) Data - bibliographic data on the Semantic Web. Report of the Working Group on Linked Data to the plenary assembly of the Austrian Library Network (translation of the title). Linked Data stands for a certain approach to publishing data on the Web. The underlying idea is to harmonise heterogeneous data sources of different origin in order to improve their accessibility and interoperability, effectively making them queryable as a big distributed database. This report summarises relevant developments in Europe as well as the Linked Data Working Group‘s strategic and technical considerations regarding the publishing of the Austrian Library Network’s (OBV’s) bibliographic datasets. It concludes with the mutual agreement that the implementation of Linked Data principles within the OBV can only be taken into consideration accompanied by a discussion about the provision of the datasets under a free license. - lang: ger text: "Linked Data steht für eine bestimmte Form der Veröffentlichung von Daten via Internet. Die zu Grunde liegende Idee ist es, Daten verschiedenster Provenienz, die derzeit teilweise gar nicht oder nur schwer zugänglich sind, in möglichst \r\neinheitlicher Form miteinander zu verknüpfen und dadurch in ihrer Gesamtheit abfragbar zu machen.\r\nDieser Bericht fasst die Entwicklungen im europäischen Raum, sowie strategische und technische Überlegungen der AG Linked Data hinsichtlich der Veröffentlichung von bibliothekarischen Daten des Österreichischen Bibliothekenverbundes (OBV) zusammen und schließt mit der gemeinsamen Übereinkunft, dass die Umsetzung von Linked Data-Prinzipien im OBV nur in Zusammenhang mit einer Diskussion über die damit einhergehende Veröffentlichung der Daten unter einer freien Lizenz angedacht werden sollte." author: - first_name: Patrick full_name: Danowski, Patrick id: 2EBD1598-F248-11E8-B48F-1D18A9856A87 last_name: Danowski orcid: 0000-0002-6026-4409 - first_name: Doron full_name: Goldfarb, Doron last_name: Goldfarb - first_name: Verena full_name: Schaffner, Verena last_name: Schaffner - first_name: Wolfram full_name: Seidler, Wolfram last_name: Seidler citation: ama: Danowski P, Goldfarb D, Schaffner V, Seidler W. Linked (Open) Data - Bibliographische Daten im Semantic Web. VÖB Mitteilungen. 2013;66(3/4):559-587. apa: Danowski, P., Goldfarb, D., Schaffner, V., & Seidler, W. (2013). Linked (Open) Data - Bibliographische Daten im Semantic Web. VÖB Mitteilungen. Verein Österreichischer Bibliothekarinnen und Bibliothekare. chicago: Danowski, Patrick, Doron Goldfarb, Verena Schaffner, and Wolfram Seidler. “Linked (Open) Data - Bibliographische Daten Im Semantic Web.” VÖB Mitteilungen. Verein Österreichischer Bibliothekarinnen und Bibliothekare, 2013. ieee: P. Danowski, D. Goldfarb, V. Schaffner, and W. Seidler, “Linked (Open) Data - Bibliographische Daten im Semantic Web,” VÖB Mitteilungen, vol. 66, no. 3/4. Verein Österreichischer Bibliothekarinnen und Bibliothekare, pp. 559–587, 2013. ista: Danowski P, Goldfarb D, Schaffner V, Seidler W. 2013. Linked (Open) Data - Bibliographische Daten im Semantic Web. VÖB Mitteilungen. 66(3/4), 559–587. mla: Danowski, Patrick, et al. “Linked (Open) Data - Bibliographische Daten Im Semantic Web.” VÖB Mitteilungen, vol. 66, no. 3/4, Verein Österreichischer Bibliothekarinnen und Bibliothekare, 2013, pp. 559–87. short: P. Danowski, D. Goldfarb, V. Schaffner, W. Seidler, VÖB Mitteilungen 66 (2013) 559–587. date_created: 2018-12-11T11:56:36Z date_published: 2013-12-01T00:00:00Z date_updated: 2021-01-12T06:56:20Z day: '01' ddc: - '020' department: - _id: E-Lib file: - access_level: open_access checksum: ae57ffcee3720adcc27b0f2767a1e04b content_type: application/pdf creator: system date_created: 2018-12-12T10:08:09Z date_updated: 2020-07-14T12:45:35Z file_id: '4669' file_name: IST-2016-719-v1+1_Patrick_Danowski__Doron_Goldfarb__Verena_Schaffner__Wolfram_Seidler_Linked__Open__Data_Bibliographische_Daten_im_Semantic_Web.pdf file_size: 881545 relation: main_file file_date_updated: 2020-07-14T12:45:35Z has_accepted_license: '1' intvolume: ' 66' issue: 3/4 language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 559 - 587 popular_science: '1' publication: VÖB Mitteilungen publication_status: published publisher: Verein Österreichischer Bibliothekarinnen und Bibliothekare publist_id: '4690' pubrep_id: '719' status: public title: Linked (Open) Data - Bibliographische Daten im Semantic Web tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 66 year: '2013' ... --- _id: '2260' abstract: - lang: eng text: "Direct Anonymous Attestation (DAA) is one of the most complex cryptographic protocols deployed in practice. It allows an embedded secure processor known as a Trusted Platform Module (TPM) to attest to the configuration of its host computer without violating the owner’s privacy. DAA has been standardized by the Trusted Computing Group and ISO/IEC.\r\n\r\nThe security of the DAA standard and all existing schemes is analyzed in the random-oracle model. We provide the first constructions of DAA in the standard model, that is, without relying on random oracles. Our constructions use new building blocks, including the first efficient signatures of knowledge in the standard model, which have many applications beyond DAA.\r\n" alternative_title: - LNCS author: - first_name: David full_name: Bernhard, David last_name: Bernhard - first_name: Georg full_name: Fuchsbauer, Georg id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87 last_name: Fuchsbauer - first_name: Essam full_name: Ghadafi, Essam last_name: Ghadafi citation: ama: Bernhard D, Fuchsbauer G, Ghadafi E. Efficient signatures of knowledge and DAA in the standard model. 2013;7954:518-533. doi:10.1007/978-3-642-38980-1_33 apa: 'Bernhard, D., Fuchsbauer, G., & Ghadafi, E. (2013). Efficient signatures of knowledge and DAA in the standard model. Presented at the ACNS: Applied Cryptography and Network Security, Banff, AB, Canada: Springer. https://doi.org/10.1007/978-3-642-38980-1_33' chicago: Bernhard, David, Georg Fuchsbauer, and Essam Ghadafi. “Efficient Signatures of Knowledge and DAA in the Standard Model.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-38980-1_33. ieee: D. Bernhard, G. Fuchsbauer, and E. Ghadafi, “Efficient signatures of knowledge and DAA in the standard model,” vol. 7954. Springer, pp. 518–533, 2013. ista: Bernhard D, Fuchsbauer G, Ghadafi E. 2013. Efficient signatures of knowledge and DAA in the standard model. 7954, 518–533. mla: Bernhard, David, et al. Efficient Signatures of Knowledge and DAA in the Standard Model. Vol. 7954, Springer, 2013, pp. 518–33, doi:10.1007/978-3-642-38980-1_33. short: D. Bernhard, G. Fuchsbauer, E. Ghadafi, 7954 (2013) 518–533. conference: end_date: 2013-06-28 location: Banff, AB, Canada name: 'ACNS: Applied Cryptography and Network Security' start_date: 2013-06-25 date_created: 2018-12-11T11:56:37Z date_published: 2013-06-01T00:00:00Z date_updated: 2020-08-11T10:09:44Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-642-38980-1_33 intvolume: ' 7954' language: - iso: eng main_file_link: - open_access: '1' url: http://eprint.iacr.org/2012/475 month: '06' oa: 1 oa_version: Submitted Version page: 518 - 533 publication_status: published publisher: Springer publist_id: '4686' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Efficient signatures of knowledge and DAA in the standard model type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7954 year: '2013' ... --- _id: '2264' abstract: - lang: eng text: Faithful progression through the cell cycle is crucial to the maintenance and developmental potential of stem cells. Here, we demonstrate that neural stem cells (NSCs) and intermediate neural progenitor cells (NPCs) employ a zinc-finger transcription factor specificity protein 2 (Sp2) as a cell cycle regulator in two temporally and spatially distinct progenitor domains. Differential conditional deletion of Sp2 in early embryonic cerebral cortical progenitors, and perinatal olfactory bulb progenitors disrupted transitions through G1, G2 and M phases, whereas DNA synthesis appeared intact. Cell-autonomous function of Sp2 was identified by deletion of Sp2 using mosaic analysis with double markers, which clearly established that conditional Sp2-null NSCs and NPCs are M phase arrested in vivo. Importantly, conditional deletion of Sp2 led to a decline in the generation of NPCs and neurons in the developing and postnatal brains. Our findings implicate Sp2-dependent mechanisms as novel regulators of cell cycle progression, the absence of which disrupts neurogenesis in the embryonic and postnatal brain. article_processing_charge: No author: - first_name: Huixuan full_name: Liang, Huixuan last_name: Liang - first_name: Guanxi full_name: Xiao, Guanxi last_name: Xiao - first_name: Haifeng full_name: Yin, Haifeng last_name: Yin - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Jonathan full_name: Horowitz, Jonathan last_name: Horowitz - first_name: Troy full_name: Ghashghaei, Troy last_name: Ghashghaei citation: ama: Liang H, Xiao G, Yin H, Hippenmeyer S, Horowitz J, Ghashghaei T. Neural development is dependent on the function of specificity protein 2 in cell cycle progression. Development. 2013;140(3):552-561. doi:10.1242/dev.085621 apa: Liang, H., Xiao, G., Yin, H., Hippenmeyer, S., Horowitz, J., & Ghashghaei, T. (2013). Neural development is dependent on the function of specificity protein 2 in cell cycle progression. Development. Company of Biologists. https://doi.org/10.1242/dev.085621 chicago: Liang, Huixuan, Guanxi Xiao, Haifeng Yin, Simon Hippenmeyer, Jonathan Horowitz, and Troy Ghashghaei. “Neural Development Is Dependent on the Function of Specificity Protein 2 in Cell Cycle Progression.” Development. Company of Biologists, 2013. https://doi.org/10.1242/dev.085621. ieee: H. Liang, G. Xiao, H. Yin, S. Hippenmeyer, J. Horowitz, and T. Ghashghaei, “Neural development is dependent on the function of specificity protein 2 in cell cycle progression,” Development, vol. 140, no. 3. Company of Biologists, pp. 552–561, 2013. ista: Liang H, Xiao G, Yin H, Hippenmeyer S, Horowitz J, Ghashghaei T. 2013. Neural development is dependent on the function of specificity protein 2 in cell cycle progression. Development. 140(3), 552–561. mla: Liang, Huixuan, et al. “Neural Development Is Dependent on the Function of Specificity Protein 2 in Cell Cycle Progression.” Development, vol. 140, no. 3, Company of Biologists, 2013, pp. 552–61, doi:10.1242/dev.085621. short: H. Liang, G. Xiao, H. Yin, S. Hippenmeyer, J. Horowitz, T. Ghashghaei, Development 140 (2013) 552–561. date_created: 2018-12-11T11:56:39Z date_published: 2013-02-01T00:00:00Z date_updated: 2021-01-12T06:56:23Z day: '01' department: - _id: SiHi doi: 10.1242/dev.085621 external_id: pmid: - '23293287' intvolume: ' 140' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561788/ month: '02' oa: 1 oa_version: Submitted Version page: 552 - 561 pmid: 1 publication: Development publication_status: published publisher: Company of Biologists publist_id: '4681' quality_controlled: '1' scopus_import: 1 status: public title: Neural development is dependent on the function of specificity protein 2 in cell cycle progression type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 140 year: '2013' ... --- _id: '2269' abstract: - lang: eng text: This paper presents a parallel, implementation-friendly analytic visibility method for triangular meshes. Together with an analytic filter convolution, it allows for a fully analytic solution to anti-aliased 3D mesh rendering on parallel hardware. Building on recent works in computational geometry, we present a new edge-triangle intersection algorithm and a novel method to complete the boundaries of all visible triangle regions after a hidden line elimination step. All stages of the method are embarrassingly parallel and easily implementable on parallel hardware. A GPU implementation is discussed and performance characteristics of the method are shown and compared to traditional sampling-based rendering methods. acknowledgement: "Funding was provided by the FWF grant P20768-N13.\nWe want to thank the reviewers for their insightful and helpful remarks and Gernot Ziegler for providing help with CUDA. " author: - first_name: Thomas full_name: Thomas Auzinger id: 4718F954-F248-11E8-B48F-1D18A9856A87 last_name: Auzinger orcid: 0000-0002-1546-3265 - first_name: Michael full_name: Wimmer, Michael last_name: Wimmer - first_name: Stefan full_name: Stefan Jeschke id: 44D6411A-F248-11E8-B48F-1D18A9856A87 last_name: Jeschke citation: ama: 'Auzinger T, Wimmer M, Jeschke S. Analytic Visibility on the GPU. Computer Graphics Forum. 2013;32(124):409-418. doi:DOI: 10.1111/cgf.12061' apa: 'Auzinger, T., Wimmer, M., & Jeschke, S. (2013). Analytic Visibility on the GPU. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/DOI: 10.1111/cgf.12061' chicago: 'Auzinger, Thomas, Michael Wimmer, and Stefan Jeschke. “Analytic Visibility on the GPU.” Computer Graphics Forum. Wiley-Blackwell, 2013. https://doi.org/DOI: 10.1111/cgf.12061.' ieee: T. Auzinger, M. Wimmer, and S. Jeschke, “Analytic Visibility on the GPU,” Computer Graphics Forum, vol. 32, no. 124. Wiley-Blackwell, pp. 409–418, 2013. ista: Auzinger T, Wimmer M, Jeschke S. 2013. Analytic Visibility on the GPU. Computer Graphics Forum. 32(124), 409–418. mla: 'Auzinger, Thomas, et al. “Analytic Visibility on the GPU.” Computer Graphics Forum, vol. 32, no. 124, Wiley-Blackwell, 2013, pp. 409–18, doi:DOI: 10.1111/cgf.12061.' short: T. Auzinger, M. Wimmer, S. Jeschke, Computer Graphics Forum 32 (2013) 409–418. date_created: 2018-12-11T11:56:40Z date_published: 2013-05-06T00:00:00Z date_updated: 2021-01-12T06:56:25Z day: '06' doi: 'DOI: 10.1111/cgf.12061' extern: 1 intvolume: ' 32' issue: 124 month: '05' page: 409 - 418 publication: Computer Graphics Forum publication_status: published publisher: Wiley-Blackwell publist_id: '4675' quality_controlled: 0 status: public title: Analytic Visibility on the GPU type: journal_article volume: 32 year: '2013' ... --- _id: '2270' abstract: - lang: eng text: "Representation languages for coalitional games are a key research area in algorithmic game theory. There is an inher-\r\nent tradeoff between how general a language is, allowing it to capture more elaborate games, and how hard \ it is computationally to optimize and solve such games. One prominent such \ language is the simple yet expressive\r\nWeighted Graph Games (WGGs) representation (Deng and Papadimitriou 1994), which maintains knowledge about synergies between agents in the form of an edge weighted graph. We consider the problem of finding \ the optimal coalition structure in WGGs. The agents in such games are vertices in a graph, and the value of a coalition is the sum of the weights of the edges present between coalition members. The optimal coalition structure is a partition of the agents to coalitions, that maximizes the sum of utilities obtained by the coalitions. We show that finding the optimal coalition structure is not only hard for general graphs, but is also intractable for restricted families such as planar graphs which are amenable for many other combinatorial problems. \ We then provide algorithms with constant factor approximations for planar, minorfree and bounded degree graphs." author: - first_name: Yoram full_name: Bachrach, Yoram last_name: Bachrach - first_name: Pushmeet full_name: Kohli, Pushmeet last_name: Kohli - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Morteza full_name: Zadimoghaddam, Morteza last_name: Zadimoghaddam citation: ama: 'Bachrach Y, Kohli P, Kolmogorov V, Zadimoghaddam M. Optimal Coalition Structures in Cooperative Graph Games. In: AAAI Press; 2013:81-87.' apa: 'Bachrach, Y., Kohli, P., Kolmogorov, V., & Zadimoghaddam, M. (2013). Optimal Coalition Structures in Cooperative Graph Games (pp. 81–87). Presented at the AAAI: Conference on Artificial Intelligence, Bellevue, WA, United States: AAAI Press.' chicago: Bachrach, Yoram, Pushmeet Kohli, Vladimir Kolmogorov, and Morteza Zadimoghaddam. “Optimal Coalition Structures in Cooperative Graph Games,” 81–87. AAAI Press, 2013. ieee: 'Y. Bachrach, P. Kohli, V. Kolmogorov, and M. Zadimoghaddam, “Optimal Coalition Structures in Cooperative Graph Games,” presented at the AAAI: Conference on Artificial Intelligence, Bellevue, WA, United States, 2013, pp. 81–87.' ista: 'Bachrach Y, Kohli P, Kolmogorov V, Zadimoghaddam M. 2013. Optimal Coalition Structures in Cooperative Graph Games. AAAI: Conference on Artificial Intelligence, 81–87.' mla: Bachrach, Yoram, et al. Optimal Coalition Structures in Cooperative Graph Games. AAAI Press, 2013, pp. 81–87. short: Y. Bachrach, P. Kohli, V. Kolmogorov, M. Zadimoghaddam, in:, AAAI Press, 2013, pp. 81–87. conference: end_date: 2013-07-18 location: Bellevue, WA, United States name: 'AAAI: Conference on Artificial Intelligence' start_date: 2013-07-14 date_created: 2018-12-11T11:56:41Z date_published: 2013-12-31T00:00:00Z date_updated: 2021-01-12T06:56:25Z day: '31' department: - _id: VlKo external_id: arxiv: - '1108.5248' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1108.5248 month: '12' oa: 1 oa_version: None page: 81-87 publication_status: published publisher: AAAI Press publist_id: '4674' quality_controlled: '1' status: public title: Optimal Coalition Structures in Cooperative Graph Games type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2273' abstract: - lang: eng text: We propose a new family of message passing techniques for MAP estimation in graphical models which we call Sequential Reweighted Message Passing (SRMP). Special cases include well-known techniques such as Min-Sum Diusion (MSD) and a faster Sequential Tree-Reweighted Message Passing (TRW-S). Importantly, our derivation is simpler than the original derivation of TRW-S, and does not involve a decomposition into trees. This allows easy generalizations. We present such a generalization for the case of higher-order graphical models, and test it on several real-world problems with promising results. author: - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: Kolmogorov V. Reweighted Message Passing Revisited. IST Austria; 2013. apa: Kolmogorov, V. (2013). Reweighted message passing revisited. IST Austria. chicago: Kolmogorov, Vladimir. Reweighted Message Passing Revisited. IST Austria, 2013. ieee: V. Kolmogorov, Reweighted message passing revisited. IST Austria, 2013. ista: Kolmogorov V. 2013. Reweighted message passing revisited, IST Austria,p. mla: Kolmogorov, Vladimir. Reweighted Message Passing Revisited. IST Austria, 2013. short: V. Kolmogorov, Reweighted Message Passing Revisited, IST Austria, 2013. date_created: 2018-12-11T11:56:42Z date_published: 2013-09-22T00:00:00Z date_updated: 2019-01-24T13:07:32Z day: '22' department: - _id: VlKo extern: 0 main_file_link: - open_access: '1' url: http://arxiv.org/abs/1309.5655 month: '09' oa: 1 publication_status: published publisher: IST Austria publist_id: '4671' quality_controlled: 0 status: public title: Reweighted message passing revisited type: report year: '2013' ... --- _id: '2278' abstract: - lang: eng text: It is firmly established that interactions between neurons and glia are fundamental across species for the correct establishment of a functional brain. Here, we found that the glia of the Drosophila larval brain display an essential non-autonomous role during the development of the optic lobe. The optic lobe develops from neuroepithelial cells that proliferate by dividing symmetrically until they switch to asymmetric/differentiative divisions that generate neuroblasts. The proneural gene lethal of scute (l9sc) is transiently activated by the epidermal growth factor receptor (EGFR)-Ras signal transduction pathway at the leading edge of a proneural wave that sweeps from medial to lateral neuroepithelium, promoting this switch. This process is tightly regulated by the tissue-autonomous function within the neuroepithelium of multiple signaling pathways, including EGFR-Ras and Notch. This study shows that the Notch ligand Serrate (Ser) is expressed in the glia and it forms a complex in vivo with Notch and Canoe, which colocalize at the adherens junctions of neuroepithelial cells. This complex is crucial for interactions between glia and neuroepithelial cells during optic lobe development. Ser is tissue-autonomously required in the glia where it activates Notch to regulate its proliferation, and non-autonomously in the neuroepithelium where Ser induces Notch signaling to avoid the premature activation of the EGFR-Ras pathway and hence of L9sc. Interestingly, different Notch activity reporters showed very different expression patterns in the glia and in the neuroepithelium, suggesting the existence of tissue-specific factors that promote the expression of particular Notch target genes or/and a reporter response dependent on different thresholds of Notch signaling. author: - first_name: Raquel full_name: Pérez Gómez, Raquel last_name: Pérez Gómez - first_name: Jana full_name: Slovakova, Jana id: 30F3F2F0-F248-11E8-B48F-1D18A9856A87 last_name: Slovakova - first_name: Noemí full_name: Rives Quinto, Noemí last_name: Rives Quinto - first_name: Alena full_name: Krejčí, Alena last_name: Krejčí - first_name: Ana full_name: Carmena, Ana last_name: Carmena citation: ama: Pérez Gómez R, Slovakova J, Rives Quinto N, Krejčí A, Carmena A. A serrate-notch-canoe complex mediates essential interactions between glia and neuroepithelial cells during Drosophila optic lobe development. Journal of Cell Science. 2013;126(21):4873-4884. doi:10.1242/jcs.125617 apa: Pérez Gómez, R., Slovakova, J., Rives Quinto, N., Krejčí, A., & Carmena, A. (2013). A serrate-notch-canoe complex mediates essential interactions between glia and neuroepithelial cells during Drosophila optic lobe development. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.125617 chicago: Pérez Gómez, Raquel, Jana Slovakova, Noemí Rives Quinto, Alena Krejčí, and Ana Carmena. “A Serrate-Notch-Canoe Complex Mediates Essential Interactions between Glia and Neuroepithelial Cells during Drosophila Optic Lobe Development.” Journal of Cell Science. Company of Biologists, 2013. https://doi.org/10.1242/jcs.125617. ieee: R. Pérez Gómez, J. Slovakova, N. Rives Quinto, A. Krejčí, and A. Carmena, “A serrate-notch-canoe complex mediates essential interactions between glia and neuroepithelial cells during Drosophila optic lobe development,” Journal of Cell Science, vol. 126, no. 21. Company of Biologists, pp. 4873–4884, 2013. ista: Pérez Gómez R, Slovakova J, Rives Quinto N, Krejčí A, Carmena A. 2013. A serrate-notch-canoe complex mediates essential interactions between glia and neuroepithelial cells during Drosophila optic lobe development. Journal of Cell Science. 126(21), 4873–4884. mla: Pérez Gómez, Raquel, et al. “A Serrate-Notch-Canoe Complex Mediates Essential Interactions between Glia and Neuroepithelial Cells during Drosophila Optic Lobe Development.” Journal of Cell Science, vol. 126, no. 21, Company of Biologists, 2013, pp. 4873–84, doi:10.1242/jcs.125617. short: R. Pérez Gómez, J. Slovakova, N. Rives Quinto, A. Krejčí, A. Carmena, Journal of Cell Science 126 (2013) 4873–4884. date_created: 2018-12-11T11:56:43Z date_published: 2013-11-01T00:00:00Z date_updated: 2021-01-12T06:56:29Z day: '01' department: - _id: CaHe doi: 10.1242/jcs.125617 intvolume: ' 126' issue: '21' language: - iso: eng month: '11' oa_version: None page: 4873 - 4884 publication: Journal of Cell Science publication_status: published publisher: Company of Biologists publist_id: '4658' quality_controlled: '1' scopus_import: 1 status: public title: A serrate-notch-canoe complex mediates essential interactions between glia and neuroepithelial cells during Drosophila optic lobe development type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 126 year: '2013' ... --- _id: '2276' abstract: - lang: eng text: The problem of minimizing the Potts energy function frequently occurs in computer vision applications. One way to tackle this NP-hard problem was proposed by Kovtun [19, 20]. It identifies a part of an optimal solution by running k maxflow computations, where k is the number of labels. The number of “labeled” pixels can be significant in some applications, e.g. 50-93% in our tests for stereo. We show how to reduce the runtime to O (log k) maxflow computations (or one parametric maxflow computation). Furthermore, the output of our algorithm allows to speed-up the subsequent alpha expansion for the unlabeled part, or can be used as it is for time-critical applications. To derive our technique, we generalize the algorithm of Felzenszwalb et al. [7] for Tree Metrics . We also show a connection to k-submodular functions from combinatorial optimization, and discuss k-submodular relaxations for general energy functions. author: - first_name: Igor full_name: Gridchyn, Igor id: 4B60654C-F248-11E8-B48F-1D18A9856A87 last_name: Gridchyn - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Gridchyn I, Kolmogorov V. Potts model, parametric maxflow and k-submodular functions. In: IEEE; 2013:2320-2327. doi:10.1109/ICCV.2013.288' apa: 'Gridchyn, I., & Kolmogorov, V. (2013). Potts model, parametric maxflow and k-submodular functions (pp. 2320–2327). Presented at the ICCV: International Conference on Computer Vision, Sydney, Australia: IEEE. https://doi.org/10.1109/ICCV.2013.288' chicago: Gridchyn, Igor, and Vladimir Kolmogorov. “Potts Model, Parametric Maxflow and k-Submodular Functions,” 2320–27. IEEE, 2013. https://doi.org/10.1109/ICCV.2013.288. ieee: 'I. Gridchyn and V. Kolmogorov, “Potts model, parametric maxflow and k-submodular functions,” presented at the ICCV: International Conference on Computer Vision, Sydney, Australia, 2013, pp. 2320–2327.' ista: 'Gridchyn I, Kolmogorov V. 2013. Potts model, parametric maxflow and k-submodular functions. ICCV: International Conference on Computer Vision, 2320–2327.' mla: Gridchyn, Igor, and Vladimir Kolmogorov. Potts Model, Parametric Maxflow and k-Submodular Functions. IEEE, 2013, pp. 2320–27, doi:10.1109/ICCV.2013.288. short: I. Gridchyn, V. Kolmogorov, in:, IEEE, 2013, pp. 2320–2327. conference: end_date: 2013-12-08 location: Sydney, Australia name: 'ICCV: International Conference on Computer Vision' start_date: 2013-12-01 date_created: 2018-12-11T11:56:43Z date_published: 2013-12-01T00:00:00Z date_updated: 2021-01-12T06:56:28Z day: '01' department: - _id: JoCs - _id: VlKo doi: 10.1109/ICCV.2013.288 external_id: arxiv: - '1310.1771' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1310.1771 month: '12' oa: 1 oa_version: Preprint page: 2320 - 2327 publication_status: published publisher: IEEE publist_id: '4668' quality_controlled: '1' status: public title: Potts model, parametric maxflow and k-submodular functions type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2280' abstract: - lang: eng text: The problem of packing ellipsoids of different sizes and shapes into an ellipsoidal container so as to minimize a measure of overlap between ellipsoids is considered. A bilevel optimization formulation is given, together with an algorithm for the general case and a simpler algorithm for the special case in which all ellipsoids are in fact spheres. Convergence results are proved and computational experience is described and illustrated. The motivating application-chromosome organization in the human cell nucleus-is discussed briefly, and some illustrative results are presented. author: - first_name: Caroline full_name: Uhler, Caroline id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 - first_name: Stephen full_name: Wright, Stephen last_name: Wright citation: ama: Uhler C, Wright S. Packing ellipsoids with overlap. SIAM Review. 2013;55(4):671-706. doi:10.1137/120872309 apa: Uhler, C., & Wright, S. (2013). Packing ellipsoids with overlap. SIAM Review. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/120872309 chicago: Uhler, Caroline, and Stephen Wright. “Packing Ellipsoids with Overlap.” SIAM Review. Society for Industrial and Applied Mathematics , 2013. https://doi.org/10.1137/120872309. ieee: C. Uhler and S. Wright, “Packing ellipsoids with overlap,” SIAM Review, vol. 55, no. 4. Society for Industrial and Applied Mathematics , pp. 671–706, 2013. ista: Uhler C, Wright S. 2013. Packing ellipsoids with overlap. SIAM Review. 55(4), 671–706. mla: Uhler, Caroline, and Stephen Wright. “Packing Ellipsoids with Overlap.” SIAM Review, vol. 55, no. 4, Society for Industrial and Applied Mathematics , 2013, pp. 671–706, doi:10.1137/120872309. short: C. Uhler, S. Wright, SIAM Review 55 (2013) 671–706. date_created: 2018-12-11T11:56:44Z date_published: 2013-11-07T00:00:00Z date_updated: 2021-01-12T06:56:30Z day: '07' department: - _id: CaUh doi: 10.1137/120872309 external_id: arxiv: - '1204.0235' intvolume: ' 55' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1204.0235 month: '11' oa: 1 oa_version: Preprint page: 671 - 706 publication: SIAM Review publication_status: published publisher: 'Society for Industrial and Applied Mathematics ' publist_id: '4655' quality_controlled: '1' scopus_import: 1 status: public title: Packing ellipsoids with overlap type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 55 year: '2013' ... --- _id: '2287' abstract: - lang: eng text: Negative frequency-dependent selection should result in equal sex ratios in large populations of dioecious flowering plants, but deviations from equality are commonly reported. A variety of ecological and genetic factors can explain biased sex ratios, although the mechanisms involved are not well understood. Most dioecious species are long-lived and/or clonal complicating efforts to identify stages during the life cycle when biases develop. We investigated the demographic correlates of sex-ratio variation in two chromosome races of Rumex hastatulus, an annual, wind-pollinated colonizer of open habitats from the southern USA. We examined sex ratios in 46 populations and evaluated the hypothesis that the proximity of males in the local mating environment, through its influence on gametophytic selection, is the primary cause of female-biased sex ratios. Female-biased sex ratios characterized most populations of R. hastatulus (mean sex ratio = 0.62), with significant female bias in 89% of populations. Large, high-density populations had the highest proportion of females, whereas smaller, low-density populations had sex ratios closer to equality. Progeny sex ratios were more female biased when males were in closer proximity to females, a result consistent with the gametophytic selection hypothesis. Our results suggest that interactions between demographic and genetic factors are probably the main cause of female-biased sex ratios in R. hastatulus. The annual life cycle of this species may limit the scope for selection against males and may account for the weaker degree of bias in comparison with perennial Rumex species. author: - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - first_name: Spencer full_name: Barrett, Spencer last_name: Barrett citation: ama: Pickup M, Barrett S. The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant. Ecology and Evolution. 2013;3(3):629-639. doi:10.1002/ece3.465 apa: Pickup, M., & Barrett, S. (2013). The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.465 chicago: Pickup, Melinda, and Spencer Barrett. “The Influence of Demography and Local Mating Environment on Sex Ratios in a Wind-Pollinated Dioecious Plant.” Ecology and Evolution. Wiley-Blackwell, 2013. https://doi.org/10.1002/ece3.465. ieee: M. Pickup and S. Barrett, “The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant,” Ecology and Evolution, vol. 3, no. 3. Wiley-Blackwell, pp. 629–639, 2013. ista: Pickup M, Barrett S. 2013. The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant. Ecology and Evolution. 3(3), 629–639. mla: Pickup, Melinda, and Spencer Barrett. “The Influence of Demography and Local Mating Environment on Sex Ratios in a Wind-Pollinated Dioecious Plant.” Ecology and Evolution, vol. 3, no. 3, Wiley-Blackwell, 2013, pp. 629–39, doi:10.1002/ece3.465. short: M. Pickup, S. Barrett, Ecology and Evolution 3 (2013) 629–639. date_created: 2018-12-11T11:56:47Z date_published: 2013-03-01T00:00:00Z date_updated: 2021-01-12T06:56:32Z day: '01' ddc: - '576' department: - _id: NiBa doi: 10.1002/ece3.465 file: - access_level: open_access checksum: b5531bab4c0dec396bf5c8497fe178bf content_type: application/pdf creator: system date_created: 2018-12-12T10:17:35Z date_updated: 2020-07-14T12:45:37Z file_id: '5290' file_name: IST-2016-416-v1+1_Pickup_et_al-2013-Ecology_and_Evolution.pdf file_size: 626949 relation: main_file file_date_updated: 2020-07-14T12:45:37Z has_accepted_license: '1' intvolume: ' 3' issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 629 - 639 publication: Ecology and Evolution publication_status: published publisher: Wiley-Blackwell publist_id: '4644' pubrep_id: '416' quality_controlled: '1' scopus_import: 1 status: public title: The influence of demography and local mating environment on sex ratios in a wind-pollinated dioecious plant tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2013' ... --- _id: '2282' abstract: - lang: eng text: Epithelial spreading is a common and fundamental aspect of various developmental and disease-related processes such as epithelial closure and wound healing. A key challenge for epithelial tissues undergoing spreading is to increase their surface area without disrupting epithelial integrity. Here we show that orienting cell divisions by tension constitutes an efficient mechanism by which the enveloping cell layer (EVL) releases anisotropic tension while undergoing spreading during zebrafish epiboly. The control of EVL cell-division orientation by tension involves cell elongation and requires myosin II activity to align the mitotic spindle with the main tension axis. We also found that in the absence of tension-oriented cell divisions and in the presence of increased tissue tension, EVL cells undergo ectopic fusions, suggesting that the reduction of tension anisotropy by oriented cell divisions is required to prevent EVL cells from fusing. We conclude that cell-division orientation by tension constitutes a key mechanism for limiting tension anisotropy and thus promoting tissue spreading during EVL epiboly. acknowledged_ssus: - _id: PreCl - _id: Bio acknowledgement: 'This work was supported by the IST Austria and MPI-CBG ' author: - first_name: Pedro full_name: Campinho, Pedro id: 3AFBBC42-F248-11E8-B48F-1D18A9856A87 last_name: Campinho orcid: 0000-0002-8526-5416 - first_name: Martin full_name: Behrndt, Martin id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87 last_name: Behrndt - first_name: Jonas full_name: Ranft, Jonas last_name: Ranft - first_name: Thomas full_name: Risler, Thomas last_name: Risler - first_name: Nicolas full_name: Minc, Nicolas last_name: Minc - 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: Campinho P, Behrndt M, Ranft J, Risler T, Minc N, Heisenberg C-PJ. Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly. Nature Cell Biology. 2013;15:1405-1414. doi:10.1038/ncb2869 apa: Campinho, P., Behrndt, M., Ranft, J., Risler, T., Minc, N., & Heisenberg, C.-P. J. (2013). Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb2869 chicago: Campinho, Pedro, Martin Behrndt, Jonas Ranft, Thomas Risler, Nicolas Minc, and Carl-Philipp J Heisenberg. “Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading during Zebrafish Epiboly.” Nature Cell Biology. Nature Publishing Group, 2013. https://doi.org/10.1038/ncb2869. ieee: P. Campinho, M. Behrndt, J. Ranft, T. Risler, N. Minc, and C.-P. J. Heisenberg, “Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly,” Nature Cell Biology, vol. 15. Nature Publishing Group, pp. 1405–1414, 2013. ista: Campinho P, Behrndt M, Ranft J, Risler T, Minc N, Heisenberg C-PJ. 2013. Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly. Nature Cell Biology. 15, 1405–1414. mla: Campinho, Pedro, et al. “Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading during Zebrafish Epiboly.” Nature Cell Biology, vol. 15, Nature Publishing Group, 2013, pp. 1405–14, doi:10.1038/ncb2869. short: P. Campinho, M. Behrndt, J. Ranft, T. Risler, N. Minc, C.-P.J. Heisenberg, Nature Cell Biology 15 (2013) 1405–1414. date_created: 2018-12-11T11:56:45Z date_published: 2013-11-10T00:00:00Z date_updated: 2023-02-21T17:02:44Z day: '10' department: - _id: CaHe doi: 10.1038/ncb2869 intvolume: ' 15' language: - iso: eng main_file_link: - open_access: '1' url: http://hal.upmc.fr/hal-00983313/ month: '11' oa: 1 oa_version: Submitted Version page: 1405 - 1414 project: - _id: 252ABD0A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I 930-B20 name: Control of Epithelial Cell Layer Spreading in Zebrafish publication: Nature Cell Biology publication_status: published publisher: Nature Publishing Group publist_id: '4652' quality_controlled: '1' related_material: record: - id: '1403' relation: dissertation_contains status: public scopus_import: 1 status: public title: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2013' ... --- _id: '2283' abstract: - lang: eng text: Pathogens exert a strong selection pressure on organisms to evolve effective immune defences. In addition to individual immunity, social organisms can act cooperatively to produce collective defences. In many ant species, queens have the option to found a colony alone or in groups with other, often unrelated, conspecifics. These associations are transient, usually lasting only as long as each queen benefits from the presence of others. In fact, once the first workers emerge, queens fight to the death for dominance. One potential advantage of co-founding may be that queens benefit from collective disease defences, such as mutual grooming, that act against common soil pathogens. We test this hypothesis by exposing single and co-founding queens to a fungal parasite, in order to assess whether queens in co-founding associations have improved survival. Surprisingly, co-foundresses exposed to the entomopathogenic fungus Metarhizium did not engage in cooperative disease defences, and consequently, we find no direct benefit of multiple queens on survival. However, an indirect benefit was observed, with parasite-exposed queens producing more brood when they co-founded, than when they were alone. We suggest this is due to a trade-off between reproduction and immunity. Additionally, we report an extraordinary ability of the queens to tolerate an infection for long periods after parasite exposure. Our study suggests that there are no social immunity benefits for co-founding ant queens, but that in parasite-rich environments, the presence of additional queens may nevertheless improve the chances of colony founding success. author: - first_name: Christopher full_name: Pull, Christopher id: 3C7F4840-F248-11E8-B48F-1D18A9856A87 last_name: Pull orcid: 0000-0003-1122-3982 - first_name: William full_name: Hughes, William last_name: Hughes - first_name: Markus full_name: Brown, Markus id: 3DAB9AFC-F248-11E8-B48F-1D18A9856A87 last_name: Brown citation: ama: 'Pull C, Hughes W, Brown M. Tolerating an infection: an indirect benefit of co-founding queen associations in the ant Lasius niger . Naturwissenschaften. 2013;100(12):1125-1136. doi:10.1007/s00114-013-1115-5' apa: 'Pull, C., Hughes, W., & Brown, M. (2013). Tolerating an infection: an indirect benefit of co-founding queen associations in the ant Lasius niger . Naturwissenschaften. Springer. https://doi.org/10.1007/s00114-013-1115-5' chicago: 'Pull, Christopher, William Hughes, and Markus Brown. “Tolerating an Infection: An Indirect Benefit of Co-Founding Queen Associations in the Ant Lasius Niger .” Naturwissenschaften. Springer, 2013. https://doi.org/10.1007/s00114-013-1115-5.' ieee: 'C. Pull, W. Hughes, and M. Brown, “Tolerating an infection: an indirect benefit of co-founding queen associations in the ant Lasius niger ,” Naturwissenschaften, vol. 100, no. 12. Springer, pp. 1125–1136, 2013.' ista: 'Pull C, Hughes W, Brown M. 2013. Tolerating an infection: an indirect benefit of co-founding queen associations in the ant Lasius niger . Naturwissenschaften. 100(12), 1125–1136.' mla: 'Pull, Christopher, et al. “Tolerating an Infection: An Indirect Benefit of Co-Founding Queen Associations in the Ant Lasius Niger .” Naturwissenschaften, vol. 100, no. 12, Springer, 2013, pp. 1125–36, doi:10.1007/s00114-013-1115-5.' short: C. Pull, W. Hughes, M. Brown, Naturwissenschaften 100 (2013) 1125–1136. date_created: 2018-12-11T11:56:45Z date_published: 2013-11-14T00:00:00Z date_updated: 2021-01-12T06:56:31Z day: '14' department: - _id: SyCr doi: 10.1007/s00114-013-1115-5 intvolume: ' 100' issue: '12' language: - iso: eng month: '11' oa_version: None page: 1125 - 1136 publication: Naturwissenschaften publication_status: published publisher: Springer publist_id: '4649' quality_controlled: '1' scopus_import: 1 status: public title: 'Tolerating an infection: an indirect benefit of co-founding queen associations in the ant Lasius niger ' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 100 year: '2013' ... --- _id: '2286' abstract: - lang: eng text: The spatiotemporal control of cell divisions is a key factor in epithelial morphogenesis and patterning. Mao et al (2013) now describe how differential rates of proliferation within the Drosophila wing disc epithelium give rise to anisotropic tissue tension in peripheral/proximal regions of the disc. Such global tissue tension anisotropy in turn determines the orientation of cell divisions by controlling epithelial cell elongation. author: - first_name: Pedro full_name: Campinho, Pedro id: 3AFBBC42-F248-11E8-B48F-1D18A9856A87 last_name: Campinho orcid: 0000-0002-8526-5416 - 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: Campinho P, Heisenberg C-PJ. The force and effect of cell proliferation. EMBO Journal. 2013;32(21):2783-2784. doi:10.1038/emboj.2013.225 apa: Campinho, P., & Heisenberg, C.-P. J. (2013). The force and effect of cell proliferation. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2013.225 chicago: Campinho, Pedro, and Carl-Philipp J Heisenberg. “The Force and Effect of Cell Proliferation.” EMBO Journal. Wiley-Blackwell, 2013. https://doi.org/10.1038/emboj.2013.225. ieee: P. Campinho and C.-P. J. Heisenberg, “The force and effect of cell proliferation,” EMBO Journal, vol. 32, no. 21. Wiley-Blackwell, pp. 2783–2784, 2013. ista: Campinho P, Heisenberg C-PJ. 2013. The force and effect of cell proliferation. EMBO Journal. 32(21), 2783–2784. mla: Campinho, Pedro, and Carl-Philipp J. Heisenberg. “The Force and Effect of Cell Proliferation.” EMBO Journal, vol. 32, no. 21, Wiley-Blackwell, 2013, pp. 2783–84, doi:10.1038/emboj.2013.225. short: P. Campinho, C.-P.J. Heisenberg, EMBO Journal 32 (2013) 2783–2784. date_created: 2018-12-11T11:56:46Z date_published: 2013-10-04T00:00:00Z date_updated: 2021-01-12T06:56:32Z day: '04' department: - _id: CaHe doi: 10.1038/emboj.2013.225 external_id: pmid: - '24097062' intvolume: ' 32' issue: '21' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3817470/ month: '10' oa: 1 oa_version: Submitted Version page: 2783 - 2784 pmid: 1 publication: EMBO Journal publication_status: published publisher: Wiley-Blackwell publist_id: '4645' quality_controlled: '1' scopus_import: 1 status: public title: The force and effect of cell proliferation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2013' ... --- _id: '2289' abstract: - lang: eng text: Formal verification aims to improve the quality of software by detecting errors before they do harm. At the basis of formal verification is the logical notion of correctness, which purports to capture whether or not a program behaves as desired. We suggest that the boolean partition of software into correct and incorrect programs falls short of the practical need to assess the behavior of software in a more nuanced fashion against multiple criteria. We therefore propose to introduce quantitative fitness measures for programs, specifically for measuring the function, performance, and robustness of reactive programs such as concurrent processes. This article describes the goals of the ERC Advanced Investigator Project QUAREM. The project aims to build and evaluate a theory of quantitative fitness measures for reactive models. Such a theory must strive to obtain quantitative generalizations of the paradigms that have been success stories in qualitative reactive modeling, such as compositionality, property-preserving abstraction and abstraction refinement, model checking, and synthesis. The theory will be evaluated not only in the context of software and hardware engineering, but also in the context of systems biology. In particular, we will use the quantitative reactive models and fitness measures developed in this project for testing hypotheses about the mechanisms behind data from biological experiments. author: - 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: Henzinger TA. Quantitative reactive modeling and verification. Computer Science Research and Development. 2013;28(4):331-344. doi:10.1007/s00450-013-0251-7 apa: Henzinger, T. A. (2013). Quantitative reactive modeling and verification. Computer Science Research and Development. Springer. https://doi.org/10.1007/s00450-013-0251-7 chicago: Henzinger, Thomas A. “Quantitative Reactive Modeling and Verification.” Computer Science Research and Development. Springer, 2013. https://doi.org/10.1007/s00450-013-0251-7. ieee: T. A. Henzinger, “Quantitative reactive modeling and verification,” Computer Science Research and Development, vol. 28, no. 4. Springer, pp. 331–344, 2013. ista: Henzinger TA. 2013. Quantitative reactive modeling and verification. Computer Science Research and Development. 28(4), 331–344. mla: Henzinger, Thomas A. “Quantitative Reactive Modeling and Verification.” Computer Science Research and Development, vol. 28, no. 4, Springer, 2013, pp. 331–44, doi:10.1007/s00450-013-0251-7. short: T.A. Henzinger, Computer Science Research and Development 28 (2013) 331–344. date_created: 2018-12-11T11:56:47Z date_published: 2013-10-05T00:00:00Z date_updated: 2021-01-12T06:56:33Z day: '05' ddc: - '000' department: - _id: ToHe doi: 10.1007/s00450-013-0251-7 ec_funded: 1 file: - access_level: open_access checksum: f117a00f9f046165bfa95595681e08a0 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:51Z date_updated: 2020-07-14T12:45:37Z file_id: '5308' file_name: IST-2016-626-v1+1_s00450-013-0251-7.pdf file_size: 570361 relation: main_file file_date_updated: 2020-07-14T12:45:37Z has_accepted_license: '1' intvolume: ' 28' issue: '4' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 331 - 344 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling publication: Computer Science Research and Development publication_status: published publisher: Springer publist_id: '4642' pubrep_id: '626' quality_controlled: '1' scopus_import: 1 status: public title: Quantitative reactive modeling and verification tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 28 year: '2013' ...