--- _id: '1442' abstract: - lang: eng text: We give a cohomological interpretation of both the Kac polynomial and the refined Donaldson-Thomas-invariants of quivers. This interpretation yields a proof of a conjecture of Kac from 1982 and gives a new perspective on recent work of Kontsevich-Soibelman. Thisis achieved by computing, via an arithmetic Fourier transform, the dimensions of the isotypical components of the cohomology of associated Nakajima quiver varieties under the action of a Weyl group. The generating function of the corresponding Poincare polynomials is an extension of Hua's formula for Kac polynomials of quivers involving Hall-Littlewood symmetric functions. The resulting formulae contain a wide range of information on the geometry of the quiver varieties. acknowledgement: |- The first author thanks the Royal Society for funding his research 2005-2012 in the form of a Royal Society University Research Fellowship as well as the Mathematical Institute and Wadham College in Oxford for a very productive environment. The second author is supported by Agence Nationale de la Recherche grant ANR-09-JCJC-0102-01. The third author is supported by the NSF grant DMS-1101484 and a Research Scholarship from the Clay Mathematical Institute. author: - first_name: Tamas full_name: Tamas Hausel id: 4A0666D8-F248-11E8-B48F-1D18A9856A87 last_name: Hausel - first_name: Emmanuel full_name: Letellier, Emmanuel last_name: Letellier - first_name: Fernando full_name: Rodríguez Villegas, Fernando last_name: Rodríguez Villegas citation: ama: Hausel T, Letellier E, Rodríguez Villegas F. Positivity for Kac polynomials and DT-invariants of quivers. Annals of Mathematics. 2013;177(3):1147-1168. doi:10.4007/annals.2013.177.3.8 apa: Hausel, T., Letellier, E., & Rodríguez Villegas, F. (2013). Positivity for Kac polynomials and DT-invariants of quivers. Annals of Mathematics. Princeton University Press. https://doi.org/10.4007/annals.2013.177.3.8 chicago: Hausel, Tamás, Emmanuel Letellier, and Fernando Rodríguez Villegas. “Positivity for Kac Polynomials and DT-Invariants of Quivers.” Annals of Mathematics. Princeton University Press, 2013. https://doi.org/10.4007/annals.2013.177.3.8. ieee: T. Hausel, E. Letellier, and F. Rodríguez Villegas, “Positivity for Kac polynomials and DT-invariants of quivers,” Annals of Mathematics, vol. 177, no. 3. Princeton University Press, pp. 1147–1168, 2013. ista: Hausel T, Letellier E, Rodríguez Villegas F. 2013. Positivity for Kac polynomials and DT-invariants of quivers. Annals of Mathematics. 177(3), 1147–1168. mla: Hausel, Tamás, et al. “Positivity for Kac Polynomials and DT-Invariants of Quivers.” Annals of Mathematics, vol. 177, no. 3, Princeton University Press, 2013, pp. 1147–68, doi:10.4007/annals.2013.177.3.8. short: T. Hausel, E. Letellier, F. Rodríguez Villegas, Annals of Mathematics 177 (2013) 1147–1168. date_created: 2018-12-11T11:52:02Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T06:50:47Z day: '01' doi: 10.4007/annals.2013.177.3.8 extern: 1 intvolume: ' 177' issue: '3' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1204.2375 month: '01' oa: 1 page: 1147 - 1168 publication: Annals of Mathematics publication_status: published publisher: Princeton University Press publist_id: '5754' quality_controlled: 0 status: public title: Positivity for Kac polynomials and DT-invariants of quivers type: journal_article volume: 177 year: '2013' ... --- _id: '1443' abstract: - lang: eng text: 'Here we survey several results and conjectures on the cohomology of the total space of the Hitchin system: the moduli space of semi-stable rank n and degree d Higgs bundles on a complex algebraic curve C. The picture emerging is a dynamic mixture of ideas originating in theoretical physics such as gauge theory and mirror symmetry, Weil conjectures in arithmetic algebraic geometry, representation theory of finite groups of Lie type and Langlands duality in number theory.' alternative_title: - Advanced Lectures in Mathematics author: - first_name: Tamas full_name: Tamas Hausel id: 4A0666D8-F248-11E8-B48F-1D18A9856A87 last_name: Hausel citation: ama: 'Hausel T. Global topology of the Hitchin system. In: Handbook of Moduli: Volume II. Vol 25. International Press; 2013:29-70.' apa: 'Hausel, T. (2013). Global topology of the Hitchin system. In Handbook of Moduli: Volume II (Vol. 25, pp. 29–70). International Press.' chicago: 'Hausel, Tamás. “Global Topology of the Hitchin System.” In Handbook of Moduli: Volume II, 25:29–70. International Press, 2013.' ieee: 'T. Hausel, “Global topology of the Hitchin system,” in Handbook of Moduli: Volume II, vol. 25, International Press, 2013, pp. 29–70.' ista: 'Hausel T. 2013.Global topology of the Hitchin system. In: Handbook of Moduli: Volume II. Advanced Lectures in Mathematics, vol. 25, 29–70.' mla: 'Hausel, Tamás. “Global Topology of the Hitchin System.” Handbook of Moduli: Volume II, vol. 25, International Press, 2013, pp. 29–70.' short: 'T. Hausel, in:, Handbook of Moduli: Volume II, International Press, 2013, pp. 29–70.' date_created: 2018-12-11T11:52:03Z date_published: 2013-03-15T00:00:00Z date_updated: 2021-01-12T06:50:47Z day: '15' extern: 1 intvolume: ' 25' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1102.1717 month: '03' oa: 1 page: 29 - 70 publication: 'Handbook of Moduli: Volume II' publication_status: published publisher: International Press publist_id: '5753' quality_controlled: 0 status: public title: Global topology of the Hitchin system type: book_chapter volume: 25 year: '2013' ... --- _id: '1469' abstract: - lang: eng text: We study connections between the topology of generic character varieties of fundamental groups of punctured Riemann surfaces, Macdonald polynomials, quiver representations, Hilbert schemes on Cx × Cx, modular forms and multiplicities in tensor products of irreducible characters of finite general linear groups. acknowledgement: During the preparation of this paper TH was supported by a Royal Society University Research Fellowship at the University of Oxford. EL was supported by ANR-09-JCJC-0102-01. FRV was supported by NSF grant DMS-0200605, an FRA from the University of Texas at Austin, EPSRC grant EP/G027110/1, Visiting Fellowships at All Souls and Wadham Colleges in Oxford and a Research Scholarship from the Clay Mathematical Institute. author: - first_name: Tamas full_name: Tamas Hausel id: 4A0666D8-F248-11E8-B48F-1D18A9856A87 last_name: Hausel - first_name: Emmanuel full_name: Letellier, Emmanuel last_name: Letellier - first_name: Fernando full_name: Rodríguez Villegas, Fernando last_name: Rodríguez Villegas citation: ama: Hausel T, Letellier E, Rodríguez Villegas F. Arithmetic harmonic analysis on character and quiver varieties II. Advances in Mathematics. 2013;234:85-128. doi:10.1016/j.aim.2012.10.009 apa: Hausel, T., Letellier, E., & Rodríguez Villegas, F. (2013). Arithmetic harmonic analysis on character and quiver varieties II. Advances in Mathematics. Academic Press. https://doi.org/10.1016/j.aim.2012.10.009 chicago: Hausel, Tamás, Emmanuel Letellier, and Fernando Rodríguez Villegas. “Arithmetic Harmonic Analysis on Character and Quiver Varieties II.” Advances in Mathematics. Academic Press, 2013. https://doi.org/10.1016/j.aim.2012.10.009. ieee: T. Hausel, E. Letellier, and F. Rodríguez Villegas, “Arithmetic harmonic analysis on character and quiver varieties II,” Advances in Mathematics, vol. 234. Academic Press, pp. 85–128, 2013. ista: Hausel T, Letellier E, Rodríguez Villegas F. 2013. Arithmetic harmonic analysis on character and quiver varieties II. Advances in Mathematics. 234, 85–128. mla: Hausel, Tamás, et al. “Arithmetic Harmonic Analysis on Character and Quiver Varieties II.” Advances in Mathematics, vol. 234, Academic Press, 2013, pp. 85–128, doi:10.1016/j.aim.2012.10.009. short: T. Hausel, E. Letellier, F. Rodríguez Villegas, Advances in Mathematics 234 (2013) 85–128. date_created: 2018-12-11T11:52:12Z date_published: 2013-02-15T00:00:00Z date_updated: 2021-01-12T06:50:57Z day: '15' doi: 10.1016/j.aim.2012.10.009 extern: 1 intvolume: ' 234' month: '02' page: 85 - 128 publication: Advances in Mathematics publication_status: published publisher: Academic Press publist_id: '5724' quality_controlled: 0 status: public title: Arithmetic harmonic analysis on character and quiver varieties II type: journal_article volume: 234 year: '2013' ... --- _id: '1470' abstract: - lang: eng text: We show that a natural isomorphism between the rational cohomology groups of the two zero-dimensional Hilbert schemes of n-points of two surfaces, the affine plane minus the axes and the cotangent bundle of an elliptic curve, exchanges the weight filtration on the first set of cohomology groups with the perverse Leray filtration associated with a natural fibration on the second set of cohomology groups. We discuss some associated hard Lefschetz phenomena. acknowledgement: Mark Andrea A. de Cataldo was partially supported by N.S.A. and N.S.F. Tamás Hausel was supported by a Royal Society University Research Fellowship. Luca Migliorini was partially supported by PRIN 2007 project "Spazi di moduli e teoria di Lie" author: - first_name: Mark full_name: De Cataldo, Mark A last_name: De Cataldo - first_name: Tamas full_name: Tamas Hausel id: 4A0666D8-F248-11E8-B48F-1D18A9856A87 last_name: Hausel - first_name: Luca full_name: Migliorini, Luca last_name: Migliorini citation: ama: De Cataldo M, Hausel T, Migliorini L. Exchange between perverse and weight filtration for the Hilbert schemes of points of two surfaces. Journal of Singularities. 2013;7:23-38. doi:10.5427/jsing.2013.7c apa: De Cataldo, M., Hausel, T., & Migliorini, L. (2013). Exchange between perverse and weight filtration for the Hilbert schemes of points of two surfaces. Journal of Singularities. Worldwide Center of Mathematics. https://doi.org/10.5427/jsing.2013.7c chicago: De Cataldo, Mark, Tamás Hausel, and Luca Migliorini. “Exchange between Perverse and Weight Filtration for the Hilbert Schemes of Points of Two Surfaces.” Journal of Singularities. Worldwide Center of Mathematics, 2013. https://doi.org/10.5427/jsing.2013.7c. ieee: M. De Cataldo, T. Hausel, and L. Migliorini, “Exchange between perverse and weight filtration for the Hilbert schemes of points of two surfaces,” Journal of Singularities, vol. 7. Worldwide Center of Mathematics, pp. 23–38, 2013. ista: De Cataldo M, Hausel T, Migliorini L. 2013. Exchange between perverse and weight filtration for the Hilbert schemes of points of two surfaces. Journal of Singularities. 7, 23–38. mla: De Cataldo, Mark, et al. “Exchange between Perverse and Weight Filtration for the Hilbert Schemes of Points of Two Surfaces.” Journal of Singularities, vol. 7, Worldwide Center of Mathematics, 2013, pp. 23–38, doi:10.5427/jsing.2013.7c. short: M. De Cataldo, T. Hausel, L. Migliorini, Journal of Singularities 7 (2013) 23–38. date_created: 2018-12-11T11:52:12Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T06:50:58Z day: '01' doi: 10.5427/jsing.2013.7c extern: 1 intvolume: ' 7' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1012.2583 month: '01' oa: 1 page: 23 - 38 publication: Journal of Singularities publication_status: published publisher: Worldwide Center of Mathematics publist_id: '5725' quality_controlled: 0 status: public title: Exchange between perverse and weight filtration for the Hilbert schemes of points of two surfaces type: journal_article volume: 7 year: '2013' ... --- _id: '11758' article_processing_charge: No article_type: letter_note author: - first_name: Luca full_name: Aceto, Luca last_name: Aceto - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Jiří full_name: Sgall, Jiří last_name: Sgall citation: ama: Aceto L, Henzinger MH, Sgall J. 38th International Colloquium on Automata, Languages and Programming. Information and Computation. 2013;222(1):1. doi:10.1016/j.ic.2012.11.002 apa: Aceto, L., Henzinger, M. H., & Sgall, J. (2013). 38th International Colloquium on Automata, Languages and Programming. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2012.11.002 chicago: Aceto, Luca, Monika H Henzinger, and Jiří Sgall. “38th International Colloquium on Automata, Languages and Programming.” Information and Computation. Elsevier, 2013. https://doi.org/10.1016/j.ic.2012.11.002. ieee: L. Aceto, M. H. Henzinger, and J. Sgall, “38th International Colloquium on Automata, Languages and Programming,” Information and Computation, vol. 222, no. 1. Elsevier, p. 1, 2013. ista: Aceto L, Henzinger MH, Sgall J. 2013. 38th International Colloquium on Automata, Languages and Programming. Information and Computation. 222(1), 1. mla: Aceto, Luca, et al. “38th International Colloquium on Automata, Languages and Programming.” Information and Computation, vol. 222, no. 1, Elsevier, 2013, p. 1, doi:10.1016/j.ic.2012.11.002. short: L. Aceto, M.H. Henzinger, J. Sgall, Information and Computation 222 (2013) 1. date_created: 2022-08-08T11:25:34Z date_published: 2013-01-01T00:00:00Z date_updated: 2023-02-23T10:09:19Z day: '01' doi: 10.1016/j.ic.2012.11.002 extern: '1' intvolume: ' 222' issue: '1' language: - iso: eng month: '01' oa_version: None page: '1' publication: Information and Computation publication_identifier: issn: - 0890-5401 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 38th International Colloquium on Automata, Languages and Programming type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 222 year: '2013' ... --- _id: '1726' abstract: - lang: eng text: The development of a functional tissue requires coordination of the amplification of progenitors and their differentiation into specific cell types. The molecular basis for this coordination during myotome ontogeny is not well understood. Dermomytome progenitors that colonize the myotome first acquire myocyte identity and subsequently proliferate as Pax7-expressing progenitors before undergoing terminal differentiation. We show that the dynamics of sonic hedgehog (Shh) signaling is crucial for this transition in both avian and mouse embryos. Initially, Shh ligand emanating from notochord/floor plate reaches the dermomyotome, where it both maintains the proliferation of dermomyotome cells and promotes myogenic differentiation of progenitors that colonized the myotome. Interfering with Shh signaling at this stage produces small myotomes and accumulation of Pax7-expressing progenitors. An in vivo reporter of Shh activity combined with mouse genetics revealed the existence of both activator and repressor Shh activities operating on distinct subsets of cells during the epaxial myotomal maturation. In contrast to observations in mice, in avians Shh promotes the differentiation of both epaxial and hypaxial myotome domains. Subsequently, myogenic progenitors become refractory to Shh; this is likely to occur at the level of, or upstream of, smoothened signaling. The end of responsiveness to Shh coincides with, and is thus likely to enable, the transition into the growth phase of the myotome. acknowledgement: This study was supported by grants from the Israel Science Foundation (ISF) [11/09 to C.K.]; the Association Francaise contre les Myopathies (AFM) [15642 to C.K.]; the German Research Foundation (DFG) [UN 34/27-1 to C.K.]; the UK Medical Research Council (MRC) [U117560541 to J.B. and A.K.]; Fondation Pour la Recherche Médicale (FRM) (post-doctoral fellowship to V.R.). Deposited in PMC for release after 6 months author: - first_name: Nitza full_name: Kahane, Nitza last_name: Kahane - first_name: Vanessa full_name: Ribes, Vanessa last_name: Ribes - first_name: Anna full_name: Anna Kicheva id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 - first_name: James full_name: Briscoe, James last_name: Briscoe - first_name: Chaya full_name: Kalcheim, Chaya last_name: Kalcheim citation: ama: Kahane N, Ribes V, Kicheva A, Briscoe J, Kalcheim C. The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling. Development. 2013;140(8):1740-1750. doi:10.1242/dev.092726 apa: Kahane, N., Ribes, V., Kicheva, A., Briscoe, J., & Kalcheim, C. (2013). The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling. Development. Company of Biologists. https://doi.org/10.1242/dev.092726 chicago: Kahane, Nitza, Vanessa Ribes, Anna Kicheva, James Briscoe, and Chaya Kalcheim. “The Transition from Differentiation to Growth during Dermomyotome-Derived Myogenesis Depends on Temporally Restricted Hedgehog Signaling.” Development. Company of Biologists, 2013. https://doi.org/10.1242/dev.092726. ieee: N. Kahane, V. Ribes, A. Kicheva, J. Briscoe, and C. Kalcheim, “The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling,” Development, vol. 140, no. 8. Company of Biologists, pp. 1740–1750, 2013. ista: Kahane N, Ribes V, Kicheva A, Briscoe J, Kalcheim C. 2013. The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling. Development. 140(8), 1740–1750. mla: Kahane, Nitza, et al. “The Transition from Differentiation to Growth during Dermomyotome-Derived Myogenesis Depends on Temporally Restricted Hedgehog Signaling.” Development, vol. 140, no. 8, Company of Biologists, 2013, pp. 1740–50, doi:10.1242/dev.092726. short: N. Kahane, V. Ribes, A. Kicheva, J. Briscoe, C. Kalcheim, Development 140 (2013) 1740–1750. date_created: 2018-12-11T11:53:41Z date_published: 2013-04-18T00:00:00Z date_updated: 2021-01-12T06:52:47Z day: '18' doi: 10.1242/dev.092726 extern: 1 intvolume: ' 140' issue: '8' month: '04' page: 1740 - 1750 publication: Development publication_status: published publisher: Company of Biologists publist_id: '5402' quality_controlled: 0 status: public title: The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling type: journal_article volume: 140 year: '2013' ... --- _id: '1727' abstract: - lang: eng text: 'Cells at different positions in a developing tissue receive different concentrations of signaling molecules, called morphogens, and this influences their cell fate. Morphogen concentration gradients have been proposed to control patterning as well as growth in many developing tissues. Some outstanding questions about tissue patterning by morphogen gradients are the following: What are the mechanisms that regulate gradient formation and shape? Is the positional information encoded in the gradient sufficiently precise to determine the positions of target gene domain boundaries? What are the temporal dynamics of gradients and how do they relate to patterning and growth? These questions are inherently quantitative in nature and addressing them requires measuring morphogen concentrations in cells, levels of downstream signaling activity, and kinetics of morphogen transport. Here we first present methods for quantifying morphogen gradient shape in which the measurements can be calibrated to reflect actual morphogen concentrations. We then discuss using fluorescence recovery after photobleaching to study the kinetics of morphogen transport at the tissue level. Finally, we present particle tracking as a method to study morphogen intracellular trafficking.' author: - first_name: Anna full_name: Anna Kicheva id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 - first_name: Laurent full_name: Holtzer, Laurent last_name: Holtzer - first_name: Ortrud full_name: Wartlick, Ortrud last_name: Wartlick - first_name: Thomas full_name: Schmidt, Thomas S last_name: Schmidt - first_name: Marcos full_name: González-Gaitán, Marcos A last_name: González Gaitán citation: ama: Kicheva A, Holtzer L, Wartlick O, Schmidt T, González Gaitán M. Quantitative imaging of morphogen gradients in drosophila imaginal discs. Cold Spring Harbor Protocols. 2013;8(5):387-403. doi:10.1101/pdb.top074237 apa: Kicheva, A., Holtzer, L., Wartlick, O., Schmidt, T., & González Gaitán, M. (2013). Quantitative imaging of morphogen gradients in drosophila imaginal discs. Cold Spring Harbor Protocols. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/pdb.top074237 chicago: Kicheva, Anna, Laurent Holtzer, Ortrud Wartlick, Thomas Schmidt, and Marcos González Gaitán. “Quantitative Imaging of Morphogen Gradients in Drosophila Imaginal Discs.” Cold Spring Harbor Protocols. Cold Spring Harbor Laboratory Press, 2013. https://doi.org/10.1101/pdb.top074237. ieee: A. Kicheva, L. Holtzer, O. Wartlick, T. Schmidt, and M. González Gaitán, “Quantitative imaging of morphogen gradients in drosophila imaginal discs,” Cold Spring Harbor Protocols, vol. 8, no. 5. Cold Spring Harbor Laboratory Press, pp. 387–403, 2013. ista: Kicheva A, Holtzer L, Wartlick O, Schmidt T, González Gaitán M. 2013. Quantitative imaging of morphogen gradients in drosophila imaginal discs. Cold Spring Harbor Protocols. 8(5), 387–403. mla: Kicheva, Anna, et al. “Quantitative Imaging of Morphogen Gradients in Drosophila Imaginal Discs.” Cold Spring Harbor Protocols, vol. 8, no. 5, Cold Spring Harbor Laboratory Press, 2013, pp. 387–403, doi:10.1101/pdb.top074237. short: A. Kicheva, L. Holtzer, O. Wartlick, T. Schmidt, M. González Gaitán, Cold Spring Harbor Protocols 8 (2013) 387–403. date_created: 2018-12-11T11:53:41Z date_published: 2013-05-01T00:00:00Z date_updated: 2021-01-12T06:52:47Z day: '01' doi: 10.1101/pdb.top074237 extern: 1 intvolume: ' 8' issue: '5' month: '05' page: 387 - 403 publication: Cold Spring Harbor Protocols publication_status: published publisher: Cold Spring Harbor Laboratory Press publist_id: '5401' quality_controlled: 0 status: public title: Quantitative imaging of morphogen gradients in drosophila imaginal discs type: journal_article volume: 8 year: '2013' ... --- _id: '1760' abstract: - lang: eng text: We report on hole g-factor measurements in three terminal SiGe self-assembled quantum dot devices with a top gate electrode positioned very close to the nanostructure. Measurements of both the perpendicular as well as the parallel g-factor reveal significant changes for a small modulation of the top gate voltage. From the observed modulations, we estimate that, for realistic experimental conditions, hole spins can be electrically manipulated with Rabi frequencies in the order of 100 MHz. This work emphasises the potential of hole-based nano-devices for efficient spin manipulation by means of the g-tensor modulation technique. acknowledgement: We acknowledge the financial support from the Nanosciences Foundation (Grenoble, France), the Commission for a Marie Curie Carrer Integration Grant, the Austrian Science Fund (FWF) for a Lise-Meitner Fellowship (M1435-N30), the DOE under Contract No. DE-FG02-08ER46482 (Yale), the European Starting Grant program, and the Agence Nationale de la Recherche author: - first_name: Natalia full_name: Ares, Natalia last_name: Ares - first_name: Georgios full_name: Georgios Katsaros id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros - first_name: Vitaly full_name: Golovach, Vitaly N last_name: Golovach - first_name: Jianjun full_name: Zhang, Jianjun last_name: Zhang - first_name: Aaron full_name: Prager, Aaron A last_name: Prager - first_name: Leonid full_name: Glazman, Leonid I last_name: Glazman - first_name: Oliver full_name: Schmidt, Oliver G last_name: Schmidt - first_name: Silvano full_name: De Franceschi, Silvano last_name: De Franceschi citation: ama: Ares N, Katsaros G, Golovach V, et al. SiGe quantum dots for fast hole spin Rabi oscillations. Applied Physics Letters. 2013;103(26). doi:10.1063/1.4858959 apa: Ares, N., Katsaros, G., Golovach, V., Zhang, J., Prager, A., Glazman, L., … De Franceschi, S. (2013). SiGe quantum dots for fast hole spin Rabi oscillations. Applied Physics Letters. American Institute of Physics. https://doi.org/10.1063/1.4858959 chicago: Ares, Natalia, Georgios Katsaros, Vitaly Golovach, Jianjun Zhang, Aaron Prager, Leonid Glazman, Oliver Schmidt, and Silvano De Franceschi. “SiGe Quantum Dots for Fast Hole Spin Rabi Oscillations.” Applied Physics Letters. American Institute of Physics, 2013. https://doi.org/10.1063/1.4858959. ieee: N. Ares et al., “SiGe quantum dots for fast hole spin Rabi oscillations,” Applied Physics Letters, vol. 103, no. 26. American Institute of Physics, 2013. ista: Ares N, Katsaros G, Golovach V, Zhang J, Prager A, Glazman L, Schmidt O, De Franceschi S. 2013. SiGe quantum dots for fast hole spin Rabi oscillations. Applied Physics Letters. 103(26). mla: Ares, Natalia, et al. “SiGe Quantum Dots for Fast Hole Spin Rabi Oscillations.” Applied Physics Letters, vol. 103, no. 26, American Institute of Physics, 2013, doi:10.1063/1.4858959. short: N. Ares, G. Katsaros, V. Golovach, J. Zhang, A. Prager, L. Glazman, O. Schmidt, S. De Franceschi, Applied Physics Letters 103 (2013). date_created: 2018-12-11T11:53:52Z date_published: 2013-01-23T00:00:00Z date_updated: 2021-01-12T06:53:02Z day: '23' doi: 10.1063/1.4858959 extern: 1 intvolume: ' 103' issue: '26' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1307.7196 month: '01' oa: 1 publication: Applied Physics Letters publication_status: published publisher: American Institute of Physics publist_id: '5364' quality_controlled: 0 status: public title: SiGe quantum dots for fast hole spin Rabi oscillations type: journal_article volume: 103 year: '2013' ... --- _id: '1759' abstract: - lang: eng text: We report an electric-field-induced giant modulation of the hole g factor in SiGe nanocrystals. The observed effect is ascribed to a so-far overlooked contribution to the g factor that stems from the mixing between heavy- and light-hole wave functions. We show that the relative displacement between the confined heavy- and light-hole states, occurring upon application of the electric field, alters their mixing strength leading to a strong nonmonotonic modulation of the g factor. acknowledgement: We acknowledge financial support from the Nanosciences Foundation (Grenoble, France), DOE under Contract No. DEFG02-08ER46482 (Yale), the Agence Nationale de la Recherche, and the European Starting Grant. G. K. acknowledges support from the European Commission via a Marie Curie Carrer Integration Grant and the FWF for a Lise-Meitner Fellowship author: - first_name: Natalia full_name: Ares, Natalia last_name: Ares - first_name: Vitaly full_name: Golovach, Vitaly N last_name: Golovach - first_name: Georgios full_name: Georgios Katsaros id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros - first_name: Mathieu full_name: Stoffel, Mathieu last_name: Stoffel - first_name: Frank full_name: Fournel, Frank last_name: Fournel - first_name: Leonid full_name: Glazman, Leonid I last_name: Glazman - first_name: Oliver full_name: Schmidt, Oliver G last_name: Schmidt - first_name: Silvano full_name: De Franceschi, Silvano last_name: De Franceschi citation: ama: Ares N, Golovach V, Katsaros G, et al. Nature of tunable hole g factors in quantum dots. Physical Review Letters. 2013;110(4). doi:10.1103/PhysRevLett.110.046602 apa: Ares, N., Golovach, V., Katsaros, G., Stoffel, M., Fournel, F., Glazman, L., … De Franceschi, S. (2013). Nature of tunable hole g factors in quantum dots. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.110.046602 chicago: Ares, Natalia, Vitaly Golovach, Georgios Katsaros, Mathieu Stoffel, Frank Fournel, Leonid Glazman, Oliver Schmidt, and Silvano De Franceschi. “Nature of Tunable Hole g Factors in Quantum Dots.” Physical Review Letters. American Physical Society, 2013. https://doi.org/10.1103/PhysRevLett.110.046602. ieee: N. Ares et al., “Nature of tunable hole g factors in quantum dots,” Physical Review Letters, vol. 110, no. 4. American Physical Society, 2013. ista: Ares N, Golovach V, Katsaros G, Stoffel M, Fournel F, Glazman L, Schmidt O, De Franceschi S. 2013. Nature of tunable hole g factors in quantum dots. Physical Review Letters. 110(4). mla: Ares, Natalia, et al. “Nature of Tunable Hole g Factors in Quantum Dots.” Physical Review Letters, vol. 110, no. 4, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.046602. short: N. Ares, V. Golovach, G. Katsaros, M. Stoffel, F. Fournel, L. Glazman, O. Schmidt, S. De Franceschi, Physical Review Letters 110 (2013). date_created: 2018-12-11T11:53:51Z date_published: 2013-01-23T00:00:00Z date_updated: 2021-01-12T06:53:01Z day: '23' doi: 10.1103/PhysRevLett.110.046602 extern: 1 intvolume: ' 110' issue: '4' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1208.0476 month: '01' oa: 1 publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '5365' quality_controlled: 0 status: public title: Nature of tunable hole g factors in quantum dots type: journal_article volume: 110 year: '2013' ... --- _id: '1785' abstract: - lang: eng text: The geometric aspects of quantum mechanics are emphasized most prominently by the concept of geometric phases, which are acquired whenever a quantum system evolves along a path in Hilbert space, that is, the space of quantum states of the system. The geometric phase is determined only by the shape of this path and is, in its simplest form, a real number. However, if the system has degenerate energy levels, then matrix-valued geometric state transformations, known as non-Abelian holonomies-the effect of which depends on the order of two consecutive paths-can be obtained. They are important, for example, for the creation of synthetic gauge fields in cold atomic gases or the description of non-Abelian anyon statistics. Moreover, there are proposals to exploit non-Abelian holonomic gates for the purposes of noise-resilient quantum computation. In contrast to Abelian geometric operations, non-Abelian ones have been observed only in nuclear quadrupole resonance experiments with a large number of spins, and without full characterization of the geometric process and its non-commutative nature. Here we realize non-Abelian non-adiabatic holonomic quantum operations on a single, superconducting, artificial three-level atom by applying a well-controlled, two-tone microwave drive. Using quantum process tomography, we determine fidelities of the resulting non-commuting gates that exceed 95 per cent. We show that two different quantum gates, originating from two distinct paths in Hilbert space, yield non-equivalent transformations when applied in different orders. This provides evidence for the non-Abelian character of the implemented holonomic quantum operations. In combination with a non-trivial two-quantum-bit gate, our method suggests a way to universal holonomic quantum computing. acknowledgement: This work is supported financially by GEOMDISS, the Swiss National Science Foundation and ETH Zurich author: - first_name: Abdufarrukh full_name: Abdumalikov, Abdufarrukh A last_name: Abdumalikov - first_name: Johannes M full_name: Johannes Fink id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: K full_name: Juliusson, K last_name: Juliusson - first_name: M full_name: Pechal, M last_name: Pechal - first_name: Stefan full_name: Berger, Stefan T last_name: Berger - first_name: Andreas full_name: Wallraff, Andreas last_name: Wallraff - first_name: Stefan full_name: Filipp, Stefan last_name: Filipp citation: ama: Abdumalikov A, Fink JM, Juliusson K, et al. Experimental realization of non-Abelian non-adiabatic geometric gates. Nature. 2013;496(7446):482-485. doi:10.1038/nature12010 apa: Abdumalikov, A., Fink, J. M., Juliusson, K., Pechal, M., Berger, S., Wallraff, A., & Filipp, S. (2013). Experimental realization of non-Abelian non-adiabatic geometric gates. Nature. Nature Publishing Group. https://doi.org/10.1038/nature12010 chicago: Abdumalikov, Abdufarrukh, Johannes M Fink, K Juliusson, M Pechal, Stefan Berger, Andreas Wallraff, and Stefan Filipp. “Experimental Realization of Non-Abelian Non-Adiabatic Geometric Gates.” Nature. Nature Publishing Group, 2013. https://doi.org/10.1038/nature12010. ieee: A. Abdumalikov et al., “Experimental realization of non-Abelian non-adiabatic geometric gates,” Nature, vol. 496, no. 7446. Nature Publishing Group, pp. 482–485, 2013. ista: Abdumalikov A, Fink JM, Juliusson K, Pechal M, Berger S, Wallraff A, Filipp S. 2013. Experimental realization of non-Abelian non-adiabatic geometric gates. Nature. 496(7446), 482–485. mla: Abdumalikov, Abdufarrukh, et al. “Experimental Realization of Non-Abelian Non-Adiabatic Geometric Gates.” Nature, vol. 496, no. 7446, Nature Publishing Group, 2013, pp. 482–85, doi:10.1038/nature12010. short: A. Abdumalikov, J.M. Fink, K. Juliusson, M. Pechal, S. Berger, A. Wallraff, S. Filipp, Nature 496 (2013) 482–485. date_created: 2018-12-11T11:54:00Z date_published: 2013-04-25T00:00:00Z date_updated: 2021-01-12T06:53:11Z day: '25' doi: 10.1038/nature12010 extern: 1 intvolume: ' 496' issue: '7446' month: '04' page: 482 - 485 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '5329' quality_controlled: 0 status: public title: Experimental realization of non-Abelian non-adiabatic geometric gates type: journal_article volume: 496 year: '2013' ... --- _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' 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' ... --- _id: '2290' abstract: - lang: eng text: The plant hormone indole-acetic acid (auxin) is essential for many aspects of plant development. Auxin-mediated growth regulation typically involves the establishment of an auxin concentration gradient mediated by polarly localized auxin transporters. The localization of auxin carriers and their amount at the plasma membrane are controlled by membrane trafficking processes such as secretion, endocytosis, and recycling. In contrast to endocytosis or recycling, how the secretory pathway mediates the localization of auxin carriers is not well understood. In this study we have used the differential cell elongation process during apical hook development to elucidate the mechanisms underlying the post-Golgi trafficking of auxin carriers in Arabidopsis. We show that differential cell elongation during apical hook development is defective in Arabidopsis mutant echidna (ech). ECH protein is required for the trans-Golgi network (TGN)-mediated trafficking of the auxin influx carrier AUX1 to the plasma membrane. In contrast, ech mutation only marginally perturbs the trafficking of the highly related auxin influx carrier LIKE-AUX1-3 or the auxin efflux carrier PIN-FORMED-3, both also involved in hook development. Electron tomography reveals that the trafficking defects in ech mutant are associated with the perturbation of secretory vesicle genesis from the TGN. Our results identify differential mechanisms for the post-Golgi trafficking of de novo-synthesized auxin carriers to plasma membrane from the TGN and reveal how trafficking of auxin influx carriers mediates the control of differential cell elongation in apical hook development. author: - first_name: Yohann full_name: Boutté, Yohann last_name: Boutté - first_name: Kristoffer full_name: Jonsson, Kristoffer last_name: Jonsson - first_name: Heather full_name: Mcfarlane, Heather last_name: Mcfarlane - first_name: Errin full_name: Johnson, Errin last_name: Johnson - first_name: Delphine full_name: Gendre, Delphine last_name: Gendre - first_name: Ranjan full_name: Swarup, Ranjan last_name: Swarup - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Lacey full_name: Samuels, Lacey last_name: Samuels - first_name: Stéphanie full_name: Robert, Stéphanie last_name: Robert - first_name: Rishikesh full_name: Bhalerao, Rishikesh last_name: Bhalerao citation: ama: Boutté Y, Jonsson K, Mcfarlane H, et al. ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation. PNAS. 2013;110(40):16259-16264. doi:10.1073/pnas.1309057110 apa: Boutté, Y., Jonsson, K., Mcfarlane, H., Johnson, E., Gendre, D., Swarup, R., … Bhalerao, R. (2013). ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1309057110 chicago: Boutté, Yohann, Kristoffer Jonsson, Heather Mcfarlane, Errin Johnson, Delphine Gendre, Ranjan Swarup, Jiří Friml, Lacey Samuels, Stéphanie Robert, and Rishikesh Bhalerao. “ECHIDNA Mediated Post Golgi Trafficking of Auxin Carriers for Differential Cell Elongation.” PNAS. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1309057110. ieee: Y. Boutté et al., “ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation,” PNAS, vol. 110, no. 40. National Academy of Sciences, pp. 16259–16264, 2013. ista: Boutté Y, Jonsson K, Mcfarlane H, Johnson E, Gendre D, Swarup R, Friml J, Samuels L, Robert S, Bhalerao R. 2013. ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation. PNAS. 110(40), 16259–16264. mla: Boutté, Yohann, et al. “ECHIDNA Mediated Post Golgi Trafficking of Auxin Carriers for Differential Cell Elongation.” PNAS, vol. 110, no. 40, National Academy of Sciences, 2013, pp. 16259–64, doi:10.1073/pnas.1309057110. short: Y. Boutté, K. Jonsson, H. Mcfarlane, E. Johnson, D. Gendre, R. Swarup, J. Friml, L. Samuels, S. Robert, R. Bhalerao, PNAS 110 (2013) 16259–16264. date_created: 2018-12-11T11:56:48Z date_published: 2013-10-01T00:00:00Z date_updated: 2021-01-12T06:56:33Z day: '01' department: - _id: JiFr doi: 10.1073/pnas.1309057110 external_id: pmid: - '24043780' intvolume: ' 110' issue: '40' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791722/ month: '10' oa: 1 oa_version: Submitted Version page: 16259 - 16264 pmid: 1 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '4639' quality_controlled: '1' scopus_import: 1 status: public title: ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2013' ... --- _id: '2294' abstract: - lang: eng text: "In this work we propose a system for automatic classification of Drosophila embryos into developmental stages.\r\nWhile the system is designed to solve an actual problem in biological research, we believe that the principle underly-\r\ning it is interesting not only for biologists, but also for researchers in computer vision. The main idea is to combine two orthogonal sources of information: one is a classifier trained on strongly invariant features, which makes it applicable to images of very different conditions, but also leads to rather noisy predictions. The other is a label propagation step based on a more powerful similarity measure that however is only consistent within specific subsets of the data at a time.\r\nIn our biological setup, the information sources are the shape and the staining patterns of embryo images. We show\r\nexperimentally that while neither of the methods \ can be used by itself to achieve satisfactory results, their combina-\r\ntion achieves prediction quality comparable to human performance." author: - first_name: Tomas full_name: Kazmar, Tomas last_name: Kazmar - first_name: Evgeny full_name: Kvon, Evgeny last_name: Kvon - first_name: Alexander full_name: Stark, Alexander last_name: Stark - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Kazmar T, Kvon E, Stark A, Lampert C. Drosophila Embryo Stage Annotation using Label Propagation. In: IEEE; 2013. doi:10.1109/ICCV.2013.139' apa: 'Kazmar, T., Kvon, E., Stark, A., & Lampert, C. (2013). Drosophila Embryo Stage Annotation using Label Propagation. Presented at the ICCV: International Conference on Computer Vision, Sydney, Australia: IEEE. https://doi.org/10.1109/ICCV.2013.139' chicago: Kazmar, Tomas, Evgeny Kvon, Alexander Stark, and Christoph Lampert. “Drosophila Embryo Stage Annotation Using Label Propagation.” IEEE, 2013. https://doi.org/10.1109/ICCV.2013.139. ieee: 'T. Kazmar, E. Kvon, A. Stark, and C. Lampert, “Drosophila Embryo Stage Annotation using Label Propagation,” presented at the ICCV: International Conference on Computer Vision, Sydney, Australia, 2013.' ista: 'Kazmar T, Kvon E, Stark A, Lampert C. 2013. Drosophila Embryo Stage Annotation using Label Propagation. ICCV: International Conference on Computer Vision.' mla: Kazmar, Tomas, et al. Drosophila Embryo Stage Annotation Using Label Propagation. IEEE, 2013, doi:10.1109/ICCV.2013.139. short: T. Kazmar, E. Kvon, A. Stark, C. Lampert, in:, IEEE, 2013. conference: end_date: 2013-12-08 location: Sydney, Australia name: 'ICCV: International Conference on Computer Vision' start_date: 2013-12-01 date_created: 2018-12-11T11:56:49Z date_published: 2013-12-01T00:00:00Z date_updated: 2021-01-12T06:56:35Z day: '01' department: - _id: ChLa doi: 10.1109/ICCV.2013.139 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://www.cv-foundation.org/openaccess/ICCV2013.py month: '12' oa: 1 oa_version: Submitted Version project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication_status: published publisher: IEEE publist_id: '4634' quality_controlled: '1' scopus_import: 1 status: public title: Drosophila Embryo Stage Annotation using Label Propagation type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2292' abstract: - lang: eng text: This book constitutes the thoroughly refereed conference proceedings of the 38th International Symposium on Mathematical Foundations of Computer Science, MFCS 2013, held in Klosterneuburg, Austria, in August 2013. The 67 revised full papers presented together with six invited talks were carefully selected from 191 submissions. Topics covered include algorithmic game theory, algorithmic learning theory, algorithms and data structures, automata, formal languages, bioinformatics, complexity, computational geometry, computer-assisted reasoning, concurrency theory, databases and knowledge-based systems, foundations of computing, logic in computer science, models of computation, semantics and verification of programs, and theoretical issues in artificial intelligence. alternative_title: - LNCS citation: ama: Chatterjee K, Sgall J, eds. Mathematical Foundations of Computer Science 2013. Vol 8087. Springer; 2013:VI-854. doi:10.1007/978-3-642-40313-2 apa: 'Chatterjee, K., & Sgall, J. (Eds.). (2013). Mathematical Foundations of Computer Science 2013 (Vol. 8087, p. VI-854). Presented at the MFCS: Mathematical Foundations of Computer Science, Klosterneuburg, Austria: Springer. https://doi.org/10.1007/978-3-642-40313-2' chicago: Chatterjee, Krishnendu, and Jiri Sgall, eds. Mathematical Foundations of Computer Science 2013. Vol. 8087. Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-40313-2. ieee: K. Chatterjee and J. Sgall, Eds., Mathematical Foundations of Computer Science 2013, vol. 8087. Springer, 2013, p. VI-854. ista: Chatterjee K, Sgall J eds. 2013. Mathematical Foundations of Computer Science 2013, Springer,p. mla: Chatterjee, Krishnendu, and Jiri Sgall, editors. Mathematical Foundations of Computer Science 2013. Vol. 8087, Springer, 2013, p. VI-854, doi:10.1007/978-3-642-40313-2. short: K. Chatterjee, J. Sgall, eds., Mathematical Foundations of Computer Science 2013, Springer, 2013. conference: end_date: 2013-08-30 location: Klosterneuburg, Austria name: 'MFCS: Mathematical Foundations of Computer Science' start_date: 2013-08-26 date_created: 2018-12-11T11:56:48Z date_published: 2013-08-08T00:00:00Z date_updated: 2020-08-11T10:09:45Z day: '08' department: - _id: KrCh doi: 10.1007/978-3-642-40313-2 editor: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Jiri full_name: Sgall, Jiri last_name: Sgall intvolume: ' 8087' language: - iso: eng month: '08' oa_version: None page: VI - 854 publication_identifier: isbn: - 978-3-642-40312-5 publication_status: published publisher: Springer publist_id: '4636' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Mathematical Foundations of Computer Science 2013 type: conference_editor user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8087 year: '2013' ... --- _id: '2293' abstract: - lang: eng text: Many computer vision problems have an asymmetric distribution of information between training and test time. In this work, we study the case where we are given additional information about the training data, which however will not be available at test time. This situation is called learning using privileged information (LUPI). We introduce two maximum-margin techniques that are able to make use of this additional source of information, and we show that the framework is applicable to several scenarios that have been studied in computer vision before. Experiments with attributes, bounding boxes, image tags and rationales as additional information in object classification show promising results. author: - first_name: Viktoriia full_name: Sharmanska, Viktoriia id: 2EA6D09E-F248-11E8-B48F-1D18A9856A87 last_name: Sharmanska orcid: 0000-0003-0192-9308 - first_name: Novi full_name: Quadrianto, Novi last_name: Quadrianto - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Sharmanska V, Quadrianto N, Lampert C. Learning to rank using privileged information. In: IEEE; 2013:825-832. doi:10.1109/ICCV.2013.107' apa: 'Sharmanska, V., Quadrianto, N., & Lampert, C. (2013). Learning to rank using privileged information (pp. 825–832). Presented at the ICCV: International Conference on Computer Vision, Sydney, Australia: IEEE. https://doi.org/10.1109/ICCV.2013.107' chicago: Sharmanska, Viktoriia, Novi Quadrianto, and Christoph Lampert. “Learning to Rank Using Privileged Information,” 825–32. IEEE, 2013. https://doi.org/10.1109/ICCV.2013.107. ieee: 'V. Sharmanska, N. Quadrianto, and C. Lampert, “Learning to rank using privileged information,” presented at the ICCV: International Conference on Computer Vision, Sydney, Australia, 2013, pp. 825–832.' ista: 'Sharmanska V, Quadrianto N, Lampert C. 2013. Learning to rank using privileged information. ICCV: International Conference on Computer Vision, 825–832.' mla: Sharmanska, Viktoriia, et al. Learning to Rank Using Privileged Information. IEEE, 2013, pp. 825–32, doi:10.1109/ICCV.2013.107. short: V. Sharmanska, N. Quadrianto, C. Lampert, in:, IEEE, 2013, pp. 825–832. conference: end_date: 2013-12-08 location: Sydney, Australia name: 'ICCV: International Conference on Computer Vision' start_date: 2013-12-01 date_created: 2018-12-11T11:56:49Z date_published: 2013-12-01T00:00:00Z date_updated: 2023-02-23T10:36:41Z day: '01' department: - _id: ChLa doi: 10.1109/ICCV.2013.107 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: www.cv-foundation.org/openaccess/content_iccv_2013/papers/Sharmanska_Learning_to_Rank_2013_ICCV_paper.pdf month: '12' oa: 1 oa_version: Submitted Version page: 825 - 832 project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication_status: published publisher: IEEE publist_id: '4635' quality_controlled: '1' scopus_import: 1 status: public title: Learning to rank using privileged information type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2291' abstract: - lang: eng text: "Cryptographic access control promises to offer easily distributed trust and broader applicability, while reducing reliance on low-level online monitors. Traditional implementations of cryptographic access control rely on simple cryptographic primitives whereas recent endeavors employ primitives with richer functionality and security guarantees. Worryingly, few of the existing cryptographic access-control schemes come with precise guarantees, the gap between the policy specification and the implementation being analyzed only informally, if at all. In this paper we begin addressing this shortcoming. Unlike prior work that targeted ad-hoc policy specification, we look at the well-established Role-Based Access Control (RBAC) model, as used in a typical file system. In short, we provide a precise syntax for a computational version of RBAC, offer rigorous definitions for cryptographic policy enforcement of a large class of RBAC security policies, and demonstrate that an implementation based on attribute-based encryption meets our security notions. We view our main contribution as being at the conceptual level. Although we work with RBAC for concreteness, our general methodology could guide future research for uses of cryptography in other access-control models. \r\n" author: - first_name: Anna full_name: Ferrara, Anna last_name: Ferrara - first_name: Georg full_name: Fuchsbauer, Georg id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87 last_name: Fuchsbauer - first_name: Bogdan full_name: Warinschi, Bogdan last_name: Warinschi citation: ama: 'Ferrara A, Fuchsbauer G, Warinschi B. Cryptographically enforced RBAC. In: IEEE; 2013:115-129. doi:10.1109/CSF.2013.15' apa: 'Ferrara, A., Fuchsbauer, G., & Warinschi, B. (2013). Cryptographically enforced RBAC (pp. 115–129). Presented at the CSF: Computer Security Foundations, New Orleans, LA, United States: IEEE. https://doi.org/10.1109/CSF.2013.15' chicago: Ferrara, Anna, Georg Fuchsbauer, and Bogdan Warinschi. “Cryptographically Enforced RBAC,” 115–29. IEEE, 2013. https://doi.org/10.1109/CSF.2013.15. ieee: 'A. Ferrara, G. Fuchsbauer, and B. Warinschi, “Cryptographically enforced RBAC,” presented at the CSF: Computer Security Foundations, New Orleans, LA, United States, 2013, pp. 115–129.' ista: 'Ferrara A, Fuchsbauer G, Warinschi B. 2013. Cryptographically enforced RBAC. CSF: Computer Security Foundations, 115–129.' mla: Ferrara, Anna, et al. Cryptographically Enforced RBAC. IEEE, 2013, pp. 115–29, doi:10.1109/CSF.2013.15. short: A. Ferrara, G. Fuchsbauer, B. Warinschi, in:, IEEE, 2013, pp. 115–129. conference: end_date: 2013-09-28 location: New Orleans, LA, United States name: 'CSF: Computer Security Foundations' start_date: 2013-09-26 date_created: 2018-12-11T11:56:48Z date_published: 2013-09-01T00:00:00Z date_updated: 2021-01-12T06:56:34Z day: '01' department: - _id: KrPi doi: 10.1109/CSF.2013.15 language: - iso: eng main_file_link: - open_access: '1' url: http://eprint.iacr.org/2013/492 month: '09' oa: 1 oa_version: Submitted Version page: 115 - 129 publication_status: published publisher: IEEE publist_id: '4637' quality_controlled: '1' scopus_import: 1 status: public title: Cryptographically enforced RBAC type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2288' abstract: - lang: eng text: This book constitutes the proceedings of the 11th International Conference on Computational Methods in Systems Biology, CMSB 2013, held in Klosterneuburg, Austria, in September 2013. The 15 regular papers included in this volume were carefully reviewed and selected from 27 submissions. They deal with computational models for all levels, from molecular and cellular, to organs and entire organisms. alternative_title: - LNCS citation: ama: Gupta A, Henzinger TA, eds. Computational Methods in Systems Biology. Vol 8130. Springer; 2013. doi:10.1007/978-3-642-40708-6 apa: 'Gupta, A., & Henzinger, T. A. (Eds.). (2013). Computational Methods in Systems Biology (Vol. 8130). Presented at the CMSB: Computational Methods in Systems Biology, Klosterneuburg, Austria: Springer. https://doi.org/10.1007/978-3-642-40708-6' chicago: Gupta, Ashutosh, and Thomas A Henzinger, eds. Computational Methods in Systems Biology. Vol. 8130. Springer, 2013. https://doi.org/10.1007/978-3-642-40708-6. ieee: A. Gupta and T. A. Henzinger, Eds., Computational Methods in Systems Biology, vol. 8130. Springer, 2013. ista: Gupta A, Henzinger TA eds. 2013. Computational Methods in Systems Biology, Springer,p. mla: Gupta, Ashutosh, and Thomas A. Henzinger, editors. Computational Methods in Systems Biology. Vol. 8130, Springer, 2013, doi:10.1007/978-3-642-40708-6. short: A. Gupta, T.A. Henzinger, eds., Computational Methods in Systems Biology, Springer, 2013. conference: end_date: 2013-09-24 location: Klosterneuburg, Austria name: 'CMSB: Computational Methods in Systems Biology' start_date: 2013-09-22 date_created: 2018-12-11T11:56:47Z date_published: 2013-07-01T00:00:00Z date_updated: 2019-08-02T12:37:44Z day: '01' department: - _id: ToHe doi: 10.1007/978-3-642-40708-6 editor: - first_name: Ashutosh full_name: Gupta, Ashutosh id: 335E5684-F248-11E8-B48F-1D18A9856A87 last_name: Gupta - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 intvolume: ' 8130' language: - iso: eng month: '07' oa_version: None publication_identifier: isbn: - 978-3-642-40707-9 publication_status: published publisher: Springer publist_id: '4643' quality_controlled: '1' status: public title: Computational Methods in Systems Biology type: conference_editor user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8130 year: '2013' ... --- _id: '2298' abstract: - lang: eng text: "We present a shape analysis for programs that manipulate overlaid data structures which share sets of objects. The abstract domain contains Separation Logic formulas that (1) combine a per-object separating conjunction with a per-field separating conjunction and (2) constrain a set of variables interpreted as sets of objects. The definition of the abstract domain operators is based on a notion of homomorphism between formulas, viewed as graphs, used recently to define optimal decision procedures for fragments of the Separation Logic. Based on a Frame Rule that supports the two versions of the separating conjunction, the analysis is able to reason in a modular manner about non-overlaid data structures and then, compose information only at a few program points, e.g., procedure returns. We have implemented this analysis in a prototype tool and applied it on several interesting case studies that manipulate overlaid and nested linked lists.\r\n" alternative_title: - LNCS author: - first_name: Cezara full_name: Dragoi, Cezara id: 2B2B5ED0-F248-11E8-B48F-1D18A9856A87 last_name: Dragoi - first_name: Constantin full_name: Enea, Constantin last_name: Enea - first_name: Mihaela full_name: Sighireanu, Mihaela last_name: Sighireanu citation: ama: 'Dragoi C, Enea C, Sighireanu M. Local shape analysis for overlaid data structures. In: Vol 7935. Springer; 2013:150-171. doi:10.1007/978-3-642-38856-9_10' apa: 'Dragoi, C., Enea, C., & Sighireanu, M. (2013). Local shape analysis for overlaid data structures (Vol. 7935, pp. 150–171). Presented at the SAS: Static Analysis Symposium, Seattle, WA, United States: Springer. https://doi.org/10.1007/978-3-642-38856-9_10' chicago: Dragoi, Cezara, Constantin Enea, and Mihaela Sighireanu. “Local Shape Analysis for Overlaid Data Structures,” 7935:150–71. Springer, 2013. https://doi.org/10.1007/978-3-642-38856-9_10. ieee: 'C. Dragoi, C. Enea, and M. Sighireanu, “Local shape analysis for overlaid data structures,” presented at the SAS: Static Analysis Symposium, Seattle, WA, United States, 2013, vol. 7935, pp. 150–171.' ista: 'Dragoi C, Enea C, Sighireanu M. 2013. Local shape analysis for overlaid data structures. SAS: Static Analysis Symposium, LNCS, vol. 7935, 150–171.' mla: Dragoi, Cezara, et al. Local Shape Analysis for Overlaid Data Structures. Vol. 7935, Springer, 2013, pp. 150–71, doi:10.1007/978-3-642-38856-9_10. short: C. Dragoi, C. Enea, M. Sighireanu, in:, Springer, 2013, pp. 150–171. conference: end_date: 2013-06-22 location: Seattle, WA, United States name: 'SAS: Static Analysis Symposium' start_date: 2013-06-20 date_created: 2018-12-11T11:56:50Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T06:56:36Z day: '01' ddc: - '000' - '004' department: - _id: ToHe doi: 10.1007/978-3-642-38856-9_10 ec_funded: 1 file: - access_level: open_access checksum: 907edd33a5892e3af093365f1fd57ed7 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:36Z date_updated: 2020-07-14T12:45:37Z file_id: '4824' file_name: IST-2014-196-v1+1_sas13.pdf file_size: 299004 relation: main_file file_date_updated: 2020-07-14T12:45:37Z has_accepted_license: '1' intvolume: ' 7935' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 150 - 171 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: Springer publist_id: '4630' pubrep_id: '196' quality_controlled: '1' scopus_import: 1 status: public title: Local shape analysis for overlaid data structures type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7935 year: '2013' ... --- _id: '2299' abstract: - lang: eng text: 'The standard hardware design flow involves: (a) design of an integrated circuit using a hardware description language, (b) extensive functional and formal verification, and (c) logical synthesis. However, the above-mentioned processes consume significant effort and time. An alternative approach is to use a formal specification language as a high-level hardware description language and synthesize hardware from formal specifications. Our work is a case study of the synthesis of the widely and industrially used AMBA AHB protocol from formal specifications. Bloem et al. presented the first formal specifications for the AMBA AHB Arbiter and synthesized the AHB Arbiter circuit. However, in the first formal specification some important assumptions were missing. Our contributions are as follows: (a) We present detailed formal specifications for the AHB Arbiter incorporating the missing details, and obtain significant improvements in the synthesis results (both with respect to the number of gates in the synthesized circuit and with respect to the time taken to synthesize the circuit), and (b) we present formal specifications to generate compact circuits for the remaining two main components of AMBA AHB, namely, AHB Master and AHB Slave. Thus with systematic description we are able to automatically and completely synthesize an important and widely used industrial protocol.' author: - first_name: Yashdeep full_name: Godhal, Yashdeep id: 5B547124-EB61-11E9-8887-89D9C04DBDF5 last_name: Godhal - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - 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: 'Godhal Y, Chatterjee K, Henzinger TA. Synthesis of AMBA AHB from formal specification: A case study. International Journal on Software Tools for Technology Transfer. 2013;15(5-6):585-601. doi:10.1007/s10009-011-0207-9' apa: 'Godhal, Y., Chatterjee, K., & Henzinger, T. A. (2013). Synthesis of AMBA AHB from formal specification: A case study. International Journal on Software Tools for Technology Transfer. Springer. https://doi.org/10.1007/s10009-011-0207-9' chicago: 'Godhal, Yashdeep, Krishnendu Chatterjee, and Thomas A Henzinger. “Synthesis of AMBA AHB from Formal Specification: A Case Study.” International Journal on Software Tools for Technology Transfer. Springer, 2013. https://doi.org/10.1007/s10009-011-0207-9.' ieee: 'Y. Godhal, K. Chatterjee, and T. A. Henzinger, “Synthesis of AMBA AHB from formal specification: A case study,” International Journal on Software Tools for Technology Transfer, vol. 15, no. 5–6. Springer, pp. 585–601, 2013.' ista: 'Godhal Y, Chatterjee K, Henzinger TA. 2013. Synthesis of AMBA AHB from formal specification: A case study. International Journal on Software Tools for Technology Transfer. 15(5–6), 585–601.' mla: 'Godhal, Yashdeep, et al. “Synthesis of AMBA AHB from Formal Specification: A Case Study.” International Journal on Software Tools for Technology Transfer, vol. 15, no. 5–6, Springer, 2013, pp. 585–601, doi:10.1007/s10009-011-0207-9.' short: Y. Godhal, K. Chatterjee, T.A. Henzinger, International Journal on Software Tools for Technology Transfer 15 (2013) 585–601. date_created: 2018-12-11T11:56:51Z date_published: 2013-10-01T00:00:00Z date_updated: 2021-01-12T06:56:37Z day: '01' ddc: - '000' department: - _id: KrCh - _id: ToHe doi: 10.1007/s10009-011-0207-9 file: - access_level: open_access checksum: 57b06a732dd8d6349190dba6b5b0d33b content_type: application/pdf creator: system date_created: 2018-12-12T10:11:53Z date_updated: 2020-07-14T12:45:37Z file_id: '4910' file_name: IST-2012-87-v1+1_Synthesis_of_AMBA_AHB_from_formal_specifications-_A_case_study.pdf file_size: 277372 relation: main_file file_date_updated: 2020-07-14T12:45:37Z has_accepted_license: '1' intvolume: ' 15' issue: 5-6 language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 585 - 601 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: International Journal on Software Tools for Technology Transfer publication_status: published publisher: Springer publist_id: '4629' pubrep_id: '87' quality_controlled: '1' scopus_import: 1 status: public title: 'Synthesis of AMBA AHB from formal specification: A case study' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2013' ... --- _id: '2297' abstract: - lang: eng text: We present an overview of mathematical results on the low temperature properties of dilute quantum gases, which have been obtained in the past few years. The presentation includes a discussion of Bose-Einstein condensation, the excitation spectrum for trapped gases and its relation to superfluidity, as well as the appearance of quantized vortices in rotating systems. All these properties are intensely being studied in current experiments on cold atomic gases. We will give a description of the mathematics involved in understanding these phenomena, starting from the underlying many-body Schrödinger equation. author: - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: 'Seiringer R. Hot topics in cold gases: A mathematical physics perspective. Japanese Journal of Mathematics. 2013;8(2):185-232. doi:10.1007/s11537-013-1264-5' apa: 'Seiringer, R. (2013). Hot topics in cold gases: A mathematical physics perspective. Japanese Journal of Mathematics. Springer. https://doi.org/10.1007/s11537-013-1264-5' chicago: 'Seiringer, Robert. “Hot Topics in Cold Gases: A Mathematical Physics Perspective.” Japanese Journal of Mathematics. Springer, 2013. https://doi.org/10.1007/s11537-013-1264-5.' ieee: 'R. Seiringer, “Hot topics in cold gases: A mathematical physics perspective,” Japanese Journal of Mathematics, vol. 8, no. 2. Springer, pp. 185–232, 2013.' ista: 'Seiringer R. 2013. Hot topics in cold gases: A mathematical physics perspective. Japanese Journal of Mathematics. 8(2), 185–232.' mla: 'Seiringer, Robert. “Hot Topics in Cold Gases: A Mathematical Physics Perspective.” Japanese Journal of Mathematics, vol. 8, no. 2, Springer, 2013, pp. 185–232, doi:10.1007/s11537-013-1264-5.' short: R. Seiringer, Japanese Journal of Mathematics 8 (2013) 185–232. date_created: 2018-12-11T11:56:50Z date_published: 2013-09-24T00:00:00Z date_updated: 2021-01-12T06:56:36Z day: '24' department: - _id: RoSe doi: 10.1007/s11537-013-1264-5 external_id: arxiv: - '0908.3686' intvolume: ' 8' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/0908.3686 month: '09' oa: 1 oa_version: Preprint page: 185 - 232 publication: Japanese Journal of Mathematics publication_status: published publisher: Springer publist_id: '4631' quality_controlled: '1' scopus_import: 1 status: public title: 'Hot topics in cold gases: A mathematical physics perspective' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2013' ... --- _id: '2306' abstract: - lang: ger text: Das Buch ist sowohl eine Einführung in die Themen Linked Data, Open Data und Open Linked Data als es auch den konkreten Bezug auf Bibliotheken behandelt. Hierzu werden konkrete Anwendungsprojekte beschrieben. Der Band wendet sich dabei sowohl an Personen aus der Bibliothekspraxis als auch an Personen aus dem Bibliotheksmanagement, die noch nicht mit dem Thema vertraut sind. alternative_title: - Bibliotheks- und Informationspraxis article_processing_charge: No author: - first_name: Patrick full_name: Danowski, Patrick id: 2EBD1598-F248-11E8-B48F-1D18A9856A87 last_name: Danowski orcid: 0000-0002-6026-4409 - first_name: Adrian full_name: Pohl, Adrian last_name: Pohl citation: ama: Danowski P, Pohl A. (Open) Linked Data in Bibliotheken. Vol 50. De Gruyter; 2013. doi:10.1515/9783110278736 apa: Danowski, P., & Pohl, A. (2013). (Open) Linked Data in Bibliotheken (Vol. 50). De Gruyter. https://doi.org/10.1515/9783110278736 chicago: Danowski, Patrick, and Adrian Pohl. (Open) Linked Data in Bibliotheken. Vol. 50. De Gruyter, 2013. https://doi.org/10.1515/9783110278736. ieee: P. Danowski and A. Pohl, (Open) Linked Data in Bibliotheken, vol. 50. De Gruyter, 2013. ista: Danowski P, Pohl A. 2013. (Open) Linked Data in Bibliotheken, De Gruyter,p. mla: Danowski, Patrick, and Adrian Pohl. (Open) Linked Data in Bibliotheken. Vol. 50, De Gruyter, 2013, doi:10.1515/9783110278736. short: P. Danowski, A. Pohl, (Open) Linked Data in Bibliotheken, De Gruyter, 2013. date_created: 2018-12-11T11:56:53Z date_published: 2013-09-13T00:00:00Z date_updated: 2021-12-21T12:17:19Z day: '13' ddc: - '020' department: - _id: E-Lib doi: 10.1515/9783110278736 file: - access_level: open_access checksum: 807a408bbee519d792702828a32c6e85 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:49Z date_updated: 2020-07-14T12:45:38Z file_id: '4774' file_name: IST-2017-725-v1+1_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Frontmatter.pdf file_size: 67731 relation: main_file - access_level: open_access checksum: 587e95c2ba24307a5a5d5bd1579429d9 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:50Z date_updated: 2020-07-14T12:45:38Z file_id: '4775' file_name: IST-2017-725-v1+2_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Inhalt.pdf file_size: 43563 relation: main_file - access_level: open_access checksum: dbcada36bb32d725d9838615706e700f content_type: application/pdf creator: system date_created: 2018-12-12T10:09:51Z date_updated: 2020-07-14T12:45:38Z file_id: '4776' file_name: IST-2017-725-v1+3_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Linked_Open_Data_in_der_Bibliothekswelt__Grundlagen_und_Überblick.pdf file_size: 11318599 relation: main_file - access_level: open_access checksum: 5235712bf0a49ccc8c2cb4f6c2560d43 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:52Z date_updated: 2020-07-14T12:45:38Z file_id: '4777' file_name: IST-2017-725-v1+4_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Vokabulare_für_bibliographische_Daten.pdf file_size: 330210 relation: main_file - access_level: open_access checksum: d851cc91f705da80617ac7df33c1c0e1 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:53Z date_updated: 2020-07-14T12:45:38Z file_id: '4778' file_name: IST-2017-725-v1+5_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_FRBR,_Serials_und_CIDOC_CRM_-_Modellierung_von_fortlaufenden_Sammelwerken_unter_Verwendung_von_FRBRoo.pdf file_size: 10652088 relation: main_file - access_level: open_access checksum: 4e77b182692c58e50fc5251bf23cc584 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:54Z date_updated: 2020-07-14T12:45:38Z file_id: '4779' file_name: IST-2017-725-v1+6_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Die_Provenienz_von_Linked_Data.pdf file_size: 6125273 relation: main_file - access_level: open_access checksum: 3debae38064d5099d22f855c353a57ec content_type: application/pdf creator: system date_created: 2018-12-12T10:09:55Z date_updated: 2020-07-14T12:45:38Z file_id: '4780' file_name: IST-2017-725-v1+7_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Forschungsdaten.pdf file_size: 1893872 relation: main_file - access_level: open_access checksum: e630b330dc0b7522d2cf204587030252 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:56Z date_updated: 2020-07-14T12:45:38Z file_id: '4781' file_name: IST-2017-725-v1+8_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Datenanreicherung_auf_LOD-Basis.pdf file_size: 1095929 relation: main_file - access_level: open_access checksum: 17edda91271bfcce8e1b6e77ca1c9d11 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:57Z date_updated: 2020-07-14T12:45:38Z file_id: '4782' file_name: IST-2017-725-v1+9_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Herausforderung_Wissensvernetzung.pdf file_size: 149699 relation: main_file - access_level: open_access checksum: aacef6734b1de58aeb58024fc47c2373 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:58Z date_updated: 2020-07-14T12:45:38Z file_id: '4783' file_name: IST-2017-725-v1+10_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Linked_Open_Data_geht_in_die_Fläche__Der_B3Kat_stellt_seine_Daten_frei.pdf file_size: 8828405 relation: main_file - access_level: open_access checksum: 0619451f7ff3ea641ce0b10c97831f47 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:59Z date_updated: 2020-07-14T12:45:38Z file_id: '4784' file_name: IST-2017-725-v1+11_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Open_Data_und_Linked_Data_in_einem_Informationssystem_für_die_Archäologie.pdf file_size: 3191208 relation: main_file - access_level: open_access checksum: 44dc8a9fc003f0edd912968958715a23 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:00Z date_updated: 2020-07-14T12:45:38Z file_id: '4785' file_name: IST-2017-725-v1+12_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Definition__Offenes_Wissen.pdf file_size: 78315 relation: main_file - access_level: open_access checksum: 48133cecebfd839b77f84f557d530c00 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:01Z date_updated: 2020-07-14T12:45:38Z file_id: '4786' file_name: IST-2017-725-v1+13_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Prinzipien_zu_offenen_bibliographischen_Daten.pdf file_size: 90532 relation: main_file - access_level: open_access checksum: a359224ddfdb178fed72b228dcfb699a content_type: application/pdf creator: system date_created: 2018-12-12T10:10:02Z date_updated: 2020-07-14T12:45:38Z file_id: '4787' file_name: IST-2017-725-v1+14_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Empfehlungen_zur_Öffnung_bibliothekarischer_Daten.pdf file_size: 90771 relation: main_file - access_level: open_access checksum: 0d2dd31d537c7a495999149d00eaffbf content_type: application/pdf creator: system date_created: 2018-12-12T10:10:03Z date_updated: 2020-07-14T12:45:38Z file_id: '4788' file_name: IST-2017-725-v1+15_[9783110278736_-__Open__Linked_Data_in_Bibliotheken]_Glossar.pdf file_size: 1830232 relation: main_file file_date_updated: 2020-07-14T12:45:38Z has_accepted_license: '1' intvolume: ' 50' language: - iso: ger month: '09' oa: 1 oa_version: Published Version publication_identifier: eisbn: - 9-783-1102-7873-6 isbn: - ' 978-3-11-027634-3' issn: - 2191-3587 publication_status: published publisher: De Gruyter publist_id: '4621' pubrep_id: '725' quality_controlled: '1' status: public title: (Open) Linked Data in Bibliotheken 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: book user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 50 year: '2013' ... --- _id: '2301' abstract: - lang: eng text: We describe the design and implementation of P, a domain-specific language to write asynchronous event driven code. P allows the programmer to specify the system as a collection of interacting state machines, which communicate with each other using events. P unifies modeling and programming into one activity for the programmer. Not only can a P program be compiled into executable code, but it can also be tested using model checking techniques. P allows the programmer to specify the environment, used to "close" the system during testing, as nondeterministic ghost machines. Ghost machines are erased during compilation to executable code; a type system ensures that the erasure is semantics preserving. The P language is designed so that a P program can be checked for responsiveness-the ability to handle every event in a timely manner. By default, a machine needs to handle every event that arrives in every state. But handling every event in every state is impractical. The language provides a notion of deferred events where the programmer can annotate when she wants to delay processing an event. The default safety checker looks for presence of unhan-dled events. The language also provides default liveness checks that an event cannot be potentially deferred forever. P was used to implement and verify the core of the USB device driver stack that ships with Microsoft Windows 8. The resulting driver is more reliable and performs better than its prior incarnation (which did not use P); we have more confidence in the robustness of its design due to the language abstractions and verification provided by P. author: - first_name: Ankush full_name: Desai, Ankush last_name: Desai - first_name: Vivek full_name: Gupta, Vivek last_name: Gupta - first_name: Ethan full_name: Jackson, Ethan last_name: Jackson - first_name: Shaz full_name: Qadeer, Shaz last_name: Qadeer - first_name: Sriram full_name: Rajamani, Sriram last_name: Rajamani - first_name: Damien full_name: Zufferey, Damien id: 4397AC76-F248-11E8-B48F-1D18A9856A87 last_name: Zufferey orcid: 0000-0002-3197-8736 citation: ama: 'Desai A, Gupta V, Jackson E, Qadeer S, Rajamani S, Zufferey D. P: Safe asynchronous event-driven programming. In: Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation. ACM; 2013:321-331. doi:10.1145/2491956.2462184' apa: 'Desai, A., Gupta, V., Jackson, E., Qadeer, S., Rajamani, S., & Zufferey, D. (2013). P: Safe asynchronous event-driven programming. In Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation (pp. 321–331). Seattle, WA, United States: ACM. https://doi.org/10.1145/2491956.2462184' chicago: 'Desai, Ankush, Vivek Gupta, Ethan Jackson, Shaz Qadeer, Sriram Rajamani, and Damien Zufferey. “P: Safe Asynchronous Event-Driven Programming.” In Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation, 321–31. ACM, 2013. https://doi.org/10.1145/2491956.2462184.' ieee: 'A. Desai, V. Gupta, E. Jackson, S. Qadeer, S. Rajamani, and D. Zufferey, “P: Safe asynchronous event-driven programming,” in Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation, Seattle, WA, United States, 2013, pp. 321–331.' ista: 'Desai A, Gupta V, Jackson E, Qadeer S, Rajamani S, Zufferey D. 2013. P: Safe asynchronous event-driven programming. Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation. PLDI: Programming Languages Design and Implementation, 321–331.' mla: 'Desai, Ankush, et al. “P: Safe Asynchronous Event-Driven Programming.” Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation, ACM, 2013, pp. 321–31, doi:10.1145/2491956.2462184.' short: A. Desai, V. Gupta, E. Jackson, S. Qadeer, S. Rajamani, D. Zufferey, in:, Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation, ACM, 2013, pp. 321–331. conference: end_date: 2013-06-19 location: Seattle, WA, United States name: 'PLDI: Programming Languages Design and Implementation' start_date: 2013-06-16 date_created: 2018-12-11T11:56:52Z date_published: 2013-06-01T00:00:00Z date_updated: 2021-01-12T06:56:38Z day: '01' department: - _id: ToHe doi: 10.1145/2491956.2462184 ec_funded: 1 language: - iso: eng main_file_link: - url: http://research.microsoft.com/pubs/191069/pldi212_desai.pdf month: '06' oa_version: None page: 321 - 331 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: Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation publication_status: published publisher: ACM publist_id: '4626' quality_controlled: '1' scopus_import: 1 status: public title: 'P: Safe asynchronous event-driven programming' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2300' abstract: - lang: eng text: We consider Ising models in two and three dimensions with nearest neighbor ferromagnetic interactions and long-range, power law decaying, antiferromagnetic interactions. If the strength of the ferromagnetic coupling J is larger than a critical value Jc, then the ground state is homogeneous and ferromagnetic. As the critical value is approached from smaller values of J, it is believed that the ground state consists of a periodic array of stripes (d=2) or slabs (d=3), all of the same size and alternating magnetization. Here we prove rigorously that the ground state energy per site converges to that of the optimal periodic striped or slabbed state, in the limit that J tends to the ferromagnetic transition point. While this theorem does not prove rigorously that the ground state is precisely striped or slabbed, it does prove that in any suitably large box the ground state is striped or slabbed with high probability. article_number: '064401' author: - first_name: Alessandro full_name: Giuliani, Alessandro last_name: Giuliani - first_name: Élliott full_name: Lieb, Élliott last_name: Lieb - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Giuliani A, Lieb É, Seiringer R. Realization of stripes and slabs in two and three dimensions. Physical Review B. 2013;88(6). doi:10.1103/PhysRevB.88.064401 apa: Giuliani, A., Lieb, É., & Seiringer, R. (2013). Realization of stripes and slabs in two and three dimensions. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.88.064401 chicago: Giuliani, Alessandro, Élliott Lieb, and Robert Seiringer. “Realization of Stripes and Slabs in Two and Three Dimensions.” Physical Review B. American Physical Society, 2013. https://doi.org/10.1103/PhysRevB.88.064401. ieee: A. Giuliani, É. Lieb, and R. Seiringer, “Realization of stripes and slabs in two and three dimensions,” Physical Review B, vol. 88, no. 6. American Physical Society, 2013. ista: Giuliani A, Lieb É, Seiringer R. 2013. Realization of stripes and slabs in two and three dimensions. Physical Review B. 88(6), 064401. mla: Giuliani, Alessandro, et al. “Realization of Stripes and Slabs in Two and Three Dimensions.” Physical Review B, vol. 88, no. 6, 064401, American Physical Society, 2013, doi:10.1103/PhysRevB.88.064401. short: A. Giuliani, É. Lieb, R. Seiringer, Physical Review B 88 (2013). date_created: 2018-12-11T11:56:51Z date_published: 2013-08-01T00:00:00Z date_updated: 2021-01-12T06:56:38Z day: '01' department: - _id: RoSe doi: 10.1103/PhysRevB.88.064401 external_id: arxiv: - '1305.5323' intvolume: ' 88' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1305.5323 month: '08' oa: 1 oa_version: Preprint publication: Physical Review B publication_status: published publisher: American Physical Society publist_id: '4627' quality_controlled: '1' scopus_import: 1 status: public title: Realization of stripes and slabs in two and three dimensions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 88 year: '2013' ... --- _id: '2303' abstract: - lang: eng text: MADM (Mosaic Analysis with Double Markers) technology offers a genetic approach in mice to visualize and concomitantly manipulate genetically defined cells at clonal level and single cell resolution. MADM employs Cre recombinase/loxP-dependent interchromosomal mitotic recombination to reconstitute two split marker genes—green GFP and red tdTomato—and can label sparse clones of homozygous mutant cells in one color and wild-type cells in the other color in an otherwise unlabeled background. At present, major MADM applications include lineage tracing, single cell labeling, conditional knockouts in small populations of cells and induction of uniparental chromosome disomy to assess effects of genomic imprinting. MADM can be applied universally in the mouse with the sole limitation being the specificity of the promoter controlling Cre recombinase expression. Here I review recent developments and extensions of the MADM technique and give an overview of the major discoveries and progresses enabled by the implementation of the novel genetic MADM tools. acknowledgement: This work was supported by IST Austria institutional funds. article_type: review author: - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Hippenmeyer S. Dissection of gene function at clonal level using mosaic analysis with double markers. Frontiers in Biology. 2013;8(6):557-568. doi:10.1007/s11515-013-1279-6 apa: Hippenmeyer, S. (2013). Dissection of gene function at clonal level using mosaic analysis with double markers. Frontiers in Biology. Springer. https://doi.org/10.1007/s11515-013-1279-6 chicago: Hippenmeyer, Simon. “Dissection of Gene Function at Clonal Level Using Mosaic Analysis with Double Markers.” Frontiers in Biology. Springer, 2013. https://doi.org/10.1007/s11515-013-1279-6. ieee: S. Hippenmeyer, “Dissection of gene function at clonal level using mosaic analysis with double markers,” Frontiers in Biology, vol. 8, no. 6. Springer, pp. 557–568, 2013. ista: Hippenmeyer S. 2013. Dissection of gene function at clonal level using mosaic analysis with double markers. Frontiers in Biology. 8(6), 557–568. mla: Hippenmeyer, Simon. “Dissection of Gene Function at Clonal Level Using Mosaic Analysis with Double Markers.” Frontiers in Biology, vol. 8, no. 6, Springer, 2013, pp. 557–68, doi:10.1007/s11515-013-1279-6. short: S. Hippenmeyer, Frontiers in Biology 8 (2013) 557–568. date_created: 2018-12-11T11:56:52Z date_published: 2013-09-03T00:00:00Z date_updated: 2021-01-12T06:56:39Z day: '03' department: - _id: SiHi doi: 10.1007/s11515-013-1279-6 intvolume: ' 8' issue: '6' language: - iso: eng month: '09' oa_version: None page: 557 - 568 publication: Frontiers in Biology publication_status: published publisher: Springer publist_id: '4624' quality_controlled: '1' scopus_import: 1 status: public title: Dissection of gene function at clonal level using mosaic analysis with double markers type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2013' ... --- _id: '2304' abstract: - lang: eng text: This extended abstract is concerned with the irregularities of distribution of one-dimensional permuted van der Corput sequences that are generated from linear permutations. We show how to obtain upper bounds for the discrepancy and diaphony of these sequences, by relating them to Kronecker sequences and applying earlier results of Faure and Niederreiter. acknowledgement: This research is supported by the Graduate school of IST Austria (Institute of Science and Technology Austria). author: - first_name: Florian full_name: Pausinger, Florian id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87 last_name: Pausinger orcid: 0000-0002-8379-3768 citation: ama: Pausinger F. Van der Corput sequences and linear permutations. Electronic Notes in Discrete Mathematics. 2013;43:43-50. doi:10.1016/j.endm.2013.07.008 apa: Pausinger, F. (2013). Van der Corput sequences and linear permutations. Electronic Notes in Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.endm.2013.07.008 chicago: Pausinger, Florian. “Van Der Corput Sequences and Linear Permutations.” Electronic Notes in Discrete Mathematics. Elsevier, 2013. https://doi.org/10.1016/j.endm.2013.07.008. ieee: F. Pausinger, “Van der Corput sequences and linear permutations,” Electronic Notes in Discrete Mathematics, vol. 43. Elsevier, pp. 43–50, 2013. ista: Pausinger F. 2013. Van der Corput sequences and linear permutations. Electronic Notes in Discrete Mathematics. 43, 43–50. mla: Pausinger, Florian. “Van Der Corput Sequences and Linear Permutations.” Electronic Notes in Discrete Mathematics, vol. 43, Elsevier, 2013, pp. 43–50, doi:10.1016/j.endm.2013.07.008. short: F. Pausinger, Electronic Notes in Discrete Mathematics 43 (2013) 43–50. date_created: 2018-12-11T11:56:53Z date_published: 2013-09-05T00:00:00Z date_updated: 2021-01-12T06:56:39Z day: '05' department: - _id: HeEd doi: 10.1016/j.endm.2013.07.008 intvolume: ' 43' language: - iso: eng month: '09' oa_version: None page: 43 - 50 publication: Electronic Notes in Discrete Mathematics publication_status: published publisher: Elsevier publist_id: '4623' quality_controlled: '1' scopus_import: 1 status: public title: Van der Corput sequences and linear permutations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 43 year: '2013' ... --- _id: '2315' abstract: - lang: eng text: ' We study the effects of random scatterers on the ground state of the one-dimensional Lieb-Liniger model of interacting bosons on the unit interval in the Gross-Pitaevskii regime. We prove that Bose Einstein condensation survives even a strong random potential with a high density of scatterers. The character of the wave function of the condensate, however, depends in an essential way on the interplay between randomness and the strength of the two-body interaction. For low density of scatterers or strong interactions the wave function extends over the whole interval. High density of scatterers and weak interaction, on the other hand, leads to localization of the wave function in a fragmented subset of the interval. ' article_processing_charge: No author: - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Jakob full_name: Yngvason, Jakob last_name: Yngvason - first_name: Valentin full_name: Zagrebnov, Valentin last_name: Zagrebnov citation: ama: 'Seiringer R, Yngvason J, Zagrebnov V. Disordered Bose-Einstein condensates with interaction. In: World Scientific Publishing; 2013:610-619. doi:10.1142/9789814449243_0063' apa: 'Seiringer, R., Yngvason, J., & Zagrebnov, V. (2013). Disordered Bose-Einstein condensates with interaction (pp. 610–619). Presented at the ICMP: International Congress on Mathematical Physics, World Scientific Publishing. https://doi.org/10.1142/9789814449243_0063' chicago: Seiringer, Robert, Jakob Yngvason, and Valentin Zagrebnov. “Disordered Bose-Einstein Condensates with Interaction,” 610–19. World Scientific Publishing, 2013. https://doi.org/10.1142/9789814449243_0063. ieee: 'R. Seiringer, J. Yngvason, and V. Zagrebnov, “Disordered Bose-Einstein condensates with interaction,” presented at the ICMP: International Congress on Mathematical Physics, 2013, pp. 610–619.' ista: 'Seiringer R, Yngvason J, Zagrebnov V. 2013. Disordered Bose-Einstein condensates with interaction. ICMP: International Congress on Mathematical Physics, 610–619.' mla: Seiringer, Robert, et al. Disordered Bose-Einstein Condensates with Interaction. World Scientific Publishing, 2013, pp. 610–19, doi:10.1142/9789814449243_0063. short: R. Seiringer, J. Yngvason, V. Zagrebnov, in:, World Scientific Publishing, 2013, pp. 610–619. conference: name: 'ICMP: International Congress on Mathematical Physics' date_created: 2018-12-11T11:56:57Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T06:56:43Z doi: 10.1142/9789814449243_0063 extern: '1' external_id: arxiv: - '1209.4046' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1209.4046 oa: 1 oa_version: None page: 610-619 publication_status: published publisher: World Scientific Publishing publist_id: '4612' status: public title: Disordered Bose-Einstein condensates with interaction type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2319' abstract: - lang: eng text: In a recent paper [7] we give the first rigorous derivation of the celebrated Ginzburg-Landau (GL)theory, starting from the microscopic Bardeen- Cooper-Schrieffer (BCS)model. Here we present our results in the simplified case of a one-dimensional system of particles interacting via a δ-potential. author: - first_name: Rupert full_name: Frank, Rupert L last_name: Frank - first_name: Christian full_name: Hainzl, Christian last_name: Hainzl - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Jan full_name: Solovej, Jan P last_name: Solovej citation: ama: 'Frank R, Hainzl C, Seiringer R, Solovej J. Derivation of Ginzburg-Landau theory for a one-dimensional system with contact interaction. In: Springer; 2013:57-88. doi:10.1007/978-3-0348-0531-5_3' apa: 'Frank, R., Hainzl, C., Seiringer, R., & Solovej, J. (2013). Derivation of Ginzburg-Landau theory for a one-dimensional system with contact interaction (pp. 57–88). Presented at the OTAMP: Operator Theory, Analysis and Mathematical Physics, Springer. https://doi.org/10.1007/978-3-0348-0531-5_3' chicago: Frank, Rupert, Christian Hainzl, Robert Seiringer, and Jan Solovej. “ Derivation of Ginzburg-Landau Theory for a One-Dimensional System with Contact Interaction,” 57–88. Springer, 2013. https://doi.org/10.1007/978-3-0348-0531-5_3. ieee: 'R. Frank, C. Hainzl, R. Seiringer, and J. Solovej, “ Derivation of Ginzburg-Landau theory for a one-dimensional system with contact interaction,” presented at the OTAMP: Operator Theory, Analysis and Mathematical Physics, 2013, pp. 57–88.' ista: 'Frank R, Hainzl C, Seiringer R, Solovej J. 2013. Derivation of Ginzburg-Landau theory for a one-dimensional system with contact interaction. OTAMP: Operator Theory, Analysis and Mathematical Physics, 57–88.' mla: Frank, Rupert, et al. Derivation of Ginzburg-Landau Theory for a One-Dimensional System with Contact Interaction. Springer, 2013, pp. 57–88, doi:10.1007/978-3-0348-0531-5_3. short: R. Frank, C. Hainzl, R. Seiringer, J. Solovej, in:, Springer, 2013, pp. 57–88. conference: name: 'OTAMP: Operator Theory, Analysis and Mathematical Physics' date_created: 2018-12-11T11:56:58Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T06:56:45Z day: '01' doi: 10.1007/978-3-0348-0531-5_3 extern: 1 main_file_link: - open_access: '1' url: http://arxiv.org/abs/1103.1866 month: '01' oa: 1 page: 57 - 88 publication_status: published publisher: Springer publist_id: '4608' quality_controlled: 0 status: public title: ' Derivation of Ginzburg-Landau theory for a one-dimensional system with contact interaction' type: conference year: '2013' ... --- _id: '2328' abstract: - lang: eng text: "Linearizability of concurrent data structures is usually proved by monolithic simulation arguments relying on identifying the so-called linearization points. Regrettably, such proofs, whether manual or automatic, are often complicated and scale poorly to advanced non-blocking concurrency patterns, such as helping and optimistic updates.\r\nIn response, we propose a more modular way of checking linearizability of concurrent queue algorithms that does not involve identifying linearization points. We reduce the task of proving linearizability with respect to the queue specification to establishing four basic properties, each of which can be proved independently by simpler arguments. As a demonstration of our approach, we verify the Herlihy and Wing queue, an algorithm that is challenging to verify by a simulation proof." alternative_title: - LNCS 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: Ali full_name: Sezgin, Ali id: 4C7638DA-F248-11E8-B48F-1D18A9856A87 last_name: Sezgin - first_name: Viktor full_name: Vafeiadis, Viktor last_name: Vafeiadis citation: ama: Henzinger TA, Sezgin A, Vafeiadis V. Aspect-oriented linearizability proofs. 2013;8052:242-256. doi:10.1007/978-3-642-40184-8_18 apa: 'Henzinger, T. A., Sezgin, A., & Vafeiadis, V. (2013). Aspect-oriented linearizability proofs. Presented at the CONCUR: Concurrency Theory, Buenos Aires, Argentina: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-642-40184-8_18' chicago: Henzinger, Thomas A, Ali Sezgin, and Viktor Vafeiadis. “Aspect-Oriented Linearizability Proofs.” Lecture Notes in Computer Science. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013. https://doi.org/10.1007/978-3-642-40184-8_18. ieee: T. A. Henzinger, A. Sezgin, and V. Vafeiadis, “Aspect-oriented linearizability proofs,” vol. 8052. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp. 242–256, 2013. ista: Henzinger TA, Sezgin A, Vafeiadis V. 2013. Aspect-oriented linearizability proofs. 8052, 242–256. mla: Henzinger, Thomas A., et al. Aspect-Oriented Linearizability Proofs. Vol. 8052, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 242–56, doi:10.1007/978-3-642-40184-8_18. short: T.A. Henzinger, A. Sezgin, V. Vafeiadis, 8052 (2013) 242–256. conference: end_date: 2013-08-30 location: Buenos Aires, Argentina name: 'CONCUR: Concurrency Theory' start_date: 2013-08-27 date_created: 2018-12-11T11:57:01Z date_published: 2013-08-01T00:00:00Z date_updated: 2023-02-23T10:16:27Z day: '01' ddc: - '000' - '004' department: - _id: ToHe doi: 10.1007/978-3-642-40184-8_18 ec_funded: 1 file: - access_level: open_access checksum: bdbb520de91751fe0136309ad4ef67e4 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:58Z date_updated: 2020-07-14T12:45:39Z file_id: '4721' file_name: IST-2014-197-v1+1_main-queue-verification.pdf file_size: 337059 relation: main_file file_date_updated: 2020-07-14T12:45:39Z has_accepted_license: '1' intvolume: ' 8052' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 242 - 256 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: '4598' pubrep_id: '197' quality_controlled: '1' related_material: record: - id: '1832' relation: later_version status: public scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Aspect-oriented linearizability proofs type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8052 year: '2013' ... --- _id: '2404' abstract: - lang: eng text: The Lieb-Thirring inequalities give a bound on the negative eigenvalues of a Schrödinger operator in terms of an Lp-norm of the potential. These are dual to bounds on the H1-norms of a system of orthonormal functions. Here we extend these bounds to analogous inequalities for perturbations of the Fermi sea of noninteracting particles (i.e., for perturbations of the continuous spectrum of the Laplacian by local potentials). author: - first_name: Rupert full_name: Frank, Rupert L last_name: Frank - first_name: Mathieu full_name: Lewin, Mathieu last_name: Lewin - first_name: Élliott full_name: Lieb, Élliott H last_name: Lieb - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Frank R, Lewin M, Lieb É, Seiringer R. A positive density analogue of the Lieb-Thirring inequality. Duke Mathematical Journal. 2013;162(3):435-495. doi:10.1215/00127094-2019477 apa: Frank, R., Lewin, M., Lieb, É., & Seiringer, R. (2013). A positive density analogue of the Lieb-Thirring inequality. Duke Mathematical Journal. Duke University Press. https://doi.org/10.1215/00127094-2019477 chicago: Frank, Rupert, Mathieu Lewin, Élliott Lieb, and Robert Seiringer. “A Positive Density Analogue of the Lieb-Thirring Inequality.” Duke Mathematical Journal. Duke University Press, 2013. https://doi.org/10.1215/00127094-2019477. ieee: R. Frank, M. Lewin, É. Lieb, and R. Seiringer, “A positive density analogue of the Lieb-Thirring inequality,” Duke Mathematical Journal, vol. 162, no. 3. Duke University Press, pp. 435–495, 2013. ista: Frank R, Lewin M, Lieb É, Seiringer R. 2013. A positive density analogue of the Lieb-Thirring inequality. Duke Mathematical Journal. 162(3), 435–495. mla: Frank, Rupert, et al. “A Positive Density Analogue of the Lieb-Thirring Inequality.” Duke Mathematical Journal, vol. 162, no. 3, Duke University Press, 2013, pp. 435–95, doi:10.1215/00127094-2019477. short: R. Frank, M. Lewin, É. Lieb, R. Seiringer, Duke Mathematical Journal 162 (2013) 435–495. date_created: 2018-12-11T11:57:28Z date_published: 2013-02-01T00:00:00Z date_updated: 2021-01-12T06:57:17Z day: '01' doi: 10.1215/00127094-2019477 extern: 1 intvolume: ' 162' issue: '3' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1108.4246 month: '02' oa: 1 page: 435 - 495 publication: Duke Mathematical Journal publication_status: published publisher: Duke University Press publist_id: '4521' quality_controlled: 0 status: public title: A positive density analogue of the Lieb-Thirring inequality type: journal_article volume: 162 year: '2013' ... --- _id: '2406' abstract: - lang: eng text: We study the effects of random scatterers on the ground state of the one-dimensional Lieb-Liniger model of interacting bosons on the unit interval. We prove that, in the Gross-Pitaevskii limit, Bose Einstein condensation takes place in the whole parameter range considered. The character of the wave function of the condensate, however, depends in an essential way on the interplay between randomness and the strength of the two-body interaction. For low density of scatterers or strong interactions the wave function extends over the whole interval. High density of scatterers and weak interaction, on the other hand, leads to localization of the wave function in a fragmented subset of the unit interval. author: - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Jakob full_name: Yngvason, Jakob last_name: Yngvason - first_name: Valentin full_name: Zagrebnov, Valentin A last_name: Zagrebnov citation: ama: 'Seiringer R, Yngvason J, Zagrebnov V. Condensation of interacting bosons in a random potential. European Physical Journal: Special Topics. 2013;217(1):103-107. doi:10.1140/epjst/e2013-01759-5' apa: 'Seiringer, R., Yngvason, J., & Zagrebnov, V. (2013). Condensation of interacting bosons in a random potential. European Physical Journal: Special Topics. Springer. https://doi.org/10.1140/epjst/e2013-01759-5' chicago: 'Seiringer, Robert, Jakob Yngvason, and Valentin Zagrebnov. “Condensation of Interacting Bosons in a Random Potential.” European Physical Journal: Special Topics. Springer, 2013. https://doi.org/10.1140/epjst/e2013-01759-5.' ieee: 'R. Seiringer, J. Yngvason, and V. Zagrebnov, “Condensation of interacting bosons in a random potential,” European Physical Journal: Special Topics, vol. 217, no. 1. Springer, pp. 103–107, 2013.' ista: 'Seiringer R, Yngvason J, Zagrebnov V. 2013. Condensation of interacting bosons in a random potential. European Physical Journal: Special Topics. 217(1), 103–107.' mla: 'Seiringer, Robert, et al. “Condensation of Interacting Bosons in a Random Potential.” European Physical Journal: Special Topics, vol. 217, no. 1, Springer, 2013, pp. 103–07, doi:10.1140/epjst/e2013-01759-5.' short: 'R. Seiringer, J. Yngvason, V. Zagrebnov, European Physical Journal: Special Topics 217 (2013) 103–107.' date_created: 2018-12-11T11:57:29Z date_published: 2013-02-01T00:00:00Z date_updated: 2021-01-12T06:57:17Z day: '01' doi: 10.1140/epjst/e2013-01759-5 extern: 1 intvolume: ' 217' issue: '1' month: '02' page: 103 - 107 publication: 'European Physical Journal: Special Topics' publication_status: published publisher: Springer publist_id: '4520' quality_controlled: 0 status: public title: Condensation of interacting bosons in a random potential type: journal_article volume: 217 year: '2013' ... --- _id: '2405' abstract: - lang: eng text: We consider the bipolaron in the Pekar-Tomasevich approximation and address the question whether the ground state is spherically symmetric or not. Numerical analysis has, so far, not completely settled the question. Our contribution is to prove rigorously that the ground state remains spherical for small values of the electron-electron Coulomb repulsion. author: - first_name: Rupert full_name: Frank, Rupert L last_name: Frank - first_name: Élliott full_name: Lieb, Élliott H last_name: Lieb - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Frank R, Lieb É, Seiringer R. Symmetry of bipolaron bound states for small Coulomb repulsion. Communications in Mathematical Physics. 2013;319(2):557-573. doi:10.1007/s00220-012-1604-y apa: Frank, R., Lieb, É., & Seiringer, R. (2013). Symmetry of bipolaron bound states for small Coulomb repulsion. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-012-1604-y chicago: Frank, Rupert, Élliott Lieb, and Robert Seiringer. “Symmetry of Bipolaron Bound States for Small Coulomb Repulsion.” Communications in Mathematical Physics. Springer, 2013. https://doi.org/10.1007/s00220-012-1604-y. ieee: R. Frank, É. Lieb, and R. Seiringer, “Symmetry of bipolaron bound states for small Coulomb repulsion,” Communications in Mathematical Physics, vol. 319, no. 2. Springer, pp. 557–573, 2013. ista: Frank R, Lieb É, Seiringer R. 2013. Symmetry of bipolaron bound states for small Coulomb repulsion. Communications in Mathematical Physics. 319(2), 557–573. mla: Frank, Rupert, et al. “Symmetry of Bipolaron Bound States for Small Coulomb Repulsion.” Communications in Mathematical Physics, vol. 319, no. 2, Springer, 2013, pp. 557–73, doi:10.1007/s00220-012-1604-y. short: R. Frank, É. Lieb, R. Seiringer, Communications in Mathematical Physics 319 (2013) 557–573. date_created: 2018-12-11T11:57:28Z date_published: 2013-04-01T00:00:00Z date_updated: 2021-01-12T06:57:17Z day: '01' doi: 10.1007/s00220-012-1604-y extern: 1 intvolume: ' 319' issue: '2' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1201.3954 month: '04' oa: 1 page: 557 - 573 publication: Communications in Mathematical Physics publication_status: published publisher: Springer publist_id: '4522' quality_controlled: 0 status: public title: Symmetry of bipolaron bound states for small Coulomb repulsion type: journal_article volume: 319 year: '2013' ... --- _id: '2408' abstract: - lang: eng text: We investigate the low-energy excitation spectrum of a Bose gas confined in a trap, with weak long-range repulsive interactions. In particular, we prove that the spectrum can be described in terms of the eigenvalues of an effective one-particle operator, as predicted by the Bogoliubov approximation. author: - first_name: Philip full_name: Grech, Philip last_name: Grech - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Grech P, Seiringer R. The excitation spectrum for weakly interacting Bosons in a trap. Communications in Mathematical Physics. 2013;322(2):559-591. doi:10.1007/s00220-013-1736-8 apa: Grech, P., & Seiringer, R. (2013). The excitation spectrum for weakly interacting Bosons in a trap. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-013-1736-8 chicago: Grech, Philip, and Robert Seiringer. “The Excitation Spectrum for Weakly Interacting Bosons in a Trap.” Communications in Mathematical Physics. Springer, 2013. https://doi.org/10.1007/s00220-013-1736-8. ieee: P. Grech and R. Seiringer, “The excitation spectrum for weakly interacting Bosons in a trap,” Communications in Mathematical Physics, vol. 322, no. 2. Springer, pp. 559–591, 2013. ista: Grech P, Seiringer R. 2013. The excitation spectrum for weakly interacting Bosons in a trap. Communications in Mathematical Physics. 322(2), 559–591. mla: Grech, Philip, and Robert Seiringer. “The Excitation Spectrum for Weakly Interacting Bosons in a Trap.” Communications in Mathematical Physics, vol. 322, no. 2, Springer, 2013, pp. 559–91, doi:10.1007/s00220-013-1736-8. short: P. Grech, R. Seiringer, Communications in Mathematical Physics 322 (2013) 559–591. date_created: 2018-12-11T11:57:29Z date_published: 2013-09-01T00:00:00Z date_updated: 2021-01-12T06:57:18Z day: '01' doi: 10.1007/s00220-013-1736-8 extern: 1 intvolume: ' 322' issue: '2' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1205.5259 month: '09' oa: 1 page: 559 - 591 publication: Communications in Mathematical Physics publication_status: published publisher: Springer publist_id: '4518' quality_controlled: 0 status: public title: The excitation spectrum for weakly interacting Bosons in a trap type: journal_article volume: 322 year: '2013' ... --- _id: '2412' abstract: - lang: eng text: 'Background: The CRISPR/Cas system is known to act as an adaptive and heritable immune system in Eubacteria and Archaea. Immunity is encoded in an array of spacer sequences. Each spacer can provide specific immunity to invasive elements that carry the same or a similar sequence. Even in closely related strains, spacer content is very dynamic and evolves quickly. Standard models of nucleotide evolutioncannot be applied to quantify its rate of change since processes other than single nucleotide changes determine its evolution.Methods We present probabilistic models that are specific for spacer content evolution. They account for the different processes of insertion and deletion. Insertions can be constrained to occur on one end only or are allowed to occur throughout the array. One deletion event can affect one spacer or a whole fragment of adjacent spacers. Parameters of the underlying models are estimated for a pair of arrays by maximum likelihood using explicit ancestor enumeration.Results Simulations show that parameters are well estimated on average under the models presented here. There is a bias in the rate estimation when including fragment deletions. The models also estimate times between pairs of strains. But with increasing time, spacer overlap goes to zero, and thus there is an upper bound on the distance that can be estimated. Spacer content similarities are displayed in a distance based phylogeny using the estimated times.We use the presented models to analyze different Yersinia pestis data sets and find that the results among them are largely congruent. The models also capture the variation in diversity of spacers among the data sets. A comparison of spacer-based phylogenies and Cas gene phylogenies shows that they resolve very different time scales for this data set.Conclusions The simulations and data analyses show that the presented models are useful for quantifying spacer content evolution and for displaying spacer content similarities of closely related strains in a phylogeny. This allows for comparisons of different CRISPR arrays or for comparisons between CRISPR arrays and nucleotide substitution rates.' author: - first_name: Anne full_name: Kupczok, Anne id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87 last_name: Kupczok - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: Kupczok A, Bollback JP. Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. 2013;13(1):54-54. doi:10.1186/1471-2148-13-54 apa: Kupczok, A., & Bollback, J. P. (2013). Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-13-54 chicago: Kupczok, Anne, and Jonathan P Bollback. “Probabilistic Models for CRISPR Spacer Content Evolution .” BMC Evolutionary Biology. BioMed Central, 2013. https://doi.org/10.1186/1471-2148-13-54. ieee: A. Kupczok and J. P. Bollback, “Probabilistic models for CRISPR spacer content evolution ,” BMC Evolutionary Biology, vol. 13, no. 1. BioMed Central, pp. 54–54, 2013. ista: Kupczok A, Bollback JP. 2013. Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. 13(1), 54–54. mla: Kupczok, Anne, and Jonathan P. Bollback. “Probabilistic Models for CRISPR Spacer Content Evolution .” BMC Evolutionary Biology, vol. 13, no. 1, BioMed Central, 2013, pp. 54–54, doi:10.1186/1471-2148-13-54. short: A. Kupczok, J.P. Bollback, BMC Evolutionary Biology 13 (2013) 54–54. date_created: 2018-12-11T11:57:31Z date_published: 2013-02-26T00:00:00Z date_updated: 2021-01-12T06:57:20Z day: '26' ddc: - '576' department: - _id: JoBo doi: 10.1186/1471-2148-13-54 file: - access_level: open_access checksum: 029c7e0b198c19312b66ecce3cabb22f content_type: application/pdf creator: system date_created: 2018-12-12T10:17:15Z date_updated: 2020-07-14T12:45:40Z file_id: '5268' file_name: IST-2015-397-v1+1_1471-2148-13-54.pdf file_size: 518729 relation: main_file file_date_updated: 2020-07-14T12:45:40Z has_accepted_license: '1' intvolume: ' 13' issue: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 54 - 54 publication: BMC Evolutionary Biology publication_status: published publisher: BioMed Central publist_id: '4514' pubrep_id: '397' quality_controlled: '1' scopus_import: 1 status: public title: 'Probabilistic models for CRISPR spacer content evolution ' 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: 13 year: '2013' ... --- _id: '2413' abstract: - lang: eng text: 'Progress in understanding the global brain dynamics has remained slow to date in large part because of the highly multiscale nature of brain activity. Indeed, normal brain dynamics is characterized by complex interactions between multiple levels: from the microscopic scale of single neurons to the mesoscopic level of local groups of neurons, and finally to the macroscopic level of the whole brain. Among the most difficult tasks are those of identifying which scales are significant for a given particular function and describing how the scales affect each other. It is important to realize that the scales of time and space are linked together, or even intertwined, and that causal inference is far more ambiguous between than within levels. We approach this problem from the perspective of our recent work on simultaneous recording from micro- and macroelectrodes in the human brain. We propose a physiological description of these multilevel interactions, based on phase–amplitude coupling of neuronal oscillations that operate at multiple frequencies and on different spatial scales. Specifically, the amplitude of the oscillations on a particular spatial scale is modulated by phasic variations in neuronal excitability induced by lower frequency oscillations that emerge on a larger spatial scale. Following this general principle, it is possible to scale up or scale down the multiscale brain dynamics. It is expected that large-scale network oscillations in the low-frequency range, mediating downward effects, may play an important role in attention and consciousness.' alternative_title: - Reviews of Nonlinear Dynamics and Complexity author: - first_name: Mario full_name: Valderrama, Mario last_name: Valderrama - first_name: Vicente full_name: Botella Soler, Vicente id: 421234E8-F248-11E8-B48F-1D18A9856A87 last_name: Botella Soler orcid: 0000-0002-8790-1914 - first_name: Michel full_name: Le Van Quyen, Michel last_name: Le Van Quyen citation: ama: 'Valderrama M, Botella Soler V, Le Van Quyen M. Neuronal oscillations scale up and scale down the brain dynamics . In: Meyer M, Pesenson Z, eds. Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain. Wiley-VCH; 2013. doi:10.1002/9783527671632.ch08' apa: 'Valderrama, M., Botella Soler, V., & Le Van Quyen, M. (2013). Neuronal oscillations scale up and scale down the brain dynamics . In M. Meyer & Z. Pesenson (Eds.), Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain. Wiley-VCH. https://doi.org/10.1002/9783527671632.ch08' chicago: 'Valderrama, Mario, Vicente Botella Soler, and Michel Le Van Quyen. “Neuronal Oscillations Scale up and Scale down the Brain Dynamics .” In Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, edited by Misha Meyer and Z. Pesenson. Wiley-VCH, 2013. https://doi.org/10.1002/9783527671632.ch08.' ieee: 'M. Valderrama, V. Botella Soler, and M. Le Van Quyen, “Neuronal oscillations scale up and scale down the brain dynamics ,” in Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, M. Meyer and Z. Pesenson, Eds. Wiley-VCH, 2013.' ista: 'Valderrama M, Botella Soler V, Le Van Quyen M. 2013.Neuronal oscillations scale up and scale down the brain dynamics . In: Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain. Reviews of Nonlinear Dynamics and Complexity, .' mla: 'Valderrama, Mario, et al. “Neuronal Oscillations Scale up and Scale down the Brain Dynamics .” Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, edited by Misha Meyer and Z. Pesenson, Wiley-VCH, 2013, doi:10.1002/9783527671632.ch08.' short: 'M. Valderrama, V. Botella Soler, M. Le Van Quyen, in:, M. Meyer, Z. Pesenson (Eds.), Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, Wiley-VCH, 2013.' date_created: 2018-12-11T11:57:31Z date_published: 2013-08-01T00:00:00Z date_updated: 2021-01-12T06:57:20Z day: '01' department: - _id: GaTk doi: 10.1002/9783527671632.ch08 editor: - first_name: Misha full_name: Meyer, Misha last_name: Meyer - first_name: Z. full_name: Pesenson, Z. last_name: Pesenson language: - iso: eng month: '08' oa_version: None publication: 'Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain' publication_identifier: eisbn: - '9783527671632' isbn: - '9783527411986 ' publication_status: published publisher: Wiley-VCH publist_id: '4513' quality_controlled: '1' scopus_import: 1 status: public title: 'Neuronal oscillations scale up and scale down the brain dynamics ' type: book_chapter user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2410' abstract: - lang: eng text: 'Here, we describe a novel virulent bacteriophage that infects Bacillus weihenstephanensis, isolated from soil in Austria. It is the first phage to be discovered that infects this species. Here, we present the complete genome sequence of this podovirus. ' author: - first_name: Rodrigo A full_name: Fernandes Redondo, Rodrigo A id: 409D5C96-F248-11E8-B48F-1D18A9856A87 last_name: Fernandes Redondo orcid: 0000-0002-5837-2793 - first_name: Anne full_name: Kupczok, Anne id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87 last_name: Kupczok - first_name: Gertraud full_name: Stift, Gertraud id: 2DB195CA-F248-11E8-B48F-1D18A9856A87 last_name: Stift - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements. 2013;1(3). doi:10.1128/genomeA.00216-13 apa: Fernandes Redondo, R. A., Kupczok, A., Stift, G., & Bollback, J. P. (2013). Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements. American Society for Microbiology. https://doi.org/10.1128/genomeA.00216-13 chicago: Fernandes Redondo, Rodrigo A, Anne Kupczok, Gertraud Stift, and Jonathan P Bollback. “Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus Weihenstephanensis.” Genome Announcements. American Society for Microbiology, 2013. https://doi.org/10.1128/genomeA.00216-13. ieee: R. A. Fernandes Redondo, A. Kupczok, G. Stift, and J. P. Bollback, “Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis,” Genome Announcements, vol. 1, no. 3. American Society for Microbiology, 2013. ista: Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. 2013. Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements. 1(3). mla: Fernandes Redondo, Rodrigo A., et al. “Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus Weihenstephanensis.” Genome Announcements, vol. 1, no. 3, American Society for Microbiology, 2013, doi:10.1128/genomeA.00216-13. short: R.A. Fernandes Redondo, A. Kupczok, G. Stift, J.P. Bollback, Genome Announcements 1 (2013). date_created: 2018-12-11T11:57:30Z date_published: 2013-06-13T00:00:00Z date_updated: 2021-01-12T06:57:19Z day: '13' ddc: - '576' department: - _id: JoBo - _id: LifeSc doi: 10.1128/genomeA.00216-13 file: - access_level: open_access checksum: 0751ec74b695567e0cdf02aaf9c26829 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:36Z date_updated: 2020-07-14T12:45:40Z file_id: '5291' file_name: IST-2015-398-v1+1_Genome_Announc.-2013-Redondo-.pdf file_size: 130026 relation: main_file file_date_updated: 2020-07-14T12:45:40Z has_accepted_license: '1' intvolume: ' 1' issue: '3' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Genome Announcements publication_status: published publisher: American Society for Microbiology publist_id: '4516' pubrep_id: '398' quality_controlled: '1' scopus_import: 1 status: public title: Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2013' ... --- _id: '2447' abstract: - lang: eng text: "Separation logic (SL) has gained widespread popularity because of its ability to succinctly express complex invariants of a program’s heap configurations. Several specialized provers have been developed for decidable SL fragments. However, these provers cannot be easily extended or combined with solvers for other theories that are important in program verification, e.g., linear arithmetic. In this paper, we present a reduction of decidable SL fragments to a decidable first-order theory that fits well into the satisfiability modulo theories (SMT) framework. We show how to use this reduction to automate satisfiability, entailment, frame inference, and abduction problems for separation logic using SMT solvers. Our approach provides a simple method of integrating separation logic into existing verification tools that provide SMT backends, and an elegant way of combining SL fragments with other decidable first-order theories. We implemented this approach in a verification tool and applied it to heap-manipulating programs whose verification involves reasoning in theory combinations.\r\n" alternative_title: - LNCS article_processing_charge: No author: - first_name: Ruzica full_name: Piskac, Ruzica last_name: Piskac - first_name: Thomas full_name: Wies, Thomas id: 447BFB88-F248-11E8-B48F-1D18A9856A87 last_name: Wies - first_name: Damien full_name: Zufferey, Damien id: 4397AC76-F248-11E8-B48F-1D18A9856A87 last_name: Zufferey orcid: 0000-0002-3197-8736 citation: ama: Piskac R, Wies T, Zufferey D. Automating separation logic using SMT. 2013;8044:773-789. doi:10.1007/978-3-642-39799-8_54 apa: 'Piskac, R., Wies, T., & Zufferey, D. (2013). Automating separation logic using SMT. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_54' chicago: Piskac, Ruzica, Thomas Wies, and Damien Zufferey. “Automating Separation Logic Using SMT.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-39799-8_54. ieee: R. Piskac, T. Wies, and D. Zufferey, “Automating separation logic using SMT,” vol. 8044. Springer, pp. 773–789, 2013. ista: Piskac R, Wies T, Zufferey D. 2013. Automating separation logic using SMT. 8044, 773–789. mla: Piskac, Ruzica, et al. Automating Separation Logic Using SMT. Vol. 8044, Springer, 2013, pp. 773–89, doi:10.1007/978-3-642-39799-8_54. short: R. Piskac, T. Wies, D. Zufferey, 8044 (2013) 773–789. conference: end_date: 2013-07-19 location: St. Petersburg, Russia name: 'CAV: Computer Aided Verification' start_date: 2013-07-13 date_created: 2018-12-11T11:57:43Z date_published: 2013-07-01T00:00:00Z date_updated: 2020-08-11T10:09:47Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-642-39799-8_54 file: - access_level: open_access checksum: 2e866932ab688f47ecd504acb4d5c7d4 content_type: application/pdf creator: dernst date_created: 2020-05-15T11:13:01Z date_updated: 2020-07-14T12:45:41Z file_id: '7859' file_name: 2013_CAV_Piskac.pdf file_size: 309182 relation: main_file file_date_updated: 2020-07-14T12:45:41Z has_accepted_license: '1' intvolume: ' 8044' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 773 - 789 publication_status: published publisher: Springer publist_id: '4456' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Automating separation logic using SMT type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8044 year: '2013' ... --- _id: '2443' abstract: - lang: eng text: The mode of action of auxin is based on its non-uniform distribution within tissues and organs. Despite the wide use of several auxin analogues in research and agriculture, little is known about the specificity of different auxin-related transport and signalling processes towards these compounds. Using seedlings of Arabidopsis thaliana and suspension-cultured cells of Nicotiana tabacum (BY-2), the physiological activity of several auxin analogues was investigated, together with their capacity to induce auxin-dependent gene expression, to inhibit endocytosis and to be transported across the plasma membrane. This study shows that the specificity criteria for different auxin-related processes vary widely. Notably, the special behaviour of some synthetic auxin analogues suggests that they might be useful tools in investigations of the molecular mechanism of auxin action. Thus, due to their differential stimulatory effects on DR5 expression, indole-3-propionic (IPA) and 2,4,5-trichlorophenoxy acetic (2,4,5-T) acids can serve in studies of TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALLING F-BOX (TIR1/AFB)-mediated auxin signalling, and 5-fluoroindole-3-acetic acid (5-F-IAA) can help to discriminate between transcriptional and non-transcriptional pathways of auxin signalling. The results demonstrate that the major determinants for the auxin-like physiological potential of a particular compound are very complex and involve its chemical and metabolic stability, its ability to distribute in tissues in a polar manner and its activity towards auxin signalling machinery. acknowledgement: The authors thank Dr Christian Luschnig (University of Natural Resources and Life Sciences (BOKU), Vienna, Austria) for the anti-PIN2 antibody, Professor Mark Estelle (University of California, San Diego, CA, USA) for tir1-1 mutant seeds and, last but not least, to Dr David Morris for critical reading of the manuscript. We also thank Markéta Pařezová and Jana Stýblová for excellent technical assistance. This work was supported by the Grant Agency of the Czech Republic (P305/11/0797 to E.Z. and 13-40637S to J.F.), the Central European Institute of Technology project CZ.1.05/1.1.00/02.0068 from the European Regional Development Fund and by a European Research Council starting independent research grant ERC-2011-StG-20101109-PSDP (to J.F.). article_processing_charge: No article_type: original author: - first_name: Sibu full_name: Simon, Sibu id: 4542EF9A-F248-11E8-B48F-1D18A9856A87 last_name: Simon orcid: 0000-0002-1998-6741 - first_name: Martin full_name: Kubeš, Martin last_name: Kubeš - first_name: Pawel full_name: Baster, Pawel id: 3028BD74-F248-11E8-B48F-1D18A9856A87 last_name: Baster - first_name: Stéphanie full_name: Robert, Stéphanie last_name: Robert - first_name: Petre full_name: Dobrev, Petre last_name: Dobrev - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová citation: ama: 'Simon S, Kubeš M, Baster P, et al. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. New Phytologist. 2013;200(4):1034-1048. doi:10.1111/nph.12437' apa: 'Simon, S., Kubeš, M., Baster, P., Robert, S., Dobrev, P., Friml, J., … Zažímalová, E. (2013). Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. New Phytologist. Wiley. https://doi.org/10.1111/nph.12437' chicago: 'Simon, Sibu, Martin Kubeš, Pawel Baster, Stéphanie Robert, Petre Dobrev, Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” New Phytologist. Wiley, 2013. https://doi.org/10.1111/nph.12437.' ieee: 'S. Simon et al., “Defining the selectivity of processes along the auxin response chain: A study using auxin analogues,” New Phytologist, vol. 200, no. 4. Wiley, pp. 1034–1048, 2013.' ista: 'Simon S, Kubeš M, Baster P, Robert S, Dobrev P, Friml J, Petrášek J, Zažímalová E. 2013. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. New Phytologist. 200(4), 1034–1048.' mla: 'Simon, Sibu, et al. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” New Phytologist, vol. 200, no. 4, Wiley, 2013, pp. 1034–48, doi:10.1111/nph.12437.' short: S. Simon, M. Kubeš, P. Baster, S. Robert, P. Dobrev, J. Friml, J. Petrášek, E. Zažímalová, New Phytologist 200 (2013) 1034–1048. date_created: 2018-12-11T11:57:41Z date_published: 2013-12-01T00:00:00Z date_updated: 2022-06-07T08:57:52Z day: '01' department: - _id: JiFr doi: 10.1111/nph.12437 ec_funded: 1 intvolume: ' 200' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/nph.12437 month: '12' oa: 1 oa_version: Published Version page: 1034 - 1048 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: New Phytologist publication_status: published publisher: Wiley publist_id: '4460' quality_controlled: '1' scopus_import: '1' status: public title: 'Defining the selectivity of processes along the auxin response chain: A study using auxin analogues' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 200 year: '2013' ... --- _id: '2446' abstract: - lang: eng text: The model-checking problem for probabilistic systems crucially relies on the translation of LTL to deterministic Rabin automata (DRW). Our recent Safraless translation [KE12, GKE12] for the LTL(F,G) fragment produces smaller automata as compared to the traditional approach. In this work, instead of DRW we consider deterministic automata with acceptance condition given as disjunction of generalized Rabin pairs (DGRW). The Safraless translation of LTL(F,G) formulas to DGRW results in smaller automata as compared to DRW. We present algorithms for probabilistic model-checking as well as game solving for DGRW conditions. Our new algorithms lead to improvement both in terms of theoretical bounds as well as practical evaluation. We compare PRISM with and without our new translation, and show that the new translation leads to significant improvements. 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: Andreas full_name: Gaiser, Andreas last_name: Gaiser - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 citation: ama: Chatterjee K, Gaiser A, Kretinsky J. Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. 2013;8044:559-575. doi:10.1007/978-3-642-39799-8_37 apa: 'Chatterjee, K., Gaiser, A., & Kretinsky, J. (2013). Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_37' chicago: Chatterjee, Krishnendu, Andreas Gaiser, and Jan Kretinsky. “Automata with Generalized Rabin Pairs for Probabilistic Model Checking and LTL Synthesis.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-39799-8_37. ieee: K. Chatterjee, A. Gaiser, and J. Kretinsky, “Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis,” vol. 8044. Springer, pp. 559–575, 2013. ista: Chatterjee K, Gaiser A, Kretinsky J. 2013. Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. 8044, 559–575. mla: Chatterjee, Krishnendu, et al. Automata with Generalized Rabin Pairs for Probabilistic Model Checking and LTL Synthesis. Vol. 8044, Springer, 2013, pp. 559–75, doi:10.1007/978-3-642-39799-8_37. short: K. Chatterjee, A. Gaiser, J. Kretinsky, 8044 (2013) 559–575. conference: end_date: 2013-07-19 location: St. Petersburg, Russia name: 'CAV: Computer Aided Verification' start_date: 2013-07-13 date_created: 2018-12-11T11:57:42Z date_published: 2013-07-01T00:00:00Z date_updated: 2020-08-11T10:09:47Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-642-39799-8_37 ec_funded: 1 external_id: arxiv: - '1304.5281' intvolume: ' 8044' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1304.5281 month: '07' oa: 1 oa_version: Preprint page: 559 - 575 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication_status: published publisher: Springer publist_id: '4457' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8044 year: '2013' ... --- _id: '2444' abstract: - lang: eng text: 'We consider two core algorithmic problems for probabilistic verification: the maximal end-component decomposition and the almost-sure reachability set computation for Markov decision processes (MDPs). For MDPs with treewidth k, we present two improved static algorithms for both the problems that run in time O(n·k 2.38·2k ) and O(m·logn· k), respectively, where n is the number of states and m is the number of edges, significantly improving the previous known O(n·k·√n· k) bound for low treewidth. We also present decremental algorithms for both problems for MDPs with constant treewidth that run in amortized logarithmic time, which is a huge improvement over the previously known algorithms that require amortized linear time.' 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: Jakub full_name: Ła̧Cki, Jakub last_name: Ła̧Cki citation: ama: Chatterjee K, Ła̧Cki J. Faster algorithms for Markov decision processes with low treewidth. 2013;8044:543-558. doi:10.1007/978-3-642-39799-8_36 apa: 'Chatterjee, K., & Ła̧Cki, J. (2013). Faster algorithms for Markov decision processes with low treewidth. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_36' chicago: Chatterjee, Krishnendu, and Jakub Ła̧Cki. “Faster Algorithms for Markov Decision Processes with Low Treewidth.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-39799-8_36. ieee: K. Chatterjee and J. Ła̧Cki, “Faster algorithms for Markov decision processes with low treewidth,” vol. 8044. Springer, pp. 543–558, 2013. ista: Chatterjee K, Ła̧Cki J. 2013. Faster algorithms for Markov decision processes with low treewidth. 8044, 543–558. mla: Chatterjee, Krishnendu, and Jakub Ła̧Cki. Faster Algorithms for Markov Decision Processes with Low Treewidth. Vol. 8044, Springer, 2013, pp. 543–58, doi:10.1007/978-3-642-39799-8_36. short: K. Chatterjee, J. Ła̧Cki, 8044 (2013) 543–558. conference: end_date: 2013-07-19 location: St. Petersburg, Russia name: 'CAV: Computer Aided Verification' start_date: 2013-07-13 date_created: 2018-12-11T11:57:42Z date_published: 2013-07-01T00:00:00Z date_updated: 2020-08-11T10:09:47Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-642-39799-8_36 ec_funded: 1 external_id: arxiv: - '1304.0084' intvolume: ' 8044' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1304.0084 month: '07' oa: 1 oa_version: Preprint page: 543 - 558 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication_status: published publisher: Springer publist_id: '4459' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Faster algorithms for Markov decision processes with low treewidth type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8044 year: '2013' ... --- _id: '2449' abstract: - lang: eng text: 'Intracellular protein routing is mediated by vesicular transport which is tightly regulated in eukaryotes. The protein and lipid homeostasis depends on coordinated delivery of de novo synthesized or recycled cargoes to the plasma membrane by exocytosis and their subsequent removal by rerouting them for recycling or degradation. Here, we report the characterization of protein affected trafficking 3 (pat3) mutant that we identified by an epifluorescence-based forward genetic screen for mutants defective in subcellular distribution of Arabidopsis auxin transporter PIN1–GFP. While pat3 displays largely normal plant morphology and development in nutrient-rich conditions, it shows strong ectopic intracellular accumulations of different plasma membrane cargoes in structures that resemble prevacuolar compartments (PVC) with an aberrant morphology. Genetic mapping revealed that pat3 is defective in vacuolar protein sorting 35A (VPS35A), a putative subunit of the retromer complex that mediates retrograde trafficking between the PVC and trans-Golgi network. Similarly, a mutant defective in another retromer subunit, vps29, shows comparable subcellular defects in PVC morphology and protein accumulation. Thus, our data provide evidence that the retromer components VPS35A and VPS29 are essential for normal PVC morphology and normal trafficking of plasma membrane proteins in plants. In addition, we show that, out of the three VPS35 retromer subunits present in Arabidopsis thaliana genome, the VPS35 homolog A plays a prevailing role in trafficking to the lytic vacuole, presenting another level of complexity in the retromer-dependent vacuolar sorting. ' author: - first_name: Tomasz full_name: Nodzyński, Tomasz last_name: Nodzyński - first_name: Murguel full_name: Feraru, Murguel last_name: Feraru - first_name: Sibylle full_name: Hirsch, Sibylle last_name: Hirsch - first_name: Riet full_name: De Rycke, Riet last_name: De Rycke - first_name: Claudiu full_name: Nicuales, Claudiu last_name: Nicuales - first_name: Jelle full_name: Van Leene, Jelle last_name: Van Leene - first_name: Geert full_name: De Jaeger, Geert last_name: De Jaeger - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Nodzyński T, Feraru M, Hirsch S, et al. Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis. Molecular Plant. 2013;6(6):1849-1862. doi:10.1093/mp/sst044 apa: Nodzyński, T., Feraru, M., Hirsch, S., De Rycke, R., Nicuales, C., Van Leene, J., … Friml, J. (2013). Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis. Molecular Plant. Cell Press. https://doi.org/10.1093/mp/sst044 chicago: Nodzyński, Tomasz, Murguel Feraru, Sibylle Hirsch, Riet De Rycke, Claudiu Nicuales, Jelle Van Leene, Geert De Jaeger, Steffen Vanneste, and Jiří Friml. “Retromer Subunits VPS35A and VPS29 Mediate Prevacuolar Compartment (PVC) Function in Arabidopsis.” Molecular Plant. Cell Press, 2013. https://doi.org/10.1093/mp/sst044. ieee: T. Nodzyński et al., “Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis,” Molecular Plant, vol. 6, no. 6. Cell Press, pp. 1849–1862, 2013. ista: Nodzyński T, Feraru M, Hirsch S, De Rycke R, Nicuales C, Van Leene J, De Jaeger G, Vanneste S, Friml J. 2013. Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis. Molecular Plant. 6(6), 1849–1862. mla: Nodzyński, Tomasz, et al. “Retromer Subunits VPS35A and VPS29 Mediate Prevacuolar Compartment (PVC) Function in Arabidopsis.” Molecular Plant, vol. 6, no. 6, Cell Press, 2013, pp. 1849–62, doi:10.1093/mp/sst044. short: T. Nodzyński, M. Feraru, S. Hirsch, R. De Rycke, C. Nicuales, J. Van Leene, G. De Jaeger, S. Vanneste, J. Friml, Molecular Plant 6 (2013) 1849–1862. date_created: 2018-12-11T11:57:44Z date_published: 2013-11-01T00:00:00Z date_updated: 2021-01-12T06:57:33Z day: '01' department: - _id: JiFr doi: 10.1093/mp/sst044 intvolume: ' 6' issue: '6' language: - iso: eng month: '11' oa_version: None page: 1849 - 1862 publication: Molecular Plant publication_status: published publisher: Cell Press publist_id: '4454' quality_controlled: '1' scopus_import: 1 status: public title: Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2013' ... --- _id: '2452' abstract: - lang: eng text: 'Background: Abundance and distribution of the plant hormone auxin play important roles in plant development. Besides other metabolic processes, various auxin carriers control the cellular level of active auxin and, hence, are major regulators of cellular auxin homeostasis. Despite the developmental importance of auxin transporters, a simple medium-to-high throughput approach to assess carrier activities is still missing. Here we show that carrier driven depletion of cellular auxin correlates with reduced nuclear auxin signaling in tobacco Bright Yellow-2 (BY-2) cell cultures.Results: We developed an easy to use transient single-cell-based system to detect carrier activity. We use the relative changes in signaling output of the auxin responsive promoter element DR5 to indirectly visualize auxin carrier activity. The feasibility of the transient approach was demonstrated by pharmacological and genetic interference with auxin signaling and transport. As a proof of concept, we provide visual evidence that the prominent auxin transport proteins PIN-FORMED (PIN)2 and PIN5 regulate cellular auxin homeostasis at the plasma membrane and endoplasmic reticulum (ER), respectively. Our data suggest that PIN2 and PIN5 have different sensitivities to the auxin transport inhibitor 1-naphthylphthalamic acid (NPA). Also the putative PIN-LIKES (PILS) auxin carrier activity at the ER is insensitive to NPA in our system, indicating that NPA blocks intercellular, but not intracellular auxin transport.Conclusions: This single-cell-based system is a useful tool by which the activity of putative auxin carriers, such as PINs, PILS and WALLS ARE THIN1 (WAT1), can be indirectly visualized in a medium-to-high throughput manner. Moreover, our single cell system might be useful to investigate also other hormonal signaling pathways, such as cytokinin.' author: - first_name: Elke full_name: Barbez, Elke last_name: Barbez - first_name: Martina full_name: Laňková, Martina last_name: Laňková - first_name: Markéta full_name: Pařezová, Markéta last_name: Pařezová - first_name: Alexis full_name: Maizel, Alexis last_name: Maizel - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Jürgen full_name: Kleine-Vehn, Jürgen last_name: Kleine Vehn citation: ama: Barbez E, Laňková M, Pařezová M, et al. Single-cell-based system to monitor carrier driven cellular auxin homeostasis. BMC Plant Biology. 2013;13(1). doi:10.1186/1471-2229-13-20 apa: Barbez, E., Laňková, M., Pařezová, M., Maizel, A., Zažímalová, E., Petrášek, J., … Kleine Vehn, J. (2013). Single-cell-based system to monitor carrier driven cellular auxin homeostasis. BMC Plant Biology. BioMed Central. https://doi.org/10.1186/1471-2229-13-20 chicago: Barbez, Elke, Martina Laňková, Markéta Pařezová, Alexis Maizel, Eva Zažímalová, Jan Petrášek, Jiří Friml, and Jürgen Kleine Vehn. “Single-Cell-Based System to Monitor Carrier Driven Cellular Auxin Homeostasis.” BMC Plant Biology. BioMed Central, 2013. https://doi.org/10.1186/1471-2229-13-20. ieee: E. Barbez et al., “Single-cell-based system to monitor carrier driven cellular auxin homeostasis,” BMC Plant Biology, vol. 13, no. 1. BioMed Central, 2013. ista: Barbez E, Laňková M, Pařezová M, Maizel A, Zažímalová E, Petrášek J, Friml J, Kleine Vehn J. 2013. Single-cell-based system to monitor carrier driven cellular auxin homeostasis. BMC Plant Biology. 13(1). mla: Barbez, Elke, et al. “Single-Cell-Based System to Monitor Carrier Driven Cellular Auxin Homeostasis.” BMC Plant Biology, vol. 13, no. 1, BioMed Central, 2013, doi:10.1186/1471-2229-13-20. short: E. Barbez, M. Laňková, M. Pařezová, A. Maizel, E. Zažímalová, J. Petrášek, J. Friml, J. Kleine Vehn, BMC Plant Biology 13 (2013). date_created: 2018-12-11T11:57:45Z date_published: 2013-02-01T00:00:00Z date_updated: 2021-01-12T06:57:34Z day: '01' doi: 10.1186/1471-2229-13-20 extern: 1 intvolume: ' 13' issue: '1' month: '02' publication: BMC Plant Biology publication_status: published publisher: BioMed Central publist_id: '4451' quality_controlled: 0 status: public title: Single-cell-based system to monitor carrier driven cellular auxin homeostasis type: journal_article volume: 13 year: '2013' ... --- _id: '2450' abstract: - lang: eng text: 'Understanding how hormones and genes interact to coordinate plant growth is a major challenge in developmental biology. The activities of auxin, ethylene, and cytokinin depend on cellular context and exhibit either synergistic or antagonistic interactions. Here we use experimentation and network construction to elucidate the role of the interaction of the POLARIS peptide (PLS) and the auxin efflux carrier PIN proteins in the crosstalk of three hormones (auxin, ethylene, and cytokinin) in Arabidopsis root development. In ethylene hypersignaling mutants such as polaris (pls), we show experimentally that expression of both PIN1 and PIN2 significantly increases. This relationship is analyzed in the context of the crosstalk between auxin, ethylene, and cytokinin: in pls, endogenous auxin, ethylene and cytokinin concentration decreases, approximately remains unchanged and increases, respectively. Experimental data are integrated into a hormonal crosstalk network through combination with information in literature. Network construction reveals that the regulation of both PIN1 and PIN2 is predominantly via ethylene signaling. In addition, it is deduced that the relationship between cytokinin and PIN1 and PIN2 levels implies a regulatory role of cytokinin in addition to its regulation to auxin, ethylene, and PLS levels. We discuss how the network of hormones and genes coordinates plant growth by simultaneously regulating the activities of auxin, ethylene, and cytokinin signaling pathways.hormonal crosstalk, root development, auxin flux, PIN proteins, PLS protein, signaling network' author: - first_name: Junli full_name: Liu, Junli last_name: Liu - first_name: Saher full_name: Menhi, Saher last_name: Menhi - first_name: Jennifer full_name: Topping, Jennifer last_name: Topping - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Keith full_name: Lindsey, Keith last_name: Lindsey citation: ama: Liu J, Menhi S, Topping J, Friml J, Lindsey K. Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development. Frontiers in Plant Science. 2013;4(75). doi:10.3389/fpls.2013.00075 apa: Liu, J., Menhi, S., Topping, J., Friml, J., & Lindsey, K. (2013). Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development. Frontiers in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2013.00075 chicago: Liu, Junli, Saher Menhi, Jennifer Topping, Jiří Friml, and Keith Lindsey. “Interaction of PLS and PIN and Hormonal Crosstalk in Arabidopsis Root Development.” Frontiers in Plant Science. Frontiers Research Foundation, 2013. https://doi.org/10.3389/fpls.2013.00075. ieee: J. Liu, S. Menhi, J. Topping, J. Friml, and K. Lindsey, “Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development,” Frontiers in Plant Science, vol. 4, no. 75. Frontiers Research Foundation, 2013. ista: Liu J, Menhi S, Topping J, Friml J, Lindsey K. 2013. Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development. Frontiers in Plant Science. 4(75). mla: Liu, Junli, et al. “Interaction of PLS and PIN and Hormonal Crosstalk in Arabidopsis Root Development.” Frontiers in Plant Science, vol. 4, no. 75, Frontiers Research Foundation, 2013, doi:10.3389/fpls.2013.00075. short: J. Liu, S. Menhi, J. Topping, J. Friml, K. Lindsey, Frontiers in Plant Science 4 (2013). date_created: 2018-12-11T11:57:44Z date_published: 2013-04-01T00:00:00Z date_updated: 2021-01-12T06:57:34Z day: '01' doi: 10.3389/fpls.2013.00075 extern: 1 intvolume: ' 4' issue: '75' month: '04' publication: Frontiers in Plant Science publication_status: published publisher: Frontiers Research Foundation publist_id: '4453' quality_controlled: 0 status: public title: Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development type: journal_article volume: 4 year: '2013' ... --- _id: '245' abstract: - lang: eng text: For given non-zero integers a, b, q we investigate the density of solutions (x; y) ∈ ℤ2 to the binary cubic congruence ax2 + by3 ≡ 0 mod q, and use it to establish the Manin conjecture for a singular del Pezzo surface of degree 2 defined over ℚ. author: - first_name: Stephan full_name: Baier, Stephan last_name: Baier - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 citation: ama: Baier S, Browning TD. Inhomogeneous cubic congruences and rational points on del Pezzo surfaces. Journal fur die Reine und Angewandte Mathematik. 2013;(680):69-151. doi:10.1515/crelle.2012.039 apa: Baier, S., & Browning, T. D. (2013). Inhomogeneous cubic congruences and rational points on del Pezzo surfaces. Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter. https://doi.org/10.1515/crelle.2012.039 chicago: Baier, Stephan, and Timothy D Browning. “Inhomogeneous Cubic Congruences and Rational Points on Del Pezzo Surfaces.” Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter, 2013. https://doi.org/10.1515/crelle.2012.039. ieee: S. Baier and T. D. Browning, “Inhomogeneous cubic congruences and rational points on del Pezzo surfaces,” Journal fur die Reine und Angewandte Mathematik, no. 680. Walter de Gruyter, pp. 69–151, 2013. ista: Baier S, Browning TD. 2013. Inhomogeneous cubic congruences and rational points on del Pezzo surfaces. Journal fur die Reine und Angewandte Mathematik. (680), 69–151. mla: Baier, Stephan, and Timothy D. Browning. “Inhomogeneous Cubic Congruences and Rational Points on Del Pezzo Surfaces.” Journal Fur Die Reine Und Angewandte Mathematik, no. 680, Walter de Gruyter, 2013, pp. 69–151, doi:10.1515/crelle.2012.039. short: S. Baier, T.D. Browning, Journal Fur Die Reine Und Angewandte Mathematik (2013) 69–151. date_created: 2018-12-11T11:45:24Z date_published: 2013-07-01T00:00:00Z date_updated: 2021-01-12T06:57:33Z day: '01' doi: 10.1515/crelle.2012.039 extern: 1 issue: '680' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1011.3434 month: '07' oa: 1 page: 69 - 151 publication: Journal fur die Reine und Angewandte Mathematik publication_status: published publisher: Walter de Gruyter publist_id: '7659' quality_controlled: 0 status: public title: Inhomogeneous cubic congruences and rational points on del Pezzo surfaces type: journal_article year: '2013' ... --- _id: '2457' author: - first_name: Tom full_name: Viaene, Tom last_name: Viaene - first_name: Charles full_name: Delwiche, Charles last_name: Delwiche - first_name: Stefan full_name: Rensing, Stefan last_name: Rensing - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Viaene T, Delwiche C, Rensing S, Friml J. Origin and evolution of PIN auxin transporters in the green lineage. Trends in Plant Science. 2013;18(1):5-10. doi:10.1016/j.tplants.2012.08.009 apa: Viaene, T., Delwiche, C., Rensing, S., & Friml, J. (2013). Origin and evolution of PIN auxin transporters in the green lineage. Trends in Plant Science. Cell Press. https://doi.org/10.1016/j.tplants.2012.08.009 chicago: Viaene, Tom, Charles Delwiche, Stefan Rensing, and Jiří Friml. “Origin and Evolution of PIN Auxin Transporters in the Green Lineage.” Trends in Plant Science. Cell Press, 2013. https://doi.org/10.1016/j.tplants.2012.08.009. ieee: T. Viaene, C. Delwiche, S. Rensing, and J. Friml, “Origin and evolution of PIN auxin transporters in the green lineage,” Trends in Plant Science, vol. 18, no. 1. Cell Press, pp. 5–10, 2013. ista: Viaene T, Delwiche C, Rensing S, Friml J. 2013. Origin and evolution of PIN auxin transporters in the green lineage. Trends in Plant Science. 18(1), 5–10. mla: Viaene, Tom, et al. “Origin and Evolution of PIN Auxin Transporters in the Green Lineage.” Trends in Plant Science, vol. 18, no. 1, Cell Press, 2013, pp. 5–10, doi:10.1016/j.tplants.2012.08.009. short: T. Viaene, C. Delwiche, S. Rensing, J. Friml, Trends in Plant Science 18 (2013) 5–10. date_created: 2018-12-11T11:57:46Z date_published: 2013-01-01T00:00:00Z date_updated: 2021-01-12T06:57:36Z day: '01' doi: 10.1016/j.tplants.2012.08.009 extern: '1' intvolume: ' 18' issue: '1' language: - iso: eng month: '01' oa_version: None page: 5 - 10 publication: Trends in Plant Science publication_status: published publisher: Cell Press publist_id: '4446' quality_controlled: '1' status: public title: Origin and evolution of PIN auxin transporters in the green lineage type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2013' ... --- _id: '246' abstract: - lang: eng text: Given an intersection of two quadrics X Pm1, with m > 9, the quantitative arithmetic of the set X(Q) is investigated under the assumption that the singular locus of X consists of a pair of conjugate singular points defined over Q(i). acknowledgement: "EP/E053262/1\tEngineering and Physical Sciences Research Council" author: - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Ritabrata full_name: Munshi, Ritabrata last_name: Munshi citation: ama: Browning TD, Munshi R. Rational points on singular intersections of quadrics. Compositio Mathematica. 2013;149(9):1457-1494. doi:10.1112/S0010437X13007185 apa: Browning, T. D., & Munshi, R. (2013). Rational points on singular intersections of quadrics. Compositio Mathematica. Cambridge University Press. https://doi.org/10.1112/S0010437X13007185 chicago: Browning, Timothy D, and Ritabrata Munshi. “Rational Points on Singular Intersections of Quadrics.” Compositio Mathematica. Cambridge University Press, 2013. https://doi.org/10.1112/S0010437X13007185. ieee: T. D. Browning and R. Munshi, “Rational points on singular intersections of quadrics,” Compositio Mathematica, vol. 149, no. 9. Cambridge University Press, pp. 1457–1494, 2013. ista: Browning TD, Munshi R. 2013. Rational points on singular intersections of quadrics. Compositio Mathematica. 149(9), 1457–1494. mla: Browning, Timothy D., and Ritabrata Munshi. “Rational Points on Singular Intersections of Quadrics.” Compositio Mathematica, vol. 149, no. 9, Cambridge University Press, 2013, pp. 1457–94, doi:10.1112/S0010437X13007185. short: T.D. Browning, R. Munshi, Compositio Mathematica 149 (2013) 1457–1494. date_created: 2018-12-11T11:45:25Z date_published: 2013-09-01T00:00:00Z date_updated: 2021-01-12T06:57:37Z day: '01' doi: 10.1112/S0010437X13007185 extern: 1 intvolume: ' 149' issue: '9' month: '09' page: 1457 - 1494 publication: Compositio Mathematica publication_status: published publisher: Cambridge University Press publist_id: '7658' quality_controlled: 0 status: public title: Rational points on singular intersections of quadrics type: journal_article volume: 149 year: '2013' ... --- _id: '2471' abstract: - lang: eng text: The impact of disulfide bonds on protein stability goes beyond simple equilibrium thermodynamics effects associated with the conformational entropy of the unfolded state. Indeed, disulfide crosslinks may play a role in the prevention of dysfunctional association and strongly affect the rates of irreversible enzyme inactivation, highly relevant in biotechnological applications. While these kinetic-stability effects remain poorly understood, by analogy with proposed mechanisms for processes of protein aggregation and fibrillogenesis, we propose that they may be determined by the properties of sparsely-populated, partially-unfolded intermediates. Here we report the successful design, on the basis of high temperature molecular-dynamics simulations, of six thermodynamically and kinetically stabilized variants of phytase from Citrobacter braakii (a biotechnologically important enzyme) with one, two or three engineered disulfides. Activity measurements and 3D crystal structure determination demonstrate that the engineered crosslinks do not cause dramatic alterations in the native structure. The inactivation kinetics for all the variants displays a strongly non-Arrhenius temperature dependence, with the time-scale for the irreversible denaturation process reaching a minimum at a given temperature within the range of the denaturation transition. We show this striking feature to be a signature of a key role played by a partially unfolded, intermediate state/ensemble. Energetic and mutational analyses confirm that the intermediate is highly unfolded (akin to a proposed critical intermediate in the misfolding of the prion protein), a result that explains the observed kinetic stabilization. Our results provide a rationale for the kinetic-stability consequences of disulfide-crosslink engineering and an experimental methodology to arrive at energetic/structural descriptions of the sparsely populated and elusive intermediates that play key roles in irreversible protein denaturation. article_number: e70013 author: - first_name: Inmaculada full_name: Sanchez Romero, Inmaculada id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87 last_name: Sanchez Romero - first_name: Antonio full_name: Ariza, Antonio last_name: Ariza - first_name: Keith full_name: Wilson, Keith last_name: Wilson - first_name: Michael full_name: Skjøt, Michael last_name: Skjøt - first_name: Jesper full_name: Vind, Jesper last_name: Vind - first_name: Leonardo full_name: De Maria, Leonardo last_name: De Maria - first_name: Lars full_name: Skov, Lars last_name: Skov - first_name: Jose full_name: Sánchez Ruiz, Jose last_name: Sánchez Ruiz citation: ama: Sanchez-Romero I, Ariza A, Wilson K, et al. Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. PLoS One. 2013;8(7). doi:10.1371/journal.pone.0070013 apa: Sanchez-Romero, I., Ariza, A., Wilson, K., Skjøt, M., Vind, J., De Maria, L., … Sánchez Ruiz, J. (2013). Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0070013 chicago: Sanchez-Romero, Inmaculada, Antonio Ariza, Keith Wilson, Michael Skjøt, Jesper Vind, Leonardo De Maria, Lars Skov, and Jose Sánchez Ruiz. “Mechanism of Protein Kinetic Stabilization by Engineered Disulfide Crosslinks.” PLoS One. Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0070013. ieee: I. Sanchez-Romero et al., “Mechanism of protein kinetic stabilization by engineered disulfide crosslinks,” PLoS One, vol. 8, no. 7. Public Library of Science, 2013. ista: Sanchez-Romero I, Ariza A, Wilson K, Skjøt M, Vind J, De Maria L, Skov L, Sánchez Ruiz J. 2013. Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. PLoS One. 8(7), e70013. mla: Sanchez-Romero, Inmaculada, et al. “Mechanism of Protein Kinetic Stabilization by Engineered Disulfide Crosslinks.” PLoS One, vol. 8, no. 7, e70013, Public Library of Science, 2013, doi:10.1371/journal.pone.0070013. short: I. Sanchez-Romero, A. Ariza, K. Wilson, M. Skjøt, J. Vind, L. De Maria, L. Skov, J. Sánchez Ruiz, PLoS One 8 (2013). date_created: 2018-12-11T11:57:51Z date_published: 2013-07-30T00:00:00Z date_updated: 2021-01-12T06:57:41Z day: '30' ddc: - '570' department: - _id: HaJa doi: 10.1371/journal.pone.0070013 file: - access_level: open_access checksum: c0c96cc76ed7ef0d036a31a7e33c9a37 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:07Z date_updated: 2020-07-14T12:45:41Z file_id: '5124' file_name: IST-2016-414-v1+1_journal.pone.0070013.pdf file_size: 1323666 relation: main_file file_date_updated: 2020-07-14T12:45:41Z has_accepted_license: '1' intvolume: ' 8' issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '4430' pubrep_id: '414' quality_controlled: '1' scopus_import: 1 status: public title: Mechanism of protein kinetic stabilization by engineered disulfide crosslinks 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: 8 year: '2013' ... --- _id: '2472' abstract: - lang: eng text: Plant-specific PIN-formed (PIN) efflux transporters for the plant hormone auxin are required for tissue-specific directional auxin transport and cellular auxin homeostasis. The Arabidopsis PIN protein family has been shown to play important roles in developmental processes such as embryogenesis, organogenesis, vascular tissue differentiation, root meristem patterning and tropic growth. Here we analyzed roles of the less characterised Arabidopsis PIN6 auxin transporter. PIN6 is auxin-inducible and is expressed during multiple auxin-regulated developmental processes. Loss of pin6 function interfered with primary root growth and lateral root development. Misexpression of PIN6 affected auxin transport and interfered with auxin homeostasis in other growth processes such as shoot apical dominance, lateral root primordia development, adventitious root formation, root hair outgrowth and root waving. These changes in auxin-regulated growth correlated with a reduction in total auxin transport as well as with an altered activity of DR5-GUS auxin response reporter. Overall, the data indicate that PIN6 regulates auxin homeostasis during plant development. article_number: e70069 author: - first_name: Christopher full_name: Cazzonelli, Christopher last_name: Cazzonelli - first_name: Marleen full_name: Vanstraelen, Marleen last_name: Vanstraelen - first_name: Sibu full_name: Simon, Sibu id: 4542EF9A-F248-11E8-B48F-1D18A9856A87 last_name: Simon orcid: 0000-0002-1998-6741 - first_name: Kuide full_name: Yin, Kuide last_name: Yin - first_name: Ashley full_name: Carron Arthur, Ashley last_name: Carron Arthur - first_name: Nazia full_name: Nisar, Nazia last_name: Nisar - first_name: Gauri full_name: Tarle, Gauri last_name: Tarle - first_name: Abby full_name: Cuttriss, Abby last_name: Cuttriss - first_name: Iain full_name: Searle, Iain last_name: Searle - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Ulrike full_name: Mathesius, Ulrike last_name: Mathesius - first_name: Josette full_name: Masle, Josette last_name: Masle - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Barry full_name: Pogson, Barry last_name: Pogson citation: ama: Cazzonelli C, Vanstraelen M, Simon S, et al. Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. PLoS One. 2013;8(7). doi:10.1371/journal.pone.0070069 apa: Cazzonelli, C., Vanstraelen, M., Simon, S., Yin, K., Carron Arthur, A., Nisar, N., … Pogson, B. (2013). Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0070069 chicago: Cazzonelli, Christopher, Marleen Vanstraelen, Sibu Simon, Kuide Yin, Ashley Carron Arthur, Nazia Nisar, Gauri Tarle, et al. “Role of the Arabidopsis PIN6 Auxin Transporter in Auxin Homeostasis and Auxin-Mediated Development.” PLoS One. Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0070069. ieee: C. Cazzonelli et al., “Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development,” PLoS One, vol. 8, no. 7. Public Library of Science, 2013. ista: Cazzonelli C, Vanstraelen M, Simon S, Yin K, Carron Arthur A, Nisar N, Tarle G, Cuttriss A, Searle I, Benková E, Mathesius U, Masle J, Friml J, Pogson B. 2013. Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. PLoS One. 8(7), e70069. mla: Cazzonelli, Christopher, et al. “Role of the Arabidopsis PIN6 Auxin Transporter in Auxin Homeostasis and Auxin-Mediated Development.” PLoS One, vol. 8, no. 7, e70069, Public Library of Science, 2013, doi:10.1371/journal.pone.0070069. short: C. Cazzonelli, M. Vanstraelen, S. Simon, K. Yin, A. Carron Arthur, N. Nisar, G. Tarle, A. Cuttriss, I. Searle, E. Benková, U. Mathesius, J. Masle, J. Friml, B. Pogson, PLoS One 8 (2013). date_created: 2018-12-11T11:57:52Z date_published: 2013-07-29T00:00:00Z date_updated: 2021-01-12T06:57:41Z day: '29' ddc: - '580' - '570' department: - _id: JiFr - _id: EvBe doi: 10.1371/journal.pone.0070069 ec_funded: 1 file: - access_level: open_access checksum: 3be71828b6c2ba9c90eb7056e3f7f57a content_type: application/pdf creator: system date_created: 2018-12-12T10:16:34Z date_updated: 2020-07-14T12:45:41Z file_id: '5222' file_name: IST-2015-393-v1+1_journal.pone.0070069.pdf file_size: 9003465 relation: main_file file_date_updated: 2020-07-14T12:45:41Z has_accepted_license: '1' intvolume: ' 8' issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 253FCA6A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '207362' name: Hormonal cross-talk in plant organogenesis - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '4431' pubrep_id: '393' quality_controlled: '1' scopus_import: 1 status: public title: Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development 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: 8 year: '2013' ... --- _id: '2470' abstract: - lang: eng text: Background:Auxin binding protein 1 (ABP1) is a putative auxin receptor and its function is indispensable for plant growth and development. ABP1 has been shown to be involved in auxin-dependent regulation of cell division and expansion, in plasma-membrane-related processes such as changes in transmembrane potential, and in the regulation of clathrin-dependent endocytosis. However, the ABP1-regulated downstream pathway remains elusive.Methodology/Principal Findings:Using auxin transport assays and quantitative analysis of cellular morphology we show that ABP1 regulates auxin efflux from tobacco BY-2 cells. The overexpression of ABP1can counterbalance increased auxin efflux and auxin starvation phenotypes caused by the overexpression of PIN auxin efflux carrier. Relevant mechanism involves the ABP1-controlled vesicle trafficking processes, including positive regulation of endocytosis of PIN auxin efflux carriers, as indicated by fluorescence recovery after photobleaching (FRAP) and pharmacological manipulations.Conclusions/Significance:The findings indicate the involvement of ABP1 in control of rate of auxin transport across plasma membrane emphasizing the role of ABP1 in regulation of PIN activity at the plasma membrane, and highlighting the relevance of ABP1 for the formation of developmentally important, PIN-dependent auxin gradients. article_number: e70050 author: - first_name: Milada full_name: Čovanová, Milada last_name: Čovanová - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Jan full_name: Rychtář, Jan last_name: Rychtář - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová citation: ama: Čovanová M, Sauer M, Rychtář J, Friml J, Petrášek J, Zažímalová E. Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells. PLoS One. 2013;8(7). doi:10.1371/journal.pone.0070050 apa: Čovanová, M., Sauer, M., Rychtář, J., Friml, J., Petrášek, J., & Zažímalová, E. (2013). Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0070050 chicago: Čovanová, Milada, Michael Sauer, Jan Rychtář, Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Overexpression of the Auxin Binding PROTEIN1 Modulates PIN-Dependent Auxin Transport in Tobacco Cells.” PLoS One. Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0070050. ieee: M. Čovanová, M. Sauer, J. Rychtář, J. Friml, J. Petrášek, and E. Zažímalová, “Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells,” PLoS One, vol. 8, no. 7. Public Library of Science, 2013. ista: Čovanová M, Sauer M, Rychtář J, Friml J, Petrášek J, Zažímalová E. 2013. Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells. PLoS One. 8(7), e70050. mla: Čovanová, Milada, et al. “Overexpression of the Auxin Binding PROTEIN1 Modulates PIN-Dependent Auxin Transport in Tobacco Cells.” PLoS One, vol. 8, no. 7, e70050, Public Library of Science, 2013, doi:10.1371/journal.pone.0070050. short: M. Čovanová, M. Sauer, J. Rychtář, J. Friml, J. Petrášek, E. Zažímalová, PLoS One 8 (2013). date_created: 2018-12-11T11:57:51Z date_published: 2013-07-23T00:00:00Z date_updated: 2021-01-12T06:57:40Z day: '23' ddc: - '570' department: - _id: JiFr doi: 10.1371/journal.pone.0070050 file: - access_level: open_access checksum: 2d47ef47616ef4de1d517d146548184e content_type: application/pdf creator: system date_created: 2018-12-12T10:08:21Z date_updated: 2020-07-14T12:45:41Z file_id: '4681' file_name: IST-2016-413-v1+1_journal.pone.0070050.pdf file_size: 2294955 relation: main_file file_date_updated: 2020-07-14T12:45:41Z has_accepted_license: '1' intvolume: ' 8' issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '4432' pubrep_id: '413' quality_controlled: '1' scopus_import: 1 status: public title: Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells 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: 8 year: '2013' ... --- _id: '2466' abstract: - lang: eng text: 'We introduce a new method for efficiently simulating liquid with extreme amounts of spatial adaptivity. Our method combines several key components to drastically speed up the simulation of large-scale fluid phenomena: We leverage an alternative Eulerian tetrahedral mesh discretization to significantly reduce the complexity of the pressure solve while increasing the robustness with respect to element quality and removing the possibility of locking. Next, we enable subtle free-surface phenomena by deriving novel second-order boundary conditions consistent with our discretization. We couple this discretization with a spatially adaptive Fluid-Implicit Particle (FLIP) method, enabling efficient, robust, minimally-dissipative simulations that can undergo sharp changes in spatial resolution while minimizing artifacts. Along the way, we provide a new method for generating a smooth and detailed surface from a set of particles with variable sizes. Finally, we explore several new sizing functions for determining spatially adaptive simulation resolutions, and we show how to couple them to our simulator. We combine each of these elements to produce a simulation algorithm that is capable of creating animations at high maximum resolutions while avoiding common pitfalls like inaccurate boundary conditions and inefficient computation.' article_number: '103' author: - first_name: Ryoichi full_name: Ando, Ryoichi last_name: Ando - first_name: Nils full_name: Thuerey, Nils last_name: Thuerey - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Ando R, Thuerey N, Wojtan C. Highly adaptive liquid simulations on tetrahedral meshes. ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2461982 apa: Ando, R., Thuerey, N., & Wojtan, C. (2013). Highly adaptive liquid simulations on tetrahedral meshes. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2461982 chicago: Ando, Ryoichi, Nils Thuerey, and Chris Wojtan. “Highly Adaptive Liquid Simulations on Tetrahedral Meshes.” ACM Transactions on Graphics. ACM, 2013. https://doi.org/10.1145/2461912.2461982. ieee: R. Ando, N. Thuerey, and C. Wojtan, “Highly adaptive liquid simulations on tetrahedral meshes,” ACM Transactions on Graphics, vol. 32, no. 4. ACM, 2013. ista: Ando R, Thuerey N, Wojtan C. 2013. Highly adaptive liquid simulations on tetrahedral meshes. ACM Transactions on Graphics. 32(4), 103. mla: Ando, Ryoichi, et al. “Highly Adaptive Liquid Simulations on Tetrahedral Meshes.” ACM Transactions on Graphics, vol. 32, no. 4, 103, ACM, 2013, doi:10.1145/2461912.2461982. short: R. Ando, N. Thuerey, C. Wojtan, ACM Transactions on Graphics 32 (2013). date_created: 2018-12-11T11:57:50Z date_published: 2013-07-01T00:00:00Z date_updated: 2023-02-23T10:44:14Z day: '01' ddc: - '000' department: - _id: ChWo doi: 10.1145/2461912.2461982 file: - access_level: open_access checksum: aeea6b0ff2b27c695aeb8408c7d2fc50 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:25Z date_updated: 2020-07-14T12:45:41Z file_id: '5279' file_name: IST-2016-605-v1+1_tetflip_fixed.pdf file_size: 8601561 relation: main_file file_date_updated: 2020-07-14T12:45:41Z has_accepted_license: '1' intvolume: ' 32' issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '4436' pubrep_id: '605' quality_controlled: '1' scopus_import: 1 status: public title: Highly adaptive liquid simulations on tetrahedral meshes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2013' ... --- _id: '2467' abstract: - lang: eng text: This paper presents a method for computing topology changes for triangle meshes in an interactive geometric modeling environment. Most triangle meshes in practice do not exhibit desirable geometric properties, so we develop a solution that is independent of standard assumptions and robust to geometric errors. Specifically, we provide the first method for topology change applicable to arbitrary non-solid, non-manifold, non-closed, self-intersecting surfaces. We prove that this new method for topology change produces the expected conventional results when applied to solid (closed, manifold, non-self-intersecting) surfaces---that is, we prove a backwards-compatibility property relative to prior work. Beyond solid surfaces, we present empirical evidence that our method remains tolerant to a variety of surface aberrations through the incorporation of a novel error correction scheme. Finally, we demonstrate how topology change applied to non-solid objects enables wholly new and useful behaviors. article_number: '34' author: - first_name: Gilbert full_name: Bernstein, Gilbert last_name: Bernstein - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: 'Bernstein G, Wojtan C. Putting holes in holey geometry: Topology change for arbitrary surfaces. ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2462027' apa: 'Bernstein, G., & Wojtan, C. (2013). Putting holes in holey geometry: Topology change for arbitrary surfaces. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2462027' chicago: 'Bernstein, Gilbert, and Chris Wojtan. “Putting Holes in Holey Geometry: Topology Change for Arbitrary Surfaces.” ACM Transactions on Graphics. ACM, 2013. https://doi.org/10.1145/2461912.2462027.' ieee: 'G. Bernstein and C. Wojtan, “Putting holes in holey geometry: Topology change for arbitrary surfaces,” ACM Transactions on Graphics, vol. 32, no. 4. ACM, 2013.' ista: 'Bernstein G, Wojtan C. 2013. Putting holes in holey geometry: Topology change for arbitrary surfaces. ACM Transactions on Graphics. 32(4), 34.' mla: 'Bernstein, Gilbert, and Chris Wojtan. “Putting Holes in Holey Geometry: Topology Change for Arbitrary Surfaces.” ACM Transactions on Graphics, vol. 32, no. 4, 34, ACM, 2013, doi:10.1145/2461912.2462027.' short: G. Bernstein, C. Wojtan, ACM Transactions on Graphics 32 (2013). date_created: 2018-12-11T11:57:50Z date_published: 2013-07-01T00:00:00Z date_updated: 2023-02-23T10:44:16Z day: '01' ddc: - '000' department: - _id: ChWo doi: 10.1145/2461912.2462027 file: - access_level: open_access checksum: 9c8425d62246996ca632c5a01870515b content_type: application/pdf creator: system date_created: 2018-12-12T10:09:43Z date_updated: 2020-07-14T12:45:41Z file_id: '4768' file_name: IST-2016-604-v1+1_toptop2013.pdf file_size: 3514674 relation: main_file file_date_updated: 2020-07-14T12:45:41Z has_accepted_license: '1' intvolume: ' 32' issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '4435' pubrep_id: '604' quality_controlled: '1' scopus_import: 1 status: public title: 'Putting holes in holey geometry: Topology change for arbitrary surfaces' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2013' ... --- _id: '2468' abstract: - lang: eng text: Our work concerns the combination of an Eulerian liquid simulation with a high-resolution surface tracker (e.g. the level set method or a Lagrangian triangle mesh). The naive application of a high-resolution surface tracker to a low-resolution velocity field can produce many visually disturbing physical and topological artifacts that limit their use in practice. We address these problems by defining an error function which compares the current state of the surface tracker to the set of physically valid surface states. By reducing this error with a gradient descent technique, we introduce a novel physics-based surface fairing method. Similarly, by treating this error function as a potential energy, we derive a new surface correction force that mimics the vortex sheet equations. We demonstrate our results with both level set and mesh-based surface trackers. article_number: '68' author: - first_name: Morten full_name: Bojsen-Hansen, Morten id: 439F0C8C-F248-11E8-B48F-1D18A9856A87 last_name: Bojsen-Hansen orcid: 0000-0002-4417-3224 - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Bojsen-Hansen M, Wojtan C. Liquid surface tracking with error compensation. ACM Transactions on Graphics. 2013;32(4). doi:10.1145/2461912.2461991 apa: Bojsen-Hansen, M., & Wojtan, C. (2013). Liquid surface tracking with error compensation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2461912.2461991 chicago: Bojsen-Hansen, Morten, and Chris Wojtan. “Liquid Surface Tracking with Error Compensation.” ACM Transactions on Graphics. ACM, 2013. https://doi.org/10.1145/2461912.2461991. ieee: M. Bojsen-Hansen and C. Wojtan, “Liquid surface tracking with error compensation,” ACM Transactions on Graphics, vol. 32, no. 4. ACM, 2013. ista: Bojsen-Hansen M, Wojtan C. 2013. Liquid surface tracking with error compensation. ACM Transactions on Graphics. 32(4), 68. mla: Bojsen-Hansen, Morten, and Chris Wojtan. “Liquid Surface Tracking with Error Compensation.” ACM Transactions on Graphics, vol. 32, no. 4, 68, ACM, 2013, doi:10.1145/2461912.2461991. short: M. Bojsen-Hansen, C. Wojtan, ACM Transactions on Graphics 32 (2013). date_created: 2018-12-11T11:57:50Z date_published: 2013-07-01T00:00:00Z date_updated: 2023-02-23T10:44:18Z day: '01' ddc: - '000' department: - _id: ChWo doi: 10.1145/2461912.2461991 file: - access_level: open_access checksum: 53d905e0180e23ef3e813b969ffed4e1 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:37Z date_updated: 2020-07-14T12:45:41Z file_id: '4761' file_name: IST-2016-603-v1+1_liquidError_web.pdf file_size: 5813685 relation: main_file file_date_updated: 2020-07-14T12:45:41Z has_accepted_license: '1' intvolume: ' 32' issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '4434' pubrep_id: '603' quality_controlled: '1' scopus_import: 1 status: public title: Liquid surface tracking with error compensation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2013' ...