--- _id: '1299' abstract: - lang: eng text: Recent experiments have shown that motion detection in Drosophila starts with splitting the visual input into two parallel channels encoding brightness increments (ON) or decrements (OFF). This suggests the existence of either two (ON-ON, OFF-OFF) or four (for all pairwise interactions) separate motion detectors. To decide between these possibilities, we stimulated flies using sequences of ON and OFF brightness pulses while recording from motion-sensitive tangential cells. We found direction-selective responses to sequences of same sign (ON-ON, OFF-OFF), but not of opposite sign (ON-OFF, OFF-ON), refuting the existence of four separate detectors. Based on further measurements, we propose a model that reproduces a variety of additional experimental data sets, including ones that were previously interpreted as support for four separate detectors. Our experiments and the derived model mark an important step in guiding further dissection of the fly motion detection circuit. author: - first_name: Hubert full_name: Eichner, Hubert last_name: Eichner - first_name: Maximilian A full_name: Maximilian Jösch id: 2BD278E6-F248-11E8-B48F-1D18A9856A87 last_name: Jösch orcid: 0000-0002-3937-1330 - first_name: Bettina full_name: Schnell, Bettina last_name: Schnell - first_name: Dierk full_name: Reiff, Dierk F last_name: Reiff - first_name: Alexander full_name: Borst, Alexander last_name: Borst citation: ama: Eichner H, Jösch MA, Schnell B, Reiff D, Borst A. Internal structure of the fly elementary motion detector. Neuron. 2011;70(6):1155-1164. doi:10.1016/j.neuron.2011.03.028 apa: Eichner, H., Jösch, M. A., Schnell, B., Reiff, D., & Borst, A. (2011). Internal structure of the fly elementary motion detector. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2011.03.028 chicago: Eichner, Hubert, Maximilian A Jösch, Bettina Schnell, Dierk Reiff, and Alexander Borst. “Internal Structure of the Fly Elementary Motion Detector.” Neuron. Elsevier, 2011. https://doi.org/10.1016/j.neuron.2011.03.028. ieee: H. Eichner, M. A. Jösch, B. Schnell, D. Reiff, and A. Borst, “Internal structure of the fly elementary motion detector,” Neuron, vol. 70, no. 6. Elsevier, pp. 1155–1164, 2011. ista: Eichner H, Jösch MA, Schnell B, Reiff D, Borst A. 2011. Internal structure of the fly elementary motion detector. Neuron. 70(6), 1155–1164. mla: Eichner, Hubert, et al. “Internal Structure of the Fly Elementary Motion Detector.” Neuron, vol. 70, no. 6, Elsevier, 2011, pp. 1155–64, doi:10.1016/j.neuron.2011.03.028. short: H. Eichner, M.A. Jösch, B. Schnell, D. Reiff, A. Borst, Neuron 70 (2011) 1155–1164. date_created: 2018-12-11T11:51:14Z date_published: 2011-06-23T00:00:00Z date_updated: 2021-01-12T06:49:43Z day: '23' doi: 10.1016/j.neuron.2011.03.028 extern: 1 intvolume: ' 70' issue: '6' month: '06' page: 1155 - 1164 publication: Neuron publication_status: published publisher: Elsevier publist_id: '5969' quality_controlled: 0 status: public title: Internal structure of the fly elementary motion detector type: journal_article volume: 70 year: '2011' ... --- _id: '1467' abstract: - lang: eng text: We propose a general conjecture for the mixed Hodge polynomial of the generic character varieties of representations of the fundamental group of a Riemann surface of genus g to GLn(C) with fixed generic semisimple conjugacy classes at k punctures. This conjecture generalizes the Cauchy identity for Macdonald polynomials and is a common generalization of two formulas that we prove in this paper. The first is a formula for the E-polynomial of these character varieties which we obtain using the character table of GLn(Fq). We use this formula to compute the Euler characteristic of character varieties. The second formula gives the Poincaré polynomial of certain associated quiver varieties which we obtain using the character table of gln(Fq). In the last main result we prove that the Poincaré polynomials of the quiver varieties equal certain multiplicities in the tensor product of irreducible characters of GLn(Fq). As a consequence we find a curious connection between Kac-Moody algebras associated with comet-shaped, and typically wild, quivers and the representation theory of GLn(Fq). acknowledgement: |- Hausel’s work was supported by National Science Foundation grants DMS-0305505 and DMS-0604775, by an Alfred Sloan Fellowship, and by a Royal Society University Research Fellowship. Letellier’s work supported by Agence Nationale de la Recherche grant ANR-09-JCJC-0102-01. Rodriguez-Villegas’s work supported by National Science Foundation grant DMS-0200605, by an FRA from the University of Texas at Austin, by EPSRC grant EP/G027110/1, by visiting fellowships at All Souls and Wadham Colleges in Oxford, and by 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. Duke Mathematical Journal. 2011;160(2):323-400. doi:10.1215/00127094-1444258 apa: Hausel, T., Letellier, E., & Rodríguez Villegas, F. (2011). Arithmetic harmonic analysis on character and quiver varieties. Duke Mathematical Journal. Duke University Press. https://doi.org/10.1215/00127094-1444258 chicago: Hausel, Tamás, Emmanuel Letellier, and Fernando Rodríguez Villegas. “Arithmetic Harmonic Analysis on Character and Quiver Varieties.” Duke Mathematical Journal. Duke University Press, 2011. https://doi.org/10.1215/00127094-1444258. ieee: T. Hausel, E. Letellier, and F. Rodríguez Villegas, “Arithmetic harmonic analysis on character and quiver varieties,” Duke Mathematical Journal, vol. 160, no. 2. Duke University Press, pp. 323–400, 2011. ista: Hausel T, Letellier E, Rodríguez Villegas F. 2011. Arithmetic harmonic analysis on character and quiver varieties. Duke Mathematical Journal. 160(2), 323–400. mla: Hausel, Tamás, et al. “Arithmetic Harmonic Analysis on Character and Quiver Varieties.” Duke Mathematical Journal, vol. 160, no. 2, Duke University Press, 2011, pp. 323–400, doi:10.1215/00127094-1444258. short: T. Hausel, E. Letellier, F. Rodríguez Villegas, Duke Mathematical Journal 160 (2011) 323–400. date_created: 2018-12-11T11:52:11Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T06:50:56Z day: '01' doi: 10.1215/00127094-1444258 extern: 1 intvolume: ' 160' issue: '2' main_file_link: - open_access: '1' url: http://arxiv.org/abs/0810.2076 month: '01' oa: 1 page: 323 - 400 publication: Duke Mathematical Journal publication_status: published publisher: Duke University Press publist_id: '5728' quality_controlled: 0 status: public title: Arithmetic harmonic analysis on character and quiver varieties type: journal_article volume: 160 year: '2011' ... --- _id: '1723' abstract: - lang: eng text: The emergence of differences in the arrangement of cells is the first step towards the establishment of many organs. Understanding this process is limited by the lack of systematic characterization of epithelial organisation. Here we apply network theory at the scale of individual cells to uncover patterns in cell-to-cell contacts that govern epithelial organisation. We provide an objective characterisation of epithelia using network representation, where cells are nodes and cell contacts are links. The features of individual cells, together with attributes of the cellular network, produce a defining signature that distinguishes epithelia from different organs, species, developmental stages and genetic conditions. The approach permits characterization, quantification and classification of normal and perturbed epithelia, and establishes a framework for understanding molecular mechanisms that underpin the architecture of complex tissues. acknowledgement: We acknowledge the MRC for funding, M.M.B. acknowledges Darwin College, EMBO YIP and Schlumberger Ltd for support. L.M.E. is funded by the Marie Curie and the EMBO fellowships. L.d.F.C. is grateful to FAPESP (05/00587-5) and CNPq (301303/06-1) for financial support. Part of this work was performed during a Visiting Scholarship to L.d.F.C. from St Catharine's College, University of Cambridge. J.B. is supported by the MRC (UK) and A.K. by a FEBS fellowship author: - first_name: Luis full_name: Escudero, Luis M last_name: Escudero - first_name: Luciano full_name: Costa, Luciano last_name: Costa - 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: Matthew full_name: Freeman, Matthew last_name: Freeman - first_name: Madan full_name: Babu, Madan M last_name: Babu citation: ama: Escudero L, Costa L, Kicheva A, Briscoe J, Freeman M, Babu M. Epithelial organisation revealed by a network of cellular contacts. Nature Communications. 2011;2(1). doi:10.1038/ncomms1536 apa: Escudero, L., Costa, L., Kicheva, A., Briscoe, J., Freeman, M., & Babu, M. (2011). Epithelial organisation revealed by a network of cellular contacts. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms1536 chicago: Escudero, Luis, Luciano Costa, Anna Kicheva, James Briscoe, Matthew Freeman, and Madan Babu. “Epithelial Organisation Revealed by a Network of Cellular Contacts.” Nature Communications. Nature Publishing Group, 2011. https://doi.org/10.1038/ncomms1536. ieee: L. Escudero, L. Costa, A. Kicheva, J. Briscoe, M. Freeman, and M. Babu, “Epithelial organisation revealed by a network of cellular contacts,” Nature Communications, vol. 2, no. 1. Nature Publishing Group, 2011. ista: Escudero L, Costa L, Kicheva A, Briscoe J, Freeman M, Babu M. 2011. Epithelial organisation revealed by a network of cellular contacts. Nature Communications. 2(1). mla: Escudero, Luis, et al. “Epithelial Organisation Revealed by a Network of Cellular Contacts.” Nature Communications, vol. 2, no. 1, Nature Publishing Group, 2011, doi:10.1038/ncomms1536. short: L. Escudero, L. Costa, A. Kicheva, J. Briscoe, M. Freeman, M. Babu, Nature Communications 2 (2011). date_created: 2018-12-11T11:53:40Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T06:52:46Z day: '01' doi: 10.1038/ncomms1536 extern: 1 intvolume: ' 2' issue: '1' month: '01' publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5405' quality_controlled: 0 status: public title: Epithelial organisation revealed by a network of cellular contacts type: journal_article volume: 2 year: '2011' ... --- _id: '1724' abstract: - lang: eng text: Morphogens, such as Decapentaplegic (Dpp) in the fly imaginal discs, form graded concentration profiles that control patterning and growth of developing organs. In the imaginal discs, proliferative growth is homogeneous in space, posing the conundrum of how morphogen concentration gradients could control position-independent growth. To understand the mechanism of proliferation control by the Dpp gradient, we quantified Dpp concentration and signaling levels during wing disc growth. Both Dpp concentration and signaling gradients scale with tissue size during development. On average, cells divide when Dpp signaling levels have increased by 50%. Our observations are consistent with a growth control mechanism based on temporal changes of cellular morphogen signaling levels. For a scaling gradient, this mechanism generates position-independent growth rates. acknowledgement: P.M., T.B., and F.J. were supported by the Max-Planck-Gesellschaft. O.W., A.K., C.S., and M.G.-G. were supported by Geneva University and by European Research Council advanced investigator grant (SARA), SystemsX (LipidX), Swiss National Science Foundation (SNF), National Centre of Competence in Research (NCCR) chemical biology and Frontiers in Genetics and R'equip grants author: - first_name: Ortrud full_name: Wartlick, Ortrud last_name: Wartlick - first_name: Peer full_name: Mumcu, Peer last_name: Mumcu - first_name: Anna full_name: Anna Kicheva id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 - first_name: Thomas full_name: Bittig, Thomas last_name: Bittig - first_name: Carole full_name: Seum, Carole last_name: Seum - first_name: Frank full_name: Jülicher, Frank last_name: Jülicher - first_name: Marcos full_name: González-Gaitán, Marcos A last_name: González Gaitán citation: ama: Wartlick O, Mumcu P, Kicheva A, et al. Dynamics of Dpp signaling and proliferation control. Science. 2011;331(6021):1154-1159. doi:10.1126/science.1200037 apa: Wartlick, O., Mumcu, P., Kicheva, A., Bittig, T., Seum, C., Jülicher, F., & González Gaitán, M. (2011). Dynamics of Dpp signaling and proliferation control. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1200037 chicago: Wartlick, Ortrud, Peer Mumcu, Anna Kicheva, Thomas Bittig, Carole Seum, Frank Jülicher, and Marcos González Gaitán. “Dynamics of Dpp Signaling and Proliferation Control.” Science. American Association for the Advancement of Science, 2011. https://doi.org/10.1126/science.1200037. ieee: O. Wartlick et al., “Dynamics of Dpp signaling and proliferation control,” Science, vol. 331, no. 6021. American Association for the Advancement of Science, pp. 1154–1159, 2011. ista: Wartlick O, Mumcu P, Kicheva A, Bittig T, Seum C, Jülicher F, González Gaitán M. 2011. Dynamics of Dpp signaling and proliferation control. Science. 331(6021), 1154–1159. mla: Wartlick, Ortrud, et al. “Dynamics of Dpp Signaling and Proliferation Control.” Science, vol. 331, no. 6021, American Association for the Advancement of Science, 2011, pp. 1154–59, doi:10.1126/science.1200037. short: O. Wartlick, P. Mumcu, A. Kicheva, T. Bittig, C. Seum, F. Jülicher, M. González Gaitán, Science 331 (2011) 1154–1159. date_created: 2018-12-11T11:53:40Z date_published: 2011-03-04T00:00:00Z date_updated: 2021-01-12T06:52:46Z day: '04' doi: 10.1126/science.1200037 extern: 1 intvolume: ' 331' issue: '6021' month: '03' page: 1154 - 1159 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '5406' quality_controlled: 0 status: public title: Dynamics of Dpp signaling and proliferation control type: journal_article volume: 331 year: '2011' ... --- _id: '1754' abstract: - lang: eng text: 'We report on a technique enabling electrical control of the contact silicidation process in silicon nanowire devices. Undoped silicon nanowires were contacted by pairs of nickel electrodes and each contact was selectively silicided by means of the Joule effect. By a realtime monitoring of the nanowire electrical resistance during the contact silicidation process we were able to fabricate nickel-silicide/silicon/nickel- silicide devices with controlled silicon channel length down to 8 nm. ' acknowledgement: This work was supported by the Agence Nationale de la Recherche (ANR) through the ACCESS and COHESION projects and by the European Commission through the Chemtronics program MEST-CT-2005-020513 author: - first_name: Massimo full_name: Mongillo, Massimo last_name: Mongillo - first_name: Panayotis full_name: Spathis, Panayotis last_name: Spathis - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros - first_name: Pascal full_name: Gentile, Pascal last_name: Gentile - first_name: Marc full_name: Sanquer, Marc last_name: Sanquer - first_name: Silvano full_name: De Franceschi, Silvano last_name: De Franceschi citation: ama: Mongillo M, Spathis P, Katsaros G, Gentile P, Sanquer M, De Franceschi S. Joule-assisted silicidation for short-channel silicon nanowire devices. ACS Nano. 2011;5(9):7117-7123. doi:10.1021/nn202524j apa: Mongillo, M., Spathis, P., Katsaros, G., Gentile, P., Sanquer, M., & De Franceschi, S. (2011). Joule-assisted silicidation for short-channel silicon nanowire devices. ACS Nano. American Chemical Society. https://doi.org/10.1021/nn202524j chicago: Mongillo, Massimo, Panayotis Spathis, Georgios Katsaros, Pascal Gentile, Marc Sanquer, and Silvano De Franceschi. “Joule-Assisted Silicidation for Short-Channel Silicon Nanowire Devices.” ACS Nano. American Chemical Society, 2011. https://doi.org/10.1021/nn202524j. ieee: M. Mongillo, P. Spathis, G. Katsaros, P. Gentile, M. Sanquer, and S. De Franceschi, “Joule-assisted silicidation for short-channel silicon nanowire devices,” ACS Nano, vol. 5, no. 9. American Chemical Society, pp. 7117–7123, 2011. ista: Mongillo M, Spathis P, Katsaros G, Gentile P, Sanquer M, De Franceschi S. 2011. Joule-assisted silicidation for short-channel silicon nanowire devices. ACS Nano. 5(9), 7117–7123. mla: Mongillo, Massimo, et al. “Joule-Assisted Silicidation for Short-Channel Silicon Nanowire Devices.” ACS Nano, vol. 5, no. 9, American Chemical Society, 2011, pp. 7117–23, doi:10.1021/nn202524j. short: M. Mongillo, P. Spathis, G. Katsaros, P. Gentile, M. Sanquer, S. De Franceschi, ACS Nano 5 (2011) 7117–7123. date_created: 2018-12-11T11:53:50Z date_published: 2011-09-27T00:00:00Z date_updated: 2021-01-12T06:52:59Z day: '27' doi: 10.1021/nn202524j extern: '1' external_id: arxiv: - '1110.5668' intvolume: ' 5' issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1110.5668 month: '09' oa: 1 oa_version: Preprint page: 7117 - 7123 publication: ACS Nano publication_status: published publisher: American Chemical Society publist_id: '5370' quality_controlled: '1' status: public title: Joule-assisted silicidation for short-channel silicon nanowire devices type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2011' ... --- _id: '1755' abstract: - lang: eng text: Spin-selective tunneling of holes in SiGe nanocrystals contacted by normal-metal leads is reported. The spin selectivity arises from an interplay of the orbital effect of the magnetic field with the strong spin-orbit interaction present in the valence band of the semiconductor. We demonstrate both experimentally and theoretically that spin-selective tunneling in semiconductor nanostructures can be achieved without the use of ferromagnetic contacts. The reported effect, which relies on mixing the light and heavy holes, should be observable in a broad class of quantum-dot systems formed in semiconductors with a degenerate valence band. acknowledgement: The work was supported by the Agence Nationale de la Recherche (through the ACCESS and COHESION projects), U.S. DOE Contract No. DE-FG02-08ER46482 (Yale), and the Nanosciences Foundation at Grenoble, France. G. K. acknowledges support from the Deutsche Forschungsgemeinschaft author: - 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: Panayotis full_name: Spathis, Panayotis N last_name: Spathis - first_name: Natalia full_name: Ares, Natalia last_name: Ares - first_name: Mathieu full_name: Stoffel, Mathieu last_name: Stoffel - first_name: Frank full_name: Fournel, Frank last_name: Fournel - first_name: Oliver full_name: Schmidt, Oliver G last_name: Schmidt - first_name: Leonid full_name: Glazman, Leonid I last_name: Glazman - first_name: Silvano full_name: De Franceschi, Silvano last_name: De Franceschi citation: ama: Katsaros G, Golovach V, Spathis P, et al. Observation of spin-selective tunneling in sige nanocrystals. Physical Review Letters. 2011;107(24). doi:10.1103/PhysRevLett.107.246601 apa: Katsaros, G., Golovach, V., Spathis, P., Ares, N., Stoffel, M., Fournel, F., … De Franceschi, S. (2011). Observation of spin-selective tunneling in sige nanocrystals. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.107.246601 chicago: Katsaros, Georgios, Vitaly Golovach, Panayotis Spathis, Natalia Ares, Mathieu Stoffel, Frank Fournel, Oliver Schmidt, Leonid Glazman, and Silvano De Franceschi. “Observation of Spin-Selective Tunneling in Sige Nanocrystals.” Physical Review Letters. American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.107.246601. ieee: G. Katsaros et al., “Observation of spin-selective tunneling in sige nanocrystals,” Physical Review Letters, vol. 107, no. 24. American Physical Society, 2011. ista: Katsaros G, Golovach V, Spathis P, Ares N, Stoffel M, Fournel F, Schmidt O, Glazman L, De Franceschi S. 2011. Observation of spin-selective tunneling in sige nanocrystals. Physical Review Letters. 107(24). mla: Katsaros, Georgios, et al. “Observation of Spin-Selective Tunneling in Sige Nanocrystals.” Physical Review Letters, vol. 107, no. 24, American Physical Society, 2011, doi:10.1103/PhysRevLett.107.246601. short: G. Katsaros, V. Golovach, P. Spathis, N. Ares, M. Stoffel, F. Fournel, O. Schmidt, L. Glazman, S. De Franceschi, Physical Review Letters 107 (2011). date_created: 2018-12-11T11:53:50Z date_published: 2011-12-07T00:00:00Z date_updated: 2021-01-12T06:53:00Z day: '07' doi: 10.1103/PhysRevLett.107.246601 extern: 1 intvolume: ' 107' issue: '24' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1107.3919 month: '12' oa: 1 publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '5369' quality_controlled: 0 status: public title: Observation of spin-selective tunneling in sige nanocrystals type: journal_article volume: 107 year: '2011' ... --- _id: '1776' abstract: - lang: eng text: Superconducting circuits have been successfully established as systems to prepare and investigate microwave light fields at the quantum level. In contrast to optical experiments where light is detected using photon counters, microwaves are usually measured with well developed linear amplifiers. This makes measurements of correlation functions - one of the important tools in optics - harder to achieve because they traditionally rely on photon counters and beam splitters. Here, we demonstrate a system where we can prepare on demand single microwave photons in a cavity and detect them at the two outputs of the cavity using linear amplifiers. Together with efficient data processing, this allows us to measure different observables of the cavity photons, including the first-order correlation function. Using these techniques we demonstrate cooling of a thermal background field in the cavity. acknowledgement: Australian National University,Aust. Res. Counc. Cent. Excellence Quantum-Atom Opt.,Griffith University,Ian Potter Foundation,International Union of Pure and Applied Physics alternative_title: - 'Journal of Physics: Conference Series' author: - first_name: Deniz full_name: Bozyigit, Deniz last_name: Bozyigit - first_name: C full_name: Lang, C last_name: Lang - 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: Christopher full_name: Eichler, Christopher last_name: Eichler - first_name: Matthias full_name: Baur, Matthias P last_name: Baur - first_name: R full_name: Bianchetti, R last_name: Bianchetti - first_name: Peter full_name: Leek, Peter J last_name: Leek - first_name: Stefan full_name: Filipp, Stefan last_name: Filipp - first_name: Andreas full_name: Wallraff, Andreas last_name: Wallraff - first_name: Marcus full_name: Da Silva, Marcus P last_name: Da Silva - first_name: Alexandre full_name: Blais, Alexandre last_name: Blais citation: ama: 'Bozyigit D, Lang C, Steffen L, et al. Correlation measurements of individual microwave photons emitted from a symmetric cavity. In: Vol 264. IOP Publishing Ltd.; 2011. doi:10.1088/1742-6596/264/1/012024' apa: Bozyigit, D., Lang, C., Steffen, L., Fink, J. M., Eichler, C., Baur, M., … Blais, A. (2011). Correlation measurements of individual microwave photons emitted from a symmetric cavity (Vol. 264). Presented at the International Conference on Atomic Physics, IOP Publishing Ltd. https://doi.org/10.1088/1742-6596/264/1/012024 chicago: Bozyigit, Deniz, C Lang, L. Steffen, Johannes M Fink, Christopher Eichler, Matthias Baur, R Bianchetti, et al. “Correlation Measurements of Individual Microwave Photons Emitted from a Symmetric Cavity,” Vol. 264. IOP Publishing Ltd., 2011. https://doi.org/10.1088/1742-6596/264/1/012024. ieee: D. Bozyigit et al., “Correlation measurements of individual microwave photons emitted from a symmetric cavity,” presented at the International Conference on Atomic Physics, 2011, vol. 264, no. 1. ista: 'Bozyigit D, Lang C, Steffen L, Fink JM, Eichler C, Baur M, Bianchetti R, Leek P, Filipp S, Wallraff A, Da Silva M, Blais A. 2011. Correlation measurements of individual microwave photons emitted from a symmetric cavity. International Conference on Atomic Physics, Journal of Physics: Conference Series, vol. 264.' mla: Bozyigit, Deniz, et al. Correlation Measurements of Individual Microwave Photons Emitted from a Symmetric Cavity. Vol. 264, no. 1, IOP Publishing Ltd., 2011, doi:10.1088/1742-6596/264/1/012024. short: D. Bozyigit, C. Lang, L. Steffen, J.M. Fink, C. Eichler, M. Baur, R. Bianchetti, P. Leek, S. Filipp, A. Wallraff, M. Da Silva, A. Blais, in:, IOP Publishing Ltd., 2011. conference: name: International Conference on Atomic Physics date_created: 2018-12-11T11:53:57Z date_published: 2011-01-01T00:00:00Z date_updated: 2019-04-26T07:22:05Z day: '01' doi: 10.1088/1742-6596/264/1/012024 extern: 1 intvolume: ' 264' issue: '1' month: '01' publication_status: published publisher: IOP Publishing Ltd. publist_id: '5339' quality_controlled: 0 status: public title: Correlation measurements of individual microwave photons emitted from a symmetric cavity type: conference volume: 264 year: '2011' ... --- _id: '1777' abstract: - lang: eng text: A wide range of experiments studying microwave photons localized in superconducting cavities have made important contributions to our understanding of the quantum properties of radiation. Propagating microwave photons, however, have so far been studied much less intensely. Here we present measurements in which we reconstruct the quantum state of itinerant single photon Fock states and their superposition with the vacuum by analyzing moments of the measured amplitude distribution up to fourth order. Using linear amplifiers and quadrature amplitude detectors, we have developed efficient methods to separate the detected single photon signal from the noise added by the amplifier. From our measurement data we have also reconstructed the corresponding Wigner function. acknowledgement: This work was supported by the European Research Council (ERC) through a Starting Grant and by ETHZ article_processing_charge: No author: - first_name: Christopher full_name: Eichler, Christopher last_name: Eichler - first_name: Deniz full_name: Bozyigit, Deniz last_name: Bozyigit - first_name: C full_name: Lang, C last_name: Lang - first_name: L. full_name: Steffen, L. last_name: Steffen - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: Andreas full_name: Wallraff, Andreas last_name: Wallraff citation: ama: Eichler C, Bozyigit D, Lang C, Steffen L, Fink JM, Wallraff A. Experimental state tomography of itinerant single microwave photons. Physical Review Letters. 2011;106(22). doi:10.1103/PhysRevLett.106.220503 apa: Eichler, C., Bozyigit, D., Lang, C., Steffen, L., Fink, J. M., & Wallraff, A. (2011). Experimental state tomography of itinerant single microwave photons. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.106.220503 chicago: Eichler, Christopher, Deniz Bozyigit, C Lang, L. Steffen, Johannes M Fink, and Andreas Wallraff. “Experimental State Tomography of Itinerant Single Microwave Photons.” Physical Review Letters. American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.106.220503. ieee: C. Eichler, D. Bozyigit, C. Lang, L. Steffen, J. M. Fink, and A. Wallraff, “Experimental state tomography of itinerant single microwave photons,” Physical Review Letters, vol. 106, no. 22. American Physical Society, 2011. ista: Eichler C, Bozyigit D, Lang C, Steffen L, Fink JM, Wallraff A. 2011. Experimental state tomography of itinerant single microwave photons. Physical Review Letters. 106(22). mla: Eichler, Christopher, et al. “Experimental State Tomography of Itinerant Single Microwave Photons.” Physical Review Letters, vol. 106, no. 22, American Physical Society, 2011, doi:10.1103/PhysRevLett.106.220503. short: C. Eichler, D. Bozyigit, C. Lang, L. Steffen, J.M. Fink, A. Wallraff, Physical Review Letters 106 (2011). date_created: 2018-12-11T11:53:57Z date_published: 2011-06-01T00:00:00Z date_updated: 2021-11-16T07:57:13Z day: '01' doi: 10.1103/PhysRevLett.106.220503 extern: '1' intvolume: ' 106' issue: '22' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1011.6668 month: '06' oa: 1 oa_version: None publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '5338' related_material: link: - relation: erratum url: https://doi.org/10.1103/PhysRevLett.106.249901 status: public title: Experimental state tomography of itinerant single microwave photons type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 106 year: '2011' ... --- _id: '1778' abstract: - lang: eng text: Creating a train of single photons and monitoring its propagation and interaction is challenging in most physical systems, as photons generally interact very weakly with other systems. However, when confining microwave frequency photons in a transmission line resonator, effective photon-photon interactions can be mediated by qubits embedded in the resonator. Here, we observe the phenomenon of photon blockade through second-order correlation function measurements. The experiments clearly demonstrate antibunching in a continuously pumped source of single microwave photons measured by using microwave beam splitters, linear amplifiers, and quadrature amplitude detectors. We also investigate resonance fluorescence and Rayleigh scattering in Mollow-triplet-like spectra. acknowledgement: This work was supported by the European Research Council (ERC) through a Starting Grant and by ETHZ. M. P. d. S. was supported by NSERC. A. B. was supported by NSERC, CIFAR, and the Alfred P. Sloan Foundation author: - first_name: C full_name: Lang, C last_name: Lang - first_name: Deniz full_name: Bozyigit, Deniz last_name: Bozyigit - 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: Abdufarrukh full_name: Abdumalikov, Abdufarrukh A last_name: Abdumalikov - first_name: Matthias full_name: Baur, Matthias P last_name: Baur - first_name: Stefan full_name: Filipp, Stefan last_name: Filipp - first_name: Marcus full_name: Da Silva, Marcus P last_name: Da Silva - first_name: Alexandre full_name: Blais, Alexandre last_name: Blais - first_name: Andreas full_name: Wallraff, Andreas last_name: Wallraff citation: ama: Lang C, Bozyigit D, Eichler C, et al. Observation of resonant photon blockade at microwave frequencies using correlation function measurements. Physical Review Letters. 2011;106(24). doi:10.1103/PhysRevLett.106.243601 apa: Lang, C., Bozyigit, D., Eichler, C., Steffen, L., Fink, J. M., Abdumalikov, A., … Wallraff, A. (2011). Observation of resonant photon blockade at microwave frequencies using correlation function measurements. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.106.243601 chicago: Lang, C, Deniz Bozyigit, Christopher Eichler, L. Steffen, Johannes M Fink, Abdufarrukh Abdumalikov, Matthias Baur, et al. “Observation of Resonant Photon Blockade at Microwave Frequencies Using Correlation Function Measurements.” Physical Review Letters. American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.106.243601. ieee: C. Lang et al., “Observation of resonant photon blockade at microwave frequencies using correlation function measurements,” Physical Review Letters, vol. 106, no. 24. American Physical Society, 2011. ista: Lang C, Bozyigit D, Eichler C, Steffen L, Fink JM, Abdumalikov A, Baur M, Filipp S, Da Silva M, Blais A, Wallraff A. 2011. Observation of resonant photon blockade at microwave frequencies using correlation function measurements. Physical Review Letters. 106(24). mla: Lang, C., et al. “Observation of Resonant Photon Blockade at Microwave Frequencies Using Correlation Function Measurements.” Physical Review Letters, vol. 106, no. 24, American Physical Society, 2011, doi:10.1103/PhysRevLett.106.243601. short: C. Lang, D. Bozyigit, C. Eichler, L. Steffen, J.M. Fink, A. Abdumalikov, M. Baur, S. Filipp, M. Da Silva, A. Blais, A. Wallraff, Physical Review Letters 106 (2011). date_created: 2018-12-11T11:53:57Z date_published: 2011-06-15T00:00:00Z date_updated: 2021-01-12T06:53:08Z day: '15' doi: 10.1103/PhysRevLett.106.243601 extern: 1 intvolume: ' 106' issue: '24' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1102.0461 month: '06' oa: 1 publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '5336' quality_controlled: 0 status: public title: Observation of resonant photon blockade at microwave frequencies using correlation function measurements type: journal_article volume: 106 year: '2011' ... --- _id: '1775' abstract: - lang: eng text: At optical frequencies the radiation produced by a source, such as a laser, a black body or a single-photon emitter, is frequently characterized by analysing the temporal correlations of emitted photons using single-photon counters. At microwave frequencies, however, there are no efficient single-photon counters yet. Instead, well-developed linear amplifiers allow for efficient measurement of the amplitude of an electromagnetic field. Here, we demonstrate first- and second-order correlation function measurements of a pulsed microwave-frequency single-photon source integrated on the same chip with a 50/50 beam splitter followed by linear amplifiers and quadrature amplitude detectors. We clearly observe single-photon coherence in first-order and photon antibunching in second-order correlation function measurements of the propagating fields. acknowledgement: This work was supported by the European Research Council (ERC) through a Starting Grant and by ETHZ. M.P.d.S. was supported by a NSERC postdoctoral fellowship. A.B. was supported by NSERC, CIFAR and the Alfred P. Sloan Foundation author: - first_name: Deniz full_name: Bozyigit, Deniz last_name: Bozyigit - first_name: C full_name: Lang, C last_name: Lang - 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: Christopher full_name: Eichler, Christopher last_name: Eichler - first_name: Matthias full_name: Baur, Matthias P last_name: Baur - first_name: R full_name: Bianchetti, R last_name: Bianchetti - first_name: Peter full_name: Leek, Peter J last_name: Leek - first_name: Stefan full_name: Filipp, Stefan last_name: Filipp - first_name: Marcus full_name: Da Silva, Marcus P last_name: Da Silva - first_name: Alexandre full_name: Blais, Alexandre last_name: Blais - first_name: Andreas full_name: Wallraff, Andreas last_name: Wallraff citation: ama: Bozyigit D, Lang C, Steffen L, et al. Antibunching of microwave-frequency photons observed in correlation measurements using linear detectors. Nature Physics. 2011;7(2):154-158. doi:10.1038/nphys1845 apa: Bozyigit, D., Lang, C., Steffen, L., Fink, J. M., Eichler, C., Baur, M., … Wallraff, A. (2011). Antibunching of microwave-frequency photons observed in correlation measurements using linear detectors. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/nphys1845 chicago: Bozyigit, Deniz, C Lang, L. Steffen, Johannes M Fink, Christopher Eichler, Matthias Baur, R Bianchetti, et al. “Antibunching of Microwave-Frequency Photons Observed in Correlation Measurements Using Linear Detectors.” Nature Physics. Nature Publishing Group, 2011. https://doi.org/10.1038/nphys1845. ieee: D. Bozyigit et al., “Antibunching of microwave-frequency photons observed in correlation measurements using linear detectors,” Nature Physics, vol. 7, no. 2. Nature Publishing Group, pp. 154–158, 2011. ista: Bozyigit D, Lang C, Steffen L, Fink JM, Eichler C, Baur M, Bianchetti R, Leek P, Filipp S, Da Silva M, Blais A, Wallraff A. 2011. Antibunching of microwave-frequency photons observed in correlation measurements using linear detectors. Nature Physics. 7(2), 154–158. mla: Bozyigit, Deniz, et al. “Antibunching of Microwave-Frequency Photons Observed in Correlation Measurements Using Linear Detectors.” Nature Physics, vol. 7, no. 2, Nature Publishing Group, 2011, pp. 154–58, doi:10.1038/nphys1845. short: D. Bozyigit, C. Lang, L. Steffen, J.M. Fink, C. Eichler, M. Baur, R. Bianchetti, P. Leek, S. Filipp, M. Da Silva, A. Blais, A. Wallraff, Nature Physics 7 (2011) 154–158. date_created: 2018-12-11T11:53:57Z date_published: 2011-02-01T00:00:00Z date_updated: 2021-01-12T06:53:07Z day: '01' doi: 10.1038/nphys1845 extern: 1 intvolume: ' 7' issue: '2' month: '02' page: 154 - 158 publication: Nature Physics publication_status: published publisher: Nature Publishing Group publist_id: '5340' quality_controlled: 0 status: public title: Antibunching of microwave-frequency photons observed in correlation measurements using linear detectors type: journal_article volume: 7 year: '2011' ... --- _id: '1781' abstract: - lang: eng text: Microwave cavities with high quality factors enable coherent coupling of distant quantum systems. Virtual photons lead to a transverse interaction between qubits when they are nonresonant with the cavity but resonant with each other. We experimentally investigate the inverse scaling of the interqubit coupling with the detuning from a cavity mode and its proportionality to the qubit-cavity interaction strength. We demonstrate that the enhanced coupling at higher frequencies is mediated by multiple higher-harmonic cavity modes. Moreover, we observe dark states of the coupled qubit-qubit system and analyze their relation to the symmetry of the applied driving field at different frequencies. acknowledgement: This work was supported by the Swiss National Science Foundation (SNF), the Austrian Science Foundation (FWF), and ETH Zurich author: - first_name: Stefan full_name: Filipp, Stefan last_name: Filipp - first_name: M full_name: Göppl, M last_name: Göppl - first_name: Johannes M full_name: Johannes Fink id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: Matthias full_name: Baur, Matthias P last_name: Baur - first_name: R full_name: Bianchetti, R last_name: Bianchetti - first_name: L. full_name: Steffen, L. Kraig last_name: Steffen - first_name: Andreas full_name: Wallraff, Andreas last_name: Wallraff citation: ama: Filipp S, Göppl M, Fink JM, et al. Multimode mediated qubit-qubit coupling and dark-state symmetries in circuit quantum electrodynamics. Physical Review A - Atomic, Molecular, and Optical Physics. 2011;83(6). doi:10.1103/PhysRevA.83.063827 apa: Filipp, S., Göppl, M., Fink, J. M., Baur, M., Bianchetti, R., Steffen, L., & Wallraff, A. (2011). Multimode mediated qubit-qubit coupling and dark-state symmetries in circuit quantum electrodynamics. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.83.063827 chicago: Filipp, Stefan, M Göppl, Johannes M Fink, Matthias Baur, R Bianchetti, L. Steffen, and Andreas Wallraff. “Multimode Mediated Qubit-Qubit Coupling and Dark-State Symmetries in Circuit Quantum Electrodynamics.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2011. https://doi.org/10.1103/PhysRevA.83.063827. ieee: S. Filipp et al., “Multimode mediated qubit-qubit coupling and dark-state symmetries in circuit quantum electrodynamics,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 83, no. 6. American Physical Society, 2011. ista: Filipp S, Göppl M, Fink JM, Baur M, Bianchetti R, Steffen L, Wallraff A. 2011. Multimode mediated qubit-qubit coupling and dark-state symmetries in circuit quantum electrodynamics. Physical Review A - Atomic, Molecular, and Optical Physics. 83(6). mla: Filipp, Stefan, et al. “Multimode Mediated Qubit-Qubit Coupling and Dark-State Symmetries in Circuit Quantum Electrodynamics.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 83, no. 6, American Physical Society, 2011, doi:10.1103/PhysRevA.83.063827. short: S. Filipp, M. Göppl, J.M. Fink, M. Baur, R. Bianchetti, L. Steffen, A. Wallraff, Physical Review A - Atomic, Molecular, and Optical Physics 83 (2011). date_created: 2018-12-11T11:53:58Z date_published: 2011-06-22T00:00:00Z date_updated: 2021-01-12T06:53:09Z day: '22' doi: 10.1103/PhysRevA.83.063827 extern: 1 intvolume: ' 83' issue: '6' month: '06' publication: Physical Review A - Atomic, Molecular, and Optical Physics publication_status: published publisher: American Physical Society publist_id: '5335' quality_controlled: 0 status: public title: Multimode mediated qubit-qubit coupling and dark-state symmetries in circuit quantum electrodynamics type: journal_article volume: 83 year: '2011' ... --- _id: '1780' abstract: - lang: eng text: Continuous variable entanglement between two modes of a radiation field is usually studied at optical frequencies. Here we demonstrate experiments that show the entanglement between microwave photons of different energy in a broadband squeezed beam. We use a Josephson parametric amplifier to generate the two-mode correlated state and detect all four quadrature components simultaneously in a two-channel heterodyne setup using amplitude detectors. Analyzing two-dimensional phase space histograms for all possible pairs of quadratures allows us to determine the full covariance matrix, which is in good agreement with the one expected for a two-mode squeezed state. acknowledgement: This work was supported by the European Research Council (ERC) through a Starting grant and by ETHZ. S. F. acknowledges the Austrian Science Foundation (FWF) for support author: - first_name: Christopher full_name: Eichler, Christopher last_name: Eichler - first_name: Deniz full_name: Bozyigit, Deniz last_name: Bozyigit - first_name: C full_name: Lang, C last_name: Lang - first_name: Matthias full_name: Baur, Matthias P last_name: Baur - 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: Stefan full_name: Filipp, Stefan last_name: Filipp - first_name: Andreas full_name: Wallraff, Andreas last_name: Wallraff citation: ama: Eichler C, Bozyigit D, Lang C, et al. Observation of two-mode squeezing in the microwave frequency domain. Physical Review Letters. 2011;107(11). doi:10.1103/PhysRevLett.107.113601 apa: Eichler, C., Bozyigit, D., Lang, C., Baur, M., Steffen, L., Fink, J. M., … Wallraff, A. (2011). Observation of two-mode squeezing in the microwave frequency domain. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.107.113601 chicago: Eichler, Christopher, Deniz Bozyigit, C Lang, Matthias Baur, L. Steffen, Johannes M Fink, Stefan Filipp, and Andreas Wallraff. “Observation of Two-Mode Squeezing in the Microwave Frequency Domain.” Physical Review Letters. American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.107.113601. ieee: C. Eichler et al., “Observation of two-mode squeezing in the microwave frequency domain,” Physical Review Letters, vol. 107, no. 11. American Physical Society, 2011. ista: Eichler C, Bozyigit D, Lang C, Baur M, Steffen L, Fink JM, Filipp S, Wallraff A. 2011. Observation of two-mode squeezing in the microwave frequency domain. Physical Review Letters. 107(11). mla: Eichler, Christopher, et al. “Observation of Two-Mode Squeezing in the Microwave Frequency Domain.” Physical Review Letters, vol. 107, no. 11, American Physical Society, 2011, doi:10.1103/PhysRevLett.107.113601. short: C. Eichler, D. Bozyigit, C. Lang, M. Baur, L. Steffen, J.M. Fink, S. Filipp, A. Wallraff, Physical Review Letters 107 (2011). date_created: 2018-12-11T11:53:58Z date_published: 2011-09-06T00:00:00Z date_updated: 2021-01-12T06:53:09Z day: '06' doi: 10.1103/PhysRevLett.107.113601 extern: 1 intvolume: ' 107' issue: '11' month: '09' publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '5334' quality_controlled: 0 status: public title: Observation of two-mode squeezing in the microwave frequency domain type: journal_article volume: 107 year: '2011' ... --- _id: '1815' abstract: - lang: eng text: Many membrane channels and receptors exhibit adaptive, or desensitized, response to a strong sustained input stimulus, often supported by protein activity-dependent inactivation. Adaptive response is thought to be related to various cellular functions such as homeostasis and enlargement of dynamic range by background compensation. Here we study the quantitative relation between adaptive response and background compensation within a modeling framework. We show that any particular type of adaptive response is neither sufficient nor necessary for adaptive enlargement of dynamic range. In particular a precise adaptive response, where system activity is maintained at a constant level at steady state, does not ensure a large dynamic range neither in input signal nor in system output. A general mechanism for input dynamic range enlargement can come about from the activity-dependent modulation of protein responsiveness by multiple biochemical modification, regardless of the type of adaptive response it induces. Therefore hierarchical biochemical processes such as methylation and phosphorylation are natural candidates to induce this property in signaling systems. author: - first_name: Tamar full_name: Tamar Friedlander id: 36A5845C-F248-11E8-B48F-1D18A9856A87 last_name: Friedlander - first_name: Naama full_name: Brenner, Naama last_name: Brenner citation: ama: Friedlander T, Brenner N. Adaptive response and enlargement of dynamic range. Mathematical Biosciences and Engineering. 2011;8(2):515-526. doi:10.3934/mbe.2011.8.515 apa: Friedlander, T., & Brenner, N. (2011). Adaptive response and enlargement of dynamic range. Mathematical Biosciences and Engineering. Arizona State University. https://doi.org/10.3934/mbe.2011.8.515 chicago: Friedlander, Tamar, and Naama Brenner. “Adaptive Response and Enlargement of Dynamic Range.” Mathematical Biosciences and Engineering. Arizona State University, 2011. https://doi.org/10.3934/mbe.2011.8.515. ieee: T. Friedlander and N. Brenner, “Adaptive response and enlargement of dynamic range,” Mathematical Biosciences and Engineering, vol. 8, no. 2. Arizona State University, pp. 515–526, 2011. ista: Friedlander T, Brenner N. 2011. Adaptive response and enlargement of dynamic range. Mathematical Biosciences and Engineering. 8(2), 515–526. mla: Friedlander, Tamar, and Naama Brenner. “Adaptive Response and Enlargement of Dynamic Range.” Mathematical Biosciences and Engineering, vol. 8, no. 2, Arizona State University, 2011, pp. 515–26, doi:10.3934/mbe.2011.8.515. short: T. Friedlander, N. Brenner, Mathematical Biosciences and Engineering 8 (2011) 515–526. date_created: 2018-12-11T11:54:10Z date_published: 2011-04-02T00:00:00Z date_updated: 2021-01-12T06:53:23Z day: '02' doi: 10.3934/mbe.2011.8.515 extern: 1 intvolume: ' 8' issue: '2' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1003.2791 month: '04' oa: 1 page: 515 - 526 publication: Mathematical Biosciences and Engineering publication_status: published publisher: Arizona State University publist_id: '5291' quality_controlled: 0 status: public title: Adaptive response and enlargement of dynamic range type: journal_article volume: 8 year: '2011' ... --- _id: '1863' abstract: - lang: eng text: The Levene model is the simplest mathematical model to describe the evolution of gene frequencies in spatially subdivided populations. It provides insight into how locally varying selection promotes a population’s genetic diversity. Despite its simplicity, interesting problems have remained unsolved even in the diallelic case. In this paper we answer an open problem by establishing that for two alleles at one locus and J demes, up to 2J−1 polymorphic equilibria may coexist. We first present a proof for the case of stable monomorphisms and then show that the result also holds for protected alleles. These findings allow us to prove that any odd number (up to 2J−1) of equilibria is possible, before we extend the proof to even numbers. We conclude with some numerical results and show that for J>2, the proportion of parameter space affording this maximum is extremely small. acknowledgement: FWF 21305 author: - first_name: Sebastian full_name: Sebastian Novak id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak citation: ama: Novak S. The number of equilibria in the diallelic Levene model with multiple demes. Theoretical Population Biology. 2011;79(3):97-101. doi:10.1016/j.tpb.2010.12.002 apa: Novak, S. (2011). The number of equilibria in the diallelic Levene model with multiple demes. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2010.12.002 chicago: Novak, Sebastian. “The Number of Equilibria in the Diallelic Levene Model with Multiple Demes.” Theoretical Population Biology. Academic Press, 2011. https://doi.org/10.1016/j.tpb.2010.12.002. ieee: S. Novak, “The number of equilibria in the diallelic Levene model with multiple demes,” Theoretical Population Biology, vol. 79, no. 3. Academic Press, pp. 97–101, 2011. ista: Novak S. 2011. The number of equilibria in the diallelic Levene model with multiple demes. Theoretical Population Biology. 79(3), 97–101. mla: Novak, Sebastian. “The Number of Equilibria in the Diallelic Levene Model with Multiple Demes.” Theoretical Population Biology, vol. 79, no. 3, Academic Press, 2011, pp. 97–101, doi:10.1016/j.tpb.2010.12.002. short: S. Novak, Theoretical Population Biology 79 (2011) 97–101. date_created: 2018-12-11T11:54:25Z date_published: 2011-05-01T00:00:00Z date_updated: 2021-01-12T06:53:42Z day: '01' doi: 10.1016/j.tpb.2010.12.002 extern: 1 intvolume: ' 79' issue: '3' month: '05' page: 97 - 101 publication: Theoretical Population Biology publication_status: published publisher: Academic Press publist_id: '5236' quality_controlled: 0 status: public title: The number of equilibria in the diallelic Levene model with multiple demes tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article volume: 79 year: '2011' ... --- _id: '1975' abstract: - lang: eng text: 'Modern α-proteobacteria are thought to be closely related to the ancient symbiont of eukaryotes, an ancestor of mitochondria. Respiratory complex I from α-proteobacteria and mitochondria is well conserved at the level of the 14 "core" subunits, consistent with that notion. Mitochondrial complex I contains the core subunits, present in all species, and up to 31 "supernumerary" subunits, generally thought to have originated only within eukaryotic lineages. However, the full protein composition of an α-proteobacterial complex I has not been established previously. Here, we report the first purification and characterization of complex I from the α-proteobacterium Paracoccus denitrificans. Single particle electron microscopy shows that the complex has a well defined L-shape. Unexpectedly, in addition to the 14 core subunits, the enzyme also contains homologues of three supernumerary mitochondrial subunits as follows: B17.2, AQDQ/18, and 13 kDa (bovine nomenclature). This finding suggests that evolution of complex I via addition of supernumerary or "accessory" subunits started before the original endosymbiotic event that led to the creation of the eukaryotic cell. It also provides further confirmation that α-proteobacteria are the closest extant relatives of mitochondria.' acknowledgement: 'This work was supported by the Medical Research Council. ' author: - first_name: Chui full_name: Yip, Chui Y last_name: Yip - first_name: Michael full_name: Harbour, Michael E last_name: Harbour - first_name: Kamburapola full_name: Jayawardena, Kamburapola G last_name: Jayawardena - first_name: Ian full_name: Fearnley, Ian M last_name: Fearnley - first_name: Leonid A full_name: Leonid Sazanov id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Yip C, Harbour M, Jayawardena K, Fearnley I, Sazanov LA. Evolution of respiratory complex I &quot;Supernumerary&quot; subunits are present in the α-proteobacterial enzyme. Journal of Biological Chemistry. 2011;286(7):5023-5033. doi:10.1074/jbc.M110.194993 apa: Yip, C., Harbour, M., Jayawardena, K., Fearnley, I., & Sazanov, L. A. (2011). Evolution of respiratory complex I &quot;Supernumerary&quot; subunits are present in the α-proteobacterial enzyme. Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M110.194993 chicago: Yip, Chui, Michael Harbour, Kamburapola Jayawardena, Ian Fearnley, and Leonid A Sazanov. “Evolution of Respiratory Complex I &quot;Supernumerary&quot; Subunits Are Present in the α-Proteobacterial Enzyme.” Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology, 2011. https://doi.org/10.1074/jbc.M110.194993. ieee: C. Yip, M. Harbour, K. Jayawardena, I. Fearnley, and L. A. Sazanov, “Evolution of respiratory complex I &quot;Supernumerary&quot; subunits are present in the α-proteobacterial enzyme,” Journal of Biological Chemistry, vol. 286, no. 7. American Society for Biochemistry and Molecular Biology, pp. 5023–5033, 2011. ista: Yip C, Harbour M, Jayawardena K, Fearnley I, Sazanov LA. 2011. Evolution of respiratory complex I &quot;Supernumerary&quot; subunits are present in the α-proteobacterial enzyme. Journal of Biological Chemistry. 286(7), 5023–5033. mla: Yip, Chui, et al. “Evolution of Respiratory Complex I &quot;Supernumerary&quot; Subunits Are Present in the α-Proteobacterial Enzyme.” Journal of Biological Chemistry, vol. 286, no. 7, American Society for Biochemistry and Molecular Biology, 2011, pp. 5023–33, doi:10.1074/jbc.M110.194993. short: C. Yip, M. Harbour, K. Jayawardena, I. Fearnley, L.A. Sazanov, Journal of Biological Chemistry 286 (2011) 5023–5033. date_created: 2018-12-11T11:55:00Z date_published: 2011-02-18T00:00:00Z date_updated: 2021-01-12T06:54:27Z day: '18' doi: 10.1074/jbc.M110.194993 extern: 1 intvolume: ' 286' issue: '7' month: '02' page: 5023 - 5033 publication: Journal of Biological Chemistry publication_status: published publisher: American Society for Biochemistry and Molecular Biology publist_id: '5112' quality_controlled: 0 status: public title: Evolution of respiratory complex I "Supernumerary" subunits are present in the α-proteobacterial enzyme type: journal_article volume: 286 year: '2011' ... --- _id: '1973' abstract: - lang: eng text: Complex I is the first and largest enzyme of the respiratory chain, coupling electron transfer between NADH and ubiquinone to the translocation of four protons across the membrane. It has a central role in cellular energy production and has been implicated in many human neurodegenerative diseases. The L-shaped enzyme consists of hydrophilic and membrane domains. Previously, we determined the structure of the hydrophilic domain. Here we report the crystal structure of the Esherichia coli complex I membrane domain at 3.0 Ã. resolution. It includes six subunits, NuoL, NuoM, NuoN, NuoA, NuoJ and NuoK, with 55 transmembrane helices. The fold of the homologous antiporter-like subunits L, M and N is novel, with two inverted structural repeats of five transmembrane helices arranged, unusually, face-to-back. Each repeat includes a discontinuous transmembrane helix and forms half of a channel across the membrane. A network of conserved polar residues connects the two half-channels, completing the proton translocation pathway. Unexpectedly, lysines rather than carboxylate residues act as the main elements of the proton pump in these subunits. The fourth probable proton-translocation channel is at the interface of subunits N, K, J and A. The structure indicates that proton translocation in complex I, uniquely, involves coordinated conformational changes in six symmetrical structural elements. acknowledgement: This work was funded by the Medical Research Council. author: - first_name: Rouslan full_name: Efremov, Rouslan G last_name: Efremov - first_name: Leonid A full_name: Leonid Sazanov id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Efremov R, Sazanov LA. Structure of the membrane domain of respiratory complex i. Nature. 2011;476(7361):414-421. doi:10.1038/nature10330 apa: Efremov, R., & Sazanov, L. A. (2011). Structure of the membrane domain of respiratory complex i. Nature. Nature Publishing Group. https://doi.org/10.1038/nature10330 chicago: Efremov, Rouslan, and Leonid A Sazanov. “Structure of the Membrane Domain of Respiratory Complex I.” Nature. Nature Publishing Group, 2011. https://doi.org/10.1038/nature10330. ieee: R. Efremov and L. A. Sazanov, “Structure of the membrane domain of respiratory complex i,” Nature, vol. 476, no. 7361. Nature Publishing Group, pp. 414–421, 2011. ista: Efremov R, Sazanov LA. 2011. Structure of the membrane domain of respiratory complex i. Nature. 476(7361), 414–421. mla: Efremov, Rouslan, and Leonid A. Sazanov. “Structure of the Membrane Domain of Respiratory Complex I.” Nature, vol. 476, no. 7361, Nature Publishing Group, 2011, pp. 414–21, doi:10.1038/nature10330. short: R. Efremov, L.A. Sazanov, Nature 476 (2011) 414–421. date_created: 2018-12-11T11:54:59Z date_published: 2011-08-25T00:00:00Z date_updated: 2021-01-12T06:54:26Z day: '25' doi: 10.1038/nature10330 extern: 1 intvolume: ' 476' issue: '7361' month: '08' page: 414 - 421 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '5110' quality_controlled: 0 status: public title: Structure of the membrane domain of respiratory complex i type: journal_article volume: 476 year: '2011' ... --- _id: '1974' abstract: - lang: eng text: Complex I is the first enzyme of the respiratory chain and plays a central role in cellular energy production. It has been implicated in many human neurodegenerative diseases, as well as in ageing. One of the biggest membrane protein complexes, it is an L-shaped assembly consisting of hydrophilic and membrane domains. Previously, we have determined structures of the hydrophilic domain in several redox states. Last year was marked by fascinating breakthroughs in the understanding of the complete structure. We described the architecture of the membrane domain and of the entire bacterial complex I. X-ray analysis of the larger mitochondrial enzyme has also been published. The core subunits of the bacterial and mitochondrial enzymes have remarkably similar structures. The proposed mechanism of coupling between electron transfer and proton translocation involves long-range conformational changes, coordinated in part by a long α-helix, akin to the coupling rod of a steam engine. acknowledgement: The work in authors’ laboratory was funded by the Medical Research Council. author: - first_name: Rouslan full_name: Efremov, Rouslan G last_name: Efremov - first_name: Leonid A full_name: Leonid Sazanov id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: 'Efremov R, Sazanov LA. Respiratory complex I: “steam engine” of the cell? Current Opinion in Structural Biology. 2011;21(4):532-540. doi:10.1016/j.sbi.2011.07.002' apa: 'Efremov, R., & Sazanov, L. A. (2011). Respiratory complex I: “steam engine” of the cell? Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2011.07.002' chicago: 'Efremov, Rouslan, and Leonid A Sazanov. “Respiratory Complex I: ‘steam Engine’ of the Cell?” Current Opinion in Structural Biology. Elsevier, 2011. https://doi.org/10.1016/j.sbi.2011.07.002.' ieee: 'R. Efremov and L. A. Sazanov, “Respiratory complex I: ‘steam engine’ of the cell?,” Current Opinion in Structural Biology, vol. 21, no. 4. Elsevier, pp. 532–540, 2011.' ista: 'Efremov R, Sazanov LA. 2011. Respiratory complex I: ‘steam engine’ of the cell? Current Opinion in Structural Biology. 21(4), 532–540.' mla: 'Efremov, Rouslan, and Leonid A. Sazanov. “Respiratory Complex I: ‘steam Engine’ of the Cell?” Current Opinion in Structural Biology, vol. 21, no. 4, Elsevier, 2011, pp. 532–40, doi:10.1016/j.sbi.2011.07.002.' short: R. Efremov, L.A. Sazanov, Current Opinion in Structural Biology 21 (2011) 532–540. date_created: 2018-12-11T11:54:59Z date_published: 2011-08-01T00:00:00Z date_updated: 2021-01-12T06:54:27Z day: '01' doi: 10.1016/j.sbi.2011.07.002 extern: 1 intvolume: ' 21' issue: '4' month: '08' page: 532 - 540 publication: Current Opinion in Structural Biology publication_status: published publisher: Elsevier publist_id: '5111' quality_controlled: 0 status: public title: 'Respiratory complex I: ''steam engine'' of the cell?' type: journal_article volume: 21 year: '2011' ... --- _id: '1985' abstract: - lang: eng text: |2- In Escherichia coli, the pole-to-pole oscillation of the Min proteins directs septum formation to midcell, which is required for symmetric cell division. In vitro, protein waves emerge from the self-organization of MinD, a membrane-binding ATPase, and its activator MinE. For wave propagation, the proteins need to cycle through states of collective membrane binding and unbinding. Although MinD presumably undergoes cooperative membrane attachment, it is unclear how synchronous detachment is coordinated. We used confocal and single-molecule microscopy to elucidate the order of events during Min wave propagation. We propose that protein detachment at the rear of the wave, and the formation of the E-ring, are accomplished by two complementary processes: first, local accumulation of MinE due to rapid rebinding, leading to dynamic instability; and second, a structural change induced by membrane-interaction of MinE in an equimolar MinD-MinE (MinDE) complex, which supports the robustness of pattern formation. acknowledgement: This work was also supported by the Max Planck Society (M.L., E.F.-F., P.S.). author: - first_name: Martin full_name: Martin Loose id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - first_name: Elisabeth full_name: Fischer-Friedrich, Elisabeth last_name: Fischer Friedrich - first_name: Christoph full_name: Herold, Christoph last_name: Herold - first_name: Karsten full_name: Kruse, Karsten last_name: Kruse - first_name: Petra full_name: 'Schwille, Petra ' last_name: Schwille citation: ama: Loose M, Fischer Friedrich E, Herold C, Kruse K, Schwille P. Min protein patterns emerge from rapid rebinding and membrane interaction of MinE. Nature Structural and Molecular Biology. 2011;18(5):577-583. doi:10.1038/nsmb.2037 apa: Loose, M., Fischer Friedrich, E., Herold, C., Kruse, K., & Schwille, P. (2011). Min protein patterns emerge from rapid rebinding and membrane interaction of MinE. Nature Structural and Molecular Biology. Nature Publishing Group. https://doi.org/10.1038/nsmb.2037 chicago: Loose, Martin, Elisabeth Fischer Friedrich, Christoph Herold, Karsten Kruse, and Petra Schwille. “Min Protein Patterns Emerge from Rapid Rebinding and Membrane Interaction of MinE.” Nature Structural and Molecular Biology. Nature Publishing Group, 2011. https://doi.org/10.1038/nsmb.2037. ieee: M. Loose, E. Fischer Friedrich, C. Herold, K. Kruse, and P. Schwille, “Min protein patterns emerge from rapid rebinding and membrane interaction of MinE,” Nature Structural and Molecular Biology, vol. 18, no. 5. Nature Publishing Group, pp. 577–583, 2011. ista: Loose M, Fischer Friedrich E, Herold C, Kruse K, Schwille P. 2011. Min protein patterns emerge from rapid rebinding and membrane interaction of MinE. Nature Structural and Molecular Biology. 18(5), 577–583. mla: Loose, Martin, et al. “Min Protein Patterns Emerge from Rapid Rebinding and Membrane Interaction of MinE.” Nature Structural and Molecular Biology, vol. 18, no. 5, Nature Publishing Group, 2011, pp. 577–83, doi:10.1038/nsmb.2037. short: M. Loose, E. Fischer Friedrich, C. Herold, K. Kruse, P. Schwille, Nature Structural and Molecular Biology 18 (2011) 577–583. date_created: 2018-12-11T11:55:03Z date_published: 2011-05-01T00:00:00Z date_updated: 2021-01-12T06:54:31Z day: '01' doi: 10.1038/nsmb.2037 extern: 1 intvolume: ' 18' issue: '5' month: '05' page: 577 - 583 publication: Nature Structural and Molecular Biology publication_status: published publisher: Nature Publishing Group publist_id: '5098' quality_controlled: 0 status: public title: Min protein patterns emerge from rapid rebinding and membrane interaction of MinE type: journal_article volume: 18 year: '2011' ... --- _id: '1986' abstract: - lang: eng text: One of the most fundamental features of biological systems is probably their ability to self-organize in space and time on different scales. Despite many elaborate theoretical models of how molecular self-organization can come about, only a few experimental systems of biological origin have so far been rigorously described, due mostly to their inherent complexity. The most promising strategy of modern biophysics is thus to identify minimal biological systems showing self-organized emergent behavior. One of the best-understood examples of protein self-organization, which has recently been successfully reconstituted in vitro, is represented by the oscillations of the Min proteins in Escherichia coli. In this review, we summarize the current understanding of the mechanism of Min protein self-organization in vivo and in vitro. We discuss the potential of the Min oscillations to sense the geometry of the cell and suggest that spontaneous protein waves could be a general means of intracellular organization. We hypothesize that cooperative membrane binding and unbinding, e.g., as an energy-dependent switch, may act as an important regulatory mechanism for protein oscillations and pattern formation in the cell. author: - first_name: Martin full_name: Martin Loose id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - first_name: Karsten full_name: Kruse, Karsten last_name: Kruse - first_name: Petra full_name: 'Schwille, Petra ' last_name: Schwille citation: ama: 'Loose M, Kruse K, Schwille P. Protein self-organization: Lessons from the min system. Annual Review of Biophysics. 2011;40(1):315-336. doi:10.1146/annurev-biophys-042910-155332' apa: 'Loose, M., Kruse, K., & Schwille, P. (2011). Protein self-organization: Lessons from the min system. Annual Review of Biophysics. Annual Reviews. https://doi.org/10.1146/annurev-biophys-042910-155332' chicago: 'Loose, Martin, Karsten Kruse, and Petra Schwille. “Protein Self-Organization: Lessons from the Min System.” Annual Review of Biophysics. Annual Reviews, 2011. https://doi.org/10.1146/annurev-biophys-042910-155332.' ieee: 'M. Loose, K. Kruse, and P. Schwille, “Protein self-organization: Lessons from the min system,” Annual Review of Biophysics, vol. 40, no. 1. Annual Reviews, pp. 315–336, 2011.' ista: 'Loose M, Kruse K, Schwille P. 2011. Protein self-organization: Lessons from the min system. Annual Review of Biophysics. 40(1), 315–336.' mla: 'Loose, Martin, et al. “Protein Self-Organization: Lessons from the Min System.” Annual Review of Biophysics, vol. 40, no. 1, Annual Reviews, 2011, pp. 315–36, doi:10.1146/annurev-biophys-042910-155332.' short: M. Loose, K. Kruse, P. Schwille, Annual Review of Biophysics 40 (2011) 315–336. date_created: 2018-12-11T11:55:04Z date_published: 2011-06-09T00:00:00Z date_updated: 2021-01-12T06:54:31Z day: '09' doi: 10.1146/annurev-biophys-042910-155332 extern: 1 intvolume: ' 40' issue: '1' month: '06' page: 315 - 336 publication: Annual Review of Biophysics publication_status: published publisher: Annual Reviews publist_id: '5097' quality_controlled: 0 status: public title: 'Protein self-organization: Lessons from the min system' type: journal_article volume: 40 year: '2011' ... --- _id: '2072' abstract: - lang: eng text: Many species have morphologically and genetically differentiated sex chromosomes, such as the XY pair of mammals. Y chromosomes are often highly degenerated and carry few functional genes, so that XY males have only one copy of most Xlinked genes (whereas females have two). As a result, chromosome-wide mechanisms of dosage compensation, such as the mammalian X-inactivation, often evolve to reestablish expression balance. A similar phenomenon is expected in femaleheterogametic species, where ZW females should suffer from imbalances due to W-chromosome degeneration. However, no global dosage compensation mechanisms have been detected in the two independent ZW systems that have been studied systematically (birds and silkworm), leading to the suggestion that lack of global dosage compensation may be a general feature of female-heterogametic species. However, analyses of other independently evolved ZW systems are required to test if this is the case. In this study, we use published genomic and expression data to test for the presence of global dosage compensation in Schistosoma mansoni, a trematode parasite that causes schistosomiasis in humans. We find that Z-linked expression is reduced relative to autosomal expression in females but not males, consistent with incomplete or localized dosage compensation. This gives further support to the theory that female-heterogametic species may not require global mechanisms of dosage compensation. author: - first_name: Beatriz full_name: Vicoso, Beatriz 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. Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite. Genome Biology and Evolution. 2011;3(1):230-235. doi:10.1093/gbe/evr010 apa: Vicoso, B., & Bachtrog, D. (2011). Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evr010 chicago: Vicoso, Beatriz, and Doris Bachtrog. “Lack of Global Dosage Compensation in Schistosoma Mansoni, a Female-Heterogametic Parasite.” Genome Biology and Evolution. Oxford University Press, 2011. https://doi.org/10.1093/gbe/evr010. ieee: B. Vicoso and D. Bachtrog, “Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite,” Genome Biology and Evolution, vol. 3, no. 1. Oxford University Press, pp. 230–235, 2011. ista: Vicoso B, Bachtrog D. 2011. Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite. Genome Biology and Evolution. 3(1), 230–235. mla: Vicoso, Beatriz, and Doris Bachtrog. “Lack of Global Dosage Compensation in Schistosoma Mansoni, a Female-Heterogametic Parasite.” Genome Biology and Evolution, vol. 3, no. 1, Oxford University Press, 2011, pp. 230–35, doi:10.1093/gbe/evr010. short: B. Vicoso, D. Bachtrog, Genome Biology and Evolution 3 (2011) 230–235. date_created: 2018-12-11T11:55:33Z date_published: 2011-02-11T00:00:00Z date_updated: 2021-01-12T06:55:08Z day: '11' ddc: - '570' doi: 10.1093/gbe/evr010 extern: '1' file: - access_level: open_access checksum: 7855c134436e4f6a13d63b6606d7e8dd content_type: application/pdf creator: dernst date_created: 2019-05-10T07:41:28Z date_updated: 2020-07-14T12:45:27Z file_id: '6395' file_name: 2011_GBE_Vicoso.pdf file_size: 212547 relation: main_file file_date_updated: 2020-07-14T12:45:27Z has_accepted_license: '1' intvolume: ' 3' issue: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 230 - 235 publication: Genome Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '4966' quality_controlled: '1' status: public title: Lack of global dosage compensation in Schistosoma mansoni, a female-heterogametic parasite tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2011' ... --- _id: '2099' abstract: - lang: eng text: We present a new technique for passive and markerless facial performance capture based on anchor frames. Our method starts with high resolution per-frame geometry acquisition using state-of-theart stereo reconstruction, and proceeds to establish a single triangle mesh that is propagated through the entire performance. Leveraging the fact that facial performances often contain repetitive subsequences, we identify anchor frames as those which contain similar facial expressions to a manually chosen reference expression. Anchor frames are automatically computed over one or even multiple performances. We introduce a robust image-space tracking method that computes pixel matches directly from the reference frame to all anchor frames, and thereby to the remaining frames in the sequence via sequential matching. This allows us to propagate one reconstructed frame to an entire sequence in parallel, in contrast to previous sequential methods. Our anchored reconstruction approach also limits tracker drift and robustly handles occlusions and motion blur. The parallel tracking and mesh propagation offer low computation times. Our technique will even automatically match anchor frames across different sequences captured on different occasions, propagating a single mesh to all performances. author: - first_name: Thabo full_name: Beeler, Thabo last_name: Beeler - first_name: Fabian full_name: Hahn, Fabian last_name: Hahn - first_name: Derek full_name: Bradley, Derek J last_name: Bradley - first_name: Bernd full_name: Bernd Bickel id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Paul full_name: Beardsley, Paul A last_name: Beardsley - first_name: Craig full_name: Gotsman, Craig last_name: Gotsman - first_name: Robert full_name: Sumner, Robert W last_name: Sumner - first_name: Markus full_name: Groß, Markus S last_name: Groß citation: ama: Beeler T, Hahn F, Bradley D, et al. High-quality passive facial performance capture using anchor frames. ACM Transactions on Graphics. 2011;30(4). doi:10.1145/2010324.1964970 apa: Beeler, T., Hahn, F., Bradley, D., Bickel, B., Beardsley, P., Gotsman, C., … Groß, M. (2011). High-quality passive facial performance capture using anchor frames. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2010324.1964970 chicago: Beeler, Thabo, Fabian Hahn, Derek Bradley, Bernd Bickel, Paul Beardsley, Craig Gotsman, Robert Sumner, and Markus Groß. “High-Quality Passive Facial Performance Capture Using Anchor Frames.” ACM Transactions on Graphics. ACM, 2011. https://doi.org/10.1145/2010324.1964970. ieee: T. Beeler et al., “High-quality passive facial performance capture using anchor frames,” ACM Transactions on Graphics, vol. 30, no. 4. ACM, 2011. ista: Beeler T, Hahn F, Bradley D, Bickel B, Beardsley P, Gotsman C, Sumner R, Groß M. 2011. High-quality passive facial performance capture using anchor frames. ACM Transactions on Graphics. 30(4). mla: Beeler, Thabo, et al. “High-Quality Passive Facial Performance Capture Using Anchor Frames.” ACM Transactions on Graphics, vol. 30, no. 4, ACM, 2011, doi:10.1145/2010324.1964970. short: T. Beeler, F. Hahn, D. Bradley, B. Bickel, P. Beardsley, C. Gotsman, R. Sumner, M. Groß, ACM Transactions on Graphics 30 (2011). date_created: 2018-12-11T11:55:42Z date_published: 2011-07-01T00:00:00Z date_updated: 2021-01-12T06:55:17Z day: '01' doi: 10.1145/2010324.1964970 extern: 1 intvolume: ' 30' issue: '4' month: '07' publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '4936' quality_controlled: 0 status: public title: High-quality passive facial performance capture using anchor frames type: journal_article volume: 30 year: '2011' ... --- _id: '2098' abstract: - lang: eng text: This chapter presents a method for real-time animation of highly detailed facial expressions based on sparse motion captures data and a limited set of static example poses. The method for real-time animation of highly detailed facial expressions decomposes geometry into large-scale motion and fine-scale details, such as expression wrinkles. Both large- and fine-scale deformation algorithms run entirely on the GPU, and our implementation based on CUDA achieves an overall performance of about 30 fps. The face conveys the most relevant visual characteristics of human identity and expression. Hence, realistic facial animations or interactions with virtual avatars are important for storytelling and gameplay. However, current approaches are either computationally expensive, require very specialized capture hardware, or are extremely labor intensive. At runtime, given an arbitrary facial expression, the algorithm computes the skin strain from the relative distance between marker points and derives fine-scale corrections for the largescale deformation. During gameplay only the sparse set of marker-point positions is transmitted to the GPU. The face animation is entirely computed on the GPU where the resulting mesh can directly be used as input for the rendering stages. This data can be easily obtained by traditional capture hardware. The proposed in-game algorithm is fast. It also is easy to implement and maps well onto programmable GPUs. author: - first_name: Bernd full_name: Bernd Bickel id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Manuel full_name: Lang, Manuel last_name: Lang citation: ama: 'Bickel B, Lang M. From sparse mocap to highly detailed facial animation. In: GPU Computing Gems Emerald Edition. Science Direct; 2011:413-426. doi:10.1016/B978-0-12-384988-5.00027-9' apa: Bickel, B., & Lang, M. (2011). From sparse mocap to highly detailed facial animation. In GPU Computing Gems Emerald Edition (pp. 413–426). Science Direct. https://doi.org/10.1016/B978-0-12-384988-5.00027-9 chicago: Bickel, Bernd, and Manuel Lang. “From Sparse Mocap to Highly Detailed Facial Animation.” In GPU Computing Gems Emerald Edition, 413–26. Science Direct, 2011. https://doi.org/10.1016/B978-0-12-384988-5.00027-9. ieee: B. Bickel and M. Lang, “From sparse mocap to highly detailed facial animation,” in GPU Computing Gems Emerald Edition, Science Direct, 2011, pp. 413–426. ista: 'Bickel B, Lang M. 2011.From sparse mocap to highly detailed facial animation. In: GPU Computing Gems Emerald Edition. , 413–426.' mla: Bickel, Bernd, and Manuel Lang. “From Sparse Mocap to Highly Detailed Facial Animation.” GPU Computing Gems Emerald Edition, Science Direct, 2011, pp. 413–26, doi:10.1016/B978-0-12-384988-5.00027-9. short: B. Bickel, M. Lang, in:, GPU Computing Gems Emerald Edition, Science Direct, 2011, pp. 413–426. date_created: 2018-12-11T11:55:42Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T06:55:17Z day: '01' doi: 10.1016/B978-0-12-384988-5.00027-9 extern: 1 month: '01' page: 413 - 426 publication: GPU Computing Gems Emerald Edition publication_status: published publisher: Science Direct publist_id: '4935' quality_controlled: 0 status: public title: From sparse mocap to highly detailed facial animation type: book_chapter year: '2011' ... --- _id: '2100' abstract: - lang: eng text: Acquiring panoramic images using stitching takes a lot of time and moving objects may cause ghosting. It is also difficult to obtain a full spherical panorama, because the downward picture cannot be captured while the camera is mounted on the tripod. author: - first_name: Jonas full_name: Pfeil, Jonas last_name: Pfeil - first_name: Kristian full_name: Hildebrand, Kristian last_name: Hildebrand - first_name: Carsten full_name: Gremzow, Carsten last_name: Gremzow - 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: 'Pfeil J, Hildebrand K, Gremzow C, Bickel B, Alexa M. Throwable panoramic ball camera. In: ACM; 2011. doi:10.1145/2073370.2073373' apa: Pfeil, J., Hildebrand, K., Gremzow, C., Bickel, B., & Alexa, M. (2011). Throwable panoramic ball camera. Presented at the SIGGRAPH Asia, ACM. https://doi.org/10.1145/2073370.2073373 chicago: Pfeil, Jonas, Kristian Hildebrand, Carsten Gremzow, Bernd Bickel, and Marc Alexa. “Throwable Panoramic Ball Camera.” ACM, 2011. https://doi.org/10.1145/2073370.2073373. ieee: J. Pfeil, K. Hildebrand, C. Gremzow, B. Bickel, and M. Alexa, “Throwable panoramic ball camera,” presented at the SIGGRAPH Asia, 2011. ista: Pfeil J, Hildebrand K, Gremzow C, Bickel B, Alexa M. 2011. Throwable panoramic ball camera. SIGGRAPH Asia. mla: Pfeil, Jonas, et al. Throwable Panoramic Ball Camera. ACM, 2011, doi:10.1145/2073370.2073373. short: J. Pfeil, K. Hildebrand, C. Gremzow, B. Bickel, M. Alexa, in:, ACM, 2011. conference: name: SIGGRAPH Asia date_created: 2018-12-11T11:55:43Z date_published: 2011-12-01T00:00:00Z date_updated: 2021-01-12T06:55:19Z day: '01' doi: 10.1145/2073370.2073373 extern: 1 month: '12' publication_status: published publisher: ACM publist_id: '4934' quality_controlled: 0 status: public title: Throwable panoramic ball camera type: conference year: '2011' ... --- _id: '2116' abstract: - lang: eng text: Let P be the Ornstein-Uhlenbeck semigroup associated with the stochastic Cauchy problem dU(t)=AU(t)dt+dWH(t), where A is the generator of a C 0-semigroup S on a Banach space E, H is a Hilbert subspace of E, and W H is an H-cylindrical Brownian motion. Assuming that S restricts to a C 0-semigroup on H, we obtain L p -bounds for D H P(t). We show that if P is analytic, then the invariance assumption is fulfilled. As an application we determine the L p -domain of the generator of P explicitly in the case where S restricts to a C 0-semigroup on H which is similar to an analytic contraction semigroup. The results are applied to the 1D stochastic heat equation driven by additive space-time white noise. acknowledgement: 'The authors are supported by VIDI subsidy 639.032.201 (JM) and VICI subsidy 639.033.604 (JvN) of the Netherlands Organisation for Scientific Research (NWO). ' author: - 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 last_name: Van Neerven citation: ama: 'Maas J, Van Neerven J. Gradient estimates and domain identification for analytic Ornstein-Uhlenbeck operators. In: Parabolic Problems. Vol 80. Birkhäuser; 2011:463-477. doi:10.1007/978-3-0348-0075-4_24' apa: Maas, J., & Van Neerven, J. (2011). Gradient estimates and domain identification for analytic Ornstein-Uhlenbeck operators. In Parabolic Problems (Vol. 80, pp. 463–477). Birkhäuser. https://doi.org/10.1007/978-3-0348-0075-4_24 chicago: Maas, Jan, and Jan Van Neerven. “Gradient Estimates and Domain Identification for Analytic Ornstein-Uhlenbeck Operators.” In Parabolic Problems, 80:463–77. Birkhäuser, 2011. https://doi.org/10.1007/978-3-0348-0075-4_24. ieee: J. Maas and J. Van Neerven, “Gradient estimates and domain identification for analytic Ornstein-Uhlenbeck operators,” in Parabolic Problems, vol. 80, Birkhäuser, 2011, pp. 463–477. ista: 'Maas J, Van Neerven J. 2011.Gradient estimates and domain identification for analytic Ornstein-Uhlenbeck operators. In: Parabolic Problems. vol. 80, 463–477.' mla: Maas, Jan, and Jan Van Neerven. “Gradient Estimates and Domain Identification for Analytic Ornstein-Uhlenbeck Operators.” Parabolic Problems, vol. 80, Birkhäuser, 2011, pp. 463–77, doi:10.1007/978-3-0348-0075-4_24. short: J. Maas, J. Van Neerven, in:, Parabolic Problems, Birkhäuser, 2011, pp. 463–477. date_created: 2018-12-11T11:55:48Z date_published: 2011-06-10T00:00:00Z date_updated: 2021-01-12T06:55:24Z day: '10' doi: 10.1007/978-3-0348-0075-4_24 extern: 1 intvolume: ' 80' main_file_link: - open_access: '1' url: 'http://arxiv.org/abs/0911.4336 ' month: '06' oa: 1 page: 463 - 477 publication: Parabolic Problems publication_status: published publisher: Birkhäuser publist_id: '4918' quality_controlled: 0 status: public title: Gradient estimates and domain identification for analytic Ornstein-Uhlenbeck operators type: book_chapter volume: 80 year: '2011' ... --- _id: '2122' abstract: - lang: eng text: We study, in L1(R̃n; γ) with respect to the gaussian measure, non- tangential maximal functions and conical square functions associ- ated with the Ornstein-Uhlenbeck operator by developing a set of techniques which allow us, to some extent, to compensate for the non-doubling character of the gaussian measure. The main result asserts that conical square functions can be controlled in L1-norm by non-tangential maximal functions. Along the way we prove a change of aperture result for the latter. This complements recent results on gaussian Hardy spaces due to Mauceri and Meda. acknowledgement: The first named author is supported by Rubicon subsidy 680-50-0901 of the Netherlands Organisation for Scientific Research (NWO). The second named author is supported by VICI subsidy 639.033.604 of the Netherlands Organisation for Scientific Research (NWO author: - 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 - first_name: Pierre full_name: Portal, Pierre last_name: Portal citation: ama: Maas J, Van Neerven J, Portal P. Conical square functions and non-tangential maximal functions with respect to the Gaussian measure. Publicacions Matemàtiques. 2011;55(2):313-341. doi:10.5565/PUBLMAT_55211_03  apa: Maas, J., Van Neerven, J., & Portal, P. (2011). Conical square functions and non-tangential maximal functions with respect to the Gaussian measure. Publicacions Matemàtiques. Universitat Autònoma de Barcelona, Departament de Matemàtique. https://doi.org/10.5565/PUBLMAT_55211_03  chicago: Maas, Jan, Jan Van Neerven, and Pierre Portal. “Conical Square Functions and Non-Tangential Maximal Functions with Respect to the Gaussian Measure.” Publicacions Matemàtiques. Universitat Autònoma de Barcelona, Departament de Matemàtique, 2011. https://doi.org/10.5565/PUBLMAT_55211_03  . ieee: J. Maas, J. Van Neerven, and P. Portal, “Conical square functions and non-tangential maximal functions with respect to the Gaussian measure,” Publicacions Matemàtiques, vol. 55, no. 2. Universitat Autònoma de Barcelona, Departament de Matemàtique, pp. 313–341, 2011. ista: Maas J, Van Neerven J, Portal P. 2011. Conical square functions and non-tangential maximal functions with respect to the Gaussian measure. Publicacions Matemàtiques. 55(2), 313–341. mla: Maas, Jan, et al. “Conical Square Functions and Non-Tangential Maximal Functions with Respect to the Gaussian Measure.” Publicacions Matemàtiques, vol. 55, no. 2, Universitat Autònoma de Barcelona, Departament de Matemàtique, 2011, pp. 313–41, doi:10.5565/PUBLMAT_55211_03  . short: J. Maas, J. Van Neerven, P. Portal, Publicacions Matemàtiques 55 (2011) 313–341. date_created: 2018-12-11T11:55:50Z date_published: 2011-07-01T00:00:00Z date_updated: 2021-01-12T06:55:26Z day: '01' doi: "10.5565/PUBLMAT_55211_03\t " extern: 1 intvolume: ' 55' issue: '2' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1003.4092 month: '07' oa: 1 page: 313 - 341 publication: Publicacions Matemàtiques publication_status: published publisher: Universitat Autònoma de Barcelona, Departament de Matemàtique publist_id: '4910' quality_controlled: 0 status: public title: Conical square functions and non-tangential maximal functions with respect to the Gaussian measure type: journal_article volume: 55 year: '2011' ... --- _id: '2123' abstract: - lang: eng text: We prove a Trotter product formula for gradient flows in metric spaces. This result is applied to establish convergence in the L 2-Wasserstein metric of the splitting method for some Fokker-Planck equations and porous medium type equations perturbed by a potential. acknowledgement: The second named author is supported by Rubicon subsidy 680-50-0901 of the Netherlands Organisation for Scientific Research (NWO). article_processing_charge: No author: - first_name: Philippe full_name: Clément, Philippe last_name: Clément - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 citation: ama: Clément P, Maas J. A Trotter product formula for gradient flows in metric spaces. Journal of Evolution Equations. 2011;11(2):405-427. doi:10.1007/s00028-010-0096-5 apa: Clément, P., & Maas, J. (2011). A Trotter product formula for gradient flows in metric spaces. Journal of Evolution Equations. Birkhäuser. https://doi.org/10.1007/s00028-010-0096-5 chicago: Clément, Philippe, and Jan Maas. “A Trotter Product Formula for Gradient Flows in Metric Spaces.” Journal of Evolution Equations. Birkhäuser, 2011. https://doi.org/10.1007/s00028-010-0096-5. ieee: P. Clément and J. Maas, “A Trotter product formula for gradient flows in metric spaces,” Journal of Evolution Equations, vol. 11, no. 2. Birkhäuser, pp. 405–427, 2011. ista: Clément P, Maas J. 2011. A Trotter product formula for gradient flows in metric spaces. Journal of Evolution Equations. 11(2), 405–427. mla: Clément, Philippe, and Jan Maas. “A Trotter Product Formula for Gradient Flows in Metric Spaces.” Journal of Evolution Equations, vol. 11, no. 2, Birkhäuser, 2011, pp. 405–27, doi:10.1007/s00028-010-0096-5. short: P. Clément, J. Maas, Journal of Evolution Equations 11 (2011) 405–427. date_created: 2018-12-11T11:55:51Z date_published: 2011-01-21T00:00:00Z date_updated: 2021-11-16T08:05:46Z day: '21' doi: 10.1007/s00028-010-0096-5 extern: '1' intvolume: ' 11' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1005.0998 month: '01' oa: 1 oa_version: None page: 405 - 427 publication: Journal of Evolution Equations publication_status: published publisher: Birkhäuser publist_id: '4911' related_material: link: - relation: erratum url: https://doi.org/10.1007/s00028-012-0173-z status: public title: A Trotter product formula for gradient flows in metric spaces type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 11 year: '2011' ... --- _id: '2126' abstract: - lang: eng text: | Let K be an irreducible and reversible Markov kernel on a finite set X. We construct a metric W on the set of probability measures on X and show that with respect to this metric, the law of the continuous time Markov chain evolves as the gradient flow of the entropy. This result is a discrete counterpart of the Wasserstein gradient flow interpretation of the heat flow in Rn by Jordan, Kinderlehrer and Otto (1998). The metric W is similar to, but different from, the L2-Wasserstein metric, and is defined via a discrete variant of the Benamou–Brenier formula. acknowledgement: Supported by Rubicon subsidy 680-50-0901 of the Netherlands Organisation for Scientific Research (NWO) author: - first_name: Jan full_name: Jan Maas id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 citation: ama: Maas J. Gradient flows of the entropy for finite Markov chains. Journal of Functional Analysis. 2011;261(8):2250-2292. doi:10.1016/j.jfa.2011.06.009 apa: Maas, J. (2011). Gradient flows of the entropy for finite Markov chains. Journal of Functional Analysis. Academic Press. https://doi.org/10.1016/j.jfa.2011.06.009 chicago: Maas, Jan. “Gradient Flows of the Entropy for Finite Markov Chains.” Journal of Functional Analysis. Academic Press, 2011. https://doi.org/10.1016/j.jfa.2011.06.009 . ieee: J. Maas, “Gradient flows of the entropy for finite Markov chains,” Journal of Functional Analysis, vol. 261, no. 8. Academic Press, pp. 2250–2292, 2011. ista: Maas J. 2011. Gradient flows of the entropy for finite Markov chains. Journal of Functional Analysis. 261(8), 2250–2292. mla: Maas, Jan. “Gradient Flows of the Entropy for Finite Markov Chains.” Journal of Functional Analysis, vol. 261, no. 8, Academic Press, 2011, pp. 2250–92, doi:10.1016/j.jfa.2011.06.009 . short: J. Maas, Journal of Functional Analysis 261 (2011) 2250–2292. date_created: 2018-12-11T11:55:51Z date_published: 2011-03-04T00:00:00Z date_updated: 2021-01-12T06:55:28Z day: '04' doi: '10.1016/j.jfa.2011.06.009 ' extern: 1 intvolume: ' 261' issue: '8' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1102.5238 month: '03' oa: 1 page: 2250 - 2292 publication: Journal of Functional Analysis publication_status: published publisher: Academic Press publist_id: '4909' quality_controlled: 0 status: public title: Gradient flows of the entropy for finite Markov chains type: journal_article volume: 261 year: '2011' ... --- _id: '2138' abstract: - lang: eng text: A (diatomic) shape resonance is a metastable state of a pair of colliding atoms quasi-bound by the centrifugal barrier imposed by the angular momentum involved in the collision. The temporary trapping of the atoms' scattering wavefunction corresponds to an enhanced atom pair density at low interatomic separations. This leads to larger overlap of the wavefunctions involved in a molecule formation process such as photoassociation, rendering the process more efficient. However, for an ensemble of atoms, the atom pair density will only be enhanced if the energy of the resonance comes close to the temperature of the atomic ensemble. Herein we explore the possibility of controlling the energy of a shape resonance by shifting it toward the temperature of atoms confined in a trap. The shifts are imparted by the interaction of non-resonant light with the anisotropic polarizability of the atom pair, which affects both the centrifugal barrier and the pair's rotational and vibrational levels. We find that at laser intensities of up to 5×109 W/cm2 the pair density is increased by one order of magnitude for 87Rb atoms at 100μK and by two orders of magnitude for 88Sr atoms at 20μK. acknowledgement: Financial support from the Deutsche Forschungsgemeinschaft (Grant No. KO 2301/2), by the Spanish project FIS2008-02380 (MICINN) as well as the Grants FQM-2445 and FQM-4643 (Junta de Andaluc´ıa), Campus de Excelencia Internacional Proyecto GENIL CEB09-0010 author: - first_name: Ruzin full_name: Ağanoğlu, Ruzin last_name: Ağanoğlu - first_name: Mikhail full_name: Mikhail Lemeshko id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Břetislav full_name: Friedrich, Břetislav last_name: Friedrich - first_name: Rosario full_name: González-Férez, Rosario last_name: González Férez - first_name: Christiane full_name: Koch, Christiane P last_name: Koch citation: ama: Ağanoğlu R, Lemeshko M, Friedrich B, González Férez R, Koch C. Controlling a diatomic shape resonance with non-resonant light. Unknown. 2011. apa: Ağanoğlu, R., Lemeshko, M., Friedrich, B., González Férez, R., & Koch, C. (2011). Controlling a diatomic shape resonance with non-resonant light. Unknown. ArXiv. chicago: Ağanoğlu, Ruzin, Mikhail Lemeshko, Břetislav Friedrich, Rosario González Férez, and Christiane Koch. “Controlling a Diatomic Shape Resonance with Non-Resonant Light.” Unknown. ArXiv, 2011. ieee: R. Ağanoğlu, M. Lemeshko, B. Friedrich, R. González Férez, and C. Koch, “Controlling a diatomic shape resonance with non-resonant light,” Unknown. ArXiv, 2011. ista: Ağanoğlu R, Lemeshko M, Friedrich B, González Férez R, Koch C. 2011. Controlling a diatomic shape resonance with non-resonant light. Unknown, . mla: Ağanoğlu, Ruzin, et al. “Controlling a Diatomic Shape Resonance with Non-Resonant Light.” Unknown, ArXiv, 2011. short: R. Ağanoğlu, M. Lemeshko, B. Friedrich, R. González Férez, C. Koch, Unknown (2011). date_created: 2018-12-11T11:55:55Z date_published: 2011-05-04T00:00:00Z date_updated: 2021-01-12T06:55:32Z day: '04' extern: 1 main_file_link: - open_access: '1' url: http://arxiv.org/abs/1105.0761 month: '05' oa: 1 publication: Unknown publication_status: published publisher: ArXiv publist_id: '4886' quality_controlled: 0 status: public title: Controlling a diatomic shape resonance with non-resonant light type: preprint year: '2011' ... --- _id: '2200' abstract: - lang: eng text: We made use of supersymmetric (SUSY) quantum mechanics to find the condition under which the Stark effect problem for a polar and polarizable closed-shell diatomic molecule subjected to collinear electrostatic and nonresonant radiative fields becomes exactly solvable. The condition Δω = ω2/4(m+1)2 connects values of the dimensionless parameters ω and Δω that characterize the strengths of the permanent and induced dipole interactions of the molecule with the respective fields. The exact solutions are obtained for the \J̃ = m, m; ω, Δω) family of 'stretched' states. The field-free and strong-field limits of the combined-fields problem were found to exhibit supersymmetry and shape invariance, which is indeed the reason why they are analytically solvable. By making use of the analytic form of the \J̃ = m,m; ω, Δω) wavefunctions, we obtained simple formulae for the expectation values of the space-fixed electric dipole moment, the alignment cosine and the angular momentum squared, and derived a 'sum rule' that combines the above expectation values into a formula for the eigenenergy. The analytic expressions for the characteristics of the strongly oriented and aligned states provide direct access to the values of the interaction parameters required for creating such states in the laboratory. acknowledgement: SK thanks the ARO for financial support author: - first_name: Mikhail full_name: Mikhail Lemeshko id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Mustafa full_name: Mustafa, Mustafa K last_name: Mustafa - first_name: Sabre full_name: Kais, Sabre last_name: Kais - first_name: Břetislav full_name: Friedrich, Břetislav last_name: Friedrich citation: ama: Lemeshko M, Mustafa M, Kais S, Friedrich B. Supersymmetry identifies molecular Stark states whose eigenproperties can be obtained analytically. New Journal of Physics. 2011;13. doi:10.1088/1367-2630/13/6/063036 apa: Lemeshko, M., Mustafa, M., Kais, S., & Friedrich, B. (2011). Supersymmetry identifies molecular Stark states whose eigenproperties can be obtained analytically. New Journal of Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/13/6/063036 chicago: Lemeshko, Mikhail, Mustafa Mustafa, Sabre Kais, and Břetislav Friedrich. “Supersymmetry Identifies Molecular Stark States Whose Eigenproperties Can Be Obtained Analytically.” New Journal of Physics. IOP Publishing Ltd., 2011. https://doi.org/10.1088/1367-2630/13/6/063036. ieee: M. Lemeshko, M. Mustafa, S. Kais, and B. Friedrich, “Supersymmetry identifies molecular Stark states whose eigenproperties can be obtained analytically,” New Journal of Physics, vol. 13. IOP Publishing Ltd., 2011. ista: Lemeshko M, Mustafa M, Kais S, Friedrich B. 2011. Supersymmetry identifies molecular Stark states whose eigenproperties can be obtained analytically. New Journal of Physics. 13. mla: Lemeshko, Mikhail, et al. “Supersymmetry Identifies Molecular Stark States Whose Eigenproperties Can Be Obtained Analytically.” New Journal of Physics, vol. 13, IOP Publishing Ltd., 2011, doi:10.1088/1367-2630/13/6/063036. short: M. Lemeshko, M. Mustafa, S. Kais, B. Friedrich, New Journal of Physics 13 (2011). date_created: 2018-12-11T11:56:17Z date_published: 2011-06-20T00:00:00Z date_updated: 2021-01-12T06:55:57Z day: '20' doi: 10.1088/1367-2630/13/6/063036 extern: 1 intvolume: ' 13' main_file_link: - open_access: '1' url: 'http://arxiv.org/abs/1106.4402 ' month: '06' oa: 1 publication: New Journal of Physics publication_status: published publisher: IOP Publishing Ltd. publist_id: '4774' quality_controlled: 0 status: public title: Supersymmetry identifies molecular Stark states whose eigenproperties can be obtained analytically type: journal_article volume: 13 year: '2011' ... --- _id: '2199' abstract: - lang: eng text: By invoking supersymmetry, we found a condition under which the Stark-effect problem for a polar and polarizable molecule subject to nonresonant electric fields becomes exactly solvable for the family of stretched states. The analytic expressions for the wave function and eigenenergy and other expectation values allow one to readily reverse-engineer the problem of finding the values of the interaction parameters required for creating quantum states with preordained characteristics. The method also allows the construction of families of isospectral potentials, realizable with combined fields. acknowledgement: 'ARO ' author: - first_name: Mikhail full_name: Mikhail Lemeshko id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Mustafa full_name: Mustafa, Mustafa K last_name: Mustafa - first_name: Sabre full_name: Kais, Sabre last_name: Kais - first_name: Břetislav full_name: Friedrich, Břetislav last_name: Friedrich citation: ama: Lemeshko M, Mustafa M, Kais S, Friedrich B. Supersymmetric factorization yields exact solutions to the molecular Stark-effect problem for &quot;stretched&quot; states. Physical Review A - Atomic, Molecular, and Optical Physics. 2011;83(4). doi:10.1103/PhysRevA.83.043415 apa: Lemeshko, M., Mustafa, M., Kais, S., & Friedrich, B. (2011). Supersymmetric factorization yields exact solutions to the molecular Stark-effect problem for &quot;stretched&quot; states. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.83.043415 chicago: Lemeshko, Mikhail, Mustafa Mustafa, Sabre Kais, and Břetislav Friedrich. “Supersymmetric Factorization Yields Exact Solutions to the Molecular Stark-Effect Problem for &quot;Stretched&quot; States.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2011. https://doi.org/10.1103/PhysRevA.83.043415. ieee: M. Lemeshko, M. Mustafa, S. Kais, and B. Friedrich, “Supersymmetric factorization yields exact solutions to the molecular Stark-effect problem for &quot;stretched&quot; states,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 83, no. 4. American Physical Society, 2011. ista: Lemeshko M, Mustafa M, Kais S, Friedrich B. 2011. Supersymmetric factorization yields exact solutions to the molecular Stark-effect problem for &quot;stretched&quot; states. Physical Review A - Atomic, Molecular, and Optical Physics. 83(4). mla: Lemeshko, Mikhail, et al. “Supersymmetric Factorization Yields Exact Solutions to the Molecular Stark-Effect Problem for &quot;Stretched&quot; States.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 83, no. 4, American Physical Society, 2011, doi:10.1103/PhysRevA.83.043415. short: M. Lemeshko, M. Mustafa, S. Kais, B. Friedrich, Physical Review A - Atomic, Molecular, and Optical Physics 83 (2011). date_created: 2018-12-11T11:56:17Z date_published: 2011-04-25T00:00:00Z date_updated: 2021-01-12T06:55:56Z day: '25' doi: 10.1103/PhysRevA.83.043415 extern: 1 intvolume: ' 83' issue: '4' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1105.5262 month: '04' oa: 1 publication: Physical Review A - Atomic, Molecular, and Optical Physics publication_status: published publisher: American Physical Society publist_id: '4776' quality_controlled: 0 status: public title: Supersymmetric factorization yields exact solutions to the molecular Stark-effect problem for "stretched" states type: journal_article volume: 83 year: '2011' ... --- _id: '2198' abstract: - lang: eng text: We show that dressing polar molecules with a far-off-resonant optical field leads to new types of intermolecular potentials, which undergo a crossover from the inverse power to oscillating behavior depending on the intermolecular distance, and whose parameters can be tuned by varying the laser intensity and wavelength. We present analytic expressions for the potential energy surfaces, thereby providing direct access to the parameters of an optical field required to design intermolecular interactions experimentally. 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. Shaping interactions between polar molecules with far-off-resonant light. Physical Review A - Atomic, Molecular, and Optical Physics. 2011;83(5). doi:10.1103/PhysRevA.83.051402 apa: Lemeshko, M. (2011). Shaping interactions between polar molecules with far-off-resonant light. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.83.051402 chicago: Lemeshko, Mikhail. “Shaping Interactions between Polar Molecules with Far-off-Resonant Light.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2011. https://doi.org/10.1103/PhysRevA.83.051402. ieee: M. Lemeshko, “Shaping interactions between polar molecules with far-off-resonant light,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 83, no. 5. American Physical Society, 2011. ista: Lemeshko M. 2011. Shaping interactions between polar molecules with far-off-resonant light. Physical Review A - Atomic, Molecular, and Optical Physics. 83(5). mla: Lemeshko, Mikhail. “Shaping Interactions between Polar Molecules with Far-off-Resonant Light.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 83, no. 5, American Physical Society, 2011, doi:10.1103/PhysRevA.83.051402. short: M. Lemeshko, Physical Review A - Atomic, Molecular, and Optical Physics 83 (2011). date_created: 2018-12-11T11:56:17Z date_published: 2011-05-27T00:00:00Z date_updated: 2021-01-12T06:55:55Z day: '27' doi: 10.1103/PhysRevA.83.051402 extern: 1 intvolume: ' 83' issue: '5' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1104.1046 month: '05' oa: 1 publication: Physical Review A - Atomic, Molecular, and Optical Physics publication_status: published publisher: American Physical Society publist_id: '4775' quality_controlled: 0 status: public title: Shaping interactions between polar molecules with far-off-resonant light type: journal_article volume: 83 year: '2011' ... --- _id: '2312' abstract: - lang: eng text: Soon, the genetic basis of most human Mendelian diseases will be solved. The next challenge will be to leverage this information to uncover basic mechanisms of disease and develop new therapies. To understand how this transformation is already beginning to unfold, we focus on the ciliopathies, a class of multi-organ diseases caused by disruption of the primary cilium. Through a convergence of data involving mutant gene discovery, proteomics, and cell biology, more than a dozen phenotypically distinguishable conditions are now united as ciliopathies. Sitting at the interface between simple and complex genetic conditions, these diseases provide clues to the future direction of human genetics. author: - first_name: Gaia full_name: Gaia Novarino id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Naiara full_name: Akizu, Naiara last_name: Akizu - first_name: Joseph full_name: Gleeson, Joseph G last_name: Gleeson citation: ama: 'Novarino G, Akizu N, Gleeson J. Modeling human disease in humans: The ciliopathies. Cell. 2011;147(1):70-79. doi:10.1016/j.cell.2011.09.014' apa: 'Novarino, G., Akizu, N., & Gleeson, J. (2011). Modeling human disease in humans: The ciliopathies. Cell. Cell Press. https://doi.org/10.1016/j.cell.2011.09.014' chicago: 'Novarino, Gaia, Naiara Akizu, and Joseph Gleeson. “Modeling Human Disease in Humans: The Ciliopathies.” Cell. Cell Press, 2011. https://doi.org/10.1016/j.cell.2011.09.014.' ieee: 'G. Novarino, N. Akizu, and J. Gleeson, “Modeling human disease in humans: The ciliopathies,” Cell, vol. 147, no. 1. Cell Press, pp. 70–79, 2011.' ista: 'Novarino G, Akizu N, Gleeson J. 2011. Modeling human disease in humans: The ciliopathies. Cell. 147(1), 70–79.' mla: 'Novarino, Gaia, et al. “Modeling Human Disease in Humans: The Ciliopathies.” Cell, vol. 147, no. 1, Cell Press, 2011, pp. 70–79, doi:10.1016/j.cell.2011.09.014.' short: G. Novarino, N. Akizu, J. Gleeson, Cell 147 (2011) 70–79. date_created: 2018-12-11T11:56:55Z date_published: 2011-01-01T00:00:00Z date_updated: 2019-04-26T07:22:10Z day: '01' doi: 10.1016/j.cell.2011.09.014 extern: 1 intvolume: ' 147' issue: '1' month: '01' page: 70 - 79 publication: Cell publication_status: published publisher: Cell Press publist_id: '4615' quality_controlled: 0 status: public title: 'Modeling human disease in humans: The ciliopathies' type: review volume: 147 year: '2011' ... --- _id: '2320' abstract: - lang: eng text: The binding of polarons, or its absence, is an old and subtle topic. After defining the model we state some recent theorems of ours. First, the transition from many-body collapse to the existence of a thermodynamic limit for N polarons occurs precisely at U = 2α, where U is the electronic Coulomb repulsion and α is the polaron coupling constant. Second, if U is large enough, there is no multi-polaron binding of any kind. We also discuss the Pekar-Tomasevich approximation to the ground state energy, which is valid for large α. Finally, we derive exact results, not reported before, about the one-dimensional toy model introduced by E. P. Gross. 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 - first_name: Lawrence full_name: Thomas, Lawrence E last_name: Thomas citation: ama: 'Frank R, Lieb É, Seiringer R, Thomas L. Binding, stability, and non-binding of multi-polaron systems. In: World Scientific Publishing; 2011:21-32. doi:10.1142/9789814350365_0002' apa: 'Frank, R., Lieb, É., Seiringer, R., & Thomas, L. (2011). Binding, stability, and non-binding of multi-polaron systems (pp. 21–32). Presented at the QMath: Mathematical Results in Quantum Physics, World Scientific Publishing. https://doi.org/10.1142/9789814350365_0002' chicago: Frank, Rupert, Élliott Lieb, Robert Seiringer, and Lawrence Thomas. “Binding, Stability, and Non-Binding of Multi-Polaron Systems,” 21–32. World Scientific Publishing, 2011. https://doi.org/10.1142/9789814350365_0002. ieee: 'R. Frank, É. Lieb, R. Seiringer, and L. Thomas, “Binding, stability, and non-binding of multi-polaron systems,” presented at the QMath: Mathematical Results in Quantum Physics, 2011, pp. 21–32.' ista: 'Frank R, Lieb É, Seiringer R, Thomas L. 2011. Binding, stability, and non-binding of multi-polaron systems. QMath: Mathematical Results in Quantum Physics, 21–32.' mla: Frank, Rupert, et al. Binding, Stability, and Non-Binding of Multi-Polaron Systems. World Scientific Publishing, 2011, pp. 21–32, doi:10.1142/9789814350365_0002. short: R. Frank, É. Lieb, R. Seiringer, L. Thomas, in:, World Scientific Publishing, 2011, pp. 21–32. conference: name: 'QMath: Mathematical Results in Quantum Physics' date_created: 2018-12-11T11:56:58Z date_published: 2011-05-26T00:00:00Z date_updated: 2021-01-12T06:56:45Z day: '26' doi: 10.1142/9789814350365_0002 extern: 1 main_file_link: - open_access: '1' url: http://arxiv.org/abs/1010.0737 month: '05' oa: 1 page: 21 - 32 publication_status: published publisher: World Scientific Publishing publist_id: '4607' quality_controlled: 0 status: public title: Binding, stability, and non-binding of multi-polaron systems type: conference year: '2011' ... --- _id: '2321' abstract: - lang: eng text: We derive a sharp bound on the location of non-positive eigenvalues of Schrödinger operators on the half-line with complex-valued potentials. alternative_title: - 'Operator Theory: Advances and Applications' author: - first_name: Rupert full_name: Frank, Rupert L last_name: Frank - first_name: Ari full_name: Laptev, Ari last_name: Laptev - 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, Laptev A, Seiringer R. A sharp bound on eigenvalues of Schrödinger operators on the halfline with complex-valued potentials. In: Vol 214. Springer; 2011:39-44. doi:10.1007/978-3-7643-9994-8_3' apa: 'Frank, R., Laptev, A., & Seiringer, R. (2011). A sharp bound on eigenvalues of Schrödinger operators on the halfline with complex-valued potentials (Vol. 214, pp. 39–44). Presented at the OTAMP: Operator Theory, Analysis and Mathematical Physics, Springer. https://doi.org/10.1007/978-3-7643-9994-8_3' chicago: Frank, Rupert, Ari Laptev, and Robert Seiringer. “ A Sharp Bound on Eigenvalues of Schrödinger Operators on the Halfline with Complex-Valued Potentials,” 214:39–44. Springer, 2011. https://doi.org/10.1007/978-3-7643-9994-8_3. ieee: 'R. Frank, A. Laptev, and R. Seiringer, “ A sharp bound on eigenvalues of Schrödinger operators on the halfline with complex-valued potentials,” presented at the OTAMP: Operator Theory, Analysis and Mathematical Physics, 2011, vol. 214, pp. 39–44.' ista: 'Frank R, Laptev A, Seiringer R. 2011. A sharp bound on eigenvalues of Schrödinger operators on the halfline with complex-valued potentials. OTAMP: Operator Theory, Analysis and Mathematical Physics, Operator Theory: Advances and Applications, vol. 214, 39–44.' mla: Frank, Rupert, et al. A Sharp Bound on Eigenvalues of Schrödinger Operators on the Halfline with Complex-Valued Potentials. Vol. 214, Springer, 2011, pp. 39–44, doi:10.1007/978-3-7643-9994-8_3. short: R. Frank, A. Laptev, R. Seiringer, in:, Springer, 2011, pp. 39–44. conference: name: 'OTAMP: Operator Theory, Analysis and Mathematical Physics' date_created: 2018-12-11T11:56:59Z date_published: 2011-03-31T00:00:00Z date_updated: 2021-01-12T06:56:46Z day: '31' doi: 10.1007/978-3-7643-9994-8_3 extern: 1 intvolume: ' 214' main_file_link: - open_access: '1' url: http://arxiv.org/abs/0903.2053 month: '03' oa: 1 page: 39 - 44 publication_status: published publisher: Springer publist_id: '4606' quality_controlled: 0 status: public title: ' A sharp bound on eigenvalues of Schrödinger operators on the halfline with complex-valued potentials' type: conference volume: 214 year: '2011' ... --- _id: '233' abstract: - lang: eng text: 'For an irreducible polynomial in at most two variables the problem of representing power-free integers is investigated. ' 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 citation: ama: Browning TD. Power-free values of polynomials. Archiv der Mathematik. 2011;96(2):139-150. doi:10.1007/s00013-011-0224-7 apa: Browning, T. D. (2011). Power-free values of polynomials. Archiv Der Mathematik. Birkhäuser. https://doi.org/10.1007/s00013-011-0224-7 chicago: Browning, Timothy D. “Power-Free Values of Polynomials.” Archiv Der Mathematik. Birkhäuser, 2011. https://doi.org/10.1007/s00013-011-0224-7. ieee: T. D. Browning, “Power-free values of polynomials,” Archiv der Mathematik, vol. 96, no. 2. Birkhäuser, pp. 139–150, 2011. ista: Browning TD. 2011. Power-free values of polynomials. Archiv der Mathematik. 96(2), 139–150. mla: Browning, Timothy D. “Power-Free Values of Polynomials.” Archiv Der Mathematik, vol. 96, no. 2, Birkhäuser, 2011, pp. 139–50, doi:10.1007/s00013-011-0224-7. short: T.D. Browning, Archiv Der Mathematik 96 (2011) 139–150. date_created: 2018-12-11T11:45:21Z date_published: 2011-02-19T00:00:00Z date_updated: 2021-01-12T06:56:49Z day: '19' doi: 10.1007/s00013-011-0224-7 extern: 1 intvolume: ' 96' issue: '2' month: '02' page: 139 - 150 publication: Archiv der Mathematik publication_status: published publisher: Birkhäuser publist_id: '7670' quality_controlled: 0 status: public title: Power-free values of polynomials type: journal_article volume: 96 year: '2011' ... --- _id: '234' abstract: - lang: eng text: We investigate the average order of the divisor function at values of binary cubic forms that are reducible over Q and discuss some applications. author: - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 citation: ama: Browning TD. The divisor problem for binary cubic forms. Journal de Theorie des Nombres de Bordeaux. 2011;23(3):579-602. doi:10.5802/jtnb.778 apa: Browning, T. D. (2011). The divisor problem for binary cubic forms. Journal de Theorie Des Nombres de Bordeaux. Universite de Bordeaux. https://doi.org/10.5802/jtnb.778 chicago: Browning, Timothy D. “The Divisor Problem for Binary Cubic Forms.” Journal de Theorie Des Nombres de Bordeaux. Universite de Bordeaux, 2011. https://doi.org/10.5802/jtnb.778. ieee: T. D. Browning, “The divisor problem for binary cubic forms,” Journal de Theorie des Nombres de Bordeaux, vol. 23, no. 3. Universite de Bordeaux, pp. 579–602, 2011. ista: Browning TD. 2011. The divisor problem for binary cubic forms. Journal de Theorie des Nombres de Bordeaux. 23(3), 579–602. mla: Browning, Timothy D. “The Divisor Problem for Binary Cubic Forms.” Journal de Theorie Des Nombres de Bordeaux, vol. 23, no. 3, Universite de Bordeaux, 2011, pp. 579–602, doi:10.5802/jtnb.778. short: T.D. Browning, Journal de Theorie Des Nombres de Bordeaux 23 (2011) 579–602. date_created: 2018-12-11T11:45:21Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T06:56:53Z day: '01' doi: 10.5802/jtnb.778 extern: 1 intvolume: ' 23' issue: '3' month: '01' page: 579 - 602 publication: Journal de Theorie des Nombres de Bordeaux publication_status: published publisher: Universite de Bordeaux publist_id: '7671' quality_controlled: 0 status: public title: The divisor problem for binary cubic forms type: journal_article volume: 23 year: '2011' ... --- _id: '235' abstract: - lang: eng text: For given positive integers m and n, we consider the frequency of representations of m/n as a sum of unit fractions. article_processing_charge: No article_type: original author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Christian full_name: Elsholtz, Christian last_name: Elsholtz citation: ama: Browning TD, Elsholtz C. The number of representations of rationals as a sum of unit fractions. Illinois Journal of Mathematics. 2011;55(2):685-696. apa: Browning, T. D., & Elsholtz, C. (2011). The number of representations of rationals as a sum of unit fractions. Illinois Journal of Mathematics. University of Illinois Press. chicago: Browning, Timothy D, and Christian Elsholtz. “The Number of Representations of Rationals as a Sum of Unit Fractions.” Illinois Journal of Mathematics. University of Illinois Press, 2011. ieee: T. D. Browning and C. Elsholtz, “The number of representations of rationals as a sum of unit fractions,” Illinois Journal of Mathematics, vol. 55, no. 2. University of Illinois Press, pp. 685–696, 2011. ista: Browning TD, Elsholtz C. 2011. The number of representations of rationals as a sum of unit fractions. Illinois Journal of Mathematics. 55(2), 685–696. mla: Browning, Timothy D., and Christian Elsholtz. “The Number of Representations of Rationals as a Sum of Unit Fractions.” Illinois Journal of Mathematics, vol. 55, no. 2, University of Illinois Press, 2011, pp. 685–96. short: T.D. Browning, C. Elsholtz, Illinois Journal of Mathematics 55 (2011) 685–696. date_created: 2018-12-11T11:45:21Z date_published: 2011-07-01T00:00:00Z date_updated: 2021-01-12T06:56:57Z day: '01' extern: '1' intvolume: ' 55' issue: '2' language: - iso: eng month: '07' oa_version: None page: 685 - 696 publication: Illinois Journal of Mathematics publication_status: published publisher: University of Illinois Press publist_id: '7669' quality_controlled: '1' status: public title: The number of representations of rationals as a sum of unit fractions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 55 year: '2011' ... --- _id: '236' abstract: - lang: eng text: An asymptotic formula is established for the number of Q-rational points of bounded height on a nonsingular quartic Del Pezzo surface with a conic bundle structure. acknowledgement: "EP/E053262/1\tEngineering and Physical Sciences Research Council" author: - first_name: Régis full_name: de la Bretèche, Régis last_name: De La Bretèche - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 citation: ama: De La Bretèche R, Browning TD. Manin’s conjecture for quartic Del Pezzo surfaces with a conic fibration. Duke Mathematical Journal. 2011;160(1):1-69. doi:10.1215/00127094-1443466 apa: De La Bretèche, R., & Browning, T. D. (2011). Manin’s conjecture for quartic Del Pezzo surfaces with a conic fibration. Duke Mathematical Journal. Duke University Press. https://doi.org/10.1215/00127094-1443466 chicago: De La Bretèche, Régis, and Timothy D Browning. “Manin’s Conjecture for Quartic Del Pezzo Surfaces with a Conic Fibration.” Duke Mathematical Journal. Duke University Press, 2011. https://doi.org/10.1215/00127094-1443466. ieee: R. De La Bretèche and T. D. Browning, “Manin’s conjecture for quartic Del Pezzo surfaces with a conic fibration,” Duke Mathematical Journal, vol. 160, no. 1. Duke University Press, pp. 1–69, 2011. ista: De La Bretèche R, Browning TD. 2011. Manin’s conjecture for quartic Del Pezzo surfaces with a conic fibration. Duke Mathematical Journal. 160(1), 1–69. mla: De La Bretèche, Régis, and Timothy D. Browning. “Manin’s Conjecture for Quartic Del Pezzo Surfaces with a Conic Fibration.” Duke Mathematical Journal, vol. 160, no. 1, Duke University Press, 2011, pp. 1–69, doi:10.1215/00127094-1443466. short: R. De La Bretèche, T.D. Browning, Duke Mathematical Journal 160 (2011) 1–69. date_created: 2018-12-11T11:45:21Z date_published: 2011-09-27T00:00:00Z date_updated: 2021-01-12T06:57:00Z day: '27' doi: 10.1215/00127094-1443466 extern: 1 intvolume: ' 160' issue: '1' month: '09' page: 1 - 69 publication: Duke Mathematical Journal publication_status: published publisher: Duke University Press publist_id: '7668' quality_controlled: 0 status: public title: Manin's conjecture for quartic Del Pezzo surfaces with a conic fibration type: journal_article volume: 160 year: '2011' ... --- _id: '2390' abstract: - lang: eng text: 'We resolve several longstanding problems concerning the stability and the absence of multi-particle binding for N≥2 polarons. Fröhlich''s 1937 polaron model describes non-relativistic particles interacting with a scalar quantized field with coupling √α, and with each other by Coulomb repulsion of strength U. We prove the following: (i) While there is a known thermodynamic instability for U<2α, stability of matter does hold for U>2α, that is, the ground state energy per particle has a finite limit as N→∞. (ii) There is no binding of any kind if U exceeds a critical value that depends on α but not on N. The same results are shown to hold for the Pekar-Tomasevich model.' 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 - first_name: Lawrence full_name: Thomas, Lawrence E last_name: Thomas citation: ama: Frank R, Lieb É, Seiringer R, Thomas L. Stability and absence of binding for multi-polaron systems. Publications Mathematiques de l Institut des Hautes Etudes Scientifiques. 2011;113(1):39-67. doi:10.1007/s10240-011-0031-5 apa: Frank, R., Lieb, É., Seiringer, R., & Thomas, L. (2011). Stability and absence of binding for multi-polaron systems. Publications Mathematiques de l Institut Des Hautes Etudes Scientifiques. Springer. https://doi.org/10.1007/s10240-011-0031-5 chicago: Frank, Rupert, Élliott Lieb, Robert Seiringer, and Lawrence Thomas. “Stability and Absence of Binding for Multi-Polaron Systems.” Publications Mathematiques de l Institut Des Hautes Etudes Scientifiques. Springer, 2011. https://doi.org/10.1007/s10240-011-0031-5. ieee: R. Frank, É. Lieb, R. Seiringer, and L. Thomas, “Stability and absence of binding for multi-polaron systems,” Publications Mathematiques de l Institut des Hautes Etudes Scientifiques, vol. 113, no. 1. Springer, pp. 39–67, 2011. ista: Frank R, Lieb É, Seiringer R, Thomas L. 2011. Stability and absence of binding for multi-polaron systems. Publications Mathematiques de l Institut des Hautes Etudes Scientifiques. 113(1), 39–67. mla: Frank, Rupert, et al. “Stability and Absence of Binding for Multi-Polaron Systems.” Publications Mathematiques de l Institut Des Hautes Etudes Scientifiques, vol. 113, no. 1, Springer, 2011, pp. 39–67, doi:10.1007/s10240-011-0031-5. short: R. Frank, É. Lieb, R. Seiringer, L. Thomas, Publications Mathematiques de l Institut Des Hautes Etudes Scientifiques 113 (2011) 39–67. date_created: 2018-12-11T11:57:23Z date_published: 2011-06-01T00:00:00Z date_updated: 2021-01-12T06:57:12Z day: '01' doi: 10.1007/s10240-011-0031-5 extern: 1 intvolume: ' 113' issue: '1' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1004.4892 month: '06' oa: 1 page: 39 - 67 publication: Publications Mathematiques de l Institut des Hautes Etudes Scientifiques publication_status: published publisher: Springer publist_id: '4534' quality_controlled: 0 status: public title: Stability and absence of binding for multi-polaron systems type: journal_article volume: 113 year: '2011' ... --- _id: '2391' abstract: - lang: eng text: The change in energy of an ideal Fermi gas when a local one-body potential is inserted into the system, or when the density is changed locally, are important quantities in condensed matter physics. We show that they can be rigorously bounded from below by a universal constant times the value given by the semiclassical approximation. 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. Energy cost to make a hole in the fermi sea. Physical Review Letters. 2011;106(15). doi:10.1103/PhysRevLett.106.150402 apa: Frank, R., Lewin, M., Lieb, É., & Seiringer, R. (2011). Energy cost to make a hole in the fermi sea. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.106.150402 chicago: Frank, Rupert, Mathieu Lewin, Élliott Lieb, and Robert Seiringer. “Energy Cost to Make a Hole in the Fermi Sea.” Physical Review Letters. American Physical Society, 2011. https://doi.org/10.1103/PhysRevLett.106.150402. ieee: R. Frank, M. Lewin, É. Lieb, and R. Seiringer, “Energy cost to make a hole in the fermi sea,” Physical Review Letters, vol. 106, no. 15. American Physical Society, 2011. ista: Frank R, Lewin M, Lieb É, Seiringer R. 2011. Energy cost to make a hole in the fermi sea. Physical Review Letters. 106(15). mla: Frank, Rupert, et al. “Energy Cost to Make a Hole in the Fermi Sea.” Physical Review Letters, vol. 106, no. 15, American Physical Society, 2011, doi:10.1103/PhysRevLett.106.150402. short: R. Frank, M. Lewin, É. Lieb, R. Seiringer, Physical Review Letters 106 (2011). date_created: 2018-12-11T11:57:24Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T06:57:12Z day: '01' doi: 10.1103/PhysRevLett.106.150402 extern: 1 intvolume: ' 106' issue: '15' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1102.1414 month: '01' oa: 1 publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '4535' quality_controlled: 0 status: public title: Energy cost to make a hole in the fermi sea type: journal_article volume: 106 year: '2011' ... --- _id: '239' abstract: - lang: eng text: An effective search bound is established for the least non-trivial integer zero of an arbitrary cubic form C ε ℤ[X 1,...,X n], provided that n ≥ 17. 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: Rainer full_name: Dietmann, Rainer last_name: Dietmann - first_name: Peter full_name: Elliott, Peter last_name: Elliott citation: ama: Browning TD, Dietmann R, Elliott P. Least zero of a cubic form. Mathematische Annalen. 2011;352(3):745-778. doi:10.1007/s00208-011-0651-6 apa: Browning, T. D., Dietmann, R., & Elliott, P. (2011). Least zero of a cubic form. Mathematische Annalen. Springer. https://doi.org/10.1007/s00208-011-0651-6 chicago: Browning, Timothy D, Rainer Dietmann, and Peter Elliott. “Least Zero of a Cubic Form.” Mathematische Annalen. Springer, 2011. https://doi.org/10.1007/s00208-011-0651-6. ieee: T. D. Browning, R. Dietmann, and P. Elliott, “Least zero of a cubic form,” Mathematische Annalen, vol. 352, no. 3. Springer, pp. 745–778, 2011. ista: Browning TD, Dietmann R, Elliott P. 2011. Least zero of a cubic form. Mathematische Annalen. 352(3), 745–778. mla: Browning, Timothy D., et al. “Least Zero of a Cubic Form.” Mathematische Annalen, vol. 352, no. 3, Springer, 2011, pp. 745–78, doi:10.1007/s00208-011-0651-6. short: T.D. Browning, R. Dietmann, P. Elliott, Mathematische Annalen 352 (2011) 745–778. date_created: 2018-12-11T11:45:22Z date_published: 2011-03-06T00:00:00Z date_updated: 2021-01-12T06:57:11Z day: '06' doi: 10.1007/s00208-011-0651-6 extern: 1 intvolume: ' 352' issue: '3' month: '03' page: 745 - 778 publication: Mathematische Annalen publication_status: published publisher: Springer publist_id: '7665' quality_controlled: 0 status: public title: Least zero of a cubic form type: journal_article volume: 352 year: '2011' ... --- _id: '2393' abstract: - lang: eng text: We investigate the low energy excitation spectrum of a Bose gas with weak, long range repulsive interactions. In particular, we prove that the Bogoliubov spectrum of elementary excitations with linear dispersion relation for small momentum becomes exact in the mean-field limit. author: - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Seiringer R. The excitation spectrum for weakly interacting Bosons. Communications in Mathematical Physics. 2011;306(2):565-578. doi:10.1007/s00220-011-1261-6 apa: Seiringer, R. (2011). The excitation spectrum for weakly interacting Bosons. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-011-1261-6 chicago: Seiringer, Robert. “The Excitation Spectrum for Weakly Interacting Bosons.” Communications in Mathematical Physics. Springer, 2011. https://doi.org/10.1007/s00220-011-1261-6. ieee: R. Seiringer, “The excitation spectrum for weakly interacting Bosons,” Communications in Mathematical Physics, vol. 306, no. 2. Springer, pp. 565–578, 2011. ista: Seiringer R. 2011. The excitation spectrum for weakly interacting Bosons. Communications in Mathematical Physics. 306(2), 565–578. mla: Seiringer, Robert. “The Excitation Spectrum for Weakly Interacting Bosons.” Communications in Mathematical Physics, vol. 306, no. 2, Springer, 2011, pp. 565–78, doi:10.1007/s00220-011-1261-6. short: R. Seiringer, Communications in Mathematical Physics 306 (2011) 565–578. date_created: 2018-12-11T11:57:24Z date_published: 2011-09-01T00:00:00Z date_updated: 2021-01-12T06:57:13Z day: '01' doi: 10.1007/s00220-011-1261-6 extern: 1 intvolume: ' 306' issue: '2' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1008.5349 month: '09' oa: 1 page: 565 - 578 publication: Communications in Mathematical Physics publication_status: published publisher: Springer publist_id: '4533' quality_controlled: 0 status: public title: The excitation spectrum for weakly interacting Bosons type: journal_article volume: 306 year: '2011' ... --- _id: '2436' abstract: - lang: eng text: 'Let EMBEDk→d be the following algorithmic problem: Given a finite simplicial complex K of dimension at most k, does there exist a (piecewise linear) embedding of K into Rd? Known results easily imply the polynomiality of EMBEDk→2 (k = 1; 2; the case k = 1, d = 2 is graph planarity) and of EMBEDk→2k for all k ≥ 3. We show that the celebrated result of Novikov on the algorithmic unsolvability of recognizing the 5-sphere implies that EMBEDd→d and EMBED (d-1)→d are undecidable for each d ≥ 5. Our main result is the NP-hardness of EMBED2→4 and, more generally, of EMBED k→d for all k; d with d ≥ 4 and d ≥ k ≥ (2d - 2)/3. These dimensions fall outside the metastable range of a theorem of Haefliger and Weber, which characterizes embeddability using the deleted product obstruction. Our reductions are based on examples, due to Segal, Spież, Freedman, Krushkal, Teichner, and Skopenkov, showing that outside the metastable range the deleted product obstruction is not sufficient to characterize embeddability. ' acknowledgement: |- We would like to thank Colin Rourke for explanations concerning PL topology and for examples showing the difference between PL embeddability and topological embeddability mentioned in Section 2. We also thank Michael Joswig, Gil Kalai, Frank Lutz, Alexander Nabutovsky, and Robin Thomas for kindly answering our questions. The second author would also like to thank Sergio Cabello for helpful discussions regarding linear-time algorithms for EMBED2!2. Finally, we are grateful to two anonymous referees for careful reading and valuable suggestions. Research of U.Wagner was supported by the Swiss National Science Foundation (SNF Projects 200021-116741 and 200021-125309). author: - first_name: Jiří full_name: Matoušek, Jiří last_name: Matoušek - first_name: Martin full_name: Martin Tancer id: 38AC689C-F248-11E8-B48F-1D18A9856A87 last_name: Tancer orcid: 0000-0002-1191-6714 - first_name: Uli full_name: Uli Wagner id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: Matoušek J, Tancer M, Wagner U. Hardness of embedding simplicial complexes in Rd. Journal of the European Mathematical Society. 2011;13(2):259-295. doi:10.4171/JEMS/252 apa: Matoušek, J., Tancer, M., & Wagner, U. (2011). Hardness of embedding simplicial complexes in Rd. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/252 chicago: Matoušek, Jiří, Martin Tancer, and Uli Wagner. “Hardness of Embedding Simplicial Complexes in Rd.” Journal of the European Mathematical Society. European Mathematical Society, 2011. https://doi.org/10.4171/JEMS/252. ieee: J. Matoušek, M. Tancer, and U. Wagner, “Hardness of embedding simplicial complexes in Rd,” Journal of the European Mathematical Society, vol. 13, no. 2. European Mathematical Society, pp. 259–295, 2011. ista: Matoušek J, Tancer M, Wagner U. 2011. Hardness of embedding simplicial complexes in Rd. Journal of the European Mathematical Society. 13(2), 259–295. mla: Matoušek, Jiří, et al. “Hardness of Embedding Simplicial Complexes in Rd.” Journal of the European Mathematical Society, vol. 13, no. 2, European Mathematical Society, 2011, pp. 259–95, doi:10.4171/JEMS/252. short: J. Matoušek, M. Tancer, U. Wagner, Journal of the European Mathematical Society 13 (2011) 259–295. date_created: 2018-12-11T11:57:39Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T06:57:28Z day: '01' doi: 10.4171/JEMS/252 extern: 1 intvolume: ' 13' issue: '2' month: '01' page: 259 - 295 publication: Journal of the European Mathematical Society publication_status: published publisher: European Mathematical Society publist_id: '4470' quality_controlled: 0 status: public title: Hardness of embedding simplicial complexes in Rd type: journal_article volume: 13 year: '2011' ... --- _id: '2437' abstract: - lang: eng text: We introduce a new notion of minors for simplicial complexes (hypergraphs), so-called homological minors. Our motivation is to propose a general approach to attack certain extremal problems for sparse simplicial complexes and the corresponding threshold problems for random complexes. In this paper, we focus on threshold problems. The basic model for random complexes is the Linial-Meshulam model Xk(n, p). By definition, such a complex has n vertices, a complete (k -1)-dimensional skeleton, and every possible k-dimensional simplex is chosen independently with probability p. We show that for every k, t≥ 1, there is a constant C = C(k, t) such that for p≥ C/n, the random complex Xk(n, p) asymptotically almost surely contains K tk (the complete k-dimensional complex on t vertices) as a homological minor. As corollary, the threshold for (topological) embeddability of Xk(n, p) into R2k is at p = θ(1/n). The method can be extended to other models of random complexes (for which the lower skeleta are not necessarily complete) and also to more general Tverberg-type problems, where instead of continuous maps without doubly covered image points (embeddings), we consider maps without qfold covered image points. author: - first_name: Uli full_name: Uli Wagner id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: 'Wagner U. Minors in random and expanding hypergraphs. In: ACM; 2011:351-360. doi:10.1145/1998196.1998256' apa: 'Wagner, U. (2011). Minors in random and expanding hypergraphs (pp. 351–360). Presented at the SGC: Symposuim on Computational Geometry, ACM. https://doi.org/10.1145/1998196.1998256' chicago: Wagner, Uli. “Minors in Random and Expanding Hypergraphs,” 351–60. ACM, 2011. https://doi.org/10.1145/1998196.1998256. ieee: 'U. Wagner, “Minors in random and expanding hypergraphs,” presented at the SGC: Symposuim on Computational Geometry, 2011, pp. 351–360.' ista: 'Wagner U. 2011. Minors in random and expanding hypergraphs. SGC: Symposuim on Computational Geometry, 351–360.' mla: Wagner, Uli. Minors in Random and Expanding Hypergraphs. ACM, 2011, pp. 351–60, doi:10.1145/1998196.1998256. short: U. Wagner, in:, ACM, 2011, pp. 351–360. conference: name: 'SGC: Symposuim on Computational Geometry' date_created: 2018-12-11T11:57:39Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T06:57:29Z day: '01' doi: 10.1145/1998196.1998256 extern: 1 month: '01' page: 351 - 360 publication_status: published publisher: ACM publist_id: '4469' quality_controlled: 0 status: public title: Minors in random and expanding hypergraphs type: conference year: '2011' ... --- _id: '2454' abstract: - lang: eng text: Within a multicellular tissue cells may coordinately form a singular or multiple polar axes, but it is unclear whether a common mechanism governs different types of polar axis formation. The phosphorylation status of PIN proteins, which is directly affected by the PINOID (PID) protein kinase and the PP2A protein phosphatase, is known to regulate the apical-basal polarity of PIN localization in bipolar cells of roots and shoot apices. Here, we provide evidence that the phosphorylation status-mediated PIN polarity switch is widely used to modulate cellular processes in Arabidopsis including multipolar pavement cells (PC) with interdigitated lobes and indentations. The degree of PC interdigitation was greatly reduced either when the FYPP1 gene, which encodes a PP2A called phytochrome-associated serine/threonine protein phosphatase, was knocked out or when the PID gene was overexpressed (35S:PID). These genetic modifications caused PIN1 localization to switch from lobe to indentation regions. The PP2A and PID mediated switching of PIN1 localization is strikingly similar to their regulation of the apical-basal polarity switch of PIN proteins in other cells. Our findings suggest a common mechanism for the regulation of PIN1 polarity formation, a fundamental cellular process that is crucial for pattern formation both at the tissue/organ and cellular levels. author: - first_name: Hongjiang full_name: Hongjiang Li id: 33CA54A6-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0001-5039-9660 - first_name: Deshu full_name: Lin, Deshu last_name: Lin - first_name: Pankaj full_name: Dhonukshe, Pankaj B last_name: Dhonukshe - first_name: Shingo full_name: Nagawa, Shingo last_name: Nagawa - first_name: Dandan full_name: Chen, Dandan last_name: Chen - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Ben full_name: Scheres, Ben last_name: Scheres - first_name: Hongwei full_name: Guo, Hongwei last_name: Guo - first_name: Zhenbiao full_name: Yang, Zhenbiao last_name: Yang citation: ama: Li H, Lin D, Dhonukshe P, et al. Phosphorylation switch modulates the interdigitated pattern of PIN1 localization and cell expansion in Arabidopsis leaf epidermis. Cell Research. 2011;21(6):970-978. doi:10.1038/cr.2011.49 apa: Li, H., Lin, D., Dhonukshe, P., Nagawa, S., Chen, D., Friml, J., … Yang, Z. (2011). Phosphorylation switch modulates the interdigitated pattern of PIN1 localization and cell expansion in Arabidopsis leaf epidermis. Cell Research. Nature Publishing Group. https://doi.org/10.1038/cr.2011.49 chicago: Li, Hongjiang, Deshu Lin, Pankaj Dhonukshe, Shingo Nagawa, Dandan Chen, Jiří Friml, Ben Scheres, Hongwei Guo, and Zhenbiao Yang. “Phosphorylation Switch Modulates the Interdigitated Pattern of PIN1 Localization and Cell Expansion in Arabidopsis Leaf Epidermis.” Cell Research. Nature Publishing Group, 2011. https://doi.org/10.1038/cr.2011.49. ieee: H. Li et al., “Phosphorylation switch modulates the interdigitated pattern of PIN1 localization and cell expansion in Arabidopsis leaf epidermis,” Cell Research, vol. 21, no. 6. Nature Publishing Group, pp. 970–978, 2011. ista: Li H, Lin D, Dhonukshe P, Nagawa S, Chen D, Friml J, Scheres B, Guo H, Yang Z. 2011. Phosphorylation switch modulates the interdigitated pattern of PIN1 localization and cell expansion in Arabidopsis leaf epidermis. Cell Research. 21(6), 970–978. mla: Li, Hongjiang, et al. “Phosphorylation Switch Modulates the Interdigitated Pattern of PIN1 Localization and Cell Expansion in Arabidopsis Leaf Epidermis.” Cell Research, vol. 21, no. 6, Nature Publishing Group, 2011, pp. 970–78, doi:10.1038/cr.2011.49. short: H. Li, D. Lin, P. Dhonukshe, S. Nagawa, D. Chen, J. Friml, B. Scheres, H. Guo, Z. Yang, Cell Research 21 (2011) 970–978. date_created: 2018-12-11T11:57:45Z date_published: 2011-06-01T00:00:00Z date_updated: 2021-01-12T06:57:35Z day: '01' doi: 10.1038/cr.2011.49 extern: 1 intvolume: ' 21' issue: '6' main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203702/ month: '06' oa: 1 page: 970 - 978 publication: Cell Research publication_status: published publisher: Nature Publishing Group publist_id: '4449' quality_controlled: 0 status: public title: Phosphorylation switch modulates the interdigitated pattern of PIN1 localization and cell expansion in Arabidopsis leaf epidermis type: journal_article volume: 21 year: '2011' ... --- _id: '2460' abstract: - lang: eng text: In unicellular and multicellular organisms, cell polarity is essential for a wide range of biological processes. An important feature of cell polarity is the asymmetric distribution of proteins in or at the plasma membrane. In plants such polar localized proteins play various specific roles ranging from organizing cell morphogenesis, asymmetric cell division, pathogen defense, nutrient transport and establishment of hormone gradients for developmental patterning. Moreover, flexible respecification of cell polarities enables plants to adjust their physiology and development to environmental changes. Having evolved multicellularity independently and lacking major cell polarity mechanisms of animal cells, plants came up with alternative solutions to generate and respecify cell polarity as well as to regulate polar domains at the plasma membrane. author: - first_name: Jan full_name: Dettmer, Jan last_name: Dettmer - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Dettmer J, Friml J. Cell polarity in plants: When two do the same, it is not the same... Current Opinion in Cell Biology. 2011;23(6):686-696. doi:10.1016/j.ceb.2011.09.006' apa: 'Dettmer, J., & Friml, J. (2011). Cell polarity in plants: When two do the same, it is not the same... Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2011.09.006' chicago: 'Dettmer, Jan, and Jiří Friml. “Cell Polarity in Plants: When Two Do the Same, It Is Not the Same...” Current Opinion in Cell Biology. Elsevier, 2011. https://doi.org/10.1016/j.ceb.2011.09.006.' ieee: 'J. Dettmer and J. Friml, “Cell polarity in plants: When two do the same, it is not the same...,” Current Opinion in Cell Biology, vol. 23, no. 6. Elsevier, pp. 686–696, 2011.' ista: 'Dettmer J, Friml J. 2011. Cell polarity in plants: When two do the same, it is not the same... Current Opinion in Cell Biology. 23(6), 686–696.' mla: 'Dettmer, Jan, and Jiří Friml. “Cell Polarity in Plants: When Two Do the Same, It Is Not the Same...” Current Opinion in Cell Biology, vol. 23, no. 6, Elsevier, 2011, pp. 686–96, doi:10.1016/j.ceb.2011.09.006.' short: J. Dettmer, J. Friml, Current Opinion in Cell Biology 23 (2011) 686–696. date_created: 2018-12-11T11:57:47Z date_published: 2011-12-01T00:00:00Z date_updated: 2021-01-12T06:57:37Z day: '01' doi: 10.1016/j.ceb.2011.09.006 extern: '1' intvolume: ' 23' issue: '6' language: - iso: eng month: '12' oa_version: None page: 686 - 696 publication: Current Opinion in Cell Biology publication_status: published publisher: Elsevier publist_id: '4443' quality_controlled: '1' status: public title: 'Cell polarity in plants: When two do the same, it is not the same...' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2011' ... --- _id: '2511' abstract: - lang: eng text: Parkinson's disease is a common neurodegenerative disorder characterized by a profound motor disability that is traceable to the emergence of synchronous, rhythmic spiking in neurons of the external segment of the globus pallidus (GPe). The origins of this pathophysiology are poorly defined for the generation of pacemaking. After the induction of a parkinsonian state in mice, there was a progressive decline in autonomous GPe pacemaking, which normally serves to desynchronize activity. The loss was attributable to the downregulation of an ion channel that is essential in pacemaking, the hyperpolarization and cyclic nucleotide-gated (HCN) channel. Viral delivery of HCN2 subunits restored pacemaking and reduced burst spiking in GPe neurons. However, the motor disability induced by dopamine (DA) depletion was not reversed, suggesting that the loss of pacemaking was a consequence, rather than a cause, of key network pathophysiology, a conclusion that is consistent with the ability of L-type channel antagonists to attenuate silencing after DA depletion. author: - first_name: Savio full_name: Chan, Savio last_name: Chan - first_name: Kelly full_name: Glajch, Kelly E last_name: Glajch - first_name: Tracy full_name: Gertler, Tracy S last_name: Gertler - first_name: Jaime full_name: Guzmán, Jaime N last_name: Guzmán - first_name: Jeff full_name: Mercer, Jeff N last_name: Mercer - first_name: Alan full_name: Lewis, Alan S last_name: Lewis - first_name: Alan full_name: Goldberg, Alan B last_name: Goldberg - first_name: Tatiana full_name: Tkatch, Tatiana last_name: Tkatch - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Sheila full_name: Fleming, Sheila M last_name: Fleming - first_name: Dane full_name: Chetkovich, Dane M last_name: Chetkovich - first_name: Pavel full_name: Osten, Pavel last_name: Osten - first_name: Hitoshi full_name: Kita, Hitoshi last_name: Kita - first_name: James full_name: Surmeier, James D last_name: Surmeier citation: ama: Chan S, Glajch K, Gertler T, et al. HCN channelopathy in external globus pallidus neurons in models of Parkinson s disease. Nature Neuroscience. 2011;14(1):85-94. doi:10.1038/nn.2692 apa: Chan, S., Glajch, K., Gertler, T., Guzmán, J., Mercer, J., Lewis, A., … Surmeier, J. (2011). HCN channelopathy in external globus pallidus neurons in models of Parkinson s disease. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.2692 chicago: Chan, Savio, Kelly Glajch, Tracy Gertler, Jaime Guzmán, Jeff Mercer, Alan Lewis, Alan Goldberg, et al. “HCN Channelopathy in External Globus Pallidus Neurons in Models of Parkinson s Disease.” Nature Neuroscience. Nature Publishing Group, 2011. https://doi.org/10.1038/nn.2692. ieee: S. Chan et al., “HCN channelopathy in external globus pallidus neurons in models of Parkinson s disease,” Nature Neuroscience, vol. 14, no. 1. Nature Publishing Group, pp. 85–94, 2011. ista: Chan S, Glajch K, Gertler T, Guzmán J, Mercer J, Lewis A, Goldberg A, Tkatch T, Shigemoto R, Fleming S, Chetkovich D, Osten P, Kita H, Surmeier J. 2011. HCN channelopathy in external globus pallidus neurons in models of Parkinson s disease. Nature Neuroscience. 14(1), 85–94. mla: Chan, Savio, et al. “HCN Channelopathy in External Globus Pallidus Neurons in Models of Parkinson s Disease.” Nature Neuroscience, vol. 14, no. 1, Nature Publishing Group, 2011, pp. 85–94, doi:10.1038/nn.2692. short: S. Chan, K. Glajch, T. Gertler, J. Guzmán, J. Mercer, A. Lewis, A. Goldberg, T. Tkatch, R. Shigemoto, S. Fleming, D. Chetkovich, P. Osten, H. Kita, J. Surmeier, Nature Neuroscience 14 (2011) 85–94. date_created: 2018-12-11T11:58:06Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T06:57:56Z day: '01' doi: 10.1038/nn.2692 extern: 1 intvolume: ' 14' issue: '1' month: '01' page: 85 - 94 publication: Nature Neuroscience publication_status: published publisher: Nature Publishing Group publist_id: '4390' quality_controlled: 0 status: public title: HCN channelopathy in external globus pallidus neurons in models of Parkinson s disease type: journal_article volume: 14 year: '2011' ... --- _id: '2512' abstract: - lang: eng text: GABAergic inhibition plays a central role in the control of pyramidal cell ensemble activities; thus, any signaling mechanism that regulates inhibition is able to fine-tune network patterns. Here, we provide evidence that the retrograde nitric oxide (NO)- cGMP cascade triggered by NMDA receptor (NMDAR) activation plays a role in the control of hippocampal GABAergic transmission in mice. GABAergic synapses express neuronal nitric oxide synthase (nNOS) postsynaptically and NO receptors (NO-sensitive guanylyl cyclase) in the presynaptic terminals. We hypothesized that-similar to glutamatergic synapses-the Ca 2+ transients required to activate nNOS were provided by NMDA receptor activation. Indeed, administration of 5 μm NMDA induced a robust nNOS-dependent cGMP production in GABAergic terminals, selectively in the CA1 and CA3c areas. Furthermore, using preembedding, postembedding, and SDS-digested freeze-fracture replica immunogold labeling, we provided quantitative immunocytochemical evidence that NMDAR subunits GluN1, GluN2A, and GluN2B were present in most somatic GABAergic synapses postsynaptically. These data indicate that NMDARs can modulate hippocampal GABAergic inhibition via NO- cGMP signaling in an activity-dependent manner and that this effect is subregion specific in the mouse hippocampus. author: - first_name: Eszter full_name: Szabadits, Eszter last_name: Szabadits - first_name: Csaba full_name: Cserép, Csaba last_name: Cserép - first_name: András full_name: Szonyi, András last_name: Szonyi - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Masahiko full_name: Watanabe, Masahiko last_name: Watanabe - first_name: Shigeyoshi full_name: Itohara, Shigeyoshi last_name: Itohara - first_name: Tamás full_name: Freund, Tamás F last_name: Freund - first_name: Gábor full_name: Nyíri, Gábor last_name: Nyíri citation: ama: Szabadits E, Cserép C, Szonyi A, et al. NMDA receptors in hippocampal GABAergic synapses and their role in nitric oxide signaling. Journal of Neuroscience. 2011;31(16):5893-5904. doi:10.1523/JNEUROSCI.5938-10.2011 apa: Szabadits, E., Cserép, C., Szonyi, A., Fukazawa, Y., Shigemoto, R., Watanabe, M., … Nyíri, G. (2011). NMDA receptors in hippocampal GABAergic synapses and their role in nitric oxide signaling. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.5938-10.2011 chicago: Szabadits, Eszter, Csaba Cserép, András Szonyi, Yugo Fukazawa, Ryuichi Shigemoto, Masahiko Watanabe, Shigeyoshi Itohara, Tamás Freund, and Gábor Nyíri. “NMDA Receptors in Hippocampal GABAergic Synapses and Their Role in Nitric Oxide Signaling.” Journal of Neuroscience. Society for Neuroscience, 2011. https://doi.org/10.1523/JNEUROSCI.5938-10.2011. ieee: E. Szabadits et al., “NMDA receptors in hippocampal GABAergic synapses and their role in nitric oxide signaling,” Journal of Neuroscience, vol. 31, no. 16. Society for Neuroscience, pp. 5893–5904, 2011. ista: Szabadits E, Cserép C, Szonyi A, Fukazawa Y, Shigemoto R, Watanabe M, Itohara S, Freund T, Nyíri G. 2011. NMDA receptors in hippocampal GABAergic synapses and their role in nitric oxide signaling. Journal of Neuroscience. 31(16), 5893–5904. mla: Szabadits, Eszter, et al. “NMDA Receptors in Hippocampal GABAergic Synapses and Their Role in Nitric Oxide Signaling.” Journal of Neuroscience, vol. 31, no. 16, Society for Neuroscience, 2011, pp. 5893–904, doi:10.1523/JNEUROSCI.5938-10.2011. short: E. Szabadits, C. Cserép, A. Szonyi, Y. Fukazawa, R. Shigemoto, M. Watanabe, S. Itohara, T. Freund, G. Nyíri, Journal of Neuroscience 31 (2011) 5893–5904. date_created: 2018-12-11T11:58:06Z date_published: 2011-04-20T00:00:00Z date_updated: 2021-01-12T06:57:56Z day: '20' doi: 10.1523/JNEUROSCI.5938-10.2011 extern: 1 intvolume: ' 31' issue: '16' month: '04' page: 5893 - 5904 publication: Journal of Neuroscience publication_status: published publisher: Society for Neuroscience publist_id: '4389' quality_controlled: 0 status: public title: NMDA receptors in hippocampal GABAergic synapses and their role in nitric oxide signaling type: journal_article volume: 31 year: '2011' ... --- _id: '2513' abstract: - lang: eng text: 'SK2-containing channels are expressed in the postsynaptic density (PSD) of dendritic spines on mouse hippocampal area CA1 pyramidal neurons and influence synaptic responses, plasticity and learning. The Sk2 gene (also known as Kcnn2) encodes two isoforms that differ only in the length of their N-terminal domains. SK2-long (SK2-L) and SK2-short (SK2-S) are coexpressed in CA1 pyramidal neurons and likely form heteromeric channels. In mice lacking SK2-L (SK2-S only mice), SK2-S-containing channels were expressed in the extrasynaptic membrane, but were excluded from the PSD. The SK channel contribution to excitatory postsynaptic potentials was absent in SK2-S only mice and was restored by SK2-L re-expression. Blocking SK channels increased the amount of long-term potentiation induced in area CA1 in slices from wild-type mice but had no effect in slices from SK2-S only mice. Furthermore, SK2-S only mice outperformed wild-type mice in the novel object recognition task. These results indicate that SK2-L directs synaptic SK2-containing channel expression and is important for normal synaptic signaling, plasticity and learning. ' author: - first_name: Duane full_name: Allen, Duane H last_name: Allen - first_name: Chris full_name: Bond, Chris T last_name: Bond - first_name: Rafael full_name: Luján, Rafael last_name: Luján - first_name: Carmen full_name: Ballesteros-Merino, Carmen last_name: Ballesteros Merino - first_name: Michael full_name: Lin, Michael T last_name: Lin - first_name: Kang full_name: Wang, Kang last_name: Wang - first_name: Nathan full_name: Klett, Nathan last_name: Klett - first_name: Masahiko full_name: Watanabe, Masahiko last_name: Watanabe - first_name: Ryuichi full_name: Ryuichi Shigemoto id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Robert full_name: Stackman, Robert W last_name: Stackman - first_name: James full_name: Maylie, James G last_name: Maylie - first_name: John full_name: Adelman, John P last_name: Adelman citation: ama: Allen D, Bond C, Luján R, et al. The SK2-long isoform directs synaptic localization and function of SK2-containing channels. Nature Neuroscience. 2011;14(6):744-749. doi:10.1038/nn.2832 apa: Allen, D., Bond, C., Luján, R., Ballesteros Merino, C., Lin, M., Wang, K., … Adelman, J. (2011). The SK2-long isoform directs synaptic localization and function of SK2-containing channels. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.2832 chicago: Allen, Duane, Chris Bond, Rafael Luján, Carmen Ballesteros Merino, Michael Lin, Kang Wang, Nathan Klett, et al. “The SK2-Long Isoform Directs Synaptic Localization and Function of SK2-Containing Channels.” Nature Neuroscience. Nature Publishing Group, 2011. https://doi.org/10.1038/nn.2832. ieee: D. Allen et al., “The SK2-long isoform directs synaptic localization and function of SK2-containing channels,” Nature Neuroscience, vol. 14, no. 6. Nature Publishing Group, pp. 744–749, 2011. ista: Allen D, Bond C, Luján R, Ballesteros Merino C, Lin M, Wang K, Klett N, Watanabe M, Shigemoto R, Stackman R, Maylie J, Adelman J. 2011. The SK2-long isoform directs synaptic localization and function of SK2-containing channels. Nature Neuroscience. 14(6), 744–749. mla: Allen, Duane, et al. “The SK2-Long Isoform Directs Synaptic Localization and Function of SK2-Containing Channels.” Nature Neuroscience, vol. 14, no. 6, Nature Publishing Group, 2011, pp. 744–49, doi:10.1038/nn.2832. short: D. Allen, C. Bond, R. Luján, C. Ballesteros Merino, M. Lin, K. Wang, N. Klett, M. Watanabe, R. Shigemoto, R. Stackman, J. Maylie, J. Adelman, Nature Neuroscience 14 (2011) 744–749. date_created: 2018-12-11T11:58:07Z date_published: 2011-06-01T00:00:00Z date_updated: 2021-01-12T06:57:56Z day: '01' doi: 10.1038/nn.2832 extern: 1 intvolume: ' 14' issue: '6' month: '06' page: 744 - 749 publication: Nature Neuroscience publication_status: published publisher: Nature Publishing Group publist_id: '4388' quality_controlled: 0 status: public title: The SK2-long isoform directs synaptic localization and function of SK2-containing channels type: journal_article volume: 14 year: '2011' ... --- _id: '2717' abstract: - lang: eng text: 'We consider Hermitian and symmetric random band matrices H in d ≥ 1 dimensions. The matrix elements H xy, indexed by, are independent, uniformly distributed random variables if {pipe}x-y{pipe} is less than the band width W, and zero otherwise. We prove that the time evolution of a quantum particle subject to the Hamiltonian H is diffusive on time scales. We also show that the localization length of the eigenvectors of H is larger than a factor W d/6 times the band width. All results are uniform in the size of the matrix. ' author: - first_name: László full_name: László Erdös id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Antti full_name: Knowles, Antti last_name: Knowles citation: ama: Erdös L, Knowles A. Quantum diffusion and eigenfunction delocalization in a random band matrix model. Communications in Mathematical Physics. 2011;303(2):509-554. doi:10.1007/s00220-011-1204-2 apa: Erdös, L., & Knowles, A. (2011). Quantum diffusion and eigenfunction delocalization in a random band matrix model. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-011-1204-2 chicago: Erdös, László, and Antti Knowles. “Quantum Diffusion and Eigenfunction Delocalization in a Random Band Matrix Model.” Communications in Mathematical Physics. Springer, 2011. https://doi.org/10.1007/s00220-011-1204-2. ieee: L. Erdös and A. Knowles, “Quantum diffusion and eigenfunction delocalization in a random band matrix model,” Communications in Mathematical Physics, vol. 303, no. 2. Springer, pp. 509–554, 2011. ista: Erdös L, Knowles A. 2011. Quantum diffusion and eigenfunction delocalization in a random band matrix model. Communications in Mathematical Physics. 303(2), 509–554. mla: Erdös, László, and Antti Knowles. “Quantum Diffusion and Eigenfunction Delocalization in a Random Band Matrix Model.” Communications in Mathematical Physics, vol. 303, no. 2, Springer, 2011, pp. 509–54, doi:10.1007/s00220-011-1204-2. short: L. Erdös, A. Knowles, Communications in Mathematical Physics 303 (2011) 509–554. date_created: 2018-12-11T11:59:14Z date_published: 2011-04-01T00:00:00Z date_updated: 2021-01-12T06:59:15Z day: '01' doi: 10.1007/s00220-011-1204-2 extern: 1 intvolume: ' 303' issue: '2' month: '04' page: 509 - 554 publication: Communications in Mathematical Physics publication_status: published publisher: Springer publist_id: '4175' quality_controlled: 0 status: public title: Quantum diffusion and eigenfunction delocalization in a random band matrix model type: journal_article volume: 303 year: '2011' ... --- _id: '2765' abstract: - lang: eng text: 'This is a study of the universality of spectral statistics for large random matrices. Considered are N×N symmetric, Hermitian, or quaternion self-dual random matrices with independent identically distributed entries (Wigner matrices), where the probability distribution of each matrix element is given by a measure v with zero expectation and with subexponential decay. The main result is that the correlation functions of the local eigenvalue statistics in the bulk of the spectrum coincide with those of the Gaussian Orthogonal Ensemble (GOE), the Gaussian Unitary Ensemble (GUE), and the Gaussian Symplectic Ensemble (GSE), respectively, in the limit as N → ∞. This approach is based on a study of the Dyson Brownian motion via a related new dynamics, the local relaxation flow. As a main input, it is established that the density of the eigenvalues converges to the Wigner semicircle law, and this holds even down to the smallest possible scale. Moreover, it is shown that the eigenvectors are completely delocalized. These results hold even without the condition that the matrix elements are identically distributed: only independence is used. In fact, for the matrix elements of the Green function strong estimates are given that imply that the local statistics of any two ensembles in the bulk are identical if the first four moments of the matrix elements match. Universality at the spectral edges requires matching only two moments. A Wigner-type estimate is also proved, and it is shown that the eigenvalues repel each other on arbitrarily small scales.' author: - first_name: László full_name: László Erdös id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 citation: ama: 'Erdös L. Universality of Wigner random matrices: A survey of recent results. Russian Mathematical Surveys. 2011;66(3):507-626. doi:10.1070/RM2011v066n03ABEH004749' apa: 'Erdös, L. (2011). Universality of Wigner random matrices: A survey of recent results. Russian Mathematical Surveys. IOP Publishing Ltd. https://doi.org/10.1070/RM2011v066n03ABEH004749' chicago: 'Erdös, László. “Universality of Wigner Random Matrices: A Survey of Recent Results.” Russian Mathematical Surveys. IOP Publishing Ltd., 2011. https://doi.org/10.1070/RM2011v066n03ABEH004749.' ieee: 'L. Erdös, “Universality of Wigner random matrices: A survey of recent results,” Russian Mathematical Surveys, vol. 66, no. 3. IOP Publishing Ltd., pp. 507–626, 2011.' ista: 'Erdös L. 2011. Universality of Wigner random matrices: A survey of recent results. Russian Mathematical Surveys. 66(3), 507–626.' mla: 'Erdös, László. “Universality of Wigner Random Matrices: A Survey of Recent Results.” Russian Mathematical Surveys, vol. 66, no. 3, IOP Publishing Ltd., 2011, pp. 507–626, doi:10.1070/RM2011v066n03ABEH004749.' short: L. Erdös, Russian Mathematical Surveys 66 (2011) 507–626. date_created: 2018-12-11T11:59:29Z date_published: 2011-01-01T00:00:00Z date_updated: 2019-04-26T07:22:20Z day: '01' doi: 10.1070/RM2011v066n03ABEH004749 extern: 1 intvolume: ' 66' issue: '3' main_file_link: - open_access: '0' url: http://arxiv.org/abs/1004.0861 month: '01' page: 507 - 626 publication: Russian Mathematical Surveys publication_status: published publisher: IOP Publishing Ltd. publist_id: '4125' quality_controlled: 0 status: public title: 'Universality of Wigner random matrices: A survey of recent results' type: review volume: 66 year: '2011' ... --- _id: '2766' abstract: - lang: eng text: We consider Hermitian and symmetric random band matrices H in d ≥ dimensions. The matrix elements Hxy, indexed by x,y ∈ Λ ⊂ ℤd are independent and their variances satisfy σ2xy:= E{pipe}Hxy{pipe}2 = W-d f((x-y)/W for some probability density f. We assume that the law of each matrix element Hxy is symmetric and exhibits subexponential decay. We prove that the time evolution of a quantum particle subject to the Hamiltonian H is diffusive on time scales ≪ Wd/3. We also show that the localization length of the eigenvectors of H is larger than a factor Wd/6 times the band width W. All results are uniform in the size {pipe}Λ{pipe} of the matrix. This extends our recent result (Erdo{double acute}s and Knowles in Commun. Math. Phys., 2011) to general band matrices. As another consequence of our proof we show that, for a larger class of random matrices satisfying Σx σ2xy for all y, the largest eigenvalue of H is bounded with high probability by 2+M-2/3+e{open} for any e{open} > 0, where M:= 1/(maxx,y σ2xy). author: - first_name: László full_name: László Erdös id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Antti full_name: Knowles, Antti last_name: Knowles citation: ama: Erdös L, Knowles A. Quantum diffusion and delocalization for band matrices with general distribution. Annales Henri Poincare. 2011;12(7):1227-1319. doi:10.1007/s00023-011-0104-5 apa: Erdös, L., & Knowles, A. (2011). Quantum diffusion and delocalization for band matrices with general distribution. Annales Henri Poincare. Birkhäuser. https://doi.org/10.1007/s00023-011-0104-5 chicago: Erdös, László, and Antti Knowles. “Quantum Diffusion and Delocalization for Band Matrices with General Distribution.” Annales Henri Poincare. Birkhäuser, 2011. https://doi.org/10.1007/s00023-011-0104-5. ieee: L. Erdös and A. Knowles, “Quantum diffusion and delocalization for band matrices with general distribution,” Annales Henri Poincare, vol. 12, no. 7. Birkhäuser, pp. 1227–1319, 2011. ista: Erdös L, Knowles A. 2011. Quantum diffusion and delocalization for band matrices with general distribution. Annales Henri Poincare. 12(7), 1227–1319. mla: Erdös, László, and Antti Knowles. “Quantum Diffusion and Delocalization for Band Matrices with General Distribution.” Annales Henri Poincare, vol. 12, no. 7, Birkhäuser, 2011, pp. 1227–319, doi:10.1007/s00023-011-0104-5. short: L. Erdös, A. Knowles, Annales Henri Poincare 12 (2011) 1227–1319. date_created: 2018-12-11T11:59:29Z date_published: 2011-11-01T00:00:00Z date_updated: 2021-01-12T06:59:33Z day: '01' doi: 10.1007/s00023-011-0104-5 extern: 1 intvolume: ' 12' issue: '7' month: '11' page: 1227 - 1319 publication: Annales Henri Poincare publication_status: published publisher: Birkhäuser publist_id: '4124' quality_controlled: 0 status: public title: Quantum diffusion and delocalization for band matrices with general distribution type: journal_article volume: 12 year: '2011' ... --- _id: '2764' abstract: - lang: eng text: Consider the Dyson Brownian motion with parameter β, where β=1,2,4 corresponds to the eigenvalue flows for the eigenvalues of symmetric, hermitian and quaternion self-dual ensembles. For any β≥1, we prove that the relaxation time to local equilibrium for the Dyson Brownian motion is bounded above by N -ζ for some ζ> 0. The proof is based on an estimate of the entropy flow of the Dyson Brownian motion w. r. t. a "pseudo equilibrium measure". As an application of this estimate, we prove that the eigenvalue spacing statistics in the bulk of the spectrum for N×N symmetric Wigner ensemble is the same as that of the Gaussian Orthogonal Ensemble (GOE) in the limit N→∞. The assumptions on the probability distribution of the matrix elements of the Wigner ensemble are a subexponential decay and some minor restriction on the support. author: - first_name: László full_name: László Erdös id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Benjamin full_name: Schlein, Benjamin last_name: Schlein - first_name: Horng full_name: Yau, Horng-Tzer last_name: Yau citation: ama: Erdös L, Schlein B, Yau H. Universality of random matrices and local relaxation flow. Inventiones Mathematicae. 2011;185(1):75-119. doi:10.1007/s00222-010-0302-7 apa: Erdös, L., Schlein, B., & Yau, H. (2011). Universality of random matrices and local relaxation flow. Inventiones Mathematicae. Springer. https://doi.org/10.1007/s00222-010-0302-7 chicago: Erdös, László, Benjamin Schlein, and Horng Yau. “Universality of Random Matrices and Local Relaxation Flow.” Inventiones Mathematicae. Springer, 2011. https://doi.org/10.1007/s00222-010-0302-7. ieee: L. Erdös, B. Schlein, and H. Yau, “Universality of random matrices and local relaxation flow,” Inventiones Mathematicae, vol. 185, no. 1. Springer, pp. 75–119, 2011. ista: Erdös L, Schlein B, Yau H. 2011. Universality of random matrices and local relaxation flow. Inventiones Mathematicae. 185(1), 75–119. mla: Erdös, László, et al. “Universality of Random Matrices and Local Relaxation Flow.” Inventiones Mathematicae, vol. 185, no. 1, Springer, 2011, pp. 75–119, doi:10.1007/s00222-010-0302-7. short: L. Erdös, B. Schlein, H. Yau, Inventiones Mathematicae 185 (2011) 75–119. date_created: 2018-12-11T11:59:29Z date_published: 2011-07-01T00:00:00Z date_updated: 2021-01-12T06:59:32Z day: '01' doi: 10.1007/s00222-010-0302-7 extern: 1 intvolume: ' 185' issue: '1' month: '07' page: 75 - 119 publication: Inventiones Mathematicae publication_status: published publisher: Springer publist_id: '4126' quality_controlled: 0 status: public title: Universality of random matrices and local relaxation flow type: journal_article volume: 185 year: '2011' ... --- _id: '2799' abstract: - lang: eng text: Shear flows undergo a sudden transition from laminar to turbulent motion as the velocity increases, and the onset of turbulence radically changes transport efficiency and mixing properties. Even for the well-studied case of pipe flow, it has not been possible to determine at what Reynolds number the motion will be either persistently turbulent or ultimately laminar. We show that in pipes, turbulence that is transient at low Reynolds numbers becomes sustained at a distinct critical point. Through extensive experiments and computer simulations, we were able to identify and characterize the processes ultimately responsible for sustaining turbulence. In contrast to the classical Landau-Ruelle-Takens view that turbulence arises from an increase in the temporal complexity of fluid motion, here, spatial proliferation of chaotic domains is the decisive process and intrinsic to the nature of fluid turbulence. author: - first_name: Kerstin full_name: Avila, Kerstin last_name: Avila - first_name: David full_name: Moxey, David last_name: Moxey - first_name: Alberto full_name: de Lózar, Alberto last_name: De Lózar - first_name: Marc full_name: Avila, Marc last_name: Avila - first_name: Dwight full_name: Barkley, Dwight last_name: Barkley - first_name: Björn full_name: Björn Hof id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Avila K, Moxey D, De Lózar A, Avila M, Barkley D, Hof B. The onset of turbulence in pipe flow. Science. 2011;333(6039):192-196. doi:10.1126/science.1203223 apa: Avila, K., Moxey, D., De Lózar, A., Avila, M., Barkley, D., & Hof, B. (2011). The onset of turbulence in pipe flow. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1203223 chicago: Avila, Kerstin, David Moxey, Alberto De Lózar, Marc Avila, Dwight Barkley, and Björn Hof. “The Onset of Turbulence in Pipe Flow.” Science. American Association for the Advancement of Science, 2011. https://doi.org/10.1126/science.1203223. ieee: K. Avila, D. Moxey, A. De Lózar, M. Avila, D. Barkley, and B. Hof, “The onset of turbulence in pipe flow,” Science, vol. 333, no. 6039. American Association for the Advancement of Science, pp. 192–196, 2011. ista: Avila K, Moxey D, De Lózar A, Avila M, Barkley D, Hof B. 2011. The onset of turbulence in pipe flow. Science. 333(6039), 192–196. mla: Avila, Kerstin, et al. “The Onset of Turbulence in Pipe Flow.” Science, vol. 333, no. 6039, American Association for the Advancement of Science, 2011, pp. 192–96, doi:10.1126/science.1203223. short: K. Avila, D. Moxey, A. De Lózar, M. Avila, D. Barkley, B. Hof, Science 333 (2011) 192–196. date_created: 2018-12-11T11:59:39Z date_published: 2011-07-08T00:00:00Z date_updated: 2021-01-12T06:59:47Z day: '08' doi: 10.1126/science.1203223 extern: 1 intvolume: ' 333' issue: '6039' month: '07' page: 192 - 196 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '4090' quality_controlled: 0 status: public title: The onset of turbulence in pipe flow type: journal_article volume: 333 year: '2011' ... --- _id: '2800' abstract: - lang: eng text: In shear flows, turbulence first occurs in the form of localized structures (puffs/spots) surrounded by laminar fluid. We here investigate such spatially intermittent flows in a pipe experiment showing that turbulent puffs have a well-defined interaction distance, which sets their minimum spacing as well as the maximum observable turbulent fraction. Two methodologies are employed. Starting from a laminar flow, puffs are first created by locally injecting a jet of fluid through the pipe wall. When the perturbation is applied periodically at low frequencies, as expected, a regular sequence of puffs is observed where the puff spacing is given by the ratio of the mean flow speed to the perturbation frequency. At large frequencies however puffs are found to interact and annihilate each other. Varying the perturbation frequency, an interaction distance is determined which sets the highest possible turbulence fraction. This enables us to establish an upper bound for the friction factor in the transitional regime, which provides a well-defined link between the Blasius and the Hagen-Poiseuille friction laws. In the second set of experiments, the Reynolds number is reduced suddenly from fully turbulent to the intermittent regime. The resulting flow reorganizes itself to a sequence of constant size puffs which, unlike in Couette and Taylor–Couette flow are randomly spaced. The minimum distance between the turbulent patches is identical to the puff interaction length. The puff interaction length is found to be in agreement with the wavelength of regular stripe and spiral patterns in plane Couette and Taylor–Couette flow. author: - first_name: Devranjan full_name: Samanta, Devranjan last_name: Samanta - first_name: Alberto full_name: de Lózar, Alberto last_name: De Lózar - first_name: Björn full_name: Björn Hof id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Samanta D, De Lózar A, Hof B. Experimental investigation of laminar turbulent intermittency in pipe flow. Journal of Fluid Mechanics. 2011;681:193-204. doi:10.1017/jfm.2011.189 apa: Samanta, D., De Lózar, A., & Hof, B. (2011). Experimental investigation of laminar turbulent intermittency in pipe flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2011.189 chicago: Samanta, Devranjan, Alberto De Lózar, and Björn Hof. “Experimental Investigation of Laminar Turbulent Intermittency in Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2011. https://doi.org/10.1017/jfm.2011.189. ieee: D. Samanta, A. De Lózar, and B. Hof, “Experimental investigation of laminar turbulent intermittency in pipe flow,” Journal of Fluid Mechanics, vol. 681. Cambridge University Press, pp. 193–204, 2011. ista: Samanta D, De Lózar A, Hof B. 2011. Experimental investigation of laminar turbulent intermittency in pipe flow. Journal of Fluid Mechanics. 681, 193–204. mla: Samanta, Devranjan, et al. “Experimental Investigation of Laminar Turbulent Intermittency in Pipe Flow.” Journal of Fluid Mechanics, vol. 681, Cambridge University Press, 2011, pp. 193–204, doi:10.1017/jfm.2011.189. short: D. Samanta, A. De Lózar, B. Hof, Journal of Fluid Mechanics 681 (2011) 193–204. date_created: 2018-12-11T11:59:40Z date_published: 2011-08-25T00:00:00Z date_updated: 2021-01-12T06:59:48Z day: '25' doi: 10.1017/jfm.2011.189 extern: 1 intvolume: ' 681' month: '08' page: 193 - 204 publication: Journal of Fluid Mechanics publication_status: published publisher: Cambridge University Press publist_id: '4089' quality_controlled: 0 status: public title: Experimental investigation of laminar turbulent intermittency in pipe flow type: journal_article volume: 681 year: '2011' ... --- _id: '2801' abstract: - lang: eng text: Turbulent puffs in pipe flow are characterized by a sharp laminar-turbulent interface at the trailing edge and a more diffused leading interface. It is known that these laminar-turbulent interfaces propagate at a speed that is approximately equal to the flow rate. Our results from direct numerical simulation show that, locally, the interface velocity relative to the fluid (i) counteracts the advection due to the laminar velocity profile so that the puff can preserve its characteristic overall shape, (ii) is very small in magnitude, but involves a large interface area so that the global propagation velocity relative to the mean flow can be large and (iii) is determined by both inertial and viscous effects. The analysis provides some new insights into the mechanisms that sustain or expand localized turbulence and might be relevant for the design of new control strategies. alternative_title: - 'Journal of Physics: Conference Series' author: - first_name: Markus full_name: Holzner, Markus last_name: Holzner - first_name: Marc full_name: Avila, Marc last_name: Avila - first_name: Alberto full_name: de Lózar, Alberto last_name: De Lózar - first_name: Björn full_name: Björn Hof id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: 'Holzner M, Avila M, De Lózar A, Hof B. A Lagrangian approach to the interface velocity of turbulent puffs in pipe flow. In: Vol 318. IOP Publishing Ltd.; 2011. doi:10.1088/1742-6596/318/5/052031' apa: 'Holzner, M., Avila, M., De Lózar, A., & Hof, B. (2011). A Lagrangian approach to the interface velocity of turbulent puffs in pipe flow (Vol. 318). Presented at the ETC13: European Turbulence Conference, IOP Publishing Ltd. https://doi.org/10.1088/1742-6596/318/5/052031' chicago: Holzner, Markus, Marc Avila, Alberto De Lózar, and Björn Hof. “A Lagrangian Approach to the Interface Velocity of Turbulent Puffs in Pipe Flow,” Vol. 318. IOP Publishing Ltd., 2011. https://doi.org/10.1088/1742-6596/318/5/052031. ieee: 'M. Holzner, M. Avila, A. De Lózar, and B. Hof, “A Lagrangian approach to the interface velocity of turbulent puffs in pipe flow,” presented at the ETC13: European Turbulence Conference, 2011, vol. 318, no. 5.' ista: 'Holzner M, Avila M, De Lózar A, Hof B. 2011. A Lagrangian approach to the interface velocity of turbulent puffs in pipe flow. ETC13: European Turbulence Conference, Journal of Physics: Conference Series, vol. 318.' mla: Holzner, Markus, et al. A Lagrangian Approach to the Interface Velocity of Turbulent Puffs in Pipe Flow. Vol. 318, no. 5, IOP Publishing Ltd., 2011, doi:10.1088/1742-6596/318/5/052031. short: M. Holzner, M. Avila, A. De Lózar, B. Hof, in:, IOP Publishing Ltd., 2011. conference: name: 'ETC13: European Turbulence Conference' date_created: 2018-12-11T11:59:40Z date_published: 2011-09-01T00:00:00Z date_updated: 2019-04-26T07:22:20Z day: '01' doi: 10.1088/1742-6596/318/5/052031 extern: 1 intvolume: ' 318' issue: '5' month: '09' publication_status: published publisher: IOP Publishing Ltd. publist_id: '4088' quality_controlled: 0 status: public title: A Lagrangian approach to the interface velocity of turbulent puffs in pipe flow type: conference volume: 318 year: '2011' ... --- _id: '2874' abstract: - lang: eng text: The apical hook develops in the upper part of the hypocotyl when seeds buried in the soil germinate, and serves to protect cotyledons and the shoot apical meristem from possible damage caused by pushing through the soil. The curvature is formed through differential cell growth that occurs at the two opposite sides of the hypocotyl, and it is established by a gradient of auxin activity and refined by the coordinated action of auxin and ethylene. Here we show that gibberellins (GAs) promote hook development through the transcriptional regulation of several genes of the ethylene and auxin pathways in Arabidopsis. The level of GA activity determines the speed of hook formation and the extent of the curvature during the formation phase independently of ethylene, probably by modulating auxin transport and response through HLS1, PIN3, and PIN7. Moreover, GAs cooperate with ethylene in preventing hook opening, in part through the induction of ethylene production mediated by ACS5/ETO2 and ACS8. author: - first_name: Javier full_name: Gallego-Bartolomé, Javier last_name: Gallego Bartolomé - first_name: María full_name: Arana, María V last_name: Arana - first_name: Filip full_name: Vandenbussche, Filip last_name: Vandenbussche - first_name: Petra full_name: Žádníková, Petra last_name: Žádníková - first_name: Eugenio full_name: Minguet, Eugenio G last_name: Minguet - first_name: Vicente full_name: Guardiola, Vicente last_name: Guardiola - first_name: Dominique full_name: Van Der Straeten, Dominique last_name: Van Der Straeten - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: David full_name: Alabadí, David last_name: Alabadí - first_name: Miguel full_name: Blázquez, Miguel A last_name: Blázquez citation: ama: Gallego Bartolomé J, Arana M, Vandenbussche F, et al. Hierarchy of hormone action controlling apical hook development in Arabidopsis. Plant Journal. 2011;67(4):622-634. doi:10.1111/j.1365-313X.2011.04621.x apa: Gallego Bartolomé, J., Arana, M., Vandenbussche, F., Žádníková, P., Minguet, E., Guardiola, V., … Blázquez, M. (2011). Hierarchy of hormone action controlling apical hook development in Arabidopsis. Plant Journal. Wiley-Blackwell. https://doi.org/10.1111/j.1365-313X.2011.04621.x chicago: Gallego Bartolomé, Javier, María Arana, Filip Vandenbussche, Petra Žádníková, Eugenio Minguet, Vicente Guardiola, Dominique Van Der Straeten, Eva Benková, David Alabadí, and Miguel Blázquez. “Hierarchy of Hormone Action Controlling Apical Hook Development in Arabidopsis.” Plant Journal. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1365-313X.2011.04621.x. ieee: J. Gallego Bartolomé et al., “Hierarchy of hormone action controlling apical hook development in Arabidopsis,” Plant Journal, vol. 67, no. 4. Wiley-Blackwell, pp. 622–634, 2011. ista: Gallego Bartolomé J, Arana M, Vandenbussche F, Žádníková P, Minguet E, Guardiola V, Van Der Straeten D, Benková E, Alabadí D, Blázquez M. 2011. Hierarchy of hormone action controlling apical hook development in Arabidopsis. Plant Journal. 67(4), 622–634. mla: Gallego Bartolomé, Javier, et al. “Hierarchy of Hormone Action Controlling Apical Hook Development in Arabidopsis.” Plant Journal, vol. 67, no. 4, Wiley-Blackwell, 2011, pp. 622–34, doi:10.1111/j.1365-313X.2011.04621.x. short: J. Gallego Bartolomé, M. Arana, F. Vandenbussche, P. Žádníková, E. Minguet, V. Guardiola, D. Van Der Straeten, E. Benková, D. Alabadí, M. Blázquez, Plant Journal 67 (2011) 622–634. date_created: 2018-12-11T12:00:04Z date_published: 2011-08-01T00:00:00Z date_updated: 2021-01-12T07:00:24Z day: '01' doi: 10.1111/j.1365-313X.2011.04621.x extern: 1 intvolume: ' 67' issue: '4' month: '08' page: 622 - 634 publication: Plant Journal publication_status: published publisher: Wiley-Blackwell publist_id: '3891' quality_controlled: 0 status: public title: Hierarchy of hormone action controlling apical hook development in Arabidopsis type: journal_article volume: 67 year: '2011' ... --- _id: '2871' abstract: - lang: eng text: Despite their relatively simple appearance, roots are incredibly complex organs that are highly adapted to differing environments. Many aspects of root development are co-ordinated by subtle spatial differences in the concentrations of the phytohormones auxin and cytokinin. Events from the formation of a root during embryogenesis to the determination of the network of lateral roots are controlled by interactions between these hormones. Recently, interactions have been defined where auxin signaling promotes the expression of cytokinin signaling inhibitors, cytokinin signaling promotes the expression of auxin signaling inhibitors and finally where cytokinin signaling regulates the complex network of auxin transport proteins to position zones of high auxin signaling. We are witnessing a period of discovery in which we are beginning to understand how these hormonal pathways communicate to regulate root formation. author: - first_name: Anthony full_name: Bishopp, Anthony last_name: Bishopp - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Ykä full_name: Helariutta, Ykä last_name: Helariutta citation: ama: 'Bishopp A, Benková E, Helariutta Y. Sending mixed messages: Auxin-cytokinin crosstalk in roots. Current Opinion in Plant Biology. 2011;14(1):10-16. doi:10.1016/j.pbi.2010.08.014' apa: 'Bishopp, A., Benková, E., & Helariutta, Y. (2011). Sending mixed messages: Auxin-cytokinin crosstalk in roots. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2010.08.014' chicago: 'Bishopp, Anthony, Eva Benková, and Ykä Helariutta. “Sending Mixed Messages: Auxin-Cytokinin Crosstalk in Roots.” Current Opinion in Plant Biology. Elsevier, 2011. https://doi.org/10.1016/j.pbi.2010.08.014.' ieee: 'A. Bishopp, E. Benková, and Y. Helariutta, “Sending mixed messages: Auxin-cytokinin crosstalk in roots,” Current Opinion in Plant Biology, vol. 14, no. 1. Elsevier, pp. 10–16, 2011.' ista: 'Bishopp A, Benková E, Helariutta Y. 2011. Sending mixed messages: Auxin-cytokinin crosstalk in roots. Current Opinion in Plant Biology. 14(1), 10–16.' mla: 'Bishopp, Anthony, et al. “Sending Mixed Messages: Auxin-Cytokinin Crosstalk in Roots.” Current Opinion in Plant Biology, vol. 14, no. 1, Elsevier, 2011, pp. 10–16, doi:10.1016/j.pbi.2010.08.014.' short: A. Bishopp, E. Benková, Y. Helariutta, Current Opinion in Plant Biology 14 (2011) 10–16. date_created: 2018-12-11T12:00:03Z date_published: 2011-02-01T00:00:00Z date_updated: 2021-01-12T07:00:23Z day: '01' doi: 10.1016/j.pbi.2010.08.014 extern: 1 intvolume: ' 14' issue: '1' month: '02' page: 10 - 16 publication: Current Opinion in Plant Biology publication_status: published publisher: Elsevier publist_id: '3894' quality_controlled: 0 status: public title: 'Sending mixed messages: Auxin-cytokinin crosstalk in roots' type: journal_article volume: 14 year: '2011' ... --- _id: '2898' abstract: - lang: eng text: Sex allocation theory has been remarkably successful at explaining the prevalence of even sex ratios in natural populations and at identifying specific conditions that can result in biased sex ratios. Much of this theory focuses on parental sex determination (SD) strategies. Here, we consider instead the evolutionary causes and consequences of mixed offspring SD strategies, in which the genotype of an individual determines not its sex, but the probability of developing one of multiple sexes. We find that alleles specifying mixed offspring SD strategies can generally outcompete alleles that specify pure strategies, but generate constraints that may prevent a population from reaching an even sex ratio. We use our model to analyze sex ratios in natural populations of Tetrahymena thermophila, a ciliate with seven sexes determined by mixed SD alleles. We show that probabilistic SD is sufficient to account for the occurrence of skewed sex ratios in natural populations of T. thermophila, provided that their effective population sizes are small. Our results highlight the importance of genetic drift in sex ratio evolution and suggest that mixed offspring SD strategies should be more common than currently thought. author: - first_name: Tiago full_name: Tiago Paixao id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Sujal full_name: Phadke, Sujal S last_name: Phadke - first_name: Ricardo full_name: Azevedo, Ricardo B last_name: Azevedo - first_name: Rebecca full_name: Zufall, Rebecca A last_name: Zufall citation: ama: Paixao T, Phadke S, Azevedo R, Zufall R. Sex ratio evolution under probabilistic sex determination. Evolution; International Journal of Organic Evolution. 2011;65(7):2050-2060. doi:10.1111/j.1558-5646.2011.01266.x apa: Paixao, T., Phadke, S., Azevedo, R., & Zufall, R. (2011). Sex ratio evolution under probabilistic sex determination. Evolution; International Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.1558-5646.2011.01266.x chicago: Paixao, Tiago, Sujal Phadke, Ricardo Azevedo, and Rebecca Zufall. “Sex Ratio Evolution under Probabilistic Sex Determination.” Evolution; International Journal of Organic Evolution. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1558-5646.2011.01266.x. ieee: T. Paixao, S. Phadke, R. Azevedo, and R. Zufall, “Sex ratio evolution under probabilistic sex determination,” Evolution; International Journal of Organic Evolution, vol. 65, no. 7. Wiley-Blackwell, pp. 2050–2060, 2011. ista: Paixao T, Phadke S, Azevedo R, Zufall R. 2011. Sex ratio evolution under probabilistic sex determination. Evolution; International Journal of Organic Evolution. 65(7), 2050–2060. mla: Paixao, Tiago, et al. “Sex Ratio Evolution under Probabilistic Sex Determination.” Evolution; International Journal of Organic Evolution, vol. 65, no. 7, Wiley-Blackwell, 2011, pp. 2050–60, doi:10.1111/j.1558-5646.2011.01266.x. short: T. Paixao, S. Phadke, R. Azevedo, R. Zufall, Evolution; International Journal of Organic Evolution 65 (2011) 2050–2060. date_created: 2018-12-11T12:00:13Z date_published: 2011-03-01T00:00:00Z date_updated: 2021-01-12T07:00:33Z day: '01' doi: 10.1111/j.1558-5646.2011.01266.x extern: 1 intvolume: ' 65' issue: '7' month: '03' page: 2050 - 2060 publication: Evolution; International Journal of Organic Evolution publication_status: published publisher: Wiley-Blackwell publist_id: '3860' quality_controlled: 0 status: public title: Sex ratio evolution under probabilistic sex determination type: journal_article volume: 65 year: '2011' ... --- _id: '2897' acknowledgement: TFs regulate gene expression by binding to specific sequences in the promoter regions of their target genes. Promoters often contain multiple copies of the same TF binding sites. How does this multiplicity evolve? One possibility is that individuals with multiple, redundant binding sites have higher fitness. However, nonadaptive processes are also likely to be important. Here, we develop a mathematical model of the evolution of TF binding sites to help us disentangle how different evolutionary mechanisms contribute to the evolution of binding site redundancy and multiplicity. We show that recombination is expected to promote the evolution of multiple binding sites. This prediction is corroborated by genome-wide data from yeast. Another important factor in the evolution of multiplicity predicted in our analysis is TF promiscuity, that is, the ability of a TF to bind to multiple sequences. In addition, our analysis indicated that direct selection can have large effects on the evolution of redundancy and multiplicity. Data from yeast identified selection for changes in expression level as a candidate mechanism for the evolution of multiple binding sites. We conclude that, although selection may play a major role in the evolution of multiplicity in regulatory regions, nonadaptive forces can also lead to high levels of multiplicity. author: - first_name: Tiago full_name: Tiago Paixao id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Ricardo full_name: Azevedo, Ricardo B last_name: Azevedo citation: ama: Paixao T, Azevedo R. Redundancy and the Evolution of Cis Regulatory Element Multiplicity. PLoS Computational Biology. 2011;6(7). doi:10.1371/journal.pcbi.1000848 apa: Paixao, T., & Azevedo, R. (2011). Redundancy and the Evolution of Cis Regulatory Element Multiplicity. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1000848 chicago: Paixao, Tiago, and Ricardo Azevedo. “Redundancy and the Evolution of Cis Regulatory Element Multiplicity.” PLoS Computational Biology. Public Library of Science, 2011. https://doi.org/10.1371/journal.pcbi.1000848. ieee: T. Paixao and R. Azevedo, “Redundancy and the Evolution of Cis Regulatory Element Multiplicity,” PLoS Computational Biology, vol. 6, no. 7. Public Library of Science, 2011. ista: Paixao T, Azevedo R. 2011. Redundancy and the Evolution of Cis Regulatory Element Multiplicity. PLoS Computational Biology. 6(7). mla: Paixao, Tiago, and Ricardo Azevedo. “Redundancy and the Evolution of Cis Regulatory Element Multiplicity.” PLoS Computational Biology, vol. 6, no. 7, Public Library of Science, 2011, doi:10.1371/journal.pcbi.1000848. short: T. Paixao, R. Azevedo, PLoS Computational Biology 6 (2011). date_created: 2018-12-11T12:00:13Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:00:33Z day: '01' doi: 10.1371/journal.pcbi.1000848 extern: 1 intvolume: ' 6' issue: '7' month: '01' publication: PLoS Computational Biology publication_status: published publisher: Public Library of Science publist_id: '3861' quality_controlled: 0 status: public title: Redundancy and the Evolution of Cis Regulatory Element Multiplicity 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: 6 year: '2011' ... --- _id: '2922' author: - first_name: Sara full_name: Vicente, Sara last_name: Vicente - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Carsten full_name: Rother, Carsten last_name: Rother citation: ama: 'Vicente S, Kolmogorov V, Rother C. Graph-cut Based Image Segmentation with Connectivity Priors. In: Blake A, Kohli P, Rother C, eds. Markov Random Fields for Vision and Image Processing. Massachusetts Institute of Technology Press; 2011.' apa: Vicente, S., Kolmogorov, V., & Rother, C. (2011). Graph-cut Based Image Segmentation with Connectivity Priors. In A. Blake, P. Kohli, & C. Rother (Eds.), Markov Random Fields for Vision and Image Processing. Massachusetts Institute of Technology Press. chicago: Vicente, Sara, Vladimir Kolmogorov, and Carsten Rother. “Graph-Cut Based Image Segmentation with Connectivity Priors.” In Markov Random Fields for Vision and Image Processing, edited by Andrew Blake, Pushmeet Kohli, and Carsten Rother. Massachusetts Institute of Technology Press, 2011. ieee: S. Vicente, V. Kolmogorov, and C. Rother, “Graph-cut Based Image Segmentation with Connectivity Priors,” in Markov Random Fields for Vision and Image Processing, A. Blake, P. Kohli, and C. Rother, Eds. Massachusetts Institute of Technology Press, 2011. ista: 'Vicente S, Kolmogorov V, Rother C. 2011.Graph-cut Based Image Segmentation with Connectivity Priors. In: Markov Random Fields for Vision and Image Processing. .' mla: Vicente, Sara, et al. “Graph-Cut Based Image Segmentation with Connectivity Priors.” Markov Random Fields for Vision and Image Processing, edited by Andrew Blake et al., Massachusetts Institute of Technology Press, 2011. short: S. Vicente, V. Kolmogorov, C. Rother, in:, A. Blake, P. Kohli, C. Rother (Eds.), Markov Random Fields for Vision and Image Processing, Massachusetts Institute of Technology Press, 2011. date_created: 2018-12-11T12:00:21Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:00:43Z day: '01' editor: - first_name: Andrew full_name: Blake, Andrew last_name: Blake - first_name: Pushmeet full_name: Kohli, Pushmeet last_name: Kohli - first_name: Carsten full_name: Rother, Carsten last_name: Rother extern: 1 month: '01' publication: Markov Random Fields for Vision and Image Processing publication_status: published publisher: Massachusetts Institute of Technology Press publist_id: '3815' quality_controlled: 0 status: public title: Graph-cut Based Image Segmentation with Connectivity Priors type: book_chapter year: '2011' ... --- _id: '2923' author: - first_name: M Pawan full_name: Kumar, M Pawan last_name: Kumar - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Philip full_name: Torr, Philip H last_name: Torr citation: ama: 'Kumar MP, Kolmogorov V, Torr P. Analyzing Convex Relaxations for MAP Estimation. In: Blake A, Kohli P, Rother C, eds. Markov Random Fields for Vision and Image Processing. Massachusetts Institute of Technology Press; 2011.' apa: Kumar, M. P., Kolmogorov, V., & Torr, P. (2011). Analyzing Convex Relaxations for MAP Estimation. In A. Blake, P. Kohli, & C. Rother (Eds.), Markov Random Fields for Vision and Image Processing. Massachusetts Institute of Technology Press. chicago: Kumar, M Pawan, Vladimir Kolmogorov, and Philip Torr. “Analyzing Convex Relaxations for MAP Estimation.” In Markov Random Fields for Vision and Image Processing, edited by Andrew Blake, Pushmeet Kohli, and Carsten Rother. Massachusetts Institute of Technology Press, 2011. ieee: M. P. Kumar, V. Kolmogorov, and P. Torr, “Analyzing Convex Relaxations for MAP Estimation,” in Markov Random Fields for Vision and Image Processing, A. Blake, P. Kohli, and C. Rother, Eds. Massachusetts Institute of Technology Press, 2011. ista: 'Kumar MP, Kolmogorov V, Torr P. 2011.Analyzing Convex Relaxations for MAP Estimation. In: Markov Random Fields for Vision and Image Processing. .' mla: Kumar, M. Pawan, et al. “Analyzing Convex Relaxations for MAP Estimation.” Markov Random Fields for Vision and Image Processing, edited by Andrew Blake et al., Massachusetts Institute of Technology Press, 2011. short: M.P. Kumar, V. Kolmogorov, P. Torr, in:, A. Blake, P. Kohli, C. Rother (Eds.), Markov Random Fields for Vision and Image Processing, Massachusetts Institute of Technology Press, 2011. date_created: 2018-12-11T12:00:21Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:00:43Z day: '01' editor: - first_name: Andrew full_name: Blake, Andrew last_name: Blake - first_name: Pushmeet full_name: Kohli, Pushmeet last_name: Kohli - first_name: Carsten full_name: Rother, Carsten last_name: Rother extern: 1 month: '01' publication: Markov Random Fields for Vision and Image Processing publication_status: published publisher: Massachusetts Institute of Technology Press publist_id: '3814' quality_controlled: 0 status: public title: Analyzing Convex Relaxations for MAP Estimation type: book_chapter year: '2011' ... --- _id: '2924' author: - first_name: Antonio full_name: Criminisi, Antonio last_name: Criminisi - first_name: Geoffrey full_name: Cross, Geoffrey last_name: Cross - first_name: Andrew full_name: Blake, Andrew last_name: Blake - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Criminisi A, Cross G, Blake A, Kolmogorov V. Bilayer Segmentation of Video. In: Blake A, Kohli P, Rother C, eds. Markov Random Fields for Vision and Image Processing. Massachusetts Institute of Technology Press; 2011.' apa: Criminisi, A., Cross, G., Blake, A., & Kolmogorov, V. (2011). Bilayer Segmentation of Video. In A. Blake, P. Kohli, & C. Rother (Eds.), Markov Random Fields for Vision and Image Processing. Massachusetts Institute of Technology Press. chicago: Criminisi, Antonio, Geoffrey Cross, Andrew Blake, and Vladimir Kolmogorov. “Bilayer Segmentation of Video.” In Markov Random Fields for Vision and Image Processing, edited by Andrew Blake, Pushmeet Kohli, and Carsten Rother. Massachusetts Institute of Technology Press, 2011. ieee: A. Criminisi, G. Cross, A. Blake, and V. Kolmogorov, “Bilayer Segmentation of Video,” in Markov Random Fields for Vision and Image Processing, A. Blake, P. Kohli, and C. Rother, Eds. Massachusetts Institute of Technology Press, 2011. ista: 'Criminisi A, Cross G, Blake A, Kolmogorov V. 2011.Bilayer Segmentation of Video. In: Markov Random Fields for Vision and Image Processing. .' mla: Criminisi, Antonio, et al. “Bilayer Segmentation of Video.” Markov Random Fields for Vision and Image Processing, edited by Andrew Blake et al., Massachusetts Institute of Technology Press, 2011. short: A. Criminisi, G. Cross, A. Blake, V. Kolmogorov, in:, A. Blake, P. Kohli, C. Rother (Eds.), Markov Random Fields for Vision and Image Processing, Massachusetts Institute of Technology Press, 2011. date_created: 2018-12-11T12:00:22Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:00:43Z day: '01' editor: - first_name: Andrew full_name: Blake, Andrew last_name: Blake - first_name: Pushmeet full_name: Kohli, Pushmeet last_name: Kohli - first_name: Carsten full_name: Rother, Carsten last_name: Rother extern: 1 month: '01' publication: Markov Random Fields for Vision and Image Processing publication_status: published publisher: Massachusetts Institute of Technology Press publist_id: '3813' quality_controlled: 0 status: public title: Bilayer Segmentation of Video type: book_chapter year: '2011' ... --- _id: '2925' author: - first_name: Carsten full_name: Rother, Carsten last_name: Rother - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Yuri full_name: Boykov, Yuri last_name: Boykov - first_name: Andrew full_name: Blake, Andrew last_name: Blake citation: ama: 'Rother C, Kolmogorov V, Boykov Y, Blake A. Interactive Foreground Extraction using graph cut. In: Blake A, Kohli P, Rother C, eds. Markov Random Fields for Vision and Image Processing. Massachusetts Institute of Technology Press; 2011.' apa: Rother, C., Kolmogorov, V., Boykov, Y., & Blake, A. (2011). Interactive Foreground Extraction using graph cut. In A. Blake, P. Kohli, & C. Rother (Eds.), Markov Random Fields for Vision and Image Processing. Massachusetts Institute of Technology Press. chicago: Rother, Carsten, Vladimir Kolmogorov, Yuri Boykov, and Andrew Blake. “Interactive Foreground Extraction Using Graph Cut.” In Markov Random Fields for Vision and Image Processing, edited by Andrew Blake, Pushmeet Kohli, and Carsten Rother. Massachusetts Institute of Technology Press, 2011. ieee: C. Rother, V. Kolmogorov, Y. Boykov, and A. Blake, “Interactive Foreground Extraction using graph cut,” in Markov Random Fields for Vision and Image Processing, A. Blake, P. Kohli, and C. Rother, Eds. Massachusetts Institute of Technology Press, 2011. ista: 'Rother C, Kolmogorov V, Boykov Y, Blake A. 2011.Interactive Foreground Extraction using graph cut. In: Markov Random Fields for Vision and Image Processing. .' mla: Rother, Carsten, et al. “Interactive Foreground Extraction Using Graph Cut.” Markov Random Fields for Vision and Image Processing, edited by Andrew Blake et al., Massachusetts Institute of Technology Press, 2011. short: C. Rother, V. Kolmogorov, Y. Boykov, A. Blake, in:, A. Blake, P. Kohli, C. Rother (Eds.), Markov Random Fields for Vision and Image Processing, Massachusetts Institute of Technology Press, 2011. date_created: 2018-12-11T12:00:22Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:00:44Z day: '01' editor: - first_name: Andrew full_name: Blake, Andrew last_name: Blake - first_name: Pushmeet full_name: Kohli, Pushmeet last_name: Kohli - first_name: Carsten full_name: Rother, Carsten last_name: Rother extern: 1 month: '01' publication: Markov Random Fields for Vision and Image Processing publication_status: published publisher: Massachusetts Institute of Technology Press publist_id: '3812' quality_controlled: 0 status: public title: Interactive Foreground Extraction using graph cut type: book_chapter year: '2011' ... --- _id: '2935' author: - first_name: Yuri full_name: Boykov, Yuri last_name: Boykov - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Boykov Y, Kolmogorov V. Basic graph cut algorithms. In: Blake A, Kohli P, Rother C, eds. Markov Random Fields for Vision and Image Processing. Massachusetts Institute of Technology Press; 2011:31-50.' apa: Boykov, Y., & Kolmogorov, V. (2011). Basic graph cut algorithms. In A. Blake, P. Kohli, & C. Rother (Eds.), Markov Random Fields for Vision and Image Processing (pp. 31–50). Massachusetts Institute of Technology Press. chicago: Boykov, Yuri, and Vladimir Kolmogorov. “Basic Graph Cut Algorithms.” In Markov Random Fields for Vision and Image Processing, edited by Andrew Blake, Pushmeet Kohli, and Carsten Rother, 31–50. Massachusetts Institute of Technology Press, 2011. ieee: Y. Boykov and V. Kolmogorov, “Basic graph cut algorithms,” in Markov Random Fields for Vision and Image Processing, A. Blake, P. Kohli, and C. Rother, Eds. Massachusetts Institute of Technology Press, 2011, pp. 31–50. ista: 'Boykov Y, Kolmogorov V. 2011.Basic graph cut algorithms. In: Markov Random Fields for Vision and Image Processing. , 31–50.' mla: Boykov, Yuri, and Vladimir Kolmogorov. “Basic Graph Cut Algorithms.” Markov Random Fields for Vision and Image Processing, edited by Andrew Blake et al., Massachusetts Institute of Technology Press, 2011, pp. 31–50. short: Y. Boykov, V. Kolmogorov, in:, A. Blake, P. Kohli, C. Rother (Eds.), Markov Random Fields for Vision and Image Processing, Massachusetts Institute of Technology Press, 2011, pp. 31–50. date_created: 2018-12-11T12:00:26Z date_published: 2011-07-22T00:00:00Z date_updated: 2021-01-12T07:39:53Z day: '22' editor: - first_name: Andrew full_name: Blake, Andrew last_name: Blake - first_name: Pushmeet full_name: Kohli, Pushmeet last_name: Kohli - first_name: Carsten full_name: Rother, Carsten last_name: Rother extern: 1 month: '07' page: 31 - 50 publication: Markov Random Fields for Vision and Image Processing publication_status: published publisher: Massachusetts Institute of Technology Press publist_id: '3801' quality_controlled: 0 status: public title: Basic graph cut algorithms type: book_chapter year: '2011' ... --- _id: '2961' abstract: - lang: eng text: |- Rapid research progress in genotyping techniques have allowed large genome-wide association studies. Existing methods often focus on determining associations between single loci and a specic phenotype. However, a particular phenotype is usually the result of complex relationships between multiple loci and the environment. In this paper, we describe a two-stage method for detecting epistasis by combining the traditionally used single-locus search with a search for multiway interactions. Our method is based on an extended version of Fisher's exact test. To perform this test, a Markov chain is constructed on the space of multidimensional contingency tables using the elements of a Markov basis as moves. We test our method on simulated data and compare it to a two-stage logistic regression method and to a fully Bayesian method, showing that we are able to detect the interacting loci when other methods fail to do so. Finally, we apply our method to a genome-wide data set consisting of 685 dogs and identify epistasis associated with canine hair length for four pairs of single nucleotide polymorphisms (SNPs). acknowledgement: Anna-Sapfo Malaspinas is supported by a Janggen-Poehn Fellowship. Caroline Uhler is supported by an International Fulbright Science and Technology Fellowship. author: - first_name: Anna full_name: 'Malaspinas, Anna-Sapfo ' last_name: Malaspinas - first_name: Caroline full_name: Caroline Uhler id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 citation: ama: Malaspinas A, Uhler C. Detecting epistasis via Markov bases. Journal of Algebraic Statistics. 2011;2(1):36-53. doi:http://dx.doi.org/10.18409/jas.v2i1.27 apa: Malaspinas, A., & Uhler, C. (2011). Detecting epistasis via Markov bases. Journal of Algebraic Statistics. Public Knowledge Project. http://dx.doi.org/10.18409/jas.v2i1.27 chicago: Malaspinas, Anna, and Caroline Uhler. “Detecting Epistasis via Markov Bases.” Journal of Algebraic Statistics. Public Knowledge Project, 2011. http://dx.doi.org/10.18409/jas.v2i1.27. ieee: A. Malaspinas and C. Uhler, “Detecting epistasis via Markov bases,” Journal of Algebraic Statistics, vol. 2, no. 1. Public Knowledge Project, pp. 36–53, 2011. ista: Malaspinas A, Uhler C. 2011. Detecting epistasis via Markov bases. Journal of Algebraic Statistics. 2(1), 36–53. mla: Malaspinas, Anna, and Caroline Uhler. “Detecting Epistasis via Markov Bases.” Journal of Algebraic Statistics, vol. 2, no. 1, Public Knowledge Project, 2011, pp. 36–53, doi:http://dx.doi.org/10.18409/jas.v2i1.27. short: A. Malaspinas, C. Uhler, Journal of Algebraic Statistics 2 (2011) 36–53. date_created: 2018-12-11T12:00:34Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:40:05Z day: '01' doi: http://dx.doi.org/10.18409/jas.v2i1.27 extern: 1 intvolume: ' 2' issue: '1' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1006.4929 month: '01' oa: 1 page: 36 - 53 publication: Journal of Algebraic Statistics publication_status: published publisher: Public Knowledge Project publist_id: '3764' quality_controlled: 0 status: public title: Detecting epistasis via Markov bases type: journal_article volume: 2 year: '2011' ... --- _id: '2960' abstract: - lang: eng text: Traditional statistical methods for the confidentiality protection for statistical databases do not scale well to deal with GWAS (genome-wide association studies) databases and external information on them. 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. 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. author: - first_name: Stephen full_name: Fienberg, Stephen E last_name: Fienberg - first_name: Aleksandra full_name: Slavkovic, Aleksandra last_name: Slavkovic - first_name: Caroline full_name: Caroline Uhler id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 citation: ama: 'Fienberg S, Slavkovic A, Uhler C. Privacy Preserving GWAS Data Sharing. In: IEEE; 2011. doi:10.1109/ICDMW.2011.140' apa: Fienberg, S., Slavkovic, A., & Uhler, C. (2011). Privacy Preserving GWAS Data Sharing. Presented at the Proceedings of the 11th IEEE International Conference on Data Mining, IEEE. https://doi.org/10.1109/ICDMW.2011.140 chicago: Fienberg, Stephen, Aleksandra Slavkovic, and Caroline Uhler. “Privacy Preserving GWAS Data Sharing.” IEEE, 2011. https://doi.org/10.1109/ICDMW.2011.140. ieee: S. Fienberg, A. Slavkovic, and C. Uhler, “Privacy Preserving GWAS Data Sharing,” presented at the Proceedings of the 11th IEEE International Conference on Data Mining, 2011. ista: Fienberg S, Slavkovic A, Uhler C. 2011. Privacy Preserving GWAS Data Sharing. Proceedings of the 11th IEEE International Conference on Data Mining. mla: Fienberg, Stephen, et al. Privacy Preserving GWAS Data Sharing. IEEE, 2011, doi:10.1109/ICDMW.2011.140. short: S. Fienberg, A. Slavkovic, C. Uhler, in:, IEEE, 2011. conference: name: Proceedings of the 11th IEEE International Conference on Data Mining date_created: 2018-12-11T12:00:34Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:40:05Z day: '01' doi: 10.1109/ICDMW.2011.140 extern: 1 month: '01' publication_status: published publisher: IEEE publist_id: '3766' quality_controlled: 0 status: public title: Privacy Preserving GWAS Data Sharing type: conference year: '2011' ... --- _id: '2975' abstract: - lang: eng text: "Zero-knowledge proofs of knowledge (ZK-PoK) for discrete logarithms and related problems are indispensable for practical cryptographic protocols. Recently, Camenisch, Kiayias, and Yung provided a specification language (the CKY-language) for such protocols which allows for a modular design and protocol analysis: for every zero-knowledge proof specified in this language, protocol designers are ensured that there exists an efficient protocol which indeed proves the specified statement.\n\nHowever, the protocols resulting from their compilation techniques only satisfy the classical notion of ZK-PoK, which is not retained are when they used as building blocks for higher-level applications or composed with other protocols.\nThis problem can be tackled by moving to the Universal Composability (UC) framework, which guarantees retention of security when composing protocols in arbitrary ways. \nWhile there exist generic transformations from $\\Sigma$-protocols to UC-secure protocols, these transformation are often too inefficient for practice.\n \nIn this paper we introduce a specification language akin to the CKY-language and a compiler such that the resulting protocols are UC-secure and efficient. \nTo this end, we propose an extension of the UC-framework addressing the \nissue that UC-secure zero-knowledge proofs are by definition proofs of knowledge, and state a special composition theorem which allows one to use the weaker -- but more efficient and often sufficient -- notion of proofs of membership in the UC-framework. \nWe believe that our contributions enable the design of practically efficient protocols that are UC-secure and thus themselves can be used as building blocks." acknowledgement: This work was in part funded by the Swiss Hasler Foundation, and the EU FP7 grants 216483 and 216499, as well as by the NSF grant CNS-0716690. alternative_title: - LNCS author: - first_name: Jan full_name: Camenisch, Jan last_name: Camenisch - first_name: Stephan full_name: Stephan Krenn id: 329FCCF0-F248-11E8-B48F-1D18A9856A87 last_name: Krenn orcid: 0000-0003-2835-9093 - first_name: Victor full_name: Shoup, Victor last_name: Shoup citation: ama: 'Camenisch J, Krenn S, Shoup V. A Framework for Practical Universally Composable Zero-Knowledge Protocols. In: Lee D, Wang X, eds. Vol 7073. Springer; 2011:449-467. doi:10.1007/978-3-642-25385-0' apa: 'Camenisch, J., Krenn, S., & Shoup, V. (2011). A Framework for Practical Universally Composable Zero-Knowledge Protocols. In D. Lee & X. Wang (Eds.) (Vol. 7073, pp. 449–467). Presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Springer. https://doi.org/10.1007/978-3-642-25385-0' chicago: Camenisch, Jan, Stephan Krenn, and Victor Shoup. “A Framework for Practical Universally Composable Zero-Knowledge Protocols.” edited by Dong Lee and Xiaoyun Wang, 7073:449–67. Springer, 2011. https://doi.org/10.1007/978-3-642-25385-0. ieee: 'J. Camenisch, S. Krenn, and V. Shoup, “A Framework for Practical Universally Composable Zero-Knowledge Protocols,” presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, 2011, vol. 7073, pp. 449–467.' ista: 'Camenisch J, Krenn S, Shoup V. 2011. A Framework for Practical Universally Composable Zero-Knowledge Protocols. ASIACRYPT: Theory and Application of Cryptology and Information Security, LNCS, vol. 7073, 449–467.' mla: Camenisch, Jan, et al. A Framework for Practical Universally Composable Zero-Knowledge Protocols. Edited by Dong Lee and Xiaoyun Wang, vol. 7073, Springer, 2011, pp. 449–67, doi:10.1007/978-3-642-25385-0. short: J. Camenisch, S. Krenn, V. Shoup, in:, D. Lee, X. Wang (Eds.), Springer, 2011, pp. 449–467. conference: name: 'ASIACRYPT: Theory and Application of Cryptology and Information Security' date_created: 2018-12-11T12:00:39Z date_published: 2011-11-21T00:00:00Z date_updated: 2021-01-12T07:40:11Z day: '21' doi: 10.1007/978-3-642-25385-0 editor: - first_name: Dong full_name: Lee, Dong Hoon last_name: Lee - first_name: Xiaoyun full_name: Wang, Xiaoyun last_name: Wang extern: 1 intvolume: ' 7073' main_file_link: - open_access: '0' url: http://eprint.iacr.org/2011/228.pdf month: '11' page: 449 - 467 publication_status: published publisher: Springer publist_id: '3728' quality_controlled: 0 status: public title: A Framework for Practical Universally Composable Zero-Knowledge Protocols type: conference volume: 7073 year: '2011' ... --- _id: '2977' abstract: - lang: eng text: "Cryptographic two-party protocols are used ubiquitously in\n everyday life. While some of these protocols are easy to\n understand and implement (e.g., key exchange or transmission of\n encrypted data), many of them are much more complex (e.g.,\n e-banking and e-voting applications, or anonymous authentication\n and credential systems).\n\n For a software engineer without appropriate cryptographic skills\n the implementation of such protocols is often difficult, time\n consuming and error-prone. For this reason, a number of compilers\n supporting programmers have been published in recent\n years. However, they are either designed for very specific\n cryptographic primitives (e.g., zero-knowledge proofs of\n knowledge), or they only offer a very low level of abstraction and\n thus again demand substantial mathematical and cryptographic\n \ skills from the programmer. Finally, some of the existing\n compilers do not produce executable code, but only metacode which\n has to be instantiated with mathematical libraries, encryption\n routines, etc. before it can actually be used.\n \n In this paper we present a cryptographically aware compiler which\n is equally useful to cryptographers who want to benchmark\n protocols designed on paper, and to programmers who want to\n implement complex security sensitive protocols without having to\n understand all subtleties. Our tool offers a high level of\n abstraction and outputs well-structured and documented Java\n code. We believe that our compiler can contribute to shortening\n the development cycles of cryptographic applications and to\n reducing their error-proneness." acknowledgement: This work was in part funded by the European Community’s Seventh Framework Programme (FP7) under grant agreement no. 216499 and the Swiss Hasler Foundation under projects no. 09037 and 10069. author: - first_name: Endre full_name: Bangerter, Endre last_name: Bangerter - first_name: Stephan full_name: Stephan Krenn id: 329FCCF0-F248-11E8-B48F-1D18A9856A87 last_name: Krenn orcid: 0000-0003-2835-9093 - first_name: Martial full_name: Seifriz, Martial last_name: Seifriz - first_name: Ulrich full_name: Ultes-Nitsche, Ulrich last_name: Ultes Nitsche citation: ama: 'Bangerter E, Krenn S, Seifriz M, Ultes Nitsche U. cPLC - A Cryptographic Programming Language and Compiler. In: Venter H, Coetzee M, Loock M, eds. IEEE; 2011. doi:10.1109/ISSA.2011.6027533' apa: 'Bangerter, E., Krenn, S., Seifriz, M., & Ultes Nitsche, U. (2011). cPLC - A Cryptographic Programming Language and Compiler. In H. Venter, M. Coetzee, & M. Loock (Eds.). Presented at the ISSA: Information Security South Africa, IEEE. https://doi.org/10.1109/ISSA.2011.6027533' chicago: Bangerter, Endre, Stephan Krenn, Martial Seifriz, and Ulrich Ultes Nitsche. “CPLC - A Cryptographic Programming Language and Compiler.” edited by Hein Venter, Marijke Coetzee, and Marianne Loock. IEEE, 2011. https://doi.org/10.1109/ISSA.2011.6027533. ieee: 'E. Bangerter, S. Krenn, M. Seifriz, and U. Ultes Nitsche, “cPLC - A Cryptographic Programming Language and Compiler,” presented at the ISSA: Information Security South Africa, 2011.' ista: 'Bangerter E, Krenn S, Seifriz M, Ultes Nitsche U. 2011. cPLC - A Cryptographic Programming Language and Compiler. ISSA: Information Security South Africa.' mla: Bangerter, Endre, et al. CPLC - A Cryptographic Programming Language and Compiler. Edited by Hein Venter et al., IEEE, 2011, doi:10.1109/ISSA.2011.6027533. short: E. Bangerter, S. Krenn, M. Seifriz, U. Ultes Nitsche, in:, H. Venter, M. Coetzee, M. Loock (Eds.), IEEE, 2011. conference: name: 'ISSA: Information Security South Africa' date_created: 2018-12-11T12:00:39Z date_published: 2011-08-01T00:00:00Z date_updated: 2021-01-12T07:40:12Z day: '01' doi: 10.1109/ISSA.2011.6027533 editor: - first_name: Hein full_name: Venter, Hein S. last_name: Venter - first_name: Marijke full_name: Coetzee, Marijke last_name: Coetzee - first_name: Marianne full_name: Loock, Marianne last_name: Loock extern: 1 month: '08' publication_status: published publisher: IEEE publist_id: '3726' quality_controlled: 0 status: public title: cPLC - A Cryptographic Programming Language and Compiler type: conference year: '2011' ... --- _id: '2976' abstract: - lang: eng text: |- Side channel attacks on cryptographic systems exploit information gained from physical implementations rather than theoretical weaknesses of a scheme. In recent years, major achievements were made for the class of so called access-driven cache attacks. Such attacks exploit the leakage of the memory locations accessed by a victim process. In this paper we consider the AES block cipher and present an attack which is capable of recovering the full secret key in almost realtime for AES-128, requiring only a very limited number of observed encryptions. Unlike previous attacks, we do not require any information about the plaintext (such as its distribution, etc.). Moreover, for the first time, we also show how the plaintext can be recovered without having access to the ciphertext at all. It is the first working attack on AES implementations using compressed tables. There, no efficient techniques to identify the beginning of AES rounds is known, which is the fundamental assumption underlying previous attacks. We have a fully working implementation of our attack which is able to recover AES keys after observing as little as 100 encryptions. It works against the OpenSSL 0.9.8n implementation of AES on Linux systems. Our spy process does not require any special privileges beyond those of a standard Linux user. A contribution of probably independent interest is a denial of service attack on the task scheduler of current Linux systems (CFS), which allows one to observe (on average) every single memory access of a victim process. acknowledgement: |- This work was in part funded by the European Community’s Seventh Framework Programme (FP7) under grant agreement no. 216499 and the Swiss Hasler Foundation. An extended abstract was also accepted for COSADE 2011. author: - first_name: David full_name: Gullasch, David last_name: Gullasch - first_name: Endre full_name: Bangerter, Endre last_name: Bangerter - first_name: Stephan full_name: Stephan Krenn id: 329FCCF0-F248-11E8-B48F-1D18A9856A87 last_name: Krenn orcid: 0000-0003-2835-9093 citation: ama: 'Gullasch D, Bangerter E, Krenn S. Cache Games - Bringing Access-Based Cache Attacks on AES to Practice. In: IEEE; 2011:490-505. doi:10.1109/SP.2011.22' apa: 'Gullasch, D., Bangerter, E., & Krenn, S. (2011). Cache Games - Bringing Access-Based Cache Attacks on AES to Practice (pp. 490–505). Presented at the S&P: IEEE Symposium on Security and Privacy, IEEE. https://doi.org/10.1109/SP.2011.22' chicago: Gullasch, David, Endre Bangerter, and Stephan Krenn. “Cache Games - Bringing Access-Based Cache Attacks on AES to Practice,” 490–505. IEEE, 2011. https://doi.org/10.1109/SP.2011.22. ieee: 'D. Gullasch, E. Bangerter, and S. Krenn, “Cache Games - Bringing Access-Based Cache Attacks on AES to Practice,” presented at the S&P: IEEE Symposium on Security and Privacy, 2011, pp. 490–505.' ista: 'Gullasch D, Bangerter E, Krenn S. 2011. Cache Games - Bringing Access-Based Cache Attacks on AES to Practice. S&P: IEEE Symposium on Security and Privacy, 490–505.' mla: Gullasch, David, et al. Cache Games - Bringing Access-Based Cache Attacks on AES to Practice. IEEE, 2011, pp. 490–505, doi:10.1109/SP.2011.22. short: D. Gullasch, E. Bangerter, S. Krenn, in:, IEEE, 2011, pp. 490–505. conference: name: 'S&P: IEEE Symposium on Security and Privacy' date_created: 2018-12-11T12:00:39Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:40:11Z day: '01' doi: 10.1109/SP.2011.22 extern: 1 main_file_link: - open_access: '0' url: http://eprint.iacr.org/2010/594.pdf month: '01' page: 490 - 505 publication_status: published publisher: IEEE publist_id: '3727' quality_controlled: 0 status: public title: Cache Games - Bringing Access-Based Cache Attacks on AES to Practice type: conference year: '2011' ... --- _id: '3092' abstract: - lang: eng text: The phytohormone auxin is vital to plant growth and development. A unique property of auxin among all other plant hormones is its cell-to-cell polar transport that requires activity of polarly localized PIN-FORMED (PIN) auxin efflux transporters. Despite the substantial molecular insight into the cellular PIN polarization, the mechanistic understanding for developmentally and environmentally regulated PIN polarization is scarce. The long-standing belief that auxin modulates its own transport by means of a positive feedback mechanism has inspired both experimentalists and theoreticians for more than two decades. Recently, theoretical models for auxin-dependent patterning in plants include the feedback between auxin transport and the PIN protein localization. These computer models aid to assess the complexity of plant development by testing and predicting plausible scenarios for various developmental processes that occur in planta. Although the majority of these models rely on purely heuristic principles, the most recent mechanistic models tentatively integrate biologically testable components into known cellular processes that underlie the PIN polarity regulation. The existing and emerging computational approaches to describe PIN polarization are presented and discussed in the light of recent experimental data on the PIN polar targeting. author: - first_name: Krzysztof T full_name: Wabnik, Krzysztof T id: 4DE369A4-F248-11E8-B48F-1D18A9856A87 last_name: Wabnik orcid: 0000-0001-7263-0560 - first_name: Willy full_name: Govaerts, Willy last_name: Govaerts - first_name: Jirí full_name: Friml, Jirí 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: 'Wabnik KT, Govaerts W, Friml J, Kleine Vehn J. Feedback models for polarized auxin transport: An emerging trend. Molecular BioSystems. 2011;7(8):2352-2359. doi:10.1039/c1mb05109a' apa: 'Wabnik, K. T., Govaerts, W., Friml, J., & Kleine Vehn, J. (2011). Feedback models for polarized auxin transport: An emerging trend. Molecular BioSystems. Royal Society of Chemistry. https://doi.org/10.1039/c1mb05109a' chicago: 'Wabnik, Krzysztof T, Willy Govaerts, Jiří Friml, and Jürgen Kleine Vehn. “Feedback Models for Polarized Auxin Transport: An Emerging Trend.” Molecular BioSystems. Royal Society of Chemistry, 2011. https://doi.org/10.1039/c1mb05109a.' ieee: 'K. T. Wabnik, W. Govaerts, J. Friml, and J. Kleine Vehn, “Feedback models for polarized auxin transport: An emerging trend,” Molecular BioSystems, vol. 7, no. 8. Royal Society of Chemistry, pp. 2352–2359, 2011.' ista: 'Wabnik KT, Govaerts W, Friml J, Kleine Vehn J. 2011. Feedback models for polarized auxin transport: An emerging trend. Molecular BioSystems. 7(8), 2352–2359.' mla: 'Wabnik, Krzysztof T., et al. “Feedback Models for Polarized Auxin Transport: An Emerging Trend.” Molecular BioSystems, vol. 7, no. 8, Royal Society of Chemistry, 2011, pp. 2352–59, doi:10.1039/c1mb05109a.' short: K.T. Wabnik, W. Govaerts, J. Friml, J. Kleine Vehn, Molecular BioSystems 7 (2011) 2352–2359. date_created: 2018-12-11T12:01:20Z date_published: 2011-06-10T00:00:00Z date_updated: 2021-01-12T07:41:00Z day: '10' doi: 10.1039/c1mb05109a extern: '1' external_id: pmid: - '21660355' intvolume: ' 7' issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/21660355 month: '06' oa: 1 oa_version: Published Version page: 2352 - 2359 pmid: 1 publication: Molecular BioSystems publication_status: published publisher: Royal Society of Chemistry publist_id: '3608' quality_controlled: '1' status: public title: 'Feedback models for polarized auxin transport: An emerging trend' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2011' ... --- _id: '3089' abstract: - lang: eng text: The phytohormone auxin is an important determinant of plant development. Directional auxin flow within tissues depends on polar localization of PIN auxin transporters. To explore regulation of PIN-mediated auxin transport, we screened for suppressors of PIN1 overexpression (supo) and identified an inositol polyphosphate 1-phosphatase mutant (supo1), with elevated inositol trisphosphate (InsP 3) and cytosolic Ca 2+ levels. Pharmacological and genetic increases in InsP 3 or Ca 2+ levels also suppressed the PIN1 gain-of-function phenotypes and caused defects in basal PIN localization, auxin transport and auxin-mediated development. In contrast, the reductions in InsP 3 levels and Ca 2+ signaling antagonized the effects of the supo1 mutation and disrupted preferentially apical PIN localization. InsP 3 and Ca 2+ are evolutionarily conserved second messengers involved in various cellular functions, particularly stress responses. Our findings implicate them as modifiers of cell polarity and polar auxin transport, and highlight a potential integration point through which Ca 2+ signaling-related stimuli could influence auxin-mediated development. author: - first_name: Jing full_name: Zhang, Jing last_name: Zhang - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Philip full_name: Brewer, Philip B last_name: Brewer - first_name: Marta full_name: Michniewicz, Marta last_name: Michniewicz - first_name: Peter full_name: Peter Grones id: 399876EC-F248-11E8-B48F-1D18A9856A87 last_name: Grones - first_name: Jürgen full_name: Kleine-Vehn, Jürgen last_name: Kleine Vehn - first_name: Christian full_name: Löfke, Christian last_name: Löfke - first_name: Thomas full_name: Teichmann, Thomas last_name: Teichmann - first_name: Agnieszka full_name: Bielach, Agnieszka last_name: Bielach - first_name: Bernard full_name: Cannoot, Bernard last_name: Cannoot - first_name: Klára full_name: Hoyerová, Klára last_name: Hoyerová - first_name: Xu full_name: Xu Chen id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Hong full_name: Xue, Hong-Wei last_name: Xue - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Zhang J, Vanneste S, Brewer P, et al. Inositol trisphosphate-induced ca^2+ signaling modulates auxin transport and pin polarity. Developmental Cell. 2011;20(6):855-866. doi:10.1016/j.devcel.2011.05.013 apa: Zhang, J., Vanneste, S., Brewer, P., Michniewicz, M., Grones, P., Kleine Vehn, J., … Friml, J. (2011). Inositol trisphosphate-induced ca^2+ signaling modulates auxin transport and pin polarity. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2011.05.013 chicago: Zhang, Jing, Steffen Vanneste, Philip Brewer, Marta Michniewicz, Peter Grones, Jürgen Kleine Vehn, Christian Löfke, et al. “Inositol Trisphosphate-Induced Ca^2+ Signaling Modulates Auxin Transport and Pin Polarity.” Developmental Cell. Cell Press, 2011. https://doi.org/10.1016/j.devcel.2011.05.013. ieee: J. Zhang et al., “Inositol trisphosphate-induced ca^2+ signaling modulates auxin transport and pin polarity,” Developmental Cell, vol. 20, no. 6. Cell Press, pp. 855–866, 2011. ista: Zhang J, Vanneste S, Brewer P, Michniewicz M, Grones P, Kleine Vehn J, Löfke C, Teichmann T, Bielach A, Cannoot B, Hoyerová K, Chen X, Xue H, Benková E, Zažímalová E, Friml J. 2011. Inositol trisphosphate-induced ca^2+ signaling modulates auxin transport and pin polarity. Developmental Cell. 20(6), 855–866. mla: Zhang, Jing, et al. “Inositol Trisphosphate-Induced Ca^2+ Signaling Modulates Auxin Transport and Pin Polarity.” Developmental Cell, vol. 20, no. 6, Cell Press, 2011, pp. 855–66, doi:10.1016/j.devcel.2011.05.013. short: J. Zhang, S. Vanneste, P. Brewer, M. Michniewicz, P. Grones, J. Kleine Vehn, C. Löfke, T. Teichmann, A. Bielach, B. Cannoot, K. Hoyerová, X. Chen, H. Xue, E. Benková, E. Zažímalová, J. Friml, Developmental Cell 20 (2011) 855–866. date_created: 2018-12-11T12:01:18Z date_published: 2011-06-14T00:00:00Z date_updated: 2021-01-12T07:40:58Z day: '14' doi: 10.1016/j.devcel.2011.05.013 extern: 1 intvolume: ' 20' issue: '6' month: '06' page: 855 - 866 publication: Developmental Cell publication_status: published publisher: Cell Press publist_id: '3612' quality_controlled: 0 status: public title: Inositol trisphosphate-induced ca^2+ signaling modulates auxin transport and pin polarity type: journal_article volume: 20 year: '2011' ... --- _id: '3090' abstract: - lang: eng text: The polarized transport of the phytohormone auxin [1], which is crucial for the regulation of different stages of plant development [2, 3], depends on the asymmetric plasma membrane distribution of the PIN-FORMED (PIN) auxin efflux carriers [4, 5]. The PIN polar localization results from clathrin-mediated endocytosis (CME) from the plasma membrane and subsequent polar recycling [6]. The Arabidopsis genome encodes two groups of dynamin-related proteins (DRPs) that show homology to mammalian dynamin - a protein required for fission of endocytic vesicles during CME [7, 8]. Here we show by coimmunoprecipitation (coIP), bimolecular fluorescence complementation (BiFC), and Förster resonance energy transfer (FRET) that members of the DRP1 group closely associate with PIN proteins at the cell plate. Localization and phenotypic analysis of novel drp1 mutants revealed a requirement for DRP1 function in correct PIN distribution and in auxin-mediated development. We propose that rapid and specific internalization of PIN proteins mediated by the DRP1 proteins and the associated CME machinery from the cell plate membranes during cytokinesis is an important mechanism for proper polar PIN positioning in interphase cells. author: - first_name: Jozef full_name: Mravec, Jozef last_name: Mravec - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Na full_name: Li, Na last_name: Li - first_name: Sjef full_name: Boeren, Sjef last_name: Boeren - first_name: Rumyana full_name: Karlova, Rumyana last_name: Karlova - first_name: Saeko full_name: Kitakura, Saeko last_name: Kitakura - first_name: Markéta full_name: Pařezová, Markéta last_name: Pařezová - first_name: Satoshi full_name: Naramoto, Satoshi last_name: Naramoto - first_name: Thomasz full_name: Nodzyński, Thomasz last_name: Nodzyński - first_name: Pankaj full_name: Dhonukshe, Pankaj last_name: Dhonukshe - first_name: Sebastian full_name: Bednarek, Sebastian Y last_name: Bednarek - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová - first_name: Sacco full_name: De Vries, Sacco last_name: De Vries - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Mravec J, Petrášek J, Li N, et al. Cell plate restricted association of DRP1A and PIN proteins is required for cell polarity establishment in arabidopsis. Current Biology. 2011;21(12):1055-1060. doi:10.1016/j.cub.2011.05.018 apa: Mravec, J., Petrášek, J., Li, N., Boeren, S., Karlova, R., Kitakura, S., … Friml, J. (2011). Cell plate restricted association of DRP1A and PIN proteins is required for cell polarity establishment in arabidopsis. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2011.05.018 chicago: Mravec, Jozef, Jan Petrášek, Na Li, Sjef Boeren, Rumyana Karlova, Saeko Kitakura, Markéta Pařezová, et al. “Cell Plate Restricted Association of DRP1A and PIN Proteins Is Required for Cell Polarity Establishment in Arabidopsis.” Current Biology. Cell Press, 2011. https://doi.org/10.1016/j.cub.2011.05.018. ieee: J. Mravec et al., “Cell plate restricted association of DRP1A and PIN proteins is required for cell polarity establishment in arabidopsis,” Current Biology, vol. 21, no. 12. Cell Press, pp. 1055–1060, 2011. ista: Mravec J, Petrášek J, Li N, Boeren S, Karlova R, Kitakura S, Pařezová M, Naramoto S, Nodzyński T, Dhonukshe P, Bednarek S, Zažímalová E, De Vries S, Friml J. 2011. Cell plate restricted association of DRP1A and PIN proteins is required for cell polarity establishment in arabidopsis. Current Biology. 21(12), 1055–1060. mla: Mravec, Jozef, et al. “Cell Plate Restricted Association of DRP1A and PIN Proteins Is Required for Cell Polarity Establishment in Arabidopsis.” Current Biology, vol. 21, no. 12, Cell Press, 2011, pp. 1055–60, doi:10.1016/j.cub.2011.05.018. short: J. Mravec, J. Petrášek, N. Li, S. Boeren, R. Karlova, S. Kitakura, M. Pařezová, S. Naramoto, T. Nodzyński, P. Dhonukshe, S. Bednarek, E. Zažímalová, S. De Vries, J. Friml, Current Biology 21 (2011) 1055–1060. date_created: 2018-12-11T12:01:19Z date_published: 2011-06-21T00:00:00Z date_updated: 2021-01-12T07:40:59Z day: '21' doi: 10.1016/j.cub.2011.05.018 extern: 1 intvolume: ' 21' issue: '12' month: '06' page: 1055 - 1060 publication: Current Biology publication_status: published publisher: Cell Press publist_id: '3611' quality_controlled: 0 status: public title: Cell plate restricted association of DRP1A and PIN proteins is required for cell polarity establishment in arabidopsis type: journal_article volume: 21 year: '2011' ... --- _id: '3088' abstract: - lang: eng text: 'Background: Whereas the majority of animals develop toward a predetermined body plan, plants show iterative growth and continually produce new organs and structures from actively dividing meristems. This raises an intriguing question: How are these newly developed organs patterned? In Arabidopsis embryos, radial symmetry is broken by the bisymmetric specification of the cotyledons in the apical domain. Subsequently, this bisymmetry is propagated to the root promeristem. Results: Here we present a mutually inhibitory feedback loop between auxin and cytokinin that sets distinct boundaries of hormonal output. Cytokinins promote the bisymmetric distribution of the PIN-FORMED (PIN) auxin efflux proteins, which channel auxin toward a central domain. High auxin promotes transcription of the cytokinin signaling inhibitor AHP6, which closes the interaction loop. This bisymmetric auxin response domain specifies the differentiation of protoxylem in a bisymmetric pattern. In embryonic roots, cytokinin is required to translate a bisymmetric auxin response in the cotyledons to a bisymmetric vascular pattern in the root promeristem. Conclusions: Our results present an interactive feedback loop between hormonal signaling and transport by which small biases in hormonal input are propagated into distinct signaling domains to specify the vascular pattern in the root meristem. It is an intriguing possibility that such a mechanism could transform radial patterns and allow continuous vascular connections between other newly emerging organs.' author: - first_name: Anthony full_name: Bishopp, Anthony last_name: Bishopp - first_name: Hanna full_name: Help, Hanna last_name: Help - first_name: Sedeer full_name: El-Showk, Sedeer last_name: El Showk - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers - first_name: Ben full_name: Scheres, Ben last_name: Scheres - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Ari full_name: Mähönen, Ari Pekka last_name: Mähönen - first_name: Ykä full_name: Helariutta, Ykä last_name: Helariutta citation: ama: Bishopp A, Help H, El Showk S, et al. A mutually inhibitory interaction between auxin and cytokinin specifies vascular pattern in roots. Current Biology. 2011;21(11):917-926. doi:10.1016/j.cub.2011.04.017 apa: Bishopp, A., Help, H., El Showk, S., Weijers, D., Scheres, B., Friml, J., … Helariutta, Y. (2011). A mutually inhibitory interaction between auxin and cytokinin specifies vascular pattern in roots. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2011.04.017 chicago: Bishopp, Anthony, Hanna Help, Sedeer El Showk, Dolf Weijers, Ben Scheres, Jiří Friml, Eva Benková, Ari Mähönen, and Ykä Helariutta. “A Mutually Inhibitory Interaction between Auxin and Cytokinin Specifies Vascular Pattern in Roots.” Current Biology. Cell Press, 2011. https://doi.org/10.1016/j.cub.2011.04.017. ieee: A. Bishopp et al., “A mutually inhibitory interaction between auxin and cytokinin specifies vascular pattern in roots,” Current Biology, vol. 21, no. 11. Cell Press, pp. 917–926, 2011. ista: Bishopp A, Help H, El Showk S, Weijers D, Scheres B, Friml J, Benková E, Mähönen A, Helariutta Y. 2011. A mutually inhibitory interaction between auxin and cytokinin specifies vascular pattern in roots. Current Biology. 21(11), 917–926. mla: Bishopp, Anthony, et al. “A Mutually Inhibitory Interaction between Auxin and Cytokinin Specifies Vascular Pattern in Roots.” Current Biology, vol. 21, no. 11, Cell Press, 2011, pp. 917–26, doi:10.1016/j.cub.2011.04.017. short: A. Bishopp, H. Help, S. El Showk, D. Weijers, B. Scheres, J. Friml, E. Benková, A. Mähönen, Y. Helariutta, Current Biology 21 (2011) 917–926. date_created: 2018-12-11T12:01:18Z date_published: 2011-06-07T00:00:00Z date_updated: 2021-01-12T07:40:58Z day: '07' doi: 10.1016/j.cub.2011.04.017 extern: 1 intvolume: ' 21' issue: '11' month: '06' page: 917 - 926 publication: Current Biology publication_status: published publisher: Cell Press publist_id: '3613' quality_controlled: 0 status: public title: A mutually inhibitory interaction between auxin and cytokinin specifies vascular pattern in roots type: journal_article volume: 21 year: '2011' ... --- _id: '3093' abstract: - lang: eng text: |2- Plants take up iron from the soil using the IRON-REGULATED TRANSPORTER 1 (IRT1) high-affinity iron transporter at the root surface. Sophisticated regulatory mechanisms allow plants to tightly control the levels of IRT1, ensuring optimal absorption of essential but toxic iron. Here, we demonstrate that overexpression of Arabidopsis thaliana IRT1 leads to constitutive IRT1 protein accumulation, metal overload, and oxidative stress. IRT1 is unexpectedly found in trans-Golgi network/early endosomes of root hair cells, and its levels and localization are unaffected by iron nutrition. Using pharmacological approaches, we show that IRT1 cycles to the plasma membrane to perform iron and metal uptake at the cell surface and is sent to the vacuole for proper turnover. We also prove that IRT1 is monoubiquitinated on several cytosol-exposed residues in vivo and that mutation of two putative monoubiquitination target residues in IRT1 triggers stabilization at the plasma membrane and leads to extreme lethality. Together, these data suggest a model in which monoubiquitin-dependent internalization/sorting and turnover keep the plasma membrane pool of IRT1 low to ensure proper iron uptake and to prevent metal toxicity. More generally, our work demonstrates the existence of monoubiquitin-dependent trafficking to lytic vacuoles in plants and points to proteasome-independent turnover of plasma membrane proteins. author: - first_name: Marie full_name: Barberon, Marie last_name: Barberon - first_name: Enric full_name: Zelazny, Enric last_name: Zelazny - first_name: Stéphanie full_name: Robert, Stéphanie last_name: Robert - first_name: Geneviève full_name: Conéjéro, Geneviève last_name: Conéjéro - first_name: Cathy full_name: Curie, Cathy last_name: Curie - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Grégory full_name: Vert, Grégory last_name: Vert citation: ama: Barberon M, Zelazny E, Robert S, et al. Monoubiquitin dependent endocytosis of the Iron Regulated Transporter 1 IRT1 transporter controls iron uptake in plants. PNAS. 2011;108(32):E450-E458. doi:10.1073/pnas.1100659108 apa: Barberon, M., Zelazny, E., Robert, S., Conéjéro, G., Curie, C., Friml, J., & Vert, G. (2011). Monoubiquitin dependent endocytosis of the Iron Regulated Transporter 1 IRT1 transporter controls iron uptake in plants. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1100659108 chicago: Barberon, Marie, Enric Zelazny, Stéphanie Robert, Geneviève Conéjéro, Cathy Curie, Jiří Friml, and Grégory Vert. “Monoubiquitin Dependent Endocytosis of the Iron Regulated Transporter 1 IRT1 Transporter Controls Iron Uptake in Plants.” PNAS. National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1100659108. ieee: M. Barberon et al., “Monoubiquitin dependent endocytosis of the Iron Regulated Transporter 1 IRT1 transporter controls iron uptake in plants,” PNAS, vol. 108, no. 32. National Academy of Sciences, pp. E450–E458, 2011. ista: Barberon M, Zelazny E, Robert S, Conéjéro G, Curie C, Friml J, Vert G. 2011. Monoubiquitin dependent endocytosis of the Iron Regulated Transporter 1 IRT1 transporter controls iron uptake in plants. PNAS. 108(32), E450–E458. mla: Barberon, Marie, et al. “Monoubiquitin Dependent Endocytosis of the Iron Regulated Transporter 1 IRT1 Transporter Controls Iron Uptake in Plants.” PNAS, vol. 108, no. 32, National Academy of Sciences, 2011, pp. E450–58, doi:10.1073/pnas.1100659108. short: M. Barberon, E. Zelazny, S. Robert, G. Conéjéro, C. Curie, J. Friml, G. Vert, PNAS 108 (2011) E450–E458. date_created: 2018-12-11T12:01:20Z date_published: 2011-08-09T00:00:00Z date_updated: 2021-01-12T07:41:00Z day: '09' doi: 10.1073/pnas.1100659108 extern: 1 intvolume: ' 108' issue: '32' month: '08' page: E450 - E458 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '3607' quality_controlled: 0 status: public title: Monoubiquitin dependent endocytosis of the Iron Regulated Transporter 1 IRT1 transporter controls iron uptake in plants type: journal_article volume: 108 year: '2011' ... --- _id: '3094' abstract: - lang: eng text: Summary Gravitropism aligns plant growth with gravity. It involves gravity perception and the asymmetric distribution of the phytohormone auxin. Here we provide insights into the mechanism for hypocotyl gravitropic growth. We show that the Arabidopsis thaliana PIN3 auxin transporter is required for the asymmetric auxin distribution for the gravitropic response. Gravistimulation polarizes PIN3 to the bottom side of hypocotyl endodermal cells, which correlates with an increased auxin response at the lower hypocotyl side. Both PIN3 polarization and hypocotyl bending require the activity of the trafficking regulator GNOM and the protein kinase PINOID. Our data suggest that gravity-induced PIN3 polarization diverts the auxin flow to mediate the asymmetric distribution of auxin for gravitropic shoot bending. author: - first_name: Hana full_name: Rakusová, Hana last_name: Rakusová - first_name: Javier full_name: Gallego-Bartolomé, Javier last_name: Gallego Bartolomé - first_name: Marleen full_name: Vanstraelen, Marleen last_name: Vanstraelen - first_name: Hélène full_name: Robert, Hélène S last_name: Robert - first_name: David full_name: Alabadí, David last_name: Alabadí - first_name: Miguel full_name: Blázquez, Miguel A last_name: Blázquez - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Rakusová H, Gallego Bartolomé J, Vanstraelen M, et al. Polarization of PIN3 dependent auxin transport for hypocotyl gravitropic response in Arabidopsis thaliana. Plant Journal. 2011;67(5):817-826. doi:10.1111/j.1365-313X.2011.04636.x apa: Rakusová, H., Gallego Bartolomé, J., Vanstraelen, M., Robert, H., Alabadí, D., Blázquez, M., … Friml, J. (2011). Polarization of PIN3 dependent auxin transport for hypocotyl gravitropic response in Arabidopsis thaliana. Plant Journal. Wiley-Blackwell. https://doi.org/10.1111/j.1365-313X.2011.04636.x chicago: Rakusová, Hana, Javier Gallego Bartolomé, Marleen Vanstraelen, Hélène Robert, David Alabadí, Miguel Blázquez, Eva Benková, and Jiří Friml. “Polarization of PIN3 Dependent Auxin Transport for Hypocotyl Gravitropic Response in Arabidopsis Thaliana.” Plant Journal. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1365-313X.2011.04636.x. ieee: H. Rakusová et al., “Polarization of PIN3 dependent auxin transport for hypocotyl gravitropic response in Arabidopsis thaliana,” Plant Journal, vol. 67, no. 5. Wiley-Blackwell, pp. 817–826, 2011. ista: Rakusová H, Gallego Bartolomé J, Vanstraelen M, Robert H, Alabadí D, Blázquez M, Benková E, Friml J. 2011. Polarization of PIN3 dependent auxin transport for hypocotyl gravitropic response in Arabidopsis thaliana. Plant Journal. 67(5), 817–826. mla: Rakusová, Hana, et al. “Polarization of PIN3 Dependent Auxin Transport for Hypocotyl Gravitropic Response in Arabidopsis Thaliana.” Plant Journal, vol. 67, no. 5, Wiley-Blackwell, 2011, pp. 817–26, doi:10.1111/j.1365-313X.2011.04636.x. short: H. Rakusová, J. Gallego Bartolomé, M. Vanstraelen, H. Robert, D. Alabadí, M. Blázquez, E. Benková, J. Friml, Plant Journal 67 (2011) 817–826. date_created: 2018-12-11T12:01:21Z date_published: 2011-09-01T00:00:00Z date_updated: 2021-01-12T07:41:01Z day: '01' doi: 10.1111/j.1365-313X.2011.04636.x extern: 1 intvolume: ' 67' issue: '5' month: '09' page: 817 - 826 publication: Plant Journal publication_status: published publisher: Wiley-Blackwell publist_id: '3606' quality_controlled: 0 status: public title: Polarization of PIN3 dependent auxin transport for hypocotyl gravitropic response in Arabidopsis thaliana type: journal_article volume: 67 year: '2011' ... --- _id: '3091' author: - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Sauer M, Friml J. Fleeting hormone cues get stabilized for plant organogenesis. Molecular Systems Biology. 2011;7. doi:10.1038/msb.2011.45 apa: Sauer, M., & Friml, J. (2011). Fleeting hormone cues get stabilized for plant organogenesis. Molecular Systems Biology. Nature Publishing Group. https://doi.org/10.1038/msb.2011.45 chicago: Sauer, Michael, and Jiří Friml. “Fleeting Hormone Cues Get Stabilized for Plant Organogenesis.” Molecular Systems Biology. Nature Publishing Group, 2011. https://doi.org/10.1038/msb.2011.45. ieee: M. Sauer and J. Friml, “Fleeting hormone cues get stabilized for plant organogenesis,” Molecular Systems Biology, vol. 7. Nature Publishing Group, 2011. ista: Sauer M, Friml J. 2011. Fleeting hormone cues get stabilized for plant organogenesis. Molecular Systems Biology. 7. mla: Sauer, Michael, and Jiří Friml. “Fleeting Hormone Cues Get Stabilized for Plant Organogenesis.” Molecular Systems Biology, vol. 7, Nature Publishing Group, 2011, doi:10.1038/msb.2011.45. short: M. Sauer, J. Friml, Molecular Systems Biology 7 (2011). date_created: 2018-12-11T12:01:19Z date_published: 2011-07-05T00:00:00Z date_updated: 2021-01-12T07:41:00Z day: '05' doi: 10.1038/msb.2011.45 extern: '1' external_id: pmid: - '21734646' intvolume: ' 7' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159970/ month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: Molecular Systems Biology publication_status: published publisher: Nature Publishing Group publist_id: '3610' quality_controlled: '1' status: public title: Fleeting hormone cues get stabilized for plant organogenesis type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2011' ... --- _id: '3102' abstract: - lang: eng text: 'Multicellular organisms depend on cell production, cell fate specification, and correct patterning to shape their adult body. In plants, auxin plays a prominent role in the timely coordination of these different cellular processes. A well-studied example is lateral root initiation, in which auxin triggers founder cell specification and cell cycle activation of xylem pole–positioned pericycle cells. Here, we report that the E2Fa transcription factor of Arabidopsis thaliana is an essential component that regulates the asymmetric cell division marking lateral root initiation. Moreover, we demonstrate that E2Fa expression is regulated by the LATERAL ORGAN BOUNDARY DOMAIN18/LATERAL ORGAN BOUNDARY DOMAIN33 (LBD18/LBD33) dimer that is, in turn, regulated by the auxin signaling pathway. LBD18/LBD33 mediates lateral root organogenesis through E2Fa transcriptional activation, whereas E2Fa expression under control of the LBD18 promoter eliminates the need for LBD18. Besides lateral root initiation, vascular patterning is disrupted in E2Fa knockout plants, similarly as it is affected in auxin signaling and lbd mutants, indicating that the transcriptional induction of E2Fa through LBDs represents a general mechanism for auxin-dependent cell cycle activation. Our data illustrate how a conserved mechanism driving cell cycle entry has been adapted evolutionarily to connect auxin signaling with control of processes determining plant architecture. ' author: - first_name: Barbara full_name: Berckmans, Barbara last_name: Berckmans - first_name: Valya full_name: Vassileva, Valya last_name: Vassileva - first_name: Stephan full_name: Schmid, Stephan P last_name: Schmid - first_name: Sara full_name: Maes, Sara last_name: Maes - first_name: Boris full_name: Parizot, Boris last_name: Parizot - first_name: Satoshi full_name: Naramoto, Satoshi last_name: Naramoto - first_name: Zoltan full_name: Magyar, Zoltan last_name: Magyar - first_name: Claire full_name: Lessa Alvim Kamei, Claire last_name: Lessa Alvim Kamei - first_name: Csaba full_name: Koncz, Csaba last_name: Koncz - first_name: Laszlo full_name: Bögre, Laszlo last_name: Bögre - first_name: Geert full_name: Persiau, Geert last_name: Persiau - first_name: Geert full_name: De Jaeger, Geert last_name: De Jaeger - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Rüdiger full_name: Simon, Rüdiger last_name: Simon - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman - first_name: Lieven full_name: de Veyldera, Lieven last_name: De Veyldera citation: ama: Berckmans B, Vassileva V, Schmid S, et al. Auxin Dependent cell cycle reactivation through transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins. Plant Cell. 2011;23(10):3671-3683. doi:10.1105/tpc.111.088377 apa: Berckmans, B., Vassileva, V., Schmid, S., Maes, S., Parizot, B., Naramoto, S., … De Veyldera, L. (2011). Auxin Dependent cell cycle reactivation through transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.111.088377 chicago: Berckmans, Barbara, Valya Vassileva, Stephan Schmid, Sara Maes, Boris Parizot, Satoshi Naramoto, Zoltan Magyar, et al. “Auxin Dependent Cell Cycle Reactivation through Transcriptional Regulation of Arabidopsis E2Fa by Lateral Organ Boundary Proteins.” Plant Cell. American Society of Plant Biologists, 2011. https://doi.org/10.1105/tpc.111.088377. ieee: B. Berckmans et al., “Auxin Dependent cell cycle reactivation through transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins,” Plant Cell, vol. 23, no. 10. American Society of Plant Biologists, pp. 3671–3683, 2011. ista: Berckmans B, Vassileva V, Schmid S, Maes S, Parizot B, Naramoto S, Magyar Z, Lessa Alvim Kamei C, Koncz C, Bögre L, Persiau G, De Jaeger G, Friml J, Simon R, Beeckman T, De Veyldera L. 2011. Auxin Dependent cell cycle reactivation through transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins. Plant Cell. 23(10), 3671–3683. mla: Berckmans, Barbara, et al. “Auxin Dependent Cell Cycle Reactivation through Transcriptional Regulation of Arabidopsis E2Fa by Lateral Organ Boundary Proteins.” Plant Cell, vol. 23, no. 10, American Society of Plant Biologists, 2011, pp. 3671–83, doi:10.1105/tpc.111.088377. short: B. Berckmans, V. Vassileva, S. Schmid, S. Maes, B. Parizot, S. Naramoto, Z. Magyar, C. Lessa Alvim Kamei, C. Koncz, L. Bögre, G. Persiau, G. De Jaeger, J. Friml, R. Simon, T. Beeckman, L. De Veyldera, Plant Cell 23 (2011) 3671–3683. date_created: 2018-12-11T12:01:24Z date_published: 2011-10-14T00:00:00Z date_updated: 2021-01-12T07:41:04Z day: '14' doi: 10.1105/tpc.111.088377 extern: 1 intvolume: ' 23' issue: '10' month: '10' page: 3671 - 3683 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '3598' quality_controlled: 0 status: public title: Auxin Dependent cell cycle reactivation through transcriptional regulation of arabidopsis E2Fa by lateral organ boundary proteins type: journal_article volume: 23 year: '2011' ... --- _id: '3103' abstract: - lang: eng text: Endocytosis in plants has an essential role not only for basic cellular functions but also for growth and development, hormonal signaling and communication with the environment including nutrient delivery, toxin avoidance, and pathogen defense. The major endocytic mechanism in plants depends on the coat protein clathrin. It starts by clathrin-coated vesicle formation at the plasma membrane, where specific cargoes are recognized and packaged for internalization. Recently, genetic, biochemical and advanced microscopy studies provided initial insights into mechanisms and roles of clathrin-mediated endocytosis in plants. Here we summarize the present state of knowledge and compare mechanisms of clathrin-mediated endocytosis in plants with animal and yeast paradigms as well as review plant-specific regulations and roles of this process. author: - first_name: Xu full_name: Chen, Xu id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Niloufer full_name: Irani, Niloufer last_name: Irani - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Chen X, Irani N, Friml J. Clathrin-mediated endocytosis: The gateway into plant cells. Current Opinion in Plant Biology. 2011;14(6):674-682. doi:10.1016/j.pbi.2011.08.006' apa: 'Chen, X., Irani, N., & Friml, J. (2011). Clathrin-mediated endocytosis: The gateway into plant cells. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2011.08.006' chicago: 'Chen, Xu, Niloufer Irani, and Jiří Friml. “Clathrin-Mediated Endocytosis: The Gateway into Plant Cells.” Current Opinion in Plant Biology. Elsevier, 2011. https://doi.org/10.1016/j.pbi.2011.08.006.' ieee: 'X. Chen, N. Irani, and J. Friml, “Clathrin-mediated endocytosis: The gateway into plant cells,” Current Opinion in Plant Biology, vol. 14, no. 6. Elsevier, pp. 674–682, 2011.' ista: 'Chen X, Irani N, Friml J. 2011. Clathrin-mediated endocytosis: The gateway into plant cells. Current Opinion in Plant Biology. 14(6), 674–682.' mla: 'Chen, Xu, et al. “Clathrin-Mediated Endocytosis: The Gateway into Plant Cells.” Current Opinion in Plant Biology, vol. 14, no. 6, Elsevier, 2011, pp. 674–82, doi:10.1016/j.pbi.2011.08.006.' short: X. Chen, N. Irani, J. Friml, Current Opinion in Plant Biology 14 (2011) 674–682. date_created: 2018-12-11T12:01:24Z date_published: 2011-12-01T00:00:00Z date_updated: 2021-01-12T07:41:05Z day: '01' doi: 10.1016/j.pbi.2011.08.006 extern: '1' intvolume: ' 14' issue: '6' language: - iso: eng month: '12' oa_version: None page: 674 - 682 publication: Current Opinion in Plant Biology publication_status: published publisher: Elsevier publist_id: '3596' quality_controlled: '1' status: public title: 'Clathrin-mediated endocytosis: The gateway into plant cells' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2011' ... --- _id: '3147' abstract: - lang: eng text: Cancer cell of origin is difficult to identify by analyzing cells within terminal stage tumors, whose identity could be concealed by the acquired plasticity. Thus, an ideal approach to identify the cell of origin is to analyze proliferative abnormalities in distinct lineages prior to malignancy. Here, we use mosaic analysis with double markers (MADM) in mice to model gliomagenesis by initiating concurrent p53/Nf1 mutations sporadically in neural stem cells (NSCs). Surprisingly, MADM-based lineage tracing revealed significant aberrant growth prior to malignancy only in oligodendrocyte precursor cells (OPCs), but not in any other NSC-derived lineages or NSCs themselves. Upon tumor formation, phenotypic and transcriptome analyses of tumor cells revealed salient OPC features. Finally, introducing the same p53/Nf1 mutations directly into OPCs consistently led to gliomagenesis. Our findings suggest OPCs as the cell of origin in this model, even when initial mutations occur in NSCs, and highlight the importance of analyzing premalignant stages to identify the cancer cell of origin. author: - first_name: Chong full_name: Liu, Chong last_name: Liu - first_name: Jonathan full_name: Sage, Jonathan C last_name: Sage - first_name: Michael full_name: Miller, Michael R last_name: Miller - first_name: Roel full_name: Verhaak, Roel G last_name: Verhaak - first_name: Simon full_name: Simon Hippenmeyer id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Hannes full_name: Vogel, Hannes last_name: Vogel - first_name: Oded full_name: Foreman, Oded last_name: Foreman - first_name: Roderick full_name: Bronson, Roderick T last_name: Bronson - first_name: Akiko full_name: Nishiyama, Akiko last_name: Nishiyama - first_name: Liqun full_name: Luo, Liqun last_name: Luo - first_name: Hui full_name: Zong, Hui last_name: Zong citation: ama: Liu C, Sage J, Miller M, et al. Mosaic analysis with double markers reveals tumor cell of origin in glioma. Cell. 2011;146(2):209-221. doi:10.1016/j.cell.2011.06.014 apa: Liu, C., Sage, J., Miller, M., Verhaak, R., Hippenmeyer, S., Vogel, H., … Zong, H. (2011). Mosaic analysis with double markers reveals tumor cell of origin in glioma. Cell. Cell Press. https://doi.org/10.1016/j.cell.2011.06.014 chicago: Liu, Chong, Jonathan Sage, Michael Miller, Roel Verhaak, Simon Hippenmeyer, Hannes Vogel, Oded Foreman, et al. “Mosaic Analysis with Double Markers Reveals Tumor Cell of Origin in Glioma.” Cell. Cell Press, 2011. https://doi.org/10.1016/j.cell.2011.06.014. ieee: C. Liu et al., “Mosaic analysis with double markers reveals tumor cell of origin in glioma,” Cell, vol. 146, no. 2. Cell Press, pp. 209–221, 2011. ista: Liu C, Sage J, Miller M, Verhaak R, Hippenmeyer S, Vogel H, Foreman O, Bronson R, Nishiyama A, Luo L, Zong H. 2011. Mosaic analysis with double markers reveals tumor cell of origin in glioma. Cell. 146(2), 209–221. mla: Liu, Chong, et al. “Mosaic Analysis with Double Markers Reveals Tumor Cell of Origin in Glioma.” Cell, vol. 146, no. 2, Cell Press, 2011, pp. 209–21, doi:10.1016/j.cell.2011.06.014. short: C. Liu, J. Sage, M. Miller, R. Verhaak, S. Hippenmeyer, H. Vogel, O. Foreman, R. Bronson, A. Nishiyama, L. Luo, H. Zong, Cell 146 (2011) 209–221. date_created: 2018-12-11T12:01:40Z date_published: 2011-07-22T00:00:00Z date_updated: 2021-01-12T07:41:23Z day: '22' doi: 10.1016/j.cell.2011.06.014 extern: 1 intvolume: ' 146' issue: '2' month: '07' page: 209 - 221 publication: Cell publication_status: published publisher: Cell Press publist_id: '3548' quality_controlled: 0 status: public title: Mosaic analysis with double markers reveals tumor cell of origin in glioma type: journal_article volume: 146 year: '2011' ... --- _id: '3204' abstract: - lang: eng text: 'We introduce a new class of functions that can be minimized in polynomial time in the value oracle model. These are functions f satisfying f(x) + f(y) ≥ f(x ∏ y) + f(x ∐ y) where the domain of each variable x i corresponds to nodes of a rooted binary tree, and operations ∏,∐ are defined with respect to this tree. Special cases include previously studied L-convex and bisubmodular functions, which can be obtained with particular choices of trees. We present a polynomial-time algorithm for minimizing functions in the new class. It combines Murota''s steepest descent algorithm for L-convex functions with bisubmodular minimization algorithms. ' alternative_title: - LNCS author: - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Kolmogorov V. Submodularity on a tree: Unifying Submodularity on a tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions. In: Vol 6907. Springer; 2011:400-411. doi:10.1007/978-3-642-22993-0_37' apa: 'Kolmogorov, V. (2011). Submodularity on a tree: Unifying Submodularity on a tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions (Vol. 6907, pp. 400–411). Presented at the MFCS: Mathematical Foundations of Computer Science, Springer. https://doi.org/10.1007/978-3-642-22993-0_37' chicago: 'Kolmogorov, Vladimir. “Submodularity on a Tree: Unifying Submodularity on a Tree: Unifying L-Convex and Bisubmodular Functions Convex and Bisubmodular Functions,” 6907:400–411. Springer, 2011. https://doi.org/10.1007/978-3-642-22993-0_37.' ieee: 'V. Kolmogorov, “Submodularity on a tree: Unifying Submodularity on a tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions,” presented at the MFCS: Mathematical Foundations of Computer Science, 2011, vol. 6907, pp. 400–411.' ista: 'Kolmogorov V. 2011. Submodularity on a tree: Unifying Submodularity on a tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions. MFCS: Mathematical Foundations of Computer Science, LNCS, vol. 6907, 400–411.' mla: 'Kolmogorov, Vladimir. Submodularity on a Tree: Unifying Submodularity on a Tree: Unifying L-Convex and Bisubmodular Functions Convex and Bisubmodular Functions. Vol. 6907, Springer, 2011, pp. 400–11, doi:10.1007/978-3-642-22993-0_37.' short: V. Kolmogorov, in:, Springer, 2011, pp. 400–411. conference: name: 'MFCS: Mathematical Foundations of Computer Science' date_created: 2018-12-11T12:02:00Z date_published: 2011-08-09T00:00:00Z date_updated: 2021-01-12T07:41:47Z day: '09' doi: 10.1007/978-3-642-22993-0_37 extern: 1 intvolume: ' 6907' main_file_link: - open_access: '0' url: http://arxiv.org/pdf/1007.1229v3 month: '08' page: 400 - 411 publication_status: published publisher: Springer publist_id: '3478' quality_controlled: 0 status: public title: 'Submodularity on a tree: Unifying Submodularity on a tree: Unifying L-convex and bisubmodular functions convex and bisubmodular functions' type: conference volume: 6907 year: '2011' ... --- _id: '3206' abstract: - lang: eng text: In this paper we address the problem of finding the most probable state of discrete Markov random field (MRF) with associative pairwise terms. Although of practical importance, this problem is known to be NP-hard in general. We propose a new type of MRF decomposition, submod-ular decomposition (SMD). Unlike existing decomposition approaches SMD decomposes the initial problem into sub-problems corresponding to a specific class label while preserving the graph structure of each subproblem. Such decomposition enables us to take into account several types of global constraints in an efficient manner. We study theoretical properties of the proposed approach and demonstrate its applicability on a number of problems. author: - first_name: Anton full_name: Osokin, Anton last_name: Osokin - first_name: Dmitry full_name: Vetrov, Dmitry last_name: Vetrov - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Osokin A, Vetrov D, Kolmogorov V. Submodular decomposition framework for inference in associative Markov networks with global constraints. In: IEEE; 2011:1889-1896. doi:10.1109/CVPR.2011.5995361' apa: 'Osokin, A., Vetrov, D., & Kolmogorov, V. (2011). Submodular decomposition framework for inference in associative Markov networks with global constraints (pp. 1889–1896). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2011.5995361' chicago: Osokin, Anton, Dmitry Vetrov, and Vladimir Kolmogorov. “Submodular Decomposition Framework for Inference in Associative Markov Networks with Global Constraints,” 1889–96. IEEE, 2011. https://doi.org/10.1109/CVPR.2011.5995361. ieee: 'A. Osokin, D. Vetrov, and V. Kolmogorov, “Submodular decomposition framework for inference in associative Markov networks with global constraints,” presented at the CVPR: Computer Vision and Pattern Recognition, 2011, pp. 1889–1896.' ista: 'Osokin A, Vetrov D, Kolmogorov V. 2011. Submodular decomposition framework for inference in associative Markov networks with global constraints. CVPR: Computer Vision and Pattern Recognition, 1889–1896.' mla: Osokin, Anton, et al. Submodular Decomposition Framework for Inference in Associative Markov Networks with Global Constraints. IEEE, 2011, pp. 1889–96, doi:10.1109/CVPR.2011.5995361. short: A. Osokin, D. Vetrov, V. Kolmogorov, in:, IEEE, 2011, pp. 1889–1896. conference: name: 'CVPR: Computer Vision and Pattern Recognition' date_created: 2018-12-11T12:02:00Z date_published: 2011-08-22T00:00:00Z date_updated: 2021-01-12T07:41:47Z day: '22' doi: 10.1109/CVPR.2011.5995361 extern: 1 main_file_link: - open_access: '0' url: http://arxiv.org/pdf/1103.1077v1 month: '08' page: 1889 - 1896 publication_status: published publisher: IEEE publist_id: '3476' quality_controlled: 0 status: public title: Submodular decomposition framework for inference in associative Markov networks with global constraints type: conference year: '2011' ... --- _id: '3205' abstract: - lang: eng text: This paper proposes a novel Linear Programming (LP) based algorithm, called Dynamic Tree-Block Coordinate Ascent (DT-BCA), for performing maximum a posteriori (MAP) inference in probabilistic graphical models. Unlike traditional message passing algorithms, which operate uniformly on the whole factor graph, our method dynamically chooses regions of the factor graph on which to focus message-passing efforts. We propose two criteria for selecting regions, including an efficiently computable upper-bound on the increase in the objective possible by passing messages in any particular region. This bound is derived from the theory of primal-dual methods from combinatorial optimization, and the forest that maximizes the bounds can be chosen efficiently using a maximum-spanning-tree-like algorithm. Experimental results show that our dynamic schedules significantly speed up state-of-the-art LP-based message-passing algorithms on a wide variety of real-world problems. author: - first_name: Daniel full_name: Tarlow, Daniel last_name: Tarlow - first_name: Druv full_name: Batra, Druv last_name: Batra - first_name: Pushmeet full_name: Kohli, Pushmeet last_name: Kohli - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Tarlow D, Batra D, Kohli P, Kolmogorov V. Dynamic tree block coordinate ascent. In: Omnipress; 2011:113-120.' apa: 'Tarlow, D., Batra, D., Kohli, P., & Kolmogorov, V. (2011). Dynamic tree block coordinate ascent (pp. 113–120). Presented at the ICML: International Conference on Machine Learning, Omnipress.' chicago: Tarlow, Daniel, Druv Batra, Pushmeet Kohli, and Vladimir Kolmogorov. “Dynamic Tree Block Coordinate Ascent,” 113–20. Omnipress, 2011. ieee: 'D. Tarlow, D. Batra, P. Kohli, and V. Kolmogorov, “Dynamic tree block coordinate ascent,” presented at the ICML: International Conference on Machine Learning, 2011, pp. 113–120.' ista: 'Tarlow D, Batra D, Kohli P, Kolmogorov V. 2011. Dynamic tree block coordinate ascent. ICML: International Conference on Machine Learning, 113–120.' mla: Tarlow, Daniel, et al. Dynamic Tree Block Coordinate Ascent. Omnipress, 2011, pp. 113–20. short: D. Tarlow, D. Batra, P. Kohli, V. Kolmogorov, in:, Omnipress, 2011, pp. 113–120. conference: name: 'ICML: International Conference on Machine Learning' date_created: 2018-12-11T12:02:00Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:41:47Z day: '01' extern: 1 main_file_link: - open_access: '0' url: http://ttic.uchicago.edu/~dbatra/publications/assets/tbkk_icml11.pdf month: '01' page: 113 - 120 publication_status: published publisher: Omnipress publist_id: '3475' quality_controlled: 0 status: public title: Dynamic tree block coordinate ascent type: conference year: '2011' ... --- _id: '3207' abstract: - lang: eng text: 'Cosegmentation is typically defined as the task of jointly segmenting something similar in a given set of images. Existing methods are too generic and so far have not demonstrated competitive results for any specific task. In this paper we overcome this limitation by adding two new aspects to cosegmentation: (1) the "something" has to be an object, and (2) the "similarity" measure is learned. In this way, we are able to achieve excellent results on the recently introduced iCoseg dataset, which contains small sets of images of either the same object instance or similar objects of the same class. The challenge of this dataset lies in the extreme changes in viewpoint, lighting, and object deformations within each set. We are able to considerably outperform several competitors. To achieve this performance, we borrow recent ideas from object recognition: the use of powerful features extracted from a pool of candidate object-like segmentations. We believe that our work will be beneficial to several application areas, such as image retrieval.' author: - first_name: Sara full_name: Vicente, Sara last_name: Vicente - first_name: Carsten full_name: Rother, Carsten last_name: Rother - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Vicente S, Rother C, Kolmogorov V. Object cosegmentation. In: IEEE; 2011:2217-2224. doi:10.1109/CVPR.2011.5995530' apa: 'Vicente, S., Rother, C., & Kolmogorov, V. (2011). Object cosegmentation (pp. 2217–2224). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2011.5995530' chicago: Vicente, Sara, Carsten Rother, and Vladimir Kolmogorov. “Object Cosegmentation,” 2217–24. IEEE, 2011. https://doi.org/10.1109/CVPR.2011.5995530. ieee: 'S. Vicente, C. Rother, and V. Kolmogorov, “Object cosegmentation,” presented at the CVPR: Computer Vision and Pattern Recognition, 2011, pp. 2217–2224.' ista: 'Vicente S, Rother C, Kolmogorov V. 2011. Object cosegmentation. CVPR: Computer Vision and Pattern Recognition, 2217–2224.' mla: Vicente, Sara, et al. Object Cosegmentation. IEEE, 2011, pp. 2217–24, doi:10.1109/CVPR.2011.5995530. short: S. Vicente, C. Rother, V. Kolmogorov, in:, IEEE, 2011, pp. 2217–2224. conference: name: 'CVPR: Computer Vision and Pattern Recognition' date_created: 2018-12-11T12:02:01Z date_published: 2011-08-22T00:00:00Z date_updated: 2021-01-12T07:41:48Z day: '22' doi: 10.1109/CVPR.2011.5995530 extern: 1 month: '08' page: 2217 - 2224 publication_status: published publisher: IEEE publist_id: '3477' quality_controlled: 0 status: public title: Object cosegmentation type: conference year: '2011' ... --- _id: '3240' abstract: - lang: eng text: 'The famous Leftover Hash Lemma (LHL) states that (almost) universal hash functions are good randomness extractors. Despite its numerous applications, LHL-based extractors suffer from the following two limitations: - Large Entropy Loss: to extract v bits from distribution X of min-entropy m which are ε-close to uniform, one must set v ≤ m - 2log(1/ε), meaning that the entropy loss L = def m - v ≥ 2 log(1/ε). For many applications, such entropy loss is too large. - Large Seed Length: the seed length n of (almost) universal hash function required by the LHL must be at least n ≥ min (u - v, v + 2log(1/ε)) - O(1), where u is the length of the source, and must grow with the number of extracted bits. Quite surprisingly, we show that both limitations of the LHL - large entropy loss and large seed - can be overcome (or, at least, mitigated) in various important scenarios. First, we show that entropy loss could be reduced to L = log(1/ε) for the setting of deriving secret keys for a wide range of cryptographic applications. Specifically, the security of these schemes with an LHL-derived key gracefully degrades from ε to at most ε + √ε2-L. (Notice that, unlike standard LHL, this bound is meaningful even when one extracts more bits than the min-entropy we have!) Based on these results we build a general computational extractor that enjoys low entropy loss and can be used to instantiate a generic key derivation function for any cryptographic application. Second, we study the soundness of the natural expand-then-extract approach, where one uses a pseudorandom generator (PRG) to expand a short "input seed" S into a longer "output seed" S′, and then use the resulting S′ as the seed required by the LHL (or, more generally, by any randomness extractor). We show that, in general, the expand-then-extract approach is not sound if the Decisional Diffie-Hellman assumption is true. Despite that, we show that it is sound either: (1) when extracting a "small" (logarithmic in the security of the PRG) number of bits; or (2) in minicrypt. Implication (2) suggests that the expand-then-extract approach is likely secure when used with "practical" PRGs, despite lacking a reductionist proof of security! © 2011 International Association for Cryptologic Research.' alternative_title: - LNCS author: - first_name: Boaz full_name: Barak, Boaz last_name: Barak - first_name: Yevgeniy full_name: Dodis, Yevgeniy last_name: Dodis - first_name: Hugo full_name: Krawczyk, Hugo last_name: Krawczyk - first_name: Olivier full_name: Pereira, Olivier last_name: Pereira - first_name: Krzysztof Z full_name: Krzysztof Pietrzak id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: François full_name: Standaert, François-Xavier last_name: Standaert - first_name: Yu full_name: Yu, Yu last_name: Yu citation: ama: 'Barak B, Dodis Y, Krawczyk H, et al. Leftover hash lemma revisited. In: Vol 6841. Springer; 2011:1-20. doi: 10.1007/978-3-642-22792-9_1' apa: 'Barak, B., Dodis, Y., Krawczyk, H., Pereira, O., Pietrzak, K. Z., Standaert, F., & Yu, Y. (2011). Leftover hash lemma revisited (Vol. 6841, pp. 1–20). Presented at the CRYPTO: International Cryptology Conference, Springer. https://doi.org/ 10.1007/978-3-642-22792-9_1' chicago: Barak, Boaz, Yevgeniy Dodis, Hugo Krawczyk, Olivier Pereira, Krzysztof Z Pietrzak, François Standaert, and Yu Yu. “Leftover Hash Lemma Revisited,” 6841:1–20. Springer, 2011. https://doi.org/ 10.1007/978-3-642-22792-9_1. ieee: 'B. Barak et al., “Leftover hash lemma revisited,” presented at the CRYPTO: International Cryptology Conference, 2011, vol. 6841, pp. 1–20.' ista: 'Barak B, Dodis Y, Krawczyk H, Pereira O, Pietrzak KZ, Standaert F, Yu Y. 2011. Leftover hash lemma revisited. CRYPTO: International Cryptology Conference, LNCS, vol. 6841, 1–20.' mla: Barak, Boaz, et al. Leftover Hash Lemma Revisited. Vol. 6841, Springer, 2011, pp. 1–20, doi: 10.1007/978-3-642-22792-9_1. short: B. Barak, Y. Dodis, H. Krawczyk, O. Pereira, K.Z. Pietrzak, F. Standaert, Y. Yu, in:, Springer, 2011, pp. 1–20. conference: name: 'CRYPTO: International Cryptology Conference' date_created: 2018-12-11T12:02:12Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:42:03Z day: '01' doi: ' 10.1007/978-3-642-22792-9_1' extern: 1 intvolume: ' 6841' month: '01' page: 1 - 20 publication_status: published publisher: Springer publist_id: '3440' quality_controlled: 0 status: public title: Leftover hash lemma revisited type: conference volume: 6841 year: '2011' ... --- _id: '3264' abstract: - lang: eng text: Verification of programs with procedures, multi-threaded programs, and higher-order functional programs can be effectively au- tomated using abstraction and refinement schemes that rely on spurious counterexamples for abstraction discovery. The analysis of counterexam- ples can be automated by a series of interpolation queries, or, alterna- tively, as a constraint solving query expressed by a set of recursion free Horn clauses. (A set of interpolation queries can be formulated as a single constraint over Horn clauses with linear dependency structure between the unknown relations.) In this paper we present an algorithm for solving recursion free Horn clauses over a combined theory of linear real/rational arithmetic and uninterpreted functions. Our algorithm performs resolu- tion to deal with the clausal structure and relies on partial solutions to deal with (non-local) instances of functionality axioms. alternative_title: - LNCS author: - first_name: Ashutosh full_name: Gupta, Ashutosh id: 335E5684-F248-11E8-B48F-1D18A9856A87 last_name: Gupta - first_name: Corneliu full_name: Popeea, Corneliu last_name: Popeea - first_name: Andrey full_name: Rybalchenko, Andrey last_name: Rybalchenko citation: ama: 'Gupta A, Popeea C, Rybalchenko A. Solving recursion-free Horn clauses over LI+UIF. In: Yang H, ed. Vol 7078. Springer; 2011:188-203. doi:10.1007/978-3-642-25318-8_16' apa: 'Gupta, A., Popeea, C., & Rybalchenko, A. (2011). Solving recursion-free Horn clauses over LI+UIF. In H. Yang (Ed.) (Vol. 7078, pp. 188–203). Presented at the APLAS: Asian Symposium on Programming Languages and Systems, Kenting, Taiwan: Springer. https://doi.org/10.1007/978-3-642-25318-8_16' chicago: Gupta, Ashutosh, Corneliu Popeea, and Andrey Rybalchenko. “Solving Recursion-Free Horn Clauses over LI+UIF.” edited by Hongseok Yang, 7078:188–203. Springer, 2011. https://doi.org/10.1007/978-3-642-25318-8_16. ieee: 'A. Gupta, C. Popeea, and A. Rybalchenko, “Solving recursion-free Horn clauses over LI+UIF,” presented at the APLAS: Asian Symposium on Programming Languages and Systems, Kenting, Taiwan, 2011, vol. 7078, pp. 188–203.' ista: 'Gupta A, Popeea C, Rybalchenko A. 2011. Solving recursion-free Horn clauses over LI+UIF. APLAS: Asian Symposium on Programming Languages and Systems, LNCS, vol. 7078, 188–203.' mla: Gupta, Ashutosh, et al. Solving Recursion-Free Horn Clauses over LI+UIF. Edited by Hongseok Yang, vol. 7078, Springer, 2011, pp. 188–203, doi:10.1007/978-3-642-25318-8_16. short: A. Gupta, C. Popeea, A. Rybalchenko, in:, H. Yang (Ed.), Springer, 2011, pp. 188–203. conference: end_date: 2011-12-07 location: Kenting, Taiwan name: 'APLAS: Asian Symposium on Programming Languages and Systems' start_date: 2011-12-05 date_created: 2018-12-11T12:02:20Z date_published: 2011-12-05T00:00:00Z date_updated: 2021-01-12T07:42:15Z day: '05' department: - _id: ToHe doi: 10.1007/978-3-642-25318-8_16 ec_funded: 1 editor: - first_name: Hongseok full_name: Yang, Hongseok last_name: Yang intvolume: ' 7078' language: - iso: eng month: '12' oa_version: None page: 188 - 203 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: '3383' quality_controlled: '1' status: public title: Solving recursion-free Horn clauses over LI+UIF type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 7078 year: '2011' ... --- _id: '3266' abstract: - lang: eng text: We present a joint image segmentation and labeling model (JSL) which, given a bag of figure-ground segment hypotheses extracted at multiple image locations and scales, constructs a joint probability distribution over both the compatible image interpretations (tilings or image segmentations) composed from those segments, and over their labeling into categories. The process of drawing samples from the joint distribution can be interpreted as first sampling tilings, modeled as maximal cliques, from a graph connecting spatially non-overlapping segments in the bag [1], followed by sampling labels for those segments, conditioned on the choice of a particular tiling. We learn the segmentation and labeling parameters jointly, based on Maximum Likelihood with a novel Incremental Saddle Point estimation procedure. The partition function over tilings and labelings is increasingly more accurately approximated by including incorrect configurations that a not-yet-competent model rates probable during learning. We show that the proposed methodologymatches the current state of the art in the Stanford dataset [2], as well as in VOC2010, where 41.7% accuracy on the test set is achieved. author: - first_name: Adrian full_name: Ion, Adrian id: 29F89302-F248-11E8-B48F-1D18A9856A87 last_name: Ion - first_name: Joao full_name: Carreira, Joao last_name: Carreira - first_name: Cristian full_name: Sminchisescu, Cristian last_name: Sminchisescu citation: ama: 'Ion A, Carreira J, Sminchisescu C. Probabilistic joint image segmentation and labeling. In: NIPS Proceedings. Vol 24. Neural Information Processing Systems Foundation; 2011:1827-1835.' apa: 'Ion, A., Carreira, J., & Sminchisescu, C. (2011). Probabilistic joint image segmentation and labeling. In NIPS Proceedings (Vol. 24, pp. 1827–1835). Granada, Spain: Neural Information Processing Systems Foundation.' chicago: Ion, Adrian, Joao Carreira, and Cristian Sminchisescu. “Probabilistic Joint Image Segmentation and Labeling.” In NIPS Proceedings, 24:1827–35. Neural Information Processing Systems Foundation, 2011. ieee: A. Ion, J. Carreira, and C. Sminchisescu, “Probabilistic joint image segmentation and labeling,” in NIPS Proceedings, Granada, Spain, 2011, vol. 24, pp. 1827–1835. ista: 'Ion A, Carreira J, Sminchisescu C. 2011. Probabilistic joint image segmentation and labeling. NIPS Proceedings. NIPS: Neural Information Processing Systems vol. 24, 1827–1835.' mla: Ion, Adrian, et al. “Probabilistic Joint Image Segmentation and Labeling.” NIPS Proceedings, vol. 24, Neural Information Processing Systems Foundation, 2011, pp. 1827–35. short: A. Ion, J. Carreira, C. Sminchisescu, in:, NIPS Proceedings, Neural Information Processing Systems Foundation, 2011, pp. 1827–1835. conference: end_date: 2011-12-14 location: Granada, Spain name: 'NIPS: Neural Information Processing Systems' start_date: 2011-12-12 date_created: 2018-12-11T12:02:21Z date_published: 2011-12-01T00:00:00Z date_updated: 2021-01-12T07:42:15Z day: '01' department: - _id: HeEd intvolume: ' 24' language: - iso: eng month: '12' oa_version: None page: 1827 - 1835 publication: NIPS Proceedings publication_status: published publisher: Neural Information Processing Systems Foundation publist_id: '3381' quality_controlled: '1' scopus_import: 1 status: public title: Probabilistic joint image segmentation and labeling type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2011' ... --- _id: '3269' abstract: - lang: eng text: The unintentional scattering of light between neighboring surfaces in complex projection environments increases the brightness and decreases the contrast, disrupting the appearance of the desired imagery. To achieve satisfactory projection results, the inverse problem of global illumination must be solved to cancel this secondary scattering. In this paper, we propose a global illumination cancellation method that minimizes the perceptual difference between the desired imagery and the actual total illumination in the resulting physical environment. Using Gauss-Newton and active set methods, we design a fast solver for the bound constrained nonlinear least squares problem raised by the perceptual error metrics. Our solver is further accelerated with a CUDA implementation and multi-resolution method to achieve 1–2 fps for problems with approximately 3000 variables. We demonstrate the global illumination cancellation algorithm with our multi-projector system. Results show that our method preserves the color fidelity of the desired imagery significantly better than previous methods. article_processing_charge: No article_type: original author: - first_name: Yu full_name: Sheng, Yu last_name: Sheng - first_name: Barbara full_name: Cutler, Barbara last_name: Cutler - first_name: Chao full_name: Chen, Chao id: 3E92416E-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Joshua full_name: Nasman, Joshua last_name: Nasman citation: ama: Sheng Y, Cutler B, Chen C, Nasman J. Perceptual global illumination cancellation in complex projection environments. Computer Graphics Forum. 2011;30(4):1261-1268. doi:10.1111/j.1467-8659.2011.01985.x apa: Sheng, Y., Cutler, B., Chen, C., & Nasman, J. (2011). Perceptual global illumination cancellation in complex projection environments. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/j.1467-8659.2011.01985.x chicago: Sheng, Yu, Barbara Cutler, Chao Chen, and Joshua Nasman. “Perceptual Global Illumination Cancellation in Complex Projection Environments.” Computer Graphics Forum. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1467-8659.2011.01985.x. ieee: Y. Sheng, B. Cutler, C. Chen, and J. Nasman, “Perceptual global illumination cancellation in complex projection environments,” Computer Graphics Forum, vol. 30, no. 4. Wiley-Blackwell, pp. 1261–1268, 2011. ista: Sheng Y, Cutler B, Chen C, Nasman J. 2011. Perceptual global illumination cancellation in complex projection environments. Computer Graphics Forum. 30(4), 1261–1268. mla: Sheng, Yu, et al. “Perceptual Global Illumination Cancellation in Complex Projection Environments.” Computer Graphics Forum, vol. 30, no. 4, Wiley-Blackwell, 2011, pp. 1261–68, doi:10.1111/j.1467-8659.2011.01985.x. short: Y. Sheng, B. Cutler, C. Chen, J. Nasman, Computer Graphics Forum 30 (2011) 1261–1268. date_created: 2018-12-11T12:02:22Z date_published: 2011-07-19T00:00:00Z date_updated: 2021-01-12T07:42:16Z day: '19' department: - _id: HeEd doi: 10.1111/j.1467-8659.2011.01985.x intvolume: ' 30' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://www.cs.cmu.edu/%7Eshengyu/download/egsr2011_paper.pdf month: '07' oa: 1 oa_version: Published Version page: 1261 - 1268 publication: Computer Graphics Forum publication_status: published publisher: Wiley-Blackwell publist_id: '3377' quality_controlled: '1' scopus_import: 1 status: public title: Perceptual global illumination cancellation in complex projection environments type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2011' ... --- _id: '3267' abstract: - lang: eng text: 'We address the problem of localizing homology classes, namely, finding the cycle representing a given class with the most concise geometric measure. We study the problem with different measures: volume, diameter and radius. For volume, that is, the 1-norm of a cycle, two main results are presented. First, we prove that the problem is NP-hard to approximate within any constant factor. Second, we prove that for homology of dimension two or higher, the problem is NP-hard to approximate even when the Betti number is O(1). The latter result leads to the inapproximability of the problem of computing the nonbounding cycle with the smallest volume and computing cycles representing a homology basis with the minimal total volume. As for the other two measures defined by pairwise geodesic distance, diameter and radius, we show that the localization problem is NP-hard for diameter but is polynomial for radius. Our work is restricted to homology over the ℤ2 field.' author: - first_name: Chao full_name: Chen, Chao id: 3E92416E-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Daniel full_name: Freedman, Daniel last_name: Freedman citation: ama: Chen C, Freedman D. Hardness results for homology localization. Discrete & Computational Geometry. 2011;45(3):425-448. doi:10.1007/s00454-010-9322-8 apa: Chen, C., & Freedman, D. (2011). Hardness results for homology localization. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-010-9322-8 chicago: Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.” Discrete & Computational Geometry. Springer, 2011. https://doi.org/10.1007/s00454-010-9322-8. ieee: C. Chen and D. Freedman, “Hardness results for homology localization,” Discrete & Computational Geometry, vol. 45, no. 3. Springer, pp. 425–448, 2011. ista: Chen C, Freedman D. 2011. Hardness results for homology localization. Discrete & Computational Geometry. 45(3), 425–448. mla: Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.” Discrete & Computational Geometry, vol. 45, no. 3, Springer, 2011, pp. 425–48, doi:10.1007/s00454-010-9322-8. short: C. Chen, D. Freedman, Discrete & Computational Geometry 45 (2011) 425–448. date_created: 2018-12-11T12:02:21Z date_published: 2011-01-14T00:00:00Z date_updated: 2023-02-21T16:07:10Z day: '14' department: - _id: HeEd doi: 10.1007/s00454-010-9322-8 intvolume: ' 45' issue: '3' language: - iso: eng month: '01' oa_version: None page: 425 - 448 publication: Discrete & Computational Geometry publication_status: published publisher: Springer publist_id: '3379' quality_controlled: '1' related_material: record: - id: '10909' relation: earlier_version status: public scopus_import: 1 status: public title: Hardness results for homology localization type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 45 year: '2011' ... --- _id: '3268' abstract: - lang: eng text: 'Algebraic topology is generally considered one of the purest subfield of mathematics. However, over the last decade two interesting new lines of research have emerged, one focusing on algorithms for algebraic topology, and the other on applications of algebraic topology in engineering and science. Amongst the new areas in which the techniques have been applied are computer vision and image processing. In this paper, we survey the results of these endeavours. Because algebraic topology is an area of mathematics with which most computer vision practitioners have no experience, we review the machinery behind the theories of homology and persistent homology; our review emphasizes intuitive explanations. In terms of applications to computer vision, we focus on four illustrative problems: shape signatures, natural image statistics, image denoising, and segmentation. Our hope is that this review will stimulate interest on the part of computer vision researchers to both use and extend the tools of this new field. ' alternative_title: - Computer Science, Technology and Applications author: - first_name: Daniel full_name: Freedman, Daniel last_name: Freedman - first_name: Chao full_name: Chen, Chao id: 3E92416E-F248-11E8-B48F-1D18A9856A87 last_name: Chen citation: ama: 'Freedman D, Chen C. Algebraic topology for computer vision. In: Computer Vision. Nova Science Publishers; 2011:239-268.' apa: Freedman, D., & Chen, C. (2011). Algebraic topology for computer vision. In Computer Vision (pp. 239–268). Nova Science Publishers. chicago: Freedman, Daniel, and Chao Chen. “Algebraic Topology for Computer Vision.” In Computer Vision, 239–68. Nova Science Publishers, 2011. ieee: D. Freedman and C. Chen, “Algebraic topology for computer vision,” in Computer Vision, Nova Science Publishers, 2011, pp. 239–268. ista: 'Freedman D, Chen C. 2011.Algebraic topology for computer vision. In: Computer Vision. Computer Science, Technology and Applications, , 239–268.' mla: Freedman, Daniel, and Chao Chen. “Algebraic Topology for Computer Vision.” Computer Vision, Nova Science Publishers, 2011, pp. 239–68. short: D. Freedman, C. Chen, in:, Computer Vision, Nova Science Publishers, 2011, pp. 239–268. date_created: 2018-12-11T12:02:22Z date_published: 2011-11-30T00:00:00Z date_updated: 2021-01-12T07:42:16Z day: '30' extern: '1' language: - iso: eng main_file_link: - url: http://www.hpl.hp.com/techreports/2009/HPL-2009-375.pdf month: '11' oa_version: None page: 239 - 268 publication: Computer Vision publication_status: published publisher: Nova Science Publishers publist_id: '3378' quality_controlled: '1' status: public title: Algebraic topology for computer vision type: book_chapter user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2011' ... --- _id: '3288' abstract: - lang: eng text: 'The zonula adherens (ZA) of epithelial cells is a site of cell-cell adhesion where cellular forces are exerted and resisted. Increasing evidence indicates that E-cadherin adhesion molecules at the ZA serve to sense force applied on the junctions and coordinate cytoskeletal responses to those forces. Efforts to understand the role that cadherins play in mechanotransduction have been limited by the lack of assays to measure the impact of forces on the ZA. In this study we used 4D imaging of GFP-tagged E-cadherin to analyse the movement of the ZA. Junctions in confluent epithelial monolayers displayed prominent movements oriented orthogonal (perpendicular) to the ZA itself. Two components were identified in these movements: a relatively slow unidirectional (translational) component that could be readily fitted by least-squares regression analysis, upon which were superimposed more rapid oscillatory movements. Myosin IIB was a dominant factor responsible for driving the unilateral translational movements. In contrast, frequency spectrum analysis revealed that depletion of Myosin IIA increased the power of the oscillatory movements. This implies that Myosin IIA may serve to dampen oscillatory movements of the ZA. This extends our recent analysis of Myosin II at the ZA to demonstrate that Myosin IIA and Myosin IIB make distinct contributions to junctional movement at the ZA.' acknowledgement: his work was funded by the National Health and Medical Research Council (NHMRC) of Australia. M.S. was an Erwin Schroedinger postdoctoral fellow of the Austrian Science Fund (FWF), S.K.W. is supported by a UQ International Research Tuition Award and Research Scholarship, S.M .by an ANZ Trustees PhD Scholarship. A.S.Y. is a Research Fellow of the NHMRC. Confocal imaging was performed at the Australian Cancer Research Foundation (ACRF) Cancer Biology Imaging Centre at the Institute for Molecular Bioscience, established with the generous support of the ACRF. author: - first_name: Michael full_name: Smutny, Michael id: 3FE6E4E8-F248-11E8-B48F-1D18A9856A87 last_name: Smutny orcid: 0000-0002-5920-9090 - first_name: Selwin full_name: Wu, Selwin last_name: Wu - first_name: Guillermo full_name: Gomez, Guillermo last_name: Gomez - first_name: Sabine full_name: Mangold, Sabine last_name: Mangold - first_name: Alpha full_name: Yap, Alpha last_name: Yap - first_name: Nicholas full_name: Hamilton, Nicholas last_name: Hamilton citation: ama: Smutny M, Wu S, Gomez G, Mangold S, Yap A, Hamilton N. Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens. PLoS One. 2011;6(7). doi:10.1371/journal.pone.0022458 apa: Smutny, M., Wu, S., Gomez, G., Mangold, S., Yap, A., & Hamilton, N. (2011). Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0022458 chicago: Smutny, Michael, Selwin Wu, Guillermo Gomez, Sabine Mangold, Alpha Yap, and Nicholas Hamilton. “Multicomponent Analysis of Junctional Movements Regulated by Myosin II Isoforms at the Epithelial Zonula Adherens.” PLoS One. Public Library of Science, 2011. https://doi.org/10.1371/journal.pone.0022458. ieee: M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, and N. Hamilton, “Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens,” PLoS One, vol. 6, no. 7. Public Library of Science, 2011. ista: Smutny M, Wu S, Gomez G, Mangold S, Yap A, Hamilton N. 2011. Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens. PLoS One. 6(7). mla: Smutny, Michael, et al. “Multicomponent Analysis of Junctional Movements Regulated by Myosin II Isoforms at the Epithelial Zonula Adherens.” PLoS One, vol. 6, no. 7, Public Library of Science, 2011, doi:10.1371/journal.pone.0022458. short: M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, N. Hamilton, PLoS One 6 (2011). date_created: 2018-12-11T12:02:28Z date_published: 2011-07-22T00:00:00Z date_updated: 2021-01-12T07:42:25Z day: '22' ddc: - '570' department: - _id: CaHe doi: 10.1371/journal.pone.0022458 file: - access_level: open_access checksum: 57a5eb11dd05241c48c44f492b3ec3ac content_type: application/pdf creator: dernst date_created: 2019-05-10T10:51:43Z date_updated: 2020-07-14T12:46:06Z file_id: '6399' file_name: 2011_PLOS_Smutny.PDF file_size: 1984567 relation: main_file file_date_updated: 2020-07-14T12:46:06Z has_accepted_license: '1' intvolume: ' 6' 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: '3357' quality_controlled: '1' status: public title: Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens 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: 6 year: '2011' ... --- _id: '3286' abstract: - lang: eng text: Cationic antimicrobial peptides (CAMPs) selectively target bacterial membranes by electrostatic interactions with negatively charged lipids. It turned out that for inhibition of microbial growth a high CAMP membrane concentration is required, which can be realized by the incorporation of hydrophobic groups within the peptide. Increasing hydrophobicity, however, reduces the CAMP selectivity for bacterial over eukaryotic host membranes, thereby causing the risk of detrimental side-effects. In this study we addressed how cationic amphipathic peptides—in particular a CAMP with Lysine–Leucine–Lysine repeats (termed KLK)—affect the localization and dynamics of molecules in eukaryotic membranes. We found KLK to selectively inhibit the endocytosis of a subgroup of membrane proteins and lipids by electrostatically interacting with negatively charged sialic acid moieties. Ultrastructural characterization revealed the formation of membrane invaginations representing fission or fusion intermediates, in which the sialylated proteins and lipids were immobilized. Experiments on structurally different cationic amphipathic peptides (KLK, 6-MO-LF11-322 and NK14-2) indicated a cooperation of electrostatic and hydrophobic forces that selectively arrest sialylated membrane constituents. acknowledgement: "This work was funded by the GEN-AU project of the Austrian Research Promotion Agency, the Austrian Science Fund (FWF; project Y250-B03) and Intercell AG.\nWe thank the following colleagues for providing plasmids and cells: Daniel Legler (University of Konstanz, Switzerland), Jennifer Lippincott-Schwartz (NIH, Bethesda, USA), Hannes Stockinger (Medical University Vienna, Austria), Katharina Strub (University of Geneva, Switzerland), Lawrence Rajendran (ETH Zurich, Switzerland), Eileen M. Lafer (UTHSC San Antonio, Texas, USA), Mark McNiven (Mayo Clinic, Minnesota, USA), John Silvius (McGill University, Montreal, Canada), Christoph Romanin (JKU Linz, Austria), Herbert Stangl (Medical University Vienna, Austria) and Anton van der Merwe (Oxford University, Oxford, UK). We thank Harald Kotisch (MFPL, Vienna) for excellent technical assistance in the processing of samples for electron microscopy and Sergio Grinstein (Hospital for Sick Children Research Institute, Toronto) for fruitful discussions. " author: - first_name: Julian full_name: Weghuber, Julian last_name: Weghuber - first_name: Michael full_name: Aichinger, Michael C. last_name: Aichinger - first_name: Mario full_name: Brameshuber, Mario last_name: Brameshuber - first_name: Stefan full_name: Stefan Wieser id: 355AA5A0-F248-11E8-B48F-1D18A9856A87 last_name: Wieser orcid: 0000-0002-2670-2217 - first_name: Verena full_name: Verena Ruprecht id: 4D71A03A-F248-11E8-B48F-1D18A9856A87 last_name: Ruprecht orcid: 0000-0003-4088-8633 - first_name: Birgit full_name: Plochberger, Birgit last_name: Plochberger - first_name: Josef full_name: Madl, Josef last_name: Madl - first_name: Andreas full_name: Horner, Andreas last_name: Horner - first_name: Siegfried full_name: Reipert, Siegfried last_name: Reipert - first_name: Karl full_name: Lohner, Karl last_name: Lohner - first_name: Tamas full_name: Henics, Tamas last_name: Henics - first_name: Gerhard full_name: Schuetz, Gerhard J last_name: Schuetz citation: ama: Weghuber J, Aichinger M, Brameshuber M, et al. Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells. Biochimica et Biophysica Acta (BBA) - Biomembranes. 2011;1808(10):2581-2590. doi:10.1016/j.bbamem.2011.06.007 apa: Weghuber, J., Aichinger, M., Brameshuber, M., Wieser, S., Ruprecht, V., Plochberger, B., … Schuetz, G. (2011). Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells. Biochimica et Biophysica Acta (BBA) - Biomembranes. Elsevier. https://doi.org/10.1016/j.bbamem.2011.06.007 chicago: Weghuber, Julian, Michael Aichinger, Mario Brameshuber, Stefan Wieser, Verena Ruprecht, Birgit Plochberger, Josef Madl, et al. “Cationic Amphipathic Peptides Accumulate Sialylated Proteins and Lipids in the Plasma Membrane of Eukaryotic Host Cells.” Biochimica et Biophysica Acta (BBA) - Biomembranes. Elsevier, 2011. https://doi.org/10.1016/j.bbamem.2011.06.007. ieee: J. Weghuber et al., “Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells,” Biochimica et Biophysica Acta (BBA) - Biomembranes, vol. 1808, no. 10. Elsevier, pp. 2581–2590, 2011. ista: Weghuber J, Aichinger M, Brameshuber M, Wieser S, Ruprecht V, Plochberger B, Madl J, Horner A, Reipert S, Lohner K, Henics T, Schuetz G. 2011. Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells. Biochimica et Biophysica Acta (BBA) - Biomembranes. 1808(10), 2581–2590. mla: Weghuber, Julian, et al. “Cationic Amphipathic Peptides Accumulate Sialylated Proteins and Lipids in the Plasma Membrane of Eukaryotic Host Cells.” Biochimica et Biophysica Acta (BBA) - Biomembranes, vol. 1808, no. 10, Elsevier, 2011, pp. 2581–90, doi:10.1016/j.bbamem.2011.06.007. short: J. Weghuber, M. Aichinger, M. Brameshuber, S. Wieser, V. Ruprecht, B. Plochberger, J. Madl, A. Horner, S. Reipert, K. Lohner, T. Henics, G. Schuetz, Biochimica et Biophysica Acta (BBA) - Biomembranes 1808 (2011) 2581–2590. date_created: 2018-12-11T12:02:28Z date_published: 2011-10-01T00:00:00Z date_updated: 2021-01-12T07:42:24Z day: '01' doi: 10.1016/j.bbamem.2011.06.007 extern: 1 intvolume: ' 1808' issue: '10' month: '10' page: 2581 - 2590 publication: Biochimica et Biophysica Acta (BBA) - Biomembranes publication_status: published publisher: Elsevier publist_id: '3359' quality_controlled: 0 status: public title: Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article volume: 1808 year: '2011' ... --- _id: '3287' abstract: - lang: eng text: 'Diffusing membrane constituents are constantly exposed to a variety of forces that influence their stochastic path. Single molecule experiments allow for resolving trajectories at extremely high spatial and temporal accuracy, thereby offering insights into en route interactions of the tracer. In this review we discuss approaches to derive information about the underlying processes, based on single molecule tracking experiments. In particular, we focus on a new versatile way to analyze single molecule diffusion in the absence of a full analytical treatment. The method is based on comprehensive comparison of an experimental data set against the hypothetical outcome of multiple experiments performed on the computer. Since Monte Carlo simulations can be easily and rapidly performed even on state-of-the-art PCs, our method provides a simple way for testing various - even complicated - diffusion models. We describe the new method in detail, and show the applicability on two specific examples: firstly, kinetic rate constants can be derived for the transient interaction of mobile membrane proteins; secondly, residence time and corral size can be extracted for confined diffusion.' author: - first_name: Verena full_name: Ruprecht, Verena id: 4D71A03A-F248-11E8-B48F-1D18A9856A87 last_name: Ruprecht orcid: 0000-0003-4088-8633 - first_name: Markus full_name: Axmann, Markus last_name: Axmann - first_name: Stefan full_name: Wieser, Stefan id: 355AA5A0-F248-11E8-B48F-1D18A9856A87 last_name: Wieser orcid: 0000-0002-2670-2217 - first_name: Gerhard full_name: Schuetz, Gerhard last_name: Schuetz citation: ama: Ruprecht V, Axmann M, Wieser S, Schuetz G. What can we learn from single molecule trajectories? Current Protein & Peptide Science. 2011;12(8):714-724. doi:10.2174/138920311798841753 apa: Ruprecht, V., Axmann, M., Wieser, S., & Schuetz, G. (2011). What can we learn from single molecule trajectories? Current Protein & Peptide Science. Bentham Science Publishers. https://doi.org/10.2174/138920311798841753 chicago: Ruprecht, Verena, Markus Axmann, Stefan Wieser, and Gerhard Schuetz. “What Can We Learn from Single Molecule Trajectories?” Current Protein & Peptide Science. Bentham Science Publishers, 2011. https://doi.org/10.2174/138920311798841753. ieee: V. Ruprecht, M. Axmann, S. Wieser, and G. Schuetz, “What can we learn from single molecule trajectories?,” Current Protein & Peptide Science, vol. 12, no. 8. Bentham Science Publishers, pp. 714–724, 2011. ista: Ruprecht V, Axmann M, Wieser S, Schuetz G. 2011. What can we learn from single molecule trajectories? Current Protein & Peptide Science. 12(8), 714–724. mla: Ruprecht, Verena, et al. “What Can We Learn from Single Molecule Trajectories?” Current Protein & Peptide Science, vol. 12, no. 8, Bentham Science Publishers, 2011, pp. 714–24, doi:10.2174/138920311798841753. short: V. Ruprecht, M. Axmann, S. Wieser, G. Schuetz, Current Protein & Peptide Science 12 (2011) 714–724. date_created: 2018-12-11T12:02:28Z date_published: 2011-12-01T00:00:00Z date_updated: 2021-01-12T07:42:24Z day: '01' department: - _id: CaHe - _id: MiSi doi: 10.2174/138920311798841753 intvolume: ' 12' issue: '8' language: - iso: eng month: '12' oa_version: None page: 714 - 724 publication: Current Protein & Peptide Science publication_status: published publisher: Bentham Science Publishers publist_id: '3358' quality_controlled: '1' scopus_import: 1 status: public title: What can we learn from single molecule trajectories? type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2011' ... --- _id: '3285' abstract: - lang: eng text: Resolving the dynamical interplay of proteins and lipids in the live-cell plasma membrane represents a central goal in current cell biology. Superresolution concepts have introduced a means of capturing spatial heterogeneity at a nanoscopic length scale. Similar concepts for detecting dynamical transitions (superresolution chronoscopy) are still lacking. Here, we show that recently introduced spot-variation fluorescence correlation spectroscopy allows for sensing transient confinement times of membrane constituents at dramatically improved resolution. Using standard diffraction-limited optics, spot-variation fluorescence correlation spectroscopy captures signatures of single retardation events far below the transit time of the tracer through the focal spot. We provide an analytical description of special cases of transient binding of a tracer to pointlike traps, or association of a tracer with nanodomains. The influence of trap mobility and the underlying binding kinetics are quantified. Experimental approaches are suggested that allow for gaining quantitative mechanistic insights into the interaction processes of membrane constituents. acknowledgement: Y 250-B03/Austrian Science Fund FWF/Austria author: - first_name: Verena full_name: Ruprecht, Verena id: 4D71A03A-F248-11E8-B48F-1D18A9856A87 last_name: Ruprecht orcid: 0000-0003-4088-8633 - first_name: Stefan full_name: Wieser, Stefan id: 355AA5A0-F248-11E8-B48F-1D18A9856A87 last_name: Wieser orcid: 0000-0002-2670-2217 - first_name: Didier full_name: Marguet, Didier last_name: Marguet - first_name: Gerhard full_name: Schuetz, Gerhard last_name: Schuetz citation: ama: Ruprecht V, Wieser S, Marguet D, Schuetz G. Spot variation fluorescence correlation spectroscopy allows for superresolution chronoscopy of confinement times in membranes. Biophysical Journal. 2011;100(11):2839-2845. doi:10.1016/j.bpj.2011.04.035 apa: Ruprecht, V., Wieser, S., Marguet, D., & Schuetz, G. (2011). Spot variation fluorescence correlation spectroscopy allows for superresolution chronoscopy of confinement times in membranes. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2011.04.035 chicago: Ruprecht, Verena, Stefan Wieser, Didier Marguet, and Gerhard Schuetz. “Spot Variation Fluorescence Correlation Spectroscopy Allows for Superresolution Chronoscopy of Confinement Times in Membranes.” Biophysical Journal. Biophysical Society, 2011. https://doi.org/10.1016/j.bpj.2011.04.035. ieee: V. Ruprecht, S. Wieser, D. Marguet, and G. Schuetz, “Spot variation fluorescence correlation spectroscopy allows for superresolution chronoscopy of confinement times in membranes,” Biophysical Journal, vol. 100, no. 11. Biophysical Society, pp. 2839–2845, 2011. ista: Ruprecht V, Wieser S, Marguet D, Schuetz G. 2011. Spot variation fluorescence correlation spectroscopy allows for superresolution chronoscopy of confinement times in membranes. Biophysical Journal. 100(11), 2839–2845. mla: Ruprecht, Verena, et al. “Spot Variation Fluorescence Correlation Spectroscopy Allows for Superresolution Chronoscopy of Confinement Times in Membranes.” Biophysical Journal, vol. 100, no. 11, Biophysical Society, 2011, pp. 2839–45, doi:10.1016/j.bpj.2011.04.035. short: V. Ruprecht, S. Wieser, D. Marguet, G. Schuetz, Biophysical Journal 100 (2011) 2839–2845. date_created: 2018-12-11T12:02:27Z date_published: 2011-06-08T00:00:00Z date_updated: 2021-01-12T07:42:23Z day: '08' doi: 10.1016/j.bpj.2011.04.035 extern: '1' intvolume: ' 100' issue: '11' language: - iso: eng month: '06' oa_version: None page: 2839 - 2845 publication: Biophysical Journal publication_status: published publisher: Biophysical Society publist_id: '3360' status: public title: Spot variation fluorescence correlation spectroscopy allows for superresolution chronoscopy of confinement times in membranes type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 100 year: '2011' ... --- _id: '3302' abstract: - lang: eng text: Cloud computing aims to give users virtually unlimited pay-per-use computing resources without the burden of managing the underlying infrastructure. We present a new job execution environment Flextic that exploits scal- able static scheduling techniques to provide the user with a flexible pricing model, such as a tradeoff between dif- ferent degrees of execution speed and execution price, and at the same time, reduce scheduling overhead for the cloud provider. We have evaluated a prototype of Flextic on Amazon EC2 and compared it against Hadoop. For various data parallel jobs from machine learning, im- age processing, and gene sequencing that we considered, Flextic has low scheduling overhead and reduces job du- ration by up to 15% compared to Hadoop, a dynamic cloud scheduler. 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: Anmol full_name: Singh, Anmol id: 72A86902-E99F-11E9-9F62-915534D1B916 last_name: Singh - first_name: Vasu full_name: Singh, Vasu id: 4DAE2708-F248-11E8-B48F-1D18A9856A87 last_name: Singh - 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: 'Henzinger TA, Singh A, Singh V, Wies T, Zufferey D. Static scheduling in clouds. In: USENIX; 2011:1-6.' apa: 'Henzinger, T. A., Singh, A., Singh, V., Wies, T., & Zufferey, D. (2011). Static scheduling in clouds (pp. 1–6). Presented at the HotCloud: Workshop on Hot Topics in Cloud Computing, USENIX.' chicago: Henzinger, Thomas A, Anmol Singh, Vasu Singh, Thomas Wies, and Damien Zufferey. “Static Scheduling in Clouds,” 1–6. USENIX, 2011. ieee: 'T. A. Henzinger, A. Singh, V. Singh, T. Wies, and D. Zufferey, “Static scheduling in clouds,” presented at the HotCloud: Workshop on Hot Topics in Cloud Computing, 2011, pp. 1–6.' ista: 'Henzinger TA, Singh A, Singh V, Wies T, Zufferey D. 2011. Static scheduling in clouds. HotCloud: Workshop on Hot Topics in Cloud Computing, 1–6.' mla: Henzinger, Thomas A., et al. Static Scheduling in Clouds. USENIX, 2011, pp. 1–6. short: T.A. Henzinger, A. Singh, V. Singh, T. Wies, D. Zufferey, in:, USENIX, 2011, pp. 1–6. conference: end_date: 2011-06-15 name: 'HotCloud: Workshop on Hot Topics in Cloud Computing' start_date: 2011-06-14 date_created: 2018-12-11T12:02:33Z date_published: 2011-06-14T00:00:00Z date_updated: 2021-01-12T07:42:31Z day: '14' ddc: - '000' - '005' department: - _id: ToHe file: - access_level: open_access checksum: 21a461ac004bb535c83320fe79b30375 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:14Z date_updated: 2020-07-14T12:46:06Z file_id: '5333' file_name: IST-2012-90-v1+1_Static_scheduling_in_clouds.pdf file_size: 232770 relation: main_file file_date_updated: 2020-07-14T12:46:06Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 1 - 6 publication_status: published publisher: USENIX publist_id: '3338' pubrep_id: '90' quality_controlled: '1' status: public title: Static scheduling in clouds type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2011' ... --- _id: '3301' abstract: - lang: eng text: The chemical master equation is a differential equation describing the time evolution of the probability distribution over the possible “states” of a biochemical system. The solution of this equation is of interest within the systems biology field ever since the importance of the molec- ular noise has been acknowledged. Unfortunately, most of the systems do not have analytical solutions, and numerical solutions suffer from the course of dimensionality and therefore need to be approximated. Here, we introduce the concept of tail approximation, which retrieves an approximation of the probabilities in the tail of a distribution from the total probability of the tail and its conditional expectation. This approximation method can then be used to numerically compute the solution of the chemical master equation on a subset of the state space, thus fighting the explosion of the state space, for which this problem is renowned. 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: Maria full_name: Mateescu, Maria last_name: Mateescu citation: ama: 'Henzinger TA, Mateescu M. Tail approximation for the chemical master equation. In: Tampere International Center for Signal Processing; 2011.' apa: 'Henzinger, T. A., & Mateescu, M. (2011). Tail approximation for the chemical master equation. Presented at the WCSB: Workshop on Computational Systems Biology (TICSP), Tampere International Center for Signal Processing.' chicago: Henzinger, Thomas A, and Maria Mateescu. “Tail Approximation for the Chemical Master Equation.” Tampere International Center for Signal Processing, 2011. ieee: 'T. A. Henzinger and M. Mateescu, “Tail approximation for the chemical master equation,” presented at the WCSB: Workshop on Computational Systems Biology (TICSP), 2011.' ista: 'Henzinger TA, Mateescu M. 2011. Tail approximation for the chemical master equation. WCSB: Workshop on Computational Systems Biology (TICSP).' mla: Henzinger, Thomas A., and Maria Mateescu. Tail Approximation for the Chemical Master Equation. Tampere International Center for Signal Processing, 2011. short: T.A. Henzinger, M. Mateescu, in:, Tampere International Center for Signal Processing, 2011. conference: name: 'WCSB: Workshop on Computational Systems Biology (TICSP)' date_created: 2018-12-11T12:02:33Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:42:30Z day: '01' ddc: - '005' - '570' department: - _id: ToHe file: - access_level: open_access checksum: aa4d7a832a5419e6c0090650ebff2b9a content_type: application/pdf creator: system date_created: 2018-12-12T10:18:12Z date_updated: 2020-07-14T12:46:06Z file_id: '5331' file_name: IST-2012-91-v1+1_Tail_approximation_for_the_chemical_master_equation.pdf file_size: 240820 relation: main_file file_date_updated: 2020-07-14T12:46:06Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version publication_status: published publisher: Tampere International Center for Signal Processing publist_id: '3339' pubrep_id: '91' quality_controlled: '1' status: public title: Tail approximation for the chemical master equation type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2011' ... --- _id: '3299' abstract: - lang: eng text: 'We introduce propagation models, a formalism designed to support general and efficient data structures for the transient analysis of biochemical reaction networks. We give two use cases for propagation abstract data types: the uniformization method and numerical integration. We also sketch an implementation of a propagation abstract data type, which uses abstraction to approximate states.' 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: Maria full_name: Mateescu, Maria last_name: Mateescu citation: ama: 'Henzinger TA, Mateescu M. Propagation models for computing biochemical reaction networks. In: Springer; 2011:1-3. doi:10.1145/2037509.2037510' apa: 'Henzinger, T. A., & Mateescu, M. (2011). Propagation models for computing biochemical reaction networks (pp. 1–3). Presented at the CMSB: Computational Methods in Systems Biology, Paris, France: Springer. https://doi.org/10.1145/2037509.2037510' chicago: Henzinger, Thomas A, and Maria Mateescu. “Propagation Models for Computing Biochemical Reaction Networks,” 1–3. Springer, 2011. https://doi.org/10.1145/2037509.2037510. ieee: 'T. A. Henzinger and M. Mateescu, “Propagation models for computing biochemical reaction networks,” presented at the CMSB: Computational Methods in Systems Biology, Paris, France, 2011, pp. 1–3.' ista: 'Henzinger TA, Mateescu M. 2011. Propagation models for computing biochemical reaction networks. CMSB: Computational Methods in Systems Biology, 1–3.' mla: Henzinger, Thomas A., and Maria Mateescu. Propagation Models for Computing Biochemical Reaction Networks. Springer, 2011, pp. 1–3, doi:10.1145/2037509.2037510. short: T.A. Henzinger, M. Mateescu, in:, Springer, 2011, pp. 1–3. conference: end_date: 2011-09-23 location: Paris, France name: 'CMSB: Computational Methods in Systems Biology' start_date: 2011-09-21 date_created: 2018-12-11T12:02:32Z date_published: 2011-09-21T00:00:00Z date_updated: 2021-01-12T07:42:29Z day: '21' ddc: - '000' - '004' department: - _id: ToHe doi: 10.1145/2037509.2037510 file: - access_level: open_access checksum: 7f5c65509db1a9fb049abedd9663ed06 content_type: application/pdf creator: system date_created: 2018-12-12T10:07:50Z date_updated: 2020-07-14T12:46:06Z file_id: '4649' file_name: IST-2012-92-v1+1_Propagation_models_for_computing_biochemical_reaction_networks.pdf file_size: 255780 relation: main_file file_date_updated: 2020-07-14T12:46:06Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 1 - 3 publication_status: published publisher: Springer publist_id: '3341' pubrep_id: '92' quality_controlled: '1' scopus_import: 1 status: public title: Propagation models for computing biochemical reaction networks type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2011' ... --- _id: '3316' abstract: - lang: eng text: In addition to being correct, a system should be robust, that is, it should behave reasonably even after receiving unexpected inputs. In this paper, we summarize two formal notions of robustness that we have introduced previously for reactive systems. One of the notions is based on assigning costs for failures on a user-provided notion of incorrect transitions in a specification. Here, we define a system to be robust if a finite number of incorrect inputs does not lead to an infinite number of incorrect outputs. We also give a more refined notion of robustness that aims to minimize the ratio of output failures to input failures. The second notion is aimed at liveness. In contrast to the previous notion, it has no concept of recovery from an error. Instead, it compares the ratio of the number of liveness constraints that the system violates to the number of liveness constraints that the environment violates. article_processing_charge: No author: - first_name: Roderick full_name: Bloem, Roderick last_name: Bloem - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Karin full_name: Greimel, Karin last_name: Greimel - 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: Barbara full_name: Jobstmann, Barbara last_name: Jobstmann citation: ama: 'Bloem R, Chatterjee K, Greimel K, Henzinger TA, Jobstmann B. Specification-centered robustness. In: 6th IEEE International Symposium on Industrial and Embedded Systems. IEEE; 2011:176-185. doi:10.1109/SIES.2011.5953660' apa: 'Bloem, R., Chatterjee, K., Greimel, K., Henzinger, T. A., & Jobstmann, B. (2011). Specification-centered robustness. In 6th IEEE International Symposium on Industrial and Embedded Systems (pp. 176–185). Vasteras, Sweden: IEEE. https://doi.org/10.1109/SIES.2011.5953660' chicago: Bloem, Roderick, Krishnendu Chatterjee, Karin Greimel, Thomas A Henzinger, and Barbara Jobstmann. “Specification-Centered Robustness.” In 6th IEEE International Symposium on Industrial and Embedded Systems, 176–85. IEEE, 2011. https://doi.org/10.1109/SIES.2011.5953660. ieee: R. Bloem, K. Chatterjee, K. Greimel, T. A. Henzinger, and B. Jobstmann, “Specification-centered robustness,” in 6th IEEE International Symposium on Industrial and Embedded Systems, Vasteras, Sweden, 2011, pp. 176–185. ista: 'Bloem R, Chatterjee K, Greimel K, Henzinger TA, Jobstmann B. 2011. Specification-centered robustness. 6th IEEE International Symposium on Industrial and Embedded Systems. SIES: International Symposium on Industrial Embedded Systems, 176–185.' mla: Bloem, Roderick, et al. “Specification-Centered Robustness.” 6th IEEE International Symposium on Industrial and Embedded Systems, IEEE, 2011, pp. 176–85, doi:10.1109/SIES.2011.5953660. short: R. Bloem, K. Chatterjee, K. Greimel, T.A. Henzinger, B. Jobstmann, in:, 6th IEEE International Symposium on Industrial and Embedded Systems, IEEE, 2011, pp. 176–185. conference: end_date: 2011-06-17 location: Vasteras, Sweden name: ' SIES: International Symposium on Industrial Embedded Systems' start_date: 2011-06-15 date_created: 2018-12-11T12:02:38Z date_published: 2011-07-14T00:00:00Z date_updated: 2021-01-12T07:42:36Z day: '14' department: - _id: KrCh - _id: ToHe doi: 10.1109/SIES.2011.5953660 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://openlib.tugraz.at/download.php?id=5cb57c8a49344&location=browse month: '07' oa: 1 oa_version: Published Version page: 176 - 185 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F2ACDE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Rigorous Systems Engineering - _id: 25F1337C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '214373' name: Design for Embedded Systems - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: 6th IEEE International Symposium on Industrial and Embedded Systems publication_status: published publisher: IEEE publist_id: '3323' quality_controlled: '1' scopus_import: 1 status: public title: Specification-centered robustness type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2011' ... --- _id: '3318' abstract: - lang: eng text: Parvalbumin is thought to act in a manner similar to EGTA, but how a slow Ca2+ buffer affects nanodomain-coupling regimes at GABAergic synapses is unclear. Direct measurements of parvalbumin concentration and paired recordings in rodent hippocampus and cerebellum revealed that parvalbumin affects synaptic dynamics only when expressed at high levels. Modeling suggests that, in high concentrations, parvalbumin may exert BAPTA-like effects, modulating nanodomain coupling via competition with local saturation of endogenous fixed buffers. author: - first_name: Emmanuel full_name: Eggermann, Emmanuel last_name: Eggermann - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Eggermann E, Jonas PM. How the “slow” Ca(2+) buffer parvalbumin affects transmitter release in nanodomain coupling regimes at GABAergic synapses. Nature Neuroscience. 2011;15:20-22. doi:10.1038/nn.3002 apa: Eggermann, E., & Jonas, P. M. (2011). How the “slow” Ca(2+) buffer parvalbumin affects transmitter release in nanodomain coupling regimes at GABAergic synapses. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3002 chicago: Eggermann, Emmanuel, and Peter M Jonas. “How the ‘Slow’ Ca(2+) Buffer Parvalbumin Affects Transmitter Release in Nanodomain Coupling Regimes at GABAergic Synapses.” Nature Neuroscience. Nature Publishing Group, 2011. https://doi.org/10.1038/nn.3002. ieee: E. Eggermann and P. M. Jonas, “How the ‘slow’ Ca(2+) buffer parvalbumin affects transmitter release in nanodomain coupling regimes at GABAergic synapses,” Nature Neuroscience, vol. 15. Nature Publishing Group, pp. 20–22, 2011. ista: Eggermann E, Jonas PM. 2011. How the “slow” Ca(2+) buffer parvalbumin affects transmitter release in nanodomain coupling regimes at GABAergic synapses. Nature Neuroscience. 15, 20–22. mla: Eggermann, Emmanuel, and Peter M. Jonas. “How the ‘Slow’ Ca(2+) Buffer Parvalbumin Affects Transmitter Release in Nanodomain Coupling Regimes at GABAergic Synapses.” Nature Neuroscience, vol. 15, Nature Publishing Group, 2011, pp. 20–22, doi:10.1038/nn.3002. short: E. Eggermann, P.M. Jonas, Nature Neuroscience 15 (2011) 20–22. date_created: 2018-12-11T12:02:38Z date_published: 2011-12-04T00:00:00Z date_updated: 2021-01-12T07:42:37Z day: '04' department: - _id: PeJo doi: 10.1038/nn.3002 intvolume: ' 15' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631701/ month: '12' oa: 1 oa_version: Submitted Version page: 20 - 22 publication: Nature Neuroscience publication_status: published publisher: Nature Publishing Group publist_id: '3321' quality_controlled: '1' scopus_import: 1 status: public title: How the “slow” Ca(2+) buffer parvalbumin affects transmitter release in nanodomain coupling regimes at GABAergic synapses type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2011' ... --- _id: '3335' abstract: - lang: eng text: We study the topology of the Megaparsec Cosmic Web in terms of the scale-dependent Betti numbers, which formalize the topological information content of the cosmic mass distribution. While the Betti numbers do not fully quantify topology, they extend the information beyond conventional cosmological studies of topology in terms of genus and Euler characteristic. The richer information content of Betti numbers goes along the availability of fast algorithms to compute them. For continuous density fields, we determine the scale-dependence of Betti numbers by invoking the cosmologically familiar filtration of sublevel or superlevel sets defined by density thresholds. For the discrete galaxy distribution, however, the analysis is based on the alpha shapes of the particles. These simplicial complexes constitute an ordered sequence of nested subsets of the Delaunay tessellation, a filtration defined by the scale parameter, α. As they are homotopy equivalent to the sublevel sets of the distance field, they are an excellent tool for assessing the topological structure of a discrete point distribution. In order to develop an intuitive understanding for the behavior of Betti numbers as a function of α, and their relation to the morphological patterns in the Cosmic Web, we first study them within the context of simple heuristic Voronoi clustering models. These can be tuned to consist of specific morphological elements of the Cosmic Web, i.e. clusters, filaments, or sheets. To elucidate the relative prominence of the various Betti numbers in different stages of morphological evolution, we introduce the concept of alpha tracks. Subsequently, we address the topology of structures emerging in the standard LCDM scenario and in cosmological scenarios with alternative dark energy content. The evolution of the Betti numbers is shown to reflect the hierarchical evolution of the Cosmic Web. We also demonstrate that the scale-dependence of the Betti numbers yields a promising measure of cosmological parameters, with a potential to help in determining the nature of dark energy and to probe primordial non-Gaussianities. We also discuss the expected Betti numbers as a function of the density threshold for superlevel sets of a Gaussian random field. Finally, we introduce the concept of persistent homology. It measures scale levels of the mass distribution and allows us to separate small from large scale features. Within the context of the hierarchical cosmic structure formation, persistence provides a natural formalism for a multiscale topology study of the Cosmic Web. alternative_title: - LNCS author: - first_name: Rien full_name: Van De Weygaert, Rien last_name: Van De Weygaert - first_name: Gert full_name: Vegter, Gert last_name: Vegter - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Bernard full_name: Jones, Bernard last_name: Jones - first_name: Pratyush full_name: Pranav, Pratyush last_name: Pranav - first_name: Changbom full_name: Park, Changbom last_name: Park - first_name: Wojciech full_name: Hellwing, Wojciech last_name: Hellwing - first_name: Bob full_name: Eldering, Bob last_name: Eldering - first_name: Nico full_name: Kruithof, Nico last_name: Kruithof - first_name: Patrick full_name: Bos, Patrick last_name: Bos - first_name: Johan full_name: Hidding, Johan last_name: Hidding - first_name: Job full_name: Feldbrugge, Job last_name: Feldbrugge - first_name: Eline full_name: Ten Have, Eline last_name: Ten Have - first_name: Matti full_name: Van Engelen, Matti last_name: Van Engelen - first_name: Manuel full_name: Caroli, Manuel last_name: Caroli - first_name: Monique full_name: Teillaud, Monique last_name: Teillaud citation: ama: 'Van De Weygaert R, Vegter G, Edelsbrunner H, et al. Alpha, Betti and the Megaparsec Universe: On the topology of the Cosmic Web. In: Gavrilova M, Tan K, Mostafavi M, eds. Transactions on Computational Science XIV. Vol 6970. Special Issue on Voronoi Diagrams and Delaunay Triangulation. Springer; 2011:60-101. doi:10.1007/978-3-642-25249-5_3' apa: 'Van De Weygaert, R., Vegter, G., Edelsbrunner, H., Jones, B., Pranav, P., Park, C., … Teillaud, M. (2011). Alpha, Betti and the Megaparsec Universe: On the topology of the Cosmic Web. In M. Gavrilova, K. Tan, & M. Mostafavi (Eds.), Transactions on Computational Science XIV (Vol. 6970, pp. 60–101). Springer. https://doi.org/10.1007/978-3-642-25249-5_3' chicago: 'Van De Weygaert, Rien, Gert Vegter, Herbert Edelsbrunner, Bernard Jones, Pratyush Pranav, Changbom Park, Wojciech Hellwing, et al. “Alpha, Betti and the Megaparsec Universe: On the Topology of the Cosmic Web.” In Transactions on Computational Science XIV, edited by Marina Gavrilova, Kenneth Tan, and Mir Mostafavi, 6970:60–101. Special Issue on Voronoi Diagrams and Delaunay Triangulation. Springer, 2011. https://doi.org/10.1007/978-3-642-25249-5_3.' ieee: 'R. Van De Weygaert et al., “Alpha, Betti and the Megaparsec Universe: On the topology of the Cosmic Web,” in Transactions on Computational Science XIV, vol. 6970, M. Gavrilova, K. Tan, and M. Mostafavi, Eds. Springer, 2011, pp. 60–101.' ista: 'Van De Weygaert R, Vegter G, Edelsbrunner H, Jones B, Pranav P, Park C, Hellwing W, Eldering B, Kruithof N, Bos P, Hidding J, Feldbrugge J, Ten Have E, Van Engelen M, Caroli M, Teillaud M. 2011.Alpha, Betti and the Megaparsec Universe: On the topology of the Cosmic Web. In: Transactions on Computational Science XIV. LNCS, vol. 6970, 60–101.' mla: 'Van De Weygaert, Rien, et al. “Alpha, Betti and the Megaparsec Universe: On the Topology of the Cosmic Web.” Transactions on Computational Science XIV, edited by Marina Gavrilova et al., vol. 6970, Springer, 2011, pp. 60–101, doi:10.1007/978-3-642-25249-5_3.' short: R. Van De Weygaert, G. Vegter, H. Edelsbrunner, B. Jones, P. Pranav, C. Park, W. Hellwing, B. Eldering, N. Kruithof, P. Bos, J. Hidding, J. Feldbrugge, E. Ten Have, M. Van Engelen, M. Caroli, M. Teillaud, in:, M. Gavrilova, K. Tan, M. Mostafavi (Eds.), Transactions on Computational Science XIV, Springer, 2011, pp. 60–101. date_created: 2018-12-11T12:02:44Z date_published: 2011-11-09T00:00:00Z date_updated: 2021-01-12T07:42:44Z day: '09' department: - _id: HeEd doi: 10.1007/978-3-642-25249-5_3 editor: - first_name: Marina full_name: Gavrilova, Marina last_name: Gavrilova - first_name: Kenneth full_name: Tan, Kenneth last_name: Tan - first_name: Mir full_name: Mostafavi, Mir last_name: Mostafavi external_id: arxiv: - '1306.3640' intvolume: ' 6970' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1306.3640 month: '11' oa: 1 oa_version: Preprint page: 60 - 101 publication: Transactions on Computational Science XIV publication_status: published publisher: Springer publist_id: '3295' quality_controlled: '1' scopus_import: 1 series_title: Special Issue on Voronoi Diagrams and Delaunay Triangulation status: public title: 'Alpha, Betti and the Megaparsec Universe: On the topology of the Cosmic Web' type: book_chapter user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 6970 year: '2011' ...