[{"_id":"246","intvolume":"       149","publist_id":"7658","year":"2013","type":"journal_article","abstract":[{"lang":"eng","text":"Given an intersection of two quadrics X Pm1, with m &gt; 9, the quantitative arithmetic of the set X(Q) is investigated under the assumption that the singular locus of X consists of a pair of conjugate singular points defined over Q(i)."}],"date_published":"2013-09-01T00:00:00Z","citation":{"short":"T.D. Browning, R. Munshi, Compositio Mathematica 149 (2013) 1457–1494.","ama":"Browning TD, Munshi R. Rational points on singular intersections of quadrics. <i>Compositio Mathematica</i>. 2013;149(9):1457-1494. doi:<a href=\"https://doi.org/10.1112/S0010437X13007185\">10.1112/S0010437X13007185</a>","chicago":"Browning, Timothy D, and Ritabrata Munshi. “Rational Points on Singular Intersections of Quadrics.” <i>Compositio Mathematica</i>. Cambridge University Press, 2013. <a href=\"https://doi.org/10.1112/S0010437X13007185\">https://doi.org/10.1112/S0010437X13007185</a>.","ieee":"T. D. Browning and R. Munshi, “Rational points on singular intersections of quadrics,” <i>Compositio Mathematica</i>, vol. 149, no. 9. Cambridge University Press, pp. 1457–1494, 2013.","ista":"Browning TD, Munshi R. 2013. Rational points on singular intersections of quadrics. Compositio Mathematica. 149(9), 1457–1494.","mla":"Browning, Timothy D., and Ritabrata Munshi. “Rational Points on Singular Intersections of Quadrics.” <i>Compositio Mathematica</i>, vol. 149, no. 9, Cambridge University Press, 2013, pp. 1457–94, doi:<a href=\"https://doi.org/10.1112/S0010437X13007185\">10.1112/S0010437X13007185</a>.","apa":"Browning, T. D., &#38; Munshi, R. (2013). Rational points on singular intersections of quadrics. <i>Compositio Mathematica</i>. Cambridge University Press. <a href=\"https://doi.org/10.1112/S0010437X13007185\">https://doi.org/10.1112/S0010437X13007185</a>"},"publisher":"Cambridge University Press","extern":1,"author":[{"orcid":"0000-0002-8314-0177","last_name":"Browning","full_name":"Timothy Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D"},{"full_name":"Munshi, Ritabrata","last_name":"Munshi","first_name":"Ritabrata"}],"day":"01","date_updated":"2021-01-12T06:57:37Z","publication_status":"published","date_created":"2018-12-11T11:45:25Z","status":"public","page":"1457 - 1494","issue":"9","doi":"10.1112/S0010437X13007185","title":"Rational points on singular intersections of quadrics","quality_controlled":0,"publication":"Compositio Mathematica","acknowledgement":"EP/E053262/1\tEngineering and Physical Sciences Research Council","month":"09","volume":149},{"year":"2013","_id":"2466","intvolume":"        32","publist_id":"4436","isi":1,"day":"01","date_updated":"2025-09-29T14:13:52Z","citation":{"ama":"Ando R, Thuerey N, Wojtan C. Highly adaptive liquid simulations on tetrahedral meshes. <i>ACM Transactions on Graphics</i>. 2013;32(4). doi:<a href=\"https://doi.org/10.1145/2461912.2461982\">10.1145/2461912.2461982</a>","ieee":"R. Ando, N. Thuerey, and C. Wojtan, “Highly adaptive liquid simulations on tetrahedral meshes,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4. ACM, 2013.","ista":"Ando R, Thuerey N, Wojtan C. 2013. Highly adaptive liquid simulations on tetrahedral meshes. ACM Transactions on Graphics. 32(4), 103.","chicago":"Ando, Ryoichi, Nils Thuerey, and Chris Wojtan. “Highly Adaptive Liquid Simulations on Tetrahedral Meshes.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2461912.2461982\">https://doi.org/10.1145/2461912.2461982</a>.","short":"R. Ando, N. Thuerey, C. Wojtan, ACM Transactions on Graphics 32 (2013).","apa":"Ando, R., Thuerey, N., &#38; Wojtan, C. (2013). Highly adaptive liquid simulations on tetrahedral meshes. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2461912.2461982\">https://doi.org/10.1145/2461912.2461982</a>","mla":"Ando, Ryoichi, et al. “Highly Adaptive Liquid Simulations on Tetrahedral Meshes.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4, 103, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2461912.2461982\">10.1145/2461912.2461982</a>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1145/2461912.2461982","oa_version":"Submitted Version","quality_controlled":"1","has_accepted_license":"1","issue":"4","month":"07","volume":32,"pubrep_id":"605","article_number":"103","external_id":{"isi":["000321840100072"]},"file":[{"checksum":"aeea6b0ff2b27c695aeb8408c7d2fc50","content_type":"application/pdf","creator":"system","date_updated":"2020-07-14T12:45:41Z","relation":"main_file","date_created":"2018-12-12T10:17:25Z","file_size":8601561,"access_level":"open_access","file_id":"5279","file_name":"IST-2016-605-v1+1_tetflip_fixed.pdf"}],"author":[{"last_name":"Ando","full_name":"Ando, Ryoichi","first_name":"Ryoichi"},{"last_name":"Thuerey","full_name":"Thuerey, Nils","first_name":"Nils"},{"last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"}],"publication_status":"published","department":[{"_id":"ChWo"}],"oa":1,"file_date_updated":"2020-07-14T12:45:41Z","ddc":["000"],"date_published":"2013-07-01T00:00:00Z","type":"journal_article","abstract":[{"text":"We introduce a new method for efficiently simulating liquid with extreme amounts of spatial adaptivity. Our method combines several key components to drastically speed up the simulation of large-scale fluid phenomena: We leverage an alternative Eulerian tetrahedral mesh discretization to significantly reduce the complexity of the pressure solve while increasing the robustness with respect to element quality and removing the possibility of locking. Next, we enable subtle free-surface phenomena by deriving novel second-order boundary conditions consistent with our discretization. We couple this discretization with a spatially adaptive Fluid-Implicit Particle (FLIP) method, enabling efficient, robust, minimally-dissipative simulations that can undergo sharp changes in spatial resolution while minimizing artifacts. Along the way, we provide a new method for generating a smooth and detailed surface from a set of particles with variable sizes. Finally, we explore several new sizing functions for determining spatially adaptive simulation resolutions, and we show how to couple them to our simulator. We combine each of these elements to produce a simulation algorithm that is capable of creating animations at high maximum resolutions while avoiding common pitfalls like inaccurate boundary conditions and inefficient computation.","lang":"eng"}],"publisher":"ACM","scopus_import":"1","title":"Highly adaptive liquid simulations on tetrahedral meshes","publication":"ACM Transactions on Graphics","date_created":"2018-12-11T11:57:50Z","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}]},{"month":"07","volume":32,"pubrep_id":"604","doi":"10.1145/2461912.2462027","quality_controlled":"1","oa_version":"Submitted Version","has_accepted_license":"1","issue":"4","day":"01","date_updated":"2025-09-29T14:13:25Z","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"apa":"Bernstein, G., &#38; Wojtan, C. (2013). Putting holes in holey geometry: Topology change for arbitrary surfaces. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2461912.2462027\">https://doi.org/10.1145/2461912.2462027</a>","mla":"Bernstein, Gilbert, and Chris Wojtan. “Putting Holes in Holey Geometry: Topology Change for Arbitrary Surfaces.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4, 34, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2461912.2462027\">10.1145/2461912.2462027</a>.","chicago":"Bernstein, Gilbert, and Chris Wojtan. “Putting Holes in Holey Geometry: Topology Change for Arbitrary Surfaces.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2461912.2462027\">https://doi.org/10.1145/2461912.2462027</a>.","ieee":"G. Bernstein and C. Wojtan, “Putting holes in holey geometry: Topology change for arbitrary surfaces,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4. ACM, 2013.","ista":"Bernstein G, Wojtan C. 2013. Putting holes in holey geometry: Topology change for arbitrary surfaces. ACM Transactions on Graphics. 32(4), 34.","ama":"Bernstein G, Wojtan C. Putting holes in holey geometry: Topology change for arbitrary surfaces. <i>ACM Transactions on Graphics</i>. 2013;32(4). doi:<a href=\"https://doi.org/10.1145/2461912.2462027\">10.1145/2461912.2462027</a>","short":"G. Bernstein, C. Wojtan, ACM Transactions on Graphics 32 (2013)."},"year":"2013","_id":"2467","publist_id":"4435","intvolume":"        32","language":[{"iso":"eng"}],"title":"Putting holes in holey geometry: Topology change for arbitrary surfaces","publication":"ACM Transactions on Graphics","status":"public","date_created":"2018-12-11T11:57:50Z","article_processing_charge":"No","author":[{"first_name":"Gilbert","full_name":"Bernstein, Gilbert","last_name":"Bernstein"},{"full_name":"Wojtan, Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:45:41Z","oa":1,"department":[{"_id":"ChWo"}],"publication_status":"published","ddc":["000"],"scopus_import":"1","publisher":"ACM","date_published":"2013-07-01T00:00:00Z","type":"journal_article","abstract":[{"text":"This paper presents a method for computing topology changes for triangle meshes in an interactive geometric modeling environment. Most triangle meshes in practice do not exhibit desirable geometric properties, so we develop a solution that is independent of standard assumptions and robust to geometric errors. Specifically, we provide the first method for topology change applicable to arbitrary non-solid, non-manifold, non-closed, self-intersecting surfaces. We prove that this new method for topology change produces the expected conventional results when applied to solid (closed, manifold, non-self-intersecting) surfaces---that is, we prove a backwards-compatibility property relative to prior work. Beyond solid surfaces, we present empirical evidence that our method remains tolerant to a variety of surface aberrations through the incorporation of a novel error correction scheme. Finally, we demonstrate how topology change applied to non-solid objects enables wholly new and useful behaviors.","lang":"eng"}],"article_number":"34","external_id":{"isi":["000321840100003"]},"file":[{"creator":"system","date_updated":"2020-07-14T12:45:41Z","checksum":"9c8425d62246996ca632c5a01870515b","content_type":"application/pdf","file_size":3514674,"access_level":"open_access","file_id":"4768","file_name":"IST-2016-604-v1+1_toptop2013.pdf","relation":"main_file","date_created":"2018-12-12T10:09:43Z"}]},{"volume":32,"month":"07","pubrep_id":"603","quality_controlled":"1","oa_version":"Submitted Version","doi":"10.1145/2461912.2461991","issue":"4","has_accepted_license":"1","day":"01","date_updated":"2025-09-29T14:12:53Z","isi":1,"citation":{"mla":"Bojsen-Hansen, Morten, and Chris Wojtan. “Liquid Surface Tracking with Error Compensation.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4, 68, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2461912.2461991\">10.1145/2461912.2461991</a>.","apa":"Bojsen-Hansen, M., &#38; Wojtan, C. (2013). Liquid surface tracking with error compensation. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2461912.2461991\">https://doi.org/10.1145/2461912.2461991</a>","short":"M. Bojsen-Hansen, C. Wojtan, ACM Transactions on Graphics 32 (2013).","ieee":"M. Bojsen-Hansen and C. Wojtan, “Liquid surface tracking with error compensation,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4. ACM, 2013.","chicago":"Bojsen-Hansen, Morten, and Chris Wojtan. “Liquid Surface Tracking with Error Compensation.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2461912.2461991\">https://doi.org/10.1145/2461912.2461991</a>.","ama":"Bojsen-Hansen M, Wojtan C. Liquid surface tracking with error compensation. <i>ACM Transactions on Graphics</i>. 2013;32(4). doi:<a href=\"https://doi.org/10.1145/2461912.2461991\">10.1145/2461912.2461991</a>","ista":"Bojsen-Hansen M, Wojtan C. 2013. Liquid surface tracking with error compensation. ACM Transactions on Graphics. 32(4), 68."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2013","publist_id":"4434","intvolume":"        32","_id":"2468","language":[{"iso":"eng"}],"corr_author":"1","publication":"ACM Transactions on Graphics","title":"Liquid surface tracking with error compensation","status":"public","article_processing_charge":"No","date_created":"2018-12-11T11:57:50Z","file_date_updated":"2020-07-14T12:45:41Z","oa":1,"publication_status":"published","department":[{"_id":"ChWo"}],"author":[{"first_name":"Morten","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","full_name":"Bojsen-Hansen, Morten","orcid":"0000-0002-4417-3224","last_name":"Bojsen-Hansen"},{"last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"}],"scopus_import":"1","publisher":"ACM","date_published":"2013-07-01T00:00:00Z","type":"journal_article","abstract":[{"text":"Our work concerns the combination of an Eulerian liquid simulation with a high-resolution surface tracker (e.g. the level set method or a Lagrangian triangle mesh). The naive application of a high-resolution surface tracker to a low-resolution velocity field can produce many visually disturbing physical and topological artifacts that limit their use in practice. We address these problems by defining an error function which compares the current state of the surface tracker to the set of physically valid surface states. By reducing this error with a gradient descent technique, we introduce a novel physics-based surface fairing method. Similarly, by treating this error function as a potential energy, we derive a new surface correction force that mimics the vortex sheet equations. We demonstrate our results with both level set and mesh-based surface trackers.","lang":"eng"}],"ddc":["000"],"file":[{"date_created":"2018-12-12T10:09:37Z","relation":"main_file","file_id":"4761","file_name":"IST-2016-603-v1+1_liquidError_web.pdf","access_level":"open_access","file_size":5813685,"content_type":"application/pdf","checksum":"53d905e0180e23ef3e813b969ffed4e1","date_updated":"2020-07-14T12:45:41Z","creator":"system"}],"external_id":{"isi":["000321840100037"]},"article_number":"68"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Cadherins are transmembrane proteins that mediate cell–cell adhesion in animals. By regulating contact formation and stability, cadherins play a crucial role in tissue morphogenesis and homeostasis. Here, we review the three major  unctions of cadherins in cell–cell contact formation and stability. Two of those functions lead to a decrease in interfacial ension at the forming cell–cell contact, thereby promoting contact expansion — first, by providing adhesion tension that lowers interfacial tension at the cell–cell contact, and second, by signaling to the actomyosin cytoskeleton in order to reduce cortex tension and thus interfacial tension at the contact. The third function of cadherins in cell–cell contact formation is to stabilize the contact by resisting mechanical forces that pull on the contact."}],"date_published":"2013-07-22T00:00:00Z","publisher":"Cell Press","scopus_import":"1","ddc":["570"],"publication_status":"published","department":[{"_id":"CaHe"}],"file_date_updated":"2020-07-14T12:45:41Z","oa":1,"author":[{"first_name":"Jean-Léon","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","last_name":"Maître","orcid":"0000-0002-3688-1474","full_name":"Maître, Jean-Léon"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"file":[{"content_type":"application/pdf","checksum":"6a424b2f007b41d4955a9135793b2162","date_updated":"2020-07-14T12:45:41Z","creator":"dernst","date_created":"2019-01-24T15:40:22Z","relation":"main_file","file_id":"5881","file_name":"2013_CurrentBiology_Maitre.pdf","file_size":247320,"access_level":"open_access"}],"external_id":{"isi":["000322414200018"],"pmid":["23885883"]},"corr_author":"1","language":[{"iso":"eng"}],"page":"R626 - R633","article_processing_charge":"No","date_created":"2018-12-11T11:57:51Z","status":"public","pmid":1,"publication":"Current Biology","title":"Three functions of cadherins in cell adhesion","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"mla":"Maître, Jean-Léon, and Carl-Philipp J. Heisenberg. “Three Functions of Cadherins in Cell Adhesion.” <i>Current Biology</i>, vol. 23, no. 14, Cell Press, 2013, pp. R626–33, doi:<a href=\"https://doi.org/10.1016/j.cub.2013.06.019\">10.1016/j.cub.2013.06.019</a>.","apa":"Maître, J.-L., &#38; Heisenberg, C.-P. J. (2013). Three functions of cadherins in cell adhesion. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2013.06.019\">https://doi.org/10.1016/j.cub.2013.06.019</a>","short":"J.-L. Maître, C.-P.J. Heisenberg, Current Biology 23 (2013) R626–R633.","ieee":"J.-L. Maître and C.-P. J. Heisenberg, “Three functions of cadherins in cell adhesion,” <i>Current Biology</i>, vol. 23, no. 14. Cell Press, pp. R626–R633, 2013.","ama":"Maître J-L, Heisenberg C-PJ. Three functions of cadherins in cell adhesion. <i>Current Biology</i>. 2013;23(14):R626-R633. doi:<a href=\"https://doi.org/10.1016/j.cub.2013.06.019\">10.1016/j.cub.2013.06.019</a>","ista":"Maître J-L, Heisenberg C-PJ. 2013. Three functions of cadherins in cell adhesion. Current Biology. 23(14), R626–R633.","chicago":"Maître, Jean-Léon, and Carl-Philipp J Heisenberg. “Three Functions of Cadherins in Cell Adhesion.” <i>Current Biology</i>. Cell Press, 2013. <a href=\"https://doi.org/10.1016/j.cub.2013.06.019\">https://doi.org/10.1016/j.cub.2013.06.019</a>."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"isi":1,"day":"22","date_updated":"2025-09-29T14:12:25Z","intvolume":"        23","publist_id":"4433","license":"https://creativecommons.org/licenses/by/4.0/","_id":"2469","year":"2013","volume":23,"month":"07","issue":"14","has_accepted_license":"1","oa_version":"Published Version","quality_controlled":"1","doi":"10.1016/j.cub.2013.06.019"},{"issue":"3","page":"500 - 502","status":"public","date_created":"2018-12-11T11:45:25Z","publication":"Canadian Mathematical Bulletin","quality_controlled":0,"title":"The Lang-Weil estimate for cubic hypersurfaces","doi":"10.4153/CMB-2011-177-4","acknowledgement":"EP/E053262/1\tEngineering and Physical Sciences Research Council","volume":56,"month":"08","publist_id":"7657","intvolume":"        56","_id":"247","year":"2013","extern":1,"citation":{"short":"T.D. Browning, Canadian Mathematical Bulletin 56 (2013) 500–502.","ieee":"T. D. Browning, “The Lang-Weil estimate for cubic hypersurfaces,” <i>Canadian Mathematical Bulletin</i>, vol. 56, no. 3. Unknown, pp. 500–502, 2013.","ama":"Browning TD. The Lang-Weil estimate for cubic hypersurfaces. <i>Canadian Mathematical Bulletin</i>. 2013;56(3):500-502. doi:<a href=\"https://doi.org/10.4153/CMB-2011-177-4\">10.4153/CMB-2011-177-4</a>","ista":"Browning TD. 2013. The Lang-Weil estimate for cubic hypersurfaces. Canadian Mathematical Bulletin. 56(3), 500–502.","chicago":"Browning, Timothy D. “The Lang-Weil Estimate for Cubic Hypersurfaces.” <i>Canadian Mathematical Bulletin</i>. Unknown, 2013. <a href=\"https://doi.org/10.4153/CMB-2011-177-4\">https://doi.org/10.4153/CMB-2011-177-4</a>.","mla":"Browning, Timothy D. “The Lang-Weil Estimate for Cubic Hypersurfaces.” <i>Canadian Mathematical Bulletin</i>, vol. 56, no. 3, Unknown, 2013, pp. 500–02, doi:<a href=\"https://doi.org/10.4153/CMB-2011-177-4\">10.4153/CMB-2011-177-4</a>.","apa":"Browning, T. D. (2013). The Lang-Weil estimate for cubic hypersurfaces. <i>Canadian Mathematical Bulletin</i>. Unknown. <a href=\"https://doi.org/10.4153/CMB-2011-177-4\">https://doi.org/10.4153/CMB-2011-177-4</a>"},"publisher":"Unknown","type":"journal_article","date_published":"2013-08-31T00:00:00Z","abstract":[{"text":"An improved estimate is provided for the number of Fq-rational points on a geometrically irreducible, projective, cubic hypersurface that is not equal to a cone.","lang":"eng"}],"publication_status":"published","date_updated":"2021-01-12T06:57:40Z","day":"31","author":[{"first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","orcid":"0000-0002-8314-0177","full_name":"Timothy Browning"}]},{"title":"Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells","publication":"PLoS One","date_created":"2018-12-11T11:57:51Z","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"article_number":"e70050","external_id":{"isi":["000325211000181"]},"file":[{"relation":"main_file","date_created":"2018-12-12T10:08:21Z","file_name":"IST-2016-413-v1+1_journal.pone.0070050.pdf","file_id":"4681","access_level":"open_access","file_size":2294955,"checksum":"2d47ef47616ef4de1d517d146548184e","content_type":"application/pdf","creator":"system","date_updated":"2020-07-14T12:45:41Z"}],"author":[{"last_name":"Čovanová","full_name":"Čovanová, Milada","first_name":"Milada"},{"last_name":"Sauer","full_name":"Sauer, Michael","first_name":"Michael"},{"first_name":"Jan","last_name":"Rychtář","full_name":"Rychtář, Jan"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","full_name":"Petrášek, Jan","last_name":"Petrášek"},{"last_name":"Zažímalová","full_name":"Zažímalová, Eva","first_name":"Eva"}],"publication_status":"published","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:45:41Z","oa":1,"ddc":["570"],"abstract":[{"text":"Background:Auxin binding protein 1 (ABP1) is a putative auxin receptor and its function is indispensable for plant growth and development. ABP1 has been shown to be involved in auxin-dependent regulation of cell division and expansion, in plasma-membrane-related processes such as changes in transmembrane potential, and in the regulation of clathrin-dependent endocytosis. However, the ABP1-regulated downstream pathway remains elusive.Methodology/Principal Findings:Using auxin transport assays and quantitative analysis of cellular morphology we show that ABP1 regulates auxin efflux from tobacco BY-2 cells. The overexpression of ABP1can counterbalance increased auxin efflux and auxin starvation phenotypes caused by the overexpression of PIN auxin efflux carrier. Relevant mechanism involves the ABP1-controlled vesicle trafficking processes, including positive regulation of endocytosis of PIN auxin efflux carriers, as indicated by fluorescence recovery after photobleaching (FRAP) and pharmacological manipulations.Conclusions/Significance:The findings indicate the involvement of ABP1 in control of rate of auxin transport across plasma membrane emphasizing the role of ABP1 in regulation of PIN activity at the plasma membrane, and highlighting the relevance of ABP1 for the formation of developmentally important, PIN-dependent auxin gradients.","lang":"eng"}],"date_published":"2013-07-23T00:00:00Z","type":"journal_article","publisher":"Public Library of Science","scopus_import":"1","doi":"10.1371/journal.pone.0070050","oa_version":"Published Version","quality_controlled":"1","has_accepted_license":"1","issue":"7","month":"07","volume":8,"pubrep_id":"413","year":"2013","_id":"2470","intvolume":"         8","publist_id":"4432","isi":1,"day":"23","date_updated":"2025-09-29T14:11:54Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"citation":{"mla":"Čovanová, Milada, et al. “Overexpression of the Auxin Binding PROTEIN1 Modulates PIN-Dependent Auxin Transport in Tobacco Cells.” <i>PLoS One</i>, vol. 8, no. 7, e70050, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pone.0070050\">10.1371/journal.pone.0070050</a>.","apa":"Čovanová, M., Sauer, M., Rychtář, J., Friml, J., Petrášek, J., &#38; Zažímalová, E. (2013). Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0070050\">https://doi.org/10.1371/journal.pone.0070050</a>","short":"M. Čovanová, M. Sauer, J. Rychtář, J. Friml, J. Petrášek, E. Zažímalová, PLoS One 8 (2013).","chicago":"Čovanová, Milada, Michael Sauer, Jan Rychtář, Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Overexpression of the Auxin Binding PROTEIN1 Modulates PIN-Dependent Auxin Transport in Tobacco Cells.” <i>PLoS One</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pone.0070050\">https://doi.org/10.1371/journal.pone.0070050</a>.","ista":"Čovanová M, Sauer M, Rychtář J, Friml J, Petrášek J, Zažímalová E. 2013. Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells. PLoS One. 8(7), e70050.","ieee":"M. Čovanová, M. Sauer, J. Rychtář, J. Friml, J. Petrášek, and E. Zažímalová, “Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells,” <i>PLoS One</i>, vol. 8, no. 7. Public Library of Science, 2013.","ama":"Čovanová M, Sauer M, Rychtář J, Friml J, Petrášek J, Zažímalová E. Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells. <i>PLoS One</i>. 2013;8(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0070050\">10.1371/journal.pone.0070050</a>"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"month":"07","volume":8,"pubrep_id":"414","doi":"10.1371/journal.pone.0070013","quality_controlled":"1","oa_version":"Published Version","has_accepted_license":"1","issue":"7","date_updated":"2025-09-29T14:10:56Z","day":"30","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"citation":{"ieee":"I. Sanchez-Romero <i>et al.</i>, “Mechanism of protein kinetic stabilization by engineered disulfide crosslinks,” <i>PLoS One</i>, vol. 8, no. 7. Public Library of Science, 2013.","ista":"Sanchez-Romero I, Ariza A, Wilson K, Skjøt M, Vind J, De Maria L, Skov L, Sánchez Ruiz J. 2013. Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. PLoS One. 8(7), e70013.","ama":"Sanchez-Romero I, Ariza A, Wilson K, et al. Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. <i>PLoS One</i>. 2013;8(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0070013\">10.1371/journal.pone.0070013</a>","chicago":"Sanchez-Romero, Inmaculada, Antonio Ariza, Keith Wilson, Michael Skjøt, Jesper Vind, Leonardo De Maria, Lars Skov, and Jose Sánchez Ruiz. “Mechanism of Protein Kinetic Stabilization by Engineered Disulfide Crosslinks.” <i>PLoS One</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pone.0070013\">https://doi.org/10.1371/journal.pone.0070013</a>.","short":"I. Sanchez-Romero, A. Ariza, K. Wilson, M. Skjøt, J. Vind, L. De Maria, L. Skov, J. Sánchez Ruiz, PLoS One 8 (2013).","apa":"Sanchez-Romero, I., Ariza, A., Wilson, K., Skjøt, M., Vind, J., De Maria, L., … Sánchez Ruiz, J. (2013). Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0070013\">https://doi.org/10.1371/journal.pone.0070013</a>","mla":"Sanchez-Romero, Inmaculada, et al. “Mechanism of Protein Kinetic Stabilization by Engineered Disulfide Crosslinks.” <i>PLoS One</i>, vol. 8, no. 7, e70013, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pone.0070013\">10.1371/journal.pone.0070013</a>."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2013","_id":"2471","publist_id":"4430","intvolume":"         8","language":[{"iso":"eng"}],"title":"Mechanism of protein kinetic stabilization by engineered disulfide crosslinks","publication":"PLoS One","status":"public","article_processing_charge":"No","date_created":"2018-12-11T11:57:51Z","author":[{"last_name":"Sanchez Romero","full_name":"Sanchez Romero, Inmaculada","first_name":"Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ariza, Antonio","last_name":"Ariza","first_name":"Antonio"},{"full_name":"Wilson, Keith","last_name":"Wilson","first_name":"Keith"},{"first_name":"Michael","full_name":"Skjøt, Michael","last_name":"Skjøt"},{"first_name":"Jesper","full_name":"Vind, Jesper","last_name":"Vind"},{"first_name":"Leonardo","last_name":"De Maria","full_name":"De Maria, Leonardo"},{"first_name":"Lars","last_name":"Skov","full_name":"Skov, Lars"},{"first_name":"Jose","last_name":"Sánchez Ruiz","full_name":"Sánchez Ruiz, Jose"}],"oa":1,"file_date_updated":"2020-07-14T12:45:41Z","department":[{"_id":"HaJa"}],"publication_status":"published","ddc":["570"],"publisher":"Public Library of Science","scopus_import":"1","type":"journal_article","date_published":"2013-07-30T00:00:00Z","abstract":[{"lang":"eng","text":"The impact of disulfide bonds on protein stability goes beyond simple equilibrium thermodynamics effects associated with the conformational entropy of the unfolded state. Indeed, disulfide crosslinks may play a role in the prevention of dysfunctional association and strongly affect the rates of irreversible enzyme inactivation, highly relevant in biotechnological applications. While these kinetic-stability effects remain poorly understood, by analogy with proposed mechanisms for processes of protein aggregation and fibrillogenesis, we propose that they may be determined by the properties of sparsely-populated, partially-unfolded intermediates. Here we report the successful design, on the basis of high temperature molecular-dynamics simulations, of six thermodynamically and kinetically stabilized variants of phytase from Citrobacter braakii (a biotechnologically important enzyme) with one, two or three engineered disulfides. Activity measurements and 3D crystal structure determination demonstrate that the engineered crosslinks do not cause dramatic alterations in the native structure. The inactivation kinetics for all the variants displays a strongly non-Arrhenius temperature dependence, with the time-scale for the irreversible denaturation process reaching a minimum at a given temperature within the range of the denaturation transition. We show this striking feature to be a signature of a key role played by a partially unfolded, intermediate state/ensemble. Energetic and mutational analyses confirm that the intermediate is highly unfolded (akin to a proposed critical intermediate in the misfolding of the prion protein), a result that explains the observed kinetic stabilization. Our results provide a rationale for the kinetic-stability consequences of disulfide-crosslink engineering and an experimental methodology to arrive at energetic/structural descriptions of the sparsely populated and elusive intermediates that play key roles in irreversible protein denaturation."}],"external_id":{"isi":["000323114200054"]},"article_number":"e70013","file":[{"content_type":"application/pdf","checksum":"c0c96cc76ed7ef0d036a31a7e33c9a37","date_updated":"2020-07-14T12:45:41Z","creator":"system","date_created":"2018-12-12T10:15:07Z","relation":"main_file","file_id":"5124","file_name":"IST-2016-414-v1+1_journal.pone.0070013.pdf","file_size":1323666,"access_level":"open_access"}]},{"year":"2013","ec_funded":1,"publist_id":"4431","intvolume":"         8","_id":"2472","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"29","date_updated":"2025-09-29T14:11:25Z","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"apa":"Cazzonelli, C., Vanstraelen, M., Simon, S., Yin, K., Carron Arthur, A., Nisar, N., … Pogson, B. (2013). Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0070069\">https://doi.org/10.1371/journal.pone.0070069</a>","mla":"Cazzonelli, Christopher, et al. “Role of the Arabidopsis PIN6 Auxin Transporter in Auxin Homeostasis and Auxin-Mediated Development.” <i>PLoS One</i>, vol. 8, no. 7, e70069, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pone.0070069\">10.1371/journal.pone.0070069</a>.","chicago":"Cazzonelli, Christopher, Marleen Vanstraelen, Sibu Simon, Kuide Yin, Ashley Carron Arthur, Nazia Nisar, Gauri Tarle, et al. “Role of the Arabidopsis PIN6 Auxin Transporter in Auxin Homeostasis and Auxin-Mediated Development.” <i>PLoS One</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pone.0070069\">https://doi.org/10.1371/journal.pone.0070069</a>.","ieee":"C. Cazzonelli <i>et al.</i>, “Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development,” <i>PLoS One</i>, vol. 8, no. 7. Public Library of Science, 2013.","ama":"Cazzonelli C, Vanstraelen M, Simon S, et al. Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. <i>PLoS One</i>. 2013;8(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0070069\">10.1371/journal.pone.0070069</a>","ista":"Cazzonelli C, Vanstraelen M, Simon S, Yin K, Carron Arthur A, Nisar N, Tarle G, Cuttriss A, Searle I, Benková E, Mathesius U, Masle J, Friml J, Pogson B. 2013. Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. PLoS One. 8(7), e70069.","short":"C. Cazzonelli, M. Vanstraelen, S. Simon, K. Yin, A. Carron Arthur, N. Nisar, G. Tarle, A. Cuttriss, I. Searle, E. Benková, U. Mathesius, J. Masle, J. Friml, B. Pogson, PLoS One 8 (2013)."},"quality_controlled":"1","oa_version":"Published Version","doi":"10.1371/journal.pone.0070069","issue":"7","has_accepted_license":"1","volume":8,"month":"07","pubrep_id":"393","file":[{"date_created":"2018-12-12T10:16:34Z","relation":"main_file","file_name":"IST-2015-393-v1+1_journal.pone.0070069.pdf","file_id":"5222","access_level":"open_access","file_size":9003465,"content_type":"application/pdf","checksum":"3be71828b6c2ba9c90eb7056e3f7f57a","date_updated":"2020-07-14T12:45:41Z","creator":"system"}],"article_number":"e70069","external_id":{"isi":["000323369700128"]},"project":[{"grant_number":"207362","name":"Hormonal cross-talk in plant organogenesis","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"file_date_updated":"2020-07-14T12:45:41Z","oa":1,"publication_status":"published","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"author":[{"full_name":"Cazzonelli, Christopher","last_name":"Cazzonelli","first_name":"Christopher"},{"last_name":"Vanstraelen","full_name":"Vanstraelen, Marleen","first_name":"Marleen"},{"full_name":"Simon, Sibu","last_name":"Simon","orcid":"0000-0002-1998-6741","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","first_name":"Sibu"},{"first_name":"Kuide","last_name":"Yin","full_name":"Yin, Kuide"},{"full_name":"Carron Arthur, Ashley","last_name":"Carron Arthur","first_name":"Ashley"},{"first_name":"Nazia","last_name":"Nisar","full_name":"Nisar, Nazia"},{"first_name":"Gauri","full_name":"Tarle, Gauri","last_name":"Tarle"},{"first_name":"Abby","last_name":"Cuttriss","full_name":"Cuttriss, Abby"},{"full_name":"Searle, Iain","last_name":"Searle","first_name":"Iain"},{"orcid":"0000-0002-8510-9739","last_name":"Benková","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"},{"last_name":"Mathesius","full_name":"Mathesius, Ulrike","first_name":"Ulrike"},{"full_name":"Masle, Josette","last_name":"Masle","first_name":"Josette"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"first_name":"Barry","full_name":"Pogson, Barry","last_name":"Pogson"}],"publisher":"Public Library of Science","scopus_import":"1","abstract":[{"text":"Plant-specific PIN-formed (PIN) efflux transporters for the plant hormone auxin are required for tissue-specific directional auxin transport and cellular auxin homeostasis. The Arabidopsis PIN protein family has been shown to play important roles in developmental processes such as embryogenesis, organogenesis, vascular tissue differentiation, root meristem patterning and tropic growth. Here we analyzed roles of the less characterised Arabidopsis PIN6 auxin transporter. PIN6 is auxin-inducible and is expressed during multiple auxin-regulated developmental processes. Loss of pin6 function interfered with primary root growth and lateral root development. Misexpression of PIN6 affected auxin transport and interfered with auxin homeostasis in other growth processes such as shoot apical dominance, lateral root primordia development, adventitious root formation, root hair outgrowth and root waving. These changes in auxin-regulated growth correlated with a reduction in total auxin transport as well as with an altered activity of DR5-GUS auxin response reporter. Overall, the data indicate that PIN6 regulates auxin homeostasis during plant development.","lang":"eng"}],"date_published":"2013-07-29T00:00:00Z","type":"journal_article","ddc":["580","570"],"publication":"PLoS One","title":"Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development","status":"public","article_processing_charge":"No","date_created":"2018-12-11T11:57:52Z","language":[{"iso":"eng"}]},{"_id":"2473","intvolume":"        87","publist_id":"4428","ec_funded":1,"year":"2013","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"mla":"Barton, Nicholas H., et al. “Genetic Hitch-Hiking in Spatially Extended Populations.” <i>Theoretical Population Biology</i>, vol. 87, no. 8, Elsevier, 2013, pp. 75–89, doi:<a href=\"https://doi.org/10.1016/j.tpb.2012.12.001\">10.1016/j.tpb.2012.12.001</a>.","apa":"Barton, N. H., Etheridge, A., Kelleher, J., &#38; Véber, A. (2013). Genetic hitch-hiking in spatially extended populations. <i>Theoretical Population Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tpb.2012.12.001\">https://doi.org/10.1016/j.tpb.2012.12.001</a>","short":"N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population Biology 87 (2013) 75–89.","ieee":"N. H. Barton, A. Etheridge, J. Kelleher, and A. Véber, “Genetic hitch-hiking in spatially extended populations,” <i>Theoretical Population Biology</i>, vol. 87, no. 8. Elsevier, pp. 75–89, 2013.","chicago":"Barton, Nicholas H, Alison Etheridge, Jerome Kelleher, and Amandine Véber. “Genetic Hitch-Hiking in Spatially Extended Populations.” <i>Theoretical Population Biology</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.tpb.2012.12.001\">https://doi.org/10.1016/j.tpb.2012.12.001</a>.","ama":"Barton NH, Etheridge A, Kelleher J, Véber A. Genetic hitch-hiking in spatially extended populations. <i>Theoretical Population Biology</i>. 2013;87(8):75-89. doi:<a href=\"https://doi.org/10.1016/j.tpb.2012.12.001\">10.1016/j.tpb.2012.12.001</a>","ista":"Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Genetic hitch-hiking in spatially extended populations. Theoretical Population Biology. 87(8), 75–89."},"isi":1,"day":"03","date_updated":"2025-09-29T14:10:28Z","has_accepted_license":"1","issue":"8","doi":"10.1016/j.tpb.2012.12.001","oa_version":"Submitted Version","quality_controlled":"1","pubrep_id":"118","month":"01","volume":87,"project":[{"name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7"}],"external_id":{"isi":["000322688800008"]},"file":[{"file_name":"IST-2013-118-v1+1_bartonetalRevision.pdf","file_id":"5376","access_level":"open_access","file_size":1706282,"relation":"main_file","date_created":"2018-12-12T10:18:54Z","creator":"system","date_updated":"2020-07-14T12:45:41Z","checksum":"4274ec1f433b838a7d5b941cc9684ca7","content_type":"application/pdf"}],"ddc":["570"],"type":"journal_article","date_published":"2013-01-03T00:00:00Z","abstract":[{"lang":"eng","text":"When a mutation with selective advantage s spreads through a panmictic population, it may cause two lineages at a linked locus to coalesce; the probability of coalescence is exp(−2rT), where T∼log(2Ns)/s is the time to fixation, N is the number of haploid individuals, and r is the recombination rate. Population structure delays fixation, and so weakens the effect of a selective sweep. However, favourable alleles spread through a spatially continuous population behind a narrow wavefront; ancestral lineages are confined at the tip of this front, and so coalesce rapidly. In extremely dense populations, coalescence is dominated by rare fluctuations ahead of the front. However, we show that for moderate densities, a simple quasi-deterministic approximation applies: the rate of coalescence within the front is λ∼2g(η)/(ρℓ), where ρ is the population density and  is the characteristic scale of the wavefront; g(η) depends only on the strength of random drift,  . The net effect of a sweep on coalescence also depends crucially on whether two lineages are ever both within the wavefront at the same time: even in the extreme case when coalescence within the front is instantaneous, the net rate of coalescence may be lower than in a single panmictic population. Sweeps can also have a substantial impact on the rate of gene flow. A single lineage will jump to a new location when it is hit by a sweep, with mean square displacement  ; this can be substantial if the species’ range, L, is large, even if the species-wide rate of sweeps per map length, Λ/R, is small. This effect is half as strong in two dimensions. In contrast, the rate of coalescence between lineages, at random locations in space and on the genetic map, is proportional to (c/L)(Λ/R), where c is the wavespeed: thus, on average, one-dimensional structure is likely to reduce coalescence due to sweeps, relative to panmixis. In two dimensions, genes must move along the front before they can coalesce; this process is rapid, being dominated by rare fluctuations. This leads to a dramatically higher rate of coalescence within the wavefront than if lineages simply diffused along the front. Nevertheless, the net rate of coalescence due to a sweep through a two-dimensional population is likely to be lower than it would be with panmixis."}],"scopus_import":"1","publisher":"Elsevier","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H"},{"last_name":"Etheridge","full_name":"Etheridge, Alison","first_name":"Alison"},{"full_name":"Kelleher, Jerome","last_name":"Kelleher","first_name":"Jerome"},{"full_name":"Véber, Amandine","last_name":"Véber","first_name":"Amandine"}],"department":[{"_id":"NiBa"}],"publication_status":"published","file_date_updated":"2020-07-14T12:45:41Z","oa":1,"article_processing_charge":"No","date_created":"2018-12-11T11:57:52Z","status":"public","page":"75 - 89","title":"Genetic hitch-hiking in spatially extended populations","publication":"Theoretical Population Biology","corr_author":"1","language":[{"iso":"eng"}]},{"volume":110,"month":"01","quality_controlled":0,"publication":"PNAS","doi":"10.1073/pnas.1214718110","title":"Neuroligin-1 controls synaptic abundance of NMDA-type glutamate receptors through extracellular coupling","page":"725 - 730","issue":"2","date_created":"2018-12-11T11:57:54Z","status":"public","publication_status":"published","author":[{"full_name":"Budreck, Elaine C","last_name":"Budreck","first_name":"Elaine"},{"first_name":"Oh","last_name":"Kwon","full_name":"Kwon, Oh-Bin"},{"full_name":"Jung, Jung-Hoon","last_name":"Jung","first_name":"Jung"},{"first_name":"Stéphane","last_name":"Baudouin","full_name":"Baudouin, Stéphane J"},{"first_name":"Albert","full_name":"Thommen, Albert","last_name":"Thommen"},{"first_name":"Hye","full_name":"Kim, Hye-Sun","last_name":"Kim"},{"last_name":"Fukazawa","full_name":"Fukazawa, Yugo","first_name":"Yugo"},{"first_name":"Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Harada","orcid":"0000-0001-7429-7896","full_name":"Harumi Harada"},{"full_name":"Tabuchi, Katsuhiko","last_name":"Tabuchi","first_name":"Katsuhiko"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Ryuichi Shigemoto","last_name":"Shigemoto","orcid":"0000-0001-8761-9444"},{"first_name":"Peter","last_name":"Scheiffele","full_name":"Scheiffele, Peter"},{"first_name":"Joung","last_name":"Kim","full_name":"Kim, Joung-Hun"}],"date_updated":"2021-01-12T06:57:43Z","day":"08","type":"journal_article","abstract":[{"text":"Despite the pivotal functions of the NMDA receptor (NMDAR) for neural circuit development and synaptic plasticity, the molecular mechanisms underlying the dynamics of NMDAR trafficking are poorly understood. The cell adhesion molecule neuroligin-1 (NL1) modifies NMDAR-dependent synaptic transmission and synaptic plasticity, but it is unclear whether NL1 controls synaptic accumulation or function of the receptors. Here, we provide evidence that NL1 regulates the abundance of NMDARs at postsynaptic sites. This function relies on extracellular, NL1 isoform-specific sequences that facilitate biochemical interactions between NL1 and the NMDAR GluN1 subunit. Our work uncovers NL1 isoform-specific cisinteractions with ionotropic glutamate receptors as a key mechanism for controlling synaptic properties.","lang":"eng"}],"date_published":"2013-01-08T00:00:00Z","citation":{"mla":"Budreck, Elaine, et al. “Neuroligin-1 Controls Synaptic Abundance of NMDA-Type Glutamate Receptors through Extracellular Coupling.” <i>PNAS</i>, vol. 110, no. 2, National Academy of Sciences, 2013, pp. 725–30, doi:<a href=\"https://doi.org/10.1073/pnas.1214718110\">10.1073/pnas.1214718110</a>.","apa":"Budreck, E., Kwon, O., Jung, J., Baudouin, S., Thommen, A., Kim, H., … Kim, J. (2013). Neuroligin-1 controls synaptic abundance of NMDA-type glutamate receptors through extracellular coupling. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1214718110\">https://doi.org/10.1073/pnas.1214718110</a>","short":"E. Budreck, O. Kwon, J. Jung, S. Baudouin, A. Thommen, H. Kim, Y. Fukazawa, H. Harada, K. Tabuchi, R. Shigemoto, P. Scheiffele, J. Kim, PNAS 110 (2013) 725–730.","chicago":"Budreck, Elaine, Oh Kwon, Jung Jung, Stéphane Baudouin, Albert Thommen, Hye Kim, Yugo Fukazawa, et al. “Neuroligin-1 Controls Synaptic Abundance of NMDA-Type Glutamate Receptors through Extracellular Coupling.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1214718110\">https://doi.org/10.1073/pnas.1214718110</a>.","ista":"Budreck E, Kwon O, Jung J, Baudouin S, Thommen A, Kim H, Fukazawa Y, Harada H, Tabuchi K, Shigemoto R, Scheiffele P, Kim J. 2013. Neuroligin-1 controls synaptic abundance of NMDA-type glutamate receptors through extracellular coupling. PNAS. 110(2), 725–730.","ama":"Budreck E, Kwon O, Jung J, et al. Neuroligin-1 controls synaptic abundance of NMDA-type glutamate receptors through extracellular coupling. <i>PNAS</i>. 2013;110(2):725-730. doi:<a href=\"https://doi.org/10.1073/pnas.1214718110\">10.1073/pnas.1214718110</a>","ieee":"E. Budreck <i>et al.</i>, “Neuroligin-1 controls synaptic abundance of NMDA-type glutamate receptors through extracellular coupling,” <i>PNAS</i>, vol. 110, no. 2. National Academy of Sciences, pp. 725–730, 2013."},"publisher":"National Academy of Sciences","extern":1,"year":"2013","intvolume":"       110","publist_id":"4423","_id":"2478"},{"date_published":"2013-11-29T00:00:00Z","type":"journal_article","abstract":[{"text":"Châtelet surfaces provide a rich source of geometrically rational surfaces that do not always satisfy the Hasse principle. Restricting attention to a special class of Châtelet surfaces, we investigate the frequency that such counter-examples arise over the rational numbers.","lang":"eng"}],"citation":{"apa":"De La Bretèche, R., &#38; Browning, T. D. (2013). Density of Châtelet surfaces failing the Hasse principle. <i>Proceedings of the London Mathematical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1112/plms/pdt060\">https://doi.org/10.1112/plms/pdt060</a>","mla":"De La Bretèche, Régis, and Timothy D. Browning. “Density of Châtelet Surfaces Failing the Hasse Principle.” <i>Proceedings of the London Mathematical Society</i>, vol. 108, no. 4, Oxford University Press, 2013, pp. 1030–78, doi:<a href=\"https://doi.org/10.1112/plms/pdt060\">10.1112/plms/pdt060</a>.","ama":"De La Bretèche R, Browning TD. Density of Châtelet surfaces failing the Hasse principle. <i>Proceedings of the London Mathematical Society</i>. 2013;108(4):1030-1078. doi:<a href=\"https://doi.org/10.1112/plms/pdt060\">10.1112/plms/pdt060</a>","ista":"De La Bretèche R, Browning TD. 2013. Density of Châtelet surfaces failing the Hasse principle. Proceedings of the London Mathematical Society. 108(4), 1030–1078.","chicago":"De La Bretèche, Régis, and Timothy D Browning. “Density of Châtelet Surfaces Failing the Hasse Principle.” <i>Proceedings of the London Mathematical Society</i>. Oxford University Press, 2013. <a href=\"https://doi.org/10.1112/plms/pdt060\">https://doi.org/10.1112/plms/pdt060</a>.","ieee":"R. De La Bretèche and T. D. Browning, “Density of Châtelet surfaces failing the Hasse principle,” <i>Proceedings of the London Mathematical Society</i>, vol. 108, no. 4. Oxford University Press, pp. 1030–1078, 2013.","short":"R. De La Bretèche, T.D. Browning, Proceedings of the London Mathematical Society 108 (2013) 1030–1078."},"publisher":"Oxford University Press","extern":1,"author":[{"first_name":"Régis","last_name":"De La Bretèche","full_name":"de la Bretèche, Régis"},{"orcid":"0000-0002-8314-0177","last_name":"Browning","full_name":"Timothy Browning","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2021-01-12T06:57:51Z","day":"29","publication_status":"published","oa":1,"_id":"250","intvolume":"       108","publist_id":"7652","main_file_link":[{"url":"https://arxiv.org/abs/1210.4010","open_access":"1"}],"year":"2013","acknowledgement":"While working on this paper, the first author was supported by an IUF Junior and ANR while the second author was supported by ERC grant 306457.","month":"11","volume":108,"date_created":"2018-12-11T11:45:26Z","status":"public","page":"1030 - 1078","issue":"4","doi":"10.1112/plms/pdt060","title":"Density of Châtelet surfaces failing the Hasse principle","quality_controlled":0,"publication":"Proceedings of the London Mathematical Society"},{"publisher":"Universite de Bordeaux I","citation":{"mla":"De La Bretèche, Régis, and Timothy D. Browning. “Counter Examples to the Hasse Principle among Certain Coflasque Tori.” <i>Journal de Theorie Des Nombres de Bordeaux</i>, vol. 26, no. 1, Universite de Bordeaux I, 2013, pp. 25–44, doi:<a href=\"https://doi.org/10.5802/jtnb.857\">10.5802/jtnb.857</a>.","apa":"De La Bretèche, R., &#38; Browning, T. D. (2013). Counter examples to the Hasse principle among certain coflasque tori. <i>Journal de Theorie Des Nombres de Bordeaux</i>. Universite de Bordeaux I. <a href=\"https://doi.org/10.5802/jtnb.857\">https://doi.org/10.5802/jtnb.857</a>","short":"R. De La Bretèche, T.D. Browning, Journal de Theorie Des Nombres de Bordeaux 26 (2013) 25–44.","ieee":"R. De La Bretèche and T. D. Browning, “Counter examples to the Hasse principle among certain coflasque tori,” <i>Journal de Theorie des Nombres de Bordeaux</i>, vol. 26, no. 1. Universite de Bordeaux I, pp. 25–44, 2013.","ama":"De La Bretèche R, Browning TD. Counter examples to the Hasse principle among certain coflasque tori. <i>Journal de Theorie des Nombres de Bordeaux</i>. 2013;26(1):25-44. doi:<a href=\"https://doi.org/10.5802/jtnb.857\">10.5802/jtnb.857</a>","chicago":"De La Bretèche, Régis, and Timothy D Browning. “Counter Examples to the Hasse Principle among Certain Coflasque Tori.” <i>Journal de Theorie Des Nombres de Bordeaux</i>. Universite de Bordeaux I, 2013. <a href=\"https://doi.org/10.5802/jtnb.857\">https://doi.org/10.5802/jtnb.857</a>.","ista":"De La Bretèche R, Browning TD. 2013. Counter examples to the Hasse principle among certain coflasque tori. Journal de Theorie des Nombres de Bordeaux. 26(1), 25–44."},"extern":1,"type":"journal_article","abstract":[{"lang":"eng","text":"We study the density of varieties in a certain family which do not satisfy the Hasse principle. This work relies on results recently obtained by Colliot-Thélène [3]."}],"date_published":"2013-05-14T00:00:00Z","publication_status":"published","day":"14","date_updated":"2021-01-12T06:57:55Z","author":[{"full_name":"de la Bretèche, Régis","last_name":"De La Bretèche","first_name":"Régis"},{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D","full_name":"Timothy Browning","orcid":"0000-0002-8314-0177","last_name":"Browning"}],"publist_id":"7651","intvolume":"        26","_id":"251","year":"2013","volume":26,"month":"05","issue":"1","page":"25 - 44","status":"public","date_created":"2018-12-11T11:45:26Z","publication":"Journal de Theorie des Nombres de Bordeaux","quality_controlled":0,"doi":"10.5802/jtnb.857","title":"Counter examples to the Hasse principle among certain coflasque tori"},{"external_id":{"isi":["000331450100005"]},"type":"journal_article","date_published":"2013-07-30T00:00:00Z","abstract":[{"lang":"eng","text":"We study the problem of object recognition for categories for which we have no training examples, a task also called zero-data or zero-shot learning. This situation has hardly been studied in computer vision research, even though it occurs frequently: the world contains tens of thousands of different object classes and for only few of them image collections have been formed and suitably annotated. To tackle the problem we introduce attribute-based classification: objects are identified based on a high-level description that is phrased in terms of semantic attributes, such as the object's color or shape. Because the identification of each such property transcends the specific learning task at hand, the attribute classifiers can be pre-learned independently, e.g. from existing image datasets unrelated to the current task. Afterwards, new classes can be detected based on their attribute representation, without the need for a new training phase. In this paper we also introduce a new dataset, Animals with Attributes, of over 30,000 images of 50 animal classes, annotated with 85 semantic attributes. Extensive experiments on this and two more datasets show that attribute-based classification indeed is able to categorize images without access to any training images of the target classes."}],"scopus_import":"1","publisher":"IEEE","author":[{"last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nickisch, Hannes","last_name":"Nickisch","first_name":"Hannes"},{"first_name":"Stefan","last_name":"Harmeling","full_name":"Harmeling, Stefan"}],"publication_status":"published","department":[{"_id":"ChLa"}],"article_processing_charge":"No","date_created":"2018-12-11T11:58:08Z","status":"public","page":"453 - 465","title":"Attribute-based classification for zero-shot learning of object categories","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","language":[{"iso":"eng"}],"_id":"2516","intvolume":"        36","publist_id":"4385","year":"2013","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ista":"Lampert C, Nickisch H, Harmeling S. 2013. Attribute-based classification for zero-shot learning of object categories. IEEE Transactions on Pattern Analysis and Machine Intelligence. 36(3), 453–465.","chicago":"Lampert, Christoph, Hannes Nickisch, and Stefan Harmeling. “Attribute-Based Classification for Zero-Shot Learning of Object Categories.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE, 2013. <a href=\"https://doi.org/10.1109/TPAMI.2013.140\">https://doi.org/10.1109/TPAMI.2013.140</a>.","ieee":"C. Lampert, H. Nickisch, and S. Harmeling, “Attribute-based classification for zero-shot learning of object categories,” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 36, no. 3. IEEE, pp. 453–465, 2013.","ama":"Lampert C, Nickisch H, Harmeling S. Attribute-based classification for zero-shot learning of object categories. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. 2013;36(3):453-465. doi:<a href=\"https://doi.org/10.1109/TPAMI.2013.140\">10.1109/TPAMI.2013.140</a>","short":"C. Lampert, H. Nickisch, S. Harmeling, IEEE Transactions on Pattern Analysis and Machine Intelligence 36 (2013) 453–465.","apa":"Lampert, C., Nickisch, H., &#38; Harmeling, S. (2013). Attribute-based classification for zero-shot learning of object categories. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE. <a href=\"https://doi.org/10.1109/TPAMI.2013.140\">https://doi.org/10.1109/TPAMI.2013.140</a>","mla":"Lampert, Christoph, et al. “Attribute-Based Classification for Zero-Shot Learning of Object Categories.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 36, no. 3, IEEE, 2013, pp. 453–65, doi:<a href=\"https://doi.org/10.1109/TPAMI.2013.140\">10.1109/TPAMI.2013.140</a>."},"isi":1,"date_updated":"2025-09-29T14:09:57Z","day":"30","issue":"3","doi":"10.1109/TPAMI.2013.140","oa_version":"None","quality_controlled":"1","month":"07","volume":36},{"issue":"Part 2","has_accepted_license":"1","oa_version":"Submitted Version","quality_controlled":"1","doi":"10.1007/978-3-642-39212-2_3","acknowledgement":"ERC Grant QUALITY. ","volume":7966,"month":"07","intvolume":"      7966","publist_id":"4384","_id":"2517","ec_funded":1,"year":"2013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Almagor, S., Boker, U., &#38; Kupferman, O. (2013). Formalizing and reasoning about quality. Presented at the ICALP: Automata, Languages and Programming, Riga, Latvia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39212-2_3\">https://doi.org/10.1007/978-3-642-39212-2_3</a>","mla":"Almagor, Shaull, et al. <i>Formalizing and Reasoning about Quality</i>. Vol. 7966, no. Part 2, Springer, 2013, pp. 15–27, doi:<a href=\"https://doi.org/10.1007/978-3-642-39212-2_3\">10.1007/978-3-642-39212-2_3</a>.","chicago":"Almagor, Shaull, Udi Boker, and Orna Kupferman. “Formalizing and Reasoning about Quality.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39212-2_3\">https://doi.org/10.1007/978-3-642-39212-2_3</a>.","ista":"Almagor S, Boker U, Kupferman O. 2013. Formalizing and reasoning about quality. 7966(Part 2), 15–27.","ama":"Almagor S, Boker U, Kupferman O. Formalizing and reasoning about quality. 2013;7966(Part 2):15-27. doi:<a href=\"https://doi.org/10.1007/978-3-642-39212-2_3\">10.1007/978-3-642-39212-2_3</a>","ieee":"S. Almagor, U. Boker, and O. Kupferman, “Formalizing and reasoning about quality,” vol. 7966, no. Part 2. Springer, pp. 15–27, 2013.","short":"S. Almagor, U. Boker, O. Kupferman, 7966 (2013) 15–27."},"day":"01","date_updated":"2020-08-11T10:09:47Z","page":"15 - 27","article_processing_charge":"No","date_created":"2018-12-11T11:58:08Z","status":"public","title":"Formalizing and reasoning about quality","alternative_title":["LNCS"],"language":[{"iso":"eng"}],"conference":{"name":"ICALP: Automata, Languages and Programming","start_date":"2013-07-08","end_date":"2013-07-12","location":"Riga, Latvia"},"series_title":"Lecture Notes in Computer Science","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"file":[{"file_id":"7860","file_name":"2013_ICALP_Almagor.pdf","access_level":"open_access","file_size":363031,"relation":"main_file","date_created":"2020-05-15T11:16:12Z","creator":"dernst","date_updated":"2020-07-14T12:45:42Z","checksum":"85afbf6c18a2c7e377c52c9410e2d824","content_type":"application/pdf"}],"abstract":[{"text":"Traditional formal methods are based on a Boolean satisfaction notion: a reactive system satisfies, or not, a given specification. We generalize formal methods to also address the quality of systems. As an adequate specification formalism we introduce the linear temporal logic LTL[F]. The satisfaction value of an LTL[F] formula is a number between 0 and 1, describing the quality of the satisfaction. The logic generalizes traditional LTL by augmenting it with a (parameterized) set F of arbitrary functions over the interval [0,1]. For example, F may contain the maximum or minimum between the satisfaction values of subformulas, their product, and their average. The classical decision problems in formal methods, such as satisfiability, model checking, and synthesis, are generalized to search and optimization problems in the quantitative setting. For example, model checking asks for the quality in which a specification is satisfied, and synthesis returns a system satisfying the specification with the highest quality. Reasoning about quality gives rise to other natural questions, like the distance between specifications. We formalize these basic questions and study them for LTL[F]. By extending the automata-theoretic approach for LTL to a setting that takes quality into an account, we are able to solve the above problems and show that reasoning about LTL[F] has roughly the same complexity as reasoning about traditional LTL.","lang":"eng"}],"date_published":"2013-07-01T00:00:00Z","type":"conference","scopus_import":1,"publisher":"Springer","ddc":["000"],"publication_status":"published","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:45:42Z","oa":1,"author":[{"first_name":"Shaull","last_name":"Almagor","full_name":"Almagor, Shaull"},{"last_name":"Boker","full_name":"Boker, Udi","first_name":"Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Orna","last_name":"Kupferman","full_name":"Kupferman, Orna"}]},{"month":"07","volume":7965,"doi":"10.1007/978-3-642-39206-1_53","oa_version":"Preprint","quality_controlled":"1","issue":"1","day":"01","date_updated":"2025-09-23T14:14:56Z","citation":{"mla":"Kolmogorov, Vladimir. <i>The Power of Linear Programming for Finite-Valued CSPs: A Constructive Characterization</i>. Vol. 7965, no. 1, Springer, 2013, pp. 625–36, doi:<a href=\"https://doi.org/10.1007/978-3-642-39206-1_53\">10.1007/978-3-642-39206-1_53</a>.","apa":"Kolmogorov, V. (2013). The power of linear programming for finite-valued CSPs: A constructive characterization (Vol. 7965, pp. 625–636). Presented at the ICALP: Automata, Languages and Programming, Riga, Latvia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39206-1_53\">https://doi.org/10.1007/978-3-642-39206-1_53</a>","short":"V. Kolmogorov, in:, Springer, 2013, pp. 625–636.","ieee":"V. Kolmogorov, “The power of linear programming for finite-valued CSPs: A constructive characterization,” presented at the ICALP: Automata, Languages and Programming, Riga, Latvia, 2013, vol. 7965, no. 1, pp. 625–636.","chicago":"Kolmogorov, Vladimir. “The Power of Linear Programming for Finite-Valued CSPs: A Constructive Characterization,” 7965:625–36. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39206-1_53\">https://doi.org/10.1007/978-3-642-39206-1_53</a>.","ama":"Kolmogorov V. The power of linear programming for finite-valued CSPs: A constructive characterization. In: Vol 7965. Springer; 2013:625-636. doi:<a href=\"https://doi.org/10.1007/978-3-642-39206-1_53\">10.1007/978-3-642-39206-1_53</a>","ista":"Kolmogorov V. 2013. The power of linear programming for finite-valued CSPs: A constructive characterization. ICALP: Automata, Languages and Programming, LNCS, vol. 7965, 625–636."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2013","_id":"2518","intvolume":"      7965","publist_id":"4383","arxiv":1,"conference":{"location":"Riga, Latvia","start_date":"2013-07-08","end_date":"2013-07-12","name":"ICALP: Automata, Languages and Programming"},"language":[{"iso":"eng"}],"corr_author":"1","title":"The power of linear programming for finite-valued CSPs: A constructive characterization","alternative_title":["LNCS"],"date_created":"2018-12-11T11:58:08Z","status":"public","page":"625 - 636","author":[{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir"}],"department":[{"_id":"VlKo"}],"publication_status":"published","oa":1,"related_material":{"record":[{"id":"2271","status":"public","relation":"later_version"}]},"date_published":"2013-07-01T00:00:00Z","abstract":[{"text":"A class of valued constraint satisfaction problems (VCSPs) is characterised by a valued constraint language, a fixed set of cost functions on a finite domain. An instance of the problem is specified by a sum of cost functions from the language with the goal to minimise the sum. We study which classes of finite-valued languages can be solved exactly by the basic linear programming relaxation (BLP). Thapper and Živný showed [20] that if BLP solves the language then the language admits a binary commutative fractional polymorphism. We prove that the converse is also true. This leads to a necessary and a sufficient condition which can be checked in polynomial time for a given language. In contrast, the previous necessary and sufficient condition due to [20] involved infinitely many inequalities. More recently, Thapper and Živný [21] showed (using, in particular, a technique introduced in this paper) that core languages that do not satisfy our condition are NP-hard. Taken together, these results imply that a finite-valued language can either be solved using Linear Programming or is NP-hard.","lang":"eng"}],"type":"conference","publisher":"Springer","scopus_import":1,"external_id":{"arxiv":["1207.7213"]},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1207.7213"}]},{"pubrep_id":"137","month":"07","has_accepted_license":"1","quality_controlled":"1","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Quadrianto, Novi, Viktoriia Sharmanska, David Knowles, and Zoubin Ghahramani. “The Supervised IBP: Neighbourhood Preserving Infinite Latent Feature Models.” In <i>Proceedings of the 29th Conference Uncertainty in Artificial Intelligence</i>, 527–36. AUAI Press, 2013.","ieee":"N. Quadrianto, V. Sharmanska, D. Knowles, and Z. Ghahramani, “The supervised IBP: Neighbourhood preserving infinite latent feature models,” in <i>Proceedings of the 29th conference uncertainty in Artificial Intelligence</i>, Bellevue, WA, United States, 2013, pp. 527–536.","ama":"Quadrianto N, Sharmanska V, Knowles D, Ghahramani Z. The supervised IBP: Neighbourhood preserving infinite latent feature models. In: <i>Proceedings of the 29th Conference Uncertainty in Artificial Intelligence</i>. AUAI Press; 2013:527-536.","ista":"Quadrianto N, Sharmanska V, Knowles D, Ghahramani Z. 2013. The supervised IBP: Neighbourhood preserving infinite latent feature models. Proceedings of the 29th conference uncertainty in Artificial Intelligence. UAI: Uncertainty in Artificial Intelligence, 527–536.","short":"N. Quadrianto, V. Sharmanska, D. Knowles, Z. Ghahramani, in:, Proceedings of the 29th Conference Uncertainty in Artificial Intelligence, AUAI Press, 2013, pp. 527–536.","apa":"Quadrianto, N., Sharmanska, V., Knowles, D., &#38; Ghahramani, Z. (2013). The supervised IBP: Neighbourhood preserving infinite latent feature models. In <i>Proceedings of the 29th conference uncertainty in Artificial Intelligence</i> (pp. 527–536). Bellevue, WA, United States: AUAI Press.","mla":"Quadrianto, Novi, et al. “The Supervised IBP: Neighbourhood Preserving Infinite Latent Feature Models.” <i>Proceedings of the 29th Conference Uncertainty in Artificial Intelligence</i>, AUAI Press, 2013, pp. 527–36."},"day":"11","date_updated":"2023-02-23T10:46:36Z","publist_id":"4381","_id":"2520","year":"2013","language":[{"iso":"eng"}],"conference":{"location":"Bellevue, WA, United States","name":"UAI: Uncertainty in Artificial Intelligence","end_date":"2013-07-15","start_date":"2013-07-11"},"page":"527 - 536","status":"public","date_created":"2018-12-11T11:58:09Z","publication":"Proceedings of the 29th conference uncertainty in Artificial Intelligence","title":"The supervised IBP: Neighbourhood preserving infinite latent feature models","publisher":"AUAI Press","scopus_import":1,"abstract":[{"lang":"eng","text":"We propose a probabilistic model to infer supervised latent variables in\r\nthe Hamming space from observed data. Our model allows simultaneous\r\ninference of the number of binary latent variables, and their values. The\r\nlatent variables preserve neighbourhood structure of the data in a sense\r\nthat objects in the same semantic concept have similar latent values, and\r\nobjects in different concepts have dissimilar latent values. We formulate\r\nthe supervised infinite latent variable problem based on an intuitive\r\nprinciple of pulling objects together if they are of the same type, and\r\npushing them apart if they are not. We then combine this principle with a\r\nflexible Indian Buffet Process prior on the latent variables. We show that\r\nthe inferred supervised latent variables can be directly used to perform a\r\nnearest neighbour search for the purpose of retrieval.  We introduce a new\r\napplication of dynamically extending hash codes, and show how to\r\neffectively couple the structure of the hash codes with continuously\r\ngrowing structure of the neighbourhood preserving infinite latent feature\r\nspace."}],"date_published":"2013-07-11T00:00:00Z","type":"conference","ddc":["000"],"file_date_updated":"2020-07-14T12:45:42Z","oa":1,"publication_identifier":{"isbn":["9780974903996"]},"publication_status":"published","department":[{"_id":"ChLa"}],"author":[{"first_name":"Novi","full_name":"Quadrianto, Novi","last_name":"Quadrianto"},{"id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","first_name":"Viktoriia","last_name":"Sharmanska","orcid":"0000-0003-0192-9308","full_name":"Sharmanska, Viktoriia"},{"full_name":"Knowles, David","last_name":"Knowles","first_name":"David"},{"full_name":"Ghahramani, Zoubin","last_name":"Ghahramani","first_name":"Zoubin"}],"file":[{"checksum":"325f20c4b926bd74d39006b97df572bd","content_type":"application/pdf","creator":"system","date_updated":"2020-07-14T12:45:42Z","relation":"main_file","date_created":"2018-12-12T10:15:16Z","file_id":"5134","file_name":"IST-2013-137-v1+1_QuaShaKnoGha13.pdf","access_level":"open_access","file_size":1117100}]},{"publisher":"Unknown","citation":{"short":"T.D. Browning, Mathematika 60 (2013) 101–107.","ama":"Browning TD. Counting rational points on cubic hypersurfaces: Corrigendum. <i>Mathematika</i>. 2013;60(1):101-107. doi:<a href=\"https://doi.org/10.1112/S0025579313000132\">10.1112/S0025579313000132</a>","ieee":"T. D. Browning, “Counting rational points on cubic hypersurfaces: Corrigendum,” <i>Mathematika</i>, vol. 60, no. 1. Unknown, pp. 101–107, 2013.","ista":"Browning TD. 2013. Counting rational points on cubic hypersurfaces: Corrigendum. Mathematika. 60(1), 101–107.","chicago":"Browning, Timothy D. “Counting Rational Points on Cubic Hypersurfaces: Corrigendum.” <i>Mathematika</i>. Unknown, 2013. <a href=\"https://doi.org/10.1112/S0025579313000132\">https://doi.org/10.1112/S0025579313000132</a>.","mla":"Browning, Timothy D. “Counting Rational Points on Cubic Hypersurfaces: Corrigendum.” <i>Mathematika</i>, vol. 60, no. 1, Unknown, 2013, pp. 101–07, doi:<a href=\"https://doi.org/10.1112/S0025579313000132\">10.1112/S0025579313000132</a>.","apa":"Browning, T. D. (2013). Counting rational points on cubic hypersurfaces: Corrigendum. <i>Mathematika</i>. Unknown. <a href=\"https://doi.org/10.1112/S0025579313000132\">https://doi.org/10.1112/S0025579313000132</a>"},"extern":1,"type":"journal_article","date_published":"2013-09-06T00:00:00Z","date_updated":"2021-01-12T06:58:03Z","day":"06","author":[{"first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","orcid":"0000-0002-8314-0177","full_name":"Timothy Browning"}],"publication_status":"published","_id":"253","publist_id":"7649","intvolume":"        60","year":"2013","month":"09","volume":60,"status":"public","date_created":"2018-12-11T11:45:27Z","issue":"1","page":"101 - 107","title":"Counting rational points on cubic hypersurfaces: Corrigendum","doi":"10.1112/S0025579313000132","publication":"Mathematika","quality_controlled":0},{"doi":"10.1242/dev.092726","title":"The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling","quality_controlled":0,"publication":"Development","status":"public","date_created":"2018-12-11T11:53:41Z","issue":"8","page":"1740 - 1750","month":"04","volume":140,"acknowledgement":"This study was supported by grants from the Israel Science Foundation (ISF) [11/09 to C.K.]; the Association Francaise contre les Myopathies (AFM) [15642 to C.K.]; the German Research Foundation (DFG) [UN 34/27-1 to C.K.]; the UK Medical Research Council (MRC) [U117560541 to J.B. and A.K.]; Fondation Pour la Recherche Médicale (FRM) (post-doctoral fellowship to V.R.). Deposited in PMC for release after 6 months","year":"2013","_id":"1726","publist_id":"5402","intvolume":"       140","day":"18","date_updated":"2021-01-12T06:52:47Z","author":[{"first_name":"Nitza","full_name":"Kahane, Nitza","last_name":"Kahane"},{"first_name":"Vanessa","full_name":"Ribes, Vanessa","last_name":"Ribes"},{"full_name":"Anna Kicheva","last_name":"Kicheva","orcid":"0000-0003-4509-4998","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Briscoe, James","last_name":"Briscoe","first_name":"James"},{"last_name":"Kalcheim","full_name":"Kalcheim, Chaya","first_name":"Chaya"}],"publication_status":"published","extern":1,"publisher":"Company of Biologists","citation":{"ama":"Kahane N, Ribes V, Kicheva A, Briscoe J, Kalcheim C. The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling. <i>Development</i>. 2013;140(8):1740-1750. doi:<a href=\"https://doi.org/10.1242/dev.092726\">10.1242/dev.092726</a>","ieee":"N. Kahane, V. Ribes, A. Kicheva, J. Briscoe, and C. Kalcheim, “The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling,” <i>Development</i>, vol. 140, no. 8. Company of Biologists, pp. 1740–1750, 2013.","ista":"Kahane N, Ribes V, Kicheva A, Briscoe J, Kalcheim C. 2013. The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling. Development. 140(8), 1740–1750.","chicago":"Kahane, Nitza, Vanessa Ribes, Anna Kicheva, James Briscoe, and Chaya Kalcheim. “The Transition from Differentiation to Growth during Dermomyotome-Derived Myogenesis Depends on Temporally Restricted Hedgehog Signaling.” <i>Development</i>. Company of Biologists, 2013. <a href=\"https://doi.org/10.1242/dev.092726\">https://doi.org/10.1242/dev.092726</a>.","short":"N. Kahane, V. Ribes, A. Kicheva, J. Briscoe, C. Kalcheim, Development 140 (2013) 1740–1750.","apa":"Kahane, N., Ribes, V., Kicheva, A., Briscoe, J., &#38; Kalcheim, C. (2013). The transition from differentiation to growth during dermomyotome-derived myogenesis depends on temporally restricted hedgehog signaling. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.092726\">https://doi.org/10.1242/dev.092726</a>","mla":"Kahane, Nitza, et al. “The Transition from Differentiation to Growth during Dermomyotome-Derived Myogenesis Depends on Temporally Restricted Hedgehog Signaling.” <i>Development</i>, vol. 140, no. 8, Company of Biologists, 2013, pp. 1740–50, doi:<a href=\"https://doi.org/10.1242/dev.092726\">10.1242/dev.092726</a>."},"abstract":[{"text":"The development of a functional tissue requires coordination of the amplification of progenitors and their differentiation into specific cell types. The molecular basis for this coordination during myotome ontogeny is not well understood. Dermomytome progenitors that colonize the myotome first acquire myocyte identity and subsequently proliferate as Pax7-expressing progenitors before undergoing terminal differentiation. We show that the dynamics of sonic hedgehog (Shh) signaling is crucial for this transition in both avian and mouse embryos. Initially, Shh ligand emanating from notochord/floor plate reaches the dermomyotome, where it both maintains the proliferation of dermomyotome cells and promotes myogenic differentiation of progenitors that colonized the myotome. Interfering with Shh signaling at this stage produces small myotomes and accumulation of Pax7-expressing progenitors. An in vivo reporter of Shh activity combined with mouse genetics revealed the existence of both activator and repressor Shh activities operating on distinct subsets of cells during the epaxial myotomal maturation. In contrast to observations in mice, in avians Shh promotes the differentiation of both epaxial and hypaxial myotome domains. Subsequently, myogenic progenitors become refractory to Shh; this is likely to occur at the level of, or upstream of, smoothened signaling. The end of responsiveness to Shh coincides with, and is thus likely to enable, the transition into the growth phase of the myotome.","lang":"eng"}],"date_published":"2013-04-18T00:00:00Z","type":"journal_article"},{"intvolume":"         8","publist_id":"5401","_id":"1727","year":"2013","type":"journal_article","abstract":[{"lang":"eng","text":"Cells at different positions in a developing tissue receive different concentrations of signaling molecules, called morphogens, and this influences their cell fate. Morphogen concentration gradients have been proposed to control patterning as well as growth in many developing tissues. Some outstanding questions about tissue patterning by morphogen gradients are the following: What are the mechanisms that regulate gradient formation and shape? Is the positional information encoded in the gradient sufficiently precise to determine the positions of target gene domain boundaries? What are the temporal dynamics of gradients and how do they relate to patterning and growth? These questions are inherently quantitative in nature and addressing them requires measuring morphogen concentrations in cells, levels of downstream signaling activity, and kinetics of morphogen transport. Here we first present methods for quantifying morphogen gradient shape in which the measurements can be calibrated to reflect actual morphogen concentrations. We then discuss using fluorescence recovery after photobleaching to study the kinetics of morphogen transport at the tissue level. Finally, we present particle tracking as a method to study morphogen intracellular trafficking."}],"date_published":"2013-05-01T00:00:00Z","publisher":"Cold Spring Harbor Laboratory Press","citation":{"mla":"Kicheva, Anna, et al. “Quantitative Imaging of Morphogen Gradients in Drosophila Imaginal Discs.” <i>Cold Spring Harbor Protocols</i>, vol. 8, no. 5, Cold Spring Harbor Laboratory Press, 2013, pp. 387–403, doi:<a href=\"https://doi.org/10.1101/pdb.top074237\">10.1101/pdb.top074237</a>.","apa":"Kicheva, A., Holtzer, L., Wartlick, O., Schmidt, T., &#38; González Gaitán, M. (2013). Quantitative imaging of morphogen gradients in drosophila imaginal discs. <i>Cold Spring Harbor Protocols</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/pdb.top074237\">https://doi.org/10.1101/pdb.top074237</a>","short":"A. Kicheva, L. Holtzer, O. Wartlick, T. Schmidt, M. González Gaitán, Cold Spring Harbor Protocols 8 (2013) 387–403.","ama":"Kicheva A, Holtzer L, Wartlick O, Schmidt T, González Gaitán M. Quantitative imaging of morphogen gradients in drosophila imaginal discs. <i>Cold Spring Harbor Protocols</i>. 2013;8(5):387-403. doi:<a href=\"https://doi.org/10.1101/pdb.top074237\">10.1101/pdb.top074237</a>","chicago":"Kicheva, Anna, Laurent Holtzer, Ortrud Wartlick, Thomas Schmidt, and Marcos González Gaitán. “Quantitative Imaging of Morphogen Gradients in Drosophila Imaginal Discs.” <i>Cold Spring Harbor Protocols</i>. Cold Spring Harbor Laboratory Press, 2013. <a href=\"https://doi.org/10.1101/pdb.top074237\">https://doi.org/10.1101/pdb.top074237</a>.","ista":"Kicheva A, Holtzer L, Wartlick O, Schmidt T, González Gaitán M. 2013. Quantitative imaging of morphogen gradients in drosophila imaginal discs. Cold Spring Harbor Protocols. 8(5), 387–403.","ieee":"A. Kicheva, L. Holtzer, O. Wartlick, T. Schmidt, and M. González Gaitán, “Quantitative imaging of morphogen gradients in drosophila imaginal discs,” <i>Cold Spring Harbor Protocols</i>, vol. 8, no. 5. Cold Spring Harbor Laboratory Press, pp. 387–403, 2013."},"extern":1,"publication_status":"published","author":[{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","orcid":"0000-0003-4509-4998","last_name":"Kicheva","full_name":"Anna Kicheva"},{"last_name":"Holtzer","full_name":"Holtzer, Laurent","first_name":"Laurent"},{"full_name":"Wartlick, Ortrud","last_name":"Wartlick","first_name":"Ortrud"},{"last_name":"Schmidt","full_name":"Schmidt, Thomas S","first_name":"Thomas"},{"full_name":"González-Gaitán, Marcos A","last_name":"González Gaitán","first_name":"Marcos"}],"day":"01","date_updated":"2021-01-12T06:52:47Z","page":"387 - 403","issue":"5","date_created":"2018-12-11T11:53:41Z","status":"public","quality_controlled":0,"publication":"Cold Spring Harbor Protocols","doi":"10.1101/pdb.top074237","title":"Quantitative imaging of morphogen gradients in drosophila imaginal discs","volume":8,"month":"05"}]