[{"status":"public","date_published":"2013-02-01T00:00:00Z","publist_id":"4451","day":"01","volume":13,"year":"2013","issue":"1","date_updated":"2021-01-12T06:57:34Z","title":"Single-cell-based system to monitor carrier driven cellular auxin homeostasis","extern":1,"citation":{"ieee":"E. Barbez <i>et al.</i>, “Single-cell-based system to monitor carrier driven cellular auxin homeostasis,” <i>BMC Plant Biology</i>, vol. 13, no. 1. BioMed Central, 2013.","apa":"Barbez, E., Laňková, M., Pařezová, M., Maizel, A., Zažímalová, E., Petrášek, J., … Kleine Vehn, J. (2013). Single-cell-based system to monitor carrier driven cellular auxin homeostasis. <i>BMC Plant Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2229-13-20\">https://doi.org/10.1186/1471-2229-13-20</a>","chicago":"Barbez, Elke, Martina Laňková, Markéta Pařezová, Alexis Maizel, Eva Zažímalová, Jan Petrášek, Jiří Friml, and Jürgen Kleine Vehn. “Single-Cell-Based System to Monitor Carrier Driven Cellular Auxin Homeostasis.” <i>BMC Plant Biology</i>. BioMed Central, 2013. <a href=\"https://doi.org/10.1186/1471-2229-13-20\">https://doi.org/10.1186/1471-2229-13-20</a>.","ama":"Barbez E, Laňková M, Pařezová M, et al. Single-cell-based system to monitor carrier driven cellular auxin homeostasis. <i>BMC Plant Biology</i>. 2013;13(1). doi:<a href=\"https://doi.org/10.1186/1471-2229-13-20\">10.1186/1471-2229-13-20</a>","short":"E. Barbez, M. Laňková, M. Pařezová, A. Maizel, E. Zažímalová, J. Petrášek, J. Friml, J. Kleine Vehn, BMC Plant Biology 13 (2013).","mla":"Barbez, Elke, et al. “Single-Cell-Based System to Monitor Carrier Driven Cellular Auxin Homeostasis.” <i>BMC Plant Biology</i>, vol. 13, no. 1, BioMed Central, 2013, doi:<a href=\"https://doi.org/10.1186/1471-2229-13-20\">10.1186/1471-2229-13-20</a>.","ista":"Barbez E, Laňková M, Pařezová M, Maizel A, Zažímalová E, Petrášek J, Friml J, Kleine Vehn J. 2013. Single-cell-based system to monitor carrier driven cellular auxin homeostasis. BMC Plant Biology. 13(1)."},"doi":"10.1186/1471-2229-13-20","type":"journal_article","intvolume":"        13","publication_status":"published","_id":"2452","publication":"BMC Plant Biology","month":"02","date_created":"2018-12-11T11:57:45Z","publisher":"BioMed Central","quality_controlled":0,"author":[{"last_name":"Barbez","first_name":"Elke","full_name":"Barbez, Elke"},{"first_name":"Martina","full_name":"Laňková, Martina","last_name":"Laňková"},{"last_name":"Pařezová","full_name":"Pařezová, Markéta","first_name":"Markéta"},{"last_name":"Maizel","first_name":"Alexis","full_name":"Maizel, Alexis"},{"last_name":"Zažímalová","first_name":"Eva","full_name":"Zažímalová, Eva"},{"last_name":"Petrášek","first_name":"Jan","full_name":"Petrášek, Jan"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Jirí Friml"},{"last_name":"Kleine Vehn","full_name":"Kleine-Vehn, Jürgen","first_name":"Jürgen"}],"abstract":[{"text":"Background: Abundance and distribution of the plant hormone auxin play important roles in plant development. Besides other metabolic processes, various auxin carriers control the cellular level of active auxin and, hence, are major regulators of cellular auxin homeostasis. Despite the developmental importance of auxin transporters, a simple medium-to-high throughput approach to assess carrier activities is still missing. Here we show that carrier driven depletion of cellular auxin correlates with reduced nuclear auxin signaling in tobacco Bright Yellow-2 (BY-2) cell cultures.Results: We developed an easy to use transient single-cell-based system to detect carrier activity. We use the relative changes in signaling output of the auxin responsive promoter element DR5 to indirectly visualize auxin carrier activity. The feasibility of the transient approach was demonstrated by pharmacological and genetic interference with auxin signaling and transport. As a proof of concept, we provide visual evidence that the prominent auxin transport proteins PIN-FORMED (PIN)2 and PIN5 regulate cellular auxin homeostasis at the plasma membrane and endoplasmic reticulum (ER), respectively. Our data suggest that PIN2 and PIN5 have different sensitivities to the auxin transport inhibitor 1-naphthylphthalamic acid (NPA). Also the putative PIN-LIKES (PILS) auxin carrier activity at the ER is insensitive to NPA in our system, indicating that NPA blocks intercellular, but not intracellular auxin transport.Conclusions: This single-cell-based system is a useful tool by which the activity of putative auxin carriers, such as PINs, PILS and WALLS ARE THIN1 (WAT1), can be indirectly visualized in a medium-to-high throughput manner. Moreover, our single cell system might be useful to investigate also other hormonal signaling pathways, such as cytokinin.","lang":"eng"}]},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2013-01-01T00:00:00Z","day":"01","year":"2013","volume":18,"publist_id":"4446","doi":"10.1016/j.tplants.2012.08.009","oa_version":"None","extern":"1","citation":{"ama":"Viaene T, Delwiche C, Rensing S, Friml J. Origin and evolution of PIN auxin transporters in the green lineage. <i>Trends in Plant Science</i>. 2013;18(1):5-10. doi:<a href=\"https://doi.org/10.1016/j.tplants.2012.08.009\">10.1016/j.tplants.2012.08.009</a>","chicago":"Viaene, Tom, Charles Delwiche, Stefan Rensing, and Jiří Friml. “Origin and Evolution of PIN Auxin Transporters in the Green Lineage.” <i>Trends in Plant Science</i>. Cell Press, 2013. <a href=\"https://doi.org/10.1016/j.tplants.2012.08.009\">https://doi.org/10.1016/j.tplants.2012.08.009</a>.","ieee":"T. Viaene, C. Delwiche, S. Rensing, and J. Friml, “Origin and evolution of PIN auxin transporters in the green lineage,” <i>Trends in Plant Science</i>, vol. 18, no. 1. Cell Press, pp. 5–10, 2013.","apa":"Viaene, T., Delwiche, C., Rensing, S., &#38; Friml, J. (2013). Origin and evolution of PIN auxin transporters in the green lineage. <i>Trends in Plant Science</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.tplants.2012.08.009\">https://doi.org/10.1016/j.tplants.2012.08.009</a>","mla":"Viaene, Tom, et al. “Origin and Evolution of PIN Auxin Transporters in the Green Lineage.” <i>Trends in Plant Science</i>, vol. 18, no. 1, Cell Press, 2013, pp. 5–10, doi:<a href=\"https://doi.org/10.1016/j.tplants.2012.08.009\">10.1016/j.tplants.2012.08.009</a>.","ista":"Viaene T, Delwiche C, Rensing S, Friml J. 2013. Origin and evolution of PIN auxin transporters in the green lineage. Trends in Plant Science. 18(1), 5–10.","short":"T. Viaene, C. Delwiche, S. Rensing, J. Friml, Trends in Plant Science 18 (2013) 5–10."},"publication_status":"published","_id":"2457","intvolume":"        18","type":"journal_article","language":[{"iso":"eng"}],"date_updated":"2021-01-12T06:57:36Z","issue":"1","title":"Origin and evolution of PIN auxin transporters in the green lineage","page":"5 - 10","author":[{"first_name":"Tom","full_name":"Viaene, Tom","last_name":"Viaene"},{"first_name":"Charles","full_name":"Delwiche, Charles","last_name":"Delwiche"},{"full_name":"Rensing, Stefan","first_name":"Stefan","last_name":"Rensing"},{"full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596"}],"quality_controlled":"1","publisher":"Cell Press","publication":"Trends in Plant Science","month":"01","date_created":"2018-12-11T11:57:46Z"},{"day":"01","volume":149,"year":"2013","publist_id":"7658","acknowledgement":"EP/E053262/1\tEngineering and Physical Sciences Research Council","status":"public","date_published":"2013-09-01T00:00:00Z","quality_controlled":0,"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)."}],"author":[{"full_name":"Timothy Browning","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","last_name":"Browning"},{"last_name":"Munshi","full_name":"Munshi, Ritabrata","first_name":"Ritabrata"}],"month":"09","publication":"Compositio Mathematica","date_created":"2018-12-11T11:45:25Z","publisher":"Cambridge University Press","extern":1,"citation":{"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>.","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>","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>","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."},"doi":"10.1112/S0010437X13007185","type":"journal_article","intvolume":"       149","_id":"246","publication_status":"published","issue":"9","date_updated":"2021-01-12T06:57:37Z","title":"Rational points on singular intersections of quadrics","page":"1457 - 1494"},{"ddc":["000"],"publisher":"ACM","quality_controlled":"1","author":[{"first_name":"Ryoichi","full_name":"Ando, Ryoichi","last_name":"Ando"},{"full_name":"Thuerey, Nils","first_name":"Nils","last_name":"Thuerey"},{"first_name":"Christopher J","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"ChWo"}],"title":"Highly adaptive liquid simulations on tetrahedral meshes","article_processing_charge":"No","has_accepted_license":"1","issue":"4","date_updated":"2025-09-29T14:13:52Z","type":"journal_article","publication_status":"published","file":[{"date_updated":"2020-07-14T12:45:41Z","access_level":"open_access","checksum":"aeea6b0ff2b27c695aeb8408c7d2fc50","file_size":8601561,"date_created":"2018-12-12T10:17:25Z","file_id":"5279","relation":"main_file","content_type":"application/pdf","creator":"system","file_name":"IST-2016-605-v1+1_tetflip_fixed.pdf"}],"isi":1,"volume":32,"year":"2013","day":"01","external_id":{"isi":["000321840100072"]},"file_date_updated":"2020-07-14T12:45:41Z","month":"07","publication":"ACM Transactions on Graphics","date_created":"2018-12-11T11:57:50Z","oa":1,"abstract":[{"lang":"eng","text":"We introduce a new method for efficiently simulating liquid with extreme amounts of spatial adaptivity. Our method combines several key components to drastically speed up the simulation of large-scale fluid phenomena: We leverage an alternative Eulerian tetrahedral mesh discretization to significantly reduce the complexity of the pressure solve while increasing the robustness with respect to element quality and removing the possibility of locking. Next, we enable subtle free-surface phenomena by deriving novel second-order boundary conditions consistent with our discretization. We couple this discretization with a spatially adaptive Fluid-Implicit Particle (FLIP) method, enabling efficient, robust, minimally-dissipative simulations that can undergo sharp changes in spatial resolution while minimizing artifacts. Along the way, we provide a new method for generating a smooth and detailed surface from a set of particles with variable sizes. Finally, we explore several new sizing functions for determining spatially adaptive simulation resolutions, and we show how to couple them to our simulator. We combine each of these elements to produce a simulation algorithm that is capable of creating animations at high maximum resolutions while avoiding common pitfalls like inaccurate boundary conditions and inefficient computation."}],"scopus_import":"1","language":[{"iso":"eng"}],"intvolume":"        32","_id":"2466","citation":{"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>.","ista":"Ando R, Thuerey N, Wojtan C. 2013. Highly adaptive liquid simulations on tetrahedral meshes. ACM Transactions on Graphics. 32(4), 103.","short":"R. Ando, N. Thuerey, C. Wojtan, ACM Transactions on Graphics 32 (2013).","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>","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>","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>.","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."},"doi":"10.1145/2461912.2461982","oa_version":"Submitted Version","publist_id":"4436","pubrep_id":"605","article_number":"103","date_published":"2013-07-01T00:00:00Z","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"scopus_import":"1","abstract":[{"lang":"eng","text":"This paper presents a method for computing topology changes for triangle meshes in an interactive geometric modeling environment. Most triangle meshes in practice do not exhibit desirable geometric properties, so we develop a solution that is independent of standard assumptions and robust to geometric errors. Specifically, we provide the first method for topology change applicable to arbitrary non-solid, non-manifold, non-closed, self-intersecting surfaces. We prove that this new method for topology change produces the expected conventional results when applied to solid (closed, manifold, non-self-intersecting) surfaces---that is, we prove a backwards-compatibility property relative to prior work. Beyond solid surfaces, we present empirical evidence that our method remains tolerant to a variety of surface aberrations through the incorporation of a novel error correction scheme. Finally, we demonstrate how topology change applied to non-solid objects enables wholly new and useful behaviors."}],"month":"07","date_created":"2018-12-11T11:57:50Z","publication":"ACM Transactions on Graphics","oa":1,"intvolume":"        32","_id":"2467","citation":{"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.","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>","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>","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>.","ista":"Bernstein G, Wojtan C. 2013. Putting holes in holey geometry: Topology change for arbitrary surfaces. ACM Transactions on Graphics. 32(4), 34.","short":"G. Bernstein, C. Wojtan, ACM Transactions on Graphics 32 (2013)."},"oa_version":"Submitted Version","doi":"10.1145/2461912.2462027","language":[{"iso":"eng"}],"pubrep_id":"604","publist_id":"4435","date_published":"2013-07-01T00:00:00Z","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"34","quality_controlled":"1","author":[{"last_name":"Bernstein","first_name":"Gilbert","full_name":"Bernstein, Gilbert"},{"orcid":"0000-0001-6646-5546","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","full_name":"Wojtan, Christopher J"}],"ddc":["000"],"publisher":"ACM","type":"journal_article","publication_status":"published","file":[{"access_level":"open_access","checksum":"9c8425d62246996ca632c5a01870515b","date_updated":"2020-07-14T12:45:41Z","relation":"main_file","content_type":"application/pdf","creator":"system","file_name":"IST-2016-604-v1+1_toptop2013.pdf","file_size":3514674,"date_created":"2018-12-12T10:09:43Z","file_id":"4768"}],"title":"Putting holes in holey geometry: Topology change for arbitrary surfaces","department":[{"_id":"ChWo"}],"article_processing_charge":"No","issue":"4","has_accepted_license":"1","date_updated":"2025-09-29T14:13:25Z","volume":32,"year":"2013","day":"01","isi":1,"file_date_updated":"2020-07-14T12:45:41Z","external_id":{"isi":["000321840100003"]}},{"citation":{"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>","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>.","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.","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).","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>.","ista":"Bojsen-Hansen M, Wojtan C. 2013. Liquid surface tracking with error compensation. ACM Transactions on Graphics. 32(4), 68."},"oa_version":"Submitted Version","doi":"10.1145/2461912.2461991","intvolume":"        32","_id":"2468","corr_author":"1","language":[{"iso":"eng"}],"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"}],"scopus_import":"1","oa":1,"publication":"ACM Transactions on Graphics","date_created":"2018-12-11T11:57:50Z","month":"07","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2013-07-01T00:00:00Z","article_number":"68","pubrep_id":"603","publist_id":"4434","file":[{"file_name":"IST-2016-603-v1+1_liquidError_web.pdf","content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4761","date_created":"2018-12-12T10:09:37Z","file_size":5813685,"checksum":"53d905e0180e23ef3e813b969ffed4e1","access_level":"open_access","date_updated":"2020-07-14T12:45:41Z"}],"type":"journal_article","publication_status":"published","has_accepted_license":"1","issue":"4","date_updated":"2025-09-29T14:12:53Z","title":"Liquid surface tracking with error compensation","department":[{"_id":"ChWo"}],"article_processing_charge":"No","quality_controlled":"1","author":[{"id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","last_name":"Bojsen-Hansen","orcid":"0000-0002-4417-3224","full_name":"Bojsen-Hansen, Morten","first_name":"Morten"},{"last_name":"Wojtan","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","full_name":"Wojtan, Christopher J"}],"publisher":"ACM","ddc":["000"],"file_date_updated":"2020-07-14T12:45:41Z","external_id":{"isi":["000321840100037"]},"day":"01","volume":32,"year":"2013","isi":1},{"year":"2013","volume":23,"day":"22","isi":1,"file_date_updated":"2020-07-14T12:45:41Z","external_id":{"pmid":["23885883"],"isi":["000322414200018"]},"author":[{"full_name":"Maître, Jean-Léon","first_name":"Jean-Léon","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","last_name":"Maître","orcid":"0000-0002-3688-1474"},{"first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","ddc":["570"],"publisher":"Cell Press","publication_status":"published","type":"journal_article","file":[{"content_type":"application/pdf","creator":"dernst","file_name":"2013_CurrentBiology_Maitre.pdf","relation":"main_file","date_created":"2019-01-24T15:40:22Z","file_id":"5881","file_size":247320,"checksum":"6a424b2f007b41d4955a9135793b2162","access_level":"open_access","date_updated":"2020-07-14T12:45:41Z"}],"article_processing_charge":"No","department":[{"_id":"CaHe"}],"title":"Three functions of cadherins in cell adhesion","date_updated":"2025-09-29T14:12:25Z","issue":"14","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publist_id":"4433","date_published":"2013-07-22T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","scopus_import":"1","abstract":[{"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.","lang":"eng"}],"pmid":1,"date_created":"2018-12-11T11:57:51Z","month":"07","publication":"Current Biology","oa":1,"corr_author":"1","_id":"2469","intvolume":"        23","doi":"10.1016/j.cub.2013.06.019","oa_version":"Published Version","citation":{"short":"J.-L. Maître, C.-P.J. Heisenberg, Current Biology 23 (2013) R626–R633.","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>.","ista":"Maître J-L, Heisenberg C-PJ. 2013. Three functions of cadherins in cell adhesion. Current Biology. 23(14), R626–R633.","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>","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>.","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>","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."},"page":"R626 - R633","language":[{"iso":"eng"}]},{"day":"31","volume":56,"year":"2013","publist_id":"7657","acknowledgement":"EP/E053262/1\tEngineering and Physical Sciences Research Council","status":"public","date_published":"2013-08-31T00:00:00Z","quality_controlled":0,"author":[{"full_name":"Timothy Browning","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","orcid":"0000-0002-8314-0177"}],"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":"Canadian Mathematical Bulletin","date_created":"2018-12-11T11:45:25Z","month":"08","publisher":"Unknown","extern":1,"citation":{"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>.","ista":"Browning TD. 2013. The Lang-Weil estimate for cubic hypersurfaces. Canadian Mathematical Bulletin. 56(3), 500–502.","short":"T.D. Browning, Canadian Mathematical Bulletin 56 (2013) 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>.","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.","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>","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>"},"doi":"10.4153/CMB-2011-177-4","type":"journal_article","intvolume":"        56","_id":"247","publication_status":"published","issue":"3","date_updated":"2021-01-12T06:57:40Z","title":"The Lang-Weil estimate for cubic hypersurfaces","page":"500 - 502"},{"article_number":"e70050","date_published":"2013-07-23T00:00:00Z","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"4432","pubrep_id":"413","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"intvolume":"         8","_id":"2470","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>.","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.","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>.","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>","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>"},"oa_version":"Published Version","doi":"10.1371/journal.pone.0070050","date_created":"2018-12-11T11:57:51Z","publication":"PLoS One","month":"07","oa":1,"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"}],"scopus_import":"1","external_id":{"isi":["000325211000181"]},"file_date_updated":"2020-07-14T12:45:41Z","isi":1,"volume":8,"year":"2013","day":"23","department":[{"_id":"JiFr"}],"title":"Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells","article_processing_charge":"No","issue":"7","has_accepted_license":"1","date_updated":"2025-09-29T14:11:54Z","type":"journal_article","publication_status":"published","file":[{"checksum":"2d47ef47616ef4de1d517d146548184e","access_level":"open_access","date_updated":"2020-07-14T12:45:41Z","file_name":"IST-2016-413-v1+1_journal.pone.0070050.pdf","creator":"system","content_type":"application/pdf","relation":"main_file","file_id":"4681","date_created":"2018-12-12T10:08:21Z","file_size":2294955}],"publisher":"Public Library of Science","ddc":["570"],"quality_controlled":"1","author":[{"last_name":"Čovanová","full_name":"Čovanová, Milada","first_name":"Milada"},{"first_name":"Michael","full_name":"Sauer, Michael","last_name":"Sauer"},{"last_name":"Rychtář","first_name":"Jan","full_name":"Rychtář, Jan"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí"},{"first_name":"Jan","full_name":"Petrášek, Jan","last_name":"Petrášek"},{"last_name":"Zažímalová","first_name":"Eva","full_name":"Zažímalová, Eva"}]},{"author":[{"id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","last_name":"Sanchez Romero","full_name":"Sanchez Romero, Inmaculada","first_name":"Inmaculada"},{"first_name":"Antonio","full_name":"Ariza, Antonio","last_name":"Ariza"},{"last_name":"Wilson","first_name":"Keith","full_name":"Wilson, Keith"},{"last_name":"Skjøt","first_name":"Michael","full_name":"Skjøt, Michael"},{"first_name":"Jesper","full_name":"Vind, Jesper","last_name":"Vind"},{"full_name":"De Maria, Leonardo","first_name":"Leonardo","last_name":"De Maria"},{"first_name":"Lars","full_name":"Skov, Lars","last_name":"Skov"},{"first_name":"Jose","full_name":"Sánchez Ruiz, Jose","last_name":"Sánchez Ruiz"}],"quality_controlled":"1","publisher":"Public Library of Science","ddc":["570"],"file":[{"access_level":"open_access","checksum":"c0c96cc76ed7ef0d036a31a7e33c9a37","date_updated":"2020-07-14T12:45:41Z","relation":"main_file","creator":"system","content_type":"application/pdf","file_name":"IST-2016-414-v1+1_journal.pone.0070013.pdf","file_size":1323666,"date_created":"2018-12-12T10:15:07Z","file_id":"5124"}],"publication_status":"published","type":"journal_article","date_updated":"2025-09-29T14:10:56Z","has_accepted_license":"1","issue":"7","article_processing_charge":"No","title":"Mechanism of protein kinetic stabilization by engineered disulfide crosslinks","department":[{"_id":"HaJa"}],"day":"30","year":"2013","volume":8,"isi":1,"file_date_updated":"2020-07-14T12:45:41Z","external_id":{"isi":["000323114200054"]},"scopus_import":"1","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."}],"oa":1,"date_created":"2018-12-11T11:57:51Z","publication":"PLoS One","month":"07","doi":"10.1371/journal.pone.0070013","oa_version":"Published Version","citation":{"ista":"Sanchez-Romero I, Ariza A, Wilson K, Skjøt M, Vind J, De Maria L, Skov L, Sánchez Ruiz J. 2013. Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. PLoS One. 8(7), e70013.","mla":"Sanchez-Romero, Inmaculada, et al. “Mechanism of Protein Kinetic Stabilization by Engineered Disulfide Crosslinks.” <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>.","short":"I. Sanchez-Romero, A. Ariza, K. Wilson, M. Skjøt, J. Vind, L. De Maria, L. Skov, J. Sánchez Ruiz, PLoS One 8 (2013).","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>","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.","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>","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>."},"_id":"2471","intvolume":"         8","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"pubrep_id":"414","publist_id":"4430","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","date_published":"2013-07-30T00:00:00Z","article_number":"e70013"},{"title":"Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"article_processing_charge":"No","has_accepted_license":"1","issue":"7","date_updated":"2025-09-29T14:11:25Z","type":"journal_article","publication_status":"published","file":[{"access_level":"open_access","checksum":"3be71828b6c2ba9c90eb7056e3f7f57a","date_updated":"2020-07-14T12:45:41Z","relation":"main_file","creator":"system","content_type":"application/pdf","file_name":"IST-2015-393-v1+1_journal.pone.0070069.pdf","file_size":9003465,"date_created":"2018-12-12T10:16:34Z","file_id":"5222"}],"ddc":["580","570"],"publisher":"Public Library of Science","quality_controlled":"1","author":[{"full_name":"Cazzonelli, Christopher","first_name":"Christopher","last_name":"Cazzonelli"},{"last_name":"Vanstraelen","full_name":"Vanstraelen, Marleen","first_name":"Marleen"},{"full_name":"Simon, Sibu","first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","last_name":"Simon","orcid":"0000-0002-1998-6741"},{"full_name":"Yin, Kuide","first_name":"Kuide","last_name":"Yin"},{"last_name":"Carron Arthur","first_name":"Ashley","full_name":"Carron Arthur, Ashley"},{"first_name":"Nazia","full_name":"Nisar, Nazia","last_name":"Nisar"},{"last_name":"Tarle","full_name":"Tarle, Gauri","first_name":"Gauri"},{"full_name":"Cuttriss, Abby","first_name":"Abby","last_name":"Cuttriss"},{"last_name":"Searle","full_name":"Searle, Iain","first_name":"Iain"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva"},{"first_name":"Ulrike","full_name":"Mathesius, Ulrike","last_name":"Mathesius"},{"first_name":"Josette","full_name":"Masle, Josette","last_name":"Masle"},{"full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"last_name":"Pogson","first_name":"Barry","full_name":"Pogson, Barry"}],"project":[{"_id":"253FCA6A-B435-11E9-9278-68D0E5697425","name":"Hormonal cross-talk in plant organogenesis","call_identifier":"FP7","grant_number":"207362"},{"call_identifier":"FP7","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000323369700128"]},"file_date_updated":"2020-07-14T12:45:41Z","isi":1,"volume":8,"year":"2013","day":"29","language":[{"iso":"eng"}],"intvolume":"         8","_id":"2472","citation":{"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).","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>.","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.","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>","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.","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>"},"doi":"10.1371/journal.pone.0070069","oa_version":"Published Version","month":"07","publication":"PLoS One","date_created":"2018-12-11T11:57:52Z","oa":1,"ec_funded":1,"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"}],"article_number":"e70069","date_published":"2013-07-29T00:00:00Z","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"4431","pubrep_id":"393","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"}},{"external_id":{"isi":["000322688800008"]},"project":[{"name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7"}],"file_date_updated":"2020-07-14T12:45:41Z","isi":1,"year":"2013","volume":87,"day":"03","article_processing_charge":"No","title":"Genetic hitch-hiking in spatially extended populations","department":[{"_id":"NiBa"}],"date_updated":"2025-09-29T14:10:28Z","has_accepted_license":"1","issue":"8","publication_status":"published","type":"journal_article","file":[{"file_size":1706282,"file_id":"5376","date_created":"2018-12-12T10:18:54Z","relation":"main_file","file_name":"IST-2013-118-v1+1_bartonetalRevision.pdf","creator":"system","content_type":"application/pdf","date_updated":"2020-07-14T12:45:41Z","access_level":"open_access","checksum":"4274ec1f433b838a7d5b941cc9684ca7"}],"publisher":"Elsevier","ddc":["570"],"author":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240"},{"last_name":"Etheridge","full_name":"Etheridge, Alison","first_name":"Alison"},{"last_name":"Kelleher","first_name":"Jerome","full_name":"Kelleher, Jerome"},{"last_name":"Véber","first_name":"Amandine","full_name":"Véber, Amandine"}],"quality_controlled":"1","date_published":"2013-01-03T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","publist_id":"4428","pubrep_id":"118","page":"75 - 89","language":[{"iso":"eng"}],"_id":"2473","corr_author":"1","intvolume":"        87","doi":"10.1016/j.tpb.2012.12.001","oa_version":"Submitted Version","citation":{"ista":"Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Genetic hitch-hiking in spatially extended populations. Theoretical Population Biology. 87(8), 75–89.","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>.","short":"N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population Biology 87 (2013) 75–89.","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>","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>.","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>"},"month":"01","date_created":"2018-12-11T11:57:52Z","publication":"Theoretical Population Biology","oa":1,"abstract":[{"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.","lang":"eng"}],"scopus_import":"1","ec_funded":1},{"publist_id":"4423","year":"2013","volume":110,"day":"08","date_published":"2013-01-08T00:00:00Z","status":"public","publisher":"National Academy of Sciences","month":"01","publication":"PNAS","date_created":"2018-12-11T11:57:54Z","author":[{"last_name":"Budreck","full_name":"Budreck, Elaine C","first_name":"Elaine"},{"last_name":"Kwon","full_name":"Kwon, Oh-Bin","first_name":"Oh"},{"full_name":"Jung, Jung-Hoon","first_name":"Jung","last_name":"Jung"},{"full_name":"Baudouin, Stéphane J","first_name":"Stéphane","last_name":"Baudouin"},{"last_name":"Thommen","full_name":"Thommen, Albert","first_name":"Albert"},{"last_name":"Kim","full_name":"Kim, Hye-Sun","first_name":"Hye"},{"full_name":"Fukazawa, Yugo","first_name":"Yugo","last_name":"Fukazawa"},{"last_name":"Harada","orcid":"0000-0001-7429-7896","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Harumi","full_name":"Harumi Harada"},{"full_name":"Tabuchi, Katsuhiko","first_name":"Katsuhiko","last_name":"Tabuchi"},{"first_name":"Ryuichi","full_name":"Ryuichi Shigemoto","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Scheiffele","first_name":"Peter","full_name":"Scheiffele, Peter"},{"last_name":"Kim","first_name":"Joung","full_name":"Kim, Joung-Hun"}],"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"}],"quality_controlled":0,"page":"725 - 730","title":"Neuroligin-1 controls synaptic abundance of NMDA-type glutamate receptors through extracellular coupling","date_updated":"2021-01-12T06:57:43Z","issue":"2","publication_status":"published","_id":"2478","intvolume":"       110","type":"journal_article","doi":"10.1073/pnas.1214718110","extern":1,"citation":{"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.","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>.","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>","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>","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.","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.","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>."}},{"status":"public","date_published":"2013-11-29T00:00:00Z","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.","publist_id":"7652","day":"29","year":"2013","volume":108,"date_updated":"2021-01-12T06:57:51Z","issue":"4","page":"1030 - 1078","title":"Density of Châtelet surfaces failing the Hasse principle","doi":"10.1112/plms/pdt060","extern":1,"citation":{"short":"R. De La Bretèche, T.D. Browning, Proceedings of the London Mathematical Society 108 (2013) 1030–1078.","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>.","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.","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>","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>"},"_id":"250","publication_status":"published","type":"journal_article","intvolume":"       108","oa":1,"publisher":"Oxford University Press","publication":"Proceedings of the London Mathematical Society","month":"11","date_created":"2018-12-11T11:45:26Z","abstract":[{"lang":"eng","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."}],"author":[{"last_name":"De La Bretèche","first_name":"Régis","full_name":"de la Bretèche, Régis"},{"first_name":"Timothy D","full_name":"Timothy Browning","last_name":"Browning","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":0,"main_file_link":[{"url":"https://arxiv.org/abs/1210.4010","open_access":"1"}]},{"status":"public","date_published":"2013-05-14T00:00:00Z","publist_id":"7651","day":"14","year":"2013","volume":26,"date_updated":"2021-01-12T06:57:55Z","issue":"1","title":"Counter examples to the Hasse principle among certain coflasque tori","page":"25 - 44","doi":"10.5802/jtnb.857","extern":1,"citation":{"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>.","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.","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>","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>","short":"R. De La Bretèche, T.D. Browning, Journal de Theorie Des Nombres de Bordeaux 26 (2013) 25–44.","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.","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>."},"_id":"251","publication_status":"published","intvolume":"        26","type":"journal_article","publisher":"Universite de Bordeaux I","publication":"Journal de Theorie des Nombres de Bordeaux","date_created":"2018-12-11T11:45:26Z","month":"05","author":[{"first_name":"Régis","full_name":"de la Bretèche, Régis","last_name":"De La Bretèche"},{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","last_name":"Browning","full_name":"Timothy Browning","first_name":"Timothy D"}],"abstract":[{"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].","lang":"eng"}],"quality_controlled":0},{"isi":1,"volume":36,"year":"2013","day":"30","external_id":{"isi":["000331450100005"]},"publisher":"IEEE","quality_controlled":"1","author":[{"orcid":"0000-0001-8622-7887","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Lampert, Christoph"},{"first_name":"Hannes","full_name":"Nickisch, Hannes","last_name":"Nickisch"},{"last_name":"Harmeling","first_name":"Stefan","full_name":"Harmeling, Stefan"}],"title":"Attribute-based classification for zero-shot learning of object categories","department":[{"_id":"ChLa"}],"article_processing_charge":"No","issue":"3","date_updated":"2025-09-29T14:09:57Z","type":"journal_article","publication_status":"published","publist_id":"4385","date_published":"2013-07-30T00:00:00Z","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:58:08Z","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","month":"07","scopus_import":"1","abstract":[{"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.","lang":"eng"}],"page":"453 - 465","language":[{"iso":"eng"}],"intvolume":"        36","_id":"2516","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.","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>.","short":"C. Lampert, H. Nickisch, S. Harmeling, IEEE Transactions on Pattern Analysis and Machine Intelligence 36 (2013) 453–465.","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>","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>","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."},"oa_version":"None","doi":"10.1109/TPAMI.2013.140"},{"series_title":"Lecture Notes in Computer Science","publisher":"Springer","ddc":["000"],"quality_controlled":"1","author":[{"full_name":"Almagor, Shaull","first_name":"Shaull","last_name":"Almagor"},{"full_name":"Boker, Udi","first_name":"Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","last_name":"Boker"},{"full_name":"Kupferman, Orna","first_name":"Orna","last_name":"Kupferman"}],"title":"Formalizing and reasoning about quality","department":[{"_id":"ToHe"}],"article_processing_charge":"No","has_accepted_license":"1","issue":"Part 2","date_updated":"2020-08-11T10:09:47Z","type":"conference","publication_status":"published","file":[{"access_level":"open_access","checksum":"85afbf6c18a2c7e377c52c9410e2d824","date_updated":"2020-07-14T12:45:42Z","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_name":"2013_ICALP_Almagor.pdf","file_size":363031,"date_created":"2020-05-15T11:16:12Z","file_id":"7860"}],"acknowledgement":"ERC Grant QUALITY. ","alternative_title":["LNCS"],"volume":7966,"year":"2013","day":"01","conference":{"location":"Riga, Latvia","start_date":"2013-07-08","name":"ICALP: Automata, Languages and Programming","end_date":"2013-07-12"},"project":[{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"}],"file_date_updated":"2020-07-14T12:45:42Z","date_created":"2018-12-11T11:58:08Z","month":"07","oa":1,"ec_funded":1,"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"}],"scopus_import":1,"page":"15 - 27","language":[{"iso":"eng"}],"intvolume":"      7966","_id":"2517","citation":{"ista":"Almagor S, Boker U, Kupferman O. 2013. Formalizing and reasoning about quality. 7966(Part 2), 15–27.","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>.","short":"S. Almagor, U. Boker, O. Kupferman, 7966 (2013) 15–27.","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>","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>.","ieee":"S. Almagor, U. Boker, and O. Kupferman, “Formalizing and reasoning about quality,” vol. 7966, no. Part 2. Springer, pp. 15–27, 2013.","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>"},"oa_version":"Submitted Version","doi":"10.1007/978-3-642-39212-2_3","publist_id":"4384","date_published":"2013-07-01T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"page":"625 - 636","language":[{"iso":"eng"}],"_id":"2518","corr_author":"1","intvolume":"      7965","doi":"10.1007/978-3-642-39206-1_53","oa_version":"Preprint","citation":{"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.","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>","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>","short":"V. Kolmogorov, in:, Springer, 2013, pp. 625–636.","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.","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>."},"month":"07","date_created":"2018-12-11T11:58:08Z","oa":1,"abstract":[{"lang":"eng","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."}],"scopus_import":1,"date_published":"2013-07-01T00:00:00Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"2271"}]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","publist_id":"4383","arxiv":1,"department":[{"_id":"VlKo"}],"title":"The power of linear programming for finite-valued CSPs: A constructive characterization","date_updated":"2025-09-23T14:14:56Z","issue":"1","publication_status":"published","type":"conference","publisher":"Springer","author":[{"last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir"}],"main_file_link":[{"url":"http://arxiv.org/abs/1207.7213","open_access":"1"}],"quality_controlled":"1","conference":{"name":"ICALP: Automata, Languages and Programming","start_date":"2013-07-08","end_date":"2013-07-12","location":"Riga, Latvia"},"external_id":{"arxiv":["1207.7213"]},"alternative_title":["LNCS"],"year":"2013","volume":7965,"day":"01"},{"year":"2013","day":"11","conference":{"location":"Bellevue, WA, United States","name":"UAI: Uncertainty in Artificial Intelligence","start_date":"2013-07-11","end_date":"2013-07-15"},"file_date_updated":"2020-07-14T12:45:42Z","ddc":["000"],"publisher":"AUAI Press","quality_controlled":"1","author":[{"last_name":"Quadrianto","first_name":"Novi","full_name":"Quadrianto, Novi"},{"id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0192-9308","last_name":"Sharmanska","full_name":"Sharmanska, Viktoriia","first_name":"Viktoriia"},{"last_name":"Knowles","first_name":"David","full_name":"Knowles, David"},{"full_name":"Ghahramani, Zoubin","first_name":"Zoubin","last_name":"Ghahramani"}],"title":"The supervised IBP: Neighbourhood preserving infinite latent feature models","department":[{"_id":"ChLa"}],"has_accepted_license":"1","date_updated":"2023-02-23T10:46:36Z","type":"conference","publication_status":"published","file":[{"date_updated":"2020-07-14T12:45:42Z","access_level":"open_access","checksum":"325f20c4b926bd74d39006b97df572bd","file_size":1117100,"date_created":"2018-12-12T10:15:16Z","file_id":"5134","relation":"main_file","content_type":"application/pdf","creator":"system","file_name":"IST-2013-137-v1+1_QuaShaKnoGha13.pdf"}],"publist_id":"4381","publication_identifier":{"isbn":["9780974903996"]},"pubrep_id":"137","date_published":"2013-07-11T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","date_created":"2018-12-11T11:58:09Z","publication":"Proceedings of the 29th conference uncertainty in Artificial Intelligence","oa":1,"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."}],"page":"527 - 536","language":[{"iso":"eng"}],"_id":"2520","citation":{"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.","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.","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.","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.","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.","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."},"oa_version":"Submitted Version"},{"type":"journal_article","intvolume":"        60","_id":"253","publication_status":"published","citation":{"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.","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>","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>.","short":"T.D. Browning, Mathematika 60 (2013) 101–107.","ista":"Browning TD. 2013. Counting rational points on cubic hypersurfaces: Corrigendum. Mathematika. 60(1), 101–107.","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>."},"extern":1,"doi":"10.1112/S0025579313000132","title":"Counting rational points on cubic hypersurfaces: Corrigendum","page":"101 - 107","issue":"1","date_updated":"2021-01-12T06:58:03Z","quality_controlled":0,"author":[{"full_name":"Timothy Browning","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","orcid":"0000-0002-8314-0177"}],"date_created":"2018-12-11T11:45:27Z","month":"09","publication":"Mathematika","publisher":"Unknown","date_published":"2013-09-06T00:00:00Z","status":"public","volume":60,"year":"2013","day":"06","publist_id":"7649"}]