[{"publication":"Auxin and Its Role in Plant Development","date_updated":"2021-01-12T06:53:19Z","publication_status":"published","status":"public","page":"143 - 170","title":"Auxin on the road navigated by cellular PIN polarity","author":[{"id":"3028BD74-F248-11E8-B48F-1D18A9856A87","first_name":"Pawel","full_name":"Baster, Pawel","last_name":"Baster"},{"last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"_id":"1806","editor":[{"full_name":"Zažímalová, Eva","last_name":"Zažímalová","first_name":"Eva"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva"}],"abstract":[{"lang":"eng","text":"The generation of asymmetry, at both cellular and tissue level, is one of the most essential capabilities of all eukaryotic organisms. It mediates basically all multicellular development ranging from embryogenesis and de novo organ formation till responses to various environmental stimuli. In plants, the awe-inspiring number of such processes is regulated by phytohormone auxin and its directional, cell-to-cell transport. The mediators of this transport, PIN auxin transporters, are asymmetrically localized at the plasma membrane, and this polar localization determines the directionality of intercellular auxin flow. Thus, auxin transport contributes crucially to the generation of local auxin gradients or maxima, which instruct given cell to change its developmental program. Here, we introduce and discuss the molecular components and cellular mechanisms regulating the generation and maintenance of cellular PIN polarity, as the general hallmarks of cell polarity in plants."}],"year":"2014","doi":"10.1007/978-3-7091-1526-8_8","publisher":"Springer","language":[{"iso":"eng"}],"type":"book_chapter","quality_controlled":"1","citation":{"apa":"Baster, P., &#38; Friml, J. (2014). Auxin on the road navigated by cellular PIN polarity. In E. Zažímalová, J. Petrášek, &#38; E. Benková (Eds.), <i>Auxin and Its Role in Plant Development</i> (pp. 143–170). Springer. <a href=\"https://doi.org/10.1007/978-3-7091-1526-8_8\">https://doi.org/10.1007/978-3-7091-1526-8_8</a>","ieee":"P. Baster and J. Friml, “Auxin on the road navigated by cellular PIN polarity,” in <i>Auxin and Its Role in Plant Development</i>, E. Zažímalová, J. Petrášek, and E. Benková, Eds. Springer, 2014, pp. 143–170.","ama":"Baster P, Friml J. Auxin on the road navigated by cellular PIN polarity. In: Zažímalová E, Petrášek J, Benková E, eds. <i>Auxin and Its Role in Plant Development</i>. Springer; 2014:143-170. doi:<a href=\"https://doi.org/10.1007/978-3-7091-1526-8_8\">10.1007/978-3-7091-1526-8_8</a>","ista":"Baster P, Friml J. 2014.Auxin on the road navigated by cellular PIN polarity. In: Auxin and Its Role in Plant Development. , 143–170.","short":"P. Baster, J. Friml, in:, E. Zažímalová, J. Petrášek, E. Benková (Eds.), Auxin and Its Role in Plant Development, Springer, 2014, pp. 143–170.","chicago":"Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular PIN Polarity.” In <i>Auxin and Its Role in Plant Development</i>, edited by Eva Zažímalová, Jan Petrášek, and Eva Benková, 143–70. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-7091-1526-8_8\">https://doi.org/10.1007/978-3-7091-1526-8_8</a>.","mla":"Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular PIN Polarity.” <i>Auxin and Its Role in Plant Development</i>, edited by Eva Zažímalová et al., Springer, 2014, pp. 143–70, doi:<a href=\"https://doi.org/10.1007/978-3-7091-1526-8_8\">10.1007/978-3-7091-1526-8_8</a>."},"department":[{"_id":"JiFr"}],"day":"01","publist_id":"5304","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","month":"04","date_published":"2014-04-01T00:00:00Z","date_created":"2018-12-11T11:54:07Z","oa_version":"None","scopus_import":1},{"publication":"International Journal of Computational Geometry and Applications","date_updated":"2021-01-12T06:53:23Z","page":"61 - 86","oa":1,"year":"2014","intvolume":"        24","publisher":"World Scientific Publishing","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"HeEd"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5290","date_published":"2014-03-16T00:00:00Z","scopus_import":1,"date_created":"2018-12-11T11:54:10Z","publication_status":"published","acknowledgement":"Work by Martin Held and Stefan Huber was supported by Austrian Science Fund (FWF): L367-N15 and P25816-N15.","status":"public","author":[{"orcid":"0000-0002-8871-5814","full_name":"Huber, Stefan","last_name":"Huber","id":"4700A070-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan"},{"full_name":"Held, Martin","last_name":"Held","first_name":"Martin"},{"last_name":"Meerwald","full_name":"Meerwald, Peter","first_name":"Peter"},{"last_name":"Kwitt","full_name":"Kwitt, Roland","first_name":"Roland"}],"title":"Topology-preserving watermarking of vector graphics","_id":"1816","issue":"1","abstract":[{"text":"Watermarking techniques for vector graphics dislocate vertices in order to embed imperceptible, yet detectable, statistical features into the input data. The embedding process may result in a change of the topology of the input data, e.g., by introducing self-intersections, which is undesirable or even disastrous for many applications. In this paper we present a watermarking framework for two-dimensional vector graphics that employs conventional watermarking techniques but still provides the guarantee that the topology of the input data is preserved. The geometric part of this framework computes so-called maximum perturbation regions (MPR) of vertices. We propose two efficient algorithms to compute MPRs based on Voronoi diagrams and constrained triangulations. Furthermore, we present two algorithms to conditionally correct the watermarked data in order to increase the watermark embedding capacity and still guarantee topological correctness. While we focus on the watermarking of input formed by straight-line segments, one of our approaches can also be extended to circular arcs. We conclude the paper by demonstrating and analyzing the applicability of our framework in conjunction with two well-known watermarking techniques.","lang":"eng"}],"doi":"10.1142/S0218195914500034","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"access_level":"open_access","content_type":"application/pdf","checksum":"be45c133ab4d43351260e21beaa8f4b1","date_updated":"2020-07-14T12:45:17Z","file_name":"IST-2016-443-v1+1_S0218195914500034.pdf","relation":"main_file","file_size":991734,"creator":"system","file_id":"4704","date_created":"2018-12-12T10:08:43Z"}],"has_accepted_license":"1","volume":24,"day":"16","citation":{"chicago":"Huber, Stefan, Martin Held, Peter Meerwald, and Roland Kwitt. “Topology-Preserving Watermarking of Vector Graphics.” <i>International Journal of Computational Geometry and Applications</i>. World Scientific Publishing, 2014. <a href=\"https://doi.org/10.1142/S0218195914500034\">https://doi.org/10.1142/S0218195914500034</a>.","mla":"Huber, Stefan, et al. “Topology-Preserving Watermarking of Vector Graphics.” <i>International Journal of Computational Geometry and Applications</i>, vol. 24, no. 1, World Scientific Publishing, 2014, pp. 61–86, doi:<a href=\"https://doi.org/10.1142/S0218195914500034\">10.1142/S0218195914500034</a>.","ieee":"S. Huber, M. Held, P. Meerwald, and R. Kwitt, “Topology-preserving watermarking of vector graphics,” <i>International Journal of Computational Geometry and Applications</i>, vol. 24, no. 1. World Scientific Publishing, pp. 61–86, 2014.","apa":"Huber, S., Held, M., Meerwald, P., &#38; Kwitt, R. (2014). Topology-preserving watermarking of vector graphics. <i>International Journal of Computational Geometry and Applications</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0218195914500034\">https://doi.org/10.1142/S0218195914500034</a>","ista":"Huber S, Held M, Meerwald P, Kwitt R. 2014. Topology-preserving watermarking of vector graphics. International Journal of Computational Geometry and Applications. 24(1), 61–86.","ama":"Huber S, Held M, Meerwald P, Kwitt R. Topology-preserving watermarking of vector graphics. <i>International Journal of Computational Geometry and Applications</i>. 2014;24(1):61-86. doi:<a href=\"https://doi.org/10.1142/S0218195914500034\">10.1142/S0218195914500034</a>","short":"S. Huber, M. Held, P. Meerwald, R. Kwitt, International Journal of Computational Geometry and Applications 24 (2014) 61–86."},"pubrep_id":"443","file_date_updated":"2020-07-14T12:45:17Z","ddc":["000"],"month":"03","oa_version":"Published Version"},{"oa":1,"year":"2014","date_updated":"2021-01-12T06:53:25Z","publication":"Journal of Mathematical Physics","article_number":"1.4881536","publist_id":"5285","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"RoSe"}],"date_created":"2018-12-11T11:54:11Z","scopus_import":1,"date_published":"2014-06-26T00:00:00Z","publisher":"American Institute of Physics","intvolume":"        55","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","_id":"1821","title":"Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation","author":[{"last_name":"Seiringer","full_name":"Seiringer, Robert","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521"}],"doi":"10.1063/1.4881536","abstract":[{"lang":"eng","text":"We review recent progress towards a rigorous understanding of the Bogoliubov approximation for bosonic quantum many-body systems. We focus, in particular, on the excitation spectrum of a Bose gas in the mean-field (Hartree) limit. A list of open problems will be discussed at the end."}],"issue":"7","project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}],"status":"public","publication_status":"published","month":"06","file_date_updated":"2020-07-14T12:45:17Z","ddc":["510","530"],"pubrep_id":"532","citation":{"chicago":"Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov Approximation.” <i>Journal of Mathematical Physics</i>. American Institute of Physics, 2014. <a href=\"https://doi.org/10.1063/1.4881536\">https://doi.org/10.1063/1.4881536</a>.","mla":"Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov Approximation.” <i>Journal of Mathematical Physics</i>, vol. 55, no. 7, 1.4881536, American Institute of Physics, 2014, doi:<a href=\"https://doi.org/10.1063/1.4881536\">10.1063/1.4881536</a>.","short":"R. Seiringer, Journal of Mathematical Physics 55 (2014).","ama":"Seiringer R. Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. <i>Journal of Mathematical Physics</i>. 2014;55(7). doi:<a href=\"https://doi.org/10.1063/1.4881536\">10.1063/1.4881536</a>","ista":"Seiringer R. 2014. Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. Journal of Mathematical Physics. 55(7), 1.4881536.","ieee":"R. Seiringer, “Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation,” <i>Journal of Mathematical Physics</i>, vol. 55, no. 7. American Institute of Physics, 2014.","apa":"Seiringer, R. (2014). Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. <i>Journal of Mathematical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4881536\">https://doi.org/10.1063/1.4881536</a>"},"day":"26","oa_version":"Submitted Version","file":[{"file_id":"5172","date_created":"2018-12-12T10:15:49Z","file_name":"IST-2016-532-v1+1_J._Mathematical_Phys._2014_Seiringer.pdf","relation":"main_file","creator":"system","file_size":269171,"date_updated":"2020-07-14T12:45:17Z","access_level":"open_access","content_type":"application/pdf","checksum":"ed0efc93c10f1341155f0316af617b82"}],"volume":55,"has_accepted_license":"1"},{"publication_status":"published","status":"public","article_number":"075101","publication":"Journal of Mathematical Physics","date_updated":"2021-01-12T06:53:25Z","issue":"7","year":"2014","doi":"10.1063/1.4884877","title":"Introduction","author":[{"full_name":"Jakšić, Vojkan","last_name":"Jakšić","first_name":"Vojkan"},{"full_name":"Pillet, Claude","last_name":"Pillet","first_name":"Claude"},{"orcid":"0000-0002-6781-0521","last_name":"Seiringer","full_name":"Seiringer, Robert","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"_id":"1822","volume":55,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"American Institute of Physics","intvolume":"        55","date_published":"2014-07-01T00:00:00Z","oa_version":"None","date_created":"2018-12-11T11:54:12Z","scopus_import":1,"citation":{"ama":"Jakšić V, Pillet C, Seiringer R. Introduction. <i>Journal of Mathematical Physics</i>. 2014;55(7). doi:<a href=\"https://doi.org/10.1063/1.4884877\">10.1063/1.4884877</a>","short":"V. Jakšić, C. Pillet, R. Seiringer, Journal of Mathematical Physics 55 (2014).","ista":"Jakšić V, Pillet C, Seiringer R. 2014. Introduction. Journal of Mathematical Physics. 55(7), 075101.","apa":"Jakšić, V., Pillet, C., &#38; Seiringer, R. (2014). Introduction. <i>Journal of Mathematical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4884877\">https://doi.org/10.1063/1.4884877</a>","ieee":"V. Jakšić, C. Pillet, and R. Seiringer, “Introduction,” <i>Journal of Mathematical Physics</i>, vol. 55, no. 7. American Institute of Physics, 2014.","mla":"Jakšić, Vojkan, et al. “Introduction.” <i>Journal of Mathematical Physics</i>, vol. 55, no. 7, 075101, American Institute of Physics, 2014, doi:<a href=\"https://doi.org/10.1063/1.4884877\">10.1063/1.4884877</a>.","chicago":"Jakšić, Vojkan, Claude Pillet, and Robert Seiringer. “Introduction.” <i>Journal of Mathematical Physics</i>. American Institute of Physics, 2014. <a href=\"https://doi.org/10.1063/1.4884877\">https://doi.org/10.1063/1.4884877</a>."},"department":[{"_id":"RoSe"}],"day":"01","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5284","month":"07"},{"_id":"1829","editor":[{"first_name":"Jens","last_name":"Kober","full_name":"Kober, Jens"},{"first_name":"Jan","last_name":"Peters","full_name":"Peters, Jan"}],"author":[{"first_name":"Katharina","last_name":"Muelling","full_name":"Muelling, Katharina"},{"last_name":"Kroemer","full_name":"Kroemer, Oliver","first_name":"Oliver"},{"last_name":"Lampert","full_name":"Lampert, Christoph","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887"},{"first_name":"Bernhard","full_name":"Schölkopf, Bernhard","last_name":"Schölkopf"}],"title":"Movement templates for learning of hitting and batting","doi":"10.1007/978-3-319-03194-1_3","alternative_title":["Springer Tracts in Advanced Robotics"],"year":"2014","abstract":[{"lang":"eng","text":"Hitting and batting tasks, such as tennis forehands, ping-pong strokes, or baseball batting, depend on predictions where the ball can be intercepted and how it can properly be returned to the opponent. These predictions get more accurate over time, hence the behaviors need to be continuously modified. As a result, movement templates with a learned global shape need to be adapted during the execution so that the racket reaches a target position and velocity that will return the ball over to the other side of the net or court. It requires altering learned movements to hit a varying target with the necessary velocity at a specific instant in time. Such a task cannot be incorporated straightforwardly in most movement representations suitable for learning. For example, the standard formulation of the dynamical system based motor primitives (introduced by Ijspeert et al (2002b)) does not satisfy this property despite their flexibility which has allowed learning tasks ranging from locomotion to kendama. In order to fulfill this requirement, we reformulate the Ijspeert framework to incorporate the possibility of specifying a desired hitting point and a desired hitting velocity while maintaining all advantages of the original formulation.We show that the proposed movement template formulation works well in two scenarios, i.e., for hitting a ball on a string with a table tennis racket at a specified velocity and for returning balls launched by a ball gun successfully over the net using forehand movements."}],"date_updated":"2021-01-12T06:53:28Z","publication":"Learning Motor Skills","page":"69 - 82","publication_status":"published","status":"public","month":"01","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5274","department":[{"_id":"ChLa"}],"day":"01","citation":{"apa":"Muelling, K., Kroemer, O., Lampert, C., &#38; Schölkopf, B. (2014). Movement templates for learning of hitting and batting. In J. Kober &#38; J. Peters (Eds.), <i>Learning Motor Skills</i> (Vol. 97, pp. 69–82). Springer. <a href=\"https://doi.org/10.1007/978-3-319-03194-1_3\">https://doi.org/10.1007/978-3-319-03194-1_3</a>","ieee":"K. Muelling, O. Kroemer, C. Lampert, and B. Schölkopf, “Movement templates for learning of hitting and batting,” in <i>Learning Motor Skills</i>, vol. 97, J. Kober and J. Peters, Eds. Springer, 2014, pp. 69–82.","short":"K. Muelling, O. Kroemer, C. Lampert, B. Schölkopf, in:, J. Kober, J. Peters (Eds.), Learning Motor Skills, Springer, 2014, pp. 69–82.","ista":"Muelling K, Kroemer O, Lampert C, Schölkopf B. 2014.Movement templates for learning of hitting and batting. In: Learning Motor Skills. Springer Tracts in Advanced Robotics, vol. 97, 69–82.","ama":"Muelling K, Kroemer O, Lampert C, Schölkopf B. Movement templates for learning of hitting and batting. In: Kober J, Peters J, eds. <i>Learning Motor Skills</i>. Vol 97. From Algorithms to Robot Experiments. Springer; 2014:69-82. doi:<a href=\"https://doi.org/10.1007/978-3-319-03194-1_3\">10.1007/978-3-319-03194-1_3</a>","chicago":"Muelling, Katharina, Oliver Kroemer, Christoph Lampert, and Bernhard Schölkopf. “Movement Templates for Learning of Hitting and Batting.” In <i>Learning Motor Skills</i>, edited by Jens Kober and Jan Peters, 97:69–82. From Algorithms to Robot Experiments. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-319-03194-1_3\">https://doi.org/10.1007/978-3-319-03194-1_3</a>.","mla":"Muelling, Katharina, et al. “Movement Templates for Learning of Hitting and Batting.” <i>Learning Motor Skills</i>, edited by Jens Kober and Jan Peters, vol. 97, Springer, 2014, pp. 69–82, doi:<a href=\"https://doi.org/10.1007/978-3-319-03194-1_3\">10.1007/978-3-319-03194-1_3</a>."},"scopus_import":1,"oa_version":"None","date_created":"2018-12-11T11:54:14Z","date_published":"2014-01-01T00:00:00Z","intvolume":"        97","publisher":"Springer","series_title":"From Algorithms to Robot Experiments","type":"book_chapter","quality_controlled":"1","language":[{"iso":"eng"}],"volume":97},{"publication_status":"published","status":"public","acknowledgement":"Marek Krčál was supported by the ERC Advanced Grant No. 267165.","page":"64 - 79","publication":"Discrete & Computational Geometry","date_updated":"2021-01-12T06:53:33Z","issue":"1","year":"2014","abstract":[{"text":"We prove polynomial upper bounds of geometric Ramsey numbers of pathwidth-2 outerplanar triangulations in both convex and general cases. We also prove that the geometric Ramsey numbers of the ladder graph on 2n vertices are bounded by O(n3) and O(n10), in the convex and general case, respectively. We then apply similar methods to prove an (Formula presented.) upper bound on the Ramsey number of a path with n ordered vertices.","lang":"eng"}],"doi":"10.1007/s00454-014-9646-x","author":[{"full_name":"Cibulka, Josef","last_name":"Cibulka","first_name":"Josef"},{"full_name":"Gao, Pu","last_name":"Gao","first_name":"Pu"},{"id":"33E21118-F248-11E8-B48F-1D18A9856A87","first_name":"Marek","full_name":"Krcál, Marek","last_name":"Krcál"},{"first_name":"Tomáš","last_name":"Valla","full_name":"Valla, Tomáš"},{"first_name":"Pavel","full_name":"Valtr, Pavel","last_name":"Valtr"}],"oa":1,"title":"On the geometric ramsey number of outerplanar graphs","_id":"1842","language":[{"iso":"eng"}],"type":"journal_article","volume":53,"main_file_link":[{"url":"http://arxiv.org/abs/1310.7004","open_access":"1"}],"intvolume":"        53","publisher":"Springer","date_published":"2014-11-14T00:00:00Z","scopus_import":1,"date_created":"2018-12-11T11:54:18Z","oa_version":"Submitted Version","day":"14","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"citation":{"ama":"Cibulka J, Gao P, Krcál M, Valla T, Valtr P. On the geometric ramsey number of outerplanar graphs. <i>Discrete &#38; Computational Geometry</i>. 2014;53(1):64-79. doi:<a href=\"https://doi.org/10.1007/s00454-014-9646-x\">10.1007/s00454-014-9646-x</a>","short":"J. Cibulka, P. Gao, M. Krcál, T. Valla, P. Valtr, Discrete &#38; Computational Geometry 53 (2014) 64–79.","ista":"Cibulka J, Gao P, Krcál M, Valla T, Valtr P. 2014. On the geometric ramsey number of outerplanar graphs. Discrete &#38; Computational Geometry. 53(1), 64–79.","apa":"Cibulka, J., Gao, P., Krcál, M., Valla, T., &#38; Valtr, P. (2014). On the geometric ramsey number of outerplanar graphs. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-014-9646-x\">https://doi.org/10.1007/s00454-014-9646-x</a>","ieee":"J. Cibulka, P. Gao, M. Krcál, T. Valla, and P. Valtr, “On the geometric ramsey number of outerplanar graphs,” <i>Discrete &#38; Computational Geometry</i>, vol. 53, no. 1. Springer, pp. 64–79, 2014.","chicago":"Cibulka, Josef, Pu Gao, Marek Krcál, Tomáš Valla, and Pavel Valtr. “On the Geometric Ramsey Number of Outerplanar Graphs.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s00454-014-9646-x\">https://doi.org/10.1007/s00454-014-9646-x</a>.","mla":"Cibulka, Josef, et al. “On the Geometric Ramsey Number of Outerplanar Graphs.” <i>Discrete &#38; Computational Geometry</i>, vol. 53, no. 1, Springer, 2014, pp. 64–79, doi:<a href=\"https://doi.org/10.1007/s00454-014-9646-x\">10.1007/s00454-014-9646-x</a>."},"publist_id":"5260","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","month":"11"},{"scopus_import":1,"date_created":"2018-12-11T11:54:19Z","date_published":"2014-11-12T00:00:00Z","publist_id":"5257","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HaJa"}],"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","intvolume":"        32","publisher":"Oxford University Press","year":"2014","oa":1,"page":"440 - 455","date_updated":"2021-01-12T06:53:34Z","publication":"Molecular Biology and Evolution","oa_version":"Published Version","ddc":["571"],"file_date_updated":"2020-07-14T12:45:19Z","month":"11","day":"12","citation":{"apa":"Risso, V., Manssour Triedo, F., Delgado Delgado, A., Arco, R., Barroso Deljesús, A., Inglés Prieto, Á., … Sánchez Ruiz, J. (2014). Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msu312\">https://doi.org/10.1093/molbev/msu312</a>","ieee":"V. Risso <i>et al.</i>, “Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history,” <i>Molecular Biology and Evolution</i>, vol. 32, no. 2. Oxford University Press, pp. 440–455, 2014.","ista":"Risso V, Manssour Triedo F, Delgado Delgado A, Arco R, Barroso Deljesús A, Inglés Prieto Á, Godoy Ruiz R, Gavira J, Gaucher E, Ibarra Molero B, Sánchez Ruiz J. 2014. Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Molecular Biology and Evolution. 32(2), 440–455.","short":"V. Risso, F. Manssour Triedo, A. Delgado Delgado, R. Arco, A. Barroso Deljesús, Á. Inglés Prieto, R. Godoy Ruiz, J. Gavira, E. Gaucher, B. Ibarra Molero, J. Sánchez Ruiz, Molecular Biology and Evolution 32 (2014) 440–455.","ama":"Risso V, Manssour Triedo F, Delgado Delgado A, et al. Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. <i>Molecular Biology and Evolution</i>. 2014;32(2):440-455. doi:<a href=\"https://doi.org/10.1093/molbev/msu312\">10.1093/molbev/msu312</a>","chicago":"Risso, Valeria, Fadia Manssour Triedo, Asuncion Delgado Delgado, Rocio Arco, Alicia Barroso Deljesús, Álvaro Inglés Prieto, Raquel Godoy Ruiz, et al. “Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/molbev/msu312\">https://doi.org/10.1093/molbev/msu312</a>.","mla":"Risso, Valeria, et al. “Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History.” <i>Molecular Biology and Evolution</i>, vol. 32, no. 2, Oxford University Press, 2014, pp. 440–55, doi:<a href=\"https://doi.org/10.1093/molbev/msu312\">10.1093/molbev/msu312</a>."},"pubrep_id":"430","volume":32,"has_accepted_license":"1","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"file":[{"file_size":1545246,"creator":"system","relation":"main_file","file_name":"IST-2016-430-v1+1_Mol_Biol_Evol-2015-Risso-440-55.pdf","checksum":"06215318e66be8f3e0c33abb07e9d3da","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:19Z","date_created":"2018-12-12T10:16:56Z","file_id":"5247"}],"doi":"10.1093/molbev/msu312","issue":"2","abstract":[{"lang":"eng","text":"Local protein interactions (&quot;molecular context&quot; effects) dictate amino acid replacements and can be described in terms of site-specific, energetic preferences for any different amino acid. It has been recently debated whether these preferences remain approximately constant during evolution or whether, due to coevolution of sites, they change strongly. Such research highlights an unresolved and fundamental issue with far-reaching implications for phylogenetic analysis and molecular evolution modeling. Here, we take advantage of the recent availability of phenotypically supported laboratory resurrections of Precambrian thioredoxins and β-lactamases to experimentally address the change of site-specific amino acid preferences over long geological timescales. Extensive mutational analyses support the notion that evolutionary adjustment to a new amino acid may occur, but to a large extent this is insufficient to erase the primitive preference for amino acid replacements. Generally, site-specific amino acid preferences appear to remain conserved throughout evolutionary history despite local sequence divergence. We show such preference conservation to be readily understandable in molecular terms and we provide crystallographic evidence for an intriguing structural-switch mechanism: Energetic preference for an ancestral amino acid in a modern protein can be linked to reorganization upon mutation to the ancestral local structure around the mutated site. Finally, we point out that site-specific preference conservation naturally leads to one plausible evolutionary explanation for the existence of intragenic global suppressor mutations."}],"_id":"1844","author":[{"last_name":"Risso","full_name":"Risso, Valeria","first_name":"Valeria"},{"first_name":"Fadia","full_name":"Manssour Triedo, Fadia","last_name":"Manssour Triedo"},{"full_name":"Delgado Delgado, Asuncion","last_name":"Delgado Delgado","first_name":"Asuncion"},{"full_name":"Arco, Rocio","last_name":"Arco","first_name":"Rocio"},{"last_name":"Barroso Deljesús","full_name":"Barroso Deljesús, Alicia","first_name":"Alicia"},{"orcid":"0000-0002-5409-8571","full_name":"Inglés Prieto, Álvaro","last_name":"Inglés Prieto","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","first_name":"Álvaro"},{"first_name":"Raquel","last_name":"Godoy Ruiz","full_name":"Godoy Ruiz, Raquel"},{"full_name":"Gavira, Josè","last_name":"Gavira","first_name":"Josè"},{"first_name":"Eric","full_name":"Gaucher, Eric","last_name":"Gaucher"},{"last_name":"Ibarra Molero","full_name":"Ibarra Molero, Beatriz","first_name":"Beatriz"},{"first_name":"Jose","last_name":"Sánchez Ruiz","full_name":"Sánchez Ruiz, Jose"}],"title":"Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history","publication_status":"published","status":"public"},{"doi":"10.1016/j.cub.2014.08.036","abstract":[{"lang":"eng","text":"To control morphogenesis, molecular regulatory networks have to interfere with the mechanical properties of the individual cells of developing organs and tissues, but how this is achieved is not well known. We study this issue here in the shoot meristem of higher plants, a group of undifferentiated cells where complex changes in growth rates and directions lead to the continuous formation of new organs [1, 2]. Here, we show that the plant hormone auxin plays an important role in this process via a dual, local effect on the extracellular matrix, the cell wall, which determines cell shape. Our study reveals that auxin not only causes a limited reduction in wall stiffness but also directly interferes with wall anisotropy via the regulation of cortical microtubule dynamics. We further show that to induce growth isotropy and organ outgrowth, auxin somehow interferes with the cortical microtubule-ordering activity of a network of proteins, including AUXIN BINDING PROTEIN 1 and KATANIN 1. Numerical simulations further indicate that the induced isotropy is sufficient to amplify the effects of the relatively minor changes in wall stiffness to promote organogenesis and the establishment of new growth axes in a robust manner."}],"issue":"19","_id":"1852","title":"An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis","author":[{"first_name":"Massimiliano","last_name":"Sassi","full_name":"Sassi, Massimiliano"},{"last_name":"Ali","full_name":"Ali, Olivier","first_name":"Olivier"},{"full_name":"Boudon, Frédéric","last_name":"Boudon","first_name":"Frédéric"},{"full_name":"Cloarec, Gladys","last_name":"Cloarec","first_name":"Gladys"},{"first_name":"Ursula","last_name":"Abad","full_name":"Abad, Ursula"},{"last_name":"Cellier","full_name":"Cellier, Coralie","first_name":"Coralie"},{"full_name":"Chen, Xu","last_name":"Chen","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","first_name":"Xu"},{"first_name":"Benjamin","full_name":"Gilles, Benjamin","last_name":"Gilles"},{"first_name":"Pascale","full_name":"Milani, Pascale","last_name":"Milani"},{"last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"first_name":"Teva","last_name":"Vernoux","full_name":"Vernoux, Teva"},{"first_name":"Christophe","full_name":"Godin, Christophe","last_name":"Godin"},{"full_name":"Hamant, Olivier","last_name":"Hamant","first_name":"Olivier"},{"first_name":"Jan","last_name":"Traas","full_name":"Traas, Jan"}],"publication_status":"published","status":"public","acknowledgement":"This work was funded by grants from EraSysBio+ (iSAM) and ERC (Morphodynamics). ","oa_version":"Submitted Version","month":"10","citation":{"chicago":"Sassi, Massimiliano, Olivier Ali, Frédéric Boudon, Gladys Cloarec, Ursula Abad, Coralie Cellier, Xu Chen, et al. “An Auxin-Mediated Shift toward Growth Isotropy Promotes Organ Formation at the Shoot Meristem in Arabidopsis.” <i>Current Biology</i>. Cell Press, 2014. <a href=\"https://doi.org/10.1016/j.cub.2014.08.036\">https://doi.org/10.1016/j.cub.2014.08.036</a>.","mla":"Sassi, Massimiliano, et al. “An Auxin-Mediated Shift toward Growth Isotropy Promotes Organ Formation at the Shoot Meristem in Arabidopsis.” <i>Current Biology</i>, vol. 24, no. 19, Cell Press, 2014, pp. 2335–42, doi:<a href=\"https://doi.org/10.1016/j.cub.2014.08.036\">10.1016/j.cub.2014.08.036</a>.","short":"M. Sassi, O. Ali, F. Boudon, G. Cloarec, U. Abad, C. Cellier, X. Chen, B. Gilles, P. Milani, J. Friml, T. Vernoux, C. Godin, O. Hamant, J. Traas, Current Biology 24 (2014) 2335–2342.","ama":"Sassi M, Ali O, Boudon F, et al. An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis. <i>Current Biology</i>. 2014;24(19):2335-2342. doi:<a href=\"https://doi.org/10.1016/j.cub.2014.08.036\">10.1016/j.cub.2014.08.036</a>","ista":"Sassi M, Ali O, Boudon F, Cloarec G, Abad U, Cellier C, Chen X, Gilles B, Milani P, Friml J, Vernoux T, Godin C, Hamant O, Traas J. 2014. An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis. Current Biology. 24(19), 2335–2342.","ieee":"M. Sassi <i>et al.</i>, “An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis,” <i>Current Biology</i>, vol. 24, no. 19. Cell Press, pp. 2335–2342, 2014.","apa":"Sassi, M., Ali, O., Boudon, F., Cloarec, G., Abad, U., Cellier, C., … Traas, J. (2014). An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2014.08.036\">https://doi.org/10.1016/j.cub.2014.08.036</a>"},"day":"06","volume":24,"year":"2014","oa":1,"page":"2335 - 2342","date_updated":"2021-01-12T06:53:37Z","publication":"Current Biology","date_created":"2018-12-11T11:54:22Z","scopus_import":1,"date_published":"2014-10-06T00:00:00Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5248","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","publisher":"Cell Press","intvolume":"        24","main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-01074821"}]},{"author":[{"first_name":"Susmit","last_name":"Jha","full_name":"Jha, Susmit"},{"first_name":"Stavros","last_name":"Tripakis","full_name":"Tripakis, Stavros"},{"last_name":"Seshia","full_name":"Seshia, Sanjit","first_name":"Sanjit"},{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"title":"Game theoretic secure localization in wireless sensor networks","_id":"1853","year":"2014","abstract":[{"lang":"eng","text":"Wireless sensor networks (WSNs) composed of low-power, low-cost sensor nodes are expected to form the backbone of future intelligent networks for a broad range of civil, industrial and military applications. These sensor nodes are often deployed through random spreading, and function in dynamic environments. Many applications of WSNs such as pollution tracking, forest fire detection, and military surveillance require knowledge of the location of constituent nodes. But the use of technologies such as GPS on all nodes is prohibitive due to power and cost constraints. So, the sensor nodes need to autonomously determine their locations. Most localization techniques use anchor nodes with known locations to determine the position of remaining nodes. Localization techniques have two conflicting requirements. On one hand, an ideal localization technique should be computationally simple and on the other hand, it must be resistant to attacks that compromise anchor nodes. In this paper, we propose a computationally light-weight game theoretic secure localization technique and demonstrate its effectiveness in comparison to existing techniques."}],"doi":"10.1109/IOT.2014.7030120","date_updated":"2021-01-12T06:53:38Z","publication_status":"published","status":"public","page":"85 - 90","department":[{"_id":"KrCh"}],"day":"03","citation":{"ieee":"S. Jha, S. Tripakis, S. Seshia, and K. Chatterjee, “Game theoretic secure localization in wireless sensor networks,” presented at the IOT: Internet of Things, Cambridge, USA, 2014, pp. 85–90.","apa":"Jha, S., Tripakis, S., Seshia, S., &#38; Chatterjee, K. (2014). Game theoretic secure localization in wireless sensor networks (pp. 85–90). Presented at the IOT: Internet of Things, Cambridge, USA: IEEE. <a href=\"https://doi.org/10.1109/IOT.2014.7030120\">https://doi.org/10.1109/IOT.2014.7030120</a>","short":"S. Jha, S. Tripakis, S. Seshia, K. Chatterjee, in:, IEEE, 2014, pp. 85–90.","ama":"Jha S, Tripakis S, Seshia S, Chatterjee K. Game theoretic secure localization in wireless sensor networks. In: IEEE; 2014:85-90. doi:<a href=\"https://doi.org/10.1109/IOT.2014.7030120\">10.1109/IOT.2014.7030120</a>","ista":"Jha S, Tripakis S, Seshia S, Chatterjee K. 2014. Game theoretic secure localization in wireless sensor networks. IOT: Internet of Things, 85–90.","mla":"Jha, Susmit, et al. <i>Game Theoretic Secure Localization in Wireless Sensor Networks</i>. IEEE, 2014, pp. 85–90, doi:<a href=\"https://doi.org/10.1109/IOT.2014.7030120\">10.1109/IOT.2014.7030120</a>.","chicago":"Jha, Susmit, Stavros Tripakis, Sanjit Seshia, and Krishnendu Chatterjee. “Game Theoretic Secure Localization in Wireless Sensor Networks,” 85–90. IEEE, 2014. <a href=\"https://doi.org/10.1109/IOT.2014.7030120\">https://doi.org/10.1109/IOT.2014.7030120</a>."},"publist_id":"5247","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","month":"02","date_published":"2014-02-03T00:00:00Z","conference":{"end_date":"2014-10-08","location":"Cambridge, USA","start_date":"2014-10-06","name":"IOT: Internet of Things"},"oa_version":"None","date_created":"2018-12-11T11:54:22Z","publisher":"IEEE","language":[{"iso":"eng"}],"quality_controlled":"1","type":"conference"},{"publisher":"Wiley","intvolume":"        34","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","publist_id":"5246","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ChWo"}],"date_created":"2018-12-11T11:54:22Z","scopus_import":1,"date_published":"2014-11-05T00:00:00Z","date_updated":"2021-01-12T06:53:38Z","publication":"Computer Graphics Forum","page":"239 - 252","oa":1,"year":"2014","file":[{"creator":"system","file_size":24817484,"relation":"main_file","file_name":"IST-2016-574-v1+1_Guerrero-2014-TPS-paper.pdf","date_updated":"2020-07-14T12:45:19Z","content_type":"application/pdf","checksum":"91946bfc509c77f5fd3151a3ff2b2c8f","access_level":"open_access","date_created":"2018-12-12T10:15:58Z","file_id":"5182"}],"volume":34,"has_accepted_license":"1","ddc":["000"],"file_date_updated":"2020-07-14T12:45:19Z","month":"11","pubrep_id":"574","citation":{"mla":"Guerrero, Paul, et al. “Partial Shape Matching Using Transformation Parameter Similarity.” <i>Computer Graphics Forum</i>, vol. 34, no. 1, Wiley, 2014, pp. 239–52, doi:<a href=\"https://doi.org/10.1111/cgf.12509\">10.1111/cgf.12509</a>.","chicago":"Guerrero, Paul, Thomas Auzinger, Michael Wimmer, and Stefan Jeschke. “Partial Shape Matching Using Transformation Parameter Similarity.” <i>Computer Graphics Forum</i>. Wiley, 2014. <a href=\"https://doi.org/10.1111/cgf.12509\">https://doi.org/10.1111/cgf.12509</a>.","ieee":"P. Guerrero, T. Auzinger, M. Wimmer, and S. Jeschke, “Partial shape matching using transformation parameter similarity,” <i>Computer Graphics Forum</i>, vol. 34, no. 1. Wiley, pp. 239–252, 2014.","apa":"Guerrero, P., Auzinger, T., Wimmer, M., &#38; Jeschke, S. (2014). Partial shape matching using transformation parameter similarity. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.12509\">https://doi.org/10.1111/cgf.12509</a>","short":"P. Guerrero, T. Auzinger, M. Wimmer, S. Jeschke, Computer Graphics Forum 34 (2014) 239–252.","ama":"Guerrero P, Auzinger T, Wimmer M, Jeschke S. Partial shape matching using transformation parameter similarity. <i>Computer Graphics Forum</i>. 2014;34(1):239-252. doi:<a href=\"https://doi.org/10.1111/cgf.12509\">10.1111/cgf.12509</a>","ista":"Guerrero P, Auzinger T, Wimmer M, Jeschke S. 2014. Partial shape matching using transformation parameter similarity. Computer Graphics Forum. 34(1), 239–252."},"day":"05","oa_version":"Submitted Version","publication_status":"published","status":"public","_id":"1854","title":"Partial shape matching using transformation parameter similarity","author":[{"last_name":"Guerrero","full_name":"Guerrero, Paul","first_name":"Paul"},{"orcid":"0000-0002-1546-3265","id":"4718F954-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","full_name":"Auzinger, Thomas","last_name":"Auzinger"},{"last_name":"Wimmer","full_name":"Wimmer, Michael","first_name":"Michael"},{"first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","last_name":"Jeschke","full_name":"Jeschke, Stefan"}],"doi":"10.1111/cgf.12509","abstract":[{"lang":"eng","text":"In this paper, we present a method for non-rigid, partial shape matching in vector graphics. Given a user-specified query region in a 2D shape, similar regions are found, even if they are non-linearly distorted. Furthermore, a non-linear mapping is established between the query regions and these matches, which allows the automatic transfer of editing operations such as texturing. This is achieved by a two-step approach. First, pointwise correspondences between the query region and the whole shape are established. The transformation parameters of these correspondences are registered in an appropriate transformation space. For transformations between similar regions, these parameters form surfaces in transformation space, which are extracted in the second step of our method. The extracted regions may be related to the query region by a non-rigid transform, enabling non-rigid shape matching. In this paper, we present a method for non-rigid, partial shape matching in vector graphics. Given a user-specified query region in a 2D shape, similar regions are found, even if they are non-linearly distorted. Furthermore, a non-linear mapping is established between the query regions and these matches, which allows the automatic transfer of editing operations such as texturing. This is achieved by a two-step approach. First, pointwise correspondences between the query region and the whole shape are established. The transformation parameters of these correspondences are registered in an appropriate transformation space. For transformations between similar regions, these parameters form surfaces in transformation space, which are extracted in the second step of our method. The extracted regions may be related to the query region by a non-rigid transform, enabling non-rigid shape matching."}],"issue":"1"},{"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","status":"public","acknowledgement":"We thank R. Dixit for performing complementary experiments, D. W. Ehrhardt and T. Hashimoto for providing the seeds of TUB6–RFP and EB1b–GFP respectively, E. Zazimalova, J. Petrasek and M. Fendrych for discussing the manuscript and J. Leung for text optimization. This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP, to J.F.), ANR blanc AuxiWall project (ANR-11-BSV5-0007, to C.P.-R. and L.G.) and the Agency for Innovation by Science and Technology (IWT) (to H.R.). This work benefited from the facilities and expertise of the Imagif Cell Biology platform (http://www.imagif.cnrs.fr), which is supported by the Conseil Général de l’Essonne.","ec_funded":1,"title":"Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules","author":[{"last_name":"Chen","full_name":"Chen, Xu","first_name":"Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Laurie","last_name":"Grandont","full_name":"Grandont, Laurie"},{"orcid":"0000-0001-5039-9660","full_name":"Li, Hongjiang","last_name":"Li","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongjiang"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Hauschild, Robert","last_name":"Hauschild"},{"first_name":"Sébastien","last_name":"Paque","full_name":"Paque, Sébastien"},{"last_name":"Abuzeineh","full_name":"Abuzeineh, Anas","first_name":"Anas"},{"first_name":"Hana","id":"4CAAA450-78D2-11EA-8E57-B40A396E08BA","last_name":"Rakusova","full_name":"Rakusova, Hana"},{"last_name":"Benková","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"},{"first_name":"Catherine","last_name":"Perrot Rechenmann","full_name":"Perrot Rechenmann, Catherine"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596"}],"_id":"1862","abstract":[{"lang":"eng","text":"The prominent and evolutionarily ancient role of the plant hormone auxin is the regulation of cell expansion. Cell expansion requires ordered arrangement of the cytoskeleton but molecular mechanisms underlying its regulation by signalling molecules including auxin are unknown. Here we show in the model plant Arabidopsis thaliana that in elongating cells exogenous application of auxin or redistribution of endogenous auxin induces very rapid microtubule re-orientation from transverse to longitudinal, coherent with the inhibition of cell expansion. This fast auxin effect requires auxin binding protein 1 (ABP1) and involves a contribution of downstream signalling components such as ROP6 GTPase, ROP-interactive protein RIC1 and the microtubule-severing protein katanin. These components are required for rapid auxin-and ABP1-mediated re-orientation of microtubules to regulate cell elongation in roots and dark-grown hypocotyls as well as asymmetric growth during gravitropic responses."}],"issue":"729","doi":"10.1038/nature13889","volume":516,"article_processing_charge":"No","citation":{"ieee":"X. Chen <i>et al.</i>, “Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules,” <i>Nature</i>, vol. 516, no. 729. Nature Publishing Group, pp. 90–93, 2014.","apa":"Chen, X., Grandont, L., Li, H., Hauschild, R., Paque, S., Abuzeineh, A., … Friml, J. (2014). Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature13889\">https://doi.org/10.1038/nature13889</a>","short":"X. Chen, L. Grandont, H. Li, R. Hauschild, S. Paque, A. Abuzeineh, H. Rakusova, E. Benková, C. Perrot Rechenmann, J. Friml, Nature 516 (2014) 90–93.","ista":"Chen X, Grandont L, Li H, Hauschild R, Paque S, Abuzeineh A, Rakusova H, Benková E, Perrot Rechenmann C, Friml J. 2014. Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules. Nature. 516(729), 90–93.","ama":"Chen X, Grandont L, Li H, et al. Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules. <i>Nature</i>. 2014;516(729):90-93. doi:<a href=\"https://doi.org/10.1038/nature13889\">10.1038/nature13889</a>","mla":"Chen, Xu, et al. “Inhibition of Cell Expansion by Rapid ABP1-Mediated Auxin Effect on Microtubules.” <i>Nature</i>, vol. 516, no. 729, Nature Publishing Group, 2014, pp. 90–93, doi:<a href=\"https://doi.org/10.1038/nature13889\">10.1038/nature13889</a>.","chicago":"Chen, Xu, Laurie Grandont, Hongjiang Li, Robert Hauschild, Sébastien Paque, Anas Abuzeineh, Hana Rakusova, Eva Benková, Catherine Perrot Rechenmann, and Jiří Friml. “Inhibition of Cell Expansion by Rapid ABP1-Mediated Auxin Effect on Microtubules.” <i>Nature</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/nature13889\">https://doi.org/10.1038/nature13889</a>."},"day":"04","month":"12","pmid":1,"oa_version":"Submitted Version","publication":"Nature","date_updated":"2025-05-07T11:12:31Z","page":"90 - 93","article_type":"original","oa":1,"year":"2014","publisher":"Nature Publishing Group","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257754/"}],"intvolume":"       516","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","department":[{"_id":"JiFr"},{"_id":"Bio"},{"_id":"EvBe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5237","external_id":{"pmid":["25409144"]},"date_published":"2014-12-04T00:00:00Z","date_created":"2018-12-11T11:54:25Z","scopus_import":"1"},{"date_updated":"2021-01-12T06:53:44Z","publication":"HVC 2014","page":"68 - 74","alternative_title":["LNCS"],"year":"2014","intvolume":"      8855","publisher":"Springer","language":[{"iso":"eng"}],"type":"conference","quality_controlled":"1","publist_id":"5228","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ToHe"}],"date_created":"2018-12-11T11:54:27Z","date_published":"2014-01-01T00:00:00Z","project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"}],"ec_funded":1,"acknowledgement":"The work presented in this paper was supported in part by the European Research Council (ERC) under grant agreement QUAINT (I774-N23)","status":"public","publication_status":"published","_id":"1869","editor":[{"first_name":"Eran","full_name":"Yahav, Eran","last_name":"Yahav"}],"author":[{"last_name":"Hofferek","full_name":"Hofferek, Georg","first_name":"Georg"},{"id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh","full_name":"Gupta, Ashutosh","last_name":"Gupta"}],"title":"Suraq - a controller synthesis tool using uninterpreted functions","doi":"10.1007/978-3-319-13338-6_6","abstract":[{"text":"Boolean controllers for systems with complex datapaths are often very difficult to implement correctly, in particular when concurrency is involved. Yet, in many instances it is easy to formally specify correctness. For example, the specification for the controller of a pipelined processor only has to state that the pipelined processor gives the same results as a non-pipelined reference design. This makes such controllers a good target for automated synthesis. However, an efficient abstraction for the complex datapath elements is needed, as a bit-precise description is often infeasible. We present Suraq, the first controller synthesis tool which uses uninterpreted functions for the abstraction. Quantified firstorder formulas (with specific quantifier structure) serve as the specification language from which Suraq synthesizes Boolean controllers. Suraq transforms the specification into an unsatisfiable SMT formula, and uses Craig interpolation to compute its results. Using Suraq, we were able to synthesize a controller (consisting of two Boolean signals) for a five-stage pipelined DLX processor in roughly one hour and 15 minutes.","lang":"eng"}],"volume":8855,"month":"01","day":"01","citation":{"apa":"Hofferek, G., &#38; Gupta, A. (2014). Suraq - a controller synthesis tool using uninterpreted functions. In E. Yahav (Ed.), <i>HVC 2014</i> (Vol. 8855, pp. 68–74). Haifa, Israel: Springer. <a href=\"https://doi.org/10.1007/978-3-319-13338-6_6\">https://doi.org/10.1007/978-3-319-13338-6_6</a>","ieee":"G. Hofferek and A. Gupta, “Suraq - a controller synthesis tool using uninterpreted functions,” in <i>HVC 2014</i>, Haifa, Israel, 2014, vol. 8855, pp. 68–74.","ama":"Hofferek G, Gupta A. Suraq - a controller synthesis tool using uninterpreted functions. In: Yahav E, ed. <i>HVC 2014</i>. Vol 8855. Springer; 2014:68-74. doi:<a href=\"https://doi.org/10.1007/978-3-319-13338-6_6\">10.1007/978-3-319-13338-6_6</a>","short":"G. Hofferek, A. Gupta, in:, E. Yahav (Ed.), HVC 2014, Springer, 2014, pp. 68–74.","ista":"Hofferek G, Gupta A. 2014. Suraq - a controller synthesis tool using uninterpreted functions. HVC 2014. HVC: Haifa Verification Conference, LNCS, vol. 8855, 68–74.","chicago":"Hofferek, Georg, and Ashutosh Gupta. “Suraq - a Controller Synthesis Tool Using Uninterpreted Functions.” In <i>HVC 2014</i>, edited by Eran Yahav, 8855:68–74. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-319-13338-6_6\">https://doi.org/10.1007/978-3-319-13338-6_6</a>.","mla":"Hofferek, Georg, and Ashutosh Gupta. “Suraq - a Controller Synthesis Tool Using Uninterpreted Functions.” <i>HVC 2014</i>, edited by Eran Yahav, vol. 8855, Springer, 2014, pp. 68–74, doi:<a href=\"https://doi.org/10.1007/978-3-319-13338-6_6\">10.1007/978-3-319-13338-6_6</a>."},"conference":{"name":"HVC: Haifa Verification Conference","location":"Haifa, Israel","start_date":"2014-11-18","end_date":"2014-11-20"},"oa_version":"None"},{"date_updated":"2021-01-12T06:53:45Z","publication":"Leibniz International Proceedings in Informatics, LIPIcs","page":"431 - 443","oa":1,"alternative_title":["LIPIcs"],"year":"2014","intvolume":"        29","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","language":[{"iso":"eng"}],"type":"conference","publist_id":"5227","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ToHe"}],"date_created":"2018-12-11T11:54:27Z","date_published":"2014-12-01T00:00:00Z","status":"public","publication_status":"published","_id":"1870","author":[{"orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"last_name":"Otop","full_name":"Otop, Jan","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"},{"id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","first_name":"Roopsha","full_name":"Samanta, Roopsha","last_name":"Samanta"}],"title":"Lipschitz robustness of finite-state transducers","doi":"10.4230/LIPIcs.FSTTCS.2014.431","abstract":[{"lang":"eng","text":"We investigate the problem of checking if a finite-state transducer is robust to uncertainty in its input. Our notion of robustness is based on the analytic notion of Lipschitz continuity - a transducer is K-(Lipschitz) robust if the perturbation in its output is at most K times the perturbation in its input. We quantify input and output perturbation using similarity functions. We show that K-robustness is undecidable even for deterministic transducers. We identify a class of functional transducers, which admits a polynomial time automata-theoretic decision procedure for K-robustness. This class includes Mealy machines and functional letter-to-letter transducers. We also study K-robustness of nondeterministic transducers. Since a nondeterministic transducer generates a set of output words for each input word, we quantify output perturbation using setsimilarity functions. We show that K-robustness of nondeterministic transducers is undecidable, even for letter-to-letter transducers. We identify a class of set-similarity functions which admit decidable K-robustness of letter-to-letter transducers."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2018-12-12T10:09:11Z","file_id":"4734","date_updated":"2020-07-14T12:45:19Z","content_type":"application/pdf","checksum":"7b1aff1710a8bffb7080ec07f62d9a17","access_level":"open_access","file_size":562151,"relation":"main_file","creator":"system","file_name":"IST-2017-804-v1+1_37.pdf"}],"volume":29,"has_accepted_license":"1","month":"12","file_date_updated":"2020-07-14T12:45:19Z","ddc":["004"],"day":"01","citation":{"chicago":"Henzinger, Thomas A, Jan Otop, and Roopsha Samanta. “Lipschitz Robustness of Finite-State Transducers.” In <i>Leibniz International Proceedings in Informatics, LIPIcs</i>, 29:431–43. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431\">https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431</a>.","mla":"Henzinger, Thomas A., et al. “Lipschitz Robustness of Finite-State Transducers.” <i>Leibniz International Proceedings in Informatics, LIPIcs</i>, vol. 29, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 431–43, doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431\">10.4230/LIPIcs.FSTTCS.2014.431</a>.","ama":"Henzinger TA, Otop J, Samanta R. Lipschitz robustness of finite-state transducers. In: <i>Leibniz International Proceedings in Informatics, LIPIcs</i>. Vol 29. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:431-443. doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431\">10.4230/LIPIcs.FSTTCS.2014.431</a>","ista":"Henzinger TA, Otop J, Samanta R. 2014. Lipschitz robustness of finite-state transducers. Leibniz International Proceedings in Informatics, LIPIcs. FSTTCS: Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol. 29, 431–443.","short":"T.A. Henzinger, J. Otop, R. Samanta, in:, Leibniz International Proceedings in Informatics, LIPIcs, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 431–443.","apa":"Henzinger, T. A., Otop, J., &#38; Samanta, R. (2014). Lipschitz robustness of finite-state transducers. In <i>Leibniz International Proceedings in Informatics, LIPIcs</i> (Vol. 29, pp. 431–443). Delhi, India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431\">https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431</a>","ieee":"T. A. Henzinger, J. Otop, and R. Samanta, “Lipschitz robustness of finite-state transducers,” in <i>Leibniz International Proceedings in Informatics, LIPIcs</i>, Delhi, India, 2014, vol. 29, pp. 431–443."},"pubrep_id":"804","conference":{"end_date":"2014-12-17","location":"Delhi, India","start_date":"2014-12-15","name":"FSTTCS: Foundations of Software Technology and Theoretical Computer Science"},"oa_version":"Published Version"},{"department":[{"_id":"ToHe"}],"publist_id":"5226","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_published":"2014-01-01T00:00:00Z","scopus_import":1,"date_created":"2018-12-11T11:54:28Z","intvolume":"      8837","publisher":"Springer","quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"oa":1,"year":"2014","alternative_title":["LNCS"],"publication":"ATVA 2014","date_updated":"2021-01-12T06:53:45Z","page":"185 - 200","day":"01","pubrep_id":"641","citation":{"mla":"Gupta, Ashutosh, et al. “Extensional Crisis and Proving Identity.” <i>ATVA 2014</i>, edited by Franck Cassez and Jean-François Raskin, vol. 8837, Springer, 2014, pp. 185–200, doi:<a href=\"https://doi.org/10.1007/978-3-319-11936-6_14\">10.1007/978-3-319-11936-6_14</a>.","chicago":"Gupta, Ashutosh, Laura Kovács, Bernhard Kragl, and Andrei Voronkov. “Extensional Crisis and Proving Identity.” In <i>ATVA 2014</i>, edited by Franck Cassez and Jean-François Raskin, 8837:185–200. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-319-11936-6_14\">https://doi.org/10.1007/978-3-319-11936-6_14</a>.","ama":"Gupta A, Kovács L, Kragl B, Voronkov A. Extensional crisis and proving identity. In: Cassez F, Raskin J-F, eds. <i>ATVA 2014</i>. Vol 8837. Springer; 2014:185-200. doi:<a href=\"https://doi.org/10.1007/978-3-319-11936-6_14\">10.1007/978-3-319-11936-6_14</a>","short":"A. Gupta, L. Kovács, B. Kragl, A. Voronkov, in:, F. Cassez, J.-F. Raskin (Eds.), ATVA 2014, Springer, 2014, pp. 185–200.","ista":"Gupta A, Kovács L, Kragl B, Voronkov A. 2014. Extensional crisis and proving identity. ATVA 2014. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 8837, 185–200.","ieee":"A. Gupta, L. Kovács, B. Kragl, and A. Voronkov, “Extensional crisis and proving identity,” in <i>ATVA 2014</i>, Sydney, Australia, 2014, vol. 8837, pp. 185–200.","apa":"Gupta, A., Kovács, L., Kragl, B., &#38; Voronkov, A. (2014). Extensional crisis and proving identity. In F. Cassez &#38; J.-F. Raskin (Eds.), <i>ATVA 2014</i> (Vol. 8837, pp. 185–200). Sydney, Australia: Springer. <a href=\"https://doi.org/10.1007/978-3-319-11936-6_14\">https://doi.org/10.1007/978-3-319-11936-6_14</a>"},"ddc":["000"],"month":"01","file_date_updated":"2020-07-14T12:45:19Z","conference":{"name":"ATVA: Automated Technology for Verification and Analysis","end_date":"2014-11-07","location":"Sydney, Australia","start_date":"2014-11-03"},"oa_version":"Submitted Version","file":[{"date_created":"2018-12-12T10:10:15Z","file_id":"4801","checksum":"af4bd3fc1f4c93075e4dc5cbf625fe7b","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:19Z","creator":"system","relation":"main_file","file_size":244294,"file_name":"IST-2016-641-v1+1_atva2014.pdf"}],"has_accepted_license":"1","volume":8837,"author":[{"last_name":"Gupta","full_name":"Gupta, Ashutosh","first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Laura","full_name":"Kovács, Laura","last_name":"Kovács"},{"first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87","last_name":"Kragl","full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117"},{"last_name":"Voronkov","full_name":"Voronkov, Andrei","first_name":"Andrei"}],"title":"Extensional crisis and proving identity","_id":"1872","editor":[{"last_name":"Cassez","full_name":"Cassez, Franck","first_name":"Franck"},{"full_name":"Raskin, Jean-François","last_name":"Raskin","first_name":"Jean-François"}],"abstract":[{"text":"Extensionality axioms are common when reasoning about data collections, such as arrays and functions in program analysis, or sets in mathematics. An extensionality axiom asserts that two collections are equal if they consist of the same elements at the same indices. Using extensionality is often required to show that two collections are equal. A typical example is the set theory theorem (∀x)(∀y)x∪y = y ∪x. Interestingly, while humans have no problem with proving such set identities using extensionality, they are very hard for superposition theorem provers because of the calculi they use. In this paper we show how addition of a new inference rule, called extensionality resolution, allows first-order theorem provers to easily solve problems no modern first-order theorem prover can solve. We illustrate this by running the VAMPIRE theorem prover with extensionality resolution on a number of set theory and array problems. Extensionality resolution helps VAMPIRE to solve problems from the TPTP library of first-order problems that were never solved before by any prover.","lang":"eng"}],"doi":"10.1007/978-3-319-11936-6_14","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"}],"status":"public","acknowledgement":"This research was supported in part by the Austrian National Research Network RiSE (S11410-N23).","publication_status":"published","ec_funded":1},{"pubrep_id":"313","citation":{"ieee":"R. Samanta, O. Olivo, and E. Allen, “Cost-aware automatic program repair,” presented at the SAS: Static Analysis Symposium, Munich, Germany, 2014, vol. 8723, pp. 268–284.","apa":"Samanta, R., Olivo, O., &#38; Allen, E. (2014). Cost-aware automatic program repair. In M. Müller-Olm &#38; H. Seidl (Eds.) (Vol. 8723, pp. 268–284). Presented at the SAS: Static Analysis Symposium, Munich, Germany: Springer. <a href=\"https://doi.org/10.1007/978-3-319-10936-7_17\">https://doi.org/10.1007/978-3-319-10936-7_17</a>","ama":"Samanta R, Olivo O, Allen E. Cost-aware automatic program repair. In: Müller-Olm M, Seidl H, eds. Vol 8723. Springer; 2014:268-284. doi:<a href=\"https://doi.org/10.1007/978-3-319-10936-7_17\">10.1007/978-3-319-10936-7_17</a>","short":"R. Samanta, O. Olivo, E. Allen, in:, M. Müller-Olm, H. Seidl (Eds.), Springer, 2014, pp. 268–284.","ista":"Samanta R, Olivo O, Allen E. 2014. Cost-aware automatic program repair. SAS: Static Analysis Symposium, LNCS, vol. 8723, 268–284.","chicago":"Samanta, Roopsha, Oswaldo Olivo, and Emerson Allen. “Cost-Aware Automatic Program Repair.” edited by Markus Müller-Olm and Helmut Seidl, 8723:268–84. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-319-10936-7_17\">https://doi.org/10.1007/978-3-319-10936-7_17</a>.","mla":"Samanta, Roopsha, et al. <i>Cost-Aware Automatic Program Repair</i>. Edited by Markus Müller-Olm and Helmut Seidl, vol. 8723, Springer, 2014, pp. 268–84, doi:<a href=\"https://doi.org/10.1007/978-3-319-10936-7_17\">10.1007/978-3-319-10936-7_17</a>."},"day":"01","month":"09","file_date_updated":"2020-07-14T12:45:19Z","ddc":["000","005"],"oa_version":"Submitted Version","conference":{"name":"SAS: Static Analysis Symposium","start_date":"2014-09-11","location":"Munich, Germany","end_date":"2014-09-14"},"file":[{"file_name":"IST-2014-313-v1+1_SOE.SAS14.pdf","creator":"system","relation":"main_file","file_size":409485,"date_updated":"2020-07-14T12:45:19Z","access_level":"open_access","content_type":"application/pdf","checksum":"78ec4ea1bdecc676cd3e8cad35c6182c","file_id":"4650","date_created":"2018-12-12T10:07:51Z"}],"has_accepted_license":"1","volume":8723,"title":"Cost-aware automatic program repair","author":[{"first_name":"Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","last_name":"Samanta","full_name":"Samanta, Roopsha"},{"first_name":"Oswaldo","full_name":"Olivo, Oswaldo","last_name":"Olivo"},{"first_name":"Emerson","full_name":"Allen, Emerson","last_name":"Allen"}],"_id":"1875","editor":[{"first_name":"Markus","last_name":"Müller-Olm","full_name":"Müller-Olm, Markus"},{"full_name":"Seidl, Helmut","last_name":"Seidl","first_name":"Helmut"}],"abstract":[{"text":"We present a formal framework for repairing infinite-state, imperative, sequential programs, with (possibly recursive) procedures and multiple assertions; the framework can generate repaired programs by modifying the original erroneous program in multiple program locations, and can ensure the readability of the repaired program using user-defined expression templates; the framework also generates a set of inductive assertions that serve as a proof of correctness of the repaired program. As a step toward integrating programmer intent and intuition in automated program repair, we present a cost-aware formulation - given a cost function associated with permissible statement modifications, the goal is to ensure that the total program modification cost does not exceed a given repair budget. As part of our predicate abstractionbased solution framework, we present a sound and complete algorithm for repair of Boolean programs. We have developed a prototype tool based on SMT solving and used it successfully to repair diverse errors in benchmark C programs.","lang":"eng"}],"doi":"10.1007/978-3-319-10936-7_17","publication_status":"published","status":"public","department":[{"_id":"ToHe"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5221","date_published":"2014-09-01T00:00:00Z","date_created":"2018-12-11T11:54:29Z","scopus_import":1,"publisher":"Springer","intvolume":"      8723","quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"oa":1,"alternative_title":["LNCS"],"year":"2014","date_updated":"2021-01-12T06:53:46Z","page":"268 - 284"},{"year":"2014","oa":1,"article_type":"original","page":"491 - 504","date_updated":"2022-03-03T11:47:09Z","publication":"Moscow Mathematical Journal","scopus_import":"1","date_created":"2018-12-11T11:54:29Z","date_published":"2014-07-01T00:00:00Z","external_id":{"arxiv":["1211.7053"]},"publist_id":"5220","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"}],"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","intvolume":"        14","main_file_link":[{"url":"http://arxiv.org/abs/1211.7053","open_access":"1"}],"publisher":"Independent University of Moscow","doi":"10.17323/1609-4514-2014-14-3-491-504","issue":"3","abstract":[{"text":"We study densities of functionals over uniformly bounded triangulations of a Delaunay set of vertices, and prove that the minimum is attained for the Delaunay triangulation if this is the case for finite sets.","lang":"eng"}],"_id":"1876","author":[{"first_name":"Nikolai","full_name":"Dolbilin, Nikolai","last_name":"Dolbilin"},{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"first_name":"Alexey","last_name":"Glazyrin","full_name":"Glazyrin, Alexey"},{"last_name":"Musin","full_name":"Musin, Oleg","first_name":"Oleg"}],"title":"Functionals on triangulations of delaunay sets","publication_status":"published","status":"public","publication_identifier":{"issn":["16093321"]},"oa_version":"Submitted Version","month":"07","day":"01","citation":{"mla":"Dolbilin, Nikolai, et al. “Functionals on Triangulations of Delaunay Sets.” <i>Moscow Mathematical Journal</i>, vol. 14, no. 3, Independent University of Moscow, 2014, pp. 491–504, doi:<a href=\"https://doi.org/10.17323/1609-4514-2014-14-3-491-504\">10.17323/1609-4514-2014-14-3-491-504</a>.","chicago":"Dolbilin, Nikolai, Herbert Edelsbrunner, Alexey Glazyrin, and Oleg Musin. “Functionals on Triangulations of Delaunay Sets.” <i>Moscow Mathematical Journal</i>. Independent University of Moscow, 2014. <a href=\"https://doi.org/10.17323/1609-4514-2014-14-3-491-504\">https://doi.org/10.17323/1609-4514-2014-14-3-491-504</a>.","ieee":"N. Dolbilin, H. Edelsbrunner, A. Glazyrin, and O. Musin, “Functionals on triangulations of delaunay sets,” <i>Moscow Mathematical Journal</i>, vol. 14, no. 3. Independent University of Moscow, pp. 491–504, 2014.","apa":"Dolbilin, N., Edelsbrunner, H., Glazyrin, A., &#38; Musin, O. (2014). Functionals on triangulations of delaunay sets. <i>Moscow Mathematical Journal</i>. Independent University of Moscow. <a href=\"https://doi.org/10.17323/1609-4514-2014-14-3-491-504\">https://doi.org/10.17323/1609-4514-2014-14-3-491-504</a>","ista":"Dolbilin N, Edelsbrunner H, Glazyrin A, Musin O. 2014. Functionals on triangulations of delaunay sets. Moscow Mathematical Journal. 14(3), 491–504.","ama":"Dolbilin N, Edelsbrunner H, Glazyrin A, Musin O. Functionals on triangulations of delaunay sets. <i>Moscow Mathematical Journal</i>. 2014;14(3):491-504. doi:<a href=\"https://doi.org/10.17323/1609-4514-2014-14-3-491-504\">10.17323/1609-4514-2014-14-3-491-504</a>","short":"N. Dolbilin, H. Edelsbrunner, A. Glazyrin, O. Musin, Moscow Mathematical Journal 14 (2014) 491–504."},"volume":14,"article_processing_charge":"No","arxiv":1},{"oa_version":"None","date_created":"2018-12-11T11:54:30Z","scopus_import":1,"date_published":"2014-10-23T00:00:00Z","publist_id":"5219","month":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Sixt, Michael K., and Kari Vaahtomeri. “Physiology: Relax and Come In.” <i>Nature</i>, vol. 514, no. 7523, Springer Nature, 2014, pp. 441–42, doi:<a href=\"https://doi.org/10.1038/514441a\">10.1038/514441a</a>.","chicago":"Sixt, Michael K, and Kari Vaahtomeri. “Physiology: Relax and Come In.” <i>Nature</i>. Springer Nature, 2014. <a href=\"https://doi.org/10.1038/514441a\">https://doi.org/10.1038/514441a</a>.","short":"M.K. Sixt, K. Vaahtomeri, Nature 514 (2014) 441–442.","ista":"Sixt MK, Vaahtomeri K. 2014. Physiology: Relax and come in. Nature. 514(7523), 441–442.","ama":"Sixt MK, Vaahtomeri K. Physiology: Relax and come in. <i>Nature</i>. 2014;514(7523):441-442. doi:<a href=\"https://doi.org/10.1038/514441a\">10.1038/514441a</a>","ieee":"M. K. Sixt and K. Vaahtomeri, “Physiology: Relax and come in,” <i>Nature</i>, vol. 514, no. 7523. Springer Nature, pp. 441–442, 2014.","apa":"Sixt, M. K., &#38; Vaahtomeri, K. (2014). Physiology: Relax and come in. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/514441a\">https://doi.org/10.1038/514441a</a>"},"department":[{"_id":"MiSi"}],"day":"23","volume":514,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","publisher":"Springer Nature","intvolume":"       514","doi":"10.1038/514441a","abstract":[{"lang":"eng","text":"During inflammation, lymph nodes swell with an influx of immune cells. New findings identify a signalling pathway that induces relaxation in the contractile cells that give structure to these organs."}],"issue":"7523","year":"2014","_id":"1877","title":"Physiology: Relax and come in","author":[{"orcid":"0000-0002-6620-9179","last_name":"Sixt","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kari","id":"368EE576-F248-11E8-B48F-1D18A9856A87","last_name":"Vaahtomeri","full_name":"Vaahtomeri, Kari","orcid":"0000-0001-7829-3518"}],"page":"441 - 442","article_type":"letter_note","publication_status":"published","status":"public","date_updated":"2021-01-12T06:53:47Z","publication":"Nature"},{"publication_status":"published","status":"public","page":"1952 - 1952","publication":"Blood","date_updated":"2021-01-12T06:53:50Z","issue":"21","year":"2014","abstract":[{"lang":"eng","text":"Unbiased high-throughput massively parallel sequencing methods have transformed the process of discovery of novel putative driver gene mutations in cancer. In chronic lymphocytic leukemia (CLL), these methods have yielded several unexpected findings, including the driver genes SF3B1, NOTCH1 and POT1. Recent analysis, utilizing down-sampling of existing datasets, has shown that the discovery process of putative drivers is far from complete across cancer. In CLL, while driver gene mutations affecting >10% of patients were efficiently discovered with previously published CLL cohorts of up to 160 samples subjected to whole exome sequencing (WES), this sample size has only 0.78 power to detect drivers affecting 5% of patients, and only 0.12 power for drivers affecting 2% of patients. These calculations emphasize the need to apply unbiased WES to larger patient cohorts."}],"author":[{"last_name":"Landau","full_name":"Landau, Dan","first_name":"Dan"},{"full_name":"Stewart, Chip","last_name":"Stewart","first_name":"Chip"},{"last_name":"Reiter","full_name":"Reiter, Johannes","first_name":"Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0170-7353"},{"first_name":"Michael","full_name":"Lawrence, Michael","last_name":"Lawrence"},{"first_name":"Carrie","full_name":"Sougnez, Carrie","last_name":"Sougnez"},{"first_name":"Jennifer","full_name":"Brown, Jennifer","last_name":"Brown"},{"full_name":"Lopez Guillermo, Armando","last_name":"Lopez Guillermo","first_name":"Armando"},{"full_name":"Gabriel, Stacey","last_name":"Gabriel","first_name":"Stacey"},{"first_name":"Eric","last_name":"Lander","full_name":"Lander, Eric"},{"first_name":"Donna","last_name":"Neuberg","full_name":"Neuberg, Donna"},{"first_name":"Carlos","last_name":"López Otín","full_name":"López Otín, Carlos"},{"full_name":"Campo, Elias","last_name":"Campo","first_name":"Elias"},{"first_name":"Gad","full_name":"Getz, Gad","last_name":"Getz"},{"first_name":"Catherine","full_name":"Wu, Catherine","last_name":"Wu"}],"title":"Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples","_id":"1884","type":"journal_article","language":[{"iso":"eng"}],"volume":124,"main_file_link":[{"url":"http://www.bloodjournal.org/content/124/21/1952?sso-checked=true"}],"intvolume":"       124","publisher":"American Society of Hematology","date_published":"2014-12-04T00:00:00Z","oa_version":"None","date_created":"2018-12-11T11:54:32Z","department":[{"_id":"KrCh"}],"day":"04","citation":{"ieee":"D. Landau <i>et al.</i>, “Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples,” <i>Blood</i>, vol. 124, no. 21. American Society of Hematology, pp. 1952–1952, 2014.","apa":"Landau, D., Stewart, C., Reiter, J., Lawrence, M., Sougnez, C., Brown, J., … Wu, C. (2014). Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples. <i>Blood</i>. American Society of Hematology.","ama":"Landau D, Stewart C, Reiter J, et al. Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples. <i>Blood</i>. 2014;124(21):1952-1952.","short":"D. Landau, C. Stewart, J. Reiter, M. Lawrence, C. Sougnez, J. Brown, A. Lopez Guillermo, S. Gabriel, E. Lander, D. Neuberg, C. López Otín, E. Campo, G. Getz, C. Wu, Blood 124 (2014) 1952–1952.","ista":"Landau D, Stewart C, Reiter J, Lawrence M, Sougnez C, Brown J, Lopez Guillermo A, Gabriel S, Lander E, Neuberg D, López Otín C, Campo E, Getz G, Wu C. 2014. Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples. Blood. 124(21), 1952–1952.","mla":"Landau, Dan, et al. “Novel Putative Driver Gene Mutations in Chronic Lymphocytic Leukemia (CLL): Results from a Combined Analysis of Whole Exome Sequencing of 262 Primary CLL Aamples.” <i>Blood</i>, vol. 124, no. 21, American Society of Hematology, 2014, pp. 1952–1952.","chicago":"Landau, Dan, Chip Stewart, Johannes Reiter, Michael Lawrence, Carrie Sougnez, Jennifer Brown, Armando Lopez Guillermo, et al. “Novel Putative Driver Gene Mutations in Chronic Lymphocytic Leukemia (CLL): Results from a Combined Analysis of Whole Exome Sequencing of 262 Primary CLL Aamples.” <i>Blood</i>. American Society of Hematology, 2014."},"month":"12","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5211"},{"status":"public","publication_status":"published","project":[{"call_identifier":"FWF","name":"Sensitivity to higher-order statistics in natural scenes","grant_number":"P 25651-N26","_id":"254D1A94-B435-11E9-9278-68D0E5697425"}],"doi":"10.7554/eLife.03722","abstract":[{"lang":"eng","text":"Information processing in the sensory periphery is shaped by natural stimulus statistics. In the periphery, a transmission bottleneck constrains performance; thus efficient coding implies that natural signal components with a predictably wider range should be compressed. In a different regime—when sampling limitations constrain performance—efficient coding implies that more resources should be allocated to informative features that are more variable. We propose that this regime is relevant for sensory cortex when it extracts complex features from limited numbers of sensory samples. To test this prediction, we use central visual processing as a model: we show that visual sensitivity for local multi-point spatial correlations, described by dozens of independently-measured parameters, can be quantitatively predicted from the structure of natural images. This suggests that efficient coding applies centrally, where it extends to higher-order sensory features and operates in a regime in which sensitivity increases with feature variability."}],"issue":"November","_id":"1886","title":"Variance predicts salience in central sensory processing","author":[{"last_name":"Hermundstad","full_name":"Hermundstad, Ann","first_name":"Ann"},{"first_name":"John","full_name":"Briguglio, John","last_name":"Briguglio"},{"first_name":"Mary","last_name":"Conte","full_name":"Conte, Mary"},{"full_name":"Victor, Jonathan","last_name":"Victor","first_name":"Jonathan"},{"first_name":"Vijay","last_name":"Balasubramanian","full_name":"Balasubramanian, Vijay"},{"orcid":"0000-0002-6699-1455","last_name":"Tkacik","full_name":"Tkacik, Gasper","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","file":[{"date_updated":"2020-07-14T12:45:20Z","access_level":"open_access","content_type":"application/pdf","checksum":"766ac8999ac6e3364f10065a06024b8f","file_name":"IST-2016-420-v1+1_e03722.full.pdf","file_size":5117086,"relation":"main_file","creator":"system","file_id":"4922","date_created":"2018-12-12T10:12:04Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","ddc":["570"],"file_date_updated":"2020-07-14T12:45:20Z","month":"11","citation":{"mla":"Hermundstad, Ann, et al. “Variance Predicts Salience in Central Sensory Processing.” <i>ELife</i>, no. November, e03722, eLife Sciences Publications, 2014, doi:<a href=\"https://doi.org/10.7554/eLife.03722\">10.7554/eLife.03722</a>.","chicago":"Hermundstad, Ann, John Briguglio, Mary Conte, Jonathan Victor, Vijay Balasubramanian, and Gašper Tkačik. “Variance Predicts Salience in Central Sensory Processing.” <i>ELife</i>. eLife Sciences Publications, 2014. <a href=\"https://doi.org/10.7554/eLife.03722\">https://doi.org/10.7554/eLife.03722</a>.","ieee":"A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, and G. Tkačik, “Variance predicts salience in central sensory processing,” <i>eLife</i>, no. November. eLife Sciences Publications, 2014.","apa":"Hermundstad, A., Briguglio, J., Conte, M., Victor, J., Balasubramanian, V., &#38; Tkačik, G. (2014). Variance predicts salience in central sensory processing. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.03722\">https://doi.org/10.7554/eLife.03722</a>","short":"A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, G. Tkačik, ELife (2014).","ista":"Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkačik G. 2014. Variance predicts salience in central sensory processing. eLife. (November), e03722.","ama":"Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkačik G. Variance predicts salience in central sensory processing. <i>eLife</i>. 2014;(November). doi:<a href=\"https://doi.org/10.7554/eLife.03722\">10.7554/eLife.03722</a>"},"pubrep_id":"420","day":"14","article_number":"e03722","date_updated":"2021-01-12T06:53:50Z","publication":"eLife","year":"2014","oa":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"publisher":"eLife Sciences Publications","date_created":"2018-12-11T11:54:32Z","scopus_import":1,"date_published":"2014-11-14T00:00:00Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5209","department":[{"_id":"GaTk"}]},{"date_created":"2018-12-11T11:54:33Z","oa_version":"Published Version","date_published":"2014-01-01T00:00:00Z","month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5208","citation":{"mla":"Cremer, Sylvia. “Gemeinsame Krankheitsabwehr in Ameisengesellschaften.” <i>Zoologie</i>, Deutsche Zoologische Gesellschaft, 2014, pp. 23–30.","chicago":"Cremer, Sylvia. “Gemeinsame Krankheitsabwehr in Ameisengesellschaften.” <i>Zoologie</i>. Deutsche Zoologische Gesellschaft, 2014.","apa":"Cremer, S. (2014). Gemeinsame Krankheitsabwehr in Ameisengesellschaften. <i>Zoologie</i>. Deutsche Zoologische Gesellschaft.","ieee":"S. Cremer, “Gemeinsame Krankheitsabwehr in Ameisengesellschaften,” <i>Zoologie</i>. Deutsche Zoologische Gesellschaft, pp. 23–30, 2014.","ista":"Cremer S. 2014. Gemeinsame Krankheitsabwehr in Ameisengesellschaften. Zoologie., 23–30.","ama":"Cremer S. Gemeinsame Krankheitsabwehr in Ameisengesellschaften. <i>Zoologie</i>. 2014:23-30.","short":"S. Cremer, Zoologie (2014) 23–30."},"day":"01","department":[{"_id":"SyCr"}],"article_processing_charge":"No","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"publisher":"Deutsche Zoologische Gesellschaft","main_file_link":[{"open_access":"1","url":"https://www.dzg-ev.de/wp-content/uploads/2019/05/zoologie2014.pdf"}],"year":"2014","_id":"1887","title":"Gemeinsame Krankheitsabwehr in Ameisengesellschaften","oa":1,"author":[{"orcid":"0000-0002-2193-3868","last_name":"Cremer","full_name":"Cremer, Sylvia","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"page":"23 - 30","article_type":"original","status":"public","publication_status":"published","date_updated":"2023-10-17T07:54:57Z","publication":"Zoologie"}]