[{"author":[{"full_name":"Chen, Wenbo","first_name":"Wenbo","last_name":"Chen"},{"full_name":"Li, Haixing","first_name":"Haixing","last_name":"Li"},{"first_name":"Jonathan R.","full_name":"Widawsky, Jonathan R.","last_name":"Widawsky"},{"last_name":"Appayee","full_name":"Appayee, Chandrakumar","first_name":"Chandrakumar"},{"last_name":"Venkataraman","first_name":"Latha","orcid":"0000-0002-6957-6089","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","full_name":"Venkataraman, Latha"},{"first_name":"Ronald","full_name":"Breslow, Ronald","last_name":"Breslow"}],"issue":"3","intvolume":"       136","external_id":{"pmid":["24397414"]},"language":[{"iso":"eng"}],"quality_controlled":"1","citation":{"mla":"Chen, Wenbo, et al. “Aromaticity Decreases Single-Molecule Junction Sonductance.” <i>Journal of the American Chemical Society</i>, vol. 136, no. 3, American Chemical Society, 2014, pp. 918–20, doi:<a href=\"https://doi.org/10.1021/ja411143s\">10.1021/ja411143s</a>.","ama":"Chen W, Li H, Widawsky JR, Appayee C, Venkataraman L, Breslow R. Aromaticity decreases single-molecule junction sonductance. <i>Journal of the American Chemical Society</i>. 2014;136(3):918-920. doi:<a href=\"https://doi.org/10.1021/ja411143s\">10.1021/ja411143s</a>","apa":"Chen, W., Li, H., Widawsky, J. R., Appayee, C., Venkataraman, L., &#38; Breslow, R. (2014). Aromaticity decreases single-molecule junction sonductance. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja411143s\">https://doi.org/10.1021/ja411143s</a>","ieee":"W. Chen, H. Li, J. R. Widawsky, C. Appayee, L. Venkataraman, and R. Breslow, “Aromaticity decreases single-molecule junction sonductance,” <i>Journal of the American Chemical Society</i>, vol. 136, no. 3. American Chemical Society, pp. 918–920, 2014.","ista":"Chen W, Li H, Widawsky JR, Appayee C, Venkataraman L, Breslow R. 2014. Aromaticity decreases single-molecule junction sonductance. Journal of the American Chemical Society. 136(3), 918–920.","chicago":"Chen, Wenbo, Haixing Li, Jonathan R. Widawsky, Chandrakumar Appayee, Latha Venkataraman, and Ronald Breslow. “Aromaticity Decreases Single-Molecule Junction Sonductance.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2014. <a href=\"https://doi.org/10.1021/ja411143s\">https://doi.org/10.1021/ja411143s</a>.","short":"W. Chen, H. Li, J.R. Widawsky, C. Appayee, L. Venkataraman, R. Breslow, Journal of the American Chemical Society 136 (2014) 918–920."},"OA_type":"closed access","status":"public","extern":"1","publication_status":"published","date_published":"2014-01-07T00:00:00Z","year":"2014","publication":"Journal of the American Chemical Society","title":"Aromaticity decreases single-molecule junction sonductance","date_created":"2024-09-09T11:25:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"date_updated":"2025-01-03T07:46:41Z","abstract":[{"lang":"eng","text":"We have measured the conductance of single-molecule junctions created with three different molecular wires using the scanning tunneling microscope-based break-junction technique. Each wire contains one of three different cyclic five-membered rings: cyclopentadiene, furan, or thiophene. We find that the single-molecule conductance of these three wires correlates negatively with the resonance energy of the five-membered ring; the nonaromatic cyclopentadiene derivative has the highest conductance, while the most aromatic of this series, thiophene, has the lowest. Furthermore, we show for another wire structure that the conductance of furan-based wires is consistently higher than for analogous thiophene systems, indicating that the negative correlation between conductance and aromaticity is robust. The best conductance would be for a quinoid structure that diminishes aromaticity. The energy penalty for partly adopting the quinoid structure is less with compounds having lower initial aromatic stabilization. An additional effect may reflect the lower HOMOs of aromatic compounds."}],"publisher":"American Chemical Society","article_type":"letter_note","doi":"10.1021/ja411143s","day":"07","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"volume":136,"_id":"17989","month":"01","type":"journal_article","oa_version":"None","page":"918-920","scopus_import":"1","article_processing_charge":"No"},{"author":[{"full_name":"Kim, Taekyeong","first_name":"Taekyeong","last_name":"Kim"},{"full_name":"Liu, Zhen-Fei","first_name":"Zhen-Fei","last_name":"Liu"},{"first_name":"Chulho","full_name":"Lee, Chulho","last_name":"Lee"},{"first_name":"Jeffrey B.","full_name":"Neaton, Jeffrey B.","last_name":"Neaton"},{"last_name":"Venkataraman","first_name":"Latha","full_name":"Venkataraman, Latha","id":"9ebb78a5-cc0d-11ee-8322-fae086a32caf","orcid":"0000-0002-6957-6089"}],"intvolume":"       111","issue":"30","citation":{"chicago":"Kim, Taekyeong, Zhen-Fei Liu, Chulho Lee, Jeffrey B. Neaton, and Latha Venkataraman. “Charge Transport and Rectification in Molecular Junctions Formed with Carbon-Based Electrodes.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1406926111\">https://doi.org/10.1073/pnas.1406926111</a>.","short":"T. Kim, Z.-F. Liu, C. Lee, J.B. Neaton, L. Venkataraman, Proceedings of the National Academy of Sciences 111 (2014) 10928–10932.","mla":"Kim, Taekyeong, et al. “Charge Transport and Rectification in Molecular Junctions Formed with Carbon-Based Electrodes.” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 30, National Academy of Sciences, 2014, pp. 10928–32, doi:<a href=\"https://doi.org/10.1073/pnas.1406926111\">10.1073/pnas.1406926111</a>.","ista":"Kim T, Liu Z-F, Lee C, Neaton JB, Venkataraman L. 2014. Charge transport and rectification in molecular junctions formed with carbon-based electrodes. Proceedings of the National Academy of Sciences. 111(30), 10928–10932.","apa":"Kim, T., Liu, Z.-F., Lee, C., Neaton, J. B., &#38; Venkataraman, L. (2014). Charge transport and rectification in molecular junctions formed with carbon-based electrodes. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1406926111\">https://doi.org/10.1073/pnas.1406926111</a>","ama":"Kim T, Liu Z-F, Lee C, Neaton JB, Venkataraman L. Charge transport and rectification in molecular junctions formed with carbon-based electrodes. <i>Proceedings of the National Academy of Sciences</i>. 2014;111(30):10928-10932. doi:<a href=\"https://doi.org/10.1073/pnas.1406926111\">10.1073/pnas.1406926111</a>","ieee":"T. Kim, Z.-F. Liu, C. Lee, J. B. Neaton, and L. Venkataraman, “Charge transport and rectification in molecular junctions formed with carbon-based electrodes,” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 30. National Academy of Sciences, pp. 10928–10932, 2014."},"OA_type":"closed access","date_published":"2014-07-14T00:00:00Z","year":"2014","extern":"1","status":"public","publication_status":"published","language":[{"iso":"eng"}],"external_id":{"pmid":["25024198"]},"quality_controlled":"1","date_updated":"2025-01-03T07:49:30Z","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Charge transport and rectification in molecular junctions formed with carbon-based electrodes","publication":"Proceedings of the National Academy of Sciences","date_created":"2024-09-09T11:26:38Z","publisher":"National Academy of Sciences","abstract":[{"text":"Molecular junctions formed using the scanning-tunneling-microscope–based break-junction technique (STM-BJ) have provided unique insight into charge transport at the nanoscale. In most prior work, the same metal, typically Au, Pt, or Ag, is used for both tip and substrate. For such noble metal electrodes, the density of electronic states is approximately constant within a narrow energy window relevant to charge transport. Here, we form molecular junctions using the STM-BJ technique, with an Au metal tip and a microfabricated graphite substrate, and measure the conductance of a series of graphite/amine-terminated oligophenyl/Au molecular junctions. The remarkable mechanical strength of graphite and the single-crystal properties of our substrates allow measurements over few thousand junctions without any change in the surface properties. We show that conductance decays exponentially with molecular backbone length with a decay constant that is essentially the same as that for measurements with two Au electrodes. More importantly, despite the inherent symmetry of the oligophenylamines, we observe rectification in these junctions. State-of-art ab initio conductance calculations are in good agreement with experiment, and explain the rectification. We show that the highly energy-dependent graphite density of states contributes variations in transmission that, when coupled with an asymmetric voltage drop across the junction, leads to the observed rectification. Together, our measurements and calculations show how functionality may emerge from hybrid molecular-scale devices purposefully designed with different electrodes beyond the so-called “wide band limit,” opening up the possibility of assembling molecular junctions with dissimilar electrodes using layered 2D materials.","lang":"eng"}],"article_type":"original","_id":"17990","volume":111,"day":"14","doi":"10.1073/pnas.1406926111","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"type":"journal_article","month":"07","oa_version":"None","article_processing_charge":"No","page":"10928-10932","scopus_import":"1"},{"editor":[{"full_name":"Zažímalová, Eva","first_name":"Eva","last_name":"Zažímalová"},{"first_name":"Jan","full_name":"Petrášek, Jan","last_name":"Petrášek"},{"full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková"}],"publisher":"Springer","scopus_import":1,"department":[{"_id":"JiFr"}],"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."}],"page":"143 - 170","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-10-09T20:55:54Z","oa_version":"None","date_created":"2018-12-11T11:54:07Z","type":"book_chapter","title":"Auxin on the road navigated by cellular PIN polarity","month":"04","publication":"Auxin and Its Role in Plant Development","_id":"1806","year":"2014","date_published":"2014-04-01T00:00:00Z","publication_status":"published","status":"public","corr_author":"1","citation":{"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>.","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.","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>","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>","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>.","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."},"quality_controlled":"1","day":"01","doi":"10.1007/978-3-7091-1526-8_8","language":[{"iso":"eng"}],"author":[{"last_name":"Baster","full_name":"Baster, Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87","first_name":"Pawel"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"}],"publist_id":"5304"},{"department":[{"_id":"HeEd"}],"page":"61 - 86","scopus_import":1,"ddc":["000"],"type":"journal_article","month":"03","oa_version":"Published Version","pubrep_id":"443","doi":"10.1142/S0218195914500034","tmp":{"short":"CC BY (4.0)","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"},"day":"16","_id":"1816","volume":24,"publist_id":"5290","abstract":[{"lang":"eng","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."}],"file":[{"file_id":"4704","date_created":"2018-12-12T10:08:43Z","date_updated":"2020-07-14T12:45:17Z","access_level":"open_access","checksum":"be45c133ab4d43351260e21beaa8f4b1","relation":"main_file","content_type":"application/pdf","file_name":"IST-2016-443-v1+1_S0218195914500034.pdf","file_size":991734,"creator":"system"}],"oa":1,"publisher":"World Scientific Publishing","title":"Topology-preserving watermarking of vector graphics","publication":"International Journal of Computational Geometry and Applications","date_created":"2018-12-11T11:54:10Z","acknowledgement":"Work by Martin Held and Stefan Huber was supported by Austrian Science Fund (FWF): L367-N15 and P25816-N15.","date_updated":"2024-10-09T20:55:54Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"quality_controlled":"1","corr_author":"1","citation":{"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>.","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>","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.","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>","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.","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>.","short":"S. Huber, M. Held, P. Meerwald, R. Kwitt, International Journal of Computational Geometry and Applications 24 (2014) 61–86."},"file_date_updated":"2020-07-14T12:45:17Z","year":"2014","date_published":"2014-03-16T00:00:00Z","status":"public","publication_status":"published","has_accepted_license":"1","author":[{"full_name":"Huber, Stefan","id":"4700A070-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8871-5814","first_name":"Stefan","last_name":"Huber"},{"first_name":"Martin","full_name":"Held, Martin","last_name":"Held"},{"last_name":"Meerwald","first_name":"Peter","full_name":"Meerwald, Peter"},{"first_name":"Roland","full_name":"Kwitt, Roland","last_name":"Kwitt"}],"intvolume":"        24","issue":"1"},{"publisher":"IOP Publishing","oa":1,"abstract":[{"text":"We present an optical setup with focus-tunable lenses to dynamically control the waist and focus position of a laser beam, in which we transport a trapped ultracold cloud of 87Rb over a distance of \r\n. The scheme allows us to shift the focus position at constant waist, providing uniform trapping conditions over the full transport length. The fraction of atoms that are transported over the entire distance comes near to unity, while the heating of the cloud is in the range of a few microkelvin. We characterize the position stability of the focus and show that residual drift rates in focus position can be compensated for by counteracting with the tunable lenses. Beyond being a compact and robust scheme to transport ultracold atoms, the reported control of laser beams makes dynamic tailoring of trapping potentials possible. As an example, we steer the size of the atomic cloud by changing the waist size of the dipole beam.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1088/1367-2630/16/9/093028","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-10-07T12:07:48Z","date_created":"2024-10-07T11:50:00Z","publication":"New Journal of Physics","title":"Optical transport and manipulation of an ultracold atomic cloud using focus-tunable lenses","status":"public","publication_status":"published","extern":"1","year":"2014","date_published":"2014-09-23T00:00:00Z","citation":{"chicago":"Leonard, Julian, Moonjoo Lee, Andrea Morales, Thomas M Karg, Tilman Esslinger, and Tobias Donner. “Optical Transport and Manipulation of an Ultracold Atomic Cloud Using Focus-Tunable Lenses.” <i>New Journal of Physics</i>. IOP Publishing, 2014. <a href=\"https://doi.org/10.1088/1367-2630/16/9/093028\">https://doi.org/10.1088/1367-2630/16/9/093028</a>.","short":"J. Leonard, M. Lee, A. Morales, T.M. Karg, T. Esslinger, T. Donner, New Journal of Physics 16 (2014).","mla":"Leonard, Julian, et al. “Optical Transport and Manipulation of an Ultracold Atomic Cloud Using Focus-Tunable Lenses.” <i>New Journal of Physics</i>, vol. 16, no. 9, 093028, IOP Publishing, 2014, doi:<a href=\"https://doi.org/10.1088/1367-2630/16/9/093028\">10.1088/1367-2630/16/9/093028</a>.","ista":"Leonard J, Lee M, Morales A, Karg TM, Esslinger T, Donner T. 2014. Optical transport and manipulation of an ultracold atomic cloud using focus-tunable lenses. New Journal of Physics. 16(9), 093028.","apa":"Leonard, J., Lee, M., Morales, A., Karg, T. M., Esslinger, T., &#38; Donner, T. (2014). Optical transport and manipulation of an ultracold atomic cloud using focus-tunable lenses. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/16/9/093028\">https://doi.org/10.1088/1367-2630/16/9/093028</a>","ieee":"J. Leonard, M. Lee, A. Morales, T. M. Karg, T. Esslinger, and T. Donner, “Optical transport and manipulation of an ultracold atomic cloud using focus-tunable lenses,” <i>New Journal of Physics</i>, vol. 16, no. 9. IOP Publishing, 2014.","ama":"Leonard J, Lee M, Morales A, Karg TM, Esslinger T, Donner T. Optical transport and manipulation of an ultracold atomic cloud using focus-tunable lenses. <i>New Journal of Physics</i>. 2014;16(9). doi:<a href=\"https://doi.org/10.1088/1367-2630/16/9/093028\">10.1088/1367-2630/16/9/093028</a>"},"quality_controlled":"1","language":[{"iso":"eng"}],"issue":"9","intvolume":"        16","author":[{"full_name":"Leonard, Julian","id":"b75b3f45-7995-11ef-9bfd-9a9cd02c3577","first_name":"Julian","last_name":"Leonard"},{"full_name":"Lee, Moonjoo","first_name":"Moonjoo","last_name":"Lee"},{"first_name":"Andrea","full_name":"Morales, Andrea","last_name":"Morales"},{"full_name":"Karg, Thomas M","first_name":"Thomas M","last_name":"Karg"},{"first_name":"Tilman","full_name":"Esslinger, Tilman","last_name":"Esslinger"},{"first_name":"Tobias","full_name":"Donner, Tobias","last_name":"Donner"}],"article_processing_charge":"Yes","scopus_import":"1","oa_version":"Published Version","month":"09","type":"journal_article","volume":16,"_id":"18200","publication_identifier":{"issn":["1367-2630"]},"doi":"10.1088/1367-2630/16/9/093028","day":"23","article_number":"093028","article_type":"original"},{"intvolume":"        55","issue":"7","author":[{"last_name":"Seiringer","first_name":"Robert","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521"}],"has_accepted_license":"1","year":"2014","date_published":"2014-06-26T00:00:00Z","publication_status":"published","status":"public","citation":{"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>.","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>","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.","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>.","short":"R. Seiringer, Journal of Mathematical Physics 55 (2014)."},"corr_author":"1","file_date_updated":"2020-07-14T12:45:17Z","quality_controlled":"1","external_id":{"isi":["000341174600010"]},"language":[{"iso":"eng"}],"date_updated":"2025-09-29T13:13:35Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:54:11Z","title":"Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation","publication":"Journal of Mathematical Physics","publisher":"American Institute of Physics","oa":1,"abstract":[{"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.","lang":"eng"}],"file":[{"date_created":"2018-12-12T10:15:49Z","file_id":"5172","access_level":"open_access","date_updated":"2020-07-14T12:45:17Z","checksum":"ed0efc93c10f1341155f0316af617b82","content_type":"application/pdf","relation":"main_file","file_name":"IST-2016-532-v1+1_J._Mathematical_Phys._2014_Seiringer.pdf","file_size":269171,"creator":"system"}],"article_number":"1.4881536","publist_id":"5285","project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}],"_id":"1821","volume":55,"doi":"10.1063/1.4881536","day":"26","pubrep_id":"532","oa_version":"Submitted Version","type":"journal_article","month":"06","article_processing_charge":"No","scopus_import":"1","isi":1,"ddc":["510","530"],"department":[{"_id":"RoSe"}]},{"publisher":"American Institute of Physics","article_processing_charge":"No","department":[{"_id":"RoSe"}],"isi":1,"scopus_import":"1","date_updated":"2025-09-29T13:12:51Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"07","publication":"Journal of Mathematical Physics","type":"journal_article","title":"Introduction","oa_version":"None","date_created":"2018-12-11T11:54:12Z","citation":{"short":"V. Jakšić, C. Pillet, R. Seiringer, Journal of Mathematical Physics 55 (2014).","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>.","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.","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>","ista":"Jakšić V, Pillet C, Seiringer R. 2014. Introduction. Journal of Mathematical Physics. 55(7), 075101.","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>."},"publication_status":"published","volume":55,"status":"public","year":"2014","_id":"1822","date_published":"2014-07-01T00:00:00Z","external_id":{"isi":["000341174600001"]},"language":[{"iso":"eng"}],"day":"01","doi":"10.1063/1.4884877","quality_controlled":"1","author":[{"first_name":"Vojkan","full_name":"Jakšić, Vojkan","last_name":"Jakšić"},{"full_name":"Pillet, Claude","first_name":"Claude","last_name":"Pillet"},{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"publist_id":"5284","issue":"7","article_number":"075101","intvolume":"        55"},{"year":"2014","_id":"1829","date_published":"2014-01-01T00:00:00Z","status":"public","publication_status":"published","volume":97,"citation":{"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>.","short":"K. Muelling, O. Kroemer, C. Lampert, B. Schölkopf, in:, J. Kober, J. Peters (Eds.), Learning Motor Skills, Springer, 2014, pp. 69–82.","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>.","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.","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>","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>","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."},"alternative_title":["Springer Tracts in Advanced Robotics"],"quality_controlled":"1","day":"01","doi":"10.1007/978-3-319-03194-1_3","language":[{"iso":"eng"}],"intvolume":"        97","publist_id":"5274","author":[{"last_name":"Muelling","full_name":"Muelling, Katharina","first_name":"Katharina"},{"last_name":"Kroemer","full_name":"Kroemer, Oliver","first_name":"Oliver"},{"last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"},{"last_name":"Schölkopf","full_name":"Schölkopf, Bernhard","first_name":"Bernhard"}],"editor":[{"last_name":"Kober","full_name":"Kober, Jens","first_name":"Jens"},{"full_name":"Peters, Jan","first_name":"Jan","last_name":"Peters"}],"publisher":"Springer","scopus_import":1,"series_title":"From Algorithms to Robot Experiments","abstract":[{"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.","lang":"eng"}],"department":[{"_id":"ChLa"}],"page":"69 - 82","date_updated":"2021-01-12T06:53:28Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa_version":"None","date_created":"2018-12-11T11:54:14Z","type":"book_chapter","title":"Movement templates for learning of hitting and batting","month":"01","publication":"Learning Motor Skills"},{"citation":{"short":"D. Raviv, A.M. Bronstein, M.M. Bronstein, D. Waisman, N. Sochen, R. Kimmel, Journal of Mathematical Imaging and Vision 50 (2014) 144–163.","chicago":"Raviv, Dan, Alex M. Bronstein, Michael M. Bronstein, Dan Waisman, Nir Sochen, and Ron Kimmel. “Equi-Affine Invariant Geometry for Shape Analysis.” <i>Journal of Mathematical Imaging and Vision</i>. Springer Nature, 2014. <a href=\"https://doi.org/10.1007/s10851-013-0467-y\">https://doi.org/10.1007/s10851-013-0467-y</a>.","ama":"Raviv D, Bronstein AM, Bronstein MM, Waisman D, Sochen N, Kimmel R. Equi-affine invariant geometry for shape analysis. <i>Journal of Mathematical Imaging and Vision</i>. 2014;50:144-163. doi:<a href=\"https://doi.org/10.1007/s10851-013-0467-y\">10.1007/s10851-013-0467-y</a>","apa":"Raviv, D., Bronstein, A. M., Bronstein, M. M., Waisman, D., Sochen, N., &#38; Kimmel, R. (2014). Equi-affine invariant geometry for shape analysis. <i>Journal of Mathematical Imaging and Vision</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10851-013-0467-y\">https://doi.org/10.1007/s10851-013-0467-y</a>","ieee":"D. Raviv, A. M. Bronstein, M. M. Bronstein, D. Waisman, N. Sochen, and R. Kimmel, “Equi-affine invariant geometry for shape analysis,” <i>Journal of Mathematical Imaging and Vision</i>, vol. 50. Springer Nature, pp. 144–163, 2014.","ista":"Raviv D, Bronstein AM, Bronstein MM, Waisman D, Sochen N, Kimmel R. 2014. Equi-affine invariant geometry for shape analysis. Journal of Mathematical Imaging and Vision. 50, 144–163.","mla":"Raviv, Dan, et al. “Equi-Affine Invariant Geometry for Shape Analysis.” <i>Journal of Mathematical Imaging and Vision</i>, vol. 50, Springer Nature, 2014, pp. 144–63, doi:<a href=\"https://doi.org/10.1007/s10851-013-0467-y\">10.1007/s10851-013-0467-y</a>."},"_id":"18353","date_published":"2014-09-01T00:00:00Z","year":"2014","extern":"1","status":"public","publication_status":"published","volume":50,"doi":"10.1007/s10851-013-0467-y","day":"01","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"eissn":["1573-7683"],"issn":["0924-9907"]},"author":[{"full_name":"Raviv, Dan","first_name":"Dan","last_name":"Raviv"},{"last_name":"Bronstein","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","orcid":"0000-0001-9699-8730","full_name":"Bronstein, Alexander","first_name":"Alexander"},{"first_name":"Michael M.","full_name":"Bronstein, Michael M.","last_name":"Bronstein"},{"last_name":"Waisman","first_name":"Dan","full_name":"Waisman, Dan"},{"last_name":"Sochen","first_name":"Nir","full_name":"Sochen, Nir"},{"full_name":"Kimmel, Ron","first_name":"Ron","last_name":"Kimmel"}],"intvolume":"        50","article_type":"original","publisher":"Springer Nature","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Traditional models of bendable surfaces are based on the exact or approximate invariance to deformations that do not tear or stretch the shape, leaving intact an intrinsic geometry associated with it. These geometries are typically defined using either the shortest path length (geodesic distance), or properties of heat diffusion (diffusion distance) on the surface. Both measures are implicitly derived from the metric induced by the ambient Euclidean space. In this paper, we depart from this restrictive assumption by observing that a different choice of the metric results in a richer set of geometric invariants. We apply equi-affine geometry for analyzing arbitrary shapes with positive Gaussian curvature. The potential of the proposed framework is explored in a range of applications such as shape matching and retrieval, symmetry detection, and computation of Voroni tessellation. We show that in some shape analysis tasks, equi-affine-invariant intrinsic geometries often outperform their Euclidean-based counterparts. We further explore the potential of this metric in facial anthropometry of newborns. We show that intrinsic properties of this homogeneous group are better captured using the equi-affine metric."}],"page":"144-163","scopus_import":"1","date_updated":"2024-11-12T08:51:43Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Equi-affine invariant geometry for shape analysis","type":"journal_article","month":"09","publication":"Journal of Mathematical Imaging and Vision","date_created":"2024-10-15T11:20:54Z","oa_version":"None"},{"abstract":[{"text":"Traditionally, NMF algorithms consist of two separate stages: a training stage, in which a generative model is learned; and a testing stage in which the pre-learned model is used in a high level task such as enhancement, separation, or classification. As an alternative, we propose a task-supervised NMF method for the adaptation of the basis spectra learned in the first stage to enhance the performance on the specific task used in the second stage. We cast this problem as a bilevel optimization program that can be efficiently solved via stochastic gradient descent. The proposed approach is general enough to handle sparsity priors of the activations, and allow non-Euclidean data terms such as β-divergences. The framework is evaluated on single-channel speech enhancement tasks.","lang":"eng"}],"scopus_import":"1","publisher":"IEEE","article_processing_charge":"No","month":"06","publication":"2014 4th Joint Workshop on Hands-free Speech Communication and Microphone Arrays (HSCMA)","type":"conference","title":"Supervised non-euclidean sparse NMF via bilevel optimization with applications to speech enhancement","date_created":"2024-10-15T11:20:54Z","oa_version":"None","date_updated":"2024-12-04T13:47:13Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"day":"26","doi":"10.1109/hscma.2014.6843241","publication_identifier":{"eisbn":["9781479931095"]},"quality_controlled":"1","citation":{"mla":"Sprechmann, Pablo, et al. “Supervised Non-Euclidean Sparse NMF via Bilevel Optimization with Applications to Speech Enhancement.” <i>2014 4th Joint Workshop on Hands-Free Speech Communication and Microphone Arrays (HSCMA)</i>, 6843241, IEEE, 2014, doi:<a href=\"https://doi.org/10.1109/hscma.2014.6843241\">10.1109/hscma.2014.6843241</a>.","apa":"Sprechmann, P., Bronstein, A. M., &#38; Sapiro, G. (2014). Supervised non-euclidean sparse NMF via bilevel optimization with applications to speech enhancement. In <i>2014 4th Joint Workshop on Hands-free Speech Communication and Microphone Arrays (HSCMA)</i>. Villers-les-Nancy, France: IEEE. <a href=\"https://doi.org/10.1109/hscma.2014.6843241\">https://doi.org/10.1109/hscma.2014.6843241</a>","ama":"Sprechmann P, Bronstein AM, Sapiro G. Supervised non-euclidean sparse NMF via bilevel optimization with applications to speech enhancement. In: <i>2014 4th Joint Workshop on Hands-Free Speech Communication and Microphone Arrays (HSCMA)</i>. IEEE; 2014. doi:<a href=\"https://doi.org/10.1109/hscma.2014.6843241\">10.1109/hscma.2014.6843241</a>","ieee":"P. Sprechmann, A. M. Bronstein, and G. Sapiro, “Supervised non-euclidean sparse NMF via bilevel optimization with applications to speech enhancement,” in <i>2014 4th Joint Workshop on Hands-free Speech Communication and Microphone Arrays (HSCMA)</i>, Villers-les-Nancy, France, 2014.","ista":"Sprechmann P, Bronstein AM, Sapiro G. 2014. Supervised non-euclidean sparse NMF via bilevel optimization with applications to speech enhancement. 2014 4th Joint Workshop on Hands-free Speech Communication and Microphone Arrays (HSCMA). 4th Joint Workshop on Hands-Free Speech Communication and Microphone Arrays, 6843241.","chicago":"Sprechmann, Pablo, Alex M. Bronstein, and Guillermo Sapiro. “Supervised Non-Euclidean Sparse NMF via Bilevel Optimization with Applications to Speech Enhancement.” In <i>2014 4th Joint Workshop on Hands-Free Speech Communication and Microphone Arrays (HSCMA)</i>. IEEE, 2014. <a href=\"https://doi.org/10.1109/hscma.2014.6843241\">https://doi.org/10.1109/hscma.2014.6843241</a>.","short":"P. Sprechmann, A.M. Bronstein, G. Sapiro, in:, 2014 4th Joint Workshop on Hands-Free Speech Communication and Microphone Arrays (HSCMA), IEEE, 2014."},"conference":{"start_date":"2014-05-12","location":"Villers-les-Nancy, France","name":"4th Joint Workshop on Hands-Free Speech Communication and Microphone Arrays","end_date":"2014-05-14"},"status":"public","publication_status":"published","extern":"1","date_published":"2014-06-26T00:00:00Z","_id":"18384","year":"2014","author":[{"last_name":"Sprechmann","first_name":"Pablo","full_name":"Sprechmann, Pablo"},{"last_name":"Bronstein","first_name":"Alexander","orcid":"0000-0001-9699-8730","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","full_name":"Bronstein, Alexander"},{"last_name":"Sapiro","full_name":"Sapiro, Guillermo","first_name":"Guillermo"}],"article_number":"6843241"},{"issue":"1","intvolume":"        36","author":[{"last_name":"Litman","full_name":"Litman, R.","first_name":"R."},{"last_name":"Bronstein","full_name":"Bronstein, Alexander","orcid":"0000-0001-9699-8730","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","first_name":"Alexander"}],"quality_controlled":"1","external_id":{"pmid":["24231874"]},"language":[{"iso":"eng"}],"publication_status":"published","status":"public","extern":"1","date_published":"2014-01-01T00:00:00Z","year":"2014","citation":{"short":"R. Litman, A.M. Bronstein, IEEE Transactions on Pattern Analysis and Machine Intelligence 36 (2014) 171–180.","chicago":"Litman, R., and Alex M. Bronstein. “Learning Spectral Descriptors for Deformable Shape Correspondence.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE, 2014. <a href=\"https://doi.org/10.1109/tpami.2013.148\">https://doi.org/10.1109/tpami.2013.148</a>.","ieee":"R. Litman and A. M. Bronstein, “Learning spectral descriptors for deformable shape correspondence,” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 36, no. 1. IEEE, pp. 171–180, 2014.","apa":"Litman, R., &#38; Bronstein, A. M. (2014). Learning spectral descriptors for deformable shape correspondence. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE. <a href=\"https://doi.org/10.1109/tpami.2013.148\">https://doi.org/10.1109/tpami.2013.148</a>","ama":"Litman R, Bronstein AM. Learning spectral descriptors for deformable shape correspondence. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. 2014;36(1):171-180. doi:<a href=\"https://doi.org/10.1109/tpami.2013.148\">10.1109/tpami.2013.148</a>","ista":"Litman R, Bronstein AM. 2014. Learning spectral descriptors for deformable shape correspondence. IEEE Transactions on Pattern Analysis and Machine Intelligence. 36(1), 171–180.","mla":"Litman, R., and Alex M. Bronstein. “Learning Spectral Descriptors for Deformable Shape Correspondence.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 36, no. 1, IEEE, 2014, pp. 171–80, doi:<a href=\"https://doi.org/10.1109/tpami.2013.148\">10.1109/tpami.2013.148</a>."},"date_created":"2024-10-15T11:20:55Z","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","title":"Learning spectral descriptors for deformable shape correspondence","date_updated":"2024-12-12T12:42:56Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","pmid":1,"abstract":[{"lang":"eng","text":"Informative and discriminative feature descriptors play a fundamental role in deformable shape analysis. For example, they have been successfully employed in correspondence, registration, and retrieval tasks. In recent years, significant attention has been devoted to descriptors obtained from the spectral decomposition of the Laplace-Beltrami operator associated with the shape. Notable examples in this family are the heat kernel signature (HKS) and the recently introduced wave kernel signature (WKS). The Laplacian-based descriptors achieve state-of-the-art performance in numerous shape analysis tasks; they are computationally efficient, isometry-invariant by construction, and can gracefully cope with a variety of transformations. In this paper, we formulate a generic family of parametric spectral descriptors. We argue that to be optimized for a specific task, the descriptor should take into account the statistics of the corpus of shapes to which it is applied (the \"signal\") and those of the class of transformations to which it is made insensitive (the \"noise\"). While such statistics are hard to model axiomatically, they can be learned from examples. Following the spirit of the Wiener filter in signal processing, we show a learning scheme for the construction of optimized spectral descriptors and relate it to Mahalanobis metric learning. The superiority of the proposed approach in generating correspondences is demonstrated on synthetic and scanned human figures. We also show that the learned descriptors are robust enough to be learned on synthetic data and transferred successfully to scanned shapes."}],"publisher":"IEEE","publication_identifier":{"issn":["0162-8828"],"eissn":["1939-3539"]},"day":"01","doi":"10.1109/tpami.2013.148","volume":36,"_id":"18413","oa_version":"None","month":"01","type":"journal_article","scopus_import":"1","page":"171-180","article_processing_charge":"No"},{"day":"01","doi":"10.1109/tpami.2013.225","publication_identifier":{"issn":["0162-8828"],"eissn":["1939-3539"]},"_id":"18414","volume":36,"type":"journal_article","month":"04","oa_version":"Preprint","page":"824-830","scopus_import":"1","article_processing_charge":"No","author":[{"full_name":"Masci, Jonathan","first_name":"Jonathan","last_name":"Masci"},{"last_name":"Bronstein","full_name":"Bronstein, Michael M.","first_name":"Michael M."},{"full_name":"Bronstein, Alexander","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","orcid":"0000-0001-9699-8730","first_name":"Alexander","last_name":"Bronstein"},{"full_name":"Schmidhuber, Jurgen","first_name":"Jurgen","last_name":"Schmidhuber"}],"intvolume":"        36","issue":"4","external_id":{"arxiv":["1207.1522"],"pmid":["26353203"]},"language":[{"iso":"eng"}],"quality_controlled":"1","citation":{"short":"J. Masci, M.M. Bronstein, A.M. Bronstein, J. Schmidhuber, IEEE Transactions on Pattern Analysis and Machine Intelligence 36 (2014) 824–830.","chicago":"Masci, Jonathan, Michael M. Bronstein, Alex M. Bronstein, and Jurgen Schmidhuber. “Multimodal Similarity-Preserving Hashing.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE, 2014. <a href=\"https://doi.org/10.1109/tpami.2013.225\">https://doi.org/10.1109/tpami.2013.225</a>.","ieee":"J. Masci, M. M. Bronstein, A. M. Bronstein, and J. Schmidhuber, “Multimodal similarity-preserving hashing,” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 36, no. 4. IEEE, pp. 824–830, 2014.","apa":"Masci, J., Bronstein, M. M., Bronstein, A. M., &#38; Schmidhuber, J. (2014). Multimodal similarity-preserving hashing. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE. <a href=\"https://doi.org/10.1109/tpami.2013.225\">https://doi.org/10.1109/tpami.2013.225</a>","ama":"Masci J, Bronstein MM, Bronstein AM, Schmidhuber J. Multimodal similarity-preserving hashing. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. 2014;36(4):824-830. doi:<a href=\"https://doi.org/10.1109/tpami.2013.225\">10.1109/tpami.2013.225</a>","ista":"Masci J, Bronstein MM, Bronstein AM, Schmidhuber J. 2014. Multimodal similarity-preserving hashing. IEEE Transactions on Pattern Analysis and Machine Intelligence. 36(4), 824–830.","mla":"Masci, Jonathan, et al. “Multimodal Similarity-Preserving Hashing.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 36, no. 4, IEEE, 2014, pp. 824–30, doi:<a href=\"https://doi.org/10.1109/tpami.2013.225\">10.1109/tpami.2013.225</a>."},"year":"2014","date_published":"2014-04-01T00:00:00Z","status":"public","extern":"1","publication_status":"published","title":"Multimodal similarity-preserving hashing","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","date_created":"2024-10-15T11:20:55Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1207.1522","open_access":"1"}],"pmid":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-12-12T13:04:27Z","arxiv":1,"abstract":[{"lang":"eng","text":"We introduce an efficient computational framework for hashing data belonging to multiple modalities into a single representation space where they become mutually comparable. The proposed approach is based on a novel coupled siamese neural network architecture and allows unified treatment of intra- and inter-modality similarity learning. Unlike existing cross-modality similarity learning approaches, our hashing functions are not limited to binarized linear projections and can assume arbitrarily complex forms. We show experimentally that our method significantly outperforms state-of-the-art hashing approaches on multimedia retrieval tasks."}],"oa":1,"publisher":"IEEE"},{"intvolume":"        53","issue":"1","author":[{"full_name":"Cibulka, Josef","first_name":"Josef","last_name":"Cibulka"},{"first_name":"Pu","full_name":"Gao, Pu","last_name":"Gao"},{"last_name":"Krcál","first_name":"Marek","id":"33E21118-F248-11E8-B48F-1D18A9856A87","full_name":"Krcál, Marek"},{"last_name":"Valla","full_name":"Valla, Tomáš","first_name":"Tomáš"},{"last_name":"Valtr","full_name":"Valtr, Pavel","first_name":"Pavel"}],"year":"2014","date_published":"2014-11-14T00:00:00Z","publication_status":"published","status":"public","citation":{"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>.","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.","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>","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>.","short":"J. Cibulka, P. Gao, M. Krcál, T. Valla, P. Valtr, Discrete &#38; Computational Geometry 53 (2014) 64–79."},"language":[{"iso":"eng"}],"external_id":{"arxiv":["1310.7004"],"isi":["000346774600005"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","arxiv":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1310.7004"}],"date_updated":"2025-09-29T13:11:56Z","date_created":"2018-12-11T11:54:18Z","acknowledgement":"Marek Krčál was supported by the ERC Advanced Grant No. 267165.","title":"On the geometric ramsey number of outerplanar graphs","publication":"Discrete & Computational Geometry","publisher":"Springer","oa":1,"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"}],"publist_id":"5260","_id":"1842","volume":53,"doi":"10.1007/s00454-014-9646-x","day":"14","oa_version":"Submitted Version","type":"journal_article","month":"11","article_processing_charge":"No","scopus_import":"1","isi":1,"department":[{"_id":"UlWa"},{"_id":"HeEd"}],"page":"64 - 79"},{"date_updated":"2024-12-19T10:20:12Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"08","publication":"Computer Graphics Forum","type":"journal_article","title":"Supervised learning of bag‐of‐features shape descriptors using sparse coding","date_created":"2024-10-15T11:20:55Z","oa_version":"None","publisher":"Wiley","article_processing_charge":"No","page":"127-136","abstract":[{"text":"We present a method for supervised learning of shape descriptors for shape retrieval applications. Many content-based shape retrieval approaches follow the bag-of-features (BoF) paradigm commonly used in text and image retrieval by first computing local shape descriptors, and then representing them in a ‘geometric dictionary’ using vector quantization. A major drawback of such approaches is that the dictionary is constructed in an unsupervised manner using clustering, unaware of the last stage of the process (pooling of the local descriptors into a BoF, and comparison of the latter using some metric). In this paper, we replace the clustering with dictionary learning, where every atom acts as a feature, followed by sparse coding and pooling to get the final BoF descriptor. Both the dictionary and the sparse codes can be learned in the supervised regime via bi-level optimization using a task-specific objective that promotes invariance desired in the specific application. We show significant performance improvement on several standard shape retrieval benchmarks.","lang":"eng"}],"scopus_import":"1","author":[{"first_name":"Roee","full_name":"Litman, Roee","last_name":"Litman"},{"last_name":"Bronstein","full_name":"Bronstein, Alexander","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","orcid":"0000-0001-9699-8730","first_name":"Alexander"},{"last_name":"Bronstein","full_name":"Bronstein, Michael","first_name":"Michael"},{"first_name":"Umberto","full_name":"Castellani, Umberto","last_name":"Castellani"}],"issue":"5","intvolume":"        33","citation":{"apa":"Litman, R., Bronstein, A. M., Bronstein, M., &#38; Castellani, U. (2014). Supervised learning of bag‐of‐features shape descriptors using sparse coding. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.12438\">https://doi.org/10.1111/cgf.12438</a>","ama":"Litman R, Bronstein AM, Bronstein M, Castellani U. Supervised learning of bag‐of‐features shape descriptors using sparse coding. <i>Computer Graphics Forum</i>. 2014;33(5):127-136. doi:<a href=\"https://doi.org/10.1111/cgf.12438\">10.1111/cgf.12438</a>","ieee":"R. Litman, A. M. Bronstein, M. Bronstein, and U. Castellani, “Supervised learning of bag‐of‐features shape descriptors using sparse coding,” <i>Computer Graphics Forum</i>, vol. 33, no. 5. Wiley, pp. 127–136, 2014.","ista":"Litman R, Bronstein AM, Bronstein M, Castellani U. 2014. Supervised learning of bag‐of‐features shape descriptors using sparse coding. Computer Graphics Forum. 33(5), 127–136.","mla":"Litman, Roee, et al. “Supervised Learning of Bag‐of‐features Shape Descriptors Using Sparse Coding.” <i>Computer Graphics Forum</i>, vol. 33, no. 5, Wiley, 2014, pp. 127–36, doi:<a href=\"https://doi.org/10.1111/cgf.12438\">10.1111/cgf.12438</a>.","short":"R. Litman, A.M. Bronstein, M. Bronstein, U. Castellani, Computer Graphics Forum 33 (2014) 127–136.","chicago":"Litman, Roee, Alex M. Bronstein, Michael Bronstein, and Umberto Castellani. “Supervised Learning of Bag‐of‐features Shape Descriptors Using Sparse Coding.” <i>Computer Graphics Forum</i>. Wiley, 2014. <a href=\"https://doi.org/10.1111/cgf.12438\">https://doi.org/10.1111/cgf.12438</a>."},"status":"public","volume":33,"publication_status":"published","extern":"1","date_published":"2014-08-01T00:00:00Z","_id":"18423","year":"2014","language":[{"iso":"eng"}],"day":"01","doi":"10.1111/cgf.12438","publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"quality_controlled":"1"},{"author":[{"first_name":"Valeria","full_name":"Risso, Valeria","last_name":"Risso"},{"last_name":"Manssour Triedo","first_name":"Fadia","full_name":"Manssour Triedo, Fadia"},{"full_name":"Delgado Delgado, Asuncion","first_name":"Asuncion","last_name":"Delgado Delgado"},{"last_name":"Arco","full_name":"Arco, Rocio","first_name":"Rocio"},{"full_name":"Barroso Deljesús, Alicia","first_name":"Alicia","last_name":"Barroso Deljesús"},{"first_name":"Álvaro","full_name":"Inglés Prieto, Álvaro","orcid":"0000-0002-5409-8571","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","last_name":"Inglés Prieto"},{"first_name":"Raquel","full_name":"Godoy Ruiz, Raquel","last_name":"Godoy Ruiz"},{"last_name":"Gavira","full_name":"Gavira, Josè","first_name":"Josè"},{"full_name":"Gaucher, Eric","first_name":"Eric","last_name":"Gaucher"},{"last_name":"Ibarra Molero","full_name":"Ibarra Molero, Beatriz","first_name":"Beatriz"},{"first_name":"Jose","full_name":"Sánchez Ruiz, Jose","last_name":"Sánchez Ruiz"}],"issue":"2","intvolume":"        32","has_accepted_license":"1","citation":{"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.","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>.","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.","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>","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>","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.","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>."},"file_date_updated":"2020-07-14T12:45:19Z","publication_status":"published","status":"public","year":"2014","date_published":"2014-11-12T00:00:00Z","language":[{"iso":"eng"}],"external_id":{"isi":["000350050700012"]},"quality_controlled":"1","date_updated":"2025-09-29T13:11:19Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Molecular Biology and Evolution","title":"Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history","date_created":"2018-12-11T11:54:19Z","publisher":"Oxford University Press","abstract":[{"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.","lang":"eng"}],"file":[{"date_created":"2018-12-12T10:16:56Z","file_id":"5247","date_updated":"2020-07-14T12:45:19Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"06215318e66be8f3e0c33abb07e9d3da","creator":"system","file_size":1545246,"file_name":"IST-2016-430-v1+1_Mol_Biol_Evol-2015-Risso-440-55.pdf"}],"oa":1,"publist_id":"5257","volume":32,"_id":"1844","day":"12","tmp":{"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)","short":"CC BY-NC (4.0)"},"doi":"10.1093/molbev/msu312","pubrep_id":"430","month":"11","type":"journal_article","oa_version":"Published Version","article_processing_charge":"No","page":"440 - 455","department":[{"_id":"HaJa"}],"ddc":["571"],"isi":1,"scopus_import":"1"},{"publist_id":"5248","volume":24,"_id":"1852","day":"06","doi":"10.1016/j.cub.2014.08.036","oa_version":"Submitted Version","month":"10","type":"journal_article","article_processing_charge":"No","isi":1,"scopus_import":"1","page":"2335 - 2342","department":[{"_id":"JiFr"}],"issue":"19","intvolume":"        24","author":[{"first_name":"Massimiliano","full_name":"Sassi, Massimiliano","last_name":"Sassi"},{"full_name":"Ali, Olivier","first_name":"Olivier","last_name":"Ali"},{"last_name":"Boudon","full_name":"Boudon, Frédéric","first_name":"Frédéric"},{"first_name":"Gladys","full_name":"Cloarec, Gladys","last_name":"Cloarec"},{"last_name":"Abad","first_name":"Ursula","full_name":"Abad, Ursula"},{"last_name":"Cellier","full_name":"Cellier, Coralie","first_name":"Coralie"},{"first_name":"Xu","full_name":"Chen, Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","last_name":"Chen"},{"full_name":"Gilles, Benjamin","first_name":"Benjamin","last_name":"Gilles"},{"last_name":"Milani","first_name":"Pascale","full_name":"Milani, Pascale"},{"last_name":"Friml","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí"},{"last_name":"Vernoux","full_name":"Vernoux, Teva","first_name":"Teva"},{"last_name":"Godin","full_name":"Godin, Christophe","first_name":"Christophe"},{"first_name":"Olivier","full_name":"Hamant, Olivier","last_name":"Hamant"},{"first_name":"Jan","full_name":"Traas, Jan","last_name":"Traas"}],"status":"public","publication_status":"published","date_published":"2014-10-06T00:00:00Z","year":"2014","citation":{"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.","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>.","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.","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>","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>","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>."},"quality_controlled":"1","external_id":{"isi":["000342747600031"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-01074821"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-29T13:10:45Z","acknowledgement":"This work was funded by grants from EraSysBio+ (iSAM) and ERC (Morphodynamics). ","date_created":"2018-12-11T11:54:22Z","publication":"Current Biology","title":"An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis","publisher":"Cell Press","oa":1,"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."}]},{"title":"Game theoretic secure localization in wireless sensor networks","type":"conference","month":"02","oa_version":"None","date_created":"2018-12-11T11:54:22Z","date_updated":"2024-10-21T06:02:48Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","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."}],"department":[{"_id":"KrCh"}],"page":"85 - 90","scopus_import":"1","publisher":"IEEE","author":[{"last_name":"Jha","first_name":"Susmit","full_name":"Jha, Susmit"},{"last_name":"Tripakis","first_name":"Stavros","full_name":"Tripakis, Stavros"},{"first_name":"Sanjit","full_name":"Seshia, Sanjit","last_name":"Seshia"},{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"}],"publist_id":"5247","day":"03","doi":"10.1109/IOT.2014.7030120","language":[{"iso":"eng"}],"quality_controlled":"1","conference":{"start_date":"2014-10-06","location":"Cambridge, USA","name":"IOT: Internet of Things","end_date":"2014-10-08"},"citation":{"ista":"Jha S, Tripakis S, Seshia S, Chatterjee K. 2014. Game theoretic secure localization in wireless sensor networks. IOT: Internet of Things, 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>","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.","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>","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>.","short":"S. Jha, S. Tripakis, S. Seshia, K. Chatterjee, in:, IEEE, 2014, pp. 85–90.","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>."},"date_published":"2014-02-03T00:00:00Z","_id":"1853","year":"2014","publication_status":"published","status":"public"},{"oa":1,"abstract":[{"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.","lang":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","checksum":"91946bfc509c77f5fd3151a3ff2b2c8f","creator":"system","file_name":"IST-2016-574-v1+1_Guerrero-2014-TPS-paper.pdf","file_size":24817484,"date_created":"2018-12-12T10:15:58Z","file_id":"5182","date_updated":"2020-07-14T12:45:19Z","access_level":"open_access"}],"publisher":"Wiley","date_created":"2018-12-11T11:54:22Z","title":"Partial shape matching using transformation parameter similarity","publication":"Computer Graphics Forum","date_updated":"2025-09-23T09:47:49Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000350145600019"]},"date_published":"2014-11-05T00:00:00Z","year":"2014","status":"public","publication_status":"published","file_date_updated":"2020-07-14T12:45:19Z","citation":{"short":"P. Guerrero, T. Auzinger, M. Wimmer, S. Jeschke, Computer Graphics Forum 34 (2014) 239–252.","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>.","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>","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.","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.","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>."},"has_accepted_license":"1","intvolume":"        34","issue":"1","author":[{"last_name":"Guerrero","full_name":"Guerrero, Paul","first_name":"Paul"},{"first_name":"Thomas","full_name":"Auzinger, Thomas","id":"4718F954-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1546-3265","last_name":"Auzinger"},{"last_name":"Wimmer","full_name":"Wimmer, Michael","first_name":"Michael"},{"last_name":"Jeschke","first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","full_name":"Jeschke, Stefan"}],"scopus_import":"1","isi":1,"ddc":["000"],"department":[{"_id":"ChWo"}],"page":"239 - 252","article_processing_charge":"No","oa_version":"Submitted Version","type":"journal_article","month":"11","pubrep_id":"574","day":"05","doi":"10.1111/cgf.12509","_id":"1854","volume":34,"publist_id":"5246"},{"external_id":{"isi":["000346310800045"],"pmid":["25409144"]},"language":[{"iso":"eng"}],"quality_controlled":"1","corr_author":"1","citation":{"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.","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>","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>","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.","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>.","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.","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>."},"status":"public","publication_status":"published","year":"2014","date_published":"2014-12-04T00:00:00Z","author":[{"id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Xu","first_name":"Xu","last_name":"Chen"},{"first_name":"Laurie","full_name":"Grandont, Laurie","last_name":"Grandont"},{"first_name":"Hongjiang","full_name":"Li, Hongjiang","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5039-9660","last_name":"Li"},{"last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"last_name":"Paque","first_name":"Sébastien","full_name":"Paque, Sébastien"},{"last_name":"Abuzeineh","full_name":"Abuzeineh, Anas","first_name":"Anas"},{"last_name":"Rakusova","first_name":"Hana","full_name":"Rakusova, Hana","id":"4CAAA450-78D2-11EA-8E57-B40A396E08BA"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","first_name":"Eva"},{"full_name":"Perrot Rechenmann, Catherine","first_name":"Catherine","last_name":"Perrot Rechenmann"},{"first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"issue":"729","intvolume":"       516","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."}],"oa":1,"publisher":"Nature Publishing Group","ec_funded":1,"publication":"Nature","title":"Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules","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.","date_created":"2018-12-11T11:54:25Z","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257754/","open_access":"1"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-29T13:10:05Z","pmid":1,"day":"04","doi":"10.1038/nature13889","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"volume":516,"project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"_id":"1862","article_type":"original","publist_id":"5237","page":"90 - 93","department":[{"_id":"JiFr"},{"_id":"Bio"},{"_id":"EvBe"}],"isi":1,"scopus_import":"1","article_processing_charge":"No","month":"12","type":"journal_article","oa_version":"Submitted Version"},{"acknowledgement":"The work presented in this paper was supported in part by the European Research Council (ERC) under grant agreement QUAINT (I774-N23)","date_created":"2018-12-11T11:54:27Z","publication":"HVC 2014","title":"Suraq - a controller synthesis tool using uninterpreted functions","date_updated":"2024-10-21T06:02:48Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","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"}],"ec_funded":1,"publisher":"Springer","intvolume":"      8855","author":[{"last_name":"Hofferek","full_name":"Hofferek, Georg","first_name":"Georg"},{"id":"335E5684-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Ashutosh","first_name":"Ashutosh","last_name":"Gupta"}],"quality_controlled":"1","language":[{"iso":"eng"}],"publication_status":"published","status":"public","date_published":"2014-01-01T00:00:00Z","year":"2014","citation":{"short":"G. Hofferek, A. Gupta, in:, E. Yahav (Ed.), HVC 2014, Springer, 2014, pp. 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>.","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>","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.","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>","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.","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>."},"alternative_title":["LNCS"],"oa_version":"None","month":"01","type":"conference","scopus_import":"1","page":"68 - 74","department":[{"_id":"ToHe"}],"editor":[{"last_name":"Yahav","first_name":"Eran","full_name":"Yahav, Eran"}],"publist_id":"5228","doi":"10.1007/978-3-319-13338-6_6","day":"01","volume":8855,"_id":"1869","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"}],"conference":{"start_date":"2014-11-18","name":"HVC: Haifa Verification Conference","end_date":"2014-11-20","location":"Haifa, Israel"}}]