[{"date_updated":"2022-05-24T08:54:54Z","ddc":["570"],"file_date_updated":"2022-05-24T08:41:41Z","department":[{"_id":"RySh"}],"_id":"2018","type":"journal_article","article_type":"original","status":"public","publication_identifier":{"issn":["0270-6474"],"eissn":["1529-2401"]},"publication_status":"published","file":[{"file_size":3963728,"date_updated":"2022-05-24T08:41:41Z","creator":"dernst","file_name":"2014_JournNeuroscience_Matsukawa.pdf","date_created":"2022-05-24T08:41:41Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"11410","checksum":"6913e9bc26e9fc1c0441a739a4199229"}],"language":[{"iso":"eng"}],"volume":34,"issue":"47","abstract":[{"lang":"eng","text":"Synaptic cell adhesion molecules are increasingly gaining attention for conferring specific properties to individual synapses. Netrin-G1 and netrin-G2 are trans-synaptic adhesion molecules that distribute on distinct axons, and their presence restricts the expression of their cognate receptors, NGL1 and NGL2, respectively, to specific subdendritic segments of target neurons. However, the neural circuits and functional roles of netrin-G isoform complexes remain unclear. Here, we use netrin-G-KO and NGL-KO mice to reveal that netrin-G1/NGL1 and netrin-G2/NGL2 interactions specify excitatory synapses in independent hippocampal pathways. In the hippocampal CA1 area, netrin-G1/NGL1 and netrin-G2/NGL2 were expressed in the temporoammonic and Schaffer collateral pathways, respectively. The lack of presynaptic netrin-Gs led to the dispersion of NGLs from postsynaptic membranes. In accord, netrin-G mutant synapses displayed opposing phenotypes in long-term and short-term plasticity through discrete biochemical pathways. The plasticity phenotypes in netrin-G-KOs were phenocopied in NGL-KOs, with a corresponding loss of netrin-Gs from presynaptic membranes. Our findings show that netrin-G/NGL interactions differentially control synaptic plasticity in distinct circuits via retrograde signaling mechanisms and explain how synaptic inputs are diversified to control neuronal activity."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"11","intvolume":" 34","citation":{"chicago":"Matsukawa, Hiroshi, Sachiko Akiyoshi Nishimura, Qi Zhang, Rafael Luján, Kazuhiko Yamaguchi, Hiromichi Goto, Kunio Yaguchi, et al. “Netrin-G/NGL Complexes Encode Functional Synaptic Diversification.” Journal of Neuroscience. Society for Neuroscience, 2014. https://doi.org/10.1523/JNEUROSCI.1141-14.2014.","ista":"Matsukawa H, Akiyoshi Nishimura S, Zhang Q, Luján R, Yamaguchi K, Goto H, Yaguchi K, Hashikawa T, Sano C, Shigemoto R, Nakashiba T, Itohara S. 2014. Netrin-G/NGL complexes encode functional synaptic diversification. Journal of Neuroscience. 34(47), 15779–15792.","mla":"Matsukawa, Hiroshi, et al. “Netrin-G/NGL Complexes Encode Functional Synaptic Diversification.” Journal of Neuroscience, vol. 34, no. 47, Society for Neuroscience, 2014, pp. 15779–92, doi:10.1523/JNEUROSCI.1141-14.2014.","short":"H. Matsukawa, S. Akiyoshi Nishimura, Q. Zhang, R. Luján, K. Yamaguchi, H. Goto, K. Yaguchi, T. Hashikawa, C. Sano, R. Shigemoto, T. Nakashiba, S. Itohara, Journal of Neuroscience 34 (2014) 15779–15792.","ieee":"H. Matsukawa et al., “Netrin-G/NGL complexes encode functional synaptic diversification,” Journal of Neuroscience, vol. 34, no. 47. Society for Neuroscience, pp. 15779–15792, 2014.","ama":"Matsukawa H, Akiyoshi Nishimura S, Zhang Q, et al. Netrin-G/NGL complexes encode functional synaptic diversification. Journal of Neuroscience. 2014;34(47):15779-15792. doi:10.1523/JNEUROSCI.1141-14.2014","apa":"Matsukawa, H., Akiyoshi Nishimura, S., Zhang, Q., Luján, R., Yamaguchi, K., Goto, H., … Itohara, S. (2014). Netrin-G/NGL complexes encode functional synaptic diversification. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1141-14.2014"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Matsukawa, Hiroshi","last_name":"Matsukawa","first_name":"Hiroshi"},{"full_name":"Akiyoshi Nishimura, Sachiko","last_name":"Akiyoshi Nishimura","first_name":"Sachiko"},{"full_name":"Zhang, Qi","last_name":"Zhang","first_name":"Qi"},{"full_name":"Luján, Rafael","last_name":"Luján","first_name":"Rafael"},{"full_name":"Yamaguchi, Kazuhiko","last_name":"Yamaguchi","first_name":"Kazuhiko"},{"full_name":"Goto, Hiromichi","last_name":"Goto","first_name":"Hiromichi"},{"first_name":"Kunio","last_name":"Yaguchi","full_name":"Yaguchi, Kunio"},{"full_name":"Hashikawa, Tsutomu","last_name":"Hashikawa","first_name":"Tsutomu"},{"first_name":"Chie","last_name":"Sano","full_name":"Sano, Chie"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"},{"full_name":"Nakashiba, Toshiaki","last_name":"Nakashiba","first_name":"Toshiaki"},{"last_name":"Itohara","full_name":"Itohara, Shigeyoshi","first_name":"Shigeyoshi"}],"publist_id":"5054","external_id":{"pmid":["25411505"]},"article_processing_charge":"No","title":"Netrin-G/NGL complexes encode functional synaptic diversification","has_accepted_license":"1","year":"2014","day":"19","publication":"Journal of Neuroscience","page":"15779 - 15792","doi":"10.1523/JNEUROSCI.1141-14.2014","date_published":"2014-11-19T00:00:00Z","date_created":"2018-12-11T11:55:14Z","acknowledgement":"This work was supported by “Funding Program for World-Leading Innovative R&D on Science and Technology (FIRST Program)” initiated by the Council for Science and Technology Policy.","quality_controlled":"1","publisher":"Society for Neuroscience","oa":1},{"ec_funded":1,"issue":"3-4","volume":17,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1407.1552"}],"scopus_import":1,"intvolume":" 17","month":"12","abstract":[{"text":"We prove that the empirical density of states of quantum spin glasses on arbitrary graphs converges to a normal distribution as long as the maximal degree is negligible compared with the total number of edges. This extends the recent results of Keating et al. (2014) that were proved for graphs with bounded chromatic number and with symmetric coupling distribution. Furthermore, we generalise the result to arbitrary hypergraphs. We test the optimality of our condition on the maximal degree for p-uniform hypergraphs that correspond to p-spin glass Hamiltonians acting on n distinguishable spin- 1/2 particles. At the critical threshold p = n1/2 we find a sharp classical-quantum phase transition between the normal distribution and the Wigner semicircle law. The former is characteristic to classical systems with commuting variables, while the latter is a signature of noncommutative random matrix theory.","lang":"eng"}],"oa_version":"Submitted Version","department":[{"_id":"LaEr"}],"date_updated":"2021-01-12T06:54:45Z","type":"journal_article","status":"public","_id":"2019","page":"441 - 464","date_created":"2018-12-11T11:55:15Z","date_published":"2014-12-17T00:00:00Z","doi":"10.1007/s11040-014-9164-3","year":"2014","publication":"Mathematical Physics, Analysis and Geometry","day":"17","oa":1,"quality_controlled":"1","publisher":"Springer","author":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös"},{"last_name":"Schröder","full_name":"Schröder, Dominik J","first_name":"Dominik J"}],"publist_id":"5053","title":"Phase transition in the density of states of quantum spin glasses","citation":{"chicago":"Erdös, László, and Dominik J Schröder. “Phase Transition in the Density of States of Quantum Spin Glasses.” Mathematical Physics, Analysis and Geometry. Springer, 2014. https://doi.org/10.1007/s11040-014-9164-3.","ista":"Erdös L, Schröder DJ. 2014. Phase transition in the density of states of quantum spin glasses. Mathematical Physics, Analysis and Geometry. 17(3–4), 441–464.","mla":"Erdös, László, and Dominik J. Schröder. “Phase Transition in the Density of States of Quantum Spin Glasses.” Mathematical Physics, Analysis and Geometry, vol. 17, no. 3–4, Springer, 2014, pp. 441–64, doi:10.1007/s11040-014-9164-3.","short":"L. Erdös, D.J. Schröder, Mathematical Physics, Analysis and Geometry 17 (2014) 441–464.","ieee":"L. Erdös and D. J. Schröder, “Phase transition in the density of states of quantum spin glasses,” Mathematical Physics, Analysis and Geometry, vol. 17, no. 3–4. Springer, pp. 441–464, 2014.","apa":"Erdös, L., & Schröder, D. J. (2014). Phase transition in the density of states of quantum spin glasses. Mathematical Physics, Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-014-9164-3","ama":"Erdös L, Schröder DJ. Phase transition in the density of states of quantum spin glasses. Mathematical Physics, Analysis and Geometry. 2014;17(3-4):441-464. doi:10.1007/s11040-014-9164-3"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}]},{"department":[{"_id":"CaUh"}],"date_updated":"2021-01-12T06:54:43Z","type":"journal_article","status":"public","_id":"2013","issue":"5","volume":14,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1209.0285"}],"scopus_import":1,"intvolume":" 14","month":"10","abstract":[{"lang":"eng","text":"An asymptotic theory is developed for computing volumes of regions in the parameter space of a directed Gaussian graphical model that are obtained by bounding partial correlations. We study these volumes using the method of real log canonical thresholds from algebraic geometry. Our analysis involves the computation of the singular loci of correlation hypersurfaces. Statistical applications include the strong-faithfulness assumption for the PC algorithm and the quantification of confounder bias in causal inference. A detailed analysis is presented for trees, bow ties, tripartite graphs, and complete graphs.\r\n"}],"oa_version":"Submitted Version","author":[{"last_name":"Lin","full_name":"Lin, Shaowei","first_name":"Shaowei"},{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","orcid":"0000-0002-7008-0216","full_name":"Uhler, Caroline","last_name":"Uhler"},{"first_name":"Bernd","last_name":"Sturmfels","full_name":"Sturmfels, Bernd"},{"last_name":"Bühlmann","full_name":"Bühlmann, Peter","first_name":"Peter"}],"publist_id":"5063","title":"Hypersurfaces and their singularities in partial correlation testing","citation":{"short":"S. Lin, C. Uhler, B. Sturmfels, P. Bühlmann, Foundations of Computational Mathematics 14 (2014) 1079–1116.","ieee":"S. Lin, C. Uhler, B. Sturmfels, and P. Bühlmann, “Hypersurfaces and their singularities in partial correlation testing,” Foundations of Computational Mathematics, vol. 14, no. 5. Springer, pp. 1079–1116, 2014.","apa":"Lin, S., Uhler, C., Sturmfels, B., & Bühlmann, P. (2014). Hypersurfaces and their singularities in partial correlation testing. Foundations of Computational Mathematics. Springer. https://doi.org/10.1007/s10208-014-9205-0","ama":"Lin S, Uhler C, Sturmfels B, Bühlmann P. Hypersurfaces and their singularities in partial correlation testing. Foundations of Computational Mathematics. 2014;14(5):1079-1116. doi:10.1007/s10208-014-9205-0","mla":"Lin, Shaowei, et al. “Hypersurfaces and Their Singularities in Partial Correlation Testing.” Foundations of Computational Mathematics, vol. 14, no. 5, Springer, 2014, pp. 1079–116, doi:10.1007/s10208-014-9205-0.","ista":"Lin S, Uhler C, Sturmfels B, Bühlmann P. 2014. Hypersurfaces and their singularities in partial correlation testing. Foundations of Computational Mathematics. 14(5), 1079–1116.","chicago":"Lin, Shaowei, Caroline Uhler, Bernd Sturmfels, and Peter Bühlmann. “Hypersurfaces and Their Singularities in Partial Correlation Testing.” Foundations of Computational Mathematics. Springer, 2014. https://doi.org/10.1007/s10208-014-9205-0."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","page":"1079 - 1116","date_created":"2018-12-11T11:55:12Z","date_published":"2014-10-10T00:00:00Z","doi":"10.1007/s10208-014-9205-0","year":"2014","publication":"Foundations of Computational Mathematics","day":"10","oa":1,"publisher":"Springer","quality_controlled":"1","acknowledgement":"This work was supported in part by the US National Science Foundation (DMS-0968882) and the Defense Advanced Research Projects Agency (DARPA) Deep Learning program (FA8650-10-C-7020)."},{"publication_status":"published","year":"2014","day":"18","publication":"ArXiv","date_published":"2014-06-18T00:00:00Z","date_created":"2018-12-11T11:55:14Z","abstract":[{"text":" Gaussian graphical models have received considerable attention during the past four decades from the statistical and machine learning communities. In Bayesian treatments of this model, the G-Wishart distribution serves as the conjugate prior for inverse covariance matrices satisfying graphical constraints. While it is straightforward to posit the unnormalized densities, the normalizing constants of these distributions have been known only for graphs that are chordal, or decomposable. Up until now, it was unknown whether the normalizing constant for a general graph could be represented explicitly, and a considerable body of computational literature emerged that attempted to avoid this apparent intractability. We close this question by providing an explicit representation of the G-Wishart normalizing constant for general graphs.","lang":"eng"}],"acknowledgement":"A.L.'s research was supported by Statistics for Innovation sfi2 in Oslo.\nD.R.'s research was partially supported by the U.S. National Science Foun-dation grant DMS-1309808; and by a Romberg Guest Professorship at the Heidelberg University Graduate School for Mathematical and Computational Methods in the Sciences, funded by German Universities Excellence Initiative grant GSC 220/2.","quality_controlled":0,"publisher":"ArXiv","main_file_link":[{"url":"http://arxiv.org/abs/1406.4901","open_access":"1"}],"oa":1,"month":"06","citation":{"ista":"Uhler C, Lenkoski A, Richards D. 2014. Exact formulas for the normalizing constants of Wishart distributions for graphical models. ArXiv, .","chicago":"Uhler, Caroline, Alex Lenkoski, and Donald Richards. “ Exact Formulas for the Normalizing Constants of Wishart Distributions for Graphical Models.” ArXiv. ArXiv, 2014.","apa":"Uhler, C., Lenkoski, A., & Richards, D. (2014). Exact formulas for the normalizing constants of Wishart distributions for graphical models. ArXiv. ArXiv.","ama":"Uhler C, Lenkoski A, Richards D. Exact formulas for the normalizing constants of Wishart distributions for graphical models. ArXiv. 2014.","short":"C. Uhler, A. Lenkoski, D. Richards, ArXiv (2014).","ieee":"C. Uhler, A. Lenkoski, and D. Richards, “ Exact formulas for the normalizing constants of Wishart distributions for graphical models,” ArXiv. ArXiv, 2014.","mla":"Uhler, Caroline, et al. “ Exact Formulas for the Normalizing Constants of Wishart Distributions for Graphical Models.” ArXiv, ArXiv, 2014."},"date_updated":"2021-01-12T06:54:44Z","extern":1,"author":[{"last_name":"Uhler","orcid":"0000-0002-7008-0216","full_name":"Caroline Uhler","first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alex","full_name":"Lenkoski, Alex","last_name":"Lenkoski"},{"first_name":"Donald","full_name":"Richards, Donald","last_name":"Richards"}],"publist_id":"5058","title":" Exact formulas for the normalizing constants of Wishart distributions for graphical models","_id":"2017","type":"preprint","status":"public"},{"language":[{"iso":"eng"}],"file":[{"file_size":4435787,"date_updated":"2020-07-14T12:45:25Z","creator":"system","file_name":"IST-2016-423-v1+1_1-s2.0-S0092867414013154-main.pdf","date_created":"2018-12-12T10:08:47Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"4709","checksum":"6c5de8329bb2ffa71cba9fda750f14ce"}],"publication_status":"published","license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"volume":159,"issue":"4","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Radial glial progenitors (RGPs) are responsible for producing nearly all neocortical neurons. To gain insight into the patterns of RGP division and neuron production, we quantitatively analyzed excitatory neuron genesis in the mouse neocortex using Mosaic Analysis with Double Markers, which provides single-cell resolution of progenitor division patterns and potential in vivo. We found that RGPs progress through a coherent program in which their proliferative potential diminishes in a predictable manner. Upon entry into the neurogenic phase, individual RGPs produce ∼8–9 neurons distributed in both deep and superficial layers, indicating a unitary output in neuronal production. Removal of OTX1, a transcription factor transiently expressed in RGPs, results in both deep- and superficial-layer neuron loss and a reduction in neuronal unit size. Moreover, ∼1/6 of neurogenic RGPs proceed to produce glia. These results suggest that progenitor behavior and histogenesis in the mammalian neocortex conform to a remarkably orderly and deterministic program."}],"intvolume":" 159","month":"11","scopus_import":1,"ddc":["570"],"date_updated":"2021-01-12T06:54:47Z","file_date_updated":"2020-07-14T12:45:25Z","department":[{"_id":"SiHi"},{"_id":"Bio"}],"_id":"2022","pubrep_id":"423","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","publication":"Cell","day":"06","year":"2014","has_accepted_license":"1","date_created":"2018-12-11T11:55:16Z","date_published":"2014-11-06T00:00:00Z","doi":"10.1016/j.cell.2014.10.027","page":"775 - 788","oa":1,"publisher":"Cell Press","quality_controlled":"1","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Gao, P., Postiglione, M. P., Krieger, T., Hernandez, L., Wang, C., Han, Z., … Shi, S. (2014). Deterministic progenitor behavior and unitary production of neurons in the neocortex. Cell. Cell Press. https://doi.org/10.1016/j.cell.2014.10.027","ama":"Gao P, Postiglione MP, Krieger T, et al. Deterministic progenitor behavior and unitary production of neurons in the neocortex. Cell. 2014;159(4):775-788. doi:10.1016/j.cell.2014.10.027","short":"P. Gao, M.P. Postiglione, T. Krieger, L. Hernandez, C. Wang, Z. Han, C. Streicher, E. Papusheva, R. Insolera, K. Chugh, O. Kodish, K. Huang, B. Simons, L. Luo, S. Hippenmeyer, S. Shi, Cell 159 (2014) 775–788.","ieee":"P. Gao et al., “Deterministic progenitor behavior and unitary production of neurons in the neocortex,” Cell, vol. 159, no. 4. Cell Press, pp. 775–788, 2014.","mla":"Gao, Peng, et al. “Deterministic Progenitor Behavior and Unitary Production of Neurons in the Neocortex.” Cell, vol. 159, no. 4, Cell Press, 2014, pp. 775–88, doi:10.1016/j.cell.2014.10.027.","ista":"Gao P, Postiglione MP, Krieger T, Hernandez L, Wang C, Han Z, Streicher C, Papusheva E, Insolera R, Chugh K, Kodish O, Huang K, Simons B, Luo L, Hippenmeyer S, Shi S. 2014. Deterministic progenitor behavior and unitary production of neurons in the neocortex. Cell. 159(4), 775–788.","chicago":"Gao, Peng, Maria P Postiglione, Teresa Krieger, Luisirene Hernandez, Chao Wang, Zhi Han, Carmen Streicher, et al. “Deterministic Progenitor Behavior and Unitary Production of Neurons in the Neocortex.” Cell. Cell Press, 2014. https://doi.org/10.1016/j.cell.2014.10.027."},"title":"Deterministic progenitor behavior and unitary production of neurons in the neocortex","author":[{"first_name":"Peng","full_name":"Gao, Peng","last_name":"Gao"},{"full_name":"Postiglione, Maria P","last_name":"Postiglione","first_name":"Maria P","id":"2C67902A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Krieger","full_name":"Krieger, Teresa","first_name":"Teresa"},{"last_name":"Hernandez","full_name":"Hernandez, Luisirene","first_name":"Luisirene"},{"full_name":"Wang, Chao","last_name":"Wang","first_name":"Chao"},{"full_name":"Han, Zhi","last_name":"Han","first_name":"Zhi"},{"full_name":"Streicher, Carmen","last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen"},{"last_name":"Papusheva","full_name":"Papusheva, Ekaterina","first_name":"Ekaterina","id":"41DB591E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ryan","last_name":"Insolera","full_name":"Insolera, Ryan"},{"first_name":"Kritika","last_name":"Chugh","full_name":"Chugh, Kritika"},{"first_name":"Oren","full_name":"Kodish, Oren","last_name":"Kodish"},{"first_name":"Kun","full_name":"Huang, Kun","last_name":"Huang"},{"first_name":"Benjamin","full_name":"Simons, Benjamin","last_name":"Simons"},{"first_name":"Liqun","last_name":"Luo","full_name":"Luo, Liqun"},{"last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"first_name":"Song","full_name":"Shi, Song","last_name":"Shi"}],"publist_id":"5050","project":[{"call_identifier":"FP7","_id":"25D61E48-B435-11E9-9278-68D0E5697425","grant_number":"618444","name":"Molecular Mechanisms of Cerebral Cortex Development"},{"name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","grant_number":"RGP0053/2014","_id":"25D7962E-B435-11E9-9278-68D0E5697425"}]},{"_id":"2020","status":"public","type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:46Z","citation":{"chicago":"Ali, Shah, Simon Hippenmeyer, Lily Saadat, Liqun Luo, Irving Weissman, and Reza Ardehali. “Existing Cardiomyocytes Generate Cardiomyocytes at a Low Rate after Birth in Mice.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1408233111.","ista":"Ali S, Hippenmeyer S, Saadat L, Luo L, Weissman I, Ardehali R. 2014. Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice. PNAS. 111(24), 8850–8855.","mla":"Ali, Shah, et al. “Existing Cardiomyocytes Generate Cardiomyocytes at a Low Rate after Birth in Mice.” PNAS, vol. 111, no. 24, National Academy of Sciences, 2014, pp. 8850–55, doi:10.1073/pnas.1408233111.","apa":"Ali, S., Hippenmeyer, S., Saadat, L., Luo, L., Weissman, I., & Ardehali, R. (2014). Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1408233111","ama":"Ali S, Hippenmeyer S, Saadat L, Luo L, Weissman I, Ardehali R. Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice. PNAS. 2014;111(24):8850-8855. doi:10.1073/pnas.1408233111","ieee":"S. Ali, S. Hippenmeyer, L. Saadat, L. Luo, I. Weissman, and R. Ardehali, “Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice,” PNAS, vol. 111, no. 24. National Academy of Sciences, pp. 8850–8855, 2014.","short":"S. Ali, S. Hippenmeyer, L. Saadat, L. Luo, I. Weissman, R. Ardehali, PNAS 111 (2014) 8850–8855."},"department":[{"_id":"SiHi"}],"title":"Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in mice","author":[{"first_name":"Shah","last_name":"Ali","full_name":"Ali, Shah"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer"},{"first_name":"Lily","full_name":"Saadat, Lily","last_name":"Saadat"},{"full_name":"Luo, Liqun","last_name":"Luo","first_name":"Liqun"},{"first_name":"Irving","full_name":"Weissman, Irving","last_name":"Weissman"},{"first_name":"Reza","full_name":"Ardehali, Reza","last_name":"Ardehali"}],"publist_id":"5052","oa_version":"None","abstract":[{"lang":"eng","text":"The mammalian heart has long been considered a postmitotic organ, implying that the total number of cardiomyocytes is set at birth. Analysis of cell division in the mammalian heart is complicated by cardiomyocyte binucleation shortly after birth, which makes it challenging to interpret traditional assays of cell turnover [Laflamme MA, Murray CE (2011) Nature 473(7347):326–335; Bergmann O, et al. (2009) Science 324(5923):98–102]. An elegant multi-isotope imaging-mass spectrometry technique recently calculated the low, discrete rate of cardiomyocyte generation in mice [Senyo SE, et al. (2013) Nature 493(7432):433–436], yet our cellular-level understanding of postnatal cardiomyogenesis remains limited. Herein, we provide a new line of evidence for the differentiated α-myosin heavy chain-expressing cardiomyocyte as the cell of origin of postnatal cardiomyogenesis using the “mosaic analysis with double markers” mouse model. We show limited, life-long, symmetric division of cardiomyocytes as a rare event that is evident in utero but significantly diminishes after the first month of life in mice; daughter cardiomyocytes divide very seldom, which this study is the first to demonstrate, to our knowledge. Furthermore, ligation of the left anterior descending coronary artery, which causes a myocardial infarction in the mosaic analysis with double-marker mice, did not increase the rate of cardiomyocyte division above the basal level for up to 4 wk after the injury. The clonal analysis described here provides direct evidence of postnatal mammalian cardiomyogenesis."}],"intvolume":" 111","month":"06","scopus_import":1,"quality_controlled":"1","publisher":"National Academy of Sciences","publication":"PNAS","language":[{"iso":"eng"}],"day":"17","year":"2014","publication_status":"published","date_created":"2018-12-11T11:55:15Z","date_published":"2014-06-17T00:00:00Z","issue":"24","volume":111,"doi":"10.1073/pnas.1408233111","page":"8850 - 8855"},{"_id":"2021","status":"public","type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:47Z","citation":{"chicago":"William, Joo, Simon Hippenmeyer, and Liqun Luo. “Dendrite Morphogenesis Depends on Relative Levels of NT-3/TrkC Signaling.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1258996.","ista":"William J, Hippenmeyer S, Luo L. 2014. Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling. Science. 346(6209), 626–629.","mla":"William, Joo, et al. “Dendrite Morphogenesis Depends on Relative Levels of NT-3/TrkC Signaling.” Science, vol. 346, no. 6209, American Association for the Advancement of Science, 2014, pp. 626–29, doi:10.1126/science.1258996.","ama":"William J, Hippenmeyer S, Luo L. Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling. Science. 2014;346(6209):626-629. doi:10.1126/science.1258996","apa":"William, J., Hippenmeyer, S., & Luo, L. (2014). Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1258996","short":"J. William, S. Hippenmeyer, L. Luo, Science 346 (2014) 626–629.","ieee":"J. William, S. Hippenmeyer, and L. Luo, “Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling,” Science, vol. 346, no. 6209. American Association for the Advancement of Science, pp. 626–629, 2014."},"title":"Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling","department":[{"_id":"SiHi"}],"author":[{"last_name":"William","full_name":"William, Joo","first_name":"Joo"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061"},{"first_name":"Liqun","last_name":"Luo","full_name":"Luo, Liqun"}],"publist_id":"5051","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Neurotrophins regulate diverse aspects of neuronal development and plasticity, but their precise in vivo functions during neural circuit assembly in the central brain remain unclear. We show that the neurotrophin receptor tropomyosin-related kinase C (TrkC) is required for dendritic growth and branching of mouse cerebellar Purkinje cells. Sparse TrkC knockout reduced dendrite complexity, but global Purkinje cell knockout had no effect. Removal of the TrkC ligand neurotrophin-3 (NT-3) from cerebellar granule cells, which provide major afferent input to developing Purkinje cell dendrites, rescued the dendrite defects caused by sparse TrkC disruption in Purkinje cells. Our data demonstrate that NT-3 from presynaptic neurons (granule cells) is required for TrkC-dependent competitive dendrite morphogenesis in postsynaptic neurons (Purkinje cells)—a previously unknown mechanism of neural circuit development."}],"intvolume":" 346","month":"10","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631524/","open_access":"1"}],"oa":1,"quality_controlled":"1","publisher":"American Association for the Advancement of Science","scopus_import":1,"publication":"Science","language":[{"iso":"eng"}],"day":"31","publication_status":"published","year":"2014","date_created":"2018-12-11T11:55:15Z","doi":"10.1126/science.1258996","date_published":"2014-10-31T00:00:00Z","volume":346,"issue":"6209","page":"626 - 629"},{"acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 246967 (VERIWARE), by the EU FP7 project HIERATIC, by the Czech Science Foundation grant No P202/12/P612, by EPSRC project EP/K038575/1.","quality_controlled":"1","publisher":"Society of Industrial and Applied Mathematics","oa":1,"day":"01","publication":" Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","year":"2014","doi":"10.1007/978-3-319-11936-6_8","date_published":"2014-11-01T00:00:00Z","date_created":"2018-12-11T11:55:17Z","page":"98 - 114","project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"26241A12-B435-11E9-9278-68D0E5697425","name":"LIGHT-REGULATED LIGAND TRAPS FOR SPATIO-TEMPORAL INHIBITION OF CELL SIGNALING","grant_number":"24696"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23"},{"grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Martin Chmelik, Vojtěch Forejt, Jan Kretinsky, Marta Kwiatkowska, David Parker, and Mateusz Ujma. “Verification of Markov Decision Processes Using Learning Algorithms.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Franck Cassez and Jean-François Raskin, 8837:98–114. Society of Industrial and Applied Mathematics, 2014. https://doi.org/10.1007/978-3-319-11936-6_8.","ista":"Brázdil T, Chatterjee K, Chmelik M, Forejt V, Kretinsky J, Kwiatkowska M, Parker D, Ujma M. 2014. Verification of markov decision processes using learning algorithms. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). ALENEX: Algorithm Engineering and Experiments, LNCS, vol. 8837, 98–114.","mla":"Brázdil, Tomáš, et al. “Verification of Markov Decision Processes Using Learning Algorithms.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Franck Cassez and Jean-François Raskin, vol. 8837, Society of Industrial and Applied Mathematics, 2014, pp. 98–114, doi:10.1007/978-3-319-11936-6_8.","ieee":"T. Brázdil et al., “Verification of markov decision processes using learning algorithms,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Sydney, Australia, 2014, vol. 8837, pp. 98–114.","short":"T. Brázdil, K. Chatterjee, M. Chmelik, V. Forejt, J. Kretinsky, M. Kwiatkowska, D. Parker, M. Ujma, in:, F. Cassez, J.-F. Raskin (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Society of Industrial and Applied Mathematics, 2014, pp. 98–114.","apa":"Brázdil, T., Chatterjee, K., Chmelik, M., Forejt, V., Kretinsky, J., Kwiatkowska, M., … Ujma, M. (2014). Verification of markov decision processes using learning algorithms. In F. Cassez & J.-F. Raskin (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8837, pp. 98–114). Sydney, Australia: Society of Industrial and Applied Mathematics. https://doi.org/10.1007/978-3-319-11936-6_8","ama":"Brázdil T, Chatterjee K, Chmelik M, et al. Verification of markov decision processes using learning algorithms. In: Cassez F, Raskin J-F, eds. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8837. Society of Industrial and Applied Mathematics; 2014:98-114. doi:10.1007/978-3-319-11936-6_8"},"editor":[{"full_name":"Cassez, Franck","last_name":"Cassez","first_name":"Franck"},{"first_name":"Jean-François","last_name":"Raskin","full_name":"Raskin, Jean-François"}],"title":"Verification of markov decision processes using learning algorithms","author":[{"full_name":"Brázdil, Tomáš","last_name":"Brázdil","first_name":"Tomáš"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin","last_name":"Chmelik"},{"full_name":"Forejt, Vojtěch","last_name":"Forejt","first_name":"Vojtěch"},{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Kretinsky","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan"},{"last_name":"Kwiatkowska","full_name":"Kwiatkowska, Marta","first_name":"Marta"},{"full_name":"Parker, David","last_name":"Parker","first_name":"David"},{"last_name":"Ujma","full_name":"Ujma, Mateusz","first_name":"Mateusz"}],"publist_id":"5046","oa_version":"Submitted Version","abstract":[{"text":"We present a general framework for applying machine-learning algorithms to the verification of Markov decision processes (MDPs). The primary goal of these techniques is to improve performance by avoiding an exhaustive exploration of the state space. Our framework focuses on probabilistic reachability, which is a core property for verification, and is illustrated through two distinct instantiations. The first assumes that full knowledge of the MDP is available, and performs a heuristic-driven partial exploration of the model, yielding precise lower and upper bounds on the required probability. The second tackles the case where we may only sample the MDP, and yields probabilistic guarantees, again in terms of both the lower and upper bounds, which provides efficient stopping criteria for the approximation. The latter is the first extension of statistical model checking for unbounded properties inMDPs. In contrast with other related techniques, our approach is not restricted to time-bounded (finite-horizon) or discounted properties, nor does it assume any particular properties of the MDP. We also show how our methods extend to LTL objectives. We present experimental results showing the performance of our framework on several examples.","lang":"eng"}],"month":"11","intvolume":" 8837","alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1402.2967"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":8837,"ec_funded":1,"_id":"2027","status":"public","type":"conference","conference":{"name":"ALENEX: Algorithm Engineering and Experiments","end_date":"2014-11-07","location":"Sydney, Australia","start_date":"2014-11-03"},"date_updated":"2021-01-12T06:54:49Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}]},{"ec_funded":1,"volume":3,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"c240f915450d4ebe8f95043a2a8c7b1a","file_id":"5094","date_updated":"2020-07-14T12:45:26Z","file_size":2239563,"creator":"system","date_created":"2018-12-12T10:14:41Z","file_name":"IST-2016-421-v1+1_e04057.full.pdf"}],"publication_status":"published","intvolume":" 3","month":"12","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"text":"A puzzling property of synaptic transmission, originally established at the neuromuscular junction, is that the time course of transmitter release is independent of the extracellular Ca2+ concentration ([Ca2+]o), whereas the rate of release is highly [Ca2+]o-dependent. Here, we examine the time course of release at inhibitory basket cell-Purkinje cell synapses and show that it is independent of [Ca2+]o. Modeling of Ca2+-dependent transmitter release suggests that the invariant time course of release critically depends on tight coupling between Ca2+ channels and release sensors. Experiments with exogenous Ca2+ chelators reveal that channel-sensor coupling at basket cell-Purkinje cell synapses is very tight, with a mean distance of 10–20 nm. Thus, tight channel-sensor coupling provides a mechanistic explanation for the apparent [Ca2+]o independence of the time course of release.","lang":"eng"}],"department":[{"_id":"PeJo"}],"file_date_updated":"2020-07-14T12:45:26Z","ddc":["570"],"date_updated":"2021-01-12T06:54:51Z","pubrep_id":"421","status":"public","type":"journal_article","_id":"2031","date_created":"2018-12-11T11:55:19Z","doi":"10.7554/eLife.04057","date_published":"2014-12-09T00:00:00Z","publication":"eLife","day":"09","year":"2014","has_accepted_license":"1","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","title":"Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse","publist_id":"5041","author":[{"full_name":"Arai, Itaru","last_name":"Arai","first_name":"Itaru","id":"32A73F6C-F248-11E8-B48F-1D18A9856A87"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Arai, itaru, and Peter M Jonas. “Nanodomain Coupling Explains Ca^2+ Independence of Transmitter Release Time Course at a Fast Central Synapse.” ELife. eLife Sciences Publications, 2014. https://doi.org/10.7554/eLife.04057.","ista":"Arai itaru, Jonas PM. 2014. Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse. eLife. 3.","mla":"Arai, itaru, and Peter M. Jonas. “Nanodomain Coupling Explains Ca^2+ Independence of Transmitter Release Time Course at a Fast Central Synapse.” ELife, vol. 3, eLife Sciences Publications, 2014, doi:10.7554/eLife.04057.","short":"itaru Arai, P.M. Jonas, ELife 3 (2014).","ieee":"itaru Arai and P. M. Jonas, “Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse,” eLife, vol. 3. eLife Sciences Publications, 2014.","apa":"Arai, itaru, & Jonas, P. M. (2014). Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.04057","ama":"Arai itaru, Jonas PM. Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse. eLife. 2014;3. doi:10.7554/eLife.04057"},"project":[{"name":"Mechanisms of transmitter release at GABAergic synapses","grant_number":"P24909-B24","call_identifier":"FWF","_id":"25C26B1E-B435-11E9-9278-68D0E5697425"},{"_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"268548","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons"}]},{"quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"doi":"10.1038/ncomms4498","date_published":"2014-03-25T00:00:00Z","date_created":"2018-12-11T11:55:16Z","day":"25","publication":"Nature Communications","has_accepted_license":"1","year":"2014","article_number":"3498","title":"Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole","publist_id":"5048","author":[{"last_name":"Toshima","full_name":"Toshima, Junko","first_name":"Junko"},{"full_name":"Nishinoaki, Show","last_name":"Nishinoaki","first_name":"Show"},{"full_name":"Sato, Yoshifumi","last_name":"Sato","first_name":"Yoshifumi"},{"first_name":"Wataru","last_name":"Yamamoto","full_name":"Yamamoto, Wataru"},{"full_name":"Furukawa, Daiki","last_name":"Furukawa","first_name":"Daiki"},{"orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","last_name":"Siekhaus","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sawaguchi","full_name":"Sawaguchi, Akira","first_name":"Akira"},{"first_name":"Jiro","full_name":"Toshima, Jiro","last_name":"Toshima"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Toshima J, Nishinoaki S, Sato Y, et al. Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole. Nature Communications. 2014;5. doi:10.1038/ncomms4498","apa":"Toshima, J., Nishinoaki, S., Sato, Y., Yamamoto, W., Furukawa, D., Siekhaus, D. E., … Toshima, J. (2014). Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms4498","ieee":"J. Toshima et al., “Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole,” Nature Communications, vol. 5. Nature Publishing Group, 2014.","short":"J. Toshima, S. Nishinoaki, Y. Sato, W. Yamamoto, D. Furukawa, D.E. Siekhaus, A. Sawaguchi, J. Toshima, Nature Communications 5 (2014).","mla":"Toshima, Junko, et al. “Bifurcation of the Endocytic Pathway into Rab5-Dependent and -Independent Transport to the Vacuole.” Nature Communications, vol. 5, 3498, Nature Publishing Group, 2014, doi:10.1038/ncomms4498.","ista":"Toshima J, Nishinoaki S, Sato Y, Yamamoto W, Furukawa D, Siekhaus DE, Sawaguchi A, Toshima J. 2014. Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole. Nature Communications. 5, 3498.","chicago":"Toshima, Junko, Show Nishinoaki, Yoshifumi Sato, Wataru Yamamoto, Daiki Furukawa, Daria E Siekhaus, Akira Sawaguchi, and Jiro Toshima. “Bifurcation of the Endocytic Pathway into Rab5-Dependent and -Independent Transport to the Vacuole.” Nature Communications. Nature Publishing Group, 2014. https://doi.org/10.1038/ncomms4498."},"month":"03","intvolume":" 5","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"The yeast Rab5 homologue, Vps21p, is known to be involved both in the vacuolar protein sorting (VPS) pathway from the trans-Golgi network to the vacuole, and in the endocytic pathway from the plasma membrane to the vacuole. However, the intracellular location at which these two pathways converge remains unclear. In addition, the endocytic pathway is not completely blocked in yeast cells lacking all Rab5 genes, suggesting the existence of an unidentified route that bypasses the Rab5-dependent endocytic pathway. Here we show that convergence of the endocytic and VPS pathways occurs upstream of the requirement for Vps21p in these pathways. We also identify a previously unidentified endocytic pathway mediated by the AP-3 complex. Importantly, the AP-3-mediated pathway appears mostly intact in Rab5-disrupted cells, and thus works as an alternative route to the vacuole/lysosome. We propose that the endocytic traffic branches into two routes to reach the vacuole: a Rab5-dependent VPS pathway and a Rab5-independent AP-3-mediated pathway."}],"volume":5,"file":[{"file_id":"4864","checksum":"614fb6579c86d1f95bdd95eeb9ab01b0","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:11:11Z","file_name":"IST-2016-616-v1+1_DaSi_Bifurcation_Postprint.pdf","creator":"system","date_updated":"2020-07-14T12:45:25Z","file_size":4803515}],"language":[{"iso":"eng"}],"publication_status":"published","status":"public","pubrep_id":"616","type":"journal_article","_id":"2024","department":[{"_id":"DaSi"}],"file_date_updated":"2020-07-14T12:45:25Z","ddc":["570"],"date_updated":"2021-01-12T06:54:48Z"},{"oa":1,"publisher":"Academic Press","quality_controlled":"1","acknowledgement":"This work is supported by AFOSR grant FA 9550-11-1-0165, program grant RPG 24/2012 from the Human Frontiers of Science (DBF) and travel support from the European Commission Marie Curie International Reintegration Grant PIRG04-GA-2008-239429 (KB). DP was supported by NIHR01 GM104987 and the Wyss Institute of Biologically Inspired Engineering. ","page":"40 - 54","date_created":"2018-12-11T11:55:18Z","doi":"10.1016/j.jtbi.2014.09.041","date_published":"2014-10-12T00:00:00Z","year":"2014","has_accepted_license":"1","publication":" Journal of Theoretical Biology","day":"12","article_processing_charge":"No","author":[{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina","orcid":"0000-0002-7214-0171","full_name":"Bodova, Katarina","last_name":"Bodova"},{"first_name":"David","full_name":"Paydarfar, David","last_name":"Paydarfar"},{"first_name":"Daniel","last_name":"Forger","full_name":"Forger, Daniel"}],"publist_id":"5043","title":"Characterizing spiking in noisy type II neurons","citation":{"mla":"Bodova, Katarina, et al. “Characterizing Spiking in Noisy Type II Neurons.” Journal of Theoretical Biology, vol. 365, Academic Press, 2014, pp. 40–54, doi:10.1016/j.jtbi.2014.09.041.","apa":"Bodova, K., Paydarfar, D., & Forger, D. (2014). Characterizing spiking in noisy type II neurons. Journal of Theoretical Biology. Academic Press. https://doi.org/10.1016/j.jtbi.2014.09.041","ama":"Bodova K, Paydarfar D, Forger D. Characterizing spiking in noisy type II neurons. Journal of Theoretical Biology. 2014;365:40-54. doi:10.1016/j.jtbi.2014.09.041","short":"K. Bodova, D. Paydarfar, D. Forger, Journal of Theoretical Biology 365 (2014) 40–54.","ieee":"K. Bodova, D. Paydarfar, and D. Forger, “Characterizing spiking in noisy type II neurons,” Journal of Theoretical Biology, vol. 365. Academic Press, pp. 40–54, 2014.","chicago":"Bodova, Katarina, David Paydarfar, and Daniel Forger. “Characterizing Spiking in Noisy Type II Neurons.” Journal of Theoretical Biology. Academic Press, 2014. https://doi.org/10.1016/j.jtbi.2014.09.041.","ista":"Bodova K, Paydarfar D, Forger D. 2014. Characterizing spiking in noisy type II neurons. Journal of Theoretical Biology. 365, 40–54."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","intvolume":" 365","month":"10","abstract":[{"text":"Understanding the dynamics of noisy neurons remains an important challenge in neuroscience. Here, we describe a simple probabilistic model that accurately describes the firing behavior in a large class (type II) of neurons. To demonstrate the usefulness of this model, we show how it accurately predicts the interspike interval (ISI) distributions, bursting patterns and mean firing rates found by: (1) simulations of the classic Hodgkin-Huxley model with channel noise, (2) experimental data from squid giant axon with a noisy input current and (3) experimental data on noisy firing from a neuron within the suprachiasmatic nucleus (SCN). This simple model has 6 parameters, however, in some cases, two of these parameters are coupled and only 5 parameters account for much of the known behavior. From these parameters, many properties of spiking can be found through simple calculation. Thus, we show how the complex effects of noise can be understood through a simple and general probabilistic model.","lang":"eng"}],"oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","volume":365,"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1016/j.jtbi.2015.03.013"}]},"publication_status":"published","language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:45:25Z","file_size":2679222,"date_created":"2018-12-12T10:17:58Z","file_name":"IST-2016-444-v1+1_1-s2.0-S0022519314005888-main.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5316","checksum":"a9dbae18d3233b3dab6944fd3f2cd49e"}],"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","pubrep_id":"444","status":"public","_id":"2028","department":[{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:45:25Z","date_updated":"2022-08-25T14:00:47Z","ddc":["570"]},{"project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"}],"author":[{"first_name":"Zuzana","full_name":"Komárková, Zuzana","last_name":"Komárková"},{"last_name":"Kretinsky","full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"publist_id":"5045","title":"Rabinizer 3: Safraless translation of ltl to small deterministic automata","editor":[{"first_name":"Franck","last_name":"Cassez","full_name":"Cassez, Franck"},{"full_name":"Raskin, Jean-François","last_name":"Raskin","first_name":"Jean-François"}],"citation":{"chicago":"Komárková, Zuzana, and Jan Kretinsky. “Rabinizer 3: Safraless Translation of Ltl to Small Deterministic Automata.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Franck Cassez and Jean-François Raskin, 8837:235–41. Springer, 2014. https://doi.org/10.1007/978-3-319-11936-6_17.","ista":"Komárková Z, Kretinsky J. 2014. Rabinizer 3: Safraless translation of ltl to small deterministic automata. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 8837, 235–241.","mla":"Komárková, Zuzana, and Jan Kretinsky. “Rabinizer 3: Safraless Translation of Ltl to Small Deterministic Automata.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Franck Cassez and Jean-François Raskin, vol. 8837, Springer, 2014, pp. 235–41, doi:10.1007/978-3-319-11936-6_17.","ama":"Komárková Z, Kretinsky J. Rabinizer 3: Safraless translation of ltl to small deterministic automata. In: Cassez F, Raskin J-F, eds. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8837. Springer; 2014:235-241. doi:10.1007/978-3-319-11936-6_17","apa":"Komárková, Z., & Kretinsky, J. (2014). Rabinizer 3: Safraless translation of ltl to small deterministic automata. In F. Cassez & J.-F. Raskin (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8837, pp. 235–241). Sydney, Australia: Springer. https://doi.org/10.1007/978-3-319-11936-6_17","short":"Z. Komárková, J. Kretinsky, in:, F. Cassez, J.-F. Raskin (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 235–241.","ieee":"Z. Komárková and J. Kretinsky, “Rabinizer 3: Safraless translation of ltl to small deterministic automata,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Sydney, Australia, 2014, vol. 8837, pp. 235–241."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Springer","acknowledgement":"Sponsor: P202/12/G061; GACR; Czech Science Foundation\r\n\r\n","page":"235 - 241","date_created":"2018-12-11T11:55:17Z","doi":"10.1007/978-3-319-11936-6_17","date_published":"2014-01-01T00:00:00Z","year":"2014","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","day":"01","conference":{"start_date":"2014-11-03","location":"Sydney, Australia","end_date":"2014-11-07","name":"ATVA: Automated Technology for Verification and Analysis"},"type":"conference","status":"public","_id":"2026","department":[{"_id":"ToHe"}],"date_updated":"2021-01-12T06:54:49Z","alternative_title":["LNCS"],"intvolume":" 8837","month":"01","abstract":[{"lang":"eng","text":"We present a tool for translating LTL formulae into deterministic ω-automata. It is the first tool that covers the whole LTL that does not use Safra’s determinization or any of its variants. This leads to smaller automata. There are several outputs of the tool: firstly, deterministic Rabin automata, which are the standard input for probabilistic model checking, e.g. for the probabilistic model-checker PRISM; secondly, deterministic generalized Rabin automata, which can also be used for probabilistic model checking and are sometimes by orders of magnitude smaller. We also link our tool to PRISM and show that this leads to a significant speed-up of probabilistic LTL model checking, especially with the generalized Rabin automata."}],"oa_version":"None","ec_funded":1,"volume":8837,"publication_status":"published","language":[{"iso":"eng"}]},{"status":"public","type":"journal_article","_id":"2029","department":[{"_id":"RoSe"}],"date_updated":"2021-01-12T06:54:50Z","month":"10","intvolume":" 108","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1404.4717","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Spin-wave theory is a key ingredient in our comprehension of quantum spin systems, and is used successfully for understanding a wide range of magnetic phenomena, including magnon condensation and stability of patterns in dipolar systems. Nevertheless, several decades of research failed to establish the validity of spin-wave theory rigorously, even for the simplest models of quantum spins. A rigorous justification of the method for the three-dimensional quantum Heisenberg ferromagnet at low temperatures is presented here. We derive sharp bounds on its free energy by combining a bosonic formulation of the model introduced by Holstein and Primakoff with probabilistic estimates and operator inequalities."}],"issue":"2","volume":108,"language":[{"iso":"eng"}],"publication_status":"published","article_number":"20003","title":"Validity of spin-wave theory for the quantum Heisenberg model","author":[{"first_name":"Michele","full_name":"Correggi, Michele","last_name":"Correggi"},{"full_name":"Giuliani, Alessandro","last_name":"Giuliani","first_name":"Alessandro"},{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5044","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Correggi M, Giuliani A, Seiringer R. 2014. Validity of spin-wave theory for the quantum Heisenberg model. EPL. 108(2), 20003.","chicago":"Correggi, Michele, Alessandro Giuliani, and Robert Seiringer. “Validity of Spin-Wave Theory for the Quantum Heisenberg Model.” EPL. IOP Publishing Ltd., 2014. https://doi.org/10.1209/0295-5075/108/20003.","short":"M. Correggi, A. Giuliani, R. Seiringer, EPL 108 (2014).","ieee":"M. Correggi, A. Giuliani, and R. Seiringer, “Validity of spin-wave theory for the quantum Heisenberg model,” EPL, vol. 108, no. 2. IOP Publishing Ltd., 2014.","ama":"Correggi M, Giuliani A, Seiringer R. Validity of spin-wave theory for the quantum Heisenberg model. EPL. 2014;108(2). doi:10.1209/0295-5075/108/20003","apa":"Correggi, M., Giuliani, A., & Seiringer, R. (2014). Validity of spin-wave theory for the quantum Heisenberg model. EPL. IOP Publishing Ltd. https://doi.org/10.1209/0295-5075/108/20003","mla":"Correggi, Michele, et al. “Validity of Spin-Wave Theory for the Quantum Heisenberg Model.” EPL, vol. 108, no. 2, 20003, IOP Publishing Ltd., 2014, doi:10.1209/0295-5075/108/20003."},"quality_controlled":"1","publisher":"IOP Publishing Ltd.","oa":1,"acknowledgement":"239694; ERC; European Research Council","date_published":"2014-10-13T00:00:00Z","doi":"10.1209/0295-5075/108/20003","date_created":"2018-12-11T11:55:18Z","day":"13","publication":"EPL","year":"2014"},{"department":[{"_id":"ChLa"}],"title":"Mind the nuisance: Gaussian process classification using privileged noise","publist_id":"5038","author":[{"first_name":"Daniel","full_name":"Hernandez Lobato, Daniel","last_name":"Hernandez Lobato"},{"first_name":"Viktoriia","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","full_name":"Sharmanska, Viktoriia","orcid":"0000-0003-0192-9308","last_name":"Sharmanska"},{"last_name":"Kersting","full_name":"Kersting, Kristian","first_name":"Kristian"},{"last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Quadrianto","full_name":"Quadrianto, Novi","first_name":"Novi"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T10:25:24Z","citation":{"ista":"Hernandez Lobato D, Sharmanska V, Kersting K, Lampert C, Quadrianto N. 2014. Mind the nuisance: Gaussian process classification using privileged noise. Advances in Neural Information Processing Systems. NIPS: Neural Information Processing Systems vol. 1, 837–845.","chicago":"Hernandez Lobato, Daniel, Viktoriia Sharmanska, Kristian Kersting, Christoph Lampert, and Novi Quadrianto. “Mind the Nuisance: Gaussian Process Classification Using Privileged Noise.” In Advances in Neural Information Processing Systems, 1:837–45. Neural Information Processing Systems, 2014.","apa":"Hernandez Lobato, D., Sharmanska, V., Kersting, K., Lampert, C., & Quadrianto, N. (2014). Mind the nuisance: Gaussian process classification using privileged noise. In Advances in Neural Information Processing Systems (Vol. 1, pp. 837–845). Montreal, Canada: Neural Information Processing Systems.","ama":"Hernandez Lobato D, Sharmanska V, Kersting K, Lampert C, Quadrianto N. Mind the nuisance: Gaussian process classification using privileged noise. In: Advances in Neural Information Processing Systems. Vol 1. Neural Information Processing Systems; 2014:837-845.","short":"D. Hernandez Lobato, V. Sharmanska, K. Kersting, C. Lampert, N. Quadrianto, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems, 2014, pp. 837–845.","ieee":"D. Hernandez Lobato, V. Sharmanska, K. Kersting, C. Lampert, and N. Quadrianto, “Mind the nuisance: Gaussian process classification using privileged noise,” in Advances in Neural Information Processing Systems, Montreal, Canada, 2014, vol. 1, no. January, pp. 837–845.","mla":"Hernandez Lobato, Daniel, et al. “Mind the Nuisance: Gaussian Process Classification Using Privileged Noise.” Advances in Neural Information Processing Systems, vol. 1, no. January, Neural Information Processing Systems, 2014, pp. 837–45."},"status":"public","type":"conference","conference":{"start_date":"2014-12-08","location":"Montreal, Canada","end_date":"2014-12-13","name":"NIPS: Neural Information Processing Systems"},"_id":"2033","volume":1,"issue":"January","date_published":"2014-12-08T00:00:00Z","date_created":"2018-12-11T11:55:20Z","page":"837-845","day":"08","language":[{"iso":"eng"}],"publication":"Advances in Neural Information Processing Systems","year":"2014","publication_status":"published","month":"12","intvolume":" 1","scopus_import":1,"quality_controlled":"1","publisher":"Neural Information Processing Systems","main_file_link":[{"open_access":"1","url":"https://papers.nips.cc/paper/5373-mind-the-nuisance-gaussian-process-classification-using-privileged-noise"}],"oa":1,"oa_version":"Submitted Version","abstract":[{"text":"The learning with privileged information setting has recently attracted a lot of attention within the machine learning community, as it allows the integration of additional knowledge into the training process of a classifier, even when this comes in the form of a data modality that is not available at test time. Here, we show that privileged information can naturally be treated as noise in the latent function of a Gaussian process classifier (GPC). That is, in contrast to the standard GPC setting, the latent function is not just a nuisance but a feature: it becomes a natural measure of confidence about the training data by modulating the slope of the GPC probit likelihood function. Extensive experiments on public datasets show that the proposed GPC method using privileged noise, called GPC+, improves over a standard GPC without privileged knowledge, and also over the current state-of-the-art SVM-based method, SVM+. Moreover, we show that advanced neural networks and deep learning methods can be compressed as privileged information.","lang":"eng"}]},{"department":[{"_id":"HaJa"}],"file_date_updated":"2020-07-14T12:45:26Z","ddc":["570"],"date_updated":"2021-01-12T06:54:51Z","status":"public","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)"},"type":"journal_article","_id":"2032","license":"https://creativecommons.org/licenses/by-nc/4.0/","volume":1,"issue":"4","language":[{"iso":"eng"}],"file":[{"file_name":"2014_Taylor_Alvaro.pdf","date_created":"2019-05-16T13:39:11Z","creator":"kschuh","file_size":1765933,"date_updated":"2020-07-14T12:45:26Z","checksum":"44e17ad40577ab46eb602e88a8b0b8fd","file_id":"6464","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","intvolume":" 1","month":"12","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"As light-based control of fundamental signaling pathways is becoming a reality, the field of optogenetics is rapidly moving beyond neuroscience. We have recently developed receptor tyrosine kinases that are activated by light and control cell proliferation, epithelial–mesenchymal transition, and angiogenic sprouting—cell behaviors central to cancer progression."}],"title":"The optogenetic promise for oncology: Episode I","author":[{"first_name":"Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","last_name":"Inglés Prieto","full_name":"Inglés Prieto, Álvaro","orcid":"0000-0002-5409-8571"},{"id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-7218-7738","full_name":"Gschaider-Reichhart, Eva","last_name":"Gschaider-Reichhart"},{"first_name":"Karin","last_name":"Schelch","full_name":"Schelch, Karin"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","last_name":"Janovjak","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315"},{"first_name":"Michael","last_name":"Grusch","full_name":"Grusch, Michael"}],"publist_id":"5040","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Inglés Prieto, Álvaro, et al. “The Optogenetic Promise for Oncology: Episode I.” Molecular and Cellular Oncology, vol. 1, no. 4, e964045, Taylor & Francis, 2014, doi:10.4161/23723548.2014.964045.","short":"Á. Inglés Prieto, E. Gschaider-Reichhart, K. Schelch, H.L. Janovjak, M. Grusch, Molecular and Cellular Oncology 1 (2014).","ieee":"Á. Inglés Prieto, E. Gschaider-Reichhart, K. Schelch, H. L. Janovjak, and M. Grusch, “The optogenetic promise for oncology: Episode I,” Molecular and Cellular Oncology, vol. 1, no. 4. Taylor & Francis, 2014.","ama":"Inglés Prieto Á, Gschaider-Reichhart E, Schelch K, Janovjak HL, Grusch M. The optogenetic promise for oncology: Episode I. Molecular and Cellular Oncology. 2014;1(4). doi:10.4161/23723548.2014.964045","apa":"Inglés Prieto, Á., Gschaider-Reichhart, E., Schelch, K., Janovjak, H. L., & Grusch, M. (2014). The optogenetic promise for oncology: Episode I. Molecular and Cellular Oncology. Taylor & Francis. https://doi.org/10.4161/23723548.2014.964045","chicago":"Inglés Prieto, Álvaro, Eva Gschaider-Reichhart, Karin Schelch, Harald L Janovjak, and Michael Grusch. “The Optogenetic Promise for Oncology: Episode I.” Molecular and Cellular Oncology. Taylor & Francis, 2014. https://doi.org/10.4161/23723548.2014.964045.","ista":"Inglés Prieto Á, Gschaider-Reichhart E, Schelch K, Janovjak HL, Grusch M. 2014. The optogenetic promise for oncology: Episode I. Molecular and Cellular Oncology. 1(4), e964045."},"article_number":"e964045","date_created":"2018-12-11T11:55:19Z","doi":"10.4161/23723548.2014.964045","date_published":"2014-12-31T00:00:00Z","publication":"Molecular and Cellular Oncology","day":"31","year":"2014","has_accepted_license":"1","oa":1,"publisher":"Taylor & Francis","quality_controlled":"1"},{"project":[{"name":"Provable Security for Physical Cryptography","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"editor":[{"full_name":"Krawczyk, Hugo","last_name":"Krawczyk","first_name":"Hugo"}],"title":"Enhanced chosen-ciphertext security and applications","publist_id":"5006","author":[{"last_name":"Dachman Soled","full_name":"Dachman Soled, Dana","first_name":"Dana"},{"id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","full_name":"Fuchsbauer, Georg","last_name":"Fuchsbauer"},{"last_name":"Mohassel","full_name":"Mohassel, Payman","first_name":"Payman"},{"last_name":"O’Neill","full_name":"O’Neill, Adam","first_name":"Adam"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Dachman Soled D, Fuchsbauer G, Mohassel P, O’Neill A. Enhanced chosen-ciphertext security and applications. In: Krawczyk H, ed. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8383. Springer; 2014:329-344. doi:10.1007/978-3-642-54631-0_19","apa":"Dachman Soled, D., Fuchsbauer, G., Mohassel, P., & O’Neill, A. (2014). Enhanced chosen-ciphertext security and applications. In H. Krawczyk (Ed.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8383, pp. 329–344). Buenos Aires, Argentina: Springer. https://doi.org/10.1007/978-3-642-54631-0_19","short":"D. Dachman Soled, G. Fuchsbauer, P. Mohassel, A. O’Neill, in:, H. Krawczyk (Ed.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 329–344.","ieee":"D. Dachman Soled, G. Fuchsbauer, P. Mohassel, and A. O’Neill, “Enhanced chosen-ciphertext security and applications,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Buenos Aires, Argentina, 2014, vol. 8383, pp. 329–344.","mla":"Dachman Soled, Dana, et al. “Enhanced Chosen-Ciphertext Security and Applications.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Hugo Krawczyk, vol. 8383, Springer, 2014, pp. 329–44, doi:10.1007/978-3-642-54631-0_19.","ista":"Dachman Soled D, Fuchsbauer G, Mohassel P, O’Neill A. 2014. Enhanced chosen-ciphertext security and applications. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PKC: Public Key Crypography, LNCS, vol. 8383, 329–344.","chicago":"Dachman Soled, Dana, Georg Fuchsbauer, Payman Mohassel, and Adam O’Neill. “Enhanced Chosen-Ciphertext Security and Applications.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Hugo Krawczyk, 8383:329–44. Springer, 2014. https://doi.org/10.1007/978-3-642-54631-0_19."},"publisher":"Springer","quality_controlled":"1","oa":1,"acknowledgement":"The second author was supported by EPSRC grant EP/H043454/1.","date_published":"2014-01-01T00:00:00Z","doi":"10.1007/978-3-642-54631-0_19","date_created":"2018-12-11T11:55:24Z","page":"329 - 344","day":"01","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","year":"2014","status":"public","type":"conference","conference":{"name":"PKC: Public Key Crypography","start_date":"2014-03-26","location":"Buenos Aires, Argentina","end_date":"2014-03-28"},"_id":"2045","department":[{"_id":"KrPi"}],"date_updated":"2021-01-12T06:54:57Z","month":"01","intvolume":" 8383","alternative_title":["LNCS"],"scopus_import":1,"main_file_link":[{"url":"https://eprint.iacr.org/2012/543","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"text":"We introduce and study a new notion of enhanced chosen-ciphertext security (ECCA) for public-key encryption. Loosely speaking, in the ECCA security experiment, the decryption oracle provided to the adversary is augmented to return not only the output of the decryption algorithm on a queried ciphertext but also of a randomness-recovery algorithm associated to the scheme. Our results mainly concern the case where the randomness-recovery algorithm is efficient. We provide constructions of ECCA-secure encryption from adaptive trapdoor functions as defined by Kiltz et al. (EUROCRYPT 2010), resulting in ECCA encryption from standard number-theoretic assumptions. We then give two applications of ECCA-secure encryption: (1) We use it as a unifying concept in showing equivalence of adaptive trapdoor functions and tag-based adaptive trapdoor functions, resolving an open question of Kiltz et al. (2) We show that ECCA-secure encryption can be used to securely realize an approach to public-key encryption with non-interactive opening (PKENO) originally suggested by Damgård and Thorbek (EUROCRYPT 2007), resulting in new and practical PKENO schemes quite different from those in prior work. Our results demonstrate that ECCA security is of both practical and theoretical interest.","lang":"eng"}],"volume":8383,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published"},{"article_number":"663","citation":{"chicago":"Kupczok, Anne, and Jonathan P Bollback. “Motif Depletion in Bacteriophages Infecting Hosts with CRISPR Systems.” BMC Genomics. BioMed Central, 2014. https://doi.org/10.1186/1471-2164-15-663.","ista":"Kupczok A, Bollback JP. 2014. Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. 15(1), 663.","mla":"Kupczok, Anne, and Jonathan P. Bollback. “Motif Depletion in Bacteriophages Infecting Hosts with CRISPR Systems.” BMC Genomics, vol. 15, no. 1, 663, BioMed Central, 2014, doi:10.1186/1471-2164-15-663.","apa":"Kupczok, A., & Bollback, J. P. (2014). Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. BioMed Central. https://doi.org/10.1186/1471-2164-15-663","ama":"Kupczok A, Bollback JP. Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. 2014;15(1). doi:10.1186/1471-2164-15-663","ieee":"A. Kupczok and J. P. Bollback, “Motif depletion in bacteriophages infecting hosts with CRISPR systems,” BMC Genomics, vol. 15, no. 1. BioMed Central, 2014.","short":"A. Kupczok, J.P. Bollback, BMC Genomics 15 (2014)."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5009","author":[{"full_name":"Kupczok, Anne","last_name":"Kupczok","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Anne"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","last_name":"Bollback"}],"title":"Motif depletion in bacteriophages infecting hosts with CRISPR systems","oa":1,"quality_controlled":"1","publisher":"BioMed Central","year":"2014","has_accepted_license":"1","publication":"BMC Genomics","day":"08","date_created":"2018-12-11T11:55:23Z","doi":"10.1186/1471-2164-15-663","date_published":"2014-08-08T00:00:00Z","_id":"2042","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"journal_article","pubrep_id":"396","status":"public","date_updated":"2021-01-12T06:54:56Z","ddc":["570"],"file_date_updated":"2020-07-14T12:45:26Z","department":[{"_id":"JoBo"}],"abstract":[{"lang":"eng","text":"Background: CRISPR is a microbial immune system likely to be involved in host-parasite coevolution. It functions using target sequences encoded by the bacterial genome, which interfere with invading nucleic acids using a homology-dependent system. The system also requires protospacer associated motifs (PAMs), short motifs close to the target sequence that are required for interference in CRISPR types I and II. Here, we investigate whether PAMs are depleted in phage genomes due to selection pressure to escape recognition.Results: To this end, we analyzed two data sets. Phages infecting all bacterial hosts were analyzed first, followed by a detailed analysis of phages infecting the genus Streptococcus, where PAMs are best understood. We use two different measures of motif underrepresentation that control for codon bias and the frequency of submotifs. We compare phages infecting species with a particular CRISPR type to those infecting species without that type. Since only known PAMs were investigated, the analysis is restricted to CRISPR types I-C and I-E and in Streptococcus to types I-C and II. We found evidence for PAM depletion in Streptococcus phages infecting hosts with CRISPR type I-C, in Vibrio phages infecting hosts with CRISPR type I-E and in Streptococcus thermopilus phages infecting hosts with type II-A, known as CRISPR3.Conclusions: The observed motif depletion in phages with hosts having CRISPR can be attributed to selection rather than to mutational bias, as mutational bias should affect the phages of all hosts. This observation implies that the CRISPR system has been efficient in the groups discussed here."}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 15","month":"08","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_id":"4878","checksum":"3f6d2776b90a842a28359cc957d3d04b","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:11:24Z","file_name":"IST-2015-396-v1+1_1471-2164-15-663.pdf","creator":"system","date_updated":"2020-07-14T12:45:26Z","file_size":1489769}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","issue":"1","volume":15},{"type":"conference","conference":{"name":"ALENEX: Algorithm Engineering and Experiments","start_date":"2014-01-05","location":"Portland, USA","end_date":"2014-01-05"},"status":"public","_id":"2043","department":[{"_id":"HeEd"}],"date_updated":"2021-01-12T06:54:56Z","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1310.0710","open_access":"1"}],"month":"01","abstract":[{"text":"Persistent homology is a popular and powerful tool for capturing topological features of data. Advances in algorithms for computing persistent homology have reduced the computation time drastically – as long as the algorithm does not exhaust the available memory. Following up on a recently presented parallel method for persistence computation on shared memory systems [1], we demonstrate that a simple adaption of the standard reduction algorithm leads to a variant for distributed systems. Our algorithmic design ensures that the data is distributed over the nodes without redundancy; this permits the computation of much larger instances than on a single machine. Moreover, we observe that the parallelism at least compensates for the overhead caused by communication between nodes, and often even speeds up the computation compared to sequential and even parallel shared memory algorithms. In our experiments, we were able to compute the persistent homology of filtrations with more than a billion (109) elements within seconds on a cluster with 32 nodes using less than 6GB of memory per node.","lang":"eng"}],"oa_version":"Submitted Version","ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"project":[{"name":"Topological Complex Systems","grant_number":"318493","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"author":[{"first_name":"Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","full_name":"Bauer, Ulrich","orcid":"0000-0002-9683-0724","last_name":"Bauer"},{"first_name":"Michael","orcid":"0000-0002-8030-9299","full_name":"Kerber, Michael","last_name":"Kerber"},{"id":"4505473A-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Reininghaus","full_name":"Reininghaus, Jan"}],"publist_id":"5008","editor":[{"last_name":" McGeoch","full_name":" McGeoch, Catherine","first_name":"Catherine"},{"first_name":"Ulrich","last_name":"Meyer","full_name":"Meyer, Ulrich"}],"title":"Distributed computation of persistent homology","citation":{"ista":"Bauer U, Kerber M, Reininghaus J. 2014. Distributed computation of persistent homology. Proceedings of the Workshop on Algorithm Engineering and Experiments. ALENEX: Algorithm Engineering and Experiments, 31–38.","chicago":"Bauer, Ulrich, Michael Kerber, and Jan Reininghaus. “Distributed Computation of Persistent Homology.” In Proceedings of the Workshop on Algorithm Engineering and Experiments, edited by Catherine McGeoch and Ulrich Meyer, 31–38. Society of Industrial and Applied Mathematics, 2014. https://doi.org/10.1137/1.9781611973198.4.","apa":"Bauer, U., Kerber, M., & Reininghaus, J. (2014). Distributed computation of persistent homology. In C. McGeoch & U. Meyer (Eds.), Proceedings of the Workshop on Algorithm Engineering and Experiments (pp. 31–38). Portland, USA: Society of Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611973198.4","ama":"Bauer U, Kerber M, Reininghaus J. Distributed computation of persistent homology. In: McGeoch C, Meyer U, eds. Proceedings of the Workshop on Algorithm Engineering and Experiments. Society of Industrial and Applied Mathematics; 2014:31-38. doi:10.1137/1.9781611973198.4","ieee":"U. Bauer, M. Kerber, and J. Reininghaus, “Distributed computation of persistent homology,” in Proceedings of the Workshop on Algorithm Engineering and Experiments, Portland, USA, 2014, pp. 31–38.","short":"U. Bauer, M. Kerber, J. Reininghaus, in:, C. McGeoch, U. Meyer (Eds.), Proceedings of the Workshop on Algorithm Engineering and Experiments, Society of Industrial and Applied Mathematics, 2014, pp. 31–38.","mla":"Bauer, Ulrich, et al. “Distributed Computation of Persistent Homology.” Proceedings of the Workshop on Algorithm Engineering and Experiments, edited by Catherine McGeoch and Ulrich Meyer, Society of Industrial and Applied Mathematics, 2014, pp. 31–38, doi:10.1137/1.9781611973198.4."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"Society of Industrial and Applied Mathematics","quality_controlled":"1","oa":1,"page":"31 - 38","doi":"10.1137/1.9781611973198.4","date_published":"2014-01-01T00:00:00Z","date_created":"2018-12-11T11:55:23Z","year":"2014","day":"01","publication":"Proceedings of the Workshop on Algorithm Engineering and Experiments"},{"oa":1,"quality_controlled":"1","publisher":"Frontiers Research Foundation","publication":"Frontiers in Neural Circuits","day":"10","year":"2014","has_accepted_license":"1","date_created":"2018-12-11T11:55:22Z","date_published":"2014-09-10T00:00:00Z","doi":"10.3389/fncir.2014.00107","article_number":"2p","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Jonas, Peter M., and John Lisman. “Structure, Function and Plasticity of Hippocampal Dentate Gyrus Microcircuits.” Frontiers in Neural Circuits, vol. 8, 2p, Frontiers Research Foundation, 2014, doi:10.3389/fncir.2014.00107.","short":"P.M. Jonas, J. Lisman, Frontiers in Neural Circuits 8 (2014).","ieee":"P. M. Jonas and J. Lisman, “Structure, function and plasticity of hippocampal dentate gyrus microcircuits,” Frontiers in Neural Circuits, vol. 8. Frontiers Research Foundation, 2014.","apa":"Jonas, P. M., & Lisman, J. (2014). Structure, function and plasticity of hippocampal dentate gyrus microcircuits. Frontiers in Neural Circuits. Frontiers Research Foundation. https://doi.org/10.3389/fncir.2014.00107","ama":"Jonas PM, Lisman J. Structure, function and plasticity of hippocampal dentate gyrus microcircuits. Frontiers in Neural Circuits. 2014;8. doi:10.3389/fncir.2014.00107","chicago":"Jonas, Peter M, and John Lisman. “Structure, Function and Plasticity of Hippocampal Dentate Gyrus Microcircuits.” Frontiers in Neural Circuits. Frontiers Research Foundation, 2014. https://doi.org/10.3389/fncir.2014.00107.","ista":"Jonas PM, Lisman J. 2014. Structure, function and plasticity of hippocampal dentate gyrus microcircuits. Frontiers in Neural Circuits. 8, 2p."},"title":"Structure, function and plasticity of hippocampal dentate gyrus microcircuits","publist_id":"5010","author":[{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"},{"first_name":"John","last_name":"Lisman","full_name":"Lisman, John"}],"oa_version":"Published Version","abstract":[{"text":"The hippocampus mediates several higher brain functions, such as learning, memory, and spatial coding. The input region of the hippocampus, the dentate gyrus, plays a critical role in these processes. Several lines of evidence suggest that the dentate gyrus acts as a preprocessor of incoming information, preparing it for subsequent processing in CA3. For example, the dentate gyrus converts input from the entorhinal cortex, where cells have multiple spatial fields, into the spatially more specific place cell activity characteristic of the CA3 region. Furthermore, the dentate gyrus is involved in pattern separation, transforming relatively similar input patterns into substantially different output patterns. Finally, the dentate gyrus produces a very sparse coding scheme in which only a very small fraction of neurons are active at any one time.","lang":"eng"}],"intvolume":" 8","month":"09","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:45:26Z","file_size":201110,"creator":"system","date_created":"2018-12-12T10:17:38Z","file_name":"IST-2016-424-v1+1_fncir-08-00107.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5294","checksum":"3ca57b164045523f876407e9f13a9fb8"}],"publication_status":"published","volume":8,"_id":"2041","pubrep_id":"424","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["570"],"date_updated":"2021-01-12T06:54:55Z","file_date_updated":"2020-07-14T12:45:26Z","department":[{"_id":"PeJo"}]},{"page":"103 - 117","doi":"10.1007/978-3-319-04099-8_7","date_published":"2014-03-19T00:00:00Z","date_created":"2018-12-11T11:55:23Z","year":"2014","day":"19","publication":"Topological Methods in Data Analysis and Visualization III","publisher":"Springer","quality_controlled":"1","oa":1,"author":[{"orcid":"0000-0002-9683-0724","full_name":"Bauer, Ulrich","last_name":"Bauer","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich"},{"first_name":"Michael","orcid":"0000-0002-8030-9299","full_name":"Kerber, Michael","last_name":"Kerber"},{"full_name":"Reininghaus, Jan","last_name":"Reininghaus","id":"4505473A-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"publist_id":"5007","title":"Clear and Compress: Computing Persistent Homology in Chunks","editor":[{"first_name":"Peer-Timo","full_name":"Bremer, Peer-Timo","last_name":"Bremer"},{"full_name":"Hotz, Ingrid","last_name":"Hotz","first_name":"Ingrid"},{"first_name":"Valerio","full_name":"Pascucci, Valerio","last_name":"Pascucci"},{"full_name":"Peikert, Ronald","last_name":"Peikert","first_name":"Ronald"}],"citation":{"ista":"Bauer U, Kerber M, Reininghaus J. 2014.Clear and Compress: Computing Persistent Homology in Chunks. In: Topological Methods in Data Analysis and Visualization III. , 103–117.","chicago":"Bauer, Ulrich, Michael Kerber, and Jan Reininghaus. “Clear and Compress: Computing Persistent Homology in Chunks.” In Topological Methods in Data Analysis and Visualization III, edited by Peer-Timo Bremer, Ingrid Hotz, Valerio Pascucci, and Ronald Peikert, 103–17. Mathematics and Visualization. Springer, 2014. https://doi.org/10.1007/978-3-319-04099-8_7.","apa":"Bauer, U., Kerber, M., & Reininghaus, J. (2014). Clear and Compress: Computing Persistent Homology in Chunks. In P.-T. Bremer, I. Hotz, V. Pascucci, & R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III (pp. 103–117). Springer. https://doi.org/10.1007/978-3-319-04099-8_7","ama":"Bauer U, Kerber M, Reininghaus J. Clear and Compress: Computing Persistent Homology in Chunks. In: Bremer P-T, Hotz I, Pascucci V, Peikert R, eds. Topological Methods in Data Analysis and Visualization III. Mathematics and Visualization. Springer; 2014:103-117. doi:10.1007/978-3-319-04099-8_7","short":"U. Bauer, M. Kerber, J. Reininghaus, in:, P.-T. Bremer, I. Hotz, V. Pascucci, R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III, Springer, 2014, pp. 103–117.","ieee":"U. Bauer, M. Kerber, and J. Reininghaus, “Clear and Compress: Computing Persistent Homology in Chunks,” in Topological Methods in Data Analysis and Visualization III, P.-T. Bremer, I. Hotz, V. Pascucci, and R. Peikert, Eds. Springer, 2014, pp. 103–117.","mla":"Bauer, Ulrich, et al. “Clear and Compress: Computing Persistent Homology in Chunks.” Topological Methods in Data Analysis and Visualization III, edited by Peer-Timo Bremer et al., Springer, 2014, pp. 103–17, doi:10.1007/978-3-319-04099-8_7."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"318493","name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1303.0477","open_access":"1"}],"month":"03","abstract":[{"text":"We present a parallel algorithm for computing the persistent homology of a filtered chain complex. Our approach differs from the commonly used reduction algorithm by first computing persistence pairs within local chunks, then simplifying the unpaired columns, and finally applying standard reduction on the simplified matrix. The approach generalizes a technique by Günther et al., which uses discrete Morse Theory to compute persistence; we derive the same worst-case complexity bound in a more general context. The algorithm employs several practical optimization techniques, which are of independent interest. Our sequential implementation of the algorithm is competitive with state-of-the-art methods, and we further improve the performance through parallel computation.","lang":"eng"}],"oa_version":"Submitted Version","department":[{"_id":"HeEd"}],"date_updated":"2021-01-12T06:54:56Z","type":"book_chapter","status":"public","_id":"2044","series_title":"Mathematics and Visualization"},{"date_created":"2018-12-11T11:55:22Z","doi":"10.1126/science.1254927","volume":345,"issue":"6204","date_published":"2014-09-26T00:00:00Z","year":"2014","publication_status":"published","language":[{"iso":"eng"}],"publication":"Science","day":"26","oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4228193/","open_access":"1"}],"publisher":"American Association for the Advancement of Science","scopus_import":1,"quality_controlled":"1","intvolume":" 345","month":"09","abstract":[{"text":"Development requires tissue growth as well as cell diversification. To address how these processes are coordinated, we analyzed the development of molecularly distinct domains of neural progenitors in the mouse and chick neural tube. We show that during development, these domains undergo changes in size that do not scale with changes in overall tissue size. Our data show that domain proportions are first established by opposing morphogen gradients and subsequently controlled by domain-specific regulation of differentiation rate but not differences in proliferation rate. Regulation of differentiation rate is key to maintaining domain proportions while accommodating both intra- and interspecies variations in size. Thus, the sequential control of progenitor specification and differentiation elaborates pattern without requiring that signaling gradients grow as tissues expand. ","lang":"eng"}],"oa_version":"Submitted Version","author":[{"last_name":"Kicheva","full_name":"Kicheva, Anna","first_name":"Anna"},{"last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias"},{"first_name":"Ana","full_name":"Ribeiro, Ana","last_name":"Ribeiro"},{"last_name":"Pérez Valle","full_name":"Pérez Valle, Helena","first_name":"Helena"},{"first_name":"Robin","last_name":"Lovell Badge","full_name":"Lovell Badge, Robin"},{"first_name":"Vasso","full_name":"Episkopou, Vasso","last_name":"Episkopou"},{"first_name":"James","full_name":"Briscoe, James","last_name":"Briscoe"}],"publist_id":"5011","title":"Coordination of progenitor specification and growth in mouse and chick spinal cord","department":[{"_id":"ToBo"}],"date_updated":"2021-01-12T06:54:55Z","citation":{"mla":"Kicheva, Anna, et al. “Coordination of Progenitor Specification and Growth in Mouse and Chick Spinal Cord.” Science, vol. 345, no. 6204, 1254927, American Association for the Advancement of Science, 2014, doi:10.1126/science.1254927.","ama":"Kicheva A, Bollenbach MT, Ribeiro A, et al. Coordination of progenitor specification and growth in mouse and chick spinal cord. Science. 2014;345(6204). doi:10.1126/science.1254927","apa":"Kicheva, A., Bollenbach, M. T., Ribeiro, A., Pérez Valle, H., Lovell Badge, R., Episkopou, V., & Briscoe, J. (2014). Coordination of progenitor specification and growth in mouse and chick spinal cord. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1254927","ieee":"A. Kicheva et al., “Coordination of progenitor specification and growth in mouse and chick spinal cord,” Science, vol. 345, no. 6204. American Association for the Advancement of Science, 2014.","short":"A. Kicheva, M.T. Bollenbach, A. Ribeiro, H. Pérez Valle, R. Lovell Badge, V. Episkopou, J. Briscoe, Science 345 (2014).","chicago":"Kicheva, Anna, Mark Tobias Bollenbach, Ana Ribeiro, Helena Pérez Valle, Robin Lovell Badge, Vasso Episkopou, and James Briscoe. “Coordination of Progenitor Specification and Growth in Mouse and Chick Spinal Cord.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1254927.","ista":"Kicheva A, Bollenbach MT, Ribeiro A, Pérez Valle H, Lovell Badge R, Episkopou V, Briscoe J. 2014. Coordination of progenitor specification and growth in mouse and chick spinal cord. Science. 345(6204), 1254927."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"2040","article_number":"1254927"},{"publisher":"Springer","quality_controlled":"1","oa":1,"acknowledgement":"This research was partially supported by BCS- 0941518 to the Department of Statistics at Carnegie Mellon University.","page":"170 - 184","doi":"10.1007/978-3-319-11257-2_14","date_published":"2014-01-01T00:00:00Z","date_created":"2018-12-11T11:55:24Z","year":"2014","day":"01","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","project":[{"name":"ROOTS Genome-wide Analysis of Root Traits","grant_number":"11-NSF-1070","_id":"25636330-B435-11E9-9278-68D0E5697425"}],"publist_id":"5004","author":[{"first_name":"Fei","full_name":"Yu, Fei","last_name":"Yu"},{"full_name":"Rybar, Michal","last_name":"Rybar","first_name":"Michal","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","last_name":"Uhler","first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stephen","full_name":"Fienberg, Stephen","last_name":"Fienberg"}],"external_id":{"arxiv":["1407.8067"]},"editor":[{"full_name":"Domingo Ferrer, Josep","last_name":"Domingo Ferrer","first_name":"Josep"}],"title":"Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases","citation":{"ista":"Yu F, Rybar M, Uhler C, Fienberg S. 2014. Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PSD: Privacy in Statistical Databases, LNCS, vol. 8744, 170–184.","chicago":"Yu, Fei, Michal Rybar, Caroline Uhler, and Stephen Fienberg. “Differentially-Private Logistic Regression for Detecting Multiple-SNP Association in GWAS Databases.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Josep Domingo Ferrer, 8744:170–84. Springer, 2014. https://doi.org/10.1007/978-3-319-11257-2_14.","short":"F. Yu, M. Rybar, C. Uhler, S. Fienberg, in:, J. Domingo Ferrer (Ed.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 170–184.","ieee":"F. Yu, M. Rybar, C. Uhler, and S. Fienberg, “Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Ibiza, Spain, 2014, vol. 8744, pp. 170–184.","apa":"Yu, F., Rybar, M., Uhler, C., & Fienberg, S. (2014). Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases. In J. Domingo Ferrer (Ed.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8744, pp. 170–184). Ibiza, Spain: Springer. https://doi.org/10.1007/978-3-319-11257-2_14","ama":"Yu F, Rybar M, Uhler C, Fienberg S. Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases. In: Domingo Ferrer J, ed. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8744. Springer; 2014:170-184. doi:10.1007/978-3-319-11257-2_14","mla":"Yu, Fei, et al. “Differentially-Private Logistic Regression for Detecting Multiple-SNP Association in GWAS Databases.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Josep Domingo Ferrer, vol. 8744, Springer, 2014, pp. 170–84, doi:10.1007/978-3-319-11257-2_14."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"alternative_title":["LNCS"],"main_file_link":[{"url":"http://arxiv.org/abs/1407.8067","open_access":"1"}],"month":"01","intvolume":" 8744","abstract":[{"text":"Following the publication of an attack on genome-wide association studies (GWAS) data proposed by Homer et al., considerable attention has been given to developing methods for releasing GWAS data in a privacy-preserving way. Here, we develop an end-to-end differentially private method for solving regression problems with convex penalty functions and selecting the penalty parameters by cross-validation. In particular, we focus on penalized logistic regression with elastic-net regularization, a method widely used to in GWAS analyses to identify disease-causing genes. We show how a differentially private procedure for penalized logistic regression with elastic-net regularization can be applied to the analysis of GWAS data and evaluate our method’s performance.","lang":"eng"}],"oa_version":"Submitted Version","volume":8744,"publication_status":"published","language":[{"iso":"eng"}],"type":"conference","conference":{"end_date":"2014-09-19","location":"Ibiza, Spain","start_date":"2014-09-17","name":"PSD: Privacy in Statistical Databases"},"status":"public","_id":"2047","department":[{"_id":"KrPi"},{"_id":"CaUh"}],"date_updated":"2021-01-12T06:54:57Z"},{"date_updated":"2021-01-12T06:55:00Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"_id":"2053","conference":{"name":"CONCUR: Concurrency Theory","end_date":"2014-09-05","location":"Rome, Italy","start_date":"2014-09-02"},"type":"conference","status":"public","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":8704,"abstract":[{"lang":"eng","text":"In contrast to the usual understanding of probabilistic systems as stochastic processes, recently these systems have also been regarded as transformers of probabilities. In this paper, we give a natural definition of strong bisimulation for probabilistic systems corresponding to this view that treats probability distributions as first-class citizens. Our definition applies in the same way to discrete systems as well as to systems with uncountable state and action spaces. Several examples demonstrate that our definition refines the understanding of behavioural equivalences of probabilistic systems. In particular, it solves a longstanding open problem concerning the representation of memoryless continuous time by memoryfull continuous time. Finally, we give algorithms for computing this bisimulation not only for finite but also for classes of uncountably infinite systems."}],"oa_version":"Submitted Version","main_file_link":[{"url":"http://arxiv.org/abs/1404.5084","open_access":"1"}],"alternative_title":["LNCS"],"intvolume":" 8704","month":"09","citation":{"mla":"Hermanns, Holger, et al. “Probabilistic Bisimulation: Naturally on Distributions.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, vol. 8704, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 249–65, doi:10.1007/978-3-662-44584-6_18.","ieee":"H. Hermanns, J. Krčál, and J. Kretinsky, “Probabilistic bisimulation: Naturally on distributions,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Rome, Italy, 2014, vol. 8704, pp. 249–265.","short":"H. Hermanns, J. Krčál, J. Kretinsky, in:, P. Baldan, D. Gorla (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 249–265.","apa":"Hermanns, H., Krčál, J., & Kretinsky, J. (2014). Probabilistic bisimulation: Naturally on distributions. In P. Baldan & D. Gorla (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8704, pp. 249–265). Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-662-44584-6_18","ama":"Hermanns H, Krčál J, Kretinsky J. Probabilistic bisimulation: Naturally on distributions. In: Baldan P, Gorla D, eds. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8704. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:249-265. doi:10.1007/978-3-662-44584-6_18","chicago":"Hermanns, Holger, Jan Krčál, and Jan Kretinsky. “Probabilistic Bisimulation: Naturally on Distributions.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, 8704:249–65. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014. https://doi.org/10.1007/978-3-662-44584-6_18.","ista":"Hermanns H, Krčál J, Kretinsky J. 2014. Probabilistic bisimulation: Naturally on distributions. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). CONCUR: Concurrency Theory, LNCS, vol. 8704, 249–265."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Hermanns","full_name":"Hermanns, Holger","first_name":"Holger"},{"last_name":"Krčál","full_name":"Krčál, Jan","first_name":"Jan"},{"full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","last_name":"Kretinsky","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"4993","title":"Probabilistic bisimulation: Naturally on distributions","editor":[{"first_name":"Paolo","last_name":"Baldan","full_name":"Baldan, Paolo"},{"last_name":"Gorla","full_name":"Gorla, Daniele","first_name":"Daniele"}],"project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms"}],"year":"2014","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","day":"01","page":"249 - 265","date_created":"2018-12-11T11:55:27Z","date_published":"2014-09-01T00:00:00Z","doi":"10.1007/978-3-662-44584-6_18","acknowledgement":"This work is supported by the EU 7th Framework Programme under grant agreements 295261 (MEALS) and 318490 (SENSATION), Czech Science Foundation under grant agreement P202/12/G061, the DFG Transregional Collaborative Research Centre SFB/TR 14 AVACS, and by the CAS/SAFEA International Partnership Program for Creative Research Teams.","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik"},{"date_created":"2018-12-11T11:55:26Z","volume":8704,"date_published":"2014-09-01T00:00:00Z","doi":"10.1007/978-3-662-44584-6_9","page":"109 - 124","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2014","intvolume":" 8704","month":"09","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","alternative_title":["LNCS"],"acknowledgement":"The second, third, fourth and fifth authors were supported by the Austrian National Research Network S11403-N23 (RiSE) of the Austrian Science Fund (FWF) and by the Vienna Science and Technology Fund (WWTF) through grants PROSEED, ICT12-059, and VRG11-005.","oa_version":"None","abstract":[{"lang":"eng","text":"A standard technique for solving the parameterized model checking problem is to reduce it to the classic model checking problem of finitely many finite-state systems. This work considers some of the theoretical power and limitations of this technique. We focus on concurrent systems in which processes communicate via pairwise rendezvous, as well as the special cases of disjunctive guards and token passing; specifications are expressed in indexed temporal logic without the next operator; and the underlying network topologies are generated by suitable Monadic Second Order Logic formulas and graph operations. First, we settle the exact computational complexity of the parameterized model checking problem for some of our concurrent systems, and establish new decidability results for others. Second, we consider the cases that model checking the parameterized system can be reduced to model checking some fixed number of processes, the number is known as a cutoff. We provide many cases for when such cutoffs can be computed, establish lower bounds on the size of such cutoffs, and identify cases where no cutoff exists. Third, we consider cases for which the parameterized system is equivalent to a single finite-state system (more precisely a Büchi word automaton), and establish tight bounds on the sizes of such automata."}],"editor":[{"first_name":"Paolo","last_name":"Baldan","full_name":"Baldan, Paolo"},{"last_name":"Gorla","full_name":"Gorla, Daniele","first_name":"Daniele"}],"title":"Parameterized model checking of rendezvous systems","department":[{"_id":"KrCh"}],"publist_id":"4994","author":[{"last_name":"Aminof","full_name":"Aminof, Benjamin","id":"4A55BD00-F248-11E8-B48F-1D18A9856A87","first_name":"Benjamin"},{"last_name":"Kotek","full_name":"Kotek, Tomer","first_name":"Tomer"},{"first_name":"Sacha","full_name":"Rubin, Sacha","last_name":"Rubin"},{"first_name":"Francesco","full_name":"Spegni, Francesco","last_name":"Spegni"},{"first_name":"Helmut","full_name":"Veith, Helmut","last_name":"Veith"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:59Z","citation":{"chicago":"Aminof, Benjamin, Tomer Kotek, Sacha Rubin, Francesco Spegni, and Helmut Veith. “Parameterized Model Checking of Rendezvous Systems.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, 8704:109–24. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014. https://doi.org/10.1007/978-3-662-44584-6_9.","ista":"Aminof B, Kotek T, Rubin S, Spegni F, Veith H. 2014. Parameterized model checking of rendezvous systems. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). CONCUR: Concurrency Theory, LNCS, vol. 8704, 109–124.","mla":"Aminof, Benjamin, et al. “Parameterized Model Checking of Rendezvous Systems.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, vol. 8704, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 109–24, doi:10.1007/978-3-662-44584-6_9.","short":"B. Aminof, T. Kotek, S. Rubin, F. Spegni, H. Veith, in:, P. Baldan, D. Gorla (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 109–124.","ieee":"B. Aminof, T. Kotek, S. Rubin, F. Spegni, and H. Veith, “Parameterized model checking of rendezvous systems,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Rome, Italy, 2014, vol. 8704, pp. 109–124.","apa":"Aminof, B., Kotek, T., Rubin, S., Spegni, F., & Veith, H. (2014). Parameterized model checking of rendezvous systems. In P. Baldan & D. Gorla (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8704, pp. 109–124). Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-662-44584-6_9","ama":"Aminof B, Kotek T, Rubin S, Spegni F, Veith H. Parameterized model checking of rendezvous systems. In: Baldan P, Gorla D, eds. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8704. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:109-124. doi:10.1007/978-3-662-44584-6_9"},"status":"public","conference":{"end_date":"2014-09-05","location":"Rome, Italy","start_date":"2014-09-02","name":"CONCUR: Concurrency Theory"},"type":"conference","_id":"2052"},{"project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"259668","name":"Provable Security for Physical Cryptography"}],"citation":{"ista":"Bellare M, Fuchsbauer G. 2014. Policy-based signatures. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PKC: Public Key Crypography, LNCS, vol. 8383, 520–537.","chicago":"Bellare, Mihir, and Georg Fuchsbauer. “Policy-Based Signatures.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Hugo Krawczyk, 8383:520–37. Springer, 2014. https://doi.org/10.1007/978-3-642-54631-0_30.","ieee":"M. Bellare and G. Fuchsbauer, “Policy-based signatures,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Buenos Aires, Argentina, 2014, vol. 8383, pp. 520–537.","short":"M. Bellare, G. Fuchsbauer, in:, H. Krawczyk (Ed.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 520–537.","ama":"Bellare M, Fuchsbauer G. Policy-based signatures. In: Krawczyk H, ed. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8383. Springer; 2014:520-537. doi:10.1007/978-3-642-54631-0_30","apa":"Bellare, M., & Fuchsbauer, G. (2014). Policy-based signatures. In H. Krawczyk (Ed.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8383, pp. 520–537). Buenos Aires, Argentina: Springer. https://doi.org/10.1007/978-3-642-54631-0_30","mla":"Bellare, Mihir, and Georg Fuchsbauer. “Policy-Based Signatures.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Hugo Krawczyk, vol. 8383, Springer, 2014, pp. 520–37, doi:10.1007/978-3-642-54631-0_30."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5005","author":[{"first_name":"Mihir","last_name":"Bellare","full_name":"Bellare, Mihir"},{"last_name":"Fuchsbauer","full_name":"Fuchsbauer, Georg","first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87"}],"title":"Policy-based signatures","editor":[{"first_name":"Hugo","full_name":"Krawczyk, Hugo","last_name":"Krawczyk"}],"acknowledgement":"Part of his work was done while at Bristol University, supported by EPSRC grant EP/H043454/1.","publisher":"Springer","quality_controlled":"1","oa":1,"year":"2014","day":"01","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","page":"520 - 537","date_published":"2014-01-01T00:00:00Z","doi":"10.1007/978-3-642-54631-0_30","date_created":"2018-12-11T11:55:24Z","_id":"2046","type":"conference","conference":{"start_date":"2014-05-26","end_date":"2014-05-28","location":"Buenos Aires, Argentina","name":"PKC: Public Key Crypography"},"status":"public","date_updated":"2021-01-12T06:54:57Z","department":[{"_id":"KrPi"}],"abstract":[{"text":"We introduce policy-based signatures (PBS), where a signer can only sign messages conforming to some authority-specified policy. The main requirements are unforgeability and privacy, the latter meaning that signatures not reveal the policy. PBS offers value along two fronts: (1) On the practical side, they allow a corporation to control what messages its employees can sign under the corporate key. (2) On the theoretical side, they unify existing work, capturing other forms of signatures as special cases or allowing them to be easily built. Our work focuses on definitions of PBS, proofs that this challenging primitive is realizable for arbitrary policies, efficient constructions for specific policies, and a few representative applications.","lang":"eng"}],"oa_version":"Submitted Version","alternative_title":["LNCS"],"scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2013/413"}],"month":"01","intvolume":" 8383","publication_status":"published","language":[{"iso":"eng"}],"volume":8383,"ec_funded":1},{"_id":"2050","status":"public","type":"journal_article","date_updated":"2021-01-12T06:54:59Z","department":[{"_id":"BjHo"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"The flow instability and further transition to turbulence in a toroidal pipe (torus) with curvature ratio (tube-to-coiling diameter) 0.049 is investigated experimentally. The flow inside the toroidal pipe is driven by a steel sphere fitted to the inner pipe diameter. The sphere is moved with constant azimuthal velocity from outside the torus by a moving magnet. The experiment is designed to investigate curved pipe flow by optical measurement techniques. Using stereoscopic particle image velocimetry, laser Doppler velocimetry and pressure drop measurements, the flow is measured for Reynolds numbers ranging from 1000 to 15 000. Time- and space-resolved velocity fields are obtained and analysed. The steady axisymmetric basic flow is strongly influenced by centrifugal effects. On an increase of the Reynolds number we find a sequence of bifurcations. For Re=4075±2% a supercritical bifurcation to an oscillatory flow is found in which waves travel in the streamwise direction with a phase velocity slightly faster than the mean flow. The oscillatory flow is superseded by a presumably quasi-periodic flow at a further increase of the Reynolds number before turbulence sets in. The results are found to be compatible, in general, with earlier experimental and numerical investigations on transition to turbulence in helical and curved pipes. However, important aspects of the bifurcation scenario differ considerably."}],"intvolume":" 738","month":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1508.06546"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","volume":738,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"J. Kühnen, M. Holzner, B. Hof, and H. Kuhlmann, “Experimental investigation of transitional flow in a toroidal pipe,” Journal of Fluid Mechanics, vol. 738. Cambridge University Press, pp. 463–491, 2014.","short":"J. Kühnen, M. Holzner, B. Hof, H. Kuhlmann, Journal of Fluid Mechanics 738 (2014) 463–491.","ama":"Kühnen J, Holzner M, Hof B, Kuhlmann H. Experimental investigation of transitional flow in a toroidal pipe. Journal of Fluid Mechanics. 2014;738:463-491. doi:10.1017/jfm.2013.603","apa":"Kühnen, J., Holzner, M., Hof, B., & Kuhlmann, H. (2014). Experimental investigation of transitional flow in a toroidal pipe. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2013.603","mla":"Kühnen, Jakob, et al. “Experimental Investigation of Transitional Flow in a Toroidal Pipe.” Journal of Fluid Mechanics, vol. 738, Cambridge University Press, 2014, pp. 463–91, doi:10.1017/jfm.2013.603.","ista":"Kühnen J, Holzner M, Hof B, Kuhlmann H. 2014. Experimental investigation of transitional flow in a toroidal pipe. Journal of Fluid Mechanics. 738, 463–491.","chicago":"Kühnen, Jakob, Markus Holzner, Björn Hof, and Hendrik Kuhlmann. “Experimental Investigation of Transitional Flow in a Toroidal Pipe.” Journal of Fluid Mechanics. Cambridge University Press, 2014. https://doi.org/10.1017/jfm.2013.603."},"title":"Experimental investigation of transitional flow in a toroidal pipe","external_id":{"arxiv":["1508.06546"]},"article_processing_charge":"No","author":[{"first_name":"Jakob","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4312-0179","full_name":"Kühnen, Jakob","last_name":"Kühnen"},{"last_name":"Holzner","full_name":"Holzner, Markus","first_name":"Markus"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof"},{"first_name":"Hendrik","full_name":"Kuhlmann, Hendrik","last_name":"Kuhlmann"}],"publist_id":"5001","oa":1,"quality_controlled":"1","publisher":"Cambridge University Press","publication":"Journal of Fluid Mechanics","day":"10","year":"2014","date_created":"2018-12-11T11:55:25Z","doi":"10.1017/jfm.2013.603","date_published":"2014-01-10T00:00:00Z","page":"463 - 491"},{"extern":1,"date_updated":"2021-01-12T06:54:59Z","citation":{"short":"M. Marchand, S. Hongyu, E. Morvant, J. Rousu, J. Shawe Taylor, in:, Neural Information Processing Systems, 2014.","ieee":"M. Marchand, S. Hongyu, E. Morvant, J. Rousu, and J. Shawe Taylor, “Multilabel structured output learning with random spanning trees of max-margin Markov networks,” presented at the NIPS: Neural Information Processing Systems, 2014.","ama":"Marchand M, Hongyu S, Morvant E, Rousu J, Shawe Taylor J. Multilabel structured output learning with random spanning trees of max-margin Markov networks. In: Neural Information Processing Systems; 2014.","apa":"Marchand, M., Hongyu, S., Morvant, E., Rousu, J., & Shawe Taylor, J. (2014). Multilabel structured output learning with random spanning trees of max-margin Markov networks. Presented at the NIPS: Neural Information Processing Systems, Neural Information Processing Systems.","mla":"Marchand, Mario, et al. Multilabel Structured Output Learning with Random Spanning Trees of Max-Margin Markov Networks. Neural Information Processing Systems, 2014.","ista":"Marchand M, Hongyu S, Morvant E, Rousu J, Shawe Taylor J. 2014. Multilabel structured output learning with random spanning trees of max-margin Markov networks. NIPS: Neural Information Processing Systems.","chicago":"Marchand, Mario, Su Hongyu, Emilie Morvant, Juho Rousu, and John Shawe Taylor. “Multilabel Structured Output Learning with Random Spanning Trees of Max-Margin Markov Networks.” Neural Information Processing Systems, 2014."},"title":"Multilabel structured output learning with random spanning trees of max-margin Markov networks","publist_id":"4996","author":[{"last_name":"Marchand","full_name":"Marchand, Mario","first_name":"Mario"},{"last_name":"Hongyu","full_name":"Hongyu, Su","first_name":"Su"},{"orcid":"0000-0002-8301-7240","full_name":"Emilie Morvant","last_name":"Morvant","first_name":"Emilie","id":"4BAC2A72-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rousu, Juho","last_name":"Rousu","first_name":"Juho"},{"full_name":"Shawe-Taylor, John","last_name":"Shawe Taylor","first_name":"John"}],"_id":"2051","status":"public","conference":{"name":"NIPS: Neural Information Processing Systems"},"type":"conference","day":"01","publication_status":"published","year":"2014","date_created":"2018-12-11T11:55:26Z","date_published":"2014-01-01T00:00:00Z","abstract":[{"lang":"eng","text":"We show that the usual score function for conditional Markov networks can be written as the expectation over the scores of their spanning trees. We also show that a small random sample of these output trees can attain a significant fraction of the margin obtained by the complete graph and we provide conditions under which we can perform tractable inference. The experimental results confirm that practical learning is scalable to realistic datasets using this approach."}],"month":"01","oa":1,"main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-01065586"}],"quality_controlled":0,"publisher":"Neural Information Processing Systems"},{"publist_id":"4987","author":[{"full_name":"Dubas, Ewa","last_name":"Dubas","first_name":"Ewa"},{"full_name":"Moravčíková, Jana","last_name":"Moravčíková","first_name":"Jana"},{"full_name":"Libantová, Jana","last_name":"Libantová","first_name":"Jana"},{"full_name":"Matušíková, Ildikó","last_name":"Matušíková","first_name":"Ildikó"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková"},{"first_name":"Iwona","last_name":"Zur","full_name":"Zur, Iwona"},{"first_name":"Monika","last_name":"Krzewska","full_name":"Krzewska, Monika"}],"title":"The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos","citation":{"ama":"Dubas E, Moravčíková J, Libantová J, et al. The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos. Protoplasma. 2014;251(5):1077-1087. doi:10.1007/s00709-014-0616-1","apa":"Dubas, E., Moravčíková, J., Libantová, J., Matušíková, I., Benková, E., Zur, I., & Krzewska, M. (2014). The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos. Protoplasma. Springer. https://doi.org/10.1007/s00709-014-0616-1","ieee":"E. Dubas et al., “The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos,” Protoplasma, vol. 251, no. 5. Springer, pp. 1077–1087, 2014.","short":"E. Dubas, J. Moravčíková, J. Libantová, I. Matušíková, E. Benková, I. Zur, M. Krzewska, Protoplasma 251 (2014) 1077–1087.","mla":"Dubas, Ewa, et al. “The Influence of Heat Stress on Auxin Distribution in Transgenic B Napus Microspores and Microspore Derived Embryos.” Protoplasma, vol. 251, no. 5, Springer, 2014, pp. 1077–87, doi:10.1007/s00709-014-0616-1.","ista":"Dubas E, Moravčíková J, Libantová J, Matušíková I, Benková E, Zur I, Krzewska M. 2014. The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos. Protoplasma. 251(5), 1077–1087.","chicago":"Dubas, Ewa, Jana Moravčíková, Jana Libantová, Ildikó Matušíková, Eva Benková, Iwona Zur, and Monika Krzewska. “The Influence of Heat Stress on Auxin Distribution in Transgenic B Napus Microspores and Microspore Derived Embryos.” Protoplasma. Springer, 2014. https://doi.org/10.1007/s00709-014-0616-1."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","page":"1077 - 1087","date_created":"2018-12-11T11:55:29Z","doi":"10.1007/s00709-014-0616-1","date_published":"2014-02-20T00:00:00Z","year":"2014","has_accepted_license":"1","publication":"Protoplasma","day":"20","oa":1,"quality_controlled":"1","publisher":"Springer","acknowledgement":"The research was supported by the IPP PAS-IPGB SAS bilateral project (“Molecular analysis of auxin distribution in oilseed androgenic embryos”), IPP PAS-FWO VIB bilateral project (“Auxin as signaling molecule in doubled haploid production of rape (B. napus var. oleifera)”), individual national research project 2011/01/D/NZ9/02547, and VEGA 2-0090-14.","department":[{"_id":"EvBe"}],"file_date_updated":"2020-07-14T12:45:27Z","date_updated":"2021-01-12T06:55:02Z","ddc":["580"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"394","status":"public","_id":"2059","volume":251,"issue":"5","publication_status":"published","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"d570a6073765118fc0bb83c31d96fa53","file_id":"5353","date_updated":"2020-07-14T12:45:27Z","file_size":6377990,"creator":"system","date_created":"2018-12-12T10:18:31Z","file_name":"IST-2015-394-v1+1_s00709-014-0616-1.pdf"}],"scopus_import":1,"intvolume":" 251","month":"02","abstract":[{"text":"Plant embryogenesis is regulated by differential distribution of the plant hormone auxin. However, the cells establishing these gradients during microspore embryogenesis remain to be identified. For the first time, we describe, using the DR5 or DR5rev reporter gene systems, the GFP- and GUS-based auxin biosensors to monitor auxin during Brassica napus androgenesis at cellular resolution in the initial stages. Our study provides evidence that the distribution of auxin changes during embryo development and depends on the temperature-inducible in vitro culture conditions. For this, microspores (mcs) were induced to embryogenesis by heat treatment and then subjected to genetic modification via Agrobacterium tumefaciens. The duration of high temperature treatment had a significant influence on auxin distribution in isolated and in vitro-cultured microspores and on microspore-derived embryo development. In the “mild” heat-treated (1 day at 32 °C) mcs, auxin localized in a polar way already at the uni-nucleate microspore, which was critical for the initiation of embryos with suspensor-like structure. Assuming a mean mcs radius of 20 μm, endogenous auxin content in a single cell corresponded to concentration of 1.01 μM. In mcs subjected to a prolonged heat (5 days at 32 °C), although auxin concentration increased dozen times, auxin polarization was set up at a few-celled pro-embryos without suspensor. Those embryos were enclosed in the outer wall called the exine. The exine rupture was accompanied by the auxin gradient polarization. Relative quantitative estimation of auxin, using time-lapse imaging, revealed that primordia possess up to 1.3-fold higher amounts than those found in the root apices of transgenic MDEs in the presence of exogenous auxin. Our results show, for the first time, which concentration of endogenous auxin coincides with the first cell division and how the high temperature interplays with auxin, by what affects delay early establishing microspore polarity. Moreover, we present how the local auxin accumulation demonstrates the apical–basal axis formation of the androgenic embryo and directs the axiality of the adult haploid plant.","lang":"eng"}],"oa_version":"Published Version"},{"date_published":"2014-08-01T00:00:00Z","doi":"10.1126/science.1255263","date_created":"2018-12-11T11:55:29Z","day":"01","publication":"Science","has_accepted_license":"1","year":"2014","publisher":"American Association for the Advancement of Science","quality_controlled":"1","oa":1,"title":"Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function","author":[{"last_name":"Hu","full_name":"Hu, Hua","id":"4AC0145C-F248-11E8-B48F-1D18A9856A87","first_name":"Hua"},{"full_name":"Gan, Jian","last_name":"Gan","first_name":"Jian","id":"3614E438-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"4984","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Hu, Hua, et al. “Fast-Spiking Parvalbumin^+ GABAergic Interneurons: From Cellular Design to Microcircuit Function.” Science, vol. 345, no. 6196, 1255263, American Association for the Advancement of Science, 2014, doi:10.1126/science.1255263.","ama":"Hu H, Gan J, Jonas PM. Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function. Science. 2014;345(6196). doi:10.1126/science.1255263","apa":"Hu, H., Gan, J., & Jonas, P. M. (2014). Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1255263","short":"H. Hu, J. Gan, P.M. Jonas, Science 345 (2014).","ieee":"H. Hu, J. Gan, and P. M. Jonas, “Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function,” Science, vol. 345, no. 6196. American Association for the Advancement of Science, 2014.","chicago":"Hu, Hua, Jian Gan, and Peter M Jonas. “Fast-Spiking Parvalbumin^+ GABAergic Interneurons: From Cellular Design to Microcircuit Function.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1255263.","ista":"Hu H, Gan J, Jonas PM. 2014. Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function. Science. 345(6196), 1255263."},"project":[{"grant_number":"P24909-B24","name":"Mechanisms of transmitter release at GABAergic synapses","call_identifier":"FWF","_id":"25C26B1E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25C0F108-B435-11E9-9278-68D0E5697425","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","grant_number":"268548"}],"article_number":"1255263","issue":"6196","volume":345,"ec_funded":1,"file":[{"date_created":"2018-12-12T10:16:00Z","file_name":"IST-2017-821-v1+1_1255263JonasPVReviewTextR_Final.pdf","creator":"system","date_updated":"2020-07-14T12:45:27Z","file_size":215514,"checksum":"a0036a589037d37e86364fa25cc0a82f","file_id":"5185","access_level":"open_access","relation":"main_file","content_type":"application/pdf"},{"file_id":"5186","checksum":"e1f57d2713725449cb898fdcb8ef47b8","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-821-v1+2_1255263JonasPVReviewFigures_Final.pdf","date_created":"2018-12-12T10:16:01Z","creator":"system","file_size":1732723,"date_updated":"2020-07-14T12:45:27Z"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"08","intvolume":" 345","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"The success story of fast-spiking, parvalbumin-positive (PV+) GABAergic interneurons (GABA, γ-aminobutyric acid) in the mammalian central nervous system is noteworthy. In 1995, the properties of these interneurons were completely unknown. Twenty years later, thanks to the massive use of subcellular patch-clamp techniques, simultaneous multiple-cell recording, optogenetics, in vivo measurements, and computational approaches, our knowledge about PV+ interneurons became more extensive than for several types of pyramidal neurons. These findings have implications beyond the “small world” of basic research on GABAergic cells. For example, the results provide a first proof of principle that neuroscientists might be able to close the gaps between the molecular, cellular, network, and behavioral levels, representing one of the main challenges at the present time. Furthermore, the results may form the basis for PV+ interneurons as therapeutic targets for brain disease in the future. However, much needs to be learned about the basic function of these interneurons before clinical neuroscientists will be able to use PV+ interneurons for therapeutic purposes."}],"department":[{"_id":"PeJo"}],"file_date_updated":"2020-07-14T12:45:27Z","ddc":["570"],"date_updated":"2021-01-12T06:55:03Z","status":"public","pubrep_id":"821","type":"journal_article","_id":"2062"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Raveendran, Karthik, et al. “Blending Liquids.” ACM Transactions on Graphics, vol. 33, no. 4, 137, ACM, 2014, doi:10.1145/2601097.2601126.","ieee":"K. Raveendran, C. Wojtan, N. Thuerey, and G. Türk, “Blending liquids,” in ACM Transactions on Graphics, Vancouver, Canada, 2014, vol. 33, no. 4.","short":"K. Raveendran, C. Wojtan, N. Thuerey, G. Türk, in:, ACM Transactions on Graphics, ACM, 2014.","ama":"Raveendran K, Wojtan C, Thuerey N, Türk G. Blending liquids. In: ACM Transactions on Graphics. Vol 33. ACM; 2014. doi:10.1145/2601097.2601126","apa":"Raveendran, K., Wojtan, C., Thuerey, N., & Türk, G. (2014). Blending liquids. In ACM Transactions on Graphics (Vol. 33). Vancouver, Canada: ACM. https://doi.org/10.1145/2601097.2601126","chicago":"Raveendran, Karthik, Chris Wojtan, Nils Thuerey, and Greg Türk. “Blending Liquids.” In ACM Transactions on Graphics, Vol. 33. ACM, 2014. https://doi.org/10.1145/2601097.2601126.","ista":"Raveendran K, Wojtan C, Thuerey N, Türk G. 2014. Blending liquids. ACM Transactions on Graphics. SIGGRAPH: International Conference and Exhibition on Computer Graphics and Interactive Techniques vol. 33, 137."},"title":"Blending liquids","author":[{"last_name":"Raveendran","full_name":"Raveendran, Karthik","first_name":"Karthik"},{"orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","last_name":"Wojtan","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nils","last_name":"Thuerey","full_name":"Thuerey, Nils"},{"first_name":"Greg","full_name":"Türk, Greg","last_name":"Türk"}],"publist_id":"4988","article_processing_charge":"No","article_number":"137","project":[{"_id":"25636330-B435-11E9-9278-68D0E5697425","grant_number":"11-NSF-1070","name":"ROOTS Genome-wide Analysis of Root Traits"}],"day":"01","publication":"ACM Transactions on Graphics","has_accepted_license":"1","year":"2014","date_published":"2014-07-01T00:00:00Z","doi":"10.1145/2601097.2601126","date_created":"2018-12-11T11:55:28Z","publisher":"ACM","quality_controlled":"1","oa":1,"ddc":["000"],"date_updated":"2022-08-25T14:02:46Z","department":[{"_id":"ChWo"}],"file_date_updated":"2020-07-14T12:45:27Z","_id":"2058","status":"public","pubrep_id":"606","type":"conference","conference":{"location":"Vancouver, Canada","end_date":"2014-08-14","start_date":"2014-08-10","name":"SIGGRAPH: International Conference and Exhibition on Computer Graphics and Interactive Techniques"},"file":[{"creator":"system","date_updated":"2020-07-14T12:45:27Z","file_size":8387384,"date_created":"2018-12-12T10:08:27Z","file_name":"IST-2016-606-v1+1_BlendingLiquids-Preprint.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"4688","checksum":"1752760a2e71e254537f31c0d10d9c6c"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":33,"issue":"4","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We present a method for smoothly blending between existing liquid animations. We introduce a semi-automatic method for matching two existing liquid animations, which we use to create new fluid motion that plausibly interpolates the input. Our contributions include a new space-time non-rigid iterative closest point algorithm that incorporates user guidance, a subsampling technique for efficient registration of meshes with millions of vertices, and a fast surface extraction algorithm that produces 3D triangle meshes from a 4D space-time surface. Our technique can be used to instantly create hundreds of new simulations, or to interactively explore complex parameter spaces. Our method is guaranteed to produce output that does not deviate from the input animations, and it generalizes to multiple dimensions. Because our method runs at interactive rates after the initial precomputation step, it has potential applications in games and training simulations."}],"month":"07","intvolume":" 33","scopus_import":"1"},{"day":"01","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","year":"2014","date_published":"2014-01-01T00:00:00Z","doi":"10.1007/978-3-662-44415-3_16","date_created":"2018-12-11T11:55:28Z","page":"153 - 162","quality_controlled":"1","publisher":"Springer","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Morvant E, Habrard A, Ayache S. 2014. Majority vote of diverse classifiers for late fusion. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). IAPR: International Workshop on Structural, Syntactic, and Statistical Pattern Recognition, LNCS, vol. 8621, 153–162.","chicago":"Morvant, Emilie, Amaury Habrard, and Stéphane Ayache. “Majority Vote of Diverse Classifiers for Late Fusion.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 8621:153–62. Springer, 2014. https://doi.org/10.1007/978-3-662-44415-3_16.","ama":"Morvant E, Habrard A, Ayache S. Majority vote of diverse classifiers for late fusion. In: Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8621. Springer; 2014:153-162. doi:10.1007/978-3-662-44415-3_16","apa":"Morvant, E., Habrard, A., & Ayache, S. (2014). Majority vote of diverse classifiers for late fusion. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8621, pp. 153–162). Joensuu, Finland: Springer. https://doi.org/10.1007/978-3-662-44415-3_16","short":"E. Morvant, A. Habrard, S. Ayache, in:, Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 153–162.","ieee":"E. Morvant, A. Habrard, and S. Ayache, “Majority vote of diverse classifiers for late fusion,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Joensuu, Finland, 2014, vol. 8621, pp. 153–162.","mla":"Morvant, Emilie, et al. “Majority Vote of Diverse Classifiers for Late Fusion.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 8621, Springer, 2014, pp. 153–62, doi:10.1007/978-3-662-44415-3_16."},"title":"Majority vote of diverse classifiers for late fusion","author":[{"orcid":"0000-0002-8301-7240","full_name":"Morvant, Emilie","last_name":"Morvant","first_name":"Emilie","id":"4BAC2A72-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Amaury","full_name":"Habrard, Amaury","last_name":"Habrard"},{"last_name":"Ayache","full_name":"Ayache, Stéphane","first_name":"Stéphane"}],"publist_id":"4989","external_id":{"arxiv":["1404.7796"]},"project":[{"name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":8621,"ec_funded":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"In the past few years, a lot of attention has been devoted to multimedia indexing by fusing multimodal informations. Two kinds of fusion schemes are generally considered: The early fusion and the late fusion. We focus on late classifier fusion, where one combines the scores of each modality at the decision level. To tackle this problem, we investigate a recent and elegant well-founded quadratic program named MinCq coming from the machine learning PAC-Bayesian theory. MinCq looks for the weighted combination, over a set of real-valued functions seen as voters, leading to the lowest misclassification rate, while maximizing the voters’ diversity. We propose an extension of MinCq tailored to multimedia indexing. Our method is based on an order-preserving pairwise loss adapted to ranking that allows us to improve Mean Averaged Precision measure while taking into account the diversity of the voters that we want to fuse. We provide evidence that this method is naturally adapted to late fusion procedures and confirm the good behavior of our approach on the challenging PASCAL VOC’07 benchmark."}],"month":"01","intvolume":" 8621","scopus_import":1,"alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.7796"}],"date_updated":"2021-01-12T06:55:01Z","department":[{"_id":"ChLa"}],"_id":"2057","status":"public","type":"conference","conference":{"name":"IAPR: International Workshop on Structural, Syntactic, and Statistical Pattern Recognition","start_date":"2014-08-20","end_date":"2014-08-22","location":"Joensuu, Finland"}},{"oa":1,"quality_controlled":"1","publisher":"Springer","acknowledgement":"T. Petrov is supported by SystemsX.ch—the Swiss Inititative for Systems Biology.","page":"767 - 797","date_created":"2018-12-11T11:55:28Z","doi":"10.1007/s00285-013-0738-7","date_published":"2014-11-20T00:00:00Z","year":"2014","publication":"Journal of Mathematical Biology","day":"20","author":[{"full_name":"Ganguly, Arnab","last_name":"Ganguly","first_name":"Arnab"},{"id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","first_name":"Tatjana","orcid":"0000-0002-9041-0905","full_name":"Petrov, Tatjana","last_name":"Petrov"},{"full_name":"Koeppl, Heinz","last_name":"Koeppl","first_name":"Heinz"}],"publist_id":"4990","title":"Markov chain aggregation and its applications to combinatorial reaction networks","citation":{"ista":"Ganguly A, Petrov T, Koeppl H. 2014. Markov chain aggregation and its applications to combinatorial reaction networks. Journal of Mathematical Biology. 69(3), 767–797.","chicago":"Ganguly, Arnab, Tatjana Petrov, and Heinz Koeppl. “Markov Chain Aggregation and Its Applications to Combinatorial Reaction Networks.” Journal of Mathematical Biology. Springer, 2014. https://doi.org/10.1007/s00285-013-0738-7.","apa":"Ganguly, A., Petrov, T., & Koeppl, H. (2014). Markov chain aggregation and its applications to combinatorial reaction networks. Journal of Mathematical Biology. Springer. https://doi.org/10.1007/s00285-013-0738-7","ama":"Ganguly A, Petrov T, Koeppl H. Markov chain aggregation and its applications to combinatorial reaction networks. Journal of Mathematical Biology. 2014;69(3):767-797. doi:10.1007/s00285-013-0738-7","ieee":"A. Ganguly, T. Petrov, and H. Koeppl, “Markov chain aggregation and its applications to combinatorial reaction networks,” Journal of Mathematical Biology, vol. 69, no. 3. Springer, pp. 767–797, 2014.","short":"A. Ganguly, T. Petrov, H. Koeppl, Journal of Mathematical Biology 69 (2014) 767–797.","mla":"Ganguly, Arnab, et al. “Markov Chain Aggregation and Its Applications to Combinatorial Reaction Networks.” Journal of Mathematical Biology, vol. 69, no. 3, Springer, 2014, pp. 767–97, doi:10.1007/s00285-013-0738-7."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1303.4532"}],"scopus_import":1,"intvolume":" 69","month":"11","abstract":[{"lang":"eng","text":"We consider a continuous-time Markov chain (CTMC) whose state space is partitioned into aggregates, and each aggregate is assigned a probability measure. A sufficient condition for defining a CTMC over the aggregates is presented as a variant of weak lumpability, which also characterizes that the measure over the original process can be recovered from that of the aggregated one. We show how the applicability of de-aggregation depends on the initial distribution. The application section is devoted to illustrate how the developed theory aids in reducing CTMC models of biochemical systems particularly in connection to protein-protein interactions. We assume that the model is written by a biologist in form of site-graph-rewrite rules. Site-graph-rewrite rules compactly express that, often, only a local context of a protein (instead of a full molecular species) needs to be in a certain configuration in order to trigger a reaction event. This observation leads to suitable aggregate Markov chains with smaller state spaces, thereby providing sufficient reduction in computational complexity. This is further exemplified in two case studies: simple unbounded polymerization and early EGFR/insulin crosstalk."}],"oa_version":"Submitted Version","issue":"3","volume":69,"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"2056","department":[{"_id":"CaGu"},{"_id":"ToHe"}],"date_updated":"2021-01-12T06:55:01Z"},{"intvolume":" 251","month":"02","quality_controlled":"1","publisher":"Springer","scopus_import":1,"oa_version":"None","abstract":[{"lang":"eng","text":"Development of cambium and its activity is important for our knowledge of the mechanism of secondary growth. Arabidopsis thaliana emerges as a good model plant for such a kind of study. Thus, this paper reports on cellular events taking place in the interfascicular regions of inflorescence stems of A. thaliana, leading to the development of interfascicular cambium from differentiated interfascicular parenchyma cells (IPC). These events are as follows: appearance of auxin accumulation, PIN1 gene expression, polar PIN1 protein localization in the basal plasma membrane and periclinal divisions. Distribution of auxin was observed to be higher in differentiating into cambium parenchyma cells compared to cells within the pith and cortex. Expression of PIN1 in IPC was always preceded by auxin accumulation. Basal localization of PIN1 was already established in the cells prior to their periclinal division. These cellular events initiated within parenchyma cells adjacent to the vascular bundles and successively extended from that point towards the middle region of the interfascicular area, located between neighboring vascular bundles. The final consequence of which was the closure of the cambial ring within the stem. Changes in the chemical composition of IPC walls were also detected and included changes of pectic epitopes, xyloglucans (XG) and extensins rich in hydroxyproline (HRGPs). In summary, results presented in this paper describe interfascicular cambium ontogenesis in terms of successive cellular events in the interfascicular regions of inflorescence stems of Arabidopsis."}],"date_created":"2018-12-11T11:55:29Z","doi":"10.1007/s00709-014-0620-5","issue":"5","date_published":"2014-02-14T00:00:00Z","volume":251,"page":"1125 - 1139","language":[{"iso":"eng"}],"publication":"Protoplasma","day":"14","year":"2014","publication_status":"published","status":"public","type":"journal_article","_id":"2061","department":[{"_id":"JiFr"}],"title":"Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis","publist_id":"4985","author":[{"first_name":"Ewa","last_name":"Mazur","full_name":"Mazur, Ewa"},{"first_name":"Ewa","last_name":"Kurczyñska","full_name":"Kurczyñska, Ewa"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:55:03Z","citation":{"mla":"Mazur, Ewa, et al. “Cellular Events during Interfascicular Cambium Ontogenesis in Inflorescence Stems of Arabidopsis.” Protoplasma, vol. 251, no. 5, Springer, 2014, pp. 1125–39, doi:10.1007/s00709-014-0620-5.","ama":"Mazur E, Kurczyñska E, Friml J. Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis. Protoplasma. 2014;251(5):1125-1139. doi:10.1007/s00709-014-0620-5","apa":"Mazur, E., Kurczyñska, E., & Friml, J. (2014). Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis. Protoplasma. Springer. https://doi.org/10.1007/s00709-014-0620-5","ieee":"E. Mazur, E. Kurczyñska, and J. Friml, “Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis,” Protoplasma, vol. 251, no. 5. Springer, pp. 1125–1139, 2014.","short":"E. Mazur, E. Kurczyñska, J. Friml, Protoplasma 251 (2014) 1125–1139.","chicago":"Mazur, Ewa, Ewa Kurczyñska, and Jiří Friml. “Cellular Events during Interfascicular Cambium Ontogenesis in Inflorescence Stems of Arabidopsis.” Protoplasma. Springer, 2014. https://doi.org/10.1007/s00709-014-0620-5.","ista":"Mazur E, Kurczyñska E, Friml J. 2014. Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis. Protoplasma. 251(5), 1125–1139."}},{"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4198489/"}],"scopus_import":1,"intvolume":" 522","month":"07","abstract":[{"lang":"eng","text":"We examined the synaptic structure, quantity, and distribution of α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA)- and N-methyl-D-aspartate (NMDA)-type glutamate receptors (AMPARs and NMDARs, respectively) in rat cochlear nuclei by a highly sensitive freeze-fracture replica labeling technique. Four excitatory synapses formed by two distinct inputs, auditory nerve (AN) and parallel fibers (PF), on different cell types were analyzed. These excitatory synapse types included AN synapses on bushy cells (AN-BC synapses) and fusiform cells (AN-FC synapses) and PF synapses on FC (PF-FC synapses) and cartwheel cell spines (PF-CwC synapses). Immunogold labeling revealed differences in synaptic structure as well as AMPAR and NMDAR number and/or density in both AN and PF synapses, indicating a target-dependent organization. The immunogold receptor labeling also identified differences in the synaptic organization of FCs based on AN or PF connections, indicating an input-dependent organization in FCs. Among the four excitatory synapse types, the AN-BC synapses were the smallest and had the most densely packed intramembrane particles (IMPs), whereas the PF-CwC synapses were the largest and had sparsely packed IMPs. All four synapse types showed positive correlations between the IMP-cluster area and the AMPAR number, indicating a common intrasynapse-type relationship for glutamatergic synapses. Immunogold particles for AMPARs were distributed over the entire area of individual AN synapses; PF synapses often showed synaptic areas devoid of labeling. The gold-labeling for NMDARs occurred in a mosaic fashion, with less positive correlations between the IMP-cluster area and the NMDAR number. Our observations reveal target- and input-dependent features in the structure, number, and organization of AMPARs and NMDARs in AN and PF synapses."}],"oa_version":"Submitted Version","volume":522,"issue":"18","publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"2064","department":[{"_id":"RySh"}],"date_updated":"2021-01-12T06:55:05Z","oa":1,"publisher":"Wiley-Blackwell","quality_controlled":"1","acknowledgement":"National Institutes of Health (NIH) Grant Number: 1R01DC013048‐0; Biotechnology and Biological Sciences Research Council, UK Grant Number: BB/J015938/1\r\n","page":"4023 - 4042","date_created":"2018-12-11T11:55:30Z","date_published":"2014-07-29T00:00:00Z","doi":"10.1002/cne.23654","year":"2014","publication":"Journal of Comparative Neurology","day":"29","author":[{"full_name":"Rubio, Maía","last_name":"Rubio","first_name":"Maía"},{"first_name":"Yugo","full_name":"Fukazawa, Yugo","last_name":"Fukazawa"},{"full_name":"Kamasawa, Naomi","last_name":"Kamasawa","first_name":"Naomi"},{"first_name":"Cheryl","last_name":"Clarkson","full_name":"Clarkson, Cheryl"},{"full_name":"Molnár, Elek","last_name":"Molnár","first_name":"Elek"},{"last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"4974","title":"Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus","citation":{"chicago":"Rubio, Maía, Yugo Fukazawa, Naomi Kamasawa, Cheryl Clarkson, Elek Molnár, and Ryuichi Shigemoto. “Target- and Input-Dependent Organization of AMPA and NMDA Receptors in Synaptic Connections of the Cochlear Nucleus.” Journal of Comparative Neurology. Wiley-Blackwell, 2014. https://doi.org/10.1002/cne.23654.","ista":"Rubio M, Fukazawa Y, Kamasawa N, Clarkson C, Molnár E, Shigemoto R. 2014. Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus. Journal of Comparative Neurology. 522(18), 4023–4042.","mla":"Rubio, Maía, et al. “Target- and Input-Dependent Organization of AMPA and NMDA Receptors in Synaptic Connections of the Cochlear Nucleus.” Journal of Comparative Neurology, vol. 522, no. 18, Wiley-Blackwell, 2014, pp. 4023–42, doi:10.1002/cne.23654.","short":"M. Rubio, Y. Fukazawa, N. Kamasawa, C. Clarkson, E. Molnár, R. Shigemoto, Journal of Comparative Neurology 522 (2014) 4023–4042.","ieee":"M. Rubio, Y. Fukazawa, N. Kamasawa, C. Clarkson, E. Molnár, and R. Shigemoto, “Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus,” Journal of Comparative Neurology, vol. 522, no. 18. Wiley-Blackwell, pp. 4023–4042, 2014.","ama":"Rubio M, Fukazawa Y, Kamasawa N, Clarkson C, Molnár E, Shigemoto R. Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus. Journal of Comparative Neurology. 2014;522(18):4023-4042. doi:10.1002/cne.23654","apa":"Rubio, M., Fukazawa, Y., Kamasawa, N., Clarkson, C., Molnár, E., & Shigemoto, R. (2014). Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus. Journal of Comparative Neurology. Wiley-Blackwell. https://doi.org/10.1002/cne.23654"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"date_created":"2018-12-11T11:55:36Z","date_published":"2014-07-01T00:00:00Z","volume":33,"issue":"4","doi":"10.1145/2601097.2601166","publication_status":"published","year":"2014","language":[{"iso":"eng"}],"day":"01","publisher":"ACM","intvolume":" 33","month":"07","abstract":[{"lang":"eng","text":"We propose an interactive, optimization-in-the-loop tool for designing inflatable structures. Given a target shape, the user draws a network of seams defining desired segment boundaries in 3D. Our method computes optimally-shaped flat panels for the segments, such that the inflated structure is as close as possible to the target while satisfying the desired seam positions. Our approach is underpinned by physics-based pattern optimization, accurate coarse-scale simulation using tension field theory, and a specialized constraint-optimization method. Our system is fast enough to warrant interactive exploration of different seam layouts, including internal connections, and their effects on the inflated shape. We demonstrate the resulting design process on a varied set of simulation examples, some of which we have fabricated, demonstrating excellent agreement with the design intent."}],"acknowledgement":"This work was partly funded by the NCCR Co-Me of the Swiss NSF.","oa_version":"None","publist_id":"4957","author":[{"full_name":"Skouras, Mélina","last_name":"Skouras","first_name":"Mélina"},{"last_name":"Thomaszewski","full_name":"Thomaszewski, Bernhard","first_name":"Bernhard"},{"first_name":"Peter","full_name":"Kaufmann, Peter","last_name":"Kaufmann"},{"last_name":"Garg","full_name":"Garg, Akash","first_name":"Akash"},{"last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"},{"first_name":"Eitan","full_name":"Grinspun, Eitan","last_name":"Grinspun"},{"first_name":"Markus","full_name":"Gross, Markus","last_name":"Gross"}],"title":"Designing inflatable structures","date_updated":"2021-01-12T06:55:11Z","citation":{"mla":"Skouras, Mélina, et al. Designing Inflatable Structures. Vol. 33, no. 4, 63, ACM, 2014, doi:10.1145/2601097.2601166.","ieee":"M. Skouras et al., “Designing inflatable structures,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, 2014, vol. 33, no. 4.","short":"M. Skouras, B. Thomaszewski, P. Kaufmann, A. Garg, B. Bickel, E. Grinspun, M. Gross, in:, ACM, 2014.","apa":"Skouras, M., Thomaszewski, B., Kaufmann, P., Garg, A., Bickel, B., Grinspun, E., & Gross, M. (2014). Designing inflatable structures (Vol. 33). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, ACM. https://doi.org/10.1145/2601097.2601166","ama":"Skouras M, Thomaszewski B, Kaufmann P, et al. Designing inflatable structures. In: Vol 33. ACM; 2014. doi:10.1145/2601097.2601166","chicago":"Skouras, Mélina, Bernhard Thomaszewski, Peter Kaufmann, Akash Garg, Bernd Bickel, Eitan Grinspun, and Markus Gross. “Designing Inflatable Structures,” Vol. 33. ACM, 2014. https://doi.org/10.1145/2601097.2601166.","ista":"Skouras M, Thomaszewski B, Kaufmann P, Garg A, Bickel B, Grinspun E, Gross M. 2014. Designing inflatable structures. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 33, 63."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","conference":{"name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques"},"type":"conference","status":"public","_id":"2081","article_number":"63"},{"acknowledgement":"This project was supported in part by the ERC Starting Grant iModel (StG-2012-306877). Emily Whiting is supported by the ETH Zurich / Marie Curie COFUND Postdoctoral Fellowship.","abstract":[{"lang":"eng","text":"Spinning tops and yo-yos have long fascinated cultures around the world with their unexpected, graceful motions that seemingly elude gravity. We present an algorithm to generate designs for spinning objects by optimizing rotational dynamics properties. As input, the user provides a solid 3D model and a desired axis of rotation. Our approach then modifies the mass distribution such that the principal directions of the moment of inertia align with the target rotation frame. We augment the model by creating voids inside its volume, with interior fill represented by an adaptive multi-resolution vox-elization. The discrete voxel fill values are optimized using a continuous, nonlinear formulation. Further, we optimize for rotational stability by maximizing the dominant principal moment. We extend our technique to incorporate deformation and multiple materials for cases where internal voids alone are insufficient. Our method is well-suited for a variety of 3D printed models, ranging from characters to abstract shapes. We demonstrate tops and yo-yos that spin surprisingly stably despite their asymmetric appearance. "}],"month":"01","intvolume":" 33","quality_controlled":0,"publisher":"ACM","day":"01","year":"2014","publication_status":"published","issue":"4","date_published":"2014-01-01T00:00:00Z","doi":"10.1145/2601097.2601157","volume":33,"date_created":"2018-12-11T11:55:35Z","_id":"2080","status":"public","type":"conference","conference":{"name":"SIGGRAPH: 41st International Conference and Exhibition on Computer Graphics and Interactive Techniques"},"extern":1,"citation":{"chicago":"Bac̈Her, Moritz, Emily Whiting, Bernd Bickel, and Olga Sorkine Hornung. “Spin-It: Optimizing Moment of Inertia for Spinnable Objects,” Vol. 33. ACM, 2014. https://doi.org/10.1145/2601097.2601157.","ista":"Bac̈Her M, Whiting E, Bickel B, Sorkine Hornung O. 2014. Spin-It: Optimizing moment of inertia for spinnable objects. SIGGRAPH: 41st International Conference and Exhibition on Computer Graphics and Interactive Techniques vol. 33.","mla":"Bac̈Her, Moritz, et al. Spin-It: Optimizing Moment of Inertia for Spinnable Objects. Vol. 33, no. 4, ACM, 2014, doi:10.1145/2601097.2601157.","apa":"Bac̈Her, M., Whiting, E., Bickel, B., & Sorkine Hornung, O. (2014). Spin-It: Optimizing moment of inertia for spinnable objects (Vol. 33). Presented at the SIGGRAPH: 41st International Conference and Exhibition on Computer Graphics and Interactive Techniques, ACM. https://doi.org/10.1145/2601097.2601157","ama":"Bac̈Her M, Whiting E, Bickel B, Sorkine Hornung O. Spin-It: Optimizing moment of inertia for spinnable objects. In: Vol 33. ACM; 2014. doi:10.1145/2601097.2601157","ieee":"M. Bac̈Her, E. Whiting, B. Bickel, and O. Sorkine Hornung, “Spin-It: Optimizing moment of inertia for spinnable objects,” presented at the SIGGRAPH: 41st International Conference and Exhibition on Computer Graphics and Interactive Techniques, 2014, vol. 33, no. 4.","short":"M. Bac̈Her, E. Whiting, B. Bickel, O. Sorkine Hornung, in:, ACM, 2014."},"date_updated":"2019-04-26T07:22:07Z","title":"Spin-It: Optimizing moment of inertia for spinnable objects","author":[{"first_name":"Moritz","last_name":"Bac̈Her","full_name":"Bac̈her, Moritz"},{"full_name":"Whiting, Emily","last_name":"Whiting","first_name":"Emily"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bernd Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sorkine Hornung","full_name":"Sorkine-Hornung, Olga","first_name":"Olga"}],"publist_id":"4958"},{"publist_id":"4919","author":[{"first_name":"Amit","full_name":"Bermano, Amit H","last_name":"Bermano"},{"full_name":"Bradley, Derek J","last_name":"Bradley","first_name":"Derek"},{"first_name":"Thabo","full_name":"Beeler, Thabo","last_name":"Beeler"},{"last_name":"Zund","full_name":"Zund, Fabio","first_name":"Fabio"},{"first_name":"Derek","last_name":"Nowrouzezahrai","full_name":"Nowrouzezahrai, Derek"},{"first_name":"Ilya","full_name":"Baran, Ilya","last_name":"Baran"},{"first_name":"Olga","last_name":"Sorkine Hornung","full_name":"Sorkine-Hornung, Olga"},{"first_name":"Hanspeter","last_name":"Pfister","full_name":"Pfister, Hanspeter"},{"first_name":"Robert","last_name":"Sumner","full_name":"Sumner, Robert W"},{"last_name":"Bickel","full_name":"Bernd Bickel","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"},{"first_name":"Markus","full_name":"Groß, Markus S","last_name":"Groß"}],"title":"Facial performance enhancement using dynamic shape space analysis","citation":{"ista":"Bermano A, Bradley D, Beeler T, Zund F, Nowrouzezahrai D, Baran I, Sorkine Hornung O, Pfister H, Sumner R, Bickel B, Groß M. 2014. Facial performance enhancement using dynamic shape space analysis. ACM Transactions on Graphics. 33(2).","chicago":"Bermano, Amit, Derek Bradley, Thabo Beeler, Fabio Zund, Derek Nowrouzezahrai, Ilya Baran, Olga Sorkine Hornung, et al. “Facial Performance Enhancement Using Dynamic Shape Space Analysis.” ACM Transactions on Graphics. ACM, 2014. https://doi.org/10.1145/2546276.","ama":"Bermano A, Bradley D, Beeler T, et al. Facial performance enhancement using dynamic shape space analysis. ACM Transactions on Graphics. 2014;33(2). doi:10.1145/2546276","apa":"Bermano, A., Bradley, D., Beeler, T., Zund, F., Nowrouzezahrai, D., Baran, I., … Groß, M. (2014). Facial performance enhancement using dynamic shape space analysis. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2546276","ieee":"A. Bermano et al., “Facial performance enhancement using dynamic shape space analysis,” ACM Transactions on Graphics, vol. 33, no. 2. ACM, 2014.","short":"A. Bermano, D. Bradley, T. Beeler, F. Zund, D. Nowrouzezahrai, I. Baran, O. Sorkine Hornung, H. Pfister, R. Sumner, B. Bickel, M. Groß, ACM Transactions on Graphics 33 (2014).","mla":"Bermano, Amit, et al. “Facial Performance Enhancement Using Dynamic Shape Space Analysis.” ACM Transactions on Graphics, vol. 33, no. 2, ACM, 2014, doi:10.1145/2546276."},"date_updated":"2021-01-12T06:55:24Z","extern":1,"type":"journal_article","status":"public","_id":"2115","doi":"10.1145/2546276","issue":"2","volume":33,"date_published":"2014-03-01T00:00:00Z","date_created":"2018-12-11T11:55:48Z","publication_status":"published","year":"2014","day":"01","publication":"ACM Transactions on Graphics","publisher":"ACM","quality_controlled":0,"month":"03","intvolume":" 33","abstract":[{"lang":"eng","text":"The facial performance of an individual is inherently rich in subtle deformation and timing details. Although these subtleties make the performance realistic and compelling, they often elude both motion capture and hand animation. We present a technique for adding fine-scale details and expressiveness to low-resolution art-directed facial performances, such as those created manually using a rig, via marker-based capture, by fitting a morphable model to a video, or through Kinect reconstruction using recent faceshift technology. We employ a high-resolution facial performance capture system to acquire a representative performance of an individual in which he or she explores the full range of facial expressiveness. From the captured data, our system extracts an expressiveness model that encodes subtle spatial and temporal deformation details specific to that particular individual. Once this model has been built, these details can be transferred to low-resolution art-directed performances. We demonstrate results on various forms of input; after our enhancement, the resulting animations exhibit the same nuances and fine spatial details as the captured performance, with optional temporal enhancement to match the dynamics of the actor. Finally, we show that our technique outperforms the current state-of-the-art in example-based facial animation."}]},{"page":"887 - 926","date_created":"2018-12-11T11:55:54Z","doi":"10.1007/s00220-014-2124-8","volume":331,"date_published":"2014-11-01T00:00:00Z","issue":"3","year":"2014","publication_status":"published","publication":"Communications in Mathematical Physics","language":[{"iso":"eng"}],"day":"01","main_file_link":[{"url":"http://arxiv.org/abs/1203.5377 ","open_access":"1"}],"oa":1,"publisher":"Springer","quality_controlled":"1","intvolume":" 331","month":"11","abstract":[{"text":"Let ℭ denote the Clifford algebra over ℝ𝑛, which is the von Neumann algebra generated by n self-adjoint operators Q j , j = 1,…,n satisfying the canonical anticommutation relations, Q i Q j + Q j Q i = 2δ ij I, and let τ denote the normalized trace on ℭ. This algebra arises in quantum mechanics as the algebra of observables generated by n fermionic degrees of freedom. Let 𝔓 denote the set of all positive operators 𝜌∈ℭ such that τ(ρ) = 1; these are the non-commutative analogs of probability densities in the non-commutative probability space (ℭ,𝜏). The fermionic Fokker–Planck equation is a quantum-mechanical analog of the classical Fokker–Planck equation with which it has much in common, such as the same optimal hypercontractivity properties. In this paper we construct a Riemannian metric on 𝔓 that we show to be a natural analog of the classical 2-Wasserstein metric, and we show that, in analogy with the classical case, the fermionic Fokker–Planck equation is gradient flow in this metric for the relative entropy with respect to the ground state. We derive a number of consequences of this, such as a sharp Talagrand inequality for this metric, and we prove a number of results pertaining to this metric. Several open problems are raised.","lang":"eng"}],"oa_version":"Submitted Version","author":[{"last_name":"Carlen","full_name":"Carlen, Eric","first_name":"Eric"},{"full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","last_name":"Maas","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"4901","title":"An analog of the 2-Wasserstein metric in non-commutative probability under which the fermionic Fokker-Planck equation is gradient flow for the entropy","date_updated":"2021-01-12T06:55:30Z","citation":{"ista":"Carlen E, Maas J. 2014. An analog of the 2-Wasserstein metric in non-commutative probability under which the fermionic Fokker-Planck equation is gradient flow for the entropy. Communications in Mathematical Physics. 331(3), 887–926.","chicago":"Carlen, Eric, and Jan Maas. “An Analog of the 2-Wasserstein Metric in Non-Commutative Probability under Which the Fermionic Fokker-Planck Equation Is Gradient Flow for the Entropy.” Communications in Mathematical Physics. Springer, 2014. https://doi.org/10.1007/s00220-014-2124-8.","apa":"Carlen, E., & Maas, J. (2014). An analog of the 2-Wasserstein metric in non-commutative probability under which the fermionic Fokker-Planck equation is gradient flow for the entropy. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-014-2124-8","ama":"Carlen E, Maas J. An analog of the 2-Wasserstein metric in non-commutative probability under which the fermionic Fokker-Planck equation is gradient flow for the entropy. Communications in Mathematical Physics. 2014;331(3):887-926. doi:10.1007/s00220-014-2124-8","ieee":"E. Carlen and J. Maas, “An analog of the 2-Wasserstein metric in non-commutative probability under which the fermionic Fokker-Planck equation is gradient flow for the entropy,” Communications in Mathematical Physics, vol. 331, no. 3. Springer, pp. 887–926, 2014.","short":"E. Carlen, J. Maas, Communications in Mathematical Physics 331 (2014) 887–926.","mla":"Carlen, Eric, and Jan Maas. “An Analog of the 2-Wasserstein Metric in Non-Commutative Probability under Which the Fermionic Fokker-Planck Equation Is Gradient Flow for the Entropy.” Communications in Mathematical Physics, vol. 331, no. 3, Springer, 2014, pp. 887–926, doi:10.1007/s00220-014-2124-8."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","extern":"1","type":"journal_article","status":"public","_id":"2133"},{"acknowledgement":"JM is supported by Rubicon grant 680-50-0901 of the Netherlands Organisation for Scientific Research (NWO). MH is supported by EPSRC grant EP/D071593/1 and by the Royal Society through a Wolfson Research Merit Award. Both MH and HW are supported by the Le","abstract":[{"text":"We study approximations to a class of vector-valued equations of Burgers type driven by a multiplicative space-time white noise. A solution theory for this class of equations has been developed recently in Probability Theory Related Fields by Hairer and Weber. The key idea was to use the theory of controlled rough paths to give definitions of weak/mild solutions and to set up a Picard iteration argument. In this article the limiting behavior of a rather large class of (spatial) approximations to these equations is studied. These approximations are shown to converge and convergence rates are given, but the limit may depend on the particular choice of approximation. This effect is a spatial analogue to the Itô-Stratonovich correction in the theory of stochastic ordinary differential equations, where it is well known that different approximation schemes may converge to different solutions.","lang":"eng"}],"month":"05","intvolume":" 67","quality_controlled":0,"publisher":"Wiley-Blackwell","main_file_link":[{"url":"http://arxiv.org/abs/1202.3094 ","open_access":"1"}],"oa":1,"day":"01","publication":"Communications on Pure and Applied Mathematics","year":"2014","publication_status":"published","volume":67,"date_published":"2014-05-01T00:00:00Z","issue":"5","doi":"10.1002/cpa.21495","date_created":"2018-12-11T11:55:53Z","page":"776 - 870","_id":"2131","status":"public","type":"journal_article","extern":1,"citation":{"short":"M. Hairer, J. Maas, H. Weber, Communications on Pure and Applied Mathematics 67 (2014) 776–870.","ieee":"M. Hairer, J. Maas, and H. Weber, “Approximating Rough Stochastic PDEs,” Communications on Pure and Applied Mathematics, vol. 67, no. 5. Wiley-Blackwell, pp. 776–870, 2014.","apa":"Hairer, M., Maas, J., & Weber, H. (2014). Approximating Rough Stochastic PDEs. Communications on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21495","ama":"Hairer M, Maas J, Weber H. Approximating Rough Stochastic PDEs. Communications on Pure and Applied Mathematics. 2014;67(5):776-870. doi:10.1002/cpa.21495","mla":"Hairer, Martin, et al. “Approximating Rough Stochastic PDEs.” Communications on Pure and Applied Mathematics, vol. 67, no. 5, Wiley-Blackwell, 2014, pp. 776–870, doi:10.1002/cpa.21495.","ista":"Hairer M, Maas J, Weber H. 2014. Approximating Rough Stochastic PDEs. Communications on Pure and Applied Mathematics. 67(5), 776–870.","chicago":"Hairer, Martin, Jan Maas, and Hendrik Weber. “Approximating Rough Stochastic PDEs.” Communications on Pure and Applied Mathematics. Wiley-Blackwell, 2014. https://doi.org/10.1002/cpa.21495."},"date_updated":"2021-01-12T06:55:30Z","title":"Approximating Rough Stochastic PDEs","publist_id":"4902","author":[{"last_name":"Hairer","full_name":"Hairer, Martin M","first_name":"Martin"},{"orcid":"0000-0002-0845-1338","full_name":"Jan Maas","last_name":"Maas","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Weber","full_name":"Weber, Hendrik","first_name":"Hendrik"}]},{"abstract":[{"lang":"eng","text":"We consider discrete porous medium equations of the form ∂tρt=Δϕ(ρt), where Δ is the generator of a reversible continuous time Markov chain on a finite set χ, and ϕ is an increasing function. We show that these equations arise as gradient flows of certain entropy functionals with respect to suitable non-local transportation metrics. This may be seen as a discrete analogue of the Wasserstein gradient flow structure for porous medium equations in ℝn discovered by Otto. We present a one-dimensional counterexample to geodesic convexity and discuss Gromov-Hausdorff convergence to the Wasserstein metric."}],"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1212.1129","open_access":"1"}],"publisher":"Southwest Missouri State University","quality_controlled":0,"intvolume":" 34","month":"04","year":"2014","publication_status":"published","publication":"Discrete and Continuous Dynamical Systems- Series A","day":"01","page":"1355 - 1374","date_created":"2018-12-11T11:55:54Z","date_published":"2014-04-01T00:00:00Z","doi":"10.3934/dcds.2014.34.1355 ","issue":"4","volume":34,"_id":"2132","type":"journal_article","status":"public","date_updated":"2021-01-12T06:55:30Z","citation":{"short":"M. Erbar, J. Maas, Discrete and Continuous Dynamical Systems- Series A 34 (2014) 1355–1374.","ieee":"M. Erbar and J. Maas, “Gradient flow structures for discrete porous medium equations,” Discrete and Continuous Dynamical Systems- Series A, vol. 34, no. 4. Southwest Missouri State University, pp. 1355–1374, 2014.","apa":"Erbar, M., & Maas, J. (2014). Gradient flow structures for discrete porous medium equations. Discrete and Continuous Dynamical Systems- Series A. Southwest Missouri State University. https://doi.org/10.3934/dcds.2014.34.1355 ","ama":"Erbar M, Maas J. Gradient flow structures for discrete porous medium equations. Discrete and Continuous Dynamical Systems- Series A. 2014;34(4):1355-1374. doi:10.3934/dcds.2014.34.1355 ","mla":"Erbar, Matthias, and Jan Maas. “Gradient Flow Structures for Discrete Porous Medium Equations.” Discrete and Continuous Dynamical Systems- Series A, vol. 34, no. 4, Southwest Missouri State University, 2014, pp. 1355–74, doi:10.3934/dcds.2014.34.1355 .","ista":"Erbar M, Maas J. 2014. Gradient flow structures for discrete porous medium equations. Discrete and Continuous Dynamical Systems- Series A. 34(4), 1355–1374.","chicago":"Erbar, Matthias, and Jan Maas. “Gradient Flow Structures for Discrete Porous Medium Equations.” Discrete and Continuous Dynamical Systems- Series A. Southwest Missouri State University, 2014. https://doi.org/10.3934/dcds.2014.34.1355 ."},"extern":1,"publist_id":"4903","author":[{"first_name":"Matthias","full_name":"Erbar, Matthias","last_name":"Erbar"},{"last_name":"Maas","full_name":"Jan Maas","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"title":"Gradient flow structures for discrete porous medium equations"},{"publisher":"American Physical Society","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1308.5905"}],"oa":1,"month":"08","intvolume":" 113","abstract":[{"text":"We propose a technique for engineering momentum-dependent dissipation in Bose-Einstein condensates with non-local interactions. The scheme relies on the use of momentum-dependent dark-states in close analogy to velocity-selective coherent population trapping. During the short-time dissipative dynamics, the system is driven into a particular finite-momentum phonon mode, which in real space corresponds to an ordered structure with non-local density-density correlations. Dissipation-induced ordering can be observed and studied in present-day experiments using cold atoms with dipole-dipole or off-resonant Rydberg interactions. Due to its dissipative nature, the ordering does not require artificial breaking of translational symmetry by an opticallattice or harmonic trap. This opens up a perspective of direct cooling of quantum gases into strongly-interacting phases.","lang":"eng"}],"oa_version":"Submitted Version","acknowledgement":"This work was supported by NSF through a grant for the Institute for Theoretical Atomic, Molecular, and Optical Physics at Harvard University and Smithsonian Astrophysical Observatory as well as the Harvard Quantum Optics Center.","issue":"7","date_published":"2014-08-11T00:00:00Z","doi":"10.1103/PhysRevLett.113.070401","volume":113,"date_created":"2018-12-11T11:55:56Z","publication_status":"published","year":"2014","day":"11","language":[{"iso":"eng"}],"publication":"Physical Review Letters","type":"journal_article","status":"public","_id":"2140","article_number":"070401","publist_id":"4884","author":[{"first_name":"Johannes","full_name":"Otterbach, Johannes","last_name":"Otterbach"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko"}],"title":"Dissipative preparation of spatial order in Rydberg-dressed Bose-Einstein condensates","date_updated":"2021-01-12T06:55:33Z","citation":{"apa":"Otterbach, J., & Lemeshko, M. (2014). Dissipative preparation of spatial order in Rydberg-dressed Bose-Einstein condensates. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.113.070401","ama":"Otterbach J, Lemeshko M. Dissipative preparation of spatial order in Rydberg-dressed Bose-Einstein condensates. Physical Review Letters. 2014;113(7). doi:10.1103/PhysRevLett.113.070401","ieee":"J. Otterbach and M. Lemeshko, “Dissipative preparation of spatial order in Rydberg-dressed Bose-Einstein condensates,” Physical Review Letters, vol. 113, no. 7. American Physical Society, 2014.","short":"J. Otterbach, M. Lemeshko, Physical Review Letters 113 (2014).","mla":"Otterbach, Johannes, and Mikhail Lemeshko. “Dissipative Preparation of Spatial Order in Rydberg-Dressed Bose-Einstein Condensates.” Physical Review Letters, vol. 113, no. 7, 070401, American Physical Society, 2014, doi:10.1103/PhysRevLett.113.070401.","ista":"Otterbach J, Lemeshko M. 2014. Dissipative preparation of spatial order in Rydberg-dressed Bose-Einstein condensates. Physical Review Letters. 113(7), 070401.","chicago":"Otterbach, Johannes, and Mikhail Lemeshko. “Dissipative Preparation of Spatial Order in Rydberg-Dressed Bose-Einstein Condensates.” Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/PhysRevLett.113.070401."},"extern":"1","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"month":"06","publisher":"ACM","scopus_import":1,"quality_controlled":"1","main_file_link":[{"url":"http://arxiv.org/abs/1311.3681","open_access":"1"}],"oa":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We define a simple, explicit map sending a morphism f : M → N of pointwise finite dimensional persistence modules to a matching between the barcodes of M and N. Our main result is that, in a precise sense, the quality of this matching is tightly controlled by the lengths of the longest intervals in the barcodes of ker f and coker f . As an immediate corollary, we obtain a new proof of the algebraic stability theorem for persistence barcodes [5, 9], a fundamental result in the theory of persistent homology. In contrast to previous proofs, ours shows explicitly how a δ-interleaving morphism between two persistence modules induces a δ-matching between the barcodes of the two modules. Our main result also specializes to a structure theorem for submodules and quotients of persistence modules. Copyright is held by the owner/author(s)."}],"date_published":"2014-06-01T00:00:00Z","doi":"10.1145/2582112.2582168","date_created":"2018-12-11T11:56:01Z","ec_funded":1,"page":"355 - 364","day":"01","language":[{"iso":"eng"}],"publication":"Proceedings of the Annual Symposium on Computational Geometry","publication_status":"published","year":"2014","project":[{"call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems","grant_number":"318493"}],"status":"public","type":"conference","conference":{"location":"Kyoto, Japan","end_date":"2014-06-11","start_date":"2014-06-08","name":"SoCG: Symposium on Computational Geometry"},"_id":"2153","title":"Induced matchings of barcodes and the algebraic stability of persistence","department":[{"_id":"HeEd"}],"author":[{"orcid":"0000-0002-9683-0724","full_name":"Bauer, Ulrich","last_name":"Bauer","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich"},{"full_name":"Lesnick, Michael","last_name":"Lesnick","first_name":"Michael"}],"publist_id":"4853","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Bauer U, Lesnick M. 2014. Induced matchings of barcodes and the algebraic stability of persistence. Proceedings of the Annual Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 355–364.","chicago":"Bauer, Ulrich, and Michael Lesnick. “Induced Matchings of Barcodes and the Algebraic Stability of Persistence.” In Proceedings of the Annual Symposium on Computational Geometry, 355–64. ACM, 2014. https://doi.org/10.1145/2582112.2582168.","short":"U. Bauer, M. Lesnick, in:, Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 355–364.","ieee":"U. Bauer and M. Lesnick, “Induced matchings of barcodes and the algebraic stability of persistence,” in Proceedings of the Annual Symposium on Computational Geometry, Kyoto, Japan, 2014, pp. 355–364.","apa":"Bauer, U., & Lesnick, M. (2014). Induced matchings of barcodes and the algebraic stability of persistence. In Proceedings of the Annual Symposium on Computational Geometry (pp. 355–364). Kyoto, Japan: ACM. https://doi.org/10.1145/2582112.2582168","ama":"Bauer U, Lesnick M. Induced matchings of barcodes and the algebraic stability of persistence. In: Proceedings of the Annual Symposium on Computational Geometry. ACM; 2014:355-364. doi:10.1145/2582112.2582168","mla":"Bauer, Ulrich, and Michael Lesnick. “Induced Matchings of Barcodes and the Algebraic Stability of Persistence.” Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 355–64, doi:10.1145/2582112.2582168."},"date_updated":"2021-01-12T06:55:38Z"},{"doi":"10.1007/s00454-014-9584-7","date_published":"2014-07-01T00:00:00Z","date_created":"2018-12-11T11:56:01Z","page":"1 - 33","day":"01","publication":"Discrete & Computational Geometry","year":"2014","quality_controlled":"1","publisher":"Springer","oa":1,"acknowledgement":"Swiss National Science Foundation (SNF 200021-125309, 200020-138230, 200020-12507)","title":"On Gromov's method of selecting heavily covered points","publist_id":"4852","author":[{"full_name":"Matoušek, Jiří","last_name":"Matoušek","first_name":"Jiří"},{"first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Matoušek, Jiří, and Uli Wagner. “On Gromov’s Method of Selecting Heavily Covered Points.” Discrete & Computational Geometry. Springer, 2014. https://doi.org/10.1007/s00454-014-9584-7.","ista":"Matoušek J, Wagner U. 2014. On Gromov’s method of selecting heavily covered points. Discrete & Computational Geometry. 52(1), 1–33.","mla":"Matoušek, Jiří, and Uli Wagner. “On Gromov’s Method of Selecting Heavily Covered Points.” Discrete & Computational Geometry, vol. 52, no. 1, Springer, 2014, pp. 1–33, doi:10.1007/s00454-014-9584-7.","short":"J. Matoušek, U. Wagner, Discrete & Computational Geometry 52 (2014) 1–33.","ieee":"J. Matoušek and U. Wagner, “On Gromov’s method of selecting heavily covered points,” Discrete & Computational Geometry, vol. 52, no. 1. Springer, pp. 1–33, 2014.","ama":"Matoušek J, Wagner U. On Gromov’s method of selecting heavily covered points. Discrete & Computational Geometry. 2014;52(1):1-33. doi:10.1007/s00454-014-9584-7","apa":"Matoušek, J., & Wagner, U. (2014). On Gromov’s method of selecting heavily covered points. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-014-9584-7"},"project":[{"grant_number":"PP00P2_138948","name":"Embeddings in Higher Dimensions: Algorithms and Combinatorics","_id":"25FA3206-B435-11E9-9278-68D0E5697425"}],"volume":52,"issue":"1","language":[{"iso":"eng"}],"publication_status":"published","month":"07","intvolume":" 52","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1102.3515","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"text":"A result of Boros and Füredi (d = 2) and of Bárány (arbitrary d) asserts that for every d there exists cd > 0 such that for every n-point set P ⊂ ℝd, some point of ℝd is covered by at least (Formula presented.) of the d-simplices spanned by the points of P. The largest possible value of cd has been the subject of ongoing research. Recently Gromov improved the existing lower bounds considerably by introducing a new, topological proof method. We provide an exposition of the combinatorial component of Gromov's approach, in terms accessible to combinatorialists and discrete geometers, and we investigate the limits of his method. In particular, we give tighter bounds on the cofilling profiles for the (n - 1)-simplex. These bounds yield a minor improvement over Gromov's lower bounds on cd for large d, but they also show that the room for further improvement through the cofilling profiles alone is quite small. We also prove a slightly better lower bound for c3 by an approach using an additional structure besides the cofilling profiles. We formulate a combinatorial extremal problem whose solution might perhaps lead to a tight lower bound for cd.","lang":"eng"}],"department":[{"_id":"UlWa"}],"date_updated":"2021-01-12T06:55:38Z","status":"public","type":"journal_article","_id":"2154"},{"date_updated":"2021-01-12T06:55:39Z","department":[{"_id":"HeEd"}],"_id":"2156","conference":{"location":"Kyoto, Japan","end_date":"2014-06-11","start_date":"2014-06-08","name":"SoCG: Symposium on Computational Geometry"},"type":"conference","status":"public","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"abstract":[{"text":"We propose a metric for Reeb graphs, called the functional distortion distance. Under this distance, the Reeb graph is stable against small changes of input functions. At the same time, it remains discriminative at differentiating input functions. In particular, the main result is that the functional distortion distance between two Reeb graphs is bounded from below by the bottleneck distance between both the ordinary and extended persistence diagrams for appropriate dimensions. As an application of our results, we analyze a natural simplification scheme for Reeb graphs, and show that persistent features in Reeb graph remains persistent under simplification. Understanding the stability of important features of the Reeb graph under simplification is an interesting problem on its own right, and critical to the practical usage of Reeb graphs. Copyright is held by the owner/author(s).","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1307.2839"}],"scopus_import":1,"month":"06","citation":{"ama":"Bauer U, Ge X, Wang Y. Measuring distance between Reeb graphs. In: Proceedings of the Annual Symposium on Computational Geometry. ACM; 2014:464-473. doi:10.1145/2582112.2582169","apa":"Bauer, U., Ge, X., & Wang, Y. (2014). Measuring distance between Reeb graphs. In Proceedings of the Annual Symposium on Computational Geometry (pp. 464–473). Kyoto, Japan: ACM. https://doi.org/10.1145/2582112.2582169","ieee":"U. Bauer, X. Ge, and Y. Wang, “Measuring distance between Reeb graphs,” in Proceedings of the Annual Symposium on Computational Geometry, Kyoto, Japan, 2014, pp. 464–473.","short":"U. Bauer, X. Ge, Y. Wang, in:, Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 464–473.","mla":"Bauer, Ulrich, et al. “Measuring Distance between Reeb Graphs.” Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 464–73, doi:10.1145/2582112.2582169.","ista":"Bauer U, Ge X, Wang Y. 2014. Measuring distance between Reeb graphs. Proceedings of the Annual Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 464–473.","chicago":"Bauer, Ulrich, Xiaoyin Ge, and Yusu Wang. “Measuring Distance between Reeb Graphs.” In Proceedings of the Annual Symposium on Computational Geometry, 464–73. ACM, 2014. https://doi.org/10.1145/2582112.2582169."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich","last_name":"Bauer","full_name":"Bauer, Ulrich","orcid":"0000-0002-9683-0724"},{"first_name":"Xiaoyin","last_name":"Ge","full_name":"Ge, Xiaoyin"},{"first_name":"Yusu","full_name":"Wang, Yusu","last_name":"Wang"}],"publist_id":"4850","title":"Measuring distance between Reeb graphs","project":[{"name":"Topological Complex Systems","grant_number":"318493","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"year":"2014","publication":"Proceedings of the Annual Symposium on Computational Geometry","day":"01","page":"464 - 473","date_created":"2018-12-11T11:56:02Z","doi":"10.1145/2582112.2582169","date_published":"2014-06-01T00:00:00Z","acknowledgement":"National Science Foundation under grants CCF-1319406, CCF-1116258.","oa":1,"publisher":"ACM","quality_controlled":"1"},{"project":[{"name":"Topological Complex Systems","grant_number":"318493","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Bauer, U., & Edelsbrunner, H. (2014). The morse theory of Čech and Delaunay filtrations. In Proceedings of the Annual Symposium on Computational Geometry (pp. 484–490). Kyoto, Japan: ACM. https://doi.org/10.1145/2582112.2582167","ama":"Bauer U, Edelsbrunner H. The morse theory of Čech and Delaunay filtrations. In: Proceedings of the Annual Symposium on Computational Geometry. ACM; 2014:484-490. doi:10.1145/2582112.2582167","short":"U. Bauer, H. Edelsbrunner, in:, Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 484–490.","ieee":"U. Bauer and H. Edelsbrunner, “The morse theory of Čech and Delaunay filtrations,” in Proceedings of the Annual Symposium on Computational Geometry, Kyoto, Japan, 2014, pp. 484–490.","mla":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Filtrations.” Proceedings of the Annual Symposium on Computational Geometry, ACM, 2014, pp. 484–90, doi:10.1145/2582112.2582167.","ista":"Bauer U, Edelsbrunner H. 2014. The morse theory of Čech and Delaunay filtrations. Proceedings of the Annual Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, 484–490.","chicago":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Filtrations.” In Proceedings of the Annual Symposium on Computational Geometry, 484–90. ACM, 2014. https://doi.org/10.1145/2582112.2582167."},"title":"The morse theory of Čech and Delaunay filtrations","author":[{"first_name":"Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9683-0724","full_name":"Bauer, Ulrich","last_name":"Bauer"},{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"4851","acknowledgement":"This research is partially supported by ESF under the ACAT Research Network Programme, and by the Russian Government under mega project 11.G34.31.0053","oa":1,"publisher":"ACM","quality_controlled":"1","publication":"Proceedings of the Annual Symposium on Computational Geometry","day":"01","year":"2014","date_created":"2018-12-11T11:56:01Z","date_published":"2014-06-01T00:00:00Z","doi":"10.1145/2582112.2582167","page":"484 - 490","_id":"2155","status":"public","conference":{"start_date":"2014-06-08","end_date":"2014-06-11","location":"Kyoto, Japan","name":"SoCG: Symposium on Computational Geometry"},"type":"conference","date_updated":"2021-01-12T06:55:38Z","department":[{"_id":"HeEd"}],"oa_version":"Submitted Version","abstract":[{"text":"Given a finite set of points in Rn and a positive radius, we study the Čech, Delaunay-Čech, alpha, and wrap complexes as instances of a generalized discrete Morse theory. We prove that the latter three complexes are simple-homotopy equivalent. Our results have applications in topological data analysis and in the reconstruction of shapes from sampled data. Copyright is held by the owner/author(s).","lang":"eng"}],"month":"06","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1312.1231"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1},{"title":"New paradigms in the establishment and maintenance of gradients during directed cell migration","publist_id":"4848","author":[{"last_name":"Majumdar","full_name":"Majumdar, Ritankar","first_name":"Ritankar"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"},{"first_name":"Carole","last_name":"Parent","full_name":"Parent, Carole"}],"external_id":{"pmid":["24959970"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Majumdar, Ritankar, Michael K Sixt, and Carole Parent. “New Paradigms in the Establishment and Maintenance of Gradients during Directed Cell Migration.” Current Opinion in Cell Biology. Elsevier, 2014. https://doi.org/10.1016/j.ceb.2014.05.010.","ista":"Majumdar R, Sixt MK, Parent C. 2014. New paradigms in the establishment and maintenance of gradients during directed cell migration. Current Opinion in Cell Biology. 30(1), 33–40.","mla":"Majumdar, Ritankar, et al. “New Paradigms in the Establishment and Maintenance of Gradients during Directed Cell Migration.” Current Opinion in Cell Biology, vol. 30, no. 1, Elsevier, 2014, pp. 33–40, doi:10.1016/j.ceb.2014.05.010.","ieee":"R. Majumdar, M. K. Sixt, and C. Parent, “New paradigms in the establishment and maintenance of gradients during directed cell migration,” Current Opinion in Cell Biology, vol. 30, no. 1. Elsevier, pp. 33–40, 2014.","short":"R. Majumdar, M.K. Sixt, C. Parent, Current Opinion in Cell Biology 30 (2014) 33–40.","apa":"Majumdar, R., Sixt, M. K., & Parent, C. (2014). New paradigms in the establishment and maintenance of gradients during directed cell migration. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2014.05.010","ama":"Majumdar R, Sixt MK, Parent C. New paradigms in the establishment and maintenance of gradients during directed cell migration. Current Opinion in Cell Biology. 2014;30(1):33-40. doi:10.1016/j.ceb.2014.05.010"},"publisher":"Elsevier","quality_controlled":"1","oa":1,"acknowledgement":"This effort was supported by the Intramural Research Program of the Center for Cancer Research, NCI, National Institutes of Health and the European Research Council (ERC).","date_published":"2014-10-01T00:00:00Z","doi":"10.1016/j.ceb.2014.05.010","date_created":"2018-12-11T11:56:03Z","page":"33 - 40","day":"01","publication":"Current Opinion in Cell Biology","year":"2014","status":"public","type":"journal_article","_id":"2158","department":[{"_id":"MiSi"}],"date_updated":"2021-01-12T06:55:40Z","month":"10","intvolume":" 30","scopus_import":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4177954/","open_access":"1"}],"pmid":1,"oa_version":"Submitted Version","abstract":[{"text":"Directional guidance of migrating cells is relatively well explored in the reductionist setting of cell culture experiments. Here spatial gradients of chemical cues as well as gradients of mechanical substrate characteristics prove sufficient to attract single cells as well as their collectives. How such gradients present and act in the context of an organism is far less clear. Here we review recent advances in understanding how guidance cues emerge and operate in the physiological context.","lang":"eng"}],"issue":"1","volume":30,"language":[{"iso":"eng"}],"publication_status":"published"},{"intvolume":" 51","month":"10","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1410.0334","open_access":"1"}],"quality_controlled":"1","publisher":"Elsevier","oa_version":"Submitted Version","abstract":[{"text":"In machine learning, the domain adaptation problem arrives when the test (tar-get) and the train (source) data are generated from different distributions. A key applied issue is thus the design of algorithms able to generalize on a new distribution, for which we have no label information. We focus on learning classification models defined as a weighted majority vote over a set of real-valued functions. In this context, Germain et al. (2013) have shown that a measure of disagreement between these functions is crucial to control. The core of this measure is a theoretical bound—the C-bound (Lacasse et al., 2007)—which involves the disagreement and leads to a well performing majority vote learn-ing algorithm in usual non-adaptative supervised setting: MinCq. In this work,we propose a framework to extend MinCq to a domain adaptation scenario.This procedure takes advantage of the recent perturbed variation divergence between distributions proposed by Harel and Mannor (2012). Justified by a theoretical bound on the target risk of the vote, we provide to MinCq a tar-get sample labeled thanks to a perturbed variation-based self-labeling focused on the regions where the source and target marginals appear similar. We also study the influence of our self-labeling, from which we deduce an original process for tuning the hyperparameters. Finally, our framework called PV-MinCq shows very promising results on a rotation and translation synthetic problem.","lang":"eng"}],"date_created":"2018-12-11T11:56:05Z","ec_funded":1,"volume":51,"date_published":"2014-10-01T00:00:00Z","doi":"10.1016/j.patrec.2014.08.013","page":"37-43","publication":"Pattern Recognition Letters","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2014","project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding"}],"status":"public","type":"journal_article","_id":"2165","title":"Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling","author":[{"orcid":"0000-0002-8301-7240","full_name":"Morvant, Emilie","last_name":"Morvant","id":"4BAC2A72-F248-11E8-B48F-1D18A9856A87","first_name":"Emilie"}],"publist_id":"4819","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"mla":"Morvant, Emilie. “Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling.” Pattern Recognition Letters, vol. 51, Elsevier, 2014, pp. 37–43, doi:10.1016/j.patrec.2014.08.013.","short":"E. Morvant, Pattern Recognition Letters 51 (2014) 37–43.","ieee":"E. Morvant, “Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling,” Pattern Recognition Letters, vol. 51. Elsevier, pp. 37–43, 2014.","ama":"Morvant E. Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling. Pattern Recognition Letters. 2014;51:37-43. doi:10.1016/j.patrec.2014.08.013","apa":"Morvant, E. (2014). Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling. Pattern Recognition Letters. Elsevier. https://doi.org/10.1016/j.patrec.2014.08.013","chicago":"Morvant, Emilie. “Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling.” Pattern Recognition Letters. Elsevier, 2014. https://doi.org/10.1016/j.patrec.2014.08.013.","ista":"Morvant E. 2014. Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling. Pattern Recognition Letters. 51, 37–43."},"date_updated":"2021-01-12T06:55:43Z"},{"scopus_import":1,"quality_controlled":"1","publisher":"Oxford University Press","intvolume":" 24","month":"08","abstract":[{"lang":"eng","text":"Neuronal ectopia, such as granule cell dispersion (GCD) in temporal lobe epilepsy (TLE), has been assumed to result from a migration defect during development. Indeed, recent studies reported that aberrant migration of neonatal-generated dentate granule cells (GCs) increased the risk to develop epilepsy later in life. On the contrary, in the present study, we show that fully differentiated GCs become motile following the induction of epileptiform activity, resulting in GCD. Hippocampal slice cultures from transgenic mice expressing green fluorescent protein in differentiated, but not in newly generated GCs, were incubated with the glutamate receptor agonist kainate (KA), which induced GC burst activity and GCD. Using real-time microscopy, we observed that KA-exposed, differentiated GCs translocated their cell bodies and changed their dendritic organization. As found in human TLE, KA application was associated with decreased expression of the extracellular matrix protein Reelin, particularly in hilar interneurons. Together these findings suggest that KA-induced motility of differentiated GCs contributes to the development of GCD and establish slice cultures as a model to study neuronal changes induced by epileptiform activity. "}],"oa_version":"None","page":"2130 - 2140","date_created":"2018-12-11T11:56:04Z","doi":"10.1093/cercor/bht067","date_published":"2014-08-01T00:00:00Z","issue":"8","volume":24,"year":"2014","publication_status":"published","language":[{"iso":"eng"}],"publication":"Cerebral Cortex","day":"01","type":"journal_article","status":"public","_id":"2164","author":[{"first_name":"Xuejun","full_name":"Chai, Xuejun","last_name":"Chai"},{"last_name":"Münzner","full_name":"Münzner, Gert","first_name":"Gert"},{"last_name":"Zhao","full_name":"Zhao, Shanting","first_name":"Shanting"},{"first_name":"Stefanie","last_name":"Tinnes","full_name":"Tinnes, Stefanie"},{"last_name":"Kowalski","full_name":"Kowalski, Janina","first_name":"Janina","id":"3F3CA136-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Häussler","full_name":"Häussler, Ute","first_name":"Ute"},{"first_name":"Christina","full_name":"Young, Christina","last_name":"Young"},{"first_name":"Carola","full_name":"Haas, Carola","last_name":"Haas"},{"first_name":"Michael","full_name":"Frotscher, Michael","last_name":"Frotscher"}],"publist_id":"4820","department":[{"_id":"PeJo"}],"title":"Epilepsy-induced motility of differentiated neurons","citation":{"ieee":"X. Chai et al., “Epilepsy-induced motility of differentiated neurons,” Cerebral Cortex, vol. 24, no. 8. Oxford University Press, pp. 2130–2140, 2014.","short":"X. Chai, G. Münzner, S. Zhao, S. Tinnes, J. Kowalski, U. Häussler, C. Young, C. Haas, M. Frotscher, Cerebral Cortex 24 (2014) 2130–2140.","apa":"Chai, X., Münzner, G., Zhao, S., Tinnes, S., Kowalski, J., Häussler, U., … Frotscher, M. (2014). Epilepsy-induced motility of differentiated neurons. Cerebral Cortex. Oxford University Press. https://doi.org/10.1093/cercor/bht067","ama":"Chai X, Münzner G, Zhao S, et al. Epilepsy-induced motility of differentiated neurons. Cerebral Cortex. 2014;24(8):2130-2140. doi:10.1093/cercor/bht067","mla":"Chai, Xuejun, et al. “Epilepsy-Induced Motility of Differentiated Neurons.” Cerebral Cortex, vol. 24, no. 8, Oxford University Press, 2014, pp. 2130–40, doi:10.1093/cercor/bht067.","ista":"Chai X, Münzner G, Zhao S, Tinnes S, Kowalski J, Häussler U, Young C, Haas C, Frotscher M. 2014. Epilepsy-induced motility of differentiated neurons. Cerebral Cortex. 24(8), 2130–2140.","chicago":"Chai, Xuejun, Gert Münzner, Shanting Zhao, Stefanie Tinnes, Janina Kowalski, Ute Häussler, Christina Young, Carola Haas, and Michael Frotscher. “Epilepsy-Induced Motility of Differentiated Neurons.” Cerebral Cortex. Oxford University Press, 2014. https://doi.org/10.1093/cercor/bht067."},"date_updated":"2021-01-12T06:55:43Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"publist_id":"4816","author":[{"full_name":"Kelleher, Jerome","last_name":"Kelleher","first_name":"Jerome"},{"last_name":"Etheridge","full_name":"Etheridge, Alison","first_name":"Alison"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"title":"Coalescent simulation in continuous space: Algorithms for large neighbourhood size","citation":{"short":"J. Kelleher, A. Etheridge, N.H. Barton, Theoretical Population Biology 95 (2014) 13–23.","ieee":"J. Kelleher, A. Etheridge, and N. H. Barton, “Coalescent simulation in continuous space: Algorithms for large neighbourhood size,” Theoretical Population Biology, vol. 95. Academic Press, pp. 13–23, 2014.","ama":"Kelleher J, Etheridge A, Barton NH. Coalescent simulation in continuous space: Algorithms for large neighbourhood size. Theoretical Population Biology. 2014;95:13-23. doi:10.1016/j.tpb.2014.05.001","apa":"Kelleher, J., Etheridge, A., & Barton, N. H. (2014). Coalescent simulation in continuous space: Algorithms for large neighbourhood size. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2014.05.001","mla":"Kelleher, Jerome, et al. “Coalescent Simulation in Continuous Space: Algorithms for Large Neighbourhood Size.” Theoretical Population Biology, vol. 95, Academic Press, 2014, pp. 13–23, doi:10.1016/j.tpb.2014.05.001.","ista":"Kelleher J, Etheridge A, Barton NH. 2014. Coalescent simulation in continuous space: Algorithms for large neighbourhood size. Theoretical Population Biology. 95, 13–23.","chicago":"Kelleher, Jerome, Alison Etheridge, and Nicholas H Barton. “Coalescent Simulation in Continuous Space: Algorithms for Large Neighbourhood Size.” Theoretical Population Biology. Academic Press, 2014. https://doi.org/10.1016/j.tpb.2014.05.001."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Academic Press","oa":1,"page":"13 - 23","date_published":"2014-08-01T00:00:00Z","doi":"10.1016/j.tpb.2014.05.001","date_created":"2018-12-11T11:56:06Z","has_accepted_license":"1","year":"2014","day":"01","publication":"Theoretical Population Biology","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"391","_id":"2168","file_date_updated":"2020-07-14T12:45:31Z","department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T06:55:44Z","ddc":["570"],"scopus_import":1,"month":"08","intvolume":" 95","abstract":[{"lang":"eng","text":"Many species have an essentially continuous distribution in space, in which there are no natural divisions between randomly mating subpopulations. Yet, the standard approach to modelling these populations is to impose an arbitrary grid of demes, adjusting deme sizes and migration rates in an attempt to capture the important features of the population. Such indirect methods are required because of the failure of the classical models of isolation by distance, which have been shown to have major technical flaws. A recently introduced model of extinction and recolonisation in two dimensions solves these technical problems, and provides a rigorous technical foundation for the study of populations evolving in a spatial continuum. The coalescent process for this model is simply stated, but direct simulation is very inefficient for large neighbourhood sizes. We present efficient and exact algorithms to simulate this coalescent process for arbitrary sample sizes and numbers of loci, and analyse these algorithms in detail."}],"oa_version":"Published Version","volume":95,"ec_funded":1,"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"4839","checksum":"979d7a8034e9df198f068f0d251f31bd","date_updated":"2020-07-14T12:45:31Z","file_size":569005,"creator":"system","date_created":"2018-12-12T10:10:49Z","file_name":"IST-2015-391-v1+1_1-s2.0-S0040580914000355-main.pdf"}],"language":[{"iso":"eng"}]},{"intvolume":" 111","month":"07","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4115508/","open_access":"1"}],"oa":1,"scopus_import":1,"quality_controlled":"1","publisher":"National Academy of Sciences","oa_version":"Submitted Version","date_created":"2018-12-11T11:56:07Z","volume":111,"date_published":"2014-07-22T00:00:00Z","issue":"29","doi":"10.1073/pnas.1410107111","page":"10398 - 10399","publication":"PNAS","language":[{"iso":"eng"}],"day":"22","year":"2014","publication_status":"published","status":"public","type":"journal_article","_id":"2169","title":"Diverse forms of selection in evolution and computer science","department":[{"_id":"NiBa"}],"publist_id":"4815","author":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","full_name":"Novak, Sebastian","last_name":"Novak"},{"first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Barton, N. H., Novak, S., & Paixao, T. (2014). Diverse forms of selection in evolution and computer science. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1410107111","ama":"Barton NH, Novak S, Paixao T. Diverse forms of selection in evolution and computer science. PNAS. 2014;111(29):10398-10399. doi:10.1073/pnas.1410107111","ieee":"N. H. Barton, S. Novak, and T. Paixao, “Diverse forms of selection in evolution and computer science,” PNAS, vol. 111, no. 29. National Academy of Sciences, pp. 10398–10399, 2014.","short":"N.H. Barton, S. Novak, T. Paixao, PNAS 111 (2014) 10398–10399.","mla":"Barton, Nicholas H., et al. “Diverse Forms of Selection in Evolution and Computer Science.” PNAS, vol. 111, no. 29, National Academy of Sciences, 2014, pp. 10398–99, doi:10.1073/pnas.1410107111.","ista":"Barton NH, Novak S, Paixao T. 2014. Diverse forms of selection in evolution and computer science. PNAS. 111(29), 10398–10399.","chicago":"Barton, Nicholas H, Sebastian Novak, and Tiago Paixao. “Diverse Forms of Selection in Evolution and Computer Science.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1410107111."},"date_updated":"2021-01-12T06:55:45Z"}]