[{"publisher":"Elsevier","date_published":"2017-06-01T00:00:00Z","title":"Doomsday equilibria for omega-regular games","abstract":[{"text":"Two-player games on graphs provide the theoretical framework for many important problems such as reactive synthesis. While the traditional study of two-player zero-sum games has been extended to multi-player games with several notions of equilibria, they are decidable only for perfect-information games, whereas several applications require imperfect-information. In this paper we propose a new notion of equilibria, called doomsday equilibria, which is a strategy profile where all players satisfy their own objective, and if any coalition of players deviates and violates even one of the players' objective, then the objective of every player is violated. We present algorithms and complexity results for deciding the existence of doomsday equilibria for various classes of ω-regular objectives, both for imperfect-information games, and for perfect-information games. We provide optimal complexity bounds for imperfect-information games, and in most cases for perfect-information games.","lang":"eng"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1311.3238"]},"date_updated":"2023-02-21T16:06:02Z","department":[{"_id":"KrCh"}],"citation":{"short":"K. Chatterjee, L. Doyen, E. Filiot, J. Raskin, Information and Computation 254 (2017) 296–315.","mla":"Chatterjee, Krishnendu, et al. “Doomsday Equilibria for Omega-Regular Games.” <i>Information and Computation</i>, vol. 254, Elsevier, 2017, pp. 296–315, doi:<a href=\"https://doi.org/10.1016/j.ic.2016.10.012\">10.1016/j.ic.2016.10.012</a>.","ieee":"K. Chatterjee, L. Doyen, E. Filiot, and J. Raskin, “Doomsday equilibria for omega-regular games,” <i>Information and Computation</i>, vol. 254. Elsevier, pp. 296–315, 2017.","apa":"Chatterjee, K., Doyen, L., Filiot, E., &#38; Raskin, J. (2017). Doomsday equilibria for omega-regular games. <i>Information and Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ic.2016.10.012\">https://doi.org/10.1016/j.ic.2016.10.012</a>","ama":"Chatterjee K, Doyen L, Filiot E, Raskin J. Doomsday equilibria for omega-regular games. <i>Information and Computation</i>. 2017;254:296-315. doi:<a href=\"https://doi.org/10.1016/j.ic.2016.10.012\">10.1016/j.ic.2016.10.012</a>","ista":"Chatterjee K, Doyen L, Filiot E, Raskin J. 2017. Doomsday equilibria for omega-regular games. Information and Computation. 254, 296–315.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Emmanuel Filiot, and Jean Raskin. “Doomsday Equilibria for Omega-Regular Games.” <i>Information and Computation</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.ic.2016.10.012\">https://doi.org/10.1016/j.ic.2016.10.012</a>."},"intvolume":"       254","arxiv":1,"publist_id":"7036","publication":"Information and Computation","related_material":{"record":[{"id":"10885","relation":"earlier_version","status":"public"}]},"scopus_import":"1","day":"01","year":"2017","doi":"10.1016/j.ic.2016.10.012","page":"296 - 315","oa":1,"language":[{"iso":"eng"}],"article_processing_charge":"No","volume":254,"month":"06","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Laurent","last_name":"Doyen","full_name":"Doyen, Laurent"},{"last_name":"Filiot","first_name":"Emmanuel","full_name":"Filiot, Emmanuel"},{"full_name":"Raskin, Jean","last_name":"Raskin","first_name":"Jean"}],"project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","oa_version":"Submitted Version","ec_funded":1,"publication_identifier":{"issn":["08905401"]},"status":"public","main_file_link":[{"url":"https://arxiv.org/abs/1311.3238","open_access":"1"}],"date_created":"2018-12-11T11:47:53Z","type":"journal_article","_id":"681","article_type":"original"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"citation":{"apa":"Ukai, H., Kawahara, A., Hirayama, K., Case, M. J., Aino, S., Miyabe, M., … Ito, I. (2017). PirB regulates asymmetries in hippocampal circuitry. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0179377\">https://doi.org/10.1371/journal.pone.0179377</a>","ista":"Ukai H, Kawahara A, Hirayama K, Case MJ, Aino S, Miyabe M, Wakita K, Oogi R, Kasayuki M, Kawashima S, Sugimoto S, Chikamatsu K, Nitta N, Koga T, Shigemoto R, Takai T, Ito I. 2017. PirB regulates asymmetries in hippocampal circuitry. PLoS One. 12(6), e0179377.","chicago":"Ukai, Hikari, Aiko Kawahara, Keiko Hirayama, Matthew J Case, Shotaro Aino, Masahiro Miyabe, Ken Wakita, et al. “PirB Regulates Asymmetries in Hippocampal Circuitry.” <i>PLoS One</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pone.0179377\">https://doi.org/10.1371/journal.pone.0179377</a>.","ama":"Ukai H, Kawahara A, Hirayama K, et al. PirB regulates asymmetries in hippocampal circuitry. <i>PLoS One</i>. 2017;12(6). doi:<a href=\"https://doi.org/10.1371/journal.pone.0179377\">10.1371/journal.pone.0179377</a>","ieee":"H. Ukai <i>et al.</i>, “PirB regulates asymmetries in hippocampal circuitry,” <i>PLoS One</i>, vol. 12, no. 6. Public Library of Science, 2017.","mla":"Ukai, Hikari, et al. “PirB Regulates Asymmetries in Hippocampal Circuitry.” <i>PLoS One</i>, vol. 12, no. 6, e0179377, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pone.0179377\">10.1371/journal.pone.0179377</a>.","short":"H. Ukai, A. Kawahara, K. Hirayama, M.J. Case, S. Aino, M. Miyabe, K. Wakita, R. Oogi, M. Kasayuki, S. Kawashima, S. Sugimoto, K. Chikamatsu, N. Nitta, T. Koga, R. Shigemoto, T. Takai, I. Ito, PLoS One 12 (2017)."},"department":[{"_id":"RySh"}],"date_updated":"2024-03-25T23:30:07Z","title":"PirB regulates asymmetries in hippocampal circuitry","publisher":"Public Library of Science","date_published":"2017-06-01T00:00:00Z","file_date_updated":"2020-07-14T12:47:40Z","ddc":["571"],"publication_status":"published","abstract":[{"text":"Left-right asymmetry is a fundamental feature of higher-order brain structure; however, the molecular basis of brain asymmetry remains unclear. We recently identified structural and functional asymmetries in mouse hippocampal circuitry that result from the asymmetrical distribution of two distinct populations of pyramidal cell synapses that differ in the density of the NMDA receptor subunit GluRε2 (also known as NR2B, GRIN2B or GluN2B). By examining the synaptic distribution of ε2 subunits, we previously found that β2-microglobulin-deficient mice, which lack cell surface expression of the vast majority of major histocompatibility complex class I (MHCI) proteins, do not exhibit circuit asymmetry. In the present study, we conducted electrophysiological and anatomical analyses on the hippocampal circuitry of mice with a knockout of the paired immunoglobulin-like receptor B (PirB), an MHCI receptor. As in β2-microglobulin-deficient mice, the PirB-deficient hippocampus lacked circuit asymmetries. This finding that MHCI loss-of-function mice and PirB knockout mice have identical phenotypes suggests that MHCI signals that produce hippocampal asymmetries are transduced through PirB. Our results provide evidence for a critical role of the MHCI/PirB signaling system in the generation of asymmetries in hippocampal circuitry.","lang":"eng"}],"doi":"10.1371/journal.pone.0179377","day":"01","year":"2017","oa":1,"publication":"PLoS One","publist_id":"7034","intvolume":"        12","scopus_import":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"51","status":"public"}]},"author":[{"last_name":"Ukai","first_name":"Hikari","full_name":"Ukai, Hikari"},{"full_name":"Kawahara, Aiko","last_name":"Kawahara","first_name":"Aiko"},{"full_name":"Hirayama, Keiko","first_name":"Keiko","last_name":"Hirayama"},{"first_name":"Matthew J","last_name":"Case","id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Case, Matthew J"},{"last_name":"Aino","first_name":"Shotaro","full_name":"Aino, Shotaro"},{"last_name":"Miyabe","first_name":"Masahiro","full_name":"Miyabe, Masahiro"},{"last_name":"Wakita","first_name":"Ken","full_name":"Wakita, Ken"},{"last_name":"Oogi","first_name":"Ryohei","full_name":"Oogi, Ryohei"},{"full_name":"Kasayuki, Michiyo","first_name":"Michiyo","last_name":"Kasayuki"},{"last_name":"Kawashima","first_name":"Shihomi","full_name":"Kawashima, Shihomi"},{"first_name":"Shunichi","last_name":"Sugimoto","full_name":"Sugimoto, Shunichi"},{"last_name":"Chikamatsu","first_name":"Kanako","full_name":"Chikamatsu, Kanako"},{"full_name":"Nitta, Noritaka","first_name":"Noritaka","last_name":"Nitta"},{"full_name":"Koga, Tsuneyuki","last_name":"Koga","first_name":"Tsuneyuki"},{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto"},{"last_name":"Takai","first_name":"Toshiyuki","full_name":"Takai, Toshiyuki"},{"last_name":"Ito","first_name":"Isao","full_name":"Ito, Isao"}],"oa_version":"Published Version","quality_controlled":"1","volume":12,"language":[{"iso":"eng"}],"article_number":"e0179377","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:47:40Z","date_created":"2018-12-12T10:12:16Z","file_name":"IST-2017-897-v1+1_journal.pone.0179377.pdf","relation":"main_file","creator":"system","file_id":"4934","checksum":"24dd19c46fb1c761b0bcbbcd1025a3a8","file_size":5798454,"access_level":"open_access"}],"issue":"6","has_accepted_license":"1","month":"06","status":"public","publication_identifier":{"issn":["19326203"]},"article_type":"original","_id":"682","type":"journal_article","date_created":"2018-12-11T11:47:54Z","pubrep_id":"897"},{"alternative_title":["LIPIcs"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"citation":{"ieee":"A. Lubiw, Z. Masárová, and U. Wagner, “A proof of the orbit conjecture for flipping edge labelled triangulations,” presented at the SoCG: Symposium on Computational Geometry, Brisbane, Australia, 2017, vol. 77.","ista":"Lubiw A, Masárová Z, Wagner U. 2017. A proof of the orbit conjecture for flipping edge labelled triangulations. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 77, 49.","ama":"Lubiw A, Masárová Z, Wagner U. A proof of the orbit conjecture for flipping edge labelled triangulations. In: Vol 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2017.49\">10.4230/LIPIcs.SoCG.2017.49</a>","chicago":"Lubiw, Anna, Zuzana Masárová, and Uli Wagner. “A Proof of the Orbit Conjecture for Flipping Edge Labelled Triangulations,” Vol. 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2017.49\">https://doi.org/10.4230/LIPIcs.SoCG.2017.49</a>.","apa":"Lubiw, A., Masárová, Z., &#38; Wagner, U. (2017). A proof of the orbit conjecture for flipping edge labelled triangulations (Vol. 77). Presented at the SoCG: Symposium on Computational Geometry, Brisbane, Australia: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2017.49\">https://doi.org/10.4230/LIPIcs.SoCG.2017.49</a>","mla":"Lubiw, Anna, et al. <i>A Proof of the Orbit Conjecture for Flipping Edge Labelled Triangulations</i>. Vol. 77, 49, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2017.49\">10.4230/LIPIcs.SoCG.2017.49</a>.","short":"A. Lubiw, Z. Masárová, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017."},"department":[{"_id":"UlWa"}],"date_updated":"2023-09-05T15:01:43Z","title":"A proof of the orbit conjecture for flipping edge labelled triangulations","date_published":"2017-06-01T00:00:00Z","file_date_updated":"2020-07-14T12:47:41Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","ddc":["514","516"],"publication_status":"published","abstract":[{"lang":"eng","text":"Given a triangulation of a point set in the plane, a flip deletes an edge e whose removal leaves a convex quadrilateral, and replaces e by the opposite diagonal of the quadrilateral. It is well known that any triangulation of a point set can be reconfigured to any other triangulation by some sequence of flips. We explore this question in the setting where each edge of a triangulation has a label, and a flip transfers the label of the removed edge to the new edge. It is not true that every labelled triangulation of a point set can be reconfigured to every other labelled triangulation via a sequence of flips, but we characterize when this is possible. There is an obvious necessary condition: for each label l, if edge e has label l in the first triangulation and edge f has label l in the second triangulation, then there must be some sequence of flips that moves label l from e to f, ignoring all other labels. Bose, Lubiw, Pathak and Verdonschot formulated the Orbit Conjecture, which states that this necessary condition is also sufficient, i.e. that all labels can be simultaneously mapped to their destination if and only if each label individually can be mapped to its destination. We prove this conjecture. Furthermore, we give a polynomial-time algorithm to find a sequence of flips to reconfigure one labelled triangulation to another, if such a sequence exists, and we prove an upper bound of O(n7) on the length of the flip sequence. Our proof uses the topological result that the sets of pairwise non-crossing edges on a planar point set form a simplicial complex that is homeomorphic to a high-dimensional ball (this follows from a result of Orden and Santos; we give a different proof based on a shelling argument). The dual cell complex of this simplicial ball, called the flip complex, has the usual flip graph as its 1-skeleton. We use properties of the 2-skeleton of the flip complex to prove the Orbit Conjecture."}],"day":"01","year":"2017","doi":"10.4230/LIPIcs.SoCG.2017.49","oa":1,"publist_id":"7033","intvolume":"        77","scopus_import":1,"related_material":{"record":[{"relation":"later_version","id":"5986","status":"public"}]},"author":[{"full_name":"Lubiw, Anna","first_name":"Anna","last_name":"Lubiw"},{"id":"45CFE238-F248-11E8-B48F-1D18A9856A87","full_name":"Masárová, Zuzana","first_name":"Zuzana","last_name":"Masárová","orcid":"0000-0002-6660-1322"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","first_name":"Uli","last_name":"Wagner","orcid":"0000-0002-1494-0568"}],"oa_version":"Published Version","quality_controlled":"1","volume":77,"language":[{"iso":"eng"}],"article_number":"49","file":[{"creator":"system","file_id":"5265","checksum":"24fdde981cc513352a78dcf9b0660ae9","file_size":710007,"access_level":"open_access","relation":"main_file","file_name":"IST-2017-896-v1+1_LIPIcs-SoCG-2017-49.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:47:41Z","date_created":"2018-12-12T10:17:12Z"}],"has_accepted_license":"1","month":"06","status":"public","_id":"683","type":"conference","date_created":"2018-12-11T11:47:54Z","conference":{"name":"SoCG: Symposium on Computational Geometry","location":"Brisbane, Australia","end_date":"2017-07-07","start_date":"2017-07-04"},"pubrep_id":"896"},{"language":[{"iso":"eng"}],"article_processing_charge":"No","volume":82,"month":"06","issue":"2","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Nir","last_name":"Piterman","full_name":"Piterman, Nir"}],"quality_controlled":"1","oa_version":"Submitted Version","status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1206.5174"}],"publication_identifier":{"issn":["0022-4812"],"eissn":["1943-5886"]},"date_created":"2018-12-11T11:47:54Z","_id":"684","type":"journal_article","date_published":"2017-06-01T00:00:00Z","publisher":"Cambridge University Press","title":"Obligation blackwell games and p-automata","abstract":[{"lang":"eng","text":"We generalize winning conditions in two-player games by adding a structural acceptance condition called obligations. Obligations are orthogonal to the linear winning conditions that define whether a play is winning. Obligations are a declaration that player 0 can achieve a certain value from a configuration. If the obligation is met, the value of that configuration for player 0 is 1. We define the value in such games and show that obligation games are determined. For Markov chains with Borel objectives and obligations, and finite turn-based stochastic parity games with obligations we give an alternative and simpler characterization of the value function. Based on this simpler definition we show that the decision problem of winning finite turn-based stochastic parity games with obligations is in NP∩co-NP. We also show that obligation games provide a game framework for reasoning about p-automata. © 2017 The Association for Symbolic Logic."}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-04-16T12:10:53Z","department":[{"_id":"KrCh"}],"citation":{"mla":"Chatterjee, Krishnendu, and Nir Piterman. “Obligation Blackwell Games and P-Automata.” <i>Journal of Symbolic Logic</i>, vol. 82, no. 2, Cambridge University Press, 2017, pp. 420–52, doi:<a href=\"https://doi.org/10.1017/jsl.2016.71\">10.1017/jsl.2016.71</a>.","short":"K. Chatterjee, N. Piterman, Journal of Symbolic Logic 82 (2017) 420–452.","ista":"Chatterjee K, Piterman N. 2017. Obligation blackwell games and p-automata. Journal of Symbolic Logic. 82(2), 420–452.","ama":"Chatterjee K, Piterman N. Obligation blackwell games and p-automata. <i>Journal of Symbolic Logic</i>. 2017;82(2):420-452. doi:<a href=\"https://doi.org/10.1017/jsl.2016.71\">10.1017/jsl.2016.71</a>","chicago":"Chatterjee, Krishnendu, and Nir Piterman. “Obligation Blackwell Games and P-Automata.” <i>Journal of Symbolic Logic</i>. Cambridge University Press, 2017. <a href=\"https://doi.org/10.1017/jsl.2016.71\">https://doi.org/10.1017/jsl.2016.71</a>.","apa":"Chatterjee, K., &#38; Piterman, N. (2017). Obligation blackwell games and p-automata. <i>Journal of Symbolic Logic</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jsl.2016.71\">https://doi.org/10.1017/jsl.2016.71</a>","ieee":"K. Chatterjee and N. Piterman, “Obligation blackwell games and p-automata,” <i>Journal of Symbolic Logic</i>, vol. 82, no. 2. Cambridge University Press, pp. 420–452, 2017."},"intvolume":"        82","publist_id":"7026","publication":"Journal of Symbolic Logic","scopus_import":"1","doi":"10.1017/jsl.2016.71","day":"01","year":"2017","page":"420 - 452","oa":1},{"author":[{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","full_name":"Martius, Georg S","last_name":"Martius","first_name":"Georg S"},{"first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"}],"external_id":{"arxiv":["1610.02995"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ChLa"}],"project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7"}],"quality_controlled":"1","date_updated":"2021-01-12T08:09:17Z","citation":{"mla":"Martius, Georg S., and Christoph Lampert. “Extrapolation and Learning Equations.” <i>5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings</i>, International Conference on Learning Representations, 2017.","short":"G.S. Martius, C. Lampert, in:, 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings, International Conference on Learning Representations, 2017.","ista":"Martius GS, Lampert C. 2017. Extrapolation and learning equations. 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. ICLR: International Conference on Learning Representations.","ama":"Martius GS, Lampert C. Extrapolation and learning equations. In: <i>5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings</i>. International Conference on Learning Representations; 2017.","chicago":"Martius, Georg S, and Christoph Lampert. “Extrapolation and Learning Equations.” In <i>5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings</i>. International Conference on Learning Representations, 2017.","apa":"Martius, G. S., &#38; Lampert, C. (2017). Extrapolation and learning equations. In <i>5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings</i>. Toulon, France: International Conference on Learning Representations.","ieee":"G. S. Martius and C. Lampert, “Extrapolation and learning equations,” in <i>5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings</i>, Toulon, France, 2017."},"oa_version":"Preprint","language":[{"iso":"eng"}],"publisher":"International Conference on Learning Representations","date_published":"2017-02-21T00:00:00Z","title":"Extrapolation and learning equations","month":"02","publication_status":"published","abstract":[{"lang":"eng","text":"In classical machine learning, regression is treated as a black box process of identifying a suitable function from a hypothesis set without attempting to gain insight into the mechanism connecting inputs and outputs. In the natural sciences, however, finding an interpretable function for a phenomenon is the prime goal as it allows to understand and generalize results. This paper proposes a novel type of function learning network, called equation learner (EQL), that can learn analytical expressions and is able to extrapolate to unseen domains. It is implemented as an end-to-end differentiable feed-forward network and allows for efficient gradient based training. Due to sparsity regularization concise interpretable expressions can be obtained. Often the true underlying source expression is identified."}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1610.02995"}],"status":"public","day":"21","year":"2017","oa":1,"date_created":"2019-09-01T22:01:00Z","_id":"6841","type":"conference","conference":{"start_date":"2017-04-24","end_date":"2017-04-26","name":"ICLR: International Conference on Learning Representations","location":"Toulon, France"},"arxiv":1,"ec_funded":1,"publication":"5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings","scopus_import":1},{"pubrep_id":"985","ec_funded":1,"type":"journal_article","_id":"685","date_created":"2018-12-11T11:47:55Z","publication_identifier":{"issn":["09254773"]},"status":"public","file":[{"access_level":"open_access","file_size":652313,"file_id":"6335","checksum":"727043d2e4199fbef6b3704e6d1ac105","creator":"dernst","relation":"main_file","file_name":"2017_Briscoe_Kicheva_and_DArcy_accepted_version.pdf","date_created":"2019-04-17T07:58:48Z","date_updated":"2020-07-14T12:47:42Z","content_type":"application/pdf"}],"month":"06","has_accepted_license":"1","volume":145,"language":[{"iso":"eng"}],"oa_version":"Submitted Version","quality_controlled":"1","project":[{"name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020"}],"author":[{"last_name":"Briscoe","first_name":"James","full_name":"Briscoe, James"},{"full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","last_name":"Kicheva","first_name":"Anna"}],"scopus_import":1,"publication":"Mechanisms of Development","publist_id":"7025","intvolume":"       145","oa":1,"doi":"10.1016/j.mod.2017.03.005","page":"26 - 31","year":"2017","day":"01","ddc":["571"],"publication_status":"published","abstract":[{"lang":"eng","text":"By applying methods and principles from the physical sciences to biological problems, D'Arcy Thompson's On Growth and Form demonstrated how mathematical reasoning reveals elegant, simple explanations for seemingly complex processes. This has had a profound influence on subsequent generations of developmental biologists. We discuss how this influence can be traced through twentieth century morphologists, embryologists and theoreticians to current research that explores the molecular and cellular mechanisms of tissue growth and patterning, including our own studies of the vertebrate neural tube."}],"title":"The physics of development 100 years after D'Arcy Thompson's “on growth and form”","pmid":1,"publisher":"Elsevier","date_published":"2017-06-01T00:00:00Z","file_date_updated":"2020-07-14T12:47:42Z","citation":{"ieee":"J. Briscoe and A. Kicheva, “The physics of development 100 years after D’Arcy Thompson’s ‘on growth and form,’” <i>Mechanisms of Development</i>, vol. 145. Elsevier, pp. 26–31, 2017.","ista":"Briscoe J, Kicheva A. 2017. The physics of development 100 years after D’Arcy Thompson’s “on growth and form”. Mechanisms of Development. 145, 26–31.","ama":"Briscoe J, Kicheva A. The physics of development 100 years after D’Arcy Thompson’s “on growth and form.” <i>Mechanisms of Development</i>. 2017;145:26-31. doi:<a href=\"https://doi.org/10.1016/j.mod.2017.03.005\">10.1016/j.mod.2017.03.005</a>","chicago":"Briscoe, James, and Anna Kicheva. “The Physics of Development 100 Years after D’Arcy Thompson’s ‘on Growth and Form.’” <i>Mechanisms of Development</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.mod.2017.03.005\">https://doi.org/10.1016/j.mod.2017.03.005</a>.","apa":"Briscoe, J., &#38; Kicheva, A. (2017). The physics of development 100 years after D’Arcy Thompson’s “on growth and form.” <i>Mechanisms of Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mod.2017.03.005\">https://doi.org/10.1016/j.mod.2017.03.005</a>","mla":"Briscoe, James, and Anna Kicheva. “The Physics of Development 100 Years after D’Arcy Thompson’s ‘on Growth and Form.’” <i>Mechanisms of Development</i>, vol. 145, Elsevier, 2017, pp. 26–31, doi:<a href=\"https://doi.org/10.1016/j.mod.2017.03.005\">10.1016/j.mod.2017.03.005</a>.","short":"J. Briscoe, A. Kicheva, Mechanisms of Development 145 (2017) 26–31."},"department":[{"_id":"AnKi"}],"date_updated":"2021-01-12T08:09:20Z","external_id":{"pmid":["28366718"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"scopus_import":1,"intvolume":"       145","publist_id":"7024","publication":"Mechanisms of Development","date_created":"2018-12-11T11:47:55Z","type":"journal_article","_id":"686","year":"2017","status":"public","day":"01","publication_identifier":{"issn":["09254773"]},"page":"32 - 37","doi":"10.1016/j.mod.2017.03.006","abstract":[{"text":"Tissues are thought to behave like fluids with a given surface tension. Differences in tissue surface tension (TST) have been proposed to trigger cell sorting and tissue envelopment. D'Arcy Thompson in his seminal book ‘On Growth and Form’ has introduced this concept of differential TST as a key physical mechanism dictating tissue formation and organization within the developing organism. Over the past century, many studies have picked up the concept of differential TST and analyzed the role and cell biological basis of TST in development, underlining the importance and influence of this concept in developmental biology.","lang":"eng"}],"month":"06","publication_status":"published","publisher":"Elsevier","date_published":"2017-06-01T00:00:00Z","language":[{"iso":"eng"}],"title":"D'Arcy Thompson's ‘on growth and form’: From soap bubbles to tissue self organization","volume":145,"date_updated":"2021-01-12T08:09:23Z","quality_controlled":"1","department":[{"_id":"CaHe"}],"oa_version":"None","citation":{"apa":"Heisenberg, C.-P. J. (2017). D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. <i>Mechanisms of Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mod.2017.03.006\">https://doi.org/10.1016/j.mod.2017.03.006</a>","ista":"Heisenberg C-PJ. 2017. D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. 145, 32–37.","ama":"Heisenberg C-PJ. D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. <i>Mechanisms of Development</i>. 2017;145:32-37. doi:<a href=\"https://doi.org/10.1016/j.mod.2017.03.006\">10.1016/j.mod.2017.03.006</a>","chicago":"Heisenberg, Carl-Philipp J. “D’Arcy Thompson’s ‘on Growth and Form’: From Soap Bubbles to Tissue Self Organization.” <i>Mechanisms of Development</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.mod.2017.03.006\">https://doi.org/10.1016/j.mod.2017.03.006</a>.","ieee":"C.-P. J. Heisenberg, “D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization,” <i>Mechanisms of Development</i>, vol. 145. Elsevier, pp. 32–37, 2017.","mla":"Heisenberg, Carl-Philipp J. “D’Arcy Thompson’s ‘on Growth and Form’: From Soap Bubbles to Tissue Self Organization.” <i>Mechanisms of Development</i>, vol. 145, Elsevier, 2017, pp. 32–37, doi:<a href=\"https://doi.org/10.1016/j.mod.2017.03.006\">10.1016/j.mod.2017.03.006</a>.","short":"C.-P.J. Heisenberg, Mechanisms of Development 145 (2017) 32–37."},"author":[{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa":1,"day":"01","page":"635 - 703","doi":"10.1093/qmath/haw053","year":"2017","scopus_import":1,"publication":"Quarterly Journal of Mathematics","publist_id":"7022","intvolume":"        68","citation":{"ieee":"B. Davison, “The critical CoHA of a quiver with potential,” <i>Quarterly Journal of Mathematics</i>, vol. 68, no. 2. Oxford University Press, pp. 635–703, 2017.","ista":"Davison B. 2017. The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. 68(2), 635–703.","chicago":"Davison, Ben. “The Critical CoHA of a Quiver with Potential.” <i>Quarterly Journal of Mathematics</i>. Oxford University Press, 2017. <a href=\"https://doi.org/10.1093/qmath/haw053\">https://doi.org/10.1093/qmath/haw053</a>.","ama":"Davison B. The critical CoHA of a quiver with potential. <i>Quarterly Journal of Mathematics</i>. 2017;68(2):635-703. doi:<a href=\"https://doi.org/10.1093/qmath/haw053\">10.1093/qmath/haw053</a>","apa":"Davison, B. (2017). The critical CoHA of a quiver with potential. <i>Quarterly Journal of Mathematics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/qmath/haw053\">https://doi.org/10.1093/qmath/haw053</a>","mla":"Davison, Ben. “The Critical CoHA of a Quiver with Potential.” <i>Quarterly Journal of Mathematics</i>, vol. 68, no. 2, Oxford University Press, 2017, pp. 635–703, doi:<a href=\"https://doi.org/10.1093/qmath/haw053\">10.1093/qmath/haw053</a>.","short":"B. Davison, Quarterly Journal of Mathematics 68 (2017) 635–703."},"department":[{"_id":"TaHa"}],"date_updated":"2021-01-12T08:09:24Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"text":"Pursuing the similarity between the Kontsevich-Soibelman construction of the cohomological Hall algebra (CoHA) of BPS states and Lusztig's construction of canonical bases for quantum enveloping algebras, and the similarity between the integrality conjecture for motivic Donaldson-Thomas invariants and the PBW theorem for quantum enveloping algebras, we build a coproduct on the CoHA associated to a quiver with potential. We also prove a cohomological dimensional reduction theorem, further linking a special class of CoHAs with Yangians, and explaining how to connect the study of character varieties with the study of CoHAs.","lang":"eng"}],"title":"The critical CoHA of a quiver with potential","date_published":"2017-06-01T00:00:00Z","publisher":"Oxford University Press","_id":"687","type":"journal_article","date_created":"2018-12-11T11:47:55Z","publication_identifier":{"issn":["00335606"]},"status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1311.7172"}],"ec_funded":1,"oa_version":"Submitted Version","project":[{"call_identifier":"FP7","name":"Arithmetic and physics of Higgs moduli spaces","grant_number":"320593","_id":"25E549F4-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","author":[{"orcid":"0000-0002-8944-4390","last_name":"Davison","first_name":"Ben","full_name":"Davison, Ben","id":"4634AB1E-F248-11E8-B48F-1D18A9856A87"}],"issue":"2","month":"06","volume":68,"language":[{"iso":"eng"}]},{"abstract":[{"text":"We show that the framework of topological data analysis can be extended from metrics to general Bregman divergences, widening the scope of possible applications. Examples are the Kullback - Leibler divergence, which is commonly used for comparing text and images, and the Itakura - Saito divergence, popular for speech and sound. In particular, we prove that appropriately generalized čech and Delaunay (alpha) complexes capture the correct homotopy type, namely that of the corresponding union of Bregman balls. Consequently, their filtrations give the correct persistence diagram, namely the one generated by the uniformly growing Bregman balls. Moreover, we show that unlike the metric setting, the filtration of Vietoris-Rips complexes may fail to approximate the persistence diagram. We propose algorithms to compute the thus generalized čech, Vietoris-Rips and Delaunay complexes and experimentally test their efficiency. Lastly, we explain their surprisingly good performance by making a connection with discrete Morse theory. 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Presented at the Symposium on Computational Geometry, SoCG, Brisbane, Australia: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2017.39\">https://doi.org/10.4230/LIPIcs.SoCG.2017.39</a>","ama":"Edelsbrunner H, Wagner H. Topological data analysis with Bregman divergences. In: Vol 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017:391-3916. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2017.39\">10.4230/LIPIcs.SoCG.2017.39</a>","ista":"Edelsbrunner H, Wagner H. 2017. Topological data analysis with Bregman divergences. Symposium on Computational Geometry, SoCG, LIPIcs, vol. 77, 391–3916.","chicago":"Edelsbrunner, Herbert, and Hubert Wagner. “Topological Data Analysis with Bregman Divergences,” 77:391–3916. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2017.39\">https://doi.org/10.4230/LIPIcs.SoCG.2017.39</a>.","ieee":"H. Edelsbrunner and H. Wagner, “Topological data analysis with Bregman divergences,” presented at the Symposium on Computational Geometry, SoCG, Brisbane, Australia, 2017, vol. 77, pp. 391–3916."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"alternative_title":["LIPIcs"],"scopus_import":1,"intvolume":"        77","publist_id":"7021","oa":1,"day":"01","doi":"10.4230/LIPIcs.SoCG.2017.39","page":"391-3916","year":"2017","has_accepted_license":"1","month":"06","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:47:42Z","date_created":"2018-12-12T10:11:03Z","file_name":"IST-2017-895-v1+1_LIPIcs-SoCG-2017-39.pdf","relation":"main_file","creator":"system","file_id":"4856","checksum":"067ab0cb3f962bae6c3af6bf0094e0f3","file_size":990546,"access_level":"open_access"}],"language":[{"iso":"eng"}],"volume":77,"quality_controlled":"1","oa_version":"Published Version","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833"},{"id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Hubert","last_name":"Wagner","first_name":"Hubert"}],"pubrep_id":"895","conference":{"end_date":"2017-07-07","start_date":"2017-07-04","name":"Symposium on Computational Geometry, SoCG","location":"Brisbane, Australia"},"date_created":"2018-12-11T11:47:56Z","_id":"688","type":"conference","publication_identifier":{"issn":["18688969"]},"status":"public"},{"author":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:09:29Z","department":[{"_id":"GaNo"}],"quality_controlled":"1","oa_version":"None","citation":{"apa":"Novarino, G. (2017). Rett syndrome modeling goes simian. <i>Science Translational Medicine</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/scitranslmed.aan8196\">https://doi.org/10.1126/scitranslmed.aan8196</a>","chicago":"Novarino, Gaia. “Rett Syndrome Modeling Goes Simian.” <i>Science Translational Medicine</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/scitranslmed.aan8196\">https://doi.org/10.1126/scitranslmed.aan8196</a>.","ama":"Novarino G. Rett syndrome modeling goes simian. <i>Science Translational Medicine</i>. 2017;9(393). doi:<a href=\"https://doi.org/10.1126/scitranslmed.aan8196\">10.1126/scitranslmed.aan8196</a>","ista":"Novarino G. 2017. Rett syndrome modeling goes simian. Science Translational Medicine. 9(393), eaan8196.","ieee":"G. Novarino, “Rett syndrome modeling goes simian,” <i>Science Translational Medicine</i>, vol. 9, no. 393. American Association for the Advancement of Science, 2017.","short":"G. Novarino, Science Translational Medicine 9 (2017).","mla":"Novarino, Gaia. “Rett Syndrome Modeling Goes Simian.” <i>Science Translational Medicine</i>, vol. 9, no. 393, eaan8196, American Association for the Advancement of Science, 2017, doi:<a href=\"https://doi.org/10.1126/scitranslmed.aan8196\">10.1126/scitranslmed.aan8196</a>."},"date_published":"2017-06-07T00:00:00Z","publisher":"American Association for the Advancement of Science","language":[{"iso":"eng"}],"title":"Rett syndrome modeling goes simian","volume":9,"abstract":[{"text":"Rett syndrome modeling in monkey mirrors the human disorder.","lang":"eng"}],"publication_status":"published","month":"06","issue":"393","article_number":"eaan8196","doi":"10.1126/scitranslmed.aan8196","status":"public","publication_identifier":{"issn":["19466234"]},"day":"07","year":"2017","date_created":"2018-12-11T11:47:56Z","_id":"689","type":"journal_article","intvolume":"         9","publist_id":"7019","publication":"Science Translational Medicine","scopus_import":1},{"publist_id":"7013","intvolume":"       114","publication":"PNAS","scopus_import":1,"day":"27","page":"E5246 - E5255","doi":"10.1073/pnas.1704470114","year":"2017","oa":1,"pmid":1,"publisher":"National Academy of Sciences","date_published":"2017-06-27T00:00:00Z","file_date_updated":"2020-07-14T12:47:44Z","title":"Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses","publication_status":"published","abstract":[{"text":"Many central synapses contain a single presynaptic active zone and a single postsynaptic density. Vesicular release statistics at such “simple synapses” indicate that they contain a small complement of docking sites where vesicles repetitively dock and fuse. In this work, we investigate functional and morphological aspects of docking sites at simple synapses made between cerebellar parallel fibers and molecular layer interneurons. Using immunogold labeling of SDS-treated freeze-fracture replicas, we find that Cav2.1 channels form several clusters per active zone with about nine channels per cluster. The mean value and range of intersynaptic variation are similar for Cav2.1 cluster numbers and for functional estimates of docking-site numbers obtained from the maximum numbers of released vesicles per action potential. Both numbers grow in relation with synaptic size and decrease by a similar extent with age between 2 wk and 4 wk postnatal. Thus, the mean docking-site numbers were 3.15 at 2 wk (range: 1–10) and 2.03 at 4 wk (range: 1–4), whereas the mean numbers of Cav2.1 clusters were 2.84 at 2 wk (range: 1–8) and 2.37 at 4 wk (range: 1–5). These changes were accompanied by decreases of miniature current amplitude (from 93 pA to 56 pA), active-zone surface area (from 0.0427 μm2 to 0.0234 μm2), and initial success rate (from 0.609 to 0.353), indicating a tightening of synaptic transmission with development. Altogether, these results suggest a close correspondence between the number of functionally defined vesicular docking sites and that of clusters of voltage-gated calcium channels. ","lang":"eng"}],"ddc":["570"],"external_id":{"pmid":["28607047"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"date_updated":"2023-02-23T12:54:57Z","citation":{"short":"T. Miki, W. Kaufmann, G. Malagon, L. Gomez, K. Tabuchi, M. Watanabe, R. Shigemoto, A. Marty, PNAS 114 (2017) E5246–E5255.","mla":"Miki, Takafumi, et al. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” <i>PNAS</i>, vol. 114, no. 26, National Academy of Sciences, 2017, pp. E5246–55, doi:<a href=\"https://doi.org/10.1073/pnas.1704470114\">10.1073/pnas.1704470114</a>.","ieee":"T. Miki <i>et al.</i>, “Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses,” <i>PNAS</i>, vol. 114, no. 26. National Academy of Sciences, pp. E5246–E5255, 2017.","apa":"Miki, T., Kaufmann, W., Malagon, G., Gomez, L., Tabuchi, K., Watanabe, M., … Marty, A. (2017). Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1704470114\">https://doi.org/10.1073/pnas.1704470114</a>","chicago":"Miki, Takafumi, Walter Kaufmann, Gerardo Malagon, Laura Gomez, Katsuhiko Tabuchi, Masahiko Watanabe, Ryuichi Shigemoto, and Alain Marty. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1704470114\">https://doi.org/10.1073/pnas.1704470114</a>.","ista":"Miki T, Kaufmann W, Malagon G, Gomez L, Tabuchi K, Watanabe M, Shigemoto R, Marty A. 2017. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. 114(26), E5246–E5255.","ama":"Miki T, Kaufmann W, Malagon G, et al. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. <i>PNAS</i>. 2017;114(26):E5246-E5255. doi:<a href=\"https://doi.org/10.1073/pnas.1704470114\">10.1073/pnas.1704470114</a>"},"status":"public","publication_identifier":{"issn":["00278424"]},"date_created":"2018-12-11T11:47:57Z","_id":"693","type":"journal_article","language":[{"iso":"eng"}],"volume":114,"article_processing_charge":"Yes (in subscription journal)","month":"06","has_accepted_license":"1","file":[{"relation":"main_file","file_size":2721544,"access_level":"open_access","creator":"kschuh","checksum":"2ab75d554f3df4a34d20fa8040589b7e","file_id":"7223","date_updated":"2020-07-14T12:47:44Z","date_created":"2020-01-03T13:27:29Z","content_type":"application/pdf","file_name":"2017_PNAS_Miki.pdf"}],"issue":"26","author":[{"first_name":"Takafumi","last_name":"Miki","full_name":"Miki, Takafumi"},{"full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","first_name":"Walter","last_name":"Kaufmann"},{"full_name":"Malagon, Gerardo","first_name":"Gerardo","last_name":"Malagon"},{"full_name":"Gomez, Laura","last_name":"Gomez","first_name":"Laura"},{"first_name":"Katsuhiko","last_name":"Tabuchi","full_name":"Tabuchi, Katsuhiko"},{"full_name":"Watanabe, Masahiko","first_name":"Masahiko","last_name":"Watanabe"},{"orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alain","last_name":"Marty","full_name":"Marty, Alain"}],"quality_controlled":"1","oa_version":"Published Version"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["28515231"]},"citation":{"ieee":"A. Veß <i>et al.</i>, “A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity,” <i>Journal of Cell Science</i>, vol. 130, no. 13. Company of Biologists, pp. 2172–2184, 2017.","ama":"Veß A, Blache U, Leitner L, et al. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. <i>Journal of Cell Science</i>. 2017;130(13):2172-2184. doi:<a href=\"https://doi.org/10.1242/jcs.200899\">10.1242/jcs.200899</a>","ista":"Veß A, Blache U, Leitner L, Kurz A, Ehrenpfordt A, Sixt MK, Posern G. 2017. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. 130(13), 2172–2184.","chicago":"Veß, Astrid, Ulrich Blache, Laura Leitner, Angela Kurz, Anja Ehrenpfordt, Michael K Sixt, and Guido Posern. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” <i>Journal of Cell Science</i>. Company of Biologists, 2017. <a href=\"https://doi.org/10.1242/jcs.200899\">https://doi.org/10.1242/jcs.200899</a>.","apa":"Veß, A., Blache, U., Leitner, L., Kurz, A., Ehrenpfordt, A., Sixt, M. K., &#38; Posern, G. (2017). A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. <i>Journal of Cell Science</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.200899\">https://doi.org/10.1242/jcs.200899</a>","short":"A. Veß, U. Blache, L. Leitner, A. Kurz, A. Ehrenpfordt, M.K. Sixt, G. Posern, Journal of Cell Science 130 (2017) 2172–2184.","mla":"Veß, Astrid, et al. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” <i>Journal of Cell Science</i>, vol. 130, no. 13, Company of Biologists, 2017, pp. 2172–84, doi:<a href=\"https://doi.org/10.1242/jcs.200899\">10.1242/jcs.200899</a>."},"date_updated":"2021-01-12T08:09:41Z","department":[{"_id":"MiSi"}],"title":"A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity","publisher":"Company of Biologists","file_date_updated":"2020-07-14T12:47:45Z","date_published":"2017-07-01T00:00:00Z","pmid":1,"ddc":["570"],"abstract":[{"text":"A change regarding the extent of adhesion - hereafter referred to as adhesion plasticity - between adhesive and less-adhesive states of mammalian cells is important for their behavior. To investigate adhesion plasticity, we have selected a stable isogenic subpopulation of human MDA-MB-468 breast carcinoma cells growing in suspension. These suspension cells are unable to re-adhere to various matrices or to contract three-dimensional collagen lattices. By using transcriptome analysis, we identified the focal adhesion protein tensin3 (Tns3) as a determinant of adhesion plasticity. Tns3 is strongly reduced at mRNA and protein levels in suspension cells. Furthermore, by transiently challenging breast cancer cells to grow under non-adherent conditions markedly reduces Tns3 protein expression, which is regained upon re-adhesion. Stable knockdown of Tns3 in parental MDA-MB-468 cells results in defective adhesion, spreading and migration. Tns3-knockdown cells display impaired structure and dynamics of focal adhesion complexes as determined by immunostaining. Restoration of Tns3 protein expression in suspension cells partially rescues adhesion and focal contact composition. Our work identifies Tns3 as a crucial focal adhesion component regulated by, and functionally contributing to, the switch between adhesive and non-adhesive states in MDA-MB-468 cancer cells.","lang":"eng"}],"publication_status":"published","day":"01","year":"2017","doi":"10.1242/jcs.200899","page":"2172 - 2184","oa":1,"publication":"Journal of Cell Science","intvolume":"       130","publist_id":"7008","scopus_import":1,"author":[{"full_name":"Veß, Astrid","first_name":"Astrid","last_name":"Veß"},{"full_name":"Blache, Ulrich","last_name":"Blache","first_name":"Ulrich"},{"first_name":"Laura","last_name":"Leitner","full_name":"Leitner, Laura"},{"full_name":"Kurz, Angela","first_name":"Angela","last_name":"Kurz"},{"first_name":"Anja","last_name":"Ehrenpfordt","full_name":"Ehrenpfordt, Anja"},{"last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"first_name":"Guido","last_name":"Posern","full_name":"Posern, Guido"}],"oa_version":"Published Version","quality_controlled":"1","volume":130,"language":[{"iso":"eng"}],"issue":"13","file":[{"date_updated":"2020-07-14T12:47:45Z","date_created":"2019-10-24T09:43:56Z","content_type":"application/pdf","file_name":"2017_CellScience_Vess.pdf","relation":"main_file","file_size":10847596,"access_level":"open_access","creator":"dernst","file_id":"6966","checksum":"42c81a0a4fc3128883b391c3af3f74bc"}],"month":"07","has_accepted_license":"1","publication_identifier":{"issn":["00219533"]},"status":"public","_id":"694","type":"journal_article","article_type":"original","date_created":"2018-12-11T11:47:58Z"},{"oa_version":"Published Version","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"author":[{"orcid":"0000-0002-2519-8004","first_name":"Marta","last_name":"Lukacisinova","full_name":"Lukacisinova, Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sebastian","last_name":"Novak","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"},{"last_name":"Paixao","first_name":"Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago"}],"article_number":"e1005609","file":[{"file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:47:46Z","date_created":"2018-12-12T10:15:01Z","creator":"system","checksum":"9143c290fa6458ed2563bff4b295554a","file_id":"5117","file_size":3775716,"access_level":"open_access","relation":"main_file"}],"issue":"7","has_accepted_license":"1","month":"07","volume":13,"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","_id":"696","date_created":"2018-12-11T11:47:58Z","status":"public","publication_identifier":{"issn":["1553734X"]},"pubrep_id":"894","ec_funded":1,"citation":{"mla":"Lukacisinova, Marta, et al. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” <i>PLoS Computational Biology</i>, vol. 13, no. 7, e1005609, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">10.1371/journal.pcbi.1005609</a>.","short":"M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017).","apa":"Lukacisinova, M., Novak, S., &#38; Paixao, T. (2017). Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">https://doi.org/10.1371/journal.pcbi.1005609</a>","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 13(7), e1005609.","ama":"Lukacisinova M, Novak S, Paixao T. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. <i>PLoS Computational Biology</i>. 2017;13(7). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">10.1371/journal.pcbi.1005609</a>","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” <i>PLoS Computational Biology</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">https://doi.org/10.1371/journal.pcbi.1005609</a>.","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes,” <i>PLoS Computational Biology</i>, vol. 13, no. 7. Public Library of Science, 2017."},"department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"date_updated":"2024-03-25T23:30:14Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"publication_status":"published","abstract":[{"text":"Mutator strains are expected to evolve when the availability and effect of beneficial mutations are high enough to counteract the disadvantage from deleterious mutations that will inevitably accumulate. As the population becomes more adapted to its environment, both availability and effect of beneficial mutations necessarily decrease and mutation rates are predicted to decrease. It has been shown that certain molecular mechanisms can lead to increased mutation rates when the organism finds itself in a stressful environment. While this may be a correlated response to other functions, it could also be an adaptive mechanism, raising mutation rates only when it is most advantageous. Here, we use a mathematical model to investigate the plausibility of the adaptive hypothesis. We show that such a mechanism can be mantained if the population is subjected to diverse stresses. By simulating various antibiotic treatment schemes, we find that combination treatments can reduce the effectiveness of second-order selection on stress-induced mutagenesis. We discuss the implications of our results to strategies of antibiotic therapy.","lang":"eng"}],"title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","publisher":"Public Library of Science","date_published":"2017-07-18T00:00:00Z","file_date_updated":"2020-07-14T12:47:46Z","oa":1,"day":"18","doi":"10.1371/journal.pcbi.1005609","year":"2017","scopus_import":1,"related_material":{"record":[{"status":"public","id":"9849","relation":"research_data"},{"relation":"research_data","id":"9850","status":"public"},{"relation":"research_data","id":"9851","status":"public"},{"status":"public","relation":"research_data","id":"9852"},{"status":"public","relation":"dissertation_contains","id":"6263"}]},"publication":"PLoS Computational Biology","publist_id":"7004","intvolume":"        13"},{"day":"01","year":"2017","doi":"10.4230/LIPIcs.ICALP.2017.39","oa":1,"publist_id":"7003","intvolume":"        80","scopus_import":1,"alternative_title":["LIPIcs"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrPi"}],"date_updated":"2021-01-12T08:11:15Z","citation":{"ista":"Pietrzak KZ, Skórski M. 2017. Non uniform attacks against pseudoentropy. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 80, 39.","ama":"Pietrzak KZ, Skórski M. Non uniform attacks against pseudoentropy. In: Vol 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2017.39\">10.4230/LIPIcs.ICALP.2017.39</a>","chicago":"Pietrzak, Krzysztof Z, and Maciej Skórski. “Non Uniform Attacks against Pseudoentropy,” Vol. 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2017.39\">https://doi.org/10.4230/LIPIcs.ICALP.2017.39</a>.","apa":"Pietrzak, K. Z., &#38; Skórski, M. (2017). Non uniform attacks against pseudoentropy (Vol. 80). Presented at the ICALP: International Colloquium on Automata, Languages, and Programming, Warsaw, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2017.39\">https://doi.org/10.4230/LIPIcs.ICALP.2017.39</a>","ieee":"K. Z. Pietrzak and M. Skórski, “Non uniform attacks against pseudoentropy,” presented at the ICALP: International Colloquium on Automata, Languages, and Programming, Warsaw, Poland, 2017, vol. 80.","mla":"Pietrzak, Krzysztof Z., and Maciej Skórski. <i>Non Uniform Attacks against Pseudoentropy</i>. Vol. 80, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2017.39\">10.4230/LIPIcs.ICALP.2017.39</a>.","short":"K.Z. Pietrzak, M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017."},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file_date_updated":"2020-07-14T12:47:46Z","date_published":"2017-07-01T00:00:00Z","title":"Non uniform attacks against pseudoentropy","publication_status":"published","abstract":[{"text":"De, Trevisan and Tulsiani [CRYPTO 2010] show that every distribution over n-bit strings which has constant statistical distance to uniform (e.g., the output of a pseudorandom generator mapping n-1 to n bit strings), can be distinguished from the uniform distribution with advantage epsilon by a circuit of size O( 2^n epsilon^2). We generalize this result, showing that a distribution which has less than k bits of min-entropy, can be distinguished from any distribution with k bits of delta-smooth min-entropy with advantage epsilon by a circuit of size O(2^k epsilon^2/delta^2). As a special case, this implies that any distribution with support at most 2^k (e.g., the output of a pseudoentropy generator mapping k to n bit strings) can be distinguished from any given distribution with min-entropy k+1 with advantage epsilon by a circuit of size O(2^k epsilon^2). Our result thus shows that pseudoentropy distributions face basically the same non-uniform attacks as pseudorandom distributions. ","lang":"eng"}],"ddc":["005"],"status":"public","publication_identifier":{"issn":["18688969"]},"date_created":"2018-12-11T11:47:59Z","type":"conference","_id":"697","conference":{"end_date":"2017-07-14","start_date":"2017-07-10","name":"ICALP: International Colloquium on Automata, Languages, and Programming","location":"Warsaw, Poland"},"ec_funded":1,"pubrep_id":"893","author":[{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak"},{"last_name":"Skórski","first_name":"Maciej","full_name":"Skórski, Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD"}],"quality_controlled":"1","project":[{"call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"volume":80,"month":"07","has_accepted_license":"1","article_number":"39","file":[{"relation":"main_file","access_level":"open_access","file_size":601004,"file_id":"4701","checksum":"e95618a001692f1af2d68f5fde43bc1f","creator":"system","date_created":"2018-12-12T10:08:40Z","date_updated":"2020-07-14T12:47:46Z","content_type":"application/pdf","file_name":"IST-2017-893-v1+1_LIPIcs-ICALP-2017-39.pdf"}]},{"year":"2017","day":"07","doi":"10.1091/mbc.E16-12-0825","page":"1997 - 2009","oa":1,"publication":"Molecular Biology of the Cell","intvolume":"        28","publist_id":"7001","scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"citation":{"ieee":"Y. Wang, M. Nagarajan, C. Uhler, and G. Shivashankar, “Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression,” <i>Molecular Biology of the Cell</i>, vol. 28, no. 14. American Society for Cell Biology, pp. 1997–2009, 2017.","apa":"Wang, Y., Nagarajan, M., Uhler, C., &#38; Shivashankar, G. (2017). Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. <i>Molecular Biology of the Cell</i>. American Society for Cell Biology. <a href=\"https://doi.org/10.1091/mbc.E16-12-0825\">https://doi.org/10.1091/mbc.E16-12-0825</a>","ama":"Wang Y, Nagarajan M, Uhler C, Shivashankar G. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. <i>Molecular Biology of the Cell</i>. 2017;28(14):1997-2009. doi:<a href=\"https://doi.org/10.1091/mbc.E16-12-0825\">10.1091/mbc.E16-12-0825</a>","chicago":"Wang, Yejun, Mallika Nagarajan, Caroline Uhler, and Gv Shivashankar. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” <i>Molecular Biology of the Cell</i>. American Society for Cell Biology, 2017. <a href=\"https://doi.org/10.1091/mbc.E16-12-0825\">https://doi.org/10.1091/mbc.E16-12-0825</a>.","ista":"Wang Y, Nagarajan M, Uhler C, Shivashankar G. 2017. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. 28(14), 1997–2009.","short":"Y. Wang, M. Nagarajan, C. Uhler, G. Shivashankar, Molecular Biology of the Cell 28 (2017) 1997–2009.","mla":"Wang, Yejun, et al. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” <i>Molecular Biology of the Cell</i>, vol. 28, no. 14, American Society for Cell Biology, 2017, pp. 1997–2009, doi:<a href=\"https://doi.org/10.1091/mbc.E16-12-0825\">10.1091/mbc.E16-12-0825</a>."},"date_updated":"2021-01-12T08:11:17Z","department":[{"_id":"CaUh"}],"title":"Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression","file_date_updated":"2020-07-14T12:47:46Z","date_published":"2017-07-07T00:00:00Z","publisher":"American Society for Cell Biology","ddc":["519"],"abstract":[{"lang":"eng","text":"Extracellular matrix signals from the microenvironment regulate gene expression patterns and cell behavior. Using a combination of experiments and geometric models, we demonstrate correlations between cell geometry, three-dimensional (3D) organization of chromosome territories, and gene expression. Fluorescence in situ hybridization experiments showed that micropatterned fibroblasts cultured on anisotropic versus isotropic substrates resulted in repositioning of specific chromosomes, which contained genes that were differentially regulated by cell geometries. Experiments combined with ellipsoid packing models revealed that the mechanosensitivity of chromosomes was correlated with their orientation in the nucleus. Transcription inhibition experiments suggested that the intermingling degree was more sensitive to global changes in transcription than to chromosome radial positioning and its orientations. These results suggested that cell geometry modulated 3D chromosome arrangement, and their neighborhoods correlated with gene expression patterns in a predictable manner. This is central to understanding geometric control of genetic programs involved in cellular homeostasis and the associated diseases. "}],"publication_status":"published","status":"public","publication_identifier":{"issn":["10591524"]},"_id":"698","type":"journal_article","date_created":"2018-12-11T11:47:59Z","pubrep_id":"892","author":[{"full_name":"Wang, Yejun","first_name":"Yejun","last_name":"Wang"},{"first_name":"Mallika","last_name":"Nagarajan","full_name":"Nagarajan, Mallika"},{"full_name":"Uhler, Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","first_name":"Caroline","last_name":"Uhler"},{"last_name":"Shivashankar","first_name":"Gv","full_name":"Shivashankar, Gv"}],"oa_version":"Published Version","project":[{"call_identifier":"FWF","name":"Gaussian Graphical Models: Theory and Applications","grant_number":"Y 903-N35","_id":"2530CA10-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","volume":28,"language":[{"iso":"eng"}],"issue":"14","file":[{"file_name":"IST-2017-892-v1+1_Mol._Biol._Cell-2017-Wang-1997-2009.pdf","date_updated":"2020-07-14T12:47:46Z","date_created":"2018-12-12T10:10:53Z","content_type":"application/pdf","file_size":1086097,"access_level":"open_access","creator":"system","file_id":"4844","checksum":"de01dac9e30970cfa6ae902480a4e04d","relation":"main_file"}],"month":"07","has_accepted_license":"1"},{"intvolume":"       114","publist_id":"7002","publication":"PNAS","scopus_import":1,"day":"03","year":"2017","page":"E5396 - E5405","doi":"10.1073/pnas.1702020114","oa":1,"publisher":"National Academy of Sciences","date_published":"2017-07-03T00:00:00Z","pmid":1,"title":"The red queen and king in finite populations","abstract":[{"text":"In antagonistic symbioses, such as host–parasite interactions, one population’s success is the other’s loss. In mutualistic symbioses, such as division of labor, both parties can gain, but they might have different preferences over the possible mutualistic arrangements. The rates of evolution of the two populations in a symbiosis are important determinants of which population will be more successful: Faster evolution is thought to be favored in antagonistic symbioses (the “Red Queen effect”), but disfavored in certain mutualistic symbioses (the “Red King effect”). However, it remains unclear which biological parameters drive these effects. Here, we analyze the effects of the various determinants of evolutionary rate: generation time, mutation rate, population size, and the intensity of natural selection. Our main results hold for the case where mutation is infrequent. Slower evolution causes a long-term advantage in an important class of mutualistic interactions. Surprisingly, less intense selection is the strongest driver of this Red King effect, whereas relative mutation rates and generation times have little effect. In antagonistic interactions, faster evolution by any means is beneficial. Our results provide insight into the demographic evolution of symbionts. ","lang":"eng"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["28630336"]},"date_updated":"2021-01-12T08:11:21Z","department":[{"_id":"KrCh"}],"citation":{"ieee":"C. Veller, L. Hayward, M. Nowak, and C. Hilbe, “The red queen and king in finite populations,” <i>PNAS</i>, vol. 114, no. 27. National Academy of Sciences, pp. E5396–E5405, 2017.","ama":"Veller C, Hayward L, Nowak M, Hilbe C. The red queen and king in finite populations. <i>PNAS</i>. 2017;114(27):E5396-E5405. doi:<a href=\"https://doi.org/10.1073/pnas.1702020114\">10.1073/pnas.1702020114</a>","ista":"Veller C, Hayward L, Nowak M, Hilbe C. 2017. The red queen and king in finite populations. PNAS. 114(27), E5396–E5405.","chicago":"Veller, Carl, Laura Hayward, Martin Nowak, and Christian Hilbe. “The Red Queen and King in Finite Populations.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1702020114\">https://doi.org/10.1073/pnas.1702020114</a>.","apa":"Veller, C., Hayward, L., Nowak, M., &#38; Hilbe, C. (2017). The red queen and king in finite populations. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1702020114\">https://doi.org/10.1073/pnas.1702020114</a>","mla":"Veller, Carl, et al. “The Red Queen and King in Finite Populations.” <i>PNAS</i>, vol. 114, no. 27, National Academy of Sciences, 2017, pp. E5396–405, doi:<a href=\"https://doi.org/10.1073/pnas.1702020114\">10.1073/pnas.1702020114</a>.","short":"C. Veller, L. Hayward, M. Nowak, C. Hilbe, PNAS 114 (2017) E5396–E5405."},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502615/","open_access":"1"}],"publication_identifier":{"issn":["00278424"]},"status":"public","date_created":"2018-12-11T11:48:00Z","type":"journal_article","_id":"699","language":[{"iso":"eng"}],"volume":114,"month":"07","issue":"27","author":[{"first_name":"Carl","last_name":"Veller","full_name":"Veller, Carl"},{"first_name":"Laura","last_name":"Hayward","full_name":"Hayward, Laura"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"},{"first_name":"Christian","last_name":"Hilbe","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian"}],"quality_controlled":"1","oa_version":"Submitted Version"},{"abstract":[{"lang":"eng","text":"Microtubules provide the mechanical force required for chromosome separation during mitosis. However, little is known about the dynamic (high-frequency) mechanical properties of microtubules. Here, we theoretically propose to control the vibrations of a doubly clamped microtubule by tip electrodes and to detect its motion via the optomechanical coupling between the vibrational modes of the microtubule and an optical cavity. In the presence of a red-detuned strong pump laser, this coupling leads to optomechanical-induced transparency of an optical probe field, which can be detected with state-of-the art technology. The center frequency and line width of the transparency peak give the resonance frequency and damping rate of the microtubule, respectively, while the height of the peak reveals information about the microtubule-cavity field coupling. Our method opens the new possibilities to gain information about the physical properties of microtubules, which will enhance our capability to design physical cancer treatment protocols as alternatives to chemotherapeutic drugs."}],"publication_status":"published","date_published":"2017-07-12T00:00:00Z","publisher":"American Institute of Physics","title":"Optomechanical proposal for monitoring microtubule mechanical vibrations","date_updated":"2023-02-23T12:56:35Z","department":[{"_id":"JoFi"}],"citation":{"ieee":"S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, and C. Simon, “Optomechanical proposal for monitoring microtubule mechanical vibrations,” <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>, vol. 96, no. 1. American Institute of Physics, 2017.","apa":"Barzanjeh, S., Salari, V., Tuszynski, J., Cifra, M., &#38; Simon, C. (2017). Optomechanical proposal for monitoring microtubule mechanical vibrations. <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.96.012404\">https://doi.org/10.1103/PhysRevE.96.012404</a>","ista":"Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. 2017. Optomechanical proposal for monitoring microtubule mechanical vibrations.  Physical Review E Statistical Nonlinear and Soft Matter Physics . 96(1), 012404.","chicago":"Barzanjeh, Shabir, Vahid Salari, Jack Tuszynski, Michal Cifra, and Christoph Simon. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>. American Institute of Physics, 2017. <a href=\"https://doi.org/10.1103/PhysRevE.96.012404\">https://doi.org/10.1103/PhysRevE.96.012404</a>.","ama":"Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. Optomechanical proposal for monitoring microtubule mechanical vibrations. <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>. 2017;96(1). doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.012404\">10.1103/PhysRevE.96.012404</a>","short":"S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, C. Simon,  Physical Review E Statistical Nonlinear and Soft Matter Physics  96 (2017).","mla":"Barzanjeh, Shabir, et al. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>, vol. 96, no. 1, 012404, American Institute of Physics, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.012404\">10.1103/PhysRevE.96.012404</a>."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"intvolume":"        96","publist_id":"6997","publication":" Physical Review E Statistical Nonlinear and Soft Matter Physics ","oa":1,"day":"12","year":"2017","doi":"10.1103/PhysRevE.96.012404","month":"07","issue":"1","article_number":"012404","language":[{"iso":"eng"}],"volume":96,"project":[{"name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics","_id":"258047B6-B435-11E9-9278-68D0E5697425","grant_number":"707438","call_identifier":"H2020"}],"quality_controlled":"1","oa_version":"Submitted Version","author":[{"orcid":"0000-0003-0415-1423","last_name":"Barzanjeh","first_name":"Shabir","full_name":"Barzanjeh, Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Salari","first_name":"Vahid","full_name":"Salari, Vahid"},{"first_name":"Jack","last_name":"Tuszynski","full_name":"Tuszynski, Jack"},{"first_name":"Michal","last_name":"Cifra","full_name":"Cifra, Michal"},{"full_name":"Simon, Christoph","last_name":"Simon","first_name":"Christoph"}],"ec_funded":1,"date_created":"2018-12-11T11:48:00Z","type":"journal_article","_id":"700","status":"public","publication_identifier":{"issn":["24700045"]},"main_file_link":[{"url":"https://arxiv.org/pdf/1612.07061.pdf","open_access":"1"}]},{"language":[{"iso":"eng"}],"volume":24,"month":"07","has_accepted_license":"1","issue":"3","file":[{"content_type":"application/pdf","date_created":"2018-12-12T10:14:25Z","date_updated":"2020-07-14T12:47:47Z","file_name":"IST-2018-984-v1+1_Patakova_on_the_nonexistence_of_k-reptile_simplices_in_R_3_and_R_4_2017.pdf","relation":"main_file","file_id":"5077","checksum":"a431e573e31df13bc0f66de3061006ec","creator":"system","access_level":"open_access","file_size":544042}],"author":[{"last_name":"Kynčl","first_name":"Jan","full_name":"Kynčl, Jan"},{"full_name":"Patakova, Zuzana","id":"48B57058-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3975-1683","first_name":"Zuzana","last_name":"Patakova"}],"quality_controlled":"1","oa_version":"Submitted Version","pubrep_id":"984","publication_identifier":{"issn":["10778926"]},"status":"public","date_created":"2018-12-11T11:48:00Z","_id":"701","type":"journal_article","publisher":"International Press","date_published":"2017-07-14T00:00:00Z","file_date_updated":"2020-07-14T12:47:47Z","title":"On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4","abstract":[{"text":"A d-dimensional simplex S is called a k-reptile (or a k-reptile simplex) if it can be tiled by k simplices with disjoint interiors that are all mutually congruent and similar to S. For d = 2, triangular k-reptiles exist for all k of the form a^2, 3a^2 or a^2+b^2 and they have been completely characterized by Snover, Waiveris, and Williams. On the other hand, the only k-reptile simplices that are known for d ≥ 3, have k = m^d, where m is a positive integer. We substantially simplify the proof by Matoušek and the second author that for d = 3, k-reptile tetrahedra can exist only for k = m^3. We then prove a weaker analogue of this result for d = 4 by showing that four-dimensional k-reptile simplices can exist only for k = m^2.","lang":"eng"}],"publication_status":"published","ddc":["500"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:11:28Z","department":[{"_id":"UlWa"}],"citation":{"apa":"Kynčl, J., &#38; Patakova, Z. (2017). On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. <i>The Electronic Journal of Combinatorics</i>. International Press.","chicago":"Kynčl, Jan, and Zuzana Patakova. “On the Nonexistence of k Reptile Simplices in ℝ^3 and ℝ^4.” <i>The Electronic Journal of Combinatorics</i>. International Press, 2017.","ama":"Kynčl J, Patakova Z. On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. <i>The Electronic Journal of Combinatorics</i>. 2017;24(3):1-44.","ista":"Kynčl J, Patakova Z. 2017. On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. The Electronic Journal of Combinatorics. 24(3), 1–44.","ieee":"J. Kynčl and Z. Patakova, “On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4,” <i>The Electronic Journal of Combinatorics</i>, vol. 24, no. 3. International Press, pp. 1–44, 2017.","short":"J. Kynčl, Z. Patakova, The Electronic Journal of Combinatorics 24 (2017) 1–44.","mla":"Kynčl, Jan, and Zuzana Patakova. “On the Nonexistence of k Reptile Simplices in ℝ^3 and ℝ^4.” <i>The Electronic Journal of Combinatorics</i>, vol. 24, no. 3, International Press, 2017, pp. 1–44."},"intvolume":"        24","publist_id":"6996","publication":"The Electronic Journal of Combinatorics","year":"2017","page":"1-44","day":"14","oa":1},{"scopus_import":1,"publication":"Science Translational Medicine","publist_id":"6993","intvolume":"         9","_id":"702","type":"journal_article","date_created":"2018-12-11T11:48:01Z","day":"19","status":"public","year":"2017","publication_identifier":{"issn":["19466234"]},"doi":"10.1126/scitranslmed.aao0972","page":"eaao0972","issue":"399","month":"07","publication_status":"published","abstract":[{"text":"Leading autism-associated mutation in mouse partially mimics human disorder.\r\n\r\n","lang":"eng"}],"volume":9,"title":"The riddle of CHD8 haploinsufficiency in autism spectrum disorder","date_published":"2017-07-19T00:00:00Z","language":[{"iso":"eng"}],"publisher":"American Association for the Advancement of Science","oa_version":"None","citation":{"apa":"Novarino, G. (2017). The riddle of CHD8 haploinsufficiency in autism spectrum disorder. <i>Science Translational Medicine</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/scitranslmed.aao0972\">https://doi.org/10.1126/scitranslmed.aao0972</a>","chicago":"Novarino, Gaia. “The Riddle of CHD8 Haploinsufficiency in Autism Spectrum Disorder.” <i>Science Translational Medicine</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/scitranslmed.aao0972\">https://doi.org/10.1126/scitranslmed.aao0972</a>.","ista":"Novarino G. 2017. The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. 9(399), eaao0972.","ama":"Novarino G. The riddle of CHD8 haploinsufficiency in autism spectrum disorder. <i>Science Translational Medicine</i>. 2017;9(399):eaao0972. doi:<a href=\"https://doi.org/10.1126/scitranslmed.aao0972\">10.1126/scitranslmed.aao0972</a>","ieee":"G. Novarino, “The riddle of CHD8 haploinsufficiency in autism spectrum disorder,” <i>Science Translational Medicine</i>, vol. 9, no. 399. American Association for the Advancement of Science, p. eaao0972, 2017.","mla":"Novarino, Gaia. “The Riddle of CHD8 Haploinsufficiency in Autism Spectrum Disorder.” <i>Science Translational Medicine</i>, vol. 9, no. 399, American Association for the Advancement of Science, 2017, p. eaao0972, doi:<a href=\"https://doi.org/10.1126/scitranslmed.aao0972\">10.1126/scitranslmed.aao0972</a>.","short":"G. Novarino, Science Translational Medicine 9 (2017) eaao0972."},"department":[{"_id":"GaNo"}],"quality_controlled":"1","date_updated":"2021-01-12T08:11:31Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-7673-7178","last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}]},{"day":"25","year":"2017","doi":"10.7554/eLife.25100","oa":1,"publist_id":"6990","intvolume":"         6","publication":"eLife","scopus_import":1,"related_material":{"record":[{"id":"5564","relation":"popular_science","status":"public"},{"status":"public","relation":"dissertation_contains","id":"26"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"CaGu"}],"date_updated":"2024-03-25T23:30:14Z","citation":{"short":"M. Steinrück, C.C. Guet, ELife 6 (2017).","mla":"Steinrück, Magdalena, and Calin C. Guet. “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” <i>ELife</i>, vol. 6, e25100, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/eLife.25100\">10.7554/eLife.25100</a>.","ista":"Steinrück M, Guet CC. 2017. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. eLife. 6, e25100.","chicago":"Steinrück, Magdalena, and Calin C Guet. “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/eLife.25100\">https://doi.org/10.7554/eLife.25100</a>.","ama":"Steinrück M, Guet CC. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/eLife.25100\">10.7554/eLife.25100</a>","apa":"Steinrück, M., &#38; Guet, C. C. (2017). Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.25100\">https://doi.org/10.7554/eLife.25100</a>","ieee":"M. Steinrück and C. C. Guet, “Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017."},"publisher":"eLife Sciences Publications","file_date_updated":"2020-07-14T12:47:48Z","date_published":"2017-07-25T00:00:00Z","title":"Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection","publication_status":"published","abstract":[{"text":"How the organization of genes on a chromosome shapes adaptation is essential for understanding evolutionary paths. Here, we investigate how adaptation to rapidly increasing levels of antibiotic depends on the chromosomal neighborhood of a drug-resistance gene inserted at different positions of the Escherichia coli chromosome. Using a dual-fluorescence reporter that allows us to distinguish gene amplifications from other up-mutations, we track in real-time adaptive changes in expression of the drug-resistance gene. We find that the relative contribution of several mutation types differs systematically between loci due to properties of neighboring genes: essentiality, expression, orientation, termination, and presence of duplicates. These properties determine rate and fitness effects of gene amplification, deletions, and mutations compromising transcriptional termination. Thus, the adaptive potential of a gene under selection is a system-property with a complex genetic basis that is specific for each chromosomal locus, and it can be inferred from detailed functional and genomic data.","lang":"eng"}],"ddc":["576"],"status":"public","publication_identifier":{"issn":["2050084X"]},"date_created":"2018-12-11T11:48:01Z","_id":"704","type":"journal_article","pubrep_id":"890","author":[{"id":"2C023F40-F248-11E8-B48F-1D18A9856A87","full_name":"Steinrück, Magdalena","last_name":"Steinrück","first_name":"Magdalena","orcid":"0000-0003-1229-9719"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052"}],"quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"volume":6,"month":"07","has_accepted_license":"1","file":[{"relation":"main_file","access_level":"open_access","file_size":2092088,"file_id":"4975","checksum":"6b908b5db9f61f6820ebd7f8fa815571","creator":"system","date_created":"2018-12-12T10:12:54Z","date_updated":"2020-07-14T12:47:48Z","content_type":"application/pdf","file_name":"IST-2017-890-v1+1_elife-25100-v1.pdf"},{"date_created":"2018-12-12T10:12:55Z","date_updated":"2020-07-14T12:47:48Z","content_type":"application/pdf","file_name":"IST-2017-890-v1+2_elife-25100-figures-v1.pdf","relation":"main_file","access_level":"open_access","file_size":3428681,"checksum":"ca21530389b720243552678125fdba35","file_id":"4976","creator":"system"}],"article_number":"e25100"}]