[{"title":"Computing the M most probable modes of a graphical model","oa":1,"main_file_link":[{"url":"http://jmlr.org/proceedings/papers/v31/chen13a.html","open_access":"1"}],"type":"conference","publication":"Proceedings of the 16th International Conference on Artificial Intelligence and Statistics","author":[{"full_name":"Chen, Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","first_name":"Chao"},{"first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir"},{"last_name":"Yan","full_name":"Yan, Zhu","first_name":"Zhu"},{"last_name":"Metaxas","full_name":"Metaxas, Dimitris","first_name":"Dimitris"},{"full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph"}],"conference":{"start_date":"2013-04-29","name":"AISTATS: Conference on Uncertainty in Artificial Intelligence","end_date":"2013-05-01","location":"Scottsdale, AZ, United States"},"scopus_import":"1","quality_controlled":"1","date_created":"2018-12-11T12:00:14Z","article_processing_charge":"No","month":"01","page":"161 - 169","volume":31,"language":[{"iso":"eng"}],"department":[{"_id":"HeEd"},{"_id":"VlKo"},{"_id":"ChLa"}],"publication_status":"published","date_published":"2013-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":" We introduce the M-modes problem for graphical models: predicting the M label configurations of highest probability that are at the same time local maxima of the probability landscape. M-modes have multiple possible applications: because they are intrinsically diverse, they provide a principled alternative to non-maximum suppression techniques for structured prediction, they can act as codebook vectors for quantizing the configuration space, or they can form component centers for mixture model approximation. We present two algorithms for solving the M-modes problem. The first algorithm solves the problem in polynomial time when the underlying graphical model is a simple chain. The second algorithm solves the problem for junction chains. In synthetic and real dataset, we demonstrate how M-modes can improve the performance of prediction. We also use the generated modes as a tool to understand the topography of the probability distribution of configurations, for example with relation to the training set size and amount of noise in the data. ","lang":"eng"}],"publist_id":"3846","date_updated":"2026-07-06T13:43:58Z","alternative_title":["PMLR"],"intvolume":"        31","day":"01","das_tickbox":"1","year":"2013","citation":{"short":"C. Chen, V. Kolmogorov, Z. Yan, D. Metaxas, C. Lampert, in:, Proceedings of the 16th International Conference on Artificial Intelligence and Statistics, Journal of Machine Learning Research, 2013, pp. 161–169.","mla":"Chen, Chao, et al. “Computing the M Most Probable Modes of a Graphical Model.” <i>Proceedings of the 16th International Conference on Artificial Intelligence and Statistics</i>, vol. 31, Journal of Machine Learning Research, 2013, pp. 161–69.","chicago":"Chen, Chao, Vladimir Kolmogorov, Zhu Yan, Dimitris Metaxas, and Christoph Lampert. “Computing the M Most Probable Modes of a Graphical Model.” In <i>Proceedings of the 16th International Conference on Artificial Intelligence and Statistics</i>, 31:161–69. Journal of Machine Learning Research, 2013.","apa":"Chen, C., Kolmogorov, V., Yan, Z., Metaxas, D., &#38; Lampert, C. (2013). Computing the M most probable modes of a graphical model. In <i>Proceedings of the 16th International Conference on Artificial Intelligence and Statistics</i> (Vol. 31, pp. 161–169). Scottsdale, AZ, United States: Journal of Machine Learning Research.","ieee":"C. Chen, V. Kolmogorov, Z. Yan, D. Metaxas, and C. Lampert, “Computing the M most probable modes of a graphical model,” in <i>Proceedings of the 16th International Conference on Artificial Intelligence and Statistics</i>, Scottsdale, AZ, United States, 2013, vol. 31, pp. 161–169.","ista":"Chen C, Kolmogorov V, Yan Z, Metaxas D, Lampert C. 2013. Computing the M most probable modes of a graphical model. Proceedings of the 16th International Conference on Artificial Intelligence and Statistics. AISTATS: Conference on Uncertainty in Artificial Intelligence, PMLR, vol. 31, 161–169.","ama":"Chen C, Kolmogorov V, Yan Z, Metaxas D, Lampert C. Computing the M most probable modes of a graphical model. In: <i>Proceedings of the 16th International Conference on Artificial Intelligence and Statistics</i>. Vol 31. Journal of Machine Learning Research; 2013:161-169."},"publisher":"Journal of Machine Learning Research","_id":"2901","status":"public","oa_version":"None"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Models of neural responses to stimuli with complex spatiotemporal correlation structure often assume that neurons are selective for only a small number of linear projections of a potentially high-dimensional input. In this review, we explore recent modeling approaches where the neural response depends on the quadratic form of the input rather than on its linear projection, that is, the neuron is sensitive to the local covariance structure of the signal preceding the spike. To infer this quadratic dependence in the presence of arbitrary (e.g., naturalistic) stimulus distribution, we review several inference methods, focusing in particular on two information theory–based approaches (maximization of stimulus energy and of noise entropy) and two likelihood-based approaches (Bayesian spike-triggered covariance and extensions of generalized linear models). We analyze the formal relationship between the likelihood-based and information-based approaches to demonstrate how they lead to consistent inference. We demonstrate the practical feasibility of these procedures by using model neurons responding to a flickering variance stimulus."}],"date_updated":"2026-07-06T13:45:52Z","publist_id":"3983","date_published":"2013-07-01T00:00:00Z","fulldoi":"https://doi.org/10.1162/NECO_a_00463","isi":1,"arxiv":1,"das_tickbox":"1","day":"01","publisher":"MIT Press","citation":{"short":"K. Rajan, O. Marre, G. Tkačik, Neural Computation 25 (2013) 1661–1692.","mla":"Rajan, Kanaka, et al. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.” <i>Neural Computation</i>, vol. 25, no. 7, MIT Press, 2013, pp. 1661–92, doi:<a href=\"https://doi.org/10.1162/NECO_a_00463\">10.1162/NECO_a_00463</a>.","chicago":"Rajan, Kanaka, Olivier Marre, and Gašper Tkačik. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.” <i>Neural Computation</i>. MIT Press, 2013. <a href=\"https://doi.org/10.1162/NECO_a_00463\">https://doi.org/10.1162/NECO_a_00463</a>.","apa":"Rajan, K., Marre, O., &#38; Tkačik, G. (2013). Learning quadratic receptive fields from neural responses to natural stimuli. <i>Neural Computation</i>. MIT Press. <a href=\"https://doi.org/10.1162/NECO_a_00463\">https://doi.org/10.1162/NECO_a_00463</a>","ieee":"K. Rajan, O. Marre, and G. Tkačik, “Learning quadratic receptive fields from neural responses to natural stimuli,” <i>Neural Computation</i>, vol. 25, no. 7. MIT Press, pp. 1661–1692, 2013.","ama":"Rajan K, Marre O, Tkačik G. Learning quadratic receptive fields from neural responses to natural stimuli. <i>Neural Computation</i>. 2013;25(7):1661-1692. doi:<a href=\"https://doi.org/10.1162/NECO_a_00463\">10.1162/NECO_a_00463</a>","ista":"Rajan K, Marre O, Tkačik G. 2013. Learning quadratic receptive fields from neural responses to natural stimuli. Neural Computation. 25(7), 1661–1692."},"year":"2013","status":"public","_id":"2818","oa_version":"Preprint","issue":"7","external_id":{"isi":["000319903700001"],"arxiv":["1209.0121"]},"intvolume":"        25","publication":"Neural Computation","author":[{"first_name":"Kanaka","full_name":"Rajan, Kanaka","last_name":"Rajan"},{"last_name":"Marre","full_name":"Marre, Olivier","first_name":"Olivier"},{"last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","first_name":"Gasper"}],"scopus_import":"1","oa":1,"title":"Learning quadratic receptive fields from neural responses to natural stimuli","type":"journal_article","doi":"10.1162/NECO_a_00463","main_file_link":[{"url":"http://arxiv.org/abs/1209.0121","open_access":"1"}],"month":"07","page":"1661 - 1692","publication_status":"published","volume":25,"language":[{"iso":"eng"}],"department":[{"_id":"GaTk"}],"quality_controlled":"1","article_processing_charge":"No","date_created":"2018-12-11T11:59:45Z"},{"_id":"2859","status":"public","oa_version":"Preprint","isi":1,"day":"01","arxiv":1,"das_tickbox":"1","publisher":"International Press of Boston","year":"2013","citation":{"ama":"Bendich P, Edelsbrunner H, Morozov D, Patel A. Homology and robustness of level and interlevel sets. <i>Homology, Homotopy and Applications</i>. 2013;15(1):51-72. doi:<a href=\"https://doi.org/10.4310/HHA.2013.v15.n1.a3\">10.4310/HHA.2013.v15.n1.a3</a>","ista":"Bendich P, Edelsbrunner H, Morozov D, Patel A. 2013. Homology and robustness of level and interlevel sets. Homology, Homotopy and Applications. 15(1), 51–72.","ieee":"P. Bendich, H. Edelsbrunner, D. Morozov, and A. Patel, “Homology and robustness of level and interlevel sets,” <i>Homology, Homotopy and Applications</i>, vol. 15, no. 1. International Press of Boston, pp. 51–72, 2013.","apa":"Bendich, P., Edelsbrunner, H., Morozov, D., &#38; Patel, A. (2013). Homology and robustness of level and interlevel sets. <i>Homology, Homotopy and Applications</i>. International Press of Boston. <a href=\"https://doi.org/10.4310/HHA.2013.v15.n1.a3\">https://doi.org/10.4310/HHA.2013.v15.n1.a3</a>","chicago":"Bendich, Paul, Herbert Edelsbrunner, Dmitriy Morozov, and Amit Patel. “Homology and Robustness of Level and Interlevel Sets.” <i>Homology, Homotopy and Applications</i>. International Press of Boston, 2013. <a href=\"https://doi.org/10.4310/HHA.2013.v15.n1.a3\">https://doi.org/10.4310/HHA.2013.v15.n1.a3</a>.","short":"P. Bendich, H. Edelsbrunner, D. Morozov, A. Patel, Homology, Homotopy and Applications 15 (2013) 51–72.","mla":"Bendich, Paul, et al. “Homology and Robustness of Level and Interlevel Sets.” <i>Homology, Homotopy and Applications</i>, vol. 15, no. 1, International Press of Boston, 2013, pp. 51–72, doi:<a href=\"https://doi.org/10.4310/HHA.2013.v15.n1.a3\">10.4310/HHA.2013.v15.n1.a3</a>."},"issue":"1","external_id":{"arxiv":["1102.3389"],"isi":["000322423600003"]},"intvolume":"        15","date_updated":"2026-07-06T13:38:59Z","publist_id":"3930","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Given a continuous function f:X-R on a topological space, we consider the preimages of intervals and their homology groups and show how to read the ranks of these groups from the extended persistence diagram of f. In addition, we quantify the robustness of the homology classes under perturbations of f using well groups, and we show how to read the ranks of these groups from the same extended persistence diagram. The special case X=R3 has ramifications in the fields of medical imaging and scientific visualization.","lang":"eng"}],"date_published":"2013-05-01T00:00:00Z","fulldoi":"https://doi.org/10.4310/HHA.2013.v15.n1.a3","page":"51 - 72","publication_status":"published","department":[{"_id":"HeEd"}],"volume":15,"language":[{"iso":"eng"}],"month":"05","article_processing_charge":"No","date_created":"2018-12-11T11:59:58Z","quality_controlled":"1","scopus_import":"1","publication":"Homology, Homotopy and Applications","author":[{"first_name":"Paul","full_name":"Bendich, Paul","id":"43F6EC54-F248-11E8-B48F-1D18A9856A87","last_name":"Bendich"},{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","first_name":"Herbert"},{"last_name":"Morozov","full_name":"Morozov, Dmitriy","first_name":"Dmitriy"},{"full_name":"Patel, Amit","id":"34A254A0-F248-11E8-B48F-1D18A9856A87","last_name":"Patel","first_name":"Amit"}],"oa":1,"title":"Homology and robustness of level and interlevel sets","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1102.3389v1"}],"doi":"10.4310/HHA.2013.v15.n1.a3"},{"date_updated":"2026-07-06T13:58:55Z","publist_id":"4655","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The problem of packing ellipsoids of different sizes and shapes into an ellipsoidal container so as to minimize a measure of overlap between ellipsoids is considered. A bilevel optimization formulation is given, together with an algorithm for the general case and a simpler algorithm for the special case in which all ellipsoids are in fact spheres. Convergence results are proved and computational experience is described and illustrated. The motivating application-chromosome organization in the human cell nucleus-is discussed briefly, and some illustrative results are presented.","lang":"eng"}],"date_published":"2013-11-07T00:00:00Z","fulldoi":"https://doi.org/10.1137/120872309","status":"public","_id":"2280","oa_version":"Preprint","das_tickbox":"1","day":"07","arxiv":1,"isi":1,"citation":{"mla":"Uhler, Caroline, and Stephen Wright. “Packing Ellipsoids with Overlap.” <i>SIAM Review</i>, vol. 55, no. 4, Society for Industrial and Applied Mathematics, 2013, pp. 671–706, doi:<a href=\"https://doi.org/10.1137/120872309\">10.1137/120872309</a>.","short":"C. Uhler, S. Wright, SIAM Review 55 (2013) 671–706.","chicago":"Uhler, Caroline, and Stephen Wright. “Packing Ellipsoids with Overlap.” <i>SIAM Review</i>. Society for Industrial and Applied Mathematics, 2013. <a href=\"https://doi.org/10.1137/120872309\">https://doi.org/10.1137/120872309</a>.","apa":"Uhler, C., &#38; Wright, S. (2013). Packing ellipsoids with overlap. <i>SIAM Review</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/120872309\">https://doi.org/10.1137/120872309</a>","ieee":"C. Uhler and S. Wright, “Packing ellipsoids with overlap,” <i>SIAM Review</i>, vol. 55, no. 4. Society for Industrial and Applied Mathematics, pp. 671–706, 2013.","ista":"Uhler C, Wright S. 2013. Packing ellipsoids with overlap. SIAM Review. 55(4), 671–706.","ama":"Uhler C, Wright S. Packing ellipsoids with overlap. <i>SIAM Review</i>. 2013;55(4):671-706. doi:<a href=\"https://doi.org/10.1137/120872309\">10.1137/120872309</a>"},"year":"2013","publisher":"Society for Industrial and Applied Mathematics","external_id":{"arxiv":["1204.0235"],"isi":["000327502800002"]},"issue":"4","intvolume":"        55","scopus_import":"1","publication":"SIAM Review","author":[{"full_name":"Uhler, Caroline","last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","first_name":"Caroline"},{"first_name":"Stephen","full_name":"Wright, Stephen","last_name":"Wright"}],"oa":1,"title":"Packing ellipsoids with overlap","doi":"10.1137/120872309","main_file_link":[{"url":"http://arxiv.org/abs/1204.0235","open_access":"1"}],"type":"journal_article","page":"671 - 706","volume":55,"department":[{"_id":"CaUh"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"11","date_created":"2018-12-11T11:56:44Z","article_processing_charge":"No","quality_controlled":"1"},{"fulldoi":"https://doi.org/10.1186/1471-2148-13-225","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"has_accepted_license":"1","date_published":"2013-10-14T00:00:00Z","abstract":[{"lang":"eng","text":"Background: The brood of ants and other social insects is highly susceptible to pathogens, particularly those that penetrate the soft larval and pupal cuticle. We here test whether the presence of a pupal cocoon, which occurs in some ant species but not in others, affects the sanitary brood care and fungal infection patterns after exposure to the entomopathogenic fungus Metarhizium brunneum. We use a) a comparative approach analysing four species with either naked or cocooned pupae and b) a within-species analysis of a single ant species, in which both pupal types co-exist in the same colony. Results: We found that the presence of a cocoon did not compromise fungal pathogen detection by the ants and that species with cocooned pupae increased brood grooming after pathogen exposure. All tested ant species further removed brood from their nests, which was predominantly expressed towards larvae and naked pupae treated with the live fungal pathogen. In contrast, cocooned pupae exposed to live fungus were not removed at higher rates than cocooned pupae exposed to dead fungus or a sham control. Consistent with this, exposure to the live fungus caused high numbers of infections and fungal outgrowth in larvae and naked pupae, but not in cocooned pupae. Moreover, the ants consistently removed the brood prior to fungal outgrowth, ensuring a clean brood chamber. Conclusion: Our study suggests that the pupal cocoon has a protective effect against fungal infection, causing an adaptive change in sanitary behaviours by the ants. It further demonstrates that brood removal-originally described for honeybees as &quot;hygienic behaviour&quot;-is a widespread sanitary behaviour in ants, which likely has important implications on disease dynamics in social insect colonies."}],"file_date_updated":"2020-07-14T12:45:37Z","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-07-28T09:35:11Z","publist_id":"4647","file":[{"file_id":"5026","date_created":"2018-12-12T10:13:41Z","file_size":281736,"file_name":"IST-2016-402-v1+1_1471-2148-13-225.pdf","access_level":"open_access","checksum":"c16ef36f2a10786a7885e19c4528d707","relation":"main_file","creator":"system","content_type":"application/pdf","date_updated":"2020-07-14T12:45:37Z"}],"intvolume":"        13","external_id":{"isi":["000326620500001"]},"issue":"1","citation":{"chicago":"Tragust, Simon, Line V Ugelvig, Michel Chapuisat, Jürgen Heinze, and Sylvia Cremer. “Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies.” <i>BMC Evolutionary Biology</i>. BioMed Central, 2013. <a href=\"https://doi.org/10.1186/1471-2148-13-225\">https://doi.org/10.1186/1471-2148-13-225</a>.","mla":"Tragust, Simon, et al. “Pupal Cocoons Affect Sanitary Brood Care and Limit Fungal Infections in Ant Colonies.” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1, 225, BioMed Central, 2013, doi:<a href=\"https://doi.org/10.1186/1471-2148-13-225\">10.1186/1471-2148-13-225</a>.","short":"S. Tragust, L.V. Ugelvig, M. Chapuisat, J. Heinze, S. Cremer, BMC Evolutionary Biology 13 (2013).","ista":"Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. 2013. Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. BMC Evolutionary Biology. 13(1), 225.","ama":"Tragust S, Ugelvig LV, Chapuisat M, Heinze J, Cremer S. Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. <i>BMC Evolutionary Biology</i>. 2013;13(1). doi:<a href=\"https://doi.org/10.1186/1471-2148-13-225\">10.1186/1471-2148-13-225</a>","ieee":"S. Tragust, L. V. Ugelvig, M. Chapuisat, J. Heinze, and S. Cremer, “Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies,” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1. BioMed Central, 2013.","apa":"Tragust, S., Ugelvig, L. V., Chapuisat, M., Heinze, J., &#38; Cremer, S. (2013). Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies. <i>BMC Evolutionary Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2148-13-225\">https://doi.org/10.1186/1471-2148-13-225</a>"},"acknowledgement":"The study was funded by the European Research Council (Marie Curie ERG 036569) and Marie Curie IEF 302204 to LVU\r\nCC BY 2.0\r\n","year":"2013","publisher":"BioMed Central","day":"14","das_tickbox":"1","isi":1,"oa_version":"Published Version","_id":"2284","status":"public","article_number":"225","doi":"10.1186/1471-2148-13-225","type":"journal_article","oa":1,"title":"Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies","author":[{"first_name":"Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87","last_name":"Tragust","full_name":"Tragust, Simon"},{"last_name":"Ugelvig","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","full_name":"Ugelvig, Line V","first_name":"Line V","orcid":"0000-0003-1832-8883"},{"first_name":"Michel","full_name":"Chapuisat, Michel","last_name":"Chapuisat"},{"last_name":"Heinze","full_name":"Heinze, Jürgen","first_name":"Jürgen"},{"full_name":"Cremer, Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia"}],"publication":"BMC Evolutionary Biology","scopus_import":"1","corr_author":"1","quality_controlled":"1","related_material":{"record":[{"status":"public","id":"9753","relation":"research_data"}]},"project":[{"call_identifier":"FP7","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","_id":"25DC711C-B435-11E9-9278-68D0E5697425","grant_number":"243071"},{"grant_number":"CR-118/3-1","name":"Host-Parasite Coevolution","_id":"25DAF0B2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25DDF0F0-B435-11E9-9278-68D0E5697425","name":"Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach","grant_number":"302004"}],"date_created":"2018-12-11T11:56:46Z","article_processing_charge":"No","license":"https://creativecommons.org/licenses/by/4.0/","month":"10","language":[{"iso":"eng"}],"volume":13,"department":[{"_id":"SyCr"}],"publication_status":"published","pubrep_id":"402"},{"_id":"1387","status":"public","oa_version":"Submitted Version","day":"01","das_tickbox":"1","acknowledgement":"This work was supported in part by the Polish Ministry of Science grant no. N206 567840, Poland’s NCN grant no. DEC-2012/05/N/ST6/03254, Austrian Science Fund NFN RiSE (Rigorous Systems Engineering), ERC Advanced Grant QUAREM (Quantitative Reactive Modeling), and ERC Grant QUALITY. The full version is available at the authors’ URLs.","citation":{"ama":"Boker U, Kuperberg D, Kupferman O, Skrzypczak M. Nondeterminism in the presence of a diverse or unknown future. 2013;7966(PART 2):89-100. doi:<a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">10.1007/978-3-642-39212-2_11</a>","ista":"Boker U, Kuperberg D, Kupferman O, Skrzypczak M. 2013. Nondeterminism in the presence of a diverse or unknown future. 7966(PART 2), 89–100.","apa":"Boker, U., Kuperberg, D., Kupferman, O., &#38; Skrzypczak, M. (2013). Nondeterminism in the presence of a diverse or unknown future. Presented at the ICALP: Automata, Languages and Programming, Riga, Latvia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">https://doi.org/10.1007/978-3-642-39212-2_11</a>","ieee":"U. Boker, D. Kuperberg, O. Kupferman, and M. Skrzypczak, “Nondeterminism in the presence of a diverse or unknown future,” vol. 7966, no. PART 2. Springer, pp. 89–100, 2013.","chicago":"Boker, Udi, Denis Kuperberg, Orna Kupferman, and Michał Skrzypczak. “Nondeterminism in the Presence of a Diverse or Unknown Future.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">https://doi.org/10.1007/978-3-642-39212-2_11</a>.","mla":"Boker, Udi, et al. <i>Nondeterminism in the Presence of a Diverse or Unknown Future</i>. Vol. 7966, no. PART 2, Springer, 2013, pp. 89–100, doi:<a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">10.1007/978-3-642-39212-2_11</a>.","short":"U. Boker, D. Kuperberg, O. Kupferman, M. Skrzypczak, 7966 (2013) 89–100."},"year":"2013","publisher":"Springer","issue":"PART 2","file":[{"file_id":"7857","file_name":"2013_ICALP_Boker.pdf","date_created":"2020-05-15T11:05:50Z","file_size":276982,"checksum":"98bc02e3793072e279ec8d364b381ff3","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:44:48Z","content_type":"application/pdf","creator":"dernst"}],"intvolume":"      7966","alternative_title":["LNCS"],"publist_id":"5823","date_updated":"2026-07-28T09:26:19Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:44:48Z","ec_funded":1,"abstract":[{"lang":"eng","text":"Choices made by nondeterministic word automata depend on both the past (the prefix of the word read so far) and the future (the suffix yet to be read). In several applications, most notably synthesis, the future is diverse or unknown, leading to algorithms that are based on deterministic automata. Hoping to retain some of the advantages of nondeterministic automata, researchers have studied restricted classes of nondeterministic automata. Three such classes are nondeterministic automata that are good for trees (GFT; i.e., ones that can be expanded to tree automata accepting the derived tree languages, thus whose choices should satisfy diverse futures), good for games (GFG; i.e., ones whose choices depend only on the past), and determinizable by pruning (DBP; i.e., ones that embody equivalent deterministic automata). The theoretical properties and relative merits of the different classes are still open, having vagueness on whether they really differ from deterministic automata. In particular, while DBP ⊆ GFG ⊆ GFT, it is not known whether every GFT automaton is GFG and whether every GFG automaton is DBP. Also open is the possible succinctness of GFG and GFT automata compared to deterministic automata. We study these problems for ω-regular automata with all common acceptance conditions. We show that GFT=GFG⊃DBP, and describe a determinization construction for GFG automata."}],"ddc":["000"],"has_accepted_license":"1","date_published":"2013-07-01T00:00:00Z","fulldoi":"https://doi.org/10.1007/978-3-642-39212-2_11","page":"89 - 100","series_title":"Lecture Notes in Computer Science","volume":7966,"language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"publication_status":"published","month":"07","date_created":"2018-12-11T11:51:44Z","article_processing_charge":"No","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7"}],"quality_controlled":"1","conference":{"start_date":"2013-07-08","name":"ICALP: Automata, Languages and Programming","end_date":"2013-07-12","location":"Riga, Latvia"},"scopus_import":"1","author":[{"full_name":"Boker, Udi","last_name":"Boker","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","first_name":"Udi"},{"first_name":"Denis","last_name":"Kuperberg","full_name":"Kuperberg, Denis"},{"full_name":"Kupferman, Orna","last_name":"Kupferman","first_name":"Orna"},{"first_name":"Michał","last_name":"Skrzypczak","full_name":"Skrzypczak, Michał"}],"title":"Nondeterminism in the presence of a diverse or unknown future","oa":1,"doi":"10.1007/978-3-642-39212-2_11","type":"conference"},{"issue":"Part 2","intvolume":"      7966","file":[{"creator":"dernst","date_updated":"2020-07-14T12:45:42Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"85afbf6c18a2c7e377c52c9410e2d824","date_created":"2020-05-15T11:16:12Z","file_size":363031,"file_name":"2013_ICALP_Almagor.pdf","file_id":"7860"}],"das_tickbox":"1","day":"01","publisher":"Springer","acknowledgement":"This work was supported in part by the Austrian Science Fund NFN RiSE (Rigorous Systems Engineering), by the ERC Advanced Grant QUAREM (Quantitative Reactive Modeling), and the ERC Grant QUALITY. The full version is available at the authors’ URLs.","year":"2013","citation":{"ista":"Almagor S, Boker U, Kupferman O. 2013. Formalizing and reasoning about quality. 7966(Part 2), 15–27.","ama":"Almagor S, Boker U, Kupferman O. Formalizing and reasoning about quality. 2013;7966(Part 2):15-27. doi:<a href=\"https://doi.org/10.1007/978-3-642-39212-2_3\">10.1007/978-3-642-39212-2_3</a>","ieee":"S. Almagor, U. Boker, and O. Kupferman, “Formalizing and reasoning about quality,” vol. 7966, no. Part 2. Springer, pp. 15–27, 2013.","apa":"Almagor, S., Boker, U., &#38; Kupferman, O. (2013). Formalizing and reasoning about quality. Presented at the ICALP: Automata, Languages and Programming, Riga, Latvia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39212-2_3\">https://doi.org/10.1007/978-3-642-39212-2_3</a>","chicago":"Almagor, Shaull, Udi Boker, and Orna Kupferman. “Formalizing and Reasoning about Quality.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39212-2_3\">https://doi.org/10.1007/978-3-642-39212-2_3</a>.","mla":"Almagor, Shaull, et al. <i>Formalizing and Reasoning about Quality</i>. Vol. 7966, no. Part 2, Springer, 2013, pp. 15–27, doi:<a href=\"https://doi.org/10.1007/978-3-642-39212-2_3\">10.1007/978-3-642-39212-2_3</a>.","short":"S. Almagor, U. Boker, O. Kupferman, 7966 (2013) 15–27."},"_id":"2517","status":"public","oa_version":"Submitted Version","has_accepted_license":"1","date_published":"2013-07-01T00:00:00Z","ddc":["000"],"fulldoi":"https://doi.org/10.1007/978-3-642-39212-2_3","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:45:42Z","ec_funded":1,"abstract":[{"text":"Traditional formal methods are based on a Boolean satisfaction notion: a reactive system satisfies, or not, a given specification. We generalize formal methods to also address the quality of systems. As an adequate specification formalism we introduce the linear temporal logic LTL[F]. The satisfaction value of an LTL[F] formula is a number between 0 and 1, describing the quality of the satisfaction. The logic generalizes traditional LTL by augmenting it with a (parameterized) set F of arbitrary functions over the interval [0,1]. For example, F may contain the maximum or minimum between the satisfaction values of subformulas, their product, and their average. The classical decision problems in formal methods, such as satisfiability, model checking, and synthesis, are generalized to search and optimization problems in the quantitative setting. For example, model checking asks for the quality in which a specification is satisfied, and synthesis returns a system satisfying the specification with the highest quality. Reasoning about quality gives rise to other natural questions, like the distance between specifications. We formalize these basic questions and study them for LTL[F]. By extending the automata-theoretic approach for LTL to a setting that takes quality into an account, we are able to solve the above problems and show that reasoning about LTL[F] has roughly the same complexity as reasoning about traditional LTL.","lang":"eng"}],"alternative_title":["LNCS"],"publist_id":"4384","date_updated":"2026-07-28T09:28:40Z","project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"quality_controlled":"1","article_processing_charge":"No","date_created":"2018-12-11T11:58:08Z","month":"07","page":"15 - 27","series_title":"Lecture Notes in Computer Science","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"volume":7966,"oa":1,"title":"Formalizing and reasoning about quality","type":"conference","doi":"10.1007/978-3-642-39212-2_3","author":[{"first_name":"Shaull","full_name":"Almagor, Shaull","last_name":"Almagor"},{"full_name":"Boker, Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","last_name":"Boker","first_name":"Udi"},{"first_name":"Orna","last_name":"Kupferman","full_name":"Kupferman, Orna"}],"conference":{"start_date":"2013-07-08","location":"Riga, Latvia","end_date":"2013-07-12","name":"ICALP: Automata, Languages and Programming"},"scopus_import":"1"},{"das_tickbox":"1","day":"01","isi":1,"acknowledgement":"The authors thank Dr Christian Luschnig (University of Natural Resources and Life Sciences (BOKU), Vienna, Austria) for the anti-PIN2 antibody, Professor Mark Estelle (University of California, San Diego, CA, USA) for tir1-1 mutant seeds and, last but not least, to Dr David Morris for critical reading of the manuscript. We also thank Markéta Pařezová and Jana Stýblová for excellent technical assistance. This work was supported by the Grant Agency of the Czech Republic (P305/11/0797 to E.Z. and 13-40637S to J.F.), the Central European Institute of Technology project CZ.1.05/1.1.00/02.0068 from the European Regional Development Fund and by a European Research Council starting independent research grant ERC-2011-StG-20101109-PSDP (to J.F.).","citation":{"mla":"Simon, Sibu, et al. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” <i>New Phytologist</i>, vol. 200, no. 4, Wiley, 2013, pp. 1034–48, doi:<a href=\"https://doi.org/10.1111/nph.12437\">10.1111/nph.12437</a>.","short":"S. Simon, M. Kubeš, P. Baster, S. Robert, P. Dobrev, J. Friml, J. Petrášek, E. Zažímalová, New Phytologist 200 (2013) 1034–1048.","chicago":"Simon, Sibu, Martin Kubeš, Pawel Baster, Stéphanie Robert, Petre Dobrev, Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” <i>New Phytologist</i>. Wiley, 2013. <a href=\"https://doi.org/10.1111/nph.12437\">https://doi.org/10.1111/nph.12437</a>.","ieee":"S. Simon <i>et al.</i>, “Defining the selectivity of processes along the auxin response chain: A study using auxin analogues,” <i>New Phytologist</i>, vol. 200, no. 4. Wiley, pp. 1034–1048, 2013.","apa":"Simon, S., Kubeš, M., Baster, P., Robert, S., Dobrev, P., Friml, J., … Zažímalová, E. (2013). Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.12437\">https://doi.org/10.1111/nph.12437</a>","ista":"Simon S, Kubeš M, Baster P, Robert S, Dobrev P, Friml J, Petrášek J, Zažímalová E. 2013. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. New Phytologist. 200(4), 1034–1048.","ama":"Simon S, Kubeš M, Baster P, et al. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. <i>New Phytologist</i>. 2013;200(4):1034-1048. doi:<a href=\"https://doi.org/10.1111/nph.12437\">10.1111/nph.12437</a>"},"year":"2013","publisher":"Wiley","_id":"2443","status":"public","oa_version":"Published Version","external_id":{"isi":["000330955300012"]},"issue":"4","intvolume":"       200","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The mode of action of auxin is based on its non-uniform distribution within tissues and organs. Despite the wide use of several auxin analogues in research and agriculture, little is known about the specificity of different auxin-related transport and signalling processes towards these compounds. Using seedlings of Arabidopsis thaliana and suspension-cultured cells of Nicotiana tabacum (BY-2), the physiological activity of several auxin analogues was investigated, together with their capacity to induce auxin-dependent gene expression, to inhibit endocytosis and to be transported across the plasma membrane. This study shows that the specificity criteria for different auxin-related processes vary widely. Notably, the special behaviour of some synthetic auxin analogues suggests that they might be useful tools in investigations of the molecular mechanism of auxin action. Thus, due to their differential stimulatory effects on DR5 expression, indole-3-propionic (IPA) and 2,4,5-trichlorophenoxy acetic (2,4,5-T) acids can serve in studies of TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALLING F-BOX (TIR1/AFB)-mediated auxin signalling, and 5-fluoroindole-3-acetic acid (5-F-IAA) can help to discriminate between transcriptional and non-transcriptional pathways of auxin signalling. The results demonstrate that the major determinants for the auxin-like physiological potential of a particular compound are very complex and involve its chemical and metabolic stability, its ability to distribute in tissues in a polar manner and its activity towards auxin signalling machinery.","lang":"eng"}],"ec_funded":1,"date_updated":"2026-07-28T09:29:45Z","publist_id":"4460","ddc":["580"],"date_published":"2013-12-01T00:00:00Z","OA_type":"free access","fulldoi":"https://doi.org/10.1111/nph.12437","article_type":"original","month":"12","page":"1034 - 1048","volume":200,"department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"publication_status":"published","project":[{"grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants"}],"quality_controlled":"1","date_created":"2018-12-11T11:57:41Z","article_processing_charge":"No","publication":"New Phytologist","author":[{"first_name":"Sibu","orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu","last_name":"Simon","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kubeš","full_name":"Kubeš, Martin","first_name":"Martin"},{"full_name":"Baster, Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87","last_name":"Baster","first_name":"Pawel"},{"first_name":"Stéphanie","full_name":"Robert, Stéphanie","last_name":"Robert"},{"full_name":"Dobrev, Petre","last_name":"Dobrev","first_name":"Petre"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí","orcid":"0000-0002-8302-7596"},{"last_name":"Petrášek","full_name":"Petrášek, Jan","first_name":"Jan"},{"first_name":"Eva","full_name":"Zažímalová, Eva","last_name":"Zažímalová"}],"scopus_import":"1","oa":1,"title":"Defining the selectivity of processes along the auxin response chain: A study using auxin analogues","doi":"10.1111/nph.12437","main_file_link":[{"url":"https://doi.org/10.1111/nph.12437","open_access":"1"}],"type":"journal_article"},{"publication":"Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language","author":[{"orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"},{"first_name":"Christoph","last_name":"Kirsch","full_name":"Kirsch, Christoph"},{"first_name":"Hannes","full_name":"Payer, Hannes","last_name":"Payer"},{"first_name":"Ali","full_name":"Sezgin, Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","last_name":"Sezgin"},{"first_name":"Ana","full_name":"Sokolova, Ana","last_name":"Sokolova"}],"corr_author":"1","conference":{"location":"Rome, Italy","name":"POPL: Principles of Programming Languages","end_date":"2013-01-25","start_date":"2013-01-23"},"scopus_import":"1","publication_identifier":{"isbn":["978-1-4503-1832-7"]},"title":"Quantitative relaxation of concurrent data structures","oa":1,"doi":"10.1145/2429069.2429109","type":"conference","month":"01","page":"317 - 328","department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"pubrep_id":"198","publication_status":"published","project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"quality_controlled":"1","related_material":{"record":[{"status":"deleted","relation":"later_version","id":"10901"}]},"date_created":"2018-12-11T11:56:11Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:45:31Z","abstract":[{"text":"There is a trade-off between performance and correctness in implementing concurrent data structures. Better performance may be achieved at the expense of relaxing correctness, by redefining the semantics of data structures. We address such a redefinition of data structure semantics and present a systematic and formal framework for obtaining new data structures by quantitatively relaxing existing ones. We view a data structure as a sequential specification S containing all &quot;legal&quot; sequences over an alphabet of method calls. Relaxing the data structure corresponds to defining a distance from any sequence over the alphabet to the sequential specification: the k-relaxed sequential specification contains all sequences over the alphabet within distance k from the original specification. In contrast to other existing work, our relaxations are semantic (distance in terms of data structure states). As an instantiation of our framework, we present two simple yet generic relaxation schemes, called out-of-order and stuttering relaxation, along with several ways of computing distances. We show that the out-of-order relaxation, when further instantiated to stacks, queues, and priority queues, amounts to tolerating bounded out-of-order behavior, which cannot be captured by a purely syntactic relaxation (distance in terms of sequence manipulation, e.g. edit distance). We give concurrent implementations of relaxed data structures and demonstrate that bounded relaxations provide the means for trading correctness for performance in a controlled way. The relaxations are monotonic which further highlights the trade-off: increasing k increases the number of permitted sequences, which as we demonstrate can lead to better performance. Finally, since a relaxed stack or queue also implements a pool, we actually have new concurrent pool implementations that outperform the state-of-the-art ones.","lang":"eng"}],"ec_funded":1,"publist_id":"4801","date_updated":"2026-07-28T11:18:47Z","ddc":["000","004"],"date_published":"2013-01-01T00:00:00Z","has_accepted_license":"1","fulldoi":"https://doi.org/10.1145/2429069.2429109","day":"01","year":"2013","acknowledgement":"This work has been supported by the European Research Council\r\nadvanced grant QUAREM, the National Research Network RiSE\r\non Rigorous Systems Engineering (Austrian Science Fund S11404-\r\nN23), and an Elise Richter Fellowship (Austrian Science Fund\r\nV00125). We thank the anonymous referees for their constructive\r\nand inspiring comments and suggestions. Ana Sokolova wishes to\r\nthank Dexter Kozen and in particular Joel Ouaknine: had they not\r\nsaved her life, she would have missed a lot of the fun involved in\r\nworking on this paper and seeing it finished.","citation":{"ama":"Henzinger TA, Kirsch C, Payer H, Sezgin A, Sokolova A. Quantitative relaxation of concurrent data structures. In: <i>Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language</i>. ACM; 2013:317-328. doi:<a href=\"https://doi.org/10.1145/2429069.2429109\">10.1145/2429069.2429109</a>","ista":"Henzinger TA, Kirsch C, Payer H, Sezgin A, Sokolova A. 2013. Quantitative relaxation of concurrent data structures. Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language. POPL: Principles of Programming Languages, 317–328.","ieee":"T. A. Henzinger, C. Kirsch, H. Payer, A. Sezgin, and A. Sokolova, “Quantitative relaxation of concurrent data structures,” in <i>Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language</i>, Rome, Italy, 2013, pp. 317–328.","apa":"Henzinger, T. A., Kirsch, C., Payer, H., Sezgin, A., &#38; Sokolova, A. (2013). Quantitative relaxation of concurrent data structures. In <i>Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming language</i> (pp. 317–328). Rome, Italy: ACM. <a href=\"https://doi.org/10.1145/2429069.2429109\">https://doi.org/10.1145/2429069.2429109</a>","chicago":"Henzinger, Thomas A, Christoph Kirsch, Hannes Payer, Ali Sezgin, and Ana Sokolova. “Quantitative Relaxation of Concurrent Data Structures.” In <i>Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language</i>, 317–28. ACM, 2013. <a href=\"https://doi.org/10.1145/2429069.2429109\">https://doi.org/10.1145/2429069.2429109</a>.","mla":"Henzinger, Thomas A., et al. “Quantitative Relaxation of Concurrent Data Structures.” <i>Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language</i>, ACM, 2013, pp. 317–28, doi:<a href=\"https://doi.org/10.1145/2429069.2429109\">10.1145/2429069.2429109</a>.","short":"T.A. Henzinger, C. Kirsch, H. Payer, A. Sezgin, A. Sokolova, in:, Proceedings of the 40th Annual ACM SIGPLAN-SIGACT Symposium on Principles of Programming Language, ACM, 2013, pp. 317–328."},"publisher":"ACM","_id":"2181","status":"public","oa_version":"Submitted Version","file":[{"file_size":294689,"date_created":"2018-12-12T10:14:33Z","file_name":"IST-2014-198-v1+1_popl128-henzinger-clean.pdf","file_id":"5086","creator":"system","content_type":"application/pdf","date_updated":"2020-07-14T12:45:31Z","access_level":"open_access","checksum":"adf465e70948f4e80e48057524516456","relation":"main_file"}]},{"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1308.4767"}],"doi":"10.1109/FMCAD.2013.6679394","type":"conference","oa":1,"title":"Synthesizing multiple boolean functions using interpolation on a single proof","author":[{"first_name":"Georg","last_name":"Hofferek","full_name":"Hofferek, Georg"},{"last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Ashutosh","first_name":"Ashutosh"},{"full_name":"Könighofer, Bettina","last_name":"Könighofer","first_name":"Bettina"},{"first_name":"Jie","full_name":"Jiang, Jie","last_name":"Jiang"},{"last_name":"Bloem","full_name":"Bloem, Roderick","first_name":"Roderick"}],"publication":"2013 Formal Methods in Computer-Aided Design","scopus_import":"1","conference":{"start_date":"2013-10-20","name":"FMCAD: Formal Methods in Computer-Aided Design","end_date":"2013-10-23","location":"Portland, OR, United States"},"quality_controlled":"1","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"}],"date_created":"2018-12-11T11:51:43Z","article_processing_charge":"No","month":"12","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"publication_status":"published","page":"77 - 84","OA_place":"repository","fulldoi":"https://doi.org/10.1109/FMCAD.2013.6679394","OA_type":"green","date_published":"2013-12-11T00:00:00Z","abstract":[{"lang":"eng","text":"It is often difficult to correctly implement a Boolean controller for a complex system, especially when concurrency is involved. Yet, it may be easy to formally specify a controller. For instance, for a pipelined processor it suffices to state that the visible behavior of the pipelined system should be identical to a non-pipelined reference system (Burch-Dill paradigm). We present a novel procedure to efficiently synthesize multiple Boolean control signals from a specification given as a quantified first-order formula (with a specific quantifier structure). Our approach uses uninterpreted functions to abstract details of the design. We construct an unsatisfiable SMT formula from the given specification. Then, from just one proof of unsatisfiability, we use a variant of Craig interpolation to compute multiple coordinated interpolants that implement the Boolean control signals. Our method avoids iterative learning and back-substitution of the control functions. We applied our approach to synthesize a controller for a simple two-stage pipelined processor, and present first experimental results."}],"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-07-28T11:20:30Z","publist_id":"5825","external_id":{"arxiv":["1308.4767"]},"citation":{"chicago":"Hofferek, Georg, Ashutosh Gupta, Bettina Könighofer, Jie Jiang, and Roderick Bloem. “Synthesizing Multiple Boolean Functions Using Interpolation on a Single Proof.” In <i>2013 Formal Methods in Computer-Aided Design</i>, 77–84. IEEE, 2013. <a href=\"https://doi.org/10.1109/FMCAD.2013.6679394\">https://doi.org/10.1109/FMCAD.2013.6679394</a>.","mla":"Hofferek, Georg, et al. “Synthesizing Multiple Boolean Functions Using Interpolation on a Single Proof.” <i>2013 Formal Methods in Computer-Aided Design</i>, IEEE, 2013, pp. 77–84, doi:<a href=\"https://doi.org/10.1109/FMCAD.2013.6679394\">10.1109/FMCAD.2013.6679394</a>.","short":"G. Hofferek, A. Gupta, B. Könighofer, J. Jiang, R. Bloem, in:, 2013 Formal Methods in Computer-Aided Design, IEEE, 2013, pp. 77–84.","ista":"Hofferek G, Gupta A, Könighofer B, Jiang J, Bloem R. 2013. Synthesizing multiple boolean functions using interpolation on a single proof. 2013 Formal Methods in Computer-Aided Design. FMCAD: Formal Methods in Computer-Aided Design, 77–84.","ama":"Hofferek G, Gupta A, Könighofer B, Jiang J, Bloem R. Synthesizing multiple boolean functions using interpolation on a single proof. In: <i>2013 Formal Methods in Computer-Aided Design</i>. IEEE; 2013:77-84. doi:<a href=\"https://doi.org/10.1109/FMCAD.2013.6679394\">10.1109/FMCAD.2013.6679394</a>","ieee":"G. Hofferek, A. Gupta, B. Könighofer, J. Jiang, and R. Bloem, “Synthesizing multiple boolean functions using interpolation on a single proof,” in <i>2013 Formal Methods in Computer-Aided Design</i>, Portland, OR, United States, 2013, pp. 77–84.","apa":"Hofferek, G., Gupta, A., Könighofer, B., Jiang, J., &#38; Bloem, R. (2013). Synthesizing multiple boolean functions using interpolation on a single proof. In <i>2013 Formal Methods in Computer-Aided Design</i> (pp. 77–84). Portland, OR, United States: IEEE. <a href=\"https://doi.org/10.1109/FMCAD.2013.6679394\">https://doi.org/10.1109/FMCAD.2013.6679394</a>"},"acknowledgement":"This research was supported by the European Commission through project\r\nDIAMOND (FP7-2009-IST-4-248613), the Austrian Science Fund (FWF)\r\nthrough projects RiSE (S11406-N23) and QUAINT (I774-N23), and ERC\r\nAdvanced Grant QUAREM (Quantitative Reactive Modeling)","year":"2013","publisher":"IEEE","arxiv":1,"das_tickbox":"1","day":"11","oa_version":"Preprint","status":"public","_id":"1385"},{"abstract":[{"lang":"eng","text":"Intracellular proteins with long lifespans have recently been linked to age-dependent defects, ranging from decreased fertility to the functional decline of neurons. Why long-lived proteins exist in metabolically active cellular environments and how they are maintained over time remains poorly understood. Here, we provide a system-wide identification of proteins with exceptional lifespans in the rat brain. These proteins are inefficiently replenished despite being translated robustly throughout adulthood. Using nucleoporins as a paradigm for long-term protein persistence, we found that nuclear pore complexes (NPCs) are maintained over a cell’s life through slow but finite exchange of even its most stable subcomplexes. This maintenance is limited, however, as some nucleoporin levels decrease during aging, providing a rationale for the previously observed age-dependent deterioration of NPC function. Our identification of a long-lived proteome reveals cellular components that are at increased risk for damage accumulation, linking long-term protein persistence to the cellular aging process."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-07-28T10:15:26Z","OA_place":"publisher","article_type":"original","fulldoi":"https://doi.org/10.1016/j.cell.2013.07.037","keyword":["General Biochemistry","Genetics and Molecular Biology"],"OA_type":"free access","date_published":"2013-08-29T00:00:00Z","year":"2013","citation":{"chicago":"Toyama, Brandon H., Jeffrey N. Savas, Sung Kyu Park, Michael S. Harris, Nicholas T. Ingolia, John R. Yates, and Martin Hetzer. “Identification of Long-Lived Proteins Reveals Exceptional Stability of Essential Cellular Structures.” <i>Cell</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.cell.2013.07.037\">https://doi.org/10.1016/j.cell.2013.07.037</a>.","mla":"Toyama, Brandon H., et al. “Identification of Long-Lived Proteins Reveals Exceptional Stability of Essential Cellular Structures.” <i>Cell</i>, vol. 154, no. 5, Elsevier, 2013, pp. 971–82, doi:<a href=\"https://doi.org/10.1016/j.cell.2013.07.037\">10.1016/j.cell.2013.07.037</a>.","short":"B.H. Toyama, J.N. Savas, S.K. Park, M.S. Harris, N.T. Ingolia, J.R. Yates, M. Hetzer, Cell 154 (2013) 971–982.","ama":"Toyama BH, Savas JN, Park SK, et al. Identification of long-lived proteins reveals exceptional stability of essential cellular structures. <i>Cell</i>. 2013;154(5):971-982. doi:<a href=\"https://doi.org/10.1016/j.cell.2013.07.037\">10.1016/j.cell.2013.07.037</a>","ista":"Toyama BH, Savas JN, Park SK, Harris MS, Ingolia NT, Yates JR, Hetzer M. 2013. Identification of long-lived proteins reveals exceptional stability of essential cellular structures. Cell. 154(5), 971–982.","ieee":"B. H. Toyama <i>et al.</i>, “Identification of long-lived proteins reveals exceptional stability of essential cellular structures,” <i>Cell</i>, vol. 154, no. 5. Elsevier, pp. 971–982, 2013.","apa":"Toyama, B. H., Savas, J. N., Park, S. K., Harris, M. S., Ingolia, N. T., Yates, J. R., &#38; Hetzer, M. (2013). Identification of long-lived proteins reveals exceptional stability of essential cellular structures. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2013.07.037\">https://doi.org/10.1016/j.cell.2013.07.037</a>"},"publisher":"Elsevier","day":"29","das_tickbox":"1","oa_version":"Published Version","status":"public","_id":"11087","intvolume":"       154","external_id":{"pmid":["23993091"]},"issue":"5","author":[{"full_name":"Toyama, Brandon H.","last_name":"Toyama","first_name":"Brandon H."},{"full_name":"Savas, Jeffrey N.","last_name":"Savas","first_name":"Jeffrey N."},{"last_name":"Park","full_name":"Park, Sung Kyu","first_name":"Sung Kyu"},{"first_name":"Michael S.","last_name":"Harris","full_name":"Harris, Michael S."},{"full_name":"Ingolia, Nicholas T.","last_name":"Ingolia","first_name":"Nicholas T."},{"first_name":"John R.","full_name":"Yates, John R.","last_name":"Yates"},{"orcid":"0000-0002-2111-992X","first_name":"Martin W","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","full_name":"HETZER, Martin W"}],"publication":"Cell","scopus_import":"1","extern":"1","doi":"10.1016/j.cell.2013.07.037","main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2013.07.037","open_access":"1"}],"type":"journal_article","publication_identifier":{"issn":["0092-8674"]},"pmid":1,"title":"Identification of long-lived proteins reveals exceptional stability of essential cellular structures","oa":1,"month":"08","department":[{"_id":"MaHe"}],"language":[{"iso":"eng"}],"volume":154,"publication_status":"published","page":"971-982","quality_controlled":"1","date_created":"2022-04-07T07:51:08Z","article_processing_charge":"No"},{"abstract":[{"lang":"eng","text":"We describe new extensions of the Vampire theorem prover for computing tree interpolants. These extensions generalize Craig interpolation in Vampire, and can also be used to derive sequence interpolants. We evaluated our implementation on a large number of examples over the theory of linear integer arithmetic and integer-indexed arrays, with and without quantifiers. When compared to other methods, our experiments show that some examples could only be solved by our implementation."}],"file_date_updated":"2020-07-14T12:45:34Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4724","date_updated":"2026-07-28T10:10:38Z","alternative_title":["LNCS"],"fulldoi":"https://doi.org/10.1007/978-3-642-45221-5_13","has_accepted_license":"1","date_published":"2013-01-14T00:00:00Z","ddc":["000"],"publisher":"Springer","citation":{"short":"R. Blanc, A. Gupta, L. Kovács, B. Kragl, 8312 (2013) 173–181.","mla":"Blanc, Régis, et al. <i>Tree Interpolation in Vampire</i>. Vol. 8312, Springer, 2013, pp. 173–81, doi:<a href=\"https://doi.org/10.1007/978-3-642-45221-5_13\">10.1007/978-3-642-45221-5_13</a>.","chicago":"Blanc, Régis, Ashutosh Gupta, Laura Kovács, and Bernhard Kragl. “Tree Interpolation in Vampire.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-45221-5_13\">https://doi.org/10.1007/978-3-642-45221-5_13</a>.","apa":"Blanc, R., Gupta, A., Kovács, L., &#38; Kragl, B. (2013). Tree interpolation in Vampire. Presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Stellenbosch, South Africa: Springer. <a href=\"https://doi.org/10.1007/978-3-642-45221-5_13\">https://doi.org/10.1007/978-3-642-45221-5_13</a>","ieee":"R. Blanc, A. Gupta, L. Kovács, and B. Kragl, “Tree interpolation in Vampire,” vol. 8312. Springer, pp. 173–181, 2013.","ista":"Blanc R, Gupta A, Kovács L, Kragl B. 2013. Tree interpolation in Vampire. 8312, 173–181.","ama":"Blanc R, Gupta A, Kovács L, Kragl B. Tree interpolation in Vampire. 2013;8312:173-181. doi:<a href=\"https://doi.org/10.1007/978-3-642-45221-5_13\">10.1007/978-3-642-45221-5_13</a>"},"acknowledgement":"This research was partly supported by the Austrian National Research Network RiSE (FWF grants S11402-N23 and S11410-N23) and the WWTF PROSEED grant (ICT C-050).","year":"2013","day":"14","das_tickbox":"1","oa_version":"Submitted Version","status":"public","_id":"2237","intvolume":"      8312","file":[{"checksum":"9cebaafca032e6769d273f393305c705","access_level":"open_access","relation":"main_file","creator":"dernst","date_updated":"2020-07-14T12:45:34Z","content_type":"application/pdf","file_id":"7858","file_size":279206,"date_created":"2020-05-15T11:10:40Z","file_name":"2013_LPAR_Blanc.pdf"}],"author":[{"first_name":"Régis","last_name":"Blanc","full_name":"Blanc, Régis"},{"first_name":"Ashutosh","full_name":"Gupta, Ashutosh","last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Laura","full_name":"Kovács, Laura","last_name":"Kovács"},{"orcid":"0000-0001-7745-9117","first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87","last_name":"Kragl","full_name":"Kragl, Bernhard"}],"scopus_import":"1","conference":{"name":"LPAR: Logic for Programming, Artificial Intelligence, and Reasoning","end_date":"2013-12-19","location":"Stellenbosch, South Africa","start_date":"2013-12-14"},"type":"conference","doi":"10.1007/978-3-642-45221-5_13","title":"Tree interpolation in Vampire","oa":1,"month":"01","publication_status":"published","volume":8312,"language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"page":"173 - 181","series_title":"Lecture Notes in Computer Science","quality_controlled":"1","project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"}],"article_processing_charge":"No","date_created":"2018-12-11T11:56:29Z"},{"oa_version":"None","publication_status":"published","department":[{"_id":"CaHe"},{"_id":"GradSch"}],"language":[{"iso":"eng"}],"_id":"1406","status":"public","page":"123","publisher":"Institute of Science and Technology Austria","citation":{"chicago":"Campinho, Pedro. “Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading.” Institute of Science and Technology Austria, 2013.","short":"P. Campinho, Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading, Institute of Science and Technology Austria, 2013.","mla":"Campinho, Pedro. <i>Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading</i>. Institute of Science and Technology Austria, 2013.","ista":"Campinho P. 2013. Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading. Institute of Science and Technology Austria.","ama":"Campinho P. Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading. 2013.","apa":"Campinho, P. (2013). <i>Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading</i>. Institute of Science and Technology Austria.","ieee":"P. Campinho, “Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading,” Institute of Science and Technology Austria, 2013."},"year":"2013","supervisor":[{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"month":"10","day":"01","article_processing_charge":"No","date_created":"2018-12-11T11:51:50Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"degree_awarded":"PhD","publist_id":"5801","alternative_title":["ISTA Thesis"],"date_updated":"2026-07-29T10:00:09Z","corr_author":"1","author":[{"full_name":"Campinho, Pedro","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","last_name":"Campinho","first_name":"Pedro","orcid":"0000-0002-8526-5416"}],"abstract":[{"lang":"eng","text":"Epithelial spreading is a critical part of various developmental and wound repair processes. Here we use zebrafish epiboly as a model system to study the cellular and molecular mechanisms underlying the spreading of epithelial sheets. During zebrafish epiboly the enveloping cell layer (EVL), a simple squamous epithelium, spreads over the embryo to eventually cover the entire yolk cell by the end of gastrulation. The EVL leading edge is anchored through tight junctions to the yolk syncytial layer (YSL), where directly adjacent to the EVL margin a contractile actomyosin ring is formed that is thought to drive EVL epiboly. The prevalent view in the field was that the contractile ring exerts a pulling force on the EVL margin, which pulls the EVL towards the vegetal pole. However, how this force is generated and how it affects EVL morphology still remains elusive. Moreover, the cellular mechanisms mediating the increase in EVL surface area, while maintaining tissue integrity and function are still unclear. Here we show that the YSL actomyosin ring pulls on the EVL margin by two distinct force-generating mechanisms. One mechanism is based on contraction of the ring around its circumference, as previously proposed. The second mechanism is based on actomyosin retrogade flows, generating force through resistance against the substrate. The latter can function at any epiboly stage even in situations where the contraction-based mechanism is unproductive. Additionally, we demonstrate that during epiboly the EVL is subjected to anisotropic tension, which guides the orientation of EVL cell division along the main axis (animal-vegetal) of tension. The influence of tension in cell division orientation involves cell elongation and requires myosin-2 activity for proper spindle alignment. Strikingly, we reveal that tension-oriented cell divisions release anisotropic tension within the EVL and that in the absence of such divisions, EVL cells undergo ectopic fusions. We conclude that forces applied to the EVL by the action of the YSL actomyosin ring generate a tension anisotropy in the EVL that orients cell divisions, which in turn limit tissue tension increase thereby facilitating tissue spreading."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"dissertation","date_published":"2013-10-01T00:00:00Z","title":"Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading","publication_identifier":{"issn":["2663-337X"]},"doi_confirm":"1","OA_place":"publisher"},{"publisher":"Nature Publishing Group","citation":{"chicago":"Campinho, Pedro, Martin Behrndt, Jonas Ranft, Thomas Risler, Nicolas Minc, and Carl-Philipp J Heisenberg. “Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading during Zebrafish Epiboly.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/ncb2869\">https://doi.org/10.1038/ncb2869</a>.","mla":"Campinho, Pedro, et al. “Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading during Zebrafish Epiboly.” <i>Nature Cell Biology</i>, vol. 15, Nature Publishing Group, 2013, pp. 1405–14, doi:<a href=\"https://doi.org/10.1038/ncb2869\">10.1038/ncb2869</a>.","short":"P. Campinho, M. Behrndt, J. Ranft, T. Risler, N. Minc, C.-P.J. Heisenberg, Nature Cell Biology 15 (2013) 1405–1414.","ama":"Campinho P, Behrndt M, Ranft J, Risler T, Minc N, Heisenberg C-PJ. Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly. <i>Nature Cell Biology</i>. 2013;15:1405-1414. doi:<a href=\"https://doi.org/10.1038/ncb2869\">10.1038/ncb2869</a>","ista":"Campinho P, Behrndt M, Ranft J, Risler T, Minc N, Heisenberg C-PJ. 2013. Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly. Nature Cell Biology. 15, 1405–1414.","ieee":"P. Campinho, M. Behrndt, J. Ranft, T. Risler, N. Minc, and C.-P. J. Heisenberg, “Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly,” <i>Nature Cell Biology</i>, vol. 15. Nature Publishing Group, pp. 1405–1414, 2013.","apa":"Campinho, P., Behrndt, M., Ranft, J., Risler, T., Minc, N., &#38; Heisenberg, C.-P. J. (2013). Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb2869\">https://doi.org/10.1038/ncb2869</a>"},"year":"2013","acknowledgement":"This work was supported by the IST Austria and MPI-CBG ","isi":1,"day":"10","oa_version":"Submitted Version","status":"public","_id":"2282","intvolume":"        15","external_id":{"isi":["000327944200005"]},"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Epithelial spreading is a common and fundamental aspect of various developmental and disease-related processes such as epithelial closure and wound healing. A key challenge for epithelial tissues undergoing spreading is to increase their surface area without disrupting epithelial integrity. Here we show that orienting cell divisions by tension constitutes an efficient mechanism by which the enveloping cell layer (EVL) releases anisotropic tension while undergoing spreading during zebrafish epiboly. The control of EVL cell-division orientation by tension involves cell elongation and requires myosin II activity to align the mitotic spindle with the main tension axis. We also found that in the absence of tension-oriented cell divisions and in the presence of increased tissue tension, EVL cells undergo ectopic fusions, suggesting that the reduction of tension anisotropy by oriented cell divisions is required to prevent EVL cells from fusing. We conclude that cell-division orientation by tension constitutes a key mechanism for limiting tension anisotropy and thus promoting tissue spreading during EVL epiboly."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-07-29T10:07:18Z","publist_id":"4652","fulldoi":"https://doi.org/10.1038/ncb2869","date_published":"2013-11-10T00:00:00Z","month":"11","publication_status":"published","volume":15,"language":[{"iso":"eng"}],"department":[{"_id":"CaHe"}],"page":"1405 - 1414","quality_controlled":"1","related_material":{"record":[{"status":"public","id":"1403","relation":"dissertation_contains"}]},"project":[{"grant_number":"I930-B20","call_identifier":"FWF","name":"Control of Epithelial Cell Layer Spreading in Zebrafish","_id":"252ABD0A-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","date_created":"2018-12-11T11:56:45Z","author":[{"orcid":"0000-0002-8526-5416","first_name":"Pedro","full_name":"Campinho, Pedro","last_name":"Campinho","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Behrndt, Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","last_name":"Behrndt","first_name":"Martin"},{"first_name":"Jonas","last_name":"Ranft","full_name":"Ranft, Jonas"},{"first_name":"Thomas","full_name":"Risler, Thomas","last_name":"Risler"},{"full_name":"Minc, Nicolas","last_name":"Minc","first_name":"Nicolas"},{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"publication":"Nature Cell Biology","scopus_import":"1","corr_author":"1","type":"journal_article","doi":"10.1038/ncb2869","main_file_link":[{"open_access":"1","url":"http://hal.upmc.fr/hal-00983313/"}],"oa":1,"title":"Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading during zebrafish epiboly"},{"date_published":"2013-12-12T00:00:00Z","has_accepted_license":"1","ddc":["000"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.1371/journal.pone.0080814","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"lang":"eng","text":"Cooperative behavior, where one individual incurs a cost to help another, is a wide spread phenomenon. Here we study direct reciprocity in the context of the alternating Prisoner's Dilemma. We consider all strategies that can be implemented by one and two-state automata. We calculate the payoff matrix of all pairwise encounters in the presence of noise. We explore deterministic selection dynamics with and without mutation. Using different error rates and payoff values, we observe convergence to a small number of distinct equilibria. Two of them are uncooperative strict Nash equilibria representing always-defect (ALLD) and Grim. The third equilibrium is mixed and represents a cooperative alliance of several strategies, dominated by a strategy which we call Forgiver. Forgiver cooperates whenever the opponent has cooperated; it defects once when the opponent has defected, but subsequently Forgiver attempts to re-establish cooperation even if the opponent has defected again. Forgiver is not an evolutionarily stable strategy, but the alliance, which it rules, is asymptotically stable. For a wide range of parameter values the most commonly observed outcome is convergence to the mixed equilibrium, dominated by Forgiver. Our results show that although forgiving might incur a short-term loss it can lead to a long-term gain. Forgiveness facilitates stable cooperation in the presence of exploitation and noise."}],"ec_funded":1,"file_date_updated":"2020-07-14T12:45:34Z","date_updated":"2026-07-29T10:15:25Z","publist_id":"4702","issue":"12","external_id":{"isi":["000328731800009"]},"intvolume":"         8","file":[{"checksum":"808e8b9e6e89658bee4ffbbfac1bd19d","access_level":"open_access","relation":"main_file","creator":"system","date_updated":"2020-07-14T12:45:34Z","content_type":"application/pdf","file_id":"4868","date_created":"2018-12-12T10:11:15Z","file_size":1050042,"file_name":"IST-2016-409-v1+1_journal.pone.0080814.pdf"}],"isi":1,"day":"12","publisher":"Public Library of Science","year":"2013","citation":{"apa":"Zagorsky, B., Reiter, J., Chatterjee, K., &#38; Nowak, M. (2013). Forgiver triumphs in alternating prisoner’s dilemma . <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0080814\">https://doi.org/10.1371/journal.pone.0080814</a>","ieee":"B. Zagorsky, J. Reiter, K. Chatterjee, and M. Nowak, “Forgiver triumphs in alternating prisoner’s dilemma ,” <i>PLoS One</i>, vol. 8, no. 12. Public Library of Science, 2013.","ama":"Zagorsky B, Reiter J, Chatterjee K, Nowak M. Forgiver triumphs in alternating prisoner’s dilemma . <i>PLoS One</i>. 2013;8(12). doi:<a href=\"https://doi.org/10.1371/journal.pone.0080814\">10.1371/journal.pone.0080814</a>","ista":"Zagorsky B, Reiter J, Chatterjee K, Nowak M. 2013. Forgiver triumphs in alternating prisoner’s dilemma . PLoS One. 8(12), e80814.","mla":"Zagorsky, Benjamin, et al. “Forgiver Triumphs in Alternating Prisoner’s Dilemma .” <i>PLoS One</i>, vol. 8, no. 12, e80814, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pone.0080814\">10.1371/journal.pone.0080814</a>.","short":"B. Zagorsky, J. Reiter, K. Chatterjee, M. Nowak, PLoS One 8 (2013).","chicago":"Zagorsky, Benjamin, Johannes Reiter, Krishnendu Chatterjee, and Martin Nowak. “Forgiver Triumphs in Alternating Prisoner’s Dilemma .” <i>PLoS One</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pone.0080814\">https://doi.org/10.1371/journal.pone.0080814</a>."},"_id":"2247","status":"public","oa_version":"Published Version","article_number":"e80814","oa":1,"title":"Forgiver triumphs in alternating prisoner's dilemma ","type":"journal_article","doi":"10.1371/journal.pone.0080814","publication":"PLoS One","author":[{"first_name":"Benjamin","full_name":"Zagorsky, Benjamin","last_name":"Zagorsky"},{"full_name":"Reiter, Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","last_name":"Reiter","orcid":"0000-0002-0170-7353","first_name":"Johannes"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"scopus_import":"1","project":[{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307"},{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","related_material":{"record":[{"status":"public","relation":"research_data","id":"9749"},{"id":"1400","relation":"dissertation_contains","status":"public"}]},"article_processing_charge":"No","date_created":"2018-12-11T11:56:33Z","month":"12","publication_status":"published","pubrep_id":"409","volume":8,"language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}]},{"month":"01","volume":6,"department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"pubrep_id":"415","publication_status":"published","page":"34 - 45","quality_controlled":"1","related_material":{"record":[{"id":"1400","relation":"dissertation_contains","status":"public"}]},"project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"}],"date_created":"2018-12-11T11:59:58Z","article_processing_charge":"No","author":[{"first_name":"Johannes","orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes","last_name":"Reiter","id":"4A918E98-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Božić","full_name":"Božić, Ivana","first_name":"Ivana"},{"id":"135B5B70-E9D2-11E9-BD74-BB415DA2B523","last_name":"Allen","full_name":"Allen, Benjamin","first_name":"Benjamin"},{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"}],"publication":"Evolutionary Applications","scopus_import":"1","corr_author":"1","doi":"10.1111/eva.12020","type":"journal_article","oa":1,"title":"The effect of one additional driver mutation on tumor progression","citation":{"apa":"Reiter, J., Božić, I., Allen, B., Chatterjee, K., &#38; Nowak, M. (2013). The effect of one additional driver mutation on tumor progression. <i>Evolutionary Applications</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/eva.12020\">https://doi.org/10.1111/eva.12020</a>","ieee":"J. Reiter, I. Božić, B. Allen, K. Chatterjee, and M. Nowak, “The effect of one additional driver mutation on tumor progression,” <i>Evolutionary Applications</i>, vol. 6, no. 1. Wiley-Blackwell, pp. 34–45, 2013.","ama":"Reiter J, Božić I, Allen B, Chatterjee K, Nowak M. The effect of one additional driver mutation on tumor progression. <i>Evolutionary Applications</i>. 2013;6(1):34-45. doi:<a href=\"https://doi.org/10.1111/eva.12020\">10.1111/eva.12020</a>","ista":"Reiter J, Božić I, Allen B, Chatterjee K, Nowak M. 2013. The effect of one additional driver mutation on tumor progression. Evolutionary Applications. 6(1), 34–45.","mla":"Reiter, Johannes, et al. “The Effect of One Additional Driver Mutation on Tumor Progression.” <i>Evolutionary Applications</i>, vol. 6, no. 1, Wiley-Blackwell, 2013, pp. 34–45, doi:<a href=\"https://doi.org/10.1111/eva.12020\">10.1111/eva.12020</a>.","short":"J. Reiter, I. Božić, B. Allen, K. Chatterjee, M. Nowak, Evolutionary Applications 6 (2013) 34–45.","chicago":"Reiter, Johannes, Ivana Božić, Benjamin Allen, Krishnendu Chatterjee, and Martin Nowak. “The Effect of One Additional Driver Mutation on Tumor Progression.” <i>Evolutionary Applications</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1111/eva.12020\">https://doi.org/10.1111/eva.12020</a>."},"year":"2013","publisher":"Wiley-Blackwell","day":"01","isi":1,"oa_version":"Published Version","_id":"2858","status":"public","file":[{"relation":"main_file","checksum":"e2955b3889f8a823c3d5a72cb16f8957","access_level":"open_access","creator":"system","date_updated":"2020-07-14T12:45:51Z","content_type":"application/pdf","file_id":"5173","file_size":1172037,"date_created":"2018-12-12T10:15:50Z","file_name":"IST-2016-415-v1+1_Reiter_et_al-2013-Evolutionary_Applications.pdf"}],"intvolume":"         6","external_id":{"isi":["000313878800004"]},"issue":"1","file_date_updated":"2020-07-14T12:45:51Z","ec_funded":1,"abstract":[{"text":"Tumor growth is caused by the acquisition of driver mutations, which enhance the net reproductive rate of cells. Driver mutations may increase cell division, reduce cell death, or allow cells to overcome density-limiting effects. We study the dynamics of tumor growth as one additional driver mutation is acquired. Our models are based on two-type branching processes that terminate in either tumor disappearance or tumor detection. In our first model, both cell types grow exponentially, with a faster rate for cells carrying the additional driver. We find that the additional driver mutation does not affect the survival probability of the lesion, but can substantially reduce the time to reach the detectable size if the lesion is slow growing. In our second model, cells lacking the additional driver cannot exceed a fixed carrying capacity, due to density limitations. In this case, the time to detection depends strongly on this carrying capacity. Our model provides a quantitative framework for studying tumor dynamics during different stages of progression. We observe that early, small lesions need additional drivers, while late stage metastases are only marginally affected by them. These results help to explain why additional driver mutations are typically not detected in fast-growing metastases.","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"3931","date_updated":"2026-07-29T10:15:25Z","fulldoi":"https://doi.org/10.1111/eva.12020","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"date_published":"2013-01-01T00:00:00Z","has_accepted_license":"1"},{"month":"06","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"volume":2,"publication_status":"published","pubrep_id":"134","quality_controlled":"1","related_material":{"record":[{"id":"1400","relation":"dissertation_contains","status":"public"}]},"date_created":"2018-12-11T11:59:45Z","article_processing_charge":"No","author":[{"first_name":"Ivana","last_name":"Božić","full_name":"Božić, Ivana"},{"orcid":"0000-0002-0170-7353","first_name":"Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","last_name":"Reiter","full_name":"Reiter, Johannes"},{"full_name":"Allen, Benjamin","last_name":"Allen","first_name":"Benjamin"},{"first_name":"Tibor","last_name":"Antal","full_name":"Antal, Tibor"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Preya","full_name":"Shah, Preya","last_name":"Shah"},{"first_name":"Yo","last_name":"Moon","full_name":"Moon, Yo"},{"first_name":"Amin","last_name":"Yaqubie","full_name":"Yaqubie, Amin"},{"first_name":"Nicole","last_name":"Kelly","full_name":"Kelly, Nicole"},{"first_name":"Dung","full_name":"Le, Dung","last_name":"Le"},{"first_name":"Evan","full_name":"Lipson, Evan","last_name":"Lipson"},{"first_name":"Paul","last_name":"Chapman","full_name":"Chapman, Paul"},{"full_name":"Diaz, Luis","last_name":"Diaz","first_name":"Luis"},{"first_name":"Bert","last_name":"Vogelstein","full_name":"Vogelstein, Bert"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"publication":"eLife","scopus_import":"1","article_number":"e00747","doi":"10.7554/eLife.00747","type":"journal_article","oa":1,"title":"Evolutionary dynamics of cancer in response to targeted combination therapy","citation":{"chicago":"Božić, Ivana, Johannes Reiter, Benjamin Allen, Tibor Antal, Krishnendu Chatterjee, Preya Shah, Yo Moon, et al. “Evolutionary Dynamics of Cancer in Response to Targeted Combination Therapy.” <i>ELife</i>. eLife Sciences Publications, 2013. <a href=\"https://doi.org/10.7554/eLife.00747\">https://doi.org/10.7554/eLife.00747</a>.","mla":"Božić, Ivana, et al. “Evolutionary Dynamics of Cancer in Response to Targeted Combination Therapy.” <i>ELife</i>, vol. 2, e00747, eLife Sciences Publications, 2013, doi:<a href=\"https://doi.org/10.7554/eLife.00747\">10.7554/eLife.00747</a>.","short":"I. Božić, J. Reiter, B. Allen, T. Antal, K. Chatterjee, P. Shah, Y. Moon, A. Yaqubie, N. Kelly, D. Le, E. Lipson, P. Chapman, L. Diaz, B. Vogelstein, M. Nowak, ELife 2 (2013).","ista":"Božić I, Reiter J, Allen B, Antal T, Chatterjee K, Shah P, Moon Y, Yaqubie A, Kelly N, Le D, Lipson E, Chapman P, Diaz L, Vogelstein B, Nowak M. 2013. Evolutionary dynamics of cancer in response to targeted combination therapy. eLife. 2, e00747.","ama":"Božić I, Reiter J, Allen B, et al. Evolutionary dynamics of cancer in response to targeted combination therapy. <i>eLife</i>. 2013;2. doi:<a href=\"https://doi.org/10.7554/eLife.00747\">10.7554/eLife.00747</a>","apa":"Božić, I., Reiter, J., Allen, B., Antal, T., Chatterjee, K., Shah, P., … Nowak, M. (2013). Evolutionary dynamics of cancer in response to targeted combination therapy. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.00747\">https://doi.org/10.7554/eLife.00747</a>","ieee":"I. Božić <i>et al.</i>, “Evolutionary dynamics of cancer in response to targeted combination therapy,” <i>eLife</i>, vol. 2. eLife Sciences Publications, 2013."},"year":"2013","publisher":"eLife Sciences Publications","day":"25","isi":1,"oa_version":"Published Version","_id":"2816","status":"public","file":[{"relation":"main_file","checksum":"2c38c47815eacd8fa66cb8b404cf7c61","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:49Z","creator":"system","file_id":"4967","file_name":"IST-2013-134-v1+1_e00747.full.pdf","file_size":3358321,"date_created":"2018-12-12T10:12:48Z"}],"intvolume":"         2","external_id":{"isi":["000328619300005"]},"file_date_updated":"2020-07-14T12:45:49Z","abstract":[{"lang":"eng","text":"In solid tumors, targeted treatments can lead to dramatic regressions, but responses are often short-lived because resistant cancer cells arise. The major strategy proposed for overcoming resistance is combination therapy. We present a mathematical model describing the evolutionary dynamics of lesions in response to treatment. We first studied 20 melanoma patients receiving vemurafenib. We then applied our model to an independent set of pancreatic, colorectal, and melanoma cancer patients with metastatic disease. We find that dual therapy results in long-term disease control for most patients, if there are no single mutations that cause cross-resistance to both drugs; in patients with large disease burden, triple therapy is needed. We also find that simultaneous therapy with two drugs is much more effective than sequential therapy. Our results provide realistic expectations for the efficacy of new drug combinations and inform the design of trials for new cancer therapeutics."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-07-29T10:15:25Z","publist_id":"3985","fulldoi":"https://doi.org/10.7554/eLife.00747","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570","610"],"has_accepted_license":"1","date_published":"2013-06-25T00:00:00Z"},{"external_id":{"arxiv":["1303.5251"]},"intvolume":"      8044","status":"public","_id":"2000","oa_version":"Preprint","day":"01","arxiv":1,"publisher":"Springer","year":"2013","citation":{"chicago":"Reiter, Johannes, Ivana Božić, Krishnendu Chatterjee, and Martin Nowak. “TTP: Tool for Tumor Progression.” In <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>, 8044:101–6. Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">https://doi.org/10.1007/978-3-642-39799-8_6</a>.","short":"J. Reiter, I. Božić, K. Chatterjee, M. Nowak, in:, Proceedings of 25th Int. Conf. on Computer Aided Verification, Springer, 2013, pp. 101–106.","mla":"Reiter, Johannes, et al. “TTP: Tool for Tumor Progression.” <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>, vol. 8044, Springer, 2013, pp. 101–06, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">10.1007/978-3-642-39799-8_6</a>.","ama":"Reiter J, Božić I, Chatterjee K, Nowak M. TTP: Tool for tumor progression. In: <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>. Vol 8044. Lecture Notes in Computer Science. Springer; 2013:101-106. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">10.1007/978-3-642-39799-8_6</a>","ista":"Reiter J, Božić I, Chatterjee K, Nowak M. 2013. TTP: Tool for tumor progression. Proceedings of 25th Int. Conf. on Computer Aided Verification. CAV: Computer Aided VerificationLecture Notes in Computer Science, LNCS, vol. 8044, 101–106.","apa":"Reiter, J., Božić, I., Chatterjee, K., &#38; Nowak, M. (2013). TTP: Tool for tumor progression. In <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i> (Vol. 8044, pp. 101–106). St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">https://doi.org/10.1007/978-3-642-39799-8_6</a>","ieee":"J. Reiter, I. Božić, K. Chatterjee, and M. Nowak, “TTP: Tool for tumor progression,” in <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>, St. Petersburg, Russia, 2013, vol. 8044, pp. 101–106."},"date_published":"2013-01-01T00:00:00Z","fulldoi":"https://doi.org/10.1007/978-3-642-39799-8_6","alternative_title":["LNCS"],"publist_id":"5077","date_updated":"2026-07-29T10:15:25Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"abstract":[{"lang":"eng","text":"In this work we present a flexible tool for tumor progression, which simulates the evolutionary dynamics of cancer. Tumor progression implements a multi-type branching process where the key parameters are the fitness landscape, the mutation rate, and the average time of cell division. The fitness of a cancer cell depends on the mutations it has accumulated. The input to our tool could be any fitness landscape, mutation rate, and cell division time, and the tool produces the growth dynamics and all relevant statistics."}],"date_created":"2018-12-11T11:55:08Z","project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","related_material":{"record":[{"relation":"earlier_version","id":"5399","status":"public"},{"status":"public","relation":"dissertation_contains","id":"1400"}]},"series_title":"Lecture Notes in Computer Science","page":"101 - 106","publication_status":"published","language":[{"iso":"eng"}],"volume":8044,"department":[{"_id":"KrCh"}],"month":"01","title":"TTP: Tool for tumor progression","oa":1,"type":"conference","doi":"10.1007/978-3-642-39799-8_6","main_file_link":[{"url":"https://arxiv.org/abs/1303.5251","open_access":"1"}],"conference":{"start_date":"2013-07-13","name":"CAV: Computer Aided Verification","end_date":"2013-07-19","location":"St. Petersburg, Russia"},"scopus_import":1,"publication":"Proceedings of 25th Int. Conf. on Computer Aided Verification","author":[{"first_name":"Johannes","orcid":"0000-0002-0170-7353","last_name":"Reiter","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","full_name":"Reiter, Johannes"},{"first_name":"Ivana","full_name":"Božić, Ivana","last_name":"Božić"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}]},{"date_published":"2013-01-07T00:00:00Z","fulldoi":"https://doi.org/10.1098/rspb.2012.2058","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Understanding the relative importance of heterosis and outbreeding depression over multiple generations is a key question in evolutionary biology and is essential for identifying appropriate genetic sources for population and ecosystem restoration. Here we use 2455 experimental crosses between 12 population pairs of the rare perennial plant Rutidosis leptorrhynchoides (Asteraceae) to investigate the multi-generational (F1, F2, F3) fitness outcomes of inter-population hybridization. We detected no evidence of outbreeding depression, with inter-population hybrids and backcrosses showing either similar fitness or significant heterosis for fitness components across the three generations. Variation in heterosis among population pairs was best explained by characteristics of the foreign source or home population, and was greatest when the source population was large, with high genetic diversity and low inbreeding, and the home population was small and inbred. Our results indicate that the primary consideration for maximizing progeny fitness following population augmentation or restoration is the use of seed from large, genetically diverse populations.","lang":"eng"}],"publist_id":"7372","date_updated":"2026-08-12T06:25:53Z","external_id":{"pmid":["23173202"],"isi":["000311943100012"]},"issue":"1750","intvolume":"       280","day":"07","isi":1,"citation":{"ama":"Pickup M, Field D, Rowell D, Young A. Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2013;280(1750). doi:<a href=\"https://doi.org/10.1098/rspb.2012.2058\">10.1098/rspb.2012.2058</a>","ista":"Pickup M, Field D, Rowell D, Young A. 2013. Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. Proceedings of the Royal Society of London Series B Biological Sciences. 280(1750), 2058.","ieee":"M. Pickup, D. Field, D. Rowell, and A. Young, “Source population characteristics affect heterosis following genetic rescue of fragmented plant populations,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 280, no. 1750. Royal Society, 2013.","apa":"Pickup, M., Field, D., Rowell, D., &#38; Young, A. (2013). Source population characteristics affect heterosis following genetic rescue of fragmented plant populations. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society. <a href=\"https://doi.org/10.1098/rspb.2012.2058\">https://doi.org/10.1098/rspb.2012.2058</a>","chicago":"Pickup, Melinda, David Field, David Rowell, and Andrew Young. “Source Population Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant Populations.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, 2013. <a href=\"https://doi.org/10.1098/rspb.2012.2058\">https://doi.org/10.1098/rspb.2012.2058</a>.","short":"M. Pickup, D. Field, D. Rowell, A. Young, Proceedings of the Royal Society of London Series B Biological Sciences 280 (2013).","mla":"Pickup, Melinda, et al. “Source Population Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant Populations.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 280, no. 1750, 2058, Royal Society, 2013, doi:<a href=\"https://doi.org/10.1098/rspb.2012.2058\">10.1098/rspb.2012.2058</a>."},"year":"2013","publisher":"Royal Society","status":"public","_id":"450","oa_version":"Submitted Version","article_number":"2058","pmid":1,"title":"Source population characteristics affect heterosis following genetic rescue of fragmented plant populations","oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574427/","open_access":"1"}],"doi":"10.1098/rspb.2012.2058","type":"journal_article","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","author":[{"first_name":"Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","full_name":"Pickup, Melinda"},{"first_name":"David","orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rowell","full_name":"Rowell, David","first_name":"David"},{"full_name":"Young, Andrew","last_name":"Young","first_name":"Andrew"}],"corr_author":"1","quality_controlled":"1","date_created":"2018-12-11T11:46:32Z","article_processing_charge":"No","month":"01","volume":280,"department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"publication_status":"published"},{"language":[{"iso":"eng"}],"department":[{"_id":"BjHo"}],"volume":87,"publication_status":"published","month":"06","date_created":"2018-12-11T11:59:43Z","article_processing_charge":"No","quality_controlled":"1","project":[{"grant_number":"306589","call_identifier":"FP7","name":"Decoding the complexity of turbulence at its origin","_id":"25152F3A-B435-11E9-9278-68D0E5697425"}],"scopus_import":"1","author":[{"first_name":"Marc","last_name":"Avila","full_name":"Avila, Marc"},{"first_name":"Björn","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof"}],"publication":"Physical Review E","main_file_link":[{"url":"http://arxiv.org/abs/1306.5890","open_access":"1"}],"doi":"10.1103/PhysRevE.87.063012","type":"journal_article","title":"Nature of laminar-turbulence intermittency in shear flows","oa":1,"article_number":"063012","oa_version":"Preprint","status":"public","_id":"2811","year":"2013","citation":{"chicago":"Avila, Marc, and Björn Hof. “Nature of Laminar-Turbulence Intermittency in Shear Flows.” <i>Physical Review E</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/PhysRevE.87.063012\">https://doi.org/10.1103/PhysRevE.87.063012</a>.","mla":"Avila, Marc, and Björn Hof. “Nature of Laminar-Turbulence Intermittency in Shear Flows.” <i>Physical Review E</i>, vol. 87, no. 6, 063012, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/PhysRevE.87.063012\">10.1103/PhysRevE.87.063012</a>.","short":"M. Avila, B. Hof, Physical Review E 87 (2013).","ista":"Avila M, Hof B. 2013. Nature of laminar-turbulence intermittency in shear flows. Physical Review E. 87(6), 063012.","ama":"Avila M, Hof B. Nature of laminar-turbulence intermittency in shear flows. <i>Physical Review E</i>. 2013;87(6). doi:<a href=\"https://doi.org/10.1103/PhysRevE.87.063012\">10.1103/PhysRevE.87.063012</a>","ieee":"M. Avila and B. Hof, “Nature of laminar-turbulence intermittency in shear flows,” <i>Physical Review E</i>, vol. 87, no. 6. American Physical Society, 2013.","apa":"Avila, M., &#38; Hof, B. (2013). Nature of laminar-turbulence intermittency in shear flows. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.87.063012\">https://doi.org/10.1103/PhysRevE.87.063012</a>"},"publisher":"American Physical Society","arxiv":1,"day":"18","isi":1,"intvolume":"        87","external_id":{"arxiv":["1306.5890"],"isi":["000320645700009"]},"issue":"6","publist_id":"4074","date_updated":"2026-08-12T14:29:19Z","ec_funded":1,"abstract":[{"text":"In pipe, channel, and boundary layer flows turbulence first occurs intermittently in space and time: at moderate Reynolds numbers domains of disordered turbulent motion are separated by quiescent laminar regions. Based on direct numerical simulations of pipe flow we argue here that the spatial intermittency has its origin in a nearest neighbor interaction between turbulent regions. We further show that in this regime turbulent flows are intrinsically intermittent with a well-defined equilibrium turbulent fraction but without ever assuming a steady pattern. This transition scenario is analogous to that found in simple models such as coupled map lattices. The scaling observed implies that laminar intermissions of the turbulent flow will persist to arbitrarily large Reynolds numbers.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1103/PhysRevE.87.063012","date_published":"2013-06-18T00:00:00Z"}]