[{"has_accepted_license":"1","alternative_title":["LNCS"],"citation":{"chicago":"Kong, Hui, Ezio Bartocci, and Thomas A Henzinger. “Reachable Set Over-Approximation for Nonlinear Systems Using Piecewise Barrier Tubes,” 10981:449–67. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_24\">https://doi.org/10.1007/978-3-319-96145-3_24</a>.","ieee":"H. Kong, E. Bartocci, and T. A. Henzinger, “Reachable set over-approximation for nonlinear systems using piecewise barrier tubes,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10981, pp. 449–467.","apa":"Kong, H., Bartocci, E., &#38; Henzinger, T. A. (2018). Reachable set over-approximation for nonlinear systems using piecewise barrier tubes (Vol. 10981, pp. 449–467). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_24\">https://doi.org/10.1007/978-3-319-96145-3_24</a>","short":"H. Kong, E. Bartocci, T.A. Henzinger, in:, Springer, 2018, pp. 449–467.","mla":"Kong, Hui, et al. <i>Reachable Set Over-Approximation for Nonlinear Systems Using Piecewise Barrier Tubes</i>. Vol. 10981, Springer, 2018, pp. 449–67, doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_24\">10.1007/978-3-319-96145-3_24</a>.","ama":"Kong H, Bartocci E, Henzinger TA. Reachable set over-approximation for nonlinear systems using piecewise barrier tubes. In: Vol 10981. Springer; 2018:449-467. doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_24\">10.1007/978-3-319-96145-3_24</a>","ista":"Kong H, Bartocci E, Henzinger TA. 2018. Reachable set over-approximation for nonlinear systems using piecewise barrier tubes. CAV: Computer Aided Verification, LNCS, vol. 10981, 449–467."},"date_created":"2018-12-11T11:44:51Z","department":[{"_id":"ToHe"}],"scopus_import":"1","acknowledgement":"Austrian Science Fund FWF: S11402-N23, S11405-N23, Z211-N32","quality_controlled":"1","volume":10981,"author":[{"last_name":"Kong","first_name":"Hui","full_name":"Kong, Hui","orcid":"0000-0002-3066-6941","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bartocci","full_name":"Bartocci, Ezio","first_name":"Ezio"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"}],"publication_status":"published","ddc":["000"],"oa":1,"year":"2018","article_processing_charge":"No","intvolume":"     10981","oa_version":"Published Version","month":"07","license":"https://creativecommons.org/licenses/by/4.0/","date_updated":"2025-04-15T06:25:58Z","page":"449 - 467","abstract":[{"text":"We address the problem of analyzing the reachable set of a polynomial nonlinear continuous system by over-approximating the flowpipe of its dynamics. The common approach to tackle this problem is to perform a numerical integration over a given time horizon based on Taylor expansion and interval arithmetic. However, this method results to be very conservative when there is a large difference in speed between trajectories as time progresses. In this paper, we propose to use combinations of barrier functions, which we call piecewise barrier tube (PBT), to over-approximate flowpipe. The basic idea of PBT is that for each segment of a flowpipe, a coarse box which is big enough to contain the segment is constructed using sampled simulation and then in the box we compute by linear programming a set of barrier functions (called barrier tube or BT for short) which work together to form a tube surrounding the flowpipe. The benefit of using PBT is that (1) BT is independent of time and hence can avoid being stretched and deformed by time; and (2) a small number of BTs can form a tight over-approximation for the flowpipe, which means that the computation required to decide whether the BTs intersect the unsafe set can be reduced significantly. We implemented a prototype called PBTS in C++. Experiments on some benchmark systems show that our approach is effective.","lang":"eng"}],"conference":{"end_date":"2018-07-17","location":"Oxford, United Kingdom","start_date":"2018-07-14","name":"CAV: Computer Aided Verification"},"file_date_updated":"2020-07-14T12:44:53Z","title":"Reachable set over-approximation for nonlinear systems using piecewise barrier tubes","doi":"10.1007/978-3-319-96145-3_24","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer","status":"public","_id":"142","type":"conference","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"language":[{"iso":"eng"}],"isi":1,"fulldoi":"https://doi.org/10.1007/978-3-319-96145-3_24","publist_id":"7781","file":[{"file_name":"2018_LNCS_Kong.pdf","content_type":"application/pdf","file_id":"5718","access_level":"open_access","creator":"dernst","relation":"main_file","date_created":"2018-12-17T15:57:06Z","date_updated":"2020-07-14T12:44:53Z","checksum":"fd95e8026deacef3dc752a733bb9355f","file_size":5591566}],"external_id":{"isi":["000491481600024"]},"day":"18","date_published":"2018-07-18T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"}},{"year":"2018","oa":1,"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.01733"}],"oa_version":"Preprint","intvolume":"        84","month":"04","author":[{"last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","first_name":"Francesco"},{"last_name":"Khanna","full_name":"Khanna, Rajiv","first_name":"Rajiv"},{"last_name":"Ghosh","full_name":"Ghosh, Joydeep","first_name":"Joydeep"},{"last_name":"Rätsch","first_name":"Gunnar","full_name":"Rätsch, Gunnar"}],"publication_status":"published","quality_controlled":"1","arxiv":1,"volume":84,"extern":"1","alternative_title":["PMLR"],"citation":{"mla":"Locatello, Francesco, et al. “Boosting Variational Inference: An Optimization Perspective.” <i>Proceedings of the 21st International Conference on Artificial Intelligence and Statistics</i>, vol. 84, ML Research Press, 2018, pp. 464–72.","ama":"Locatello F, Khanna R, Ghosh J, Rätsch G. Boosting variational inference: An optimization perspective. In: <i>Proceedings of the 21st International Conference on Artificial Intelligence and Statistics</i>. Vol 84. ML Research Press; 2018:464-472.","ista":"Locatello F, Khanna R, Ghosh J, Rätsch G. 2018. Boosting variational inference: An optimization perspective. Proceedings of the 21st International Conference on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence and Statistics, PMLR, vol. 84, 464–472.","chicago":"Locatello, Francesco, Rajiv Khanna, Joydeep Ghosh, and Gunnar Rätsch. “Boosting Variational Inference: An Optimization Perspective.” In <i>Proceedings of the 21st International Conference on Artificial Intelligence and Statistics</i>, 84:464–72. ML Research Press, 2018.","ieee":"F. Locatello, R. Khanna, J. Ghosh, and G. Rätsch, “Boosting variational inference: An optimization perspective,” in <i>Proceedings of the 21st International Conference on Artificial Intelligence and Statistics</i>, Playa Blanca, Lanzarote, 2018, vol. 84, pp. 464–472.","apa":"Locatello, F., Khanna, R., Ghosh, J., &#38; Rätsch, G. (2018). Boosting variational inference: An optimization perspective. In <i>Proceedings of the 21st International Conference on Artificial Intelligence and Statistics</i> (Vol. 84, pp. 464–472). Playa Blanca, Lanzarote: ML Research Press.","short":"F. Locatello, R. Khanna, J. Ghosh, G. Rätsch, in:, Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, ML Research Press, 2018, pp. 464–472."},"publication":"Proceedings of the 21st International Conference on Artificial Intelligence and Statistics","date_created":"2023-08-22T14:15:20Z","scopus_import":"1","department":[{"_id":"FrLo"}],"language":[{"iso":"eng"}],"external_id":{"arxiv":["1708.01733"]},"day":"15","date_published":"2018-04-15T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"ML Research Press","_id":"14201","status":"public","type":"conference","page":"464-472","date_updated":"2024-10-14T12:29:27Z","abstract":[{"lang":"eng","text":"Variational inference is a popular technique to approximate a possibly\r\nintractable Bayesian posterior with a more tractable one. Recently, boosting\r\nvariational inference has been proposed as a new paradigm to approximate the\r\nposterior by a mixture of densities by greedily adding components to the\r\nmixture. However, as is the case with many other variational inference\r\nalgorithms, its theoretical properties have not been studied. In the present\r\nwork, we study the convergence properties of this approach from a modern\r\noptimization viewpoint by establishing connections to the classic Frank-Wolfe\r\nalgorithm. Our analyses yields novel theoretical insights regarding the\r\nsufficient conditions for convergence, explicit rates, and algorithmic\r\nsimplifications. Since a lot of focus in previous works for variational\r\ninference has been on tractability, our work is especially important as a much\r\nneeded attempt to bridge the gap between probabilistic models and their\r\ncorresponding theoretical properties."}],"conference":{"name":"AISTATS: Conference on Artificial Intelligence and Statistics","location":"Playa Blanca, Lanzarote","start_date":"2018-04-09","end_date":"2018-04-11"},"title":"Boosting variational inference: An optimization perspective"},{"extern":"1","citation":{"ieee":"F. Locatello, G. Dresdner, R. Khanna, I. Valera, and G. Rätsch, “Boosting black box variational inference,” in <i>Advances in Neural Information Processing Systems</i>, Montreal, Canada, 2018, vol. 31.","apa":"Locatello, F., Dresdner, G., Khanna, R., Valera, I., &#38; Rätsch, G. (2018). Boosting black box variational inference. In <i>Advances in Neural Information Processing Systems</i> (Vol. 31). Montreal, Canada: Neural Information Processing Systems Foundation.","short":"F. Locatello, G. Dresdner, R. Khanna, I. Valera, G. Rätsch, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2018.","chicago":"Locatello, Francesco, Gideon Dresdner, Rajiv Khanna, Isabel Valera, and Gunnar Rätsch. “Boosting Black Box Variational Inference.” In <i>Advances in Neural Information Processing Systems</i>, Vol. 31. Neural Information Processing Systems Foundation, 2018.","ista":"Locatello F, Dresdner G, Khanna R, Valera I, Rätsch G. 2018. Boosting black box variational inference. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 31.","mla":"Locatello, Francesco, et al. “Boosting Black Box Variational Inference.” <i>Advances in Neural Information Processing Systems</i>, vol. 31, Neural Information Processing Systems Foundation, 2018.","ama":"Locatello F, Dresdner G, Khanna R, Valera I, Rätsch G. Boosting black box variational inference. In: <i>Advances in Neural Information Processing Systems</i>. Vol 31. Neural Information Processing Systems Foundation; 2018."},"publication":"Advances in Neural Information Processing Systems","date_created":"2023-08-22T14:15:40Z","department":[{"_id":"FrLo"}],"scopus_import":"1","quality_controlled":"1","arxiv":1,"publication_identifier":{"eissn":["1049-5258"],"isbn":["9781510884472"]},"volume":31,"author":[{"last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"},{"last_name":"Dresdner","full_name":"Dresdner, Gideon","first_name":"Gideon"},{"last_name":"Khanna","first_name":"Rajiv","full_name":"Khanna, Rajiv"},{"full_name":"Valera, Isabel","first_name":"Isabel","last_name":"Valera"},{"full_name":"Rätsch, Gunnar","first_name":"Gunnar","last_name":"Rätsch"}],"publication_status":"published","oa":1,"year":"2018","article_processing_charge":"No","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.02185"}],"intvolume":"        31","month":"06","date_updated":"2023-09-13T07:38:24Z","abstract":[{"lang":"eng","text":"Approximating a probability density in a tractable manner is a central task\r\nin Bayesian statistics. Variational Inference (VI) is a popular technique that\r\nachieves tractability by choosing a relatively simple variational family.\r\nBorrowing ideas from the classic boosting framework, recent approaches attempt\r\nto \\emph{boost} VI by replacing the selection of a single density with a\r\ngreedily constructed mixture of densities. In order to guarantee convergence,\r\nprevious works impose stringent assumptions that require significant effort for\r\npractitioners. Specifically, they require a custom implementation of the greedy\r\nstep (called the LMO) for every probabilistic model with respect to an\r\nunnatural variational family of truncated distributions. Our work fixes these\r\nissues with novel theoretical and algorithmic insights. On the theoretical\r\nside, we show that boosting VI satisfies a relaxed smoothness assumption which\r\nis sufficient for the convergence of the functional Frank-Wolfe (FW) algorithm.\r\nFurthermore, we rephrase the LMO problem and propose to maximize the Residual\r\nELBO (RELBO) which replaces the standard ELBO optimization in VI. These\r\ntheoretical enhancements allow for black box implementation of the boosting\r\nsubroutine. Finally, we present a stopping criterion drawn from the duality gap\r\nin the classic FW analyses and exhaustive experiments to illustrate the\r\nusefulness of our theoretical and algorithmic contributions."}],"conference":{"end_date":"2018-12-08","name":"NeurIPS: Neural Information Processing Systems","start_date":"2018-12-03","location":"Montreal, Canada"},"title":"Boosting black box variational inference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Neural Information Processing Systems Foundation","status":"public","_id":"14202","type":"conference","language":[{"iso":"eng"}],"external_id":{"arxiv":["1806.02185"]},"day":"06","date_published":"2018-06-06T00:00:00Z"},{"publication_status":"published","author":[{"full_name":"Yurtsever, Alp","first_name":"Alp","last_name":"Yurtsever"},{"last_name":"Fercoq","full_name":"Fercoq, Olivier","first_name":"Olivier"},{"orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello"},{"last_name":"Cevher","first_name":"Volkan","full_name":"Cevher, Volkan"}],"article_processing_charge":"No","oa":1,"year":"2018","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.08544"}],"intvolume":"        80","month":"07","alternative_title":["PMLR"],"extern":"1","citation":{"chicago":"Yurtsever, Alp, Olivier Fercoq, Francesco Locatello, and Volkan Cevher. “A Conditional Gradient Framework for Composite Convex Minimization with Applications to Semidefinite Programming.” In <i>Proceedings of the 35th International Conference on Machine Learning</i>, 80:5727–36. ML Research Press, 2018.","short":"A. Yurtsever, O. Fercoq, F. Locatello, V. Cevher, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 5727–5736.","ieee":"A. Yurtsever, O. Fercoq, F. Locatello, and V. Cevher, “A conditional gradient framework for composite convex minimization with applications to semidefinite programming,” in <i>Proceedings of the 35th International Conference on Machine Learning</i>, Stockholm, Sweden, 2018, vol. 80, pp. 5727–5736.","apa":"Yurtsever, A., Fercoq, O., Locatello, F., &#38; Cevher, V. (2018). A conditional gradient framework for composite convex minimization with applications to semidefinite programming. In <i>Proceedings of the 35th International Conference on Machine Learning</i> (Vol. 80, pp. 5727–5736). Stockholm, Sweden: ML Research Press.","mla":"Yurtsever, Alp, et al. “A Conditional Gradient Framework for Composite Convex Minimization with Applications to Semidefinite Programming.” <i>Proceedings of the 35th International Conference on Machine Learning</i>, vol. 80, ML Research Press, 2018, pp. 5727–36.","ama":"Yurtsever A, Fercoq O, Locatello F, Cevher V. A conditional gradient framework for composite convex minimization with applications to semidefinite programming. In: <i>Proceedings of the 35th International Conference on Machine Learning</i>. Vol 80. ML Research Press; 2018:5727-5736.","ista":"Yurtsever A, Fercoq O, Locatello F, Cevher V. 2018. A conditional gradient framework for composite convex minimization with applications to semidefinite programming. Proceedings of the 35th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 80, 5727–5736."},"publication":"Proceedings of the 35th International Conference on Machine Learning","department":[{"_id":"FrLo"}],"date_created":"2023-08-22T14:16:01Z","quality_controlled":"1","arxiv":1,"volume":80,"language":[{"iso":"eng"}],"external_id":{"arxiv":["1804.08544"]},"day":"15","date_published":"2018-07-15T00:00:00Z","page":"5727-5736","date_updated":"2023-09-13T08:13:39Z","conference":{"location":"Stockholm, Sweden","start_date":"2018-07-10","name":"ICML: International Conference on Machine Learning","end_date":"2018-07-15"},"abstract":[{"lang":"eng","text":"We propose a conditional gradient framework for a composite convex minimization template with broad applications. Our approach combines smoothing and homotopy techniques under the CGM framework, and provably achieves the optimal O(1/k−−√) convergence rate. We demonstrate that the same rate holds if the linear subproblems are solved approximately with additive or multiplicative error. In contrast with the relevant work, we are able to characterize the convergence when the non-smooth term is an indicator function. Specific applications of our framework include the non-smooth minimization, semidefinite programming, and minimization with linear inclusion constraints over a compact domain. Numerical evidence demonstrates the benefits of our framework."}],"title":"A conditional gradient framework for composite convex minimization with applications to semidefinite programming","publisher":"ML Research Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","_id":"14203","status":"public"},{"publisher":"ML Research Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","_id":"14204","status":"public","date_updated":"2024-10-14T12:29:40Z","page":"3198-3207","abstract":[{"lang":"eng","text":"Two popular examples of first-order optimization methods over linear spaces are coordinate descent and matching pursuit algorithms, with their randomized variants. While the former targets the optimization by moving along coordinates, the latter considers a generalized notion of directions. Exploiting the connection between the two algorithms, we present a unified analysis of both, providing affine invariant sublinear O(1/t) rates on smooth objectives and linear convergence on strongly convex objectives. As a byproduct of our affine invariant analysis of matching pursuit, our rates for steepest coordinate descent are the tightest known. Furthermore, we show the first accelerated convergence rate O(1/t2) for matching pursuit and steepest coordinate descent on convex objectives."}],"title":"On matching pursuit and coordinate descent","language":[{"iso":"eng"}],"external_id":{"arxiv":["1803.09539"]},"day":"01","date_published":"2018-07-01T00:00:00Z","arxiv":1,"quality_controlled":"1","volume":80,"extern":"1","alternative_title":["PMLR"],"citation":{"chicago":"Locatello, Francesco, Anant Raj, Sai Praneeth Karimireddy, Gunnar Rätsch, Bernhard Schölkopf, Sebastian U. Stich, and Martin Jaggi. “On Matching Pursuit and Coordinate Descent.” In <i>Proceedings of the 35th International Conference on Machine Learning</i>, 80:3198–3207. ML Research Press, 2018.","short":"F. Locatello, A. Raj, S.P. Karimireddy, G. Rätsch, B. Schölkopf, S.U. Stich, M. Jaggi, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 3198–3207.","ieee":"F. Locatello <i>et al.</i>, “On matching pursuit and coordinate descent,” in <i>Proceedings of the 35th International Conference on Machine Learning</i>, 2018, vol. 80, pp. 3198–3207.","apa":"Locatello, F., Raj, A., Karimireddy, S. P., Rätsch, G., Schölkopf, B., Stich, S. U., &#38; Jaggi, M. (2018). On matching pursuit and coordinate descent. In <i>Proceedings of the 35th International Conference on Machine Learning</i> (Vol. 80, pp. 3198–3207). ML Research Press.","ama":"Locatello F, Raj A, Karimireddy SP, et al. On matching pursuit and coordinate descent. In: <i>Proceedings of the 35th International Conference on Machine Learning</i>. Vol 80. ML Research Press; 2018:3198-3207.","mla":"Locatello, Francesco, et al. “On Matching Pursuit and Coordinate Descent.” <i>Proceedings of the 35th International Conference on Machine Learning</i>, vol. 80, ML Research Press, 2018, pp. 3198–207.","ista":"Locatello F, Raj A, Karimireddy SP, Rätsch G, Schölkopf B, Stich SU, Jaggi M. 2018. On matching pursuit and coordinate descent. Proceedings of the 35th International Conference on Machine Learning. , PMLR, vol. 80, 3198–3207."},"publication":"Proceedings of the 35th International Conference on Machine Learning","department":[{"_id":"FrLo"}],"scopus_import":"1","date_created":"2023-08-22T14:16:25Z","article_processing_charge":"No","oa":1,"year":"2018","oa_version":"Preprint","intvolume":"        80","main_file_link":[{"url":"https://arxiv.org/abs/1803.09539","open_access":"1"}],"month":"07","publication_status":"published","author":[{"last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"last_name":"Raj","first_name":"Anant","full_name":"Raj, Anant"},{"full_name":"Karimireddy, Sai Praneeth","first_name":"Sai Praneeth","last_name":"Karimireddy"},{"full_name":"Rätsch, Gunnar","first_name":"Gunnar","last_name":"Rätsch"},{"first_name":"Bernhard","full_name":"Schölkopf, Bernhard","last_name":"Schölkopf"},{"last_name":"Stich","first_name":"Sebastian U.","full_name":"Stich, Sebastian U."},{"first_name":"Martin","full_name":"Jaggi, Martin","last_name":"Jaggi"}]},{"extern":"1","date_updated":"2024-10-14T12:30:32Z","citation":{"apa":"Locatello, F., Vincent, D., Tolstikhin, I., Ratsch, G., Gelly, S., &#38; Scholkopf, B. (2018). Clustering meets implicit generative models. In <i>6th International Conference on Learning Representations</i>. Vancouver, Canada.","ieee":"F. Locatello, D. Vincent, I. Tolstikhin, G. Ratsch, S. Gelly, and B. Scholkopf, “Clustering meets implicit generative models,” in <i>6th International Conference on Learning Representations</i>, Vancouver, Canada, 2018.","short":"F. Locatello, D. Vincent, I. Tolstikhin, G. Ratsch, S. Gelly, B. Scholkopf, in:, 6th International Conference on Learning Representations, 2018.","chicago":"Locatello, Francesco, Damien Vincent, Ilya Tolstikhin, Gunnar Ratsch, Sylvain Gelly, and Bernhard Scholkopf. “Clustering Meets Implicit Generative Models.” In <i>6th International Conference on Learning Representations</i>, 2018.","ista":"Locatello F, Vincent D, Tolstikhin I, Ratsch G, Gelly S, Scholkopf B. 2018. Clustering meets implicit generative models. 6th International Conference on Learning Representations. International Conference on Machine Learning.","ama":"Locatello F, Vincent D, Tolstikhin I, Ratsch G, Gelly S, Scholkopf B. Clustering meets implicit generative models. In: <i>6th International Conference on Learning Representations</i>. ; 2018.","mla":"Locatello, Francesco, et al. “Clustering Meets Implicit Generative Models.” <i>6th International Conference on Learning Representations</i>, 2018."},"conference":{"location":"Vancouver, Canada","start_date":"2018-04-30","name":"International Conference on Machine Learning","end_date":"2018-05-03"},"publication":"6th International Conference on Learning Representations","abstract":[{"text":"Clustering is a cornerstone of unsupervised learning which can be thought as disentangling multiple generative mechanisms underlying the data. In this paper we introduce an algorithmic framework to train mixtures of implicit generative models which we particularize for variational autoencoders. Relying on an additional set of discriminators, we propose a competitive procedure in which the models only need to approximate the portion of the data distribution from which they can produce realistic samples. As a byproduct, each model is simpler to train, and a clustering interpretation arises naturally from the partitioning of the training points among the models. We empirically show that our approach splits the training distribution in a reasonable way and increases the quality of the generated samples.","lang":"eng"}],"department":[{"_id":"FrLo"}],"scopus_import":"1","title":"Clustering meets implicit generative models","date_created":"2023-08-22T14:25:34Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","arxiv":1,"type":"conference","_id":"14224","status":"public","publication_status":"published","author":[{"last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","first_name":"Francesco"},{"first_name":"Damien","full_name":"Vincent, Damien","last_name":"Vincent"},{"last_name":"Tolstikhin","full_name":"Tolstikhin, Ilya","first_name":"Ilya"},{"full_name":"Ratsch, Gunnar","first_name":"Gunnar","last_name":"Ratsch"},{"last_name":"Gelly","full_name":"Gelly, Sylvain","first_name":"Sylvain"},{"last_name":"Scholkopf","full_name":"Scholkopf, Bernhard","first_name":"Bernhard"}],"language":[{"iso":"eng"}],"external_id":{"arxiv":["1804.11130"]},"day":"01","date_published":"2018-05-01T00:00:00Z","article_processing_charge":"No","oa":1,"year":"2018","oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1804.11130","open_access":"1"}],"month":"05"},{"article_processing_charge":"No","year":"2018","oa":1,"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1804.10985","open_access":"1"}],"month":"07","publication_status":"published","author":[{"last_name":"Brázdil","full_name":"Brázdil, Tomáš","first_name":"Tomáš"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"first_name":"Antonín","full_name":"Kučera, Antonín","last_name":"Kučera"},{"last_name":"Novotny","full_name":"Novotny, Petr","first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Velan","full_name":"Velan, Dominik","first_name":"Dominik"},{"full_name":"Zuleger, Florian","first_name":"Florian","last_name":"Zuleger"}],"quality_controlled":"1","arxiv":1,"publication_identifier":{"isbn":["978-1-4503-5583-4"]},"ec_funded":1,"volume":"F138033","alternative_title":["ACM/IEEE Symposium on Logic in Computer Science"],"citation":{"apa":"Brázdil, T., Chatterjee, K., Kučera, A., Novotný, P., Velan, D., &#38; Zuleger, F. (2018). Efficient algorithms for asymptotic bounds on termination time in VASS (Vol. F138033, pp. 185–194). Presented at the LICS: Logic in Computer Science, Oxford, United Kingdom: IEEE. <a href=\"https://doi.org/10.1145/3209108.3209191\">https://doi.org/10.1145/3209108.3209191</a>","ieee":"T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, and F. Zuleger, “Efficient algorithms for asymptotic bounds on termination time in VASS,” presented at the LICS: Logic in Computer Science, Oxford, United Kingdom, 2018, vol. F138033, pp. 185–194.","short":"T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, F. Zuleger, in:, IEEE, 2018, pp. 185–194.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Antonín Kučera, Petr Novotný, Dominik Velan, and Florian Zuleger. “Efficient Algorithms for Asymptotic Bounds on Termination Time in VASS,” F138033:185–94. IEEE, 2018. <a href=\"https://doi.org/10.1145/3209108.3209191\">https://doi.org/10.1145/3209108.3209191</a>.","ista":"Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. 2018. Efficient algorithms for asymptotic bounds on termination time in VASS. LICS: Logic in Computer Science, ACM/IEEE Symposium on Logic in Computer Science, vol. F138033, 185–194.","ama":"Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. Efficient algorithms for asymptotic bounds on termination time in VASS. In: Vol F138033. IEEE; 2018:185-194. doi:<a href=\"https://doi.org/10.1145/3209108.3209191\">10.1145/3209108.3209191</a>","mla":"Brázdil, Tomáš, et al. <i>Efficient Algorithms for Asymptotic Bounds on Termination Time in VASS</i>. Vol. F138033, IEEE, 2018, pp. 185–94, doi:<a href=\"https://doi.org/10.1145/3209108.3209191\">10.1145/3209108.3209191</a>."},"scopus_import":"1","department":[{"_id":"KrCh"}],"date_created":"2018-12-11T11:44:51Z","fulldoi":"https://doi.org/10.1145/3209108.3209191","isi":1,"publist_id":"7780","language":[{"iso":"eng"}],"external_id":{"isi":["000545262800020"],"arxiv":["1804.10985"]},"date_published":"2018-07-09T00:00:00Z","day":"09","doi":"10.1145/3209108.3209191","publisher":"IEEE","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","project":[{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"}],"status":"public","_id":"143","page":"185 - 194","date_updated":"2025-06-04T08:04:55Z","conference":{"end_date":"2018-07-12","start_date":"2018-07-09","location":"Oxford, United Kingdom","name":"LICS: Logic in Computer Science"},"abstract":[{"lang":"eng","text":"Vector Addition Systems with States (VASS) provide a well-known and fundamental model for the analysis of concurrent processes, parameterized systems, and are also used as abstract models of programs in resource bound analysis. In this paper we study the problem of obtaining asymptotic bounds on the termination time of a given VASS. In particular, we focus on the practically important case of obtaining polynomial bounds on termination time. Our main contributions are as follows: First, we present a polynomial-time algorithm for deciding whether a given VASS has a linear asymptotic complexity. We also show that if the complexity of a VASS is not linear, it is at least quadratic. Second, we classify VASS according to quantitative properties of their cycles. We show that certain singularities in these properties are the key reason for non-polynomial asymptotic complexity of VASS. In absence of singularities, we show that the asymptotic complexity is always polynomial and of the form Θ(nk), for some integer k d, where d is the dimension of the VASS. We present a polynomial-time algorithm computing the optimal k. For general VASS, the same algorithm, which is based on a complete technique for the construction of ranking functions in VASS, produces a valid lower bound, i.e., a k such that the termination complexity is (nk). Our results are based on new insights into the geometry of VASS dynamics, which hold the potential for further applicability to VASS analysis."}],"title":"Efficient algorithms for asymptotic bounds on termination time in VASS"},{"external_id":{"arxiv":["1804.11130"]},"language":[{"iso":"eng"}],"author":[{"first_name":"Francesco","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello"},{"last_name":"Vincent","full_name":"Vincent, Damien","first_name":"Damien"},{"last_name":"Tolstikhin","full_name":"Tolstikhin, Ilya","first_name":"Ilya"},{"last_name":"Rätsch","first_name":"Gunnar","full_name":"Rätsch, Gunnar"},{"first_name":"Sylvain","full_name":"Gelly, Sylvain","last_name":"Gelly"},{"first_name":"Bernhard","full_name":"Schölkopf, Bernhard","last_name":"Schölkopf"}],"fulldoi":"https://doi.org/10.48550/arXiv.1804.11130","publication_status":"submitted","day":"30","date_published":"2018-04-30T00:00:00Z","year":"2018","oa":1,"article_processing_charge":"No","month":"04","oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1804.11130","open_access":"1"}],"citation":{"ista":"Locatello F, Vincent D, Tolstikhin I, Rätsch G, Gelly S, Schölkopf B. Competitive training of mixtures of independent deep generative models. arXiv, 1804.11130.","mla":"Locatello, Francesco, et al. “Competitive Training of Mixtures of Independent Deep Generative Models.” <i>ArXiv</i>, 1804.11130, doi:<a href=\"https://doi.org/10.48550/arXiv.1804.11130\">10.48550/arXiv.1804.11130</a>.","ama":"Locatello F, Vincent D, Tolstikhin I, Rätsch G, Gelly S, Schölkopf B. Competitive training of mixtures of independent deep generative models. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.1804.11130\">10.48550/arXiv.1804.11130</a>","apa":"Locatello, F., Vincent, D., Tolstikhin, I., Rätsch, G., Gelly, S., &#38; Schölkopf, B. (n.d.). Competitive training of mixtures of independent deep generative models. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.1804.11130\">https://doi.org/10.48550/arXiv.1804.11130</a>","ieee":"F. Locatello, D. Vincent, I. Tolstikhin, G. Rätsch, S. Gelly, and B. Schölkopf, “Competitive training of mixtures of independent deep generative models,” <i>arXiv</i>. .","short":"F. Locatello, D. Vincent, I. Tolstikhin, G. Rätsch, S. Gelly, B. Schölkopf, ArXiv (n.d.).","chicago":"Locatello, Francesco, Damien Vincent, Ilya Tolstikhin, Gunnar Rätsch, Sylvain Gelly, and Bernhard Schölkopf. “Competitive Training of Mixtures of Independent Deep Generative Models.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.1804.11130\">https://doi.org/10.48550/arXiv.1804.11130</a>."},"date_updated":"2024-10-14T12:31:09Z","extern":"1","date_created":"2023-09-13T12:20:49Z","title":"Competitive training of mixtures of independent deep generative models","department":[{"_id":"FrLo"}],"abstract":[{"text":"A common assumption in causal modeling posits that the data is generated by a\r\nset of independent mechanisms, and algorithms should aim to recover this\r\nstructure. Standard unsupervised learning, however, is often concerned with\r\ntraining a single model to capture the overall distribution or aspects thereof.\r\nInspired by clustering approaches, we consider mixtures of implicit generative\r\nmodels that ``disentangle'' the independent generative mechanisms underlying\r\nthe data. Relying on an additional set of discriminators, we propose a\r\ncompetitive training procedure in which the models only need to capture the\r\nportion of the data distribution from which they can produce realistic samples.\r\nAs a by-product, each model is simpler and faster to train. We empirically show\r\nthat our approach splits the training distribution in a sensible way and\r\nincreases the quality of the generated samples.","lang":"eng"}],"publication":"arXiv","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"1804.11130","doi":"10.48550/arXiv.1804.11130","status":"public","_id":"14327","type":"preprint","arxiv":1},{"alternative_title":["ACM/IEEE Symposium on Logic in Computer Science"],"citation":{"short":"T. Ferrere, T.A. Henzinger, E. Saraç, in:, IEEE, 2018, pp. 394–403.","ieee":"T. Ferrere, T. A. Henzinger, and E. Saraç, “A theory of register monitors,” presented at the LICS: Logic in Computer Science, Oxford, UK, 2018, vol. Part F138033, pp. 394–403.","apa":"Ferrere, T., Henzinger, T. A., &#38; Saraç, E. (2018). A theory of register monitors (Vol. Part F138033, pp. 394–403). Presented at the LICS: Logic in Computer Science, Oxford, UK: IEEE. <a href=\"https://doi.org/10.1145/3209108.3209194\">https://doi.org/10.1145/3209108.3209194</a>","chicago":"Ferrere, Thomas, Thomas A Henzinger, and Ege Saraç. “A Theory of Register Monitors,” Part F138033:394–403. IEEE, 2018. <a href=\"https://doi.org/10.1145/3209108.3209194\">https://doi.org/10.1145/3209108.3209194</a>.","ista":"Ferrere T, Henzinger TA, Saraç E. 2018. A theory of register monitors. LICS: Logic in Computer Science, ACM/IEEE Symposium on Logic in Computer Science, vol. Part F138033, 394–403.","mla":"Ferrere, Thomas, et al. <i>A Theory of Register Monitors</i>. Vol. Part F138033, IEEE, 2018, pp. 394–403, doi:<a href=\"https://doi.org/10.1145/3209108.3209194\">10.1145/3209108.3209194</a>.","ama":"Ferrere T, Henzinger TA, Saraç E. A theory of register monitors. In: Vol Part F138033. IEEE; 2018:394-403. doi:<a href=\"https://doi.org/10.1145/3209108.3209194\">10.1145/3209108.3209194</a>"},"scopus_import":"1","department":[{"_id":"ToHe"}],"date_created":"2018-12-11T11:44:52Z","quality_controlled":"1","volume":"Part F138033","publication_status":"published","author":[{"id":"40960E6E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","first_name":"Thomas","last_name":"Ferrere"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"},{"last_name":"Saraç","full_name":"Saraç, Ege","first_name":"Ege"}],"article_processing_charge":"No","year":"2018","oa_version":"None","month":"07","page":"394 - 403","date_updated":"2023-09-08T11:49:13Z","conference":{"end_date":"2018-07-12","name":"LICS: Logic in Computer Science","start_date":"2018-07-09","location":"Oxford, UK"},"abstract":[{"lang":"eng","text":"The task of a monitor is to watch, at run-time, the execution of a reactive system, and signal the occurrence of a safety violation in the observed sequence of events. While finite-state monitors have been studied extensively, in practice, monitoring software also makes use of unbounded memory. We define a model of automata equipped with integer-valued registers which can execute only a bounded number of instructions between consecutive events, and thus can form the theoretical basis for the study of infinite-state monitors. We classify these register monitors according to the number k of available registers, and the type of register instructions. In stark contrast to the theory of computability for register machines, we prove that for every k 1, monitors with k + 1 counters (with instruction set 〈+1, =〉) are strictly more expressive than monitors with k counters. We also show that adder monitors (with instruction set 〈1, +, =〉) are strictly more expressive than counter monitors, but are complete for monitoring all computable safety -languages for k = 6. Real-time monitors are further required to signal the occurrence of a safety violation as soon as it occurs. The expressiveness hierarchy for counter monitors carries over to real-time monitors. We then show that 2 adders cannot simulate 3 counters in real-time. Finally, we show that real-time adder monitors with inequalities are as expressive as real-time Turing machines."}],"title":"A theory of register monitors","doi":"10.1145/3209108.3209194","publisher":"IEEE","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"conference","_id":"144","status":"public","fulldoi":"https://doi.org/10.1145/3209108.3209194","isi":1,"publist_id":"7779","language":[{"iso":"eng"}],"external_id":{"isi":["000545262800041"]},"day":"09","date_published":"2018-07-09T00:00:00Z"},{"author":[{"id":"45812BD4-F248-11E8-B48F-1D18A9856A87","full_name":"Truckenbrodt, Sven M","first_name":"Sven M","last_name":"Truckenbrodt"},{"last_name":"Viplav","first_name":"Abhiyan","full_name":"Viplav, Abhiyan"},{"full_name":"Jähne, Sebsatian","first_name":"Sebsatian","last_name":"Jähne"},{"first_name":"Angela","full_name":"Vogts, Angela","last_name":"Vogts"},{"first_name":"Annette","full_name":"Denker, Annette","last_name":"Denker"},{"last_name":"Wildhagen","full_name":"Wildhagen, Hanna","first_name":"Hanna"},{"first_name":"Eugenio","full_name":"Fornasiero, Eugenio","last_name":"Fornasiero"},{"first_name":"Silvio","full_name":"Rizzoli, Silvio","last_name":"Rizzoli"}],"article_type":"original","publication_status":"published","ddc":["570"],"oa":1,"year":"2018","article_processing_charge":"No","month":"08","issue":"15","intvolume":"        37","oa_version":"Published Version","citation":{"ama":"Truckenbrodt SM, Viplav A, Jähne S, et al. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. <i>The EMBO Journal</i>. 2018;37(15). doi:<a href=\"https://doi.org/10.15252/embj.201798044\">10.15252/embj.201798044</a>","mla":"Truckenbrodt, Sven M., et al. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” <i>The EMBO Journal</i>, vol. 37, no. 15, e98044, Wiley, 2018, doi:<a href=\"https://doi.org/10.15252/embj.201798044\">10.15252/embj.201798044</a>.","ista":"Truckenbrodt SM, Viplav A, Jähne S, Vogts A, Denker A, Wildhagen H, Fornasiero E, Rizzoli S. 2018. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. 37(15), e98044.","chicago":"Truckenbrodt, Sven M, Abhiyan Viplav, Sebsatian Jähne, Angela Vogts, Annette Denker, Hanna Wildhagen, Eugenio Fornasiero, and Silvio Rizzoli. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” <i>The EMBO Journal</i>. Wiley, 2018. <a href=\"https://doi.org/10.15252/embj.201798044\">https://doi.org/10.15252/embj.201798044</a>.","short":"S.M. Truckenbrodt, A. Viplav, S. Jähne, A. Vogts, A. Denker, H. Wildhagen, E. Fornasiero, S. Rizzoli, The EMBO Journal 37 (2018).","apa":"Truckenbrodt, S. M., Viplav, A., Jähne, S., Vogts, A., Denker, A., Wildhagen, H., … Rizzoli, S. (2018). Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. <i>The EMBO Journal</i>. Wiley. <a href=\"https://doi.org/10.15252/embj.201798044\">https://doi.org/10.15252/embj.201798044</a>","ieee":"S. M. Truckenbrodt <i>et al.</i>, “Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission,” <i>The EMBO Journal</i>, vol. 37, no. 15. Wiley, 2018."},"corr_author":"1","has_accepted_license":"1","date_created":"2018-12-11T11:44:52Z","scopus_import":"1","department":[{"_id":"JoDa"}],"publication":"The EMBO Journal","article_number":"e98044","acknowledgement":"We thank Reinhard Jahn for providing a plasmid for YFP-SNAP25. We thank Erwin Neher for help with the development of the mathematical model of the synaptic vesicle life cycle. We thank Martin Meschkat, Andreas Höbartner, Annedore Punge, and Peer Hoopmann for help with the experiments. We thank Burkhard Rammner for providing the illustrations of synaptic vesicle and protein dynamics. We thank Manuel Maidorn, Martin Helm, and Katharina N. Richter for critically reading the manuscript. S.T. was supported by an Excellence Stipend of the Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences (GGNB). E.F.F. is a recipient of long-term fellowships from the European Molecular Biology Organization (ALTF_797-2012) and from the Human Frontier Science Program (HFSP_LT000830/2013). The work was supported by grants to S.O.R. from the European Research Council (ERC-2013-CoG NeuroMolAnatomy) and from the Deutsche Forschungsgemeinschaft (Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, SFB1190/P09, SFB889/A05, and SFB1286/A03, and DFG RI 1967 7/1). The nanoSIMS instrument was funded by the German Federal Ministry of Education and Research (03F0626A).","volume":37,"publication_identifier":{"issn":["0261-4189"]},"quality_controlled":"1","external_id":{"pmid":["29950309"],"isi":["000440416900005"]},"language":[{"iso":"eng"}],"publist_id":"7778","fulldoi":"https://doi.org/10.15252/embj.201798044","isi":1,"file":[{"file_size":2846470,"date_updated":"2020-07-14T12:44:56Z","checksum":"a540feb6c9af6aefc78de531461a8835","relation":"main_file","date_created":"2018-12-17T14:17:29Z","creator":"dernst","access_level":"open_access","file_id":"5710","file_name":"2018_EMBO_Truckenbrodt.pdf","content_type":"application/pdf"}],"day":"01","date_published":"2018-08-01T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"pmid":1,"date_updated":"2024-10-09T20:58:32Z","title":"Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission","abstract":[{"text":"Aged proteins can become hazardous to cellular function, by accumulating molecular damage. This implies that cells should preferentially rely on newly produced ones. We tested this hypothesis in cultured hippocampal neurons, focusing on synaptic transmission. We found that newly synthesized vesicle proteins were incorporated in the actively recycling pool of vesicles responsible for all neurotransmitter release during physiological activity. We observed this for the calcium sensor Synaptotagmin 1, for the neurotransmitter transporter VGAT, and for the fusion protein VAMP2 (Synaptobrevin 2). Metabolic labeling of proteins and visualization by secondary ion mass spectrometry enabled us to query the entire protein makeup of the actively recycling vesicles, which we found to be younger than that of non-recycling vesicles. The young vesicle proteins remained in use for up to ~ 24 h, during which they participated in recycling a few hundred times. They were afterward reluctant to release and were degraded after an additional ~ 24–48 h. We suggest that the recycling pool of synaptic vesicles relies on newly synthesized proteins, while the inactive reserve pool contains older proteins.","lang":"eng"}],"file_date_updated":"2020-07-14T12:44:56Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Wiley","doi":"10.15252/embj.201798044","_id":"145","status":"public","type":"journal_article"},{"quality_controlled":"1","volume":4,"has_accepted_license":"1","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-process-in-root-development-discovered/"}]},"citation":{"ama":"Shi CL, von Wangenheim D, Herrmann U, et al. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. <i>Nature Plants</i>. 2018;4(8):596-604. doi:<a href=\"https://doi.org/10.1038/s41477-018-0212-z\">10.1038/s41477-018-0212-z</a>","mla":"Shi, Chun Lin, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” <i>Nature Plants</i>, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 596–604, doi:<a href=\"https://doi.org/10.1038/s41477-018-0212-z\">10.1038/s41477-018-0212-z</a>.","ista":"Shi CL, von Wangenheim D, Herrmann U, Wildhagen M, Kulik I, Kopf A, Ishida T, Olsson V, Anker MK, Albert M, Butenko MA, Felix G, Sawa S, Claassen M, Friml J, Aalen RB. 2018. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. 4(8), 596–604.","chicago":"Shi, Chun Lin, Daniel von Wangenheim, Ullrich Herrmann, Mari Wildhagen, Ivan Kulik, Andreas Kopf, Takashi Ishida, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” <i>Nature Plants</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0212-z\">https://doi.org/10.1038/s41477-018-0212-z</a>.","short":"C.L. Shi, D. von Wangenheim, U. Herrmann, M. Wildhagen, I. Kulik, A. Kopf, T. Ishida, V. Olsson, M.K. Anker, M. Albert, M.A. Butenko, G. Felix, S. Sawa, M. Claassen, J. Friml, R.B. Aalen, Nature Plants 4 (2018) 596–604.","ieee":"C. L. Shi <i>et al.</i>, “The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling,” <i>Nature Plants</i>, vol. 4, no. 8. Nature Publishing Group, pp. 596–604, 2018.","apa":"Shi, C. L., von Wangenheim, D., Herrmann, U., Wildhagen, M., Kulik, I., Kopf, A., … Aalen, R. B. (2018). The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. <i>Nature Plants</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41477-018-0212-z\">https://doi.org/10.1038/s41477-018-0212-z</a>"},"publication":"Nature Plants","date_created":"2018-12-11T11:44:52Z","department":[{"_id":"JiFr"}],"scopus_import":"1","year":"2018","oa":1,"article_processing_charge":"No","intvolume":"         4","issue":"8","oa_version":"Submitted Version","month":"07","author":[{"full_name":"Shi, Chun Lin","first_name":"Chun Lin","last_name":"Shi"},{"id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247","full_name":"Von Wangenheim, Daniel","first_name":"Daniel","last_name":"Von Wangenheim"},{"first_name":"Ullrich","full_name":"Herrmann, Ullrich","last_name":"Herrmann"},{"first_name":"Mari","full_name":"Wildhagen, Mari","last_name":"Wildhagen"},{"last_name":"Kulik","id":"F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB","first_name":"Ivan","full_name":"Kulik, Ivan"},{"last_name":"Kopf","first_name":"Andreas","full_name":"Kopf, Andreas"},{"last_name":"Ishida","first_name":"Takashi","full_name":"Ishida, Takashi"},{"last_name":"Olsson","first_name":"Vilde","full_name":"Olsson, Vilde"},{"full_name":"Anker, Mari Kristine","first_name":"Mari Kristine","last_name":"Anker"},{"full_name":"Albert, Markus","first_name":"Markus","last_name":"Albert"},{"last_name":"Butenko","first_name":"Melinka A","full_name":"Butenko, Melinka A"},{"last_name":"Felix","full_name":"Felix, Georg","first_name":"Georg"},{"first_name":"Shinichiro","full_name":"Sawa, Shinichiro","last_name":"Sawa"},{"last_name":"Claassen","first_name":"Manfred","full_name":"Claassen, Manfred"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"full_name":"Aalen, Reidunn B","first_name":"Reidunn B","last_name":"Aalen"}],"publication_status":"published","article_type":"original","ddc":["580"],"doi":"10.1038/s41477-018-0212-z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Nature Publishing Group","_id":"146","status":"public","type":"journal_article","page":"596 - 604","date_updated":"2023-09-19T10:08:45Z","pmid":1,"abstract":[{"text":"The root cap protects the stem cell niche of angiosperm roots from damage. In Arabidopsis, lateral root cap (LRC) cells covering the meristematic zone are regularly lost through programmed cell death, while the outermost layer of the root cap covering the tip is repeatedly sloughed. Efficient coordination with stem cells producing new layers is needed to maintain a constant size of the cap. We present a signalling pair, the peptide IDA-LIKE1 (IDL1) and its receptor HAESA-LIKE2 (HSL2), mediating such communication. Live imaging over several days characterized this process from initial fractures in LRC cell files to full separation of a layer. Enhanced expression of IDL1 in the separating root cap layers resulted in increased frequency of sloughing, balanced with generation of new layers in a HSL2-dependent manner. Transcriptome analyses linked IDL1-HSL2 signalling to the transcription factors BEARSKIN1/2 and genes associated with programmed cell death. Mutations in either IDL1 or HSL2 slowed down cell division, maturation and separation. Thus, IDL1-HSL2 signalling potentiates dynamic regulation of the homeostatic balance between stem cell division and sloughing activity.","lang":"eng"}],"file_date_updated":"2020-07-14T12:44:56Z","title":"The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling","language":[{"iso":"eng"}],"publist_id":"7777","fulldoi":"https://doi.org/10.1038/s41477-018-0212-z","file":[{"date_created":"2019-11-18T16:24:07Z","relation":"main_file","creator":"dernst","file_size":226829,"checksum":"da33101c76ee1b2dc5ab28fd2ccba9d0","date_updated":"2020-07-14T12:44:56Z","file_name":"2018_NaturePlants_Shi.pdf","content_type":"application/pdf","access_level":"open_access","file_id":"7043"}],"isi":1,"external_id":{"pmid":["30061750"],"isi":["000443861300016"]},"day":"30","date_published":"2018-07-30T00:00:00Z"},{"abstract":[{"text":"The trafficking of subcellular cargos in eukaryotic cells crucially depends on vesicle budding, a process mediated by ARF-GEFs (ADP-ribosylation factor guanine nucleotide exchange factors). In plants, ARF-GEFs play essential roles in endocytosis, vacuolar trafficking, recycling, secretion, and polar trafficking. Moreover, they are important for plant development, mainly through controlling the polar subcellular localization of PIN-FORMED (PIN) transporters of the plant hormone auxin. Here, using a chemical genetics screen in Arabidopsis thaliana, we identified Endosidin 4 (ES4), an inhibitor of eukaryotic ARF-GEFs. ES4 acts similarly to and synergistically with the established ARF-GEF inhibitor Brefeldin A and has broad effects on intracellular trafficking, including endocytosis, exocytosis, and vacuolar targeting. Additionally, Arabidopsis and yeast (Sacharomyces cerevisiae) mutants defective in ARF-GEF show altered sensitivity to ES4. ES4 interferes with the activation-based membrane association of the ARF1 GTPases, but not of their mutant variants that are activated independently of ARF-GEF activity. Biochemical approaches and docking simulations confirmed that ES4 specifically targets the SEC7 domain-containing ARF-GEFs. These observations collectively identify ES4 as a chemical tool enabling the study of ARF-GEF-mediated processes, including ARF-GEF-mediated plant development.","lang":"eng"}],"title":"The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes","page":"2553 - 2572","date_updated":"2026-06-18T17:36:26Z","pmid":1,"status":"public","_id":"147","project":[{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"},{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"type":"journal_article","doi":"10.1105/tpc.18.00127","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Oxford University Press","date_published":"2018-11-12T00:00:00Z","day":"12","language":[{"iso":"eng"}],"publist_id":"7776","fulldoi":"https://doi.org/10.1105/tpc.18.00127","isi":1,"external_id":{"pmid":["30018156"],"isi":["000450000500023"]},"publication":"The Plant Cell","date_created":"2018-12-11T11:44:52Z","department":[{"_id":"JiFr"}],"scopus_import":"1","citation":{"apa":"Kania, U., Nodzyński, T., Lu, Q., Hicks, G. R., Nerinckx, W., Mishev, K., … Friml, J. (2018). The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. <i>The Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1105/tpc.18.00127\">https://doi.org/10.1105/tpc.18.00127</a>","ieee":"U. Kania <i>et al.</i>, “The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes,” <i>The Plant Cell</i>, vol. 30, no. 10. Oxford University Press, pp. 2553–2572, 2018.","short":"U. Kania, T. Nodzyński, Q. Lu, G.R. Hicks, W. Nerinckx, K. Mishev, F. Peurois, J. Cherfils, R.R.M. De, P. Grones, S. Robert, E. Russinova, J. Friml, The Plant Cell 30 (2018) 2553–2572.","chicago":"Kania, Urszula, Tomasz Nodzyński, Qing Lu, Glenn R Hicks, Wim Nerinckx, Kiril Mishev, Francois Peurois, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.” <i>The Plant Cell</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1105/tpc.18.00127\">https://doi.org/10.1105/tpc.18.00127</a>.","ista":"Kania U, Nodzyński T, Lu Q, Hicks GR, Nerinckx W, Mishev K, Peurois F, Cherfils J, De RRM, Grones P, Robert S, Russinova E, Friml J. 2018. The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. 30(10), 2553–2572.","mla":"Kania, Urszula, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.” <i>The Plant Cell</i>, vol. 30, no. 10, Oxford University Press, 2018, pp. 2553–72, doi:<a href=\"https://doi.org/10.1105/tpc.18.00127\">10.1105/tpc.18.00127</a>.","ama":"Kania U, Nodzyński T, Lu Q, et al. The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. <i>The Plant Cell</i>. 2018;30(10):2553-2572. doi:<a href=\"https://doi.org/10.1105/tpc.18.00127\">10.1105/tpc.18.00127</a>"},"corr_author":"1","quality_controlled":"1","ec_funded":1,"volume":30,"publication_identifier":{"issn":["1040-4651"]},"acknowledgement":"We thank Gerd Jürgens, Sandra Richter, and Sheng Yang He for providing antibodies; Maciek Adamowski, Fernando Aniento, Sebastian Bednarek, Nico Callewaert, Matyás Fendrych, Elena Feraru, and Mugurel I. Feraru for helpful suggestions; Siamsa Doyle for critical reading of the manuscript and helpful comments and suggestions; and Stephanie Smith and Martine De Cock for help in editing and language corrections. We acknowledge the core facility Cellular Imaging of CEITEC supported by the Czech-BioImaging large RI project (LM2015062 funded by MEYS CR) for their support with obtaining scientific data presented in this article. Plant Sciences Core Facility of CEITEC Masaryk University is gratefully acknowledged for obtaining part of the scientific data presented in this article. We acknowledge support from the Fondation pour la Recherche Médicale and from the Institut National du Cancer (J.C.). The research leading to these results was funded by the European Research Council under the European Union's 7th Framework Program (FP7/2007-2013)/ERC grant agreement numbers 282300 and 742985 and the Czech Science Foundation GAČR (GA18-26981S; J.F.); Ministry of Education, Youth, and Sports/MEYS of the Czech Republic under the Project CEITEC 2020 (LQ1601; T.N.); the China Science Council for a predoctoral fellowship (Q.L.); a joint research project within the framework of cooperation between the Research Foundation-Flanders and the Bulgarian Academy of Sciences (VS.025.13N; K.M. and E.R.); Vetenskapsrådet and Vinnova (Verket för Innovationssystem; S.R.), Knut och Alice Wallenbergs Stiftelse via “Shapesystem” Grant 2012.0050 (S.R.), Kempe stiftelserna (P.G.), Tryggers CTS410 (P.G.).","ddc":["580"],"author":[{"last_name":"Kania","id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","full_name":"Kania, Urszula","first_name":"Urszula"},{"last_name":"Nodzyński","full_name":"Nodzyński, Tomasz","first_name":"Tomasz"},{"last_name":"Lu","full_name":"Lu, Qing","first_name":"Qing"},{"full_name":"Hicks, Glenn R","first_name":"Glenn R","last_name":"Hicks"},{"last_name":"Nerinckx","full_name":"Nerinckx, Wim","first_name":"Wim"},{"first_name":"Kiril","full_name":"Mishev, Kiril","last_name":"Mishev"},{"last_name":"Peurois","first_name":"Francois","full_name":"Peurois, Francois"},{"first_name":"Jacqueline","full_name":"Cherfils, Jacqueline","last_name":"Cherfils"},{"last_name":"De","full_name":"De, Rycke Riet Maria","first_name":"Rycke Riet Maria"},{"last_name":"Grones","id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Grones, Peter"},{"last_name":"Robert","full_name":"Robert, Stéphanie","first_name":"Stéphanie"},{"first_name":"Eugenia","full_name":"Russinova, Eugenia","last_name":"Russinova"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"}],"publication_status":"published","article_type":"original","issue":"10","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1105/tpc.18.00127"}],"intvolume":"        30","oa_version":"Published Version","month":"11","oa":1,"year":"2018","article_processing_charge":"No"},{"status":"public","_id":"148","type":"journal_article","project":[{"call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Cell Press","doi":"10.1016/j.cell.2018.06.033","title":"The Chara genome: Secondary complexity and implications for plant terrestrialization","abstract":[{"text":"Land plants evolved from charophytic algae, among which Charophyceae possess the most complex body plans. We present the genome of Chara braunii; comparison of the genome to those of land plants identified evolutionary novelties for plant terrestrialization and land plant heritage genes. C. braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C. braunii plastids are controlled via land-plant-like retrograde signaling, and transcriptional regulation is more elaborate than in other algae. The morphological complexity of this organism may result from expanded gene families, with three cases of particular note: genes effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases, and transcription factors (TFs). Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote.","lang":"eng"}],"pmid":1,"date_updated":"2026-06-18T17:39:09Z","page":"448 - 464.e24","day":"12","date_published":"2018-07-12T00:00:00Z","external_id":{"isi":["000438482800019"],"pmid":["30007417"]},"language":[{"iso":"eng"}],"isi":1,"fulldoi":"https://doi.org/10.1016/j.cell.2018.06.033","publist_id":"7774","ec_funded":1,"volume":174,"quality_controlled":"1","acknowledgement":"In-Data-Review","date_created":"2018-12-11T11:44:53Z","department":[{"_id":"JiFr"}],"scopus_import":"1","publication":"Cell","citation":{"ista":"Nishiyama T, Sakayama H, De Vries J, Buschmann H, Saint Marcoux D, Ullrich K, Haas F, Vanderstraeten L, Becker D, Lang D, Vosolsobě S, Rombauts S, Wilhelmsson P, Janitza P, Kern R, Heyl A, Rümpler F, Calderón Villalobos L, Clay J, Skokan R, Toyoda A, Suzuki Y, Kagoshima H, Schijlen E, Tajeshwar N, Catarino B, Hetherington A, Saltykova A, Bonnot C, Breuninger H, Symeonidi A, Radhakrishnan G, Van Nieuwerburgh F, Deforce D, Chang C, Karol K, Hedrich R, Ulvskov P, Glöckner G, Delwiche C, Petrášek J, Van De Peer Y, Friml J, Beilby M, Dolan L, Kohara Y, Sugano S, Fujiyama A, Delaux PM, Quint M, Theissen G, Hagemann M, Harholt J, Dunand C, Zachgo S, Langdale J, Maumus F, Van Der Straeten D, Gould SB, Rensing S. 2018. The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. 174(2), 448–464.e24.","mla":"Nishiyama, Tomoaki, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” <i>Cell</i>, vol. 174, no. 2, Cell Press, 2018, p. 448–464.e24, doi:<a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">10.1016/j.cell.2018.06.033</a>.","ama":"Nishiyama T, Sakayama H, De Vries J, et al. The Chara genome: Secondary complexity and implications for plant terrestrialization. <i>Cell</i>. 2018;174(2):448-464.e24. doi:<a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">10.1016/j.cell.2018.06.033</a>","short":"T. Nishiyama, H. Sakayama, J. De Vries, H. Buschmann, D. Saint Marcoux, K. Ullrich, F. Haas, L. Vanderstraeten, D. Becker, D. Lang, S. Vosolsobě, S. Rombauts, P. Wilhelmsson, P. Janitza, R. Kern, A. Heyl, F. Rümpler, L. Calderón Villalobos, J. Clay, R. Skokan, A. Toyoda, Y. Suzuki, H. Kagoshima, E. Schijlen, N. Tajeshwar, B. Catarino, A. Hetherington, A. Saltykova, C. Bonnot, H. Breuninger, A. Symeonidi, G. Radhakrishnan, F. Van Nieuwerburgh, D. Deforce, C. Chang, K. Karol, R. Hedrich, P. Ulvskov, G. Glöckner, C. Delwiche, J. Petrášek, Y. Van De Peer, J. Friml, M. Beilby, L. Dolan, Y. Kohara, S. Sugano, A. Fujiyama, P.M. Delaux, M. Quint, G. Theissen, M. Hagemann, J. Harholt, C. Dunand, S. Zachgo, J. Langdale, F. Maumus, D. Van Der Straeten, S.B. Gould, S. Rensing, Cell 174 (2018) 448–464.e24.","apa":"Nishiyama, T., Sakayama, H., De Vries, J., Buschmann, H., Saint Marcoux, D., Ullrich, K., … Rensing, S. (2018). The Chara genome: Secondary complexity and implications for plant terrestrialization. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">https://doi.org/10.1016/j.cell.2018.06.033</a>","ieee":"T. Nishiyama <i>et al.</i>, “The Chara genome: Secondary complexity and implications for plant terrestrialization,” <i>Cell</i>, vol. 174, no. 2. Cell Press, p. 448–464.e24, 2018.","chicago":"Nishiyama, Tomoaki, Hidetoshi Sakayama, Jan De Vries, Henrik Buschmann, Denis Saint Marcoux, Kristian Ullrich, Fabian Haas, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” <i>Cell</i>. Cell Press, 2018. <a href=\"https://doi.org/10.1016/j.cell.2018.06.033\">https://doi.org/10.1016/j.cell.2018.06.033</a>."},"month":"07","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30007417"}],"issue":"2","intvolume":"       174","oa":1,"year":"2018","article_processing_charge":"No","ddc":["580"],"author":[{"full_name":"Nishiyama, Tomoaki","first_name":"Tomoaki","last_name":"Nishiyama"},{"last_name":"Sakayama","first_name":"Hidetoshi","full_name":"Sakayama, Hidetoshi"},{"full_name":"De Vries, Jan","first_name":"Jan","last_name":"De Vries"},{"last_name":"Buschmann","full_name":"Buschmann, Henrik","first_name":"Henrik"},{"last_name":"Saint Marcoux","full_name":"Saint Marcoux, Denis","first_name":"Denis"},{"full_name":"Ullrich, Kristian","first_name":"Kristian","last_name":"Ullrich"},{"last_name":"Haas","first_name":"Fabian","full_name":"Haas, Fabian"},{"full_name":"Vanderstraeten, Lisa","first_name":"Lisa","last_name":"Vanderstraeten"},{"last_name":"Becker","full_name":"Becker, Dirk","first_name":"Dirk"},{"last_name":"Lang","full_name":"Lang, Daniel","first_name":"Daniel"},{"last_name":"Vosolsobě","full_name":"Vosolsobě, Stanislav","first_name":"Stanislav"},{"first_name":"Stephane","full_name":"Rombauts, Stephane","last_name":"Rombauts"},{"last_name":"Wilhelmsson","first_name":"Per","full_name":"Wilhelmsson, Per"},{"first_name":"Philipp","full_name":"Janitza, Philipp","last_name":"Janitza"},{"last_name":"Kern","first_name":"Ramona","full_name":"Kern, Ramona"},{"full_name":"Heyl, Alexander","first_name":"Alexander","last_name":"Heyl"},{"last_name":"Rümpler","first_name":"Florian","full_name":"Rümpler, Florian"},{"last_name":"Calderón Villalobos","first_name":"Luz","full_name":"Calderón Villalobos, Luz"},{"last_name":"Clay","first_name":"John","full_name":"Clay, John"},{"first_name":"Roman","full_name":"Skokan, Roman","last_name":"Skokan"},{"first_name":"Atsushi","full_name":"Toyoda, Atsushi","last_name":"Toyoda"},{"first_name":"Yutaka","full_name":"Suzuki, Yutaka","last_name":"Suzuki"},{"first_name":"Hiroshi","full_name":"Kagoshima, Hiroshi","last_name":"Kagoshima"},{"full_name":"Schijlen, Elio","first_name":"Elio","last_name":"Schijlen"},{"last_name":"Tajeshwar","full_name":"Tajeshwar, Navindra","first_name":"Navindra"},{"last_name":"Catarino","first_name":"Bruno","full_name":"Catarino, Bruno"},{"last_name":"Hetherington","first_name":"Alexander","full_name":"Hetherington, Alexander"},{"last_name":"Saltykova","first_name":"Assia","full_name":"Saltykova, Assia"},{"last_name":"Bonnot","first_name":"Clemence","full_name":"Bonnot, Clemence"},{"full_name":"Breuninger, Holger","first_name":"Holger","last_name":"Breuninger"},{"full_name":"Symeonidi, Aikaterini","first_name":"Aikaterini","last_name":"Symeonidi"},{"full_name":"Radhakrishnan, Guru","first_name":"Guru","last_name":"Radhakrishnan"},{"first_name":"Filip","full_name":"Van Nieuwerburgh, Filip","last_name":"Van Nieuwerburgh"},{"full_name":"Deforce, Dieter","first_name":"Dieter","last_name":"Deforce"},{"full_name":"Chang, Caren","first_name":"Caren","last_name":"Chang"},{"last_name":"Karol","first_name":"Kenneth","full_name":"Karol, Kenneth"},{"last_name":"Hedrich","full_name":"Hedrich, Rainer","first_name":"Rainer"},{"first_name":"Peter","full_name":"Ulvskov, Peter","last_name":"Ulvskov"},{"last_name":"Glöckner","first_name":"Gernot","full_name":"Glöckner, Gernot"},{"last_name":"Delwiche","first_name":"Charles","full_name":"Delwiche, Charles"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"full_name":"Van De Peer, Yves","first_name":"Yves","last_name":"Van De Peer"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí"},{"full_name":"Beilby, Mary","first_name":"Mary","last_name":"Beilby"},{"full_name":"Dolan, Liam","first_name":"Liam","last_name":"Dolan"},{"full_name":"Kohara, Yuji","first_name":"Yuji","last_name":"Kohara"},{"last_name":"Sugano","first_name":"Sumio","full_name":"Sugano, Sumio"},{"full_name":"Fujiyama, Asao","first_name":"Asao","last_name":"Fujiyama"},{"last_name":"Delaux","first_name":"Pierre Marc","full_name":"Delaux, Pierre Marc"},{"full_name":"Quint, Marcel","first_name":"Marcel","last_name":"Quint"},{"full_name":"Theissen, Gunter","first_name":"Gunter","last_name":"Theissen"},{"first_name":"Martin","full_name":"Hagemann, Martin","last_name":"Hagemann"},{"full_name":"Harholt, Jesper","first_name":"Jesper","last_name":"Harholt"},{"full_name":"Dunand, Christophe","first_name":"Christophe","last_name":"Dunand"},{"last_name":"Zachgo","full_name":"Zachgo, Sabine","first_name":"Sabine"},{"last_name":"Langdale","first_name":"Jane","full_name":"Langdale, Jane"},{"full_name":"Maumus, Florian","first_name":"Florian","last_name":"Maumus"},{"last_name":"Van Der Straeten","first_name":"Dominique","full_name":"Van Der Straeten, Dominique"},{"first_name":"Sven B","full_name":"Gould, Sven B","last_name":"Gould"},{"last_name":"Rensing","first_name":"Stefan","full_name":"Rensing, Stefan"}],"publication_status":"published"},{"publication_status":"published","article_type":"original","author":[{"first_name":"Robert","full_name":"Dick, Robert","last_name":"Dick"},{"first_name":"Kaneil K","full_name":"Zadrozny, Kaneil K","last_name":"Zadrozny"},{"first_name":"Chaoyi","full_name":"Xu, Chaoyi","last_name":"Xu"},{"last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian","orcid":"0000-0003-4790-8078","first_name":"Florian"},{"last_name":"Lyddon","first_name":"Terri D","full_name":"Lyddon, Terri D"},{"first_name":"Clifton L","full_name":"Ricana, Clifton L","last_name":"Ricana"},{"full_name":"Wagner, Jonathan M","first_name":"Jonathan M","last_name":"Wagner"},{"full_name":"Perilla, Juan R","first_name":"Juan R","last_name":"Perilla"},{"last_name":"Ganser","first_name":"Pornillos Barbie K","full_name":"Ganser, Pornillos Barbie K"},{"full_name":"Johnson, Marc C","first_name":"Marc C","last_name":"Johnson"},{"first_name":"Owen","full_name":"Pornillos, Owen","last_name":"Pornillos"},{"full_name":"Vogt, Volker","first_name":"Volker","last_name":"Vogt"}],"month":"08","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242333/","open_access":"1"}],"issue":"7719","oa_version":"Submitted Version","intvolume":"       560","article_processing_charge":"No","oa":1,"year":"2018","scopus_import":"1","department":[{"_id":"FlSc"}],"date_created":"2018-12-11T11:44:53Z","publication":"Nature","citation":{"ieee":"R. Dick <i>et al.</i>, “Inositol phosphates are assembly co-factors for HIV-1,” <i>Nature</i>, vol. 560, no. 7719. Nature Publishing Group, pp. 509–512, 2018.","apa":"Dick, R., Zadrozny, K. K., Xu, C., Schur, F. K., Lyddon, T. D., Ricana, C. L., … Vogt, V. (2018). Inositol phosphates are assembly co-factors for HIV-1. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41586-018-0396-4\">https://doi.org/10.1038/s41586-018-0396-4</a>","short":"R. Dick, K.K. Zadrozny, C. Xu, F.K. Schur, T.D. Lyddon, C.L. Ricana, J.M. Wagner, J.R. Perilla, P.B.K. Ganser, M.C. Johnson, O. Pornillos, V. Vogt, Nature 560 (2018) 509–512.","chicago":"Dick, Robert, Kaneil K Zadrozny, Chaoyi Xu, Florian KM Schur, Terri D Lyddon, Clifton L Ricana, Jonathan M Wagner, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” <i>Nature</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41586-018-0396-4\">https://doi.org/10.1038/s41586-018-0396-4</a>.","ista":"Dick R, Zadrozny KK, Xu C, Schur FK, Lyddon TD, Ricana CL, Wagner JM, Perilla JR, Ganser PBK, Johnson MC, Pornillos O, Vogt V. 2018. Inositol phosphates are assembly co-factors for HIV-1. Nature. 560(7719), 509–512.","ama":"Dick R, Zadrozny KK, Xu C, et al. Inositol phosphates are assembly co-factors for HIV-1. <i>Nature</i>. 2018;560(7719):509–512. doi:<a href=\"https://doi.org/10.1038/s41586-018-0396-4\">10.1038/s41586-018-0396-4</a>","mla":"Dick, Robert, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” <i>Nature</i>, vol. 560, no. 7719, Nature Publishing Group, 2018, pp. 509–512, doi:<a href=\"https://doi.org/10.1038/s41586-018-0396-4\">10.1038/s41586-018-0396-4</a>."},"related_material":{"link":[{"url":"https://doi.org/10.1038/s41586-018-0505-4","relation":"erratum"}]},"publication_identifier":{"eissn":["1476-4687"]},"volume":560,"quality_controlled":"1","day":"29","date_published":"2018-08-29T00:00:00Z","external_id":{"pmid":["30158708"],"isi":["000442483400046"]},"isi":1,"fulldoi":"https://doi.org/10.1038/s41586-018-0396-4","language":[{"iso":"eng"}],"title":"Inositol phosphates are assembly co-factors for HIV-1","abstract":[{"text":"A short, 14-amino-acid segment called SP1, located in the Gag structural protein1, has a critical role during the formation of the HIV-1 virus particle. During virus assembly, the SP1 peptide and seven preceding residues fold into a six-helix bundle, which holds together the Gag hexamer and facilitates the formation of a curved immature hexagonal lattice underneath the viral membrane2,3. Upon completion of assembly and budding, proteolytic cleavage of Gag leads to virus maturation, in which the immature lattice is broken down; the liberated CA domain of Gag then re-assembles into the mature conical capsid that encloses the viral genome and associated enzymes. Folding and proteolysis of the six-helix bundle are crucial rate-limiting steps of both Gag assembly and disassembly, and the six-helix bundle is an established target of HIV-1 inhibitors4,5. Here, using a combination of structural and functional analyses, we show that inositol hexakisphosphate (InsP6, also known as IP6) facilitates the formation of the six-helix bundle and assembly of the immature HIV-1 Gag lattice. IP6 makes ionic contacts with two rings of lysine residues at the centre of the Gag hexamer. Proteolytic cleavage then unmasks an alternative binding site, where IP6 interaction promotes the assembly of the mature capsid lattice. These studies identify IP6 as a naturally occurring small molecule that promotes both assembly and maturation of HIV-1.","lang":"eng"}],"pmid":1,"date_updated":"2023-09-12T07:44:37Z","page":"509–512","type":"journal_article","status":"public","_id":"150","publisher":"Nature Publishing Group","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1038/s41586-018-0396-4"},{"type":"journal_article","status":"public","_id":"152","publisher":"Elsevier","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1016/j.tcb.2018.06.006","title":"Mammalian mitochondrial complex I structure and disease causing mutations","file_date_updated":"2020-07-14T12:45:00Z","abstract":[{"text":"Complex I has an essential role in ATP production by coupling electron transfer from NADH to quinone with translocation of protons across the inner mitochondrial membrane. Isolated complex I deficiency is a frequent cause of mitochondrial inherited diseases. Complex I has also been implicated in cancer, ageing, and neurodegenerative conditions. Until recently, the understanding of complex I deficiency on the molecular level was limited due to the lack of high-resolution structures of the enzyme. However, due to developments in single particle cryo-electron microscopy (cryo-EM), recent studies have reported nearly atomic resolution maps and models of mitochondrial complex I. These structures significantly add to our understanding of complex I mechanism and assembly. The disease-causing mutations are discussed here in their structural context.","lang":"eng"}],"page":"835 - 867","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_updated":"2023-09-13T08:51:56Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"date_published":"2018-07-26T00:00:00Z","day":"26","external_id":{"isi":["000445118200007"]},"publist_id":"7769","fulldoi":"https://doi.org/10.1016/j.tcb.2018.06.006","file":[{"file_size":2185385,"date_updated":"2020-07-14T12:45:00Z","checksum":"ef6d2b4e1fd63948539639242610bfa6","relation":"main_file","date_created":"2019-11-07T12:55:20Z","creator":"lsazanov","access_level":"open_access","file_id":"6994","content_type":"application/pdf","file_name":"SasanovFinalMS+EdComments_LS_allacc_withFigs.pdf"}],"isi":1,"language":[{"iso":"eng"}],"volume":28,"quality_controlled":"1","department":[{"_id":"LeSa"}],"scopus_import":"1","date_created":"2018-12-11T11:44:54Z","publication":"Trends in Cell Biology","citation":{"ama":"Fiedorczuk K, Sazanov LA. Mammalian mitochondrial complex I structure and disease causing mutations. <i>Trends in Cell Biology</i>. 2018;28(10):835-867. doi:<a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">10.1016/j.tcb.2018.06.006</a>","mla":"Fiedorczuk, Karol, and Leonid A. Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” <i>Trends in Cell Biology</i>, vol. 28, no. 10, Elsevier, 2018, pp. 835–67, doi:<a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">10.1016/j.tcb.2018.06.006</a>.","ista":"Fiedorczuk K, Sazanov LA. 2018. Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. 28(10), 835–867.","chicago":"Fiedorczuk, Karol, and Leonid A Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” <i>Trends in Cell Biology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">https://doi.org/10.1016/j.tcb.2018.06.006</a>.","apa":"Fiedorczuk, K., &#38; Sazanov, L. A. (2018). Mammalian mitochondrial complex I structure and disease causing mutations. <i>Trends in Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcb.2018.06.006\">https://doi.org/10.1016/j.tcb.2018.06.006</a>","ieee":"K. Fiedorczuk and L. A. Sazanov, “Mammalian mitochondrial complex I structure and disease causing mutations,” <i>Trends in Cell Biology</i>, vol. 28, no. 10. Elsevier, pp. 835–867, 2018.","short":"K. Fiedorczuk, L.A. Sazanov, Trends in Cell Biology 28 (2018) 835–867."},"has_accepted_license":"1","month":"07","issue":"10","oa_version":"Submitted Version","intvolume":"        28","article_processing_charge":"No","year":"2018","oa":1,"ddc":["572"],"publication_status":"published","article_type":"original","author":[{"last_name":"Fiedorczuk","first_name":"Karol","full_name":"Fiedorczuk, Karol","id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0"},{"last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A"}]},{"publication_status":"published","author":[{"last_name":"Renkawitz","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2856-3369","full_name":"Renkawitz, Jörg","first_name":"Jörg"},{"last_name":"Reversat","id":"35B76592-F248-11E8-B48F-1D18A9856A87","first_name":"Anne","full_name":"Reversat, Anne","orcid":"0000-0003-0666-8928"},{"last_name":"Leithner","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander F","orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F"},{"last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","first_name":"Jack"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt"}],"intvolume":"       147","oa_version":"None","month":"07","article_processing_charge":"No","year":"2018","publication":"Methods in Cell Biology","department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"scopus_import":"1","date_created":"2018-12-11T11:44:54Z","citation":{"chicago":"Renkawitz, Jörg, Anne Reversat, Alexander F Leithner, Jack Merrin, and Michael K Sixt. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” In <i>Methods in Cell Biology</i>, 147:79–91. Academic Press, 2018. <a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">https://doi.org/10.1016/bs.mcb.2018.07.004</a>.","apa":"Renkawitz, J., Reversat, A., Leithner, A. F., Merrin, J., &#38; Sixt, M. K. (2018). Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In <i>Methods in Cell Biology</i> (Vol. 147, pp. 79–91). Academic Press. <a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">https://doi.org/10.1016/bs.mcb.2018.07.004</a>","ieee":"J. Renkawitz, A. Reversat, A. F. Leithner, J. Merrin, and M. K. Sixt, “Micro-engineered ‘pillar forests’ to study cell migration in complex but controlled 3D environments,” in <i>Methods in Cell Biology</i>, vol. 147, Academic Press, 2018, pp. 79–91.","short":"J. Renkawitz, A. Reversat, A.F. Leithner, J. Merrin, M.K. Sixt, in:, Methods in Cell Biology, Academic Press, 2018, pp. 79–91.","ama":"Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: <i>Methods in Cell Biology</i>. Vol 147. Academic Press; 2018:79-91. doi:<a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">10.1016/bs.mcb.2018.07.004</a>","mla":"Renkawitz, Jörg, et al. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” <i>Methods in Cell Biology</i>, vol. 147, Academic Press, 2018, pp. 79–91, doi:<a href=\"https://doi.org/10.1016/bs.mcb.2018.07.004\">10.1016/bs.mcb.2018.07.004</a>.","ista":"Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. 2018.Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: Methods in Cell Biology. vol. 147, 79–91."},"quality_controlled":"1","publication_identifier":{"issn":["0091-679X"]},"volume":147,"day":"27","date_published":"2018-07-27T00:00:00Z","isi":1,"fulldoi":"https://doi.org/10.1016/bs.mcb.2018.07.004","publist_id":"7768","language":[{"iso":"eng"}],"external_id":{"isi":["000452412300006"],"pmid":["30165964"]},"abstract":[{"text":"Cells migrating in multicellular organisms steadily traverse complex three-dimensional (3D) environments. To decipher the underlying cell biology, current experimental setups either use simplified 2D, tissue-mimetic 3D (e.g., collagen matrices) or in vivo environments. While only in vivo experiments are truly physiological, they do not allow for precise manipulation of environmental parameters. 2D in vitro experiments do allow mechanical and chemical manipulations, but increasing evidence demonstrates substantial differences of migratory mechanisms in 2D and 3D. Here, we describe simple, robust, and versatile “pillar forests” to investigate cell migration in complex but fully controllable 3D environments. Pillar forests are polydimethylsiloxane-based setups, in which two closely adjacent surfaces are interconnected by arrays of micrometer-sized pillars. Changing the pillar shape, size, height and the inter-pillar distance precisely manipulates microenvironmental parameters (e.g., pore sizes, micro-geometry, micro-topology), while being easily combined with chemotactic cues, surface coatings, diverse cell types and advanced imaging techniques. Thus, pillar forests combine the advantages of 2D cell migration assays with the precise definition of 3D environmental parameters.","lang":"eng"}],"title":"Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments","page":"79 - 91","date_updated":"2025-07-10T11:51:09Z","pmid":1,"type":"book_chapter","status":"public","_id":"153","doi":"10.1016/bs.mcb.2018.07.004","publisher":"Academic Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"type":"conference","_id":"155","status":"public","publisher":"SPIE","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1117/12.2309928","title":"Routing thermal noise through quantum networks","editor":[{"last_name":"Andrews","first_name":"D L","full_name":"Andrews, D L"},{"last_name":"Ostendorf","full_name":"Ostendorf, A","first_name":"A"},{"last_name":"Bain","full_name":"Bain, A J","first_name":"A J"},{"full_name":"Nunzi, J M","first_name":"J M","last_name":"Nunzi"}],"conference":{"end_date":"2018-04-26","location":"Strasbourg, France","start_date":"2018-04-22","name":"SPIE: The international society for optical engineering"},"abstract":[{"text":"There is currently significant interest in operating devices in the quantum regime, where their behaviour cannot be explained through classical mechanics. Quantum states, including entangled states, are fragile and easily disturbed by excessive thermal noise. Here we address the question of whether it is possible to create non-reciprocal devices that encourage the flow of thermal noise towards or away from a particular quantum device in a network. Our work makes use of the cascaded systems formalism to answer this question in the affirmative, showing how a three-port device can be used as an effective thermal transistor, and illustrates how this formalism maps onto an experimentally-realisable optomechanical system. Our results pave the way to more resilient quantum devices and to the use of thermal noise as a resource.","lang":"eng"}],"date_updated":"2023-09-18T08:12:24Z","day":"04","date_published":"2018-05-04T00:00:00Z","external_id":{"arxiv":["1806.01000"],"isi":["000453298500019"]},"publist_id":"7766","fulldoi":"https://doi.org/10.1117/12.2309928","isi":1,"language":[{"iso":"eng"}],"volume":10672,"quality_controlled":"1","arxiv":1,"article_number":"106721N","department":[{"_id":"JoFi"}],"scopus_import":"1","date_created":"2018-12-11T11:44:55Z","citation":{"chicago":"Xuereb, André, Matteo Aquilina, and Shabir Barzanjeh. “Routing Thermal Noise through Quantum Networks.” edited by D L Andrews, A Ostendorf, A J Bain, and J M Nunzi, Vol. 10672. SPIE, 2018. <a href=\"https://doi.org/10.1117/12.2309928\">https://doi.org/10.1117/12.2309928</a>.","short":"A. Xuereb, M. Aquilina, S. Barzanjeh, in:, D.L. Andrews, A. Ostendorf, A.J. Bain, J.M. Nunzi (Eds.), SPIE, 2018.","apa":"Xuereb, A., Aquilina, M., &#38; Barzanjeh, S. (2018). Routing thermal noise through quantum networks. In D. L. Andrews, A. Ostendorf, A. J. Bain, &#38; J. M. Nunzi (Eds.) (Vol. 10672). Presented at the SPIE: The international society for optical engineering, Strasbourg, France: SPIE. <a href=\"https://doi.org/10.1117/12.2309928\">https://doi.org/10.1117/12.2309928</a>","ieee":"A. Xuereb, M. Aquilina, and S. Barzanjeh, “Routing thermal noise through quantum networks,” presented at the SPIE: The international society for optical engineering, Strasbourg, France, 2018, vol. 10672.","mla":"Xuereb, André, et al. <i>Routing Thermal Noise through Quantum Networks</i>. Edited by D L Andrews et al., vol. 10672, 106721N, SPIE, 2018, doi:<a href=\"https://doi.org/10.1117/12.2309928\">10.1117/12.2309928</a>.","ama":"Xuereb A, Aquilina M, Barzanjeh S. Routing thermal noise through quantum networks. In: Andrews DL, Ostendorf A, Bain AJ, Nunzi JM, eds. Vol 10672. SPIE; 2018. doi:<a href=\"https://doi.org/10.1117/12.2309928\">10.1117/12.2309928</a>","ista":"Xuereb A, Aquilina M, Barzanjeh S. 2018. Routing thermal noise through quantum networks. SPIE: The international society for optical engineering, Proceedings of SPIE, vol. 10672, 106721N."},"alternative_title":["Proceedings of SPIE"],"month":"05","main_file_link":[{"url":"https://arxiv.org/abs/1806.01000","open_access":"1"}],"intvolume":"     10672","oa_version":"Preprint","article_processing_charge":"No","year":"2018","oa":1,"publication_status":"published","author":[{"last_name":"Xuereb","full_name":"Xuereb, André","first_name":"André"},{"first_name":"Matteo","full_name":"Aquilina, Matteo","last_name":"Aquilina"},{"last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir","first_name":"Shabir"}]},{"volume":10951,"quality_controlled":"1","citation":{"chicago":"Ferrere, Thomas. “The Compound Interest in Relaxing Punctuality,” 10951:147–64. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">https://doi.org/10.1007/978-3-319-95582-7_9</a>.","short":"T. Ferrere, in:, Springer, 2018, pp. 147–164.","apa":"Ferrere, T. (2018). The compound interest in relaxing punctuality (Vol. 10951, pp. 147–164). Presented at the FM: Formal Methods, Oxford, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">https://doi.org/10.1007/978-3-319-95582-7_9</a>","ieee":"T. Ferrere, “The compound interest in relaxing punctuality,” presented at the FM: Formal Methods, Oxford, UK, 2018, vol. 10951, pp. 147–164.","mla":"Ferrere, Thomas. <i>The Compound Interest in Relaxing Punctuality</i>. Vol. 10951, Springer, 2018, pp. 147–64, doi:<a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">10.1007/978-3-319-95582-7_9</a>.","ama":"Ferrere T. The compound interest in relaxing punctuality. In: Vol 10951. Springer; 2018:147-164. doi:<a href=\"https://doi.org/10.1007/978-3-319-95582-7_9\">10.1007/978-3-319-95582-7_9</a>","ista":"Ferrere T. 2018. The compound interest in relaxing punctuality. FM: Formal Methods, LNCS, vol. 10951, 147–164."},"alternative_title":["LNCS"],"has_accepted_license":"1","department":[{"_id":"ToHe"}],"scopus_import":"1","date_created":"2018-12-11T11:44:55Z","article_processing_charge":"No","year":"2018","oa":1,"month":"07","oa_version":"Submitted Version","intvolume":"     10951","publication_status":"published","author":[{"id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","last_name":"Ferrere"}],"ddc":["000"],"publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-319-95582-7_9","project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"type":"conference","status":"public","_id":"156","page":"147 - 164","date_updated":"2025-07-10T11:51:10Z","title":"The compound interest in relaxing punctuality","file_date_updated":"2020-10-09T06:22:41Z","conference":{"name":"FM: Formal Methods","location":"Oxford, UK","start_date":"2018-07-15","end_date":"2018-07-17"},"abstract":[{"text":"Imprecision in timing can sometimes be beneficial: Metric interval temporal logic (MITL), disabling the expression of punctuality constraints, was shown to translate to timed automata, yielding an elementary decision procedure. We show how this principle extends to other forms of dense-time specification using regular expressions. By providing a clean, automaton-based formal framework for non-punctual languages, we are able to recover and extend several results in timed systems. Metric interval regular expressions (MIRE) are introduced, providing regular expressions with non-singular duration constraints. We obtain that MIRE are expressively complete relative to a class of one-clock timed automata, which can be determinized using additional clocks. Metric interval dynamic logic (MIDL) is then defined using MIRE as temporal modalities. We show that MIDL generalizes known extensions of MITL, while translating to timed automata at comparable cost.","lang":"eng"}],"external_id":{"isi":["000489765800009"]},"file":[{"date_created":"2020-10-09T06:22:41Z","relation":"main_file","creator":"dernst","success":1,"file_size":485576,"date_updated":"2020-10-09T06:22:41Z","checksum":"a045c213c42c445f1889326f8db82a0a","file_name":"2018_LNCS_Ferrere.pdf","content_type":"application/pdf","access_level":"open_access","file_id":"8637"}],"fulldoi":"https://doi.org/10.1007/978-3-319-95582-7_9","publist_id":"7765","isi":1,"language":[{"iso":"eng"}],"date_published":"2018-07-12T00:00:00Z","day":"12"},{"publication":"Nature","date_created":"2018-12-11T11:44:56Z","department":[{"_id":"KrCh"}],"scopus_import":"1","has_accepted_license":"1","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/engineering-cooperation/","description":"News on IST Homepage"}]},"citation":{"ista":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. 2018. Evolution of cooperation in stochastic games. Nature. 559(7713), 246–249.","mla":"Hilbe, Christian, et al. “Evolution of Cooperation in Stochastic Games.” <i>Nature</i>, vol. 559, no. 7713, Nature Publishing Group, 2018, pp. 246–49, doi:<a href=\"https://doi.org/10.1038/s41586-018-0277-x\">10.1038/s41586-018-0277-x</a>.","ama":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. Evolution of cooperation in stochastic games. <i>Nature</i>. 2018;559(7713):246-249. doi:<a href=\"https://doi.org/10.1038/s41586-018-0277-x\">10.1038/s41586-018-0277-x</a>","apa":"Hilbe, C., Šimsa, Š., Chatterjee, K., &#38; Nowak, M. (2018). Evolution of cooperation in stochastic games. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41586-018-0277-x\">https://doi.org/10.1038/s41586-018-0277-x</a>","ieee":"C. Hilbe, Š. Šimsa, K. Chatterjee, and M. Nowak, “Evolution of cooperation in stochastic games,” <i>Nature</i>, vol. 559, no. 7713. Nature Publishing Group, pp. 246–249, 2018.","short":"C. Hilbe, Š. Šimsa, K. Chatterjee, M. Nowak, Nature 559 (2018) 246–249.","chicago":"Hilbe, Christian, Štepán Šimsa, Krishnendu Chatterjee, and Martin Nowak. “Evolution of Cooperation in Stochastic Games.” <i>Nature</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41586-018-0277-x\">https://doi.org/10.1038/s41586-018-0277-x</a>."},"quality_controlled":"1","ec_funded":1,"volume":559,"acknowledgement":"European Research Council Start Grant 279307, Austrian Science Fund (FWF) grant P23499-N23, \r\nC.H. acknowledges support from the ISTFELLOW programme.","ddc":["000"],"author":[{"last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","first_name":"Christian"},{"last_name":"Šimsa","full_name":"Šimsa, Štepán","first_name":"Štepán"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"publication_status":"published","oa_version":"Submitted Version","intvolume":"       559","issue":"7713","month":"07","oa":1,"year":"2018","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Social dilemmas occur when incentives for individuals are misaligned with group interests 1-7 . According to the 'tragedy of the commons', these misalignments can lead to overexploitation and collapse of public resources. The resulting behaviours can be analysed with the tools of game theory 8 . The theory of direct reciprocity 9-15 suggests that repeated interactions can alleviate such dilemmas, but previous work has assumed that the public resource remains constant over time. Here we introduce the idea that the public resource is instead changeable and depends on the strategic choices of individuals. An intuitive scenario is that cooperation increases the public resource, whereas defection decreases it. Thus, cooperation allows the possibility of playing a more valuable game with higher payoffs, whereas defection leads to a less valuable game. We analyse this idea using the theory of stochastic games 16-19 and evolutionary game theory. We find that the dependence of the public resource on previous interactions can greatly enhance the propensity for cooperation. For these results, the interaction between reciprocity and payoff feedback is crucial: neither repeated interactions in a constant environment nor single interactions in a changing environment yield similar cooperation rates. Our framework shows which feedbacks between exploitation and environment - either naturally occurring or designed - help to overcome social dilemmas."}],"file_date_updated":"2020-07-14T12:45:02Z","title":"Evolution of cooperation in stochastic games","date_updated":"2025-04-15T06:30:08Z","page":"246 - 249","_id":"157","status":"public","project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF","grant_number":"S11407"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"type":"journal_article","doi":"10.1038/s41586-018-0277-x","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Nature Publishing Group","date_published":"2018-07-04T00:00:00Z","day":"04","language":[{"iso":"eng"}],"file":[{"file_id":"7049","access_level":"open_access","file_name":"2018_Nature_Hilbe.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:45:02Z","checksum":"011ab905cf9a410bc2b96f15174d654d","file_size":2834442,"creator":"dernst","relation":"main_file","date_created":"2019-11-19T08:09:57Z"}],"fulldoi":"https://doi.org/10.1038/s41586-018-0277-x","isi":1,"publist_id":"7764","external_id":{"isi":["000438240900054"]}},{"date_created":"2018-12-11T11:44:56Z","scopus_import":"1","department":[{"_id":"JiFr"}],"publication":"Nature Plants","citation":{"mla":"Robert, Hélène, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning in Arabidopsis.” <i>Nature Plants</i>, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 548–53, doi:<a href=\"https://doi.org/10.1038/s41477-018-0204-z\">10.1038/s41477-018-0204-z</a>.","ama":"Robert H, Park C, Gutièrrez C, et al. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. <i>Nature Plants</i>. 2018;4(8):548-553. doi:<a href=\"https://doi.org/10.1038/s41477-018-0204-z\">10.1038/s41477-018-0204-z</a>","ista":"Robert H, Park C, Gutièrrez C, Wójcikowska B, Pěnčík A, Novák O, Chen J, Grunewald W, Dresselhaus T, Friml J, Laux T. 2018. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. 4(8), 548–553.","chicago":"Robert, Hélène, Chulmin Park, Carla Gutièrrez, Barbara Wójcikowska, Aleš Pěnčík, Ondřej Novák, Junyi Chen, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning in Arabidopsis.” <i>Nature Plants</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0204-z\">https://doi.org/10.1038/s41477-018-0204-z</a>.","short":"H. Robert, C. Park, C. Gutièrrez, B. Wójcikowska, A. Pěnčík, O. Novák, J. Chen, W. Grunewald, T. Dresselhaus, J. Friml, T. Laux, Nature Plants 4 (2018) 548–553.","ieee":"H. Robert <i>et al.</i>, “Maternal auxin supply contributes to early embryo patterning in Arabidopsis,” <i>Nature Plants</i>, vol. 4, no. 8. Nature Publishing Group, pp. 548–553, 2018.","apa":"Robert, H., Park, C., Gutièrrez, C., Wójcikowska, B., Pěnčík, A., Novák, O., … Laux, T. (2018). Maternal auxin supply contributes to early embryo patterning in Arabidopsis. <i>Nature Plants</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41477-018-0204-z\">https://doi.org/10.1038/s41477-018-0204-z</a>"},"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/plant-mothers-talk-to-their-embryos-via-the-hormone-auxin/"}]},"volume":4,"ec_funded":1,"quality_controlled":"1","acknowledgement":"This work was further supported by the Czech Science Foundation GACR (GA13-40637S) to J.F.;","author":[{"full_name":"Robert, Hélène","first_name":"Hélène","last_name":"Robert"},{"last_name":"Park","full_name":"Park, Chulmin","first_name":"Chulmin"},{"last_name":"Gutièrrez","first_name":"Carla","full_name":"Gutièrrez, Carla"},{"full_name":"Wójcikowska, Barbara","first_name":"Barbara","last_name":"Wójcikowska"},{"last_name":"Pěnčík","first_name":"Aleš","full_name":"Pěnčík, Aleš"},{"last_name":"Novák","full_name":"Novák, Ondřej","first_name":"Ondřej"},{"last_name":"Chen","full_name":"Chen, Junyi","first_name":"Junyi"},{"full_name":"Grunewald, Wim","first_name":"Wim","last_name":"Grunewald"},{"last_name":"Dresselhaus","full_name":"Dresselhaus, Thomas","first_name":"Thomas"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Laux","full_name":"Laux, Thomas","first_name":"Thomas"}],"publication_status":"published","month":"07","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30013211","open_access":"1"}],"oa_version":"Submitted Version","issue":"8","intvolume":"         4","year":"2018","oa":1,"article_processing_charge":"No","title":"Maternal auxin supply contributes to early embryo patterning in Arabidopsis","abstract":[{"text":"The angiosperm seed is composed of three genetically distinct tissues: the diploid embryo that originates from the fertilized egg cell, the triploid endosperm that is produced from the fertilized central cell, and the maternal sporophytic integuments that develop into the seed coat1. At the onset of embryo development in Arabidopsis thaliana, the zygote divides asymmetrically, producing a small apical embryonic cell and a larger basal cell that connects the embryo to the maternal tissue2. The coordinated and synchronous development of the embryo and the surrounding integuments, and the alignment of their growth axes, suggest communication between maternal tissues and the embryo. In contrast to animals, however, where a network of maternal factors that direct embryo patterning have been identified3,4, only a few maternal mutations have been described to affect embryo development in plants5–7. Early embryo patterning in Arabidopsis requires accumulation of the phytohormone auxin in the apical cell by directed transport from the suspensor8–10. However, the origin of this auxin has remained obscure. Here we investigate the source of auxin for early embryogenesis and provide evidence that the mother plant coordinates seed development by supplying auxin to the early embryo from the integuments of the ovule. We show that auxin response increases in ovules after fertilization, due to upregulated auxin biosynthesis in the integuments, and this maternally produced auxin is required for correct embryo development.","lang":"eng"}],"pmid":1,"page":"548 - 553","date_updated":"2025-04-15T07:48:03Z","_id":"158","status":"public","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300"}],"type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Nature Publishing Group","doi":"10.1038/s41477-018-0204-z","day":"16","date_published":"2018-07-16T00:00:00Z","external_id":{"pmid":["30013211"],"isi":["000443861300011"]},"language":[{"iso":"eng"}],"isi":1,"fulldoi":"https://doi.org/10.1038/s41477-018-0204-z","publist_id":"7763"}]