[{"oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","publication":"Nature","day":"29","year":"2018","isi":1,"date_created":"2018-12-11T11:44:53Z","doi":"10.1038/s41586-018-0396-4","date_published":"2018-08-29T00:00:00Z","page":"509–512","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Dick R, Zadrozny KK, Xu C, et al. Inositol phosphates are assembly co-factors for HIV-1. Nature. 2018;560(7719):509–512. doi:10.1038/s41586-018-0396-4","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. Nature. Nature Publishing Group. https://doi.org/10.1038/s41586-018-0396-4","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.","ieee":"R. Dick et al., “Inositol phosphates are assembly co-factors for HIV-1,” Nature, vol. 560, no. 7719. Nature Publishing Group, pp. 509–512, 2018.","mla":"Dick, Robert, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” Nature, vol. 560, no. 7719, Nature Publishing Group, 2018, pp. 509–512, doi:10.1038/s41586-018-0396-4.","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.","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.” Nature. Nature Publishing Group, 2018. https://doi.org/10.1038/s41586-018-0396-4."},"title":"Inositol phosphates are assembly co-factors for HIV-1","article_processing_charge":"No","external_id":{"pmid":["30158708"],"isi":["000442483400046"]},"author":[{"first_name":"Robert","full_name":"Dick, Robert","last_name":"Dick"},{"first_name":"Kaneil K","full_name":"Zadrozny, Kaneil K","last_name":"Zadrozny"},{"last_name":"Xu","full_name":"Xu, Chaoyi","first_name":"Chaoyi"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Schur, Florian","orcid":"0000-0003-4790-8078","last_name":"Schur"},{"full_name":"Lyddon, Terri D","last_name":"Lyddon","first_name":"Terri D"},{"first_name":"Clifton L","full_name":"Ricana, Clifton L","last_name":"Ricana"},{"full_name":"Wagner, Jonathan M","last_name":"Wagner","first_name":"Jonathan M"},{"full_name":"Perilla, Juan R","last_name":"Perilla","first_name":"Juan R"},{"last_name":"Ganser","full_name":"Ganser, Pornillos Barbie K","first_name":"Pornillos Barbie K"},{"full_name":"Johnson, Marc C","last_name":"Johnson","first_name":"Marc C"},{"first_name":"Owen","full_name":"Pornillos, Owen","last_name":"Pornillos"},{"full_name":"Vogt, Volker","last_name":"Vogt","first_name":"Volker"}],"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","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."}],"intvolume":" 560","month":"08","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242333/"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1476-4687"]},"issue":"7719","volume":560,"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-018-0505-4"}]},"_id":"150","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-09-12T07:44:37Z","department":[{"_id":"FlSc"}]},{"title":"Introduction to tropical series and wave dynamic on them","article_processing_charge":"No","external_id":{"isi":["000438818400007"],"arxiv":["1706.03062"]},"author":[{"last_name":"Kalinin","full_name":"Kalinin, Nikita","first_name":"Nikita"},{"full_name":"Shkolnikov, Mikhail","orcid":"0000-0002-4310-178X","last_name":"Shkolnikov","id":"35084A62-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"}],"publist_id":"7576","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"N. Kalinin, M. Shkolnikov, Discrete and Continuous Dynamical Systems- Series A 38 (2018) 2827–2849.","ieee":"N. Kalinin and M. Shkolnikov, “Introduction to tropical series and wave dynamic on them,” Discrete and Continuous Dynamical Systems- Series A, vol. 38, no. 6. AIMS, pp. 2827–2849, 2018.","ama":"Kalinin N, Shkolnikov M. Introduction to tropical series and wave dynamic on them. Discrete and Continuous Dynamical Systems- Series A. 2018;38(6):2827-2849. doi:10.3934/dcds.2018120","apa":"Kalinin, N., & Shkolnikov, M. (2018). Introduction to tropical series and wave dynamic on them. Discrete and Continuous Dynamical Systems- Series A. AIMS. https://doi.org/10.3934/dcds.2018120","mla":"Kalinin, Nikita, and Mikhail Shkolnikov. “Introduction to Tropical Series and Wave Dynamic on Them.” Discrete and Continuous Dynamical Systems- Series A, vol. 38, no. 6, AIMS, 2018, pp. 2827–49, doi:10.3934/dcds.2018120.","ista":"Kalinin N, Shkolnikov M. 2018. Introduction to tropical series and wave dynamic on them. Discrete and Continuous Dynamical Systems- Series A. 38(6), 2827–2849.","chicago":"Kalinin, Nikita, and Mikhail Shkolnikov. “Introduction to Tropical Series and Wave Dynamic on Them.” Discrete and Continuous Dynamical Systems- Series A. AIMS, 2018. https://doi.org/10.3934/dcds.2018120."},"date_created":"2018-12-11T11:45:43Z","date_published":"2018-06-01T00:00:00Z","doi":"10.3934/dcds.2018120","page":"2827 - 2849","publication":"Discrete and Continuous Dynamical Systems- Series A","day":"01","year":"2018","isi":1,"oa":1,"publisher":"AIMS","quality_controlled":"1","acknowledgement":"The first author, Nikita Kalinin, is funded by SNCF PostDoc.Mobility grant 168647. Support from the Basic Research Program of the National Research University Higher School of Economics is gratefully acknowledged. The second author, Mikhail Shkolnikov, is supported in part by the grant 159240 of the Swiss National Science Foundation as well as by the National Center of Competence in Research SwissMAP of the Swiss National Science Foundation.","department":[{"_id":"TaHa"}],"date_updated":"2023-09-12T07:45:37Z","status":"public","type":"journal_article","_id":"303","volume":38,"issue":"6","language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 38","month":"06","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.03062"}],"scopus_import":"1","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"The theory of tropical series, that we develop here, firstly appeared in the study of the growth of pluriharmonic functions. Motivated by waves in sandpile models we introduce a dynamic on the set of tropical series, and it is experimentally observed that this dynamic obeys a power law. So, this paper serves as a compilation of results we need for other articles and also introduces several objects interesting by themselves."}]},{"extern":"1","date_updated":"2023-09-13T07:38:24Z","department":[{"_id":"FrLo"}],"_id":"14202","status":"public","type":"conference","conference":{"location":"Montreal, Canada","end_date":"2018-12-08","start_date":"2018-12-03","name":"NeurIPS: Neural Information Processing Systems"},"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1049-5258"],"isbn":["9781510884472"]},"publication_status":"published","volume":31,"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"month":"06","intvolume":" 31","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.02185"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Locatello, Francesco, Gideon Dresdner, Rajiv Khanna, Isabel Valera, and Gunnar Rätsch. “Boosting Black Box Variational Inference.” In Advances in Neural Information Processing Systems, 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.” Advances in Neural Information Processing Systems, vol. 31, Neural Information Processing Systems Foundation, 2018.","apa":"Locatello, F., Dresdner, G., Khanna, R., Valera, I., & Rätsch, G. (2018). Boosting black box variational inference. In Advances in Neural Information Processing Systems (Vol. 31). Montreal, Canada: Neural Information Processing Systems Foundation.","ama":"Locatello F, Dresdner G, Khanna R, Valera I, Rätsch G. Boosting black box variational inference. In: Advances in Neural Information Processing Systems. Vol 31. Neural Information Processing Systems Foundation; 2018.","ieee":"F. Locatello, G. Dresdner, R. Khanna, I. Valera, and G. Rätsch, “Boosting black box variational inference,” in Advances in Neural Information Processing Systems, Montreal, Canada, 2018, vol. 31.","short":"F. Locatello, G. Dresdner, R. Khanna, I. Valera, G. Rätsch, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2018."},"title":"Boosting black box variational inference","author":[{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","last_name":"Locatello"},{"first_name":"Gideon","full_name":"Dresdner, Gideon","last_name":"Dresdner"},{"full_name":"Khanna, Rajiv","last_name":"Khanna","first_name":"Rajiv"},{"last_name":"Valera","full_name":"Valera, Isabel","first_name":"Isabel"},{"last_name":"Rätsch","full_name":"Rätsch, Gunnar","first_name":"Gunnar"}],"external_id":{"arxiv":["1806.02185"]},"article_processing_charge":"No","day":"06","publication":"Advances in Neural Information Processing Systems","year":"2018","date_published":"2018-06-06T00:00:00Z","date_created":"2023-08-22T14:15:40Z","quality_controlled":"1","publisher":"Neural Information Processing Systems Foundation","oa":1},{"day":"15","publication":"Proceedings of the 21st International Conference on Artificial Intelligence and Statistics","year":"2018","date_published":"2018-04-15T00:00:00Z","date_created":"2023-08-22T14:15:20Z","page":"464-472","quality_controlled":"1","publisher":"ML Research Press","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Locatello, F., Khanna, R., Ghosh, J., & Rätsch, G. (2018). Boosting variational inference: An optimization perspective. In Proceedings of the 21st International Conference on Artificial Intelligence and Statistics (Vol. 84, pp. 464–472). Playa Blanca, Lanzarote: ML Research Press.","ama":"Locatello F, Khanna R, Ghosh J, Rätsch G. Boosting variational inference: An optimization perspective. In: Proceedings of the 21st International Conference on Artificial Intelligence and Statistics. Vol 84. ML Research Press; 2018:464-472.","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.","ieee":"F. Locatello, R. Khanna, J. Ghosh, and G. Rätsch, “Boosting variational inference: An optimization perspective,” in Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, Playa Blanca, Lanzarote, 2018, vol. 84, pp. 464–472.","mla":"Locatello, Francesco, et al. “Boosting Variational Inference: An Optimization Perspective.” Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, vol. 84, ML Research Press, 2018, pp. 464–72.","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 Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, 84:464–72. ML Research Press, 2018."},"title":"Boosting variational inference: An optimization perspective","author":[{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"},{"full_name":"Khanna, Rajiv","last_name":"Khanna","first_name":"Rajiv"},{"first_name":"Joydeep","last_name":"Ghosh","full_name":"Ghosh, Joydeep"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"}],"external_id":{"arxiv":["1708.01733"]},"article_processing_charge":"No","language":[{"iso":"eng"}],"publication_status":"published","volume":84,"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"month":"04","intvolume":" 84","scopus_import":"1","alternative_title":["PMLR"],"main_file_link":[{"url":"https://arxiv.org/abs/1708.01733","open_access":"1"}],"extern":"1","date_updated":"2023-09-13T07:52:40Z","department":[{"_id":"FrLo"}],"_id":"14201","status":"public","type":"conference","conference":{"start_date":"2018-04-09","location":"Playa Blanca, Lanzarote","end_date":"2018-04-11","name":"AISTATS: Conference on Artificial Intelligence and Statistics"}},{"citation":{"mla":"Fortuin, Vincent, et al. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” International Conference on Learning Representations, 2018.","ieee":"V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, and G. Rätsch, “SOM-VAE: Interpretable discrete representation learning on time series,” in International Conference on Learning Representations, New Orleans, LA, United States, 2018.","short":"V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, G. Rätsch, in:, International Conference on Learning Representations, 2018.","apa":"Fortuin, V., Hüser, M., Locatello, F., Strathmann, H., & Rätsch, G. (2018). SOM-VAE: Interpretable discrete representation learning on time series. In International Conference on Learning Representations. New Orleans, LA, United States.","ama":"Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. SOM-VAE: Interpretable discrete representation learning on time series. In: International Conference on Learning Representations. ; 2018.","chicago":"Fortuin, Vincent, Matthias Hüser, Francesco Locatello, Heiko Strathmann, and Gunnar Rätsch. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” In International Conference on Learning Representations, 2018.","ista":"Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. 2018. SOM-VAE: Interpretable discrete representation learning on time series. International Conference on Learning Representations. ICLR: International Conference on Learning Representations."},"date_updated":"2023-09-13T06:35:12Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","article_processing_charge":"No","external_id":{"arxiv":["1806.02199"]},"author":[{"full_name":"Fortuin, Vincent","last_name":"Fortuin","first_name":"Vincent"},{"last_name":"Hüser","full_name":"Hüser, Matthias","first_name":"Matthias"},{"last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"first_name":"Heiko","full_name":"Strathmann, Heiko","last_name":"Strathmann"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"}],"title":"SOM-VAE: Interpretable discrete representation learning on time series","department":[{"_id":"FrLo"}],"_id":"14198","conference":{"name":"ICLR: International Conference on Learning Representations","start_date":"2019-05-06","location":"New Orleans, LA, United States","end_date":"2019-05-09"},"type":"conference","status":"public","publication_status":"published","year":"2018","language":[{"iso":"eng"}],"publication":"International Conference on Learning Representations","day":"06","date_created":"2023-08-22T14:12:48Z","date_published":"2018-06-06T00:00:00Z","abstract":[{"lang":"eng","text":"High-dimensional time series are common in many domains. Since human\r\ncognition is not optimized to work well in high-dimensional spaces, these areas\r\ncould benefit from interpretable low-dimensional representations. However, most\r\nrepresentation learning algorithms for time series data are difficult to\r\ninterpret. This is due to non-intuitive mappings from data features to salient\r\nproperties of the representation and non-smoothness over time. To address this\r\nproblem, we propose a new representation learning framework building on ideas\r\nfrom interpretable discrete dimensionality reduction and deep generative\r\nmodeling. This framework allows us to learn discrete representations of time\r\nseries, which give rise to smooth and interpretable embeddings with superior\r\nclustering performance. We introduce a new way to overcome the\r\nnon-differentiability in discrete representation learning and present a\r\ngradient-based version of the traditional self-organizing map algorithm that is\r\nmore performant than the original. Furthermore, to allow for a probabilistic\r\ninterpretation of our method, we integrate a Markov model in the representation\r\nspace. This model uncovers the temporal transition structure, improves\r\nclustering performance even further and provides additional explanatory\r\ninsights as well as a natural representation of uncertainty. We evaluate our\r\nmodel in terms of clustering performance and interpretability on static\r\n(Fashion-)MNIST data, a time series of linearly interpolated (Fashion-)MNIST\r\nimages, a chaotic Lorenz attractor system with two macro states, as well as on\r\na challenging real world medical time series application on the eICU data set.\r\nOur learned representations compare favorably with competitor methods and\r\nfacilitate downstream tasks on the real world data."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.02199"}],"oa":1,"quality_controlled":"1","month":"06"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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 Proceedings of the 35th International Conference on Machine Learning, 80:5727–36. ML Research Press, 2018.","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.","mla":"Yurtsever, Alp, et al. “A Conditional Gradient Framework for Composite Convex Minimization with Applications to Semidefinite Programming.” Proceedings of the 35th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 5727–36.","ieee":"A. Yurtsever, O. Fercoq, F. Locatello, and V. Cevher, “A conditional gradient framework for composite convex minimization with applications to semidefinite programming,” in Proceedings of the 35th International Conference on Machine Learning, Stockholm, Sweden, 2018, vol. 80, pp. 5727–5736.","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.","ama":"Yurtsever A, Fercoq O, Locatello F, Cevher V. A conditional gradient framework for composite convex minimization with applications to semidefinite programming. In: Proceedings of the 35th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:5727-5736.","apa":"Yurtsever, A., Fercoq, O., Locatello, F., & Cevher, V. (2018). A conditional gradient framework for composite convex minimization with applications to semidefinite programming. In Proceedings of the 35th International Conference on Machine Learning (Vol. 80, pp. 5727–5736). Stockholm, Sweden: ML Research Press."},"title":"A conditional gradient framework for composite convex minimization with applications to semidefinite programming","author":[{"first_name":"Alp","last_name":"Yurtsever","full_name":"Yurtsever, Alp"},{"first_name":"Olivier","last_name":"Fercoq","full_name":"Fercoq, Olivier"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","last_name":"Locatello"},{"first_name":"Volkan","full_name":"Cevher, Volkan","last_name":"Cevher"}],"article_processing_charge":"No","external_id":{"arxiv":["1804.08544"]},"day":"15","publication":"Proceedings of the 35th International Conference on Machine Learning","year":"2018","date_published":"2018-07-15T00:00:00Z","date_created":"2023-08-22T14:16:01Z","page":"5727-5736","publisher":"ML Research Press","quality_controlled":"1","oa":1,"extern":"1","date_updated":"2023-09-13T08:13:39Z","department":[{"_id":"FrLo"}],"_id":"14203","status":"public","type":"conference","conference":{"start_date":"2018-07-10","location":"Stockholm, Sweden","end_date":"2018-07-15","name":"ICML: International Conference on Machine Learning"},"language":[{"iso":"eng"}],"publication_status":"published","volume":80,"oa_version":"Preprint","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."}],"month":"07","intvolume":" 80","alternative_title":["PMLR"],"main_file_link":[{"url":"https://arxiv.org/abs/1804.08544","open_access":"1"}]},{"oa":1,"publisher":"Genetics Society of America","quality_controlled":"1","publication":"Genetics","day":"01","year":"2018","isi":1,"date_created":"2018-12-11T11:45:36Z","doi":"10.1534/genetics.118.301018","date_published":"2018-08-01T00:00:00Z","page":"1279 - 1303","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"H. Sachdeva, N.H. Barton, Genetics 209 (2018) 1279–1303.","ieee":"H. Sachdeva and N. H. Barton, “Introgression of a block of genome under infinitesimal selection,” Genetics, vol. 209, no. 4. Genetics Society of America, pp. 1279–1303, 2018.","apa":"Sachdeva, H., & Barton, N. H. (2018). Introgression of a block of genome under infinitesimal selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301018","ama":"Sachdeva H, Barton NH. Introgression of a block of genome under infinitesimal selection. Genetics. 2018;209(4):1279-1303. doi:10.1534/genetics.118.301018","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” Genetics, vol. 209, no. 4, Genetics Society of America, 2018, pp. 1279–303, doi:10.1534/genetics.118.301018.","ista":"Sachdeva H, Barton NH. 2018. Introgression of a block of genome under infinitesimal selection. Genetics. 209(4), 1279–1303.","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.301018."},"title":"Introgression of a block of genome under infinitesimal selection","article_processing_charge":"No","external_id":{"isi":["000440014100020"]},"publist_id":"7617","author":[{"full_name":"Sachdeva, Himani","last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Submitted Version","abstract":[{"text":"Adaptive introgression is common in nature and can be driven by selection acting on multiple, linked genes. We explore the effects of polygenic selection on introgression under the infinitesimal model with linkage. This model assumes that the introgressing block has an effectively infinite number of genes, each with an infinitesimal effect on the trait under selection. The block is assumed to introgress under directional selection within a native population that is genetically homogeneous. We use individual-based simulations and a branching process approximation to compute various statistics of the introgressing block, and explore how these depend on parameters such as the map length and initial trait value associated with the introgressing block, the genetic variability along the block, and the strength of selection. Our results show that the introgression dynamics of a block under infinitesimal selection is qualitatively different from the dynamics of neutral introgression. We also find that in the long run, surviving descendant blocks are likely to have intermediate lengths, and clarify how the length is shaped by the interplay between linkage and infinitesimal selection. Our results suggest that it may be difficult to distinguish introgression of single loci from that of genomic blocks with multiple, tightly linked and weakly selected loci.","lang":"eng"}],"intvolume":" 209","month":"08","main_file_link":[{"url":"https://www.biorxiv.org/content/early/2017/11/30/227082","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","volume":209,"issue":"4","_id":"282","status":"public","type":"journal_article","date_updated":"2023-09-13T08:22:32Z","department":[{"_id":"NiBa"}]},{"department":[{"_id":"KrPi"}],"date_updated":"2023-09-13T08:23:18Z","type":"conference","conference":{"start_date":"2018-06-17 ","location":"Vail, CO, USA","end_date":"2018-06-22","name":"ISIT: International Symposium on Information Theory"},"status":"public","_id":"108","volume":2018,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","alternative_title":["ISIT Proceedings"],"main_file_link":[{"url":"https://eprint.iacr.org/2017/507","open_access":"1"}],"month":"08","intvolume":" 2018","abstract":[{"lang":"eng","text":"Universal hashing found a lot of applications in computer science. In cryptography the most important fact about universal families is the so called Leftover Hash Lemma, proved by Impagliazzo, Levin and Luby. In the language of modern cryptography it states that almost universal families are good extractors. In this work we provide a somewhat surprising characterization in the opposite direction. Namely, every extractor with sufficiently good parameters yields a universal family on a noticeable fraction of its inputs. Our proof technique is based on tools from extremal graph theory applied to the \\'collision graph\\' induced by the extractor, and may be of independent interest. We discuss possible applications to the theory of randomness extractors and non-malleable codes."}],"oa_version":"Submitted Version","author":[{"last_name":"Obremski","full_name":"Obremski, Marciej","first_name":"Marciej"},{"last_name":"Skorski","full_name":"Skorski, Maciej","first_name":"Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD"}],"publist_id":"7946","external_id":{"isi":["000448139300368"]},"article_processing_charge":"No","title":"Inverted leftover hash lemma","citation":{"chicago":"Obremski, Marciej, and Maciej Skórski. “Inverted Leftover Hash Lemma,” Vol. 2018. IEEE, 2018. https://doi.org/10.1109/ISIT.2018.8437654.","ista":"Obremski M, Skórski M. 2018. Inverted leftover hash lemma. ISIT: International Symposium on Information Theory, ISIT Proceedings, vol. 2018.","mla":"Obremski, Marciej, and Maciej Skórski. Inverted Leftover Hash Lemma. Vol. 2018, IEEE, 2018, doi:10.1109/ISIT.2018.8437654.","apa":"Obremski, M., & Skórski, M. (2018). Inverted leftover hash lemma (Vol. 2018). Presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA: IEEE. https://doi.org/10.1109/ISIT.2018.8437654","ama":"Obremski M, Skórski M. Inverted leftover hash lemma. In: Vol 2018. IEEE; 2018. doi:10.1109/ISIT.2018.8437654","ieee":"M. Obremski and M. Skórski, “Inverted leftover hash lemma,” presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA, 2018, vol. 2018.","short":"M. Obremski, M. Skórski, in:, IEEE, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-08-16T00:00:00Z","doi":"10.1109/ISIT.2018.8437654","date_created":"2018-12-11T11:44:40Z","isi":1,"year":"2018","day":"16","publisher":"IEEE","quality_controlled":"1","oa":1},{"department":[{"_id":"FrLo"}],"extern":"1","date_updated":"2023-09-13T08:19:05Z","status":"public","type":"conference","_id":"14204","volume":80,"language":[{"iso":"eng"}],"publication_status":"published","month":"07","intvolume":" 80","alternative_title":["PMLR"],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1803.09539","open_access":"1"}],"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"title":"On matching pursuit and coordinate descent","author":[{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello"},{"first_name":"Anant","full_name":"Raj, Anant","last_name":"Raj"},{"first_name":"Sai Praneeth","full_name":"Karimireddy, Sai Praneeth","last_name":"Karimireddy"},{"last_name":"Rätsch","full_name":"Rätsch, Gunnar","first_name":"Gunnar"},{"first_name":"Bernhard","last_name":"Schölkopf","full_name":"Schölkopf, Bernhard"},{"full_name":"Stich, Sebastian U.","last_name":"Stich","first_name":"Sebastian U."},{"full_name":"Jaggi, Martin","last_name":"Jaggi","first_name":"Martin"}],"article_processing_charge":"No","external_id":{"arxiv":["1803.09539"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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 Proceedings of the 35th International Conference on Machine Learning, 80:3198–3207. ML Research Press, 2018.","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.","mla":"Locatello, Francesco, et al. “On Matching Pursuit and Coordinate Descent.” Proceedings of the 35th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 3198–207.","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 et al., “On matching pursuit and coordinate descent,” in Proceedings of the 35th International Conference on Machine Learning, 2018, vol. 80, pp. 3198–3207.","apa":"Locatello, F., Raj, A., Karimireddy, S. P., Rätsch, G., Schölkopf, B., Stich, S. U., & Jaggi, M. (2018). On matching pursuit and coordinate descent. In Proceedings of the 35th International Conference on Machine Learning (Vol. 80, pp. 3198–3207). ML Research Press.","ama":"Locatello F, Raj A, Karimireddy SP, et al. On matching pursuit and coordinate descent. In: Proceedings of the 35th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:3198-3207."},"date_published":"2018-07-01T00:00:00Z","date_created":"2023-08-22T14:16:25Z","page":"3198-3207","day":"01","publication":"Proceedings of the 35th International Conference on Machine Learning","year":"2018","quality_controlled":"1","publisher":"ML Research Press","oa":1},{"scopus_import":"1","alternative_title":["LNCS"],"month":"07","intvolume":" 10981","abstract":[{"lang":"eng","text":"We present layered concurrent programs, a compact and expressive notation for specifying refinement proofs of concurrent programs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. These programs are expressed in the ordinary syntax of imperative concurrent programs using gated atomic actions, sequencing, choice, and (recursive) procedure calls. Each concurrent program is automatically extracted from the layered program. We reduce refinement to the safety of a sequence of concurrent checker programs, one each to justify the connection between every two consecutive concurrent programs. These checker programs are also automatically extracted from the layered program. Layered concurrent programs have been implemented in the CIVL verifier which has been successfully used for the verification of several complex concurrent programs."}],"oa_version":"Published Version","volume":10981,"related_material":{"record":[{"relation":"dissertation_contains","id":"8332","status":"public"}]},"publication_status":"published","file":[{"checksum":"c64fff560fe5a7532ec10626ad1c215e","file_id":"5705","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_LNCS_Kragl.pdf","date_created":"2018-12-17T12:52:12Z","file_size":1603844,"date_updated":"2020-07-14T12:45:04Z","creator":"dernst"}],"language":[{"iso":"eng"}],"type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"CAV: Computer Aided Verification","start_date":"2018-07-14","end_date":"2018-07-17","location":"Oxford, UK"},"status":"public","_id":"160","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:45:04Z","date_updated":"2023-09-13T08:45:09Z","ddc":["000"],"quality_controlled":"1","publisher":"Springer","oa":1,"page":"79 - 102","date_published":"2018-07-18T00:00:00Z","doi":"10.1007/978-3-319-96145-3_5","date_created":"2018-12-11T11:44:57Z","isi":1,"has_accepted_license":"1","year":"2018","day":"18","project":[{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"publist_id":"7761","author":[{"orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard","last_name":"Kragl","first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Qadeer, Shaz","last_name":"Qadeer","first_name":"Shaz"}],"article_processing_charge":"No","external_id":{"isi":["000491481600005"]},"title":"Layered Concurrent Programs","citation":{"chicago":"Kragl, Bernhard, and Shaz Qadeer. “Layered Concurrent Programs,” 10981:79–102. Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_5.","ista":"Kragl B, Qadeer S. 2018. Layered Concurrent Programs. CAV: Computer Aided Verification, LNCS, vol. 10981, 79–102.","mla":"Kragl, Bernhard, and Shaz Qadeer. Layered Concurrent Programs. Vol. 10981, Springer, 2018, pp. 79–102, doi:10.1007/978-3-319-96145-3_5.","apa":"Kragl, B., & Qadeer, S. (2018). Layered Concurrent Programs (Vol. 10981, pp. 79–102). Presented at the CAV: Computer Aided Verification, Oxford, UK: Springer. https://doi.org/10.1007/978-3-319-96145-3_5","ama":"Kragl B, Qadeer S. Layered Concurrent Programs. In: Vol 10981. Springer; 2018:79-102. doi:10.1007/978-3-319-96145-3_5","short":"B. Kragl, S. Qadeer, in:, Springer, 2018, pp. 79–102.","ieee":"B. Kragl and S. Qadeer, “Layered Concurrent Programs,” presented at the CAV: Computer Aided Verification, Oxford, UK, 2018, vol. 10981, pp. 79–102."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"acknowledgement":"We gratefully acknowledge funding from the Chinese Scholarship Council (CSC; project number 201206910025 to Z.G.), the Fonds Wetenschappelijk Onderzoek (FWO; project number G005112N to A.D.; fellowship number 12I7417N to Z.L.), the Belgian Federal Science Policy Office (BELSPO; to Y.S.), the Agency for Innovation by Science and Technology of Belgium (IWT; fellowship number 121110 to M.V.D.), the Hercules foundation (grant AUGE-09-029 to K.D.), and the ERC StG PROCELLDEATH (project number 639234 to M.K.N.).","quality_controlled":"1","publisher":"Nature Publishing Group","publication":"Nature Plants","day":"28","year":"2018","isi":1,"date_created":"2018-12-11T11:45:35Z","doi":"10.1038/s41477-018-0160-7","date_published":"2018-05-28T00:00:00Z","page":"365 - 375","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Gao Z, Daneva A, Salanenka Y, Van Durme M, Huysmans M, Lin Z, De Winter F, Vanneste S, Karimi M, Van De Velde J, Vandepoele K, Van De Walle D, Dewettinck K, Lambrecht B, Nowack M. 2018. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. 4(6), 365–375.","chicago":"Gao, Zhen, Anna Daneva, Yuliya Salanenka, Matthias Van Durme, Marlies Huysmans, Zongcheng Lin, Freya De Winter, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” Nature Plants. Nature Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0160-7.","short":"Z. Gao, A. Daneva, Y. Salanenka, M. Van Durme, M. Huysmans, Z. Lin, F. De Winter, S. Vanneste, M. Karimi, J. Van De Velde, K. Vandepoele, D. Van De Walle, K. Dewettinck, B. Lambrecht, M. Nowack, Nature Plants 4 (2018) 365–375.","ieee":"Z. Gao et al., “KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis,” Nature Plants, vol. 4, no. 6. Nature Publishing Group, pp. 365–375, 2018.","ama":"Gao Z, Daneva A, Salanenka Y, et al. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. 2018;4(6):365-375. doi:10.1038/s41477-018-0160-7","apa":"Gao, Z., Daneva, A., Salanenka, Y., Van Durme, M., Huysmans, M., Lin, Z., … Nowack, M. (2018). KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/s41477-018-0160-7","mla":"Gao, Zhen, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” Nature Plants, vol. 4, no. 6, Nature Publishing Group, 2018, pp. 365–75, doi:10.1038/s41477-018-0160-7."},"title":"KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis","external_id":{"isi":["000435571000017"]},"article_processing_charge":"No","publist_id":"7619","author":[{"first_name":"Zhen","full_name":"Gao, Zhen","last_name":"Gao"},{"last_name":"Daneva","full_name":"Daneva, Anna","first_name":"Anna"},{"id":"46DAAE7E-F248-11E8-B48F-1D18A9856A87","first_name":"Yuliya","full_name":"Salanenka, Yuliya","last_name":"Salanenka"},{"first_name":"Matthias","last_name":"Van Durme","full_name":"Van Durme, Matthias"},{"first_name":"Marlies","last_name":"Huysmans","full_name":"Huysmans, Marlies"},{"first_name":"Zongcheng","full_name":"Lin, Zongcheng","last_name":"Lin"},{"last_name":"De Winter","full_name":"De Winter, Freya","first_name":"Freya"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"},{"full_name":"Karimi, Mansour","last_name":"Karimi","first_name":"Mansour"},{"first_name":"Jan","last_name":"Van De Velde","full_name":"Van De Velde, Jan"},{"last_name":"Vandepoele","full_name":"Vandepoele, Klaas","first_name":"Klaas"},{"first_name":"Davy","last_name":"Van De Walle","full_name":"Van De Walle, Davy"},{"first_name":"Koen","full_name":"Dewettinck, Koen","last_name":"Dewettinck"},{"first_name":"Bart","full_name":"Lambrecht, Bart","last_name":"Lambrecht"},{"last_name":"Nowack","full_name":"Nowack, Moritz","first_name":"Moritz"}],"oa_version":"None","abstract":[{"text":"Flowers have a species-specific functional life span that determines the time window in which pollination, fertilization and seed set can occur. The stigma tissue plays a key role in flower receptivity by intercepting pollen and initiating pollen tube growth toward the ovary. In this article, we show that a developmentally controlled cell death programme terminates the functional life span of stigma cells in Arabidopsis. We identified the leaf senescence regulator ORESARA1 (also known as ANAC092) and the previously uncharacterized KIRA1 (also known as ANAC074) as partially redundant transcription factors that modulate stigma longevity by controlling the expression of programmed cell death-associated genes. KIRA1 expression is sufficient to induce cell death and terminate floral receptivity, whereas lack of both KIRA1 and ORESARA1 substantially increases stigma life span. Surprisingly, the extension of stigma longevity is accompanied by only a moderate extension of flower receptivity, suggesting that additional processes participate in the control of the flower's receptive life span.","lang":"eng"}],"intvolume":" 4","month":"05","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","volume":4,"issue":"6","_id":"280","status":"public","type":"journal_article","date_updated":"2023-09-13T08:24:17Z","department":[{"_id":"JiFr"}]},{"type":"journal_article","status":"public","_id":"503","department":[{"_id":"CaGu"}],"date_updated":"2023-09-13T08:24:51Z","scopus_import":"1","month":"02","intvolume":" 268","acknowledged_ssus":[{"_id":"Bio"}],"abstract":[{"text":"Buffers are essential for diluting bacterial cultures for flow cytometry analysis in order to study bacterial physiology and gene expression parameters based on fluorescence signals. Using a variety of constitutively expressed fluorescent proteins in Escherichia coli K-12 strain MG1655, we found strong artifactual changes in fluorescence levels after dilution into the commonly used flow cytometry buffer phosphate-buffered saline (PBS) and two other buffer solutions, Tris-HCl and M9 salts. These changes appeared very rapidly after dilution, and were linked to increased membrane permeability and loss in cell viability. We observed buffer-related effects in several different E. coli strains, K-12, C and W, but not E. coli B, which can be partially explained by differences in lipopolysaccharide (LPS) and outer membrane composition. Supplementing the buffers with divalent cations responsible for outer membrane stability, Mg2+ and Ca2+, preserved fluorescence signals, membrane integrity and viability of E. coli. Thus, stabilizing the bacterial outer membrane is essential for precise and unbiased measurements of fluorescence parameters using flow cytometry.","lang":"eng"}],"oa_version":"None","volume":268,"publication_status":"published","language":[{"iso":"eng"}],"publist_id":"7317","author":[{"first_name":"Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","last_name":"Tomasek","orcid":"0000-0003-3768-877X","full_name":"Tomasek, Kathrin"},{"full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet"}],"article_processing_charge":"No","external_id":{"isi":["000425715100006"]},"title":"Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains","citation":{"mla":"Tomasek, Kathrin, et al. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” Journal of Biotechnology, vol. 268, Elsevier, 2018, pp. 40–52, doi:10.1016/j.jbiotec.2018.01.008.","short":"K. Tomasek, T. Bergmiller, C.C. Guet, Journal of Biotechnology 268 (2018) 40–52.","ieee":"K. Tomasek, T. Bergmiller, and C. C. Guet, “Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains,” Journal of Biotechnology, vol. 268. Elsevier, pp. 40–52, 2018.","apa":"Tomasek, K., Bergmiller, T., & Guet, C. C. (2018). Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. Elsevier. https://doi.org/10.1016/j.jbiotec.2018.01.008","ama":"Tomasek K, Bergmiller T, Guet CC. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. 2018;268:40-52. doi:10.1016/j.jbiotec.2018.01.008","chicago":"Tomasek, Kathrin, Tobias Bergmiller, and Calin C Guet. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” Journal of Biotechnology. Elsevier, 2018. https://doi.org/10.1016/j.jbiotec.2018.01.008.","ista":"Tomasek K, Bergmiller T, Guet CC. 2018. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. 268, 40–52."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Elsevier","quality_controlled":"1","acknowledgement":"We thank R Chait and M Lagator for sharing Bacillus subtilis CR_Y1 and pZS*_2R-cIPtet-Venus-Prm, respectively. We are grateful to T Pilizota and all members of the Guet lab for critically reading the manuscript. We also thank the Bioimaging facility at IST Austria for assistance using the FACSAria III system.\r\n\r\n","page":"40 - 52","date_published":"2018-02-20T00:00:00Z","doi":"10.1016/j.jbiotec.2018.01.008","date_created":"2018-12-11T11:46:50Z","isi":1,"year":"2018","day":"20","publication":"Journal of Biotechnology"},{"citation":{"ista":"Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC, Levin B. 2018. Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. 16(8), 2005971.","chicago":"Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005971.","short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, PLoS Biology 16 (2018).","ieee":"W. Chaudhry et al., “Leaky resistance and the conditions for the existence of lytic bacteriophage,” PLoS Biology, vol. 16, no. 8. Public Library of Science, 2018.","apa":"Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin, B. (2018). Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005971","ama":"Chaudhry W, Pleska M, Shah N, et al. Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. 2018;16(8). doi:10.1371/journal.pbio.2005971","mla":"Chaudhry, Waqas, et al. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” PLoS Biology, vol. 16, no. 8, 2005971, Public Library of Science, 2018, doi:10.1371/journal.pbio.2005971."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Waqas","full_name":"Chaudhry, Waqas","last_name":"Chaudhry"},{"id":"4569785E-F248-11E8-B48F-1D18A9856A87","first_name":"Maros","orcid":"0000-0001-7460-7479","full_name":"Pleska, Maros","last_name":"Pleska"},{"last_name":"Shah","full_name":"Shah, Nilang","first_name":"Nilang"},{"full_name":"Weiss, Howard","last_name":"Weiss","first_name":"Howard"},{"first_name":"Ingrid","last_name":"Mccall","full_name":"Mccall, Ingrid"},{"first_name":"Justin","full_name":"Meyer, Justin","last_name":"Meyer"},{"last_name":"Gupta","full_name":"Gupta, Animesh","first_name":"Animesh"},{"last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"},{"full_name":"Levin, Bruce","last_name":"Levin","first_name":"Bruce"}],"publist_id":"7972","external_id":{"isi":["000443383300024"]},"article_processing_charge":"Yes","title":"Leaky resistance and the conditions for the existence of lytic bacteriophage","article_number":"2005971","has_accepted_license":"1","isi":1,"year":"2018","day":"16","publication":"PLoS Biology","date_published":"2018-08-16T00:00:00Z","doi":"10.1371/journal.pbio.2005971","date_created":"2018-12-11T11:44:32Z","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"date_updated":"2023-09-13T08:45:41Z","ddc":["570"],"file_date_updated":"2020-07-14T12:48:10Z","department":[{"_id":"CaGu"}],"_id":"82","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_status":"published","file":[{"creator":"dernst","file_size":4007095,"date_updated":"2020-07-14T12:48:10Z","file_name":"2018_Plos_Chaudhry.pdf","date_created":"2018-12-17T12:55:31Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"527076f78265cd4ea192cd1569851587","file_id":"5706"}],"language":[{"iso":"eng"}],"volume":16,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9810"}]},"issue":"8","abstract":[{"text":"In experimental cultures, when bacteria are mixed with lytic (virulent) bacteriophage, bacterial cells resistant to the phage commonly emerge and become the dominant population of bacteria. Following the ascent of resistant mutants, the densities of bacteria in these simple communities become limited by resources rather than the phage. Despite the evolution of resistant hosts, upon which the phage cannot replicate, the lytic phage population is most commonly maintained in an apparently stable state with the resistant bacteria. Several mechanisms have been put forward to account for this result. Here we report the results of population dynamic/evolution experiments with a virulent mutant of phage Lambda, λVIR, and Escherichia coli in serial transfer cultures. We show that, following the ascent of λVIR-resistant bacteria, λVIRis maintained in the majority of cases in maltose-limited minimal media and in all cases in nutrient-rich broth. Using mathematical models and experiments, we show that the dominant mechanism responsible for maintenance of λVIRin these resource-limited populations dominated by resistant E. coli is a high rate of either phenotypic or genetic transition from resistance to susceptibility—a hitherto undemonstrated mechanism we term "leaky resistance." We discuss the implications of leaky resistance to our understanding of the conditions for the maintenance of phage in populations of bacteria—their “existence conditions.”.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"08","intvolume":" 16"},{"author":[{"last_name":"Umetani","full_name":"Umetani, Nobuyuki","first_name":"Nobuyuki"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"}],"publist_id":"8053","external_id":{"isi":["000448185000050"]},"article_processing_charge":"No","title":"Learning three-dimensional flow for interactive aerodynamic design","citation":{"chicago":"Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for Interactive Aerodynamic Design.” ACM Trans. Graph. ACM, 2018. https://doi.org/10.1145/3197517.3201325.","ista":"Umetani N, Bickel B. 2018. Learning three-dimensional flow for interactive aerodynamic design. ACM Trans. Graph. 37(4), 89.","mla":"Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for Interactive Aerodynamic Design.” ACM Trans. Graph., vol. 37, no. 4, 89, ACM, 2018, doi:10.1145/3197517.3201325.","ama":"Umetani N, Bickel B. Learning three-dimensional flow for interactive aerodynamic design. ACM Trans Graph. 2018;37(4). doi:10.1145/3197517.3201325","apa":"Umetani, N., & Bickel, B. (2018). Learning three-dimensional flow for interactive aerodynamic design. ACM Trans. Graph. ACM. https://doi.org/10.1145/3197517.3201325","ieee":"N. Umetani and B. Bickel, “Learning three-dimensional flow for interactive aerodynamic design,” ACM Trans. Graph., vol. 37, no. 4. ACM, 2018.","short":"N. Umetani, B. Bickel, ACM Trans. Graph. 37 (2018)."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"89","date_published":"2018-08-04T00:00:00Z","doi":"10.1145/3197517.3201325","date_created":"2018-12-11T11:44:06Z","isi":1,"has_accepted_license":"1","year":"2018","day":"04","publication":"ACM Trans. Graph.","publisher":"ACM","quality_controlled":"1","oa":1,"file_date_updated":"2020-07-14T12:46:22Z","department":[{"_id":"BeBi"}],"date_updated":"2023-09-13T08:46:15Z","ddc":["003","004"],"type":"journal_article","status":"public","pubrep_id":"1049","_id":"4","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/new-interactive-machine-learning-tool-makes-car-designs-more-aerodynamic/","description":"News on IST Homepage"}]},"volume":37,"issue":"4","ec_funded":1,"publication_status":"published","file":[{"file_size":22803163,"date_updated":"2020-07-14T12:46:22Z","creator":"system","file_name":"IST-2018-1049-v1+1_2018_sigg_Learning3DAerodynamics.pdf","date_created":"2018-12-12T10:16:28Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5216","checksum":"7a2243668f215821bc6aecad0320079a"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"08","intvolume":" 37","abstract":[{"text":"We present a data-driven technique to instantly predict how fluid flows around various three-dimensional objects. Such simulation is useful for computational fabrication and engineering, but is usually computationally expensive since it requires solving the Navier-Stokes equation for many time steps. To accelerate the process, we propose a machine learning framework which predicts aerodynamic forces and velocity and pressure fields given a threedimensional shape input. Handling detailed free-form three-dimensional shapes in a data-driven framework is challenging because machine learning approaches usually require a consistent parametrization of input and output. We present a novel PolyCube maps-based parametrization that can be computed for three-dimensional shapes at interactive rates. This allows us to efficiently learn the nonlinear response of the flow using a Gaussian process regression. We demonstrate the effectiveness of our approach for the interactive design and optimization of a car body.","lang":"eng"}],"oa_version":"Submitted Version"},{"date_updated":"2023-09-13T08:48:46Z","department":[{"_id":"ToHe"}],"_id":"183","status":"public","type":"conference","conference":{"location":"Porto, Portugal","end_date":"2018-04-13","start_date":"2018-04-11","name":"HSCC: Hybrid Systems: Computation and Control"},"language":[{"iso":"eng"}],"publication_status":"published","oa_version":"None","abstract":[{"text":"Fault-localization is considered to be a very tedious and time-consuming activity in the design of complex Cyber-Physical Systems (CPS). This laborious task essentially requires expert knowledge of the system in order to discover the cause of the fault. In this context, we propose a new procedure that AIDS designers in debugging Simulink/Stateflow hybrid system models, guided by Signal Temporal Logic (STL) specifications. The proposed method relies on three main ingredients: (1) a monitoring and a trace diagnostics procedure that checks whether a tested behavior satisfies or violates an STL specification, localizes time segments and interfaces variables contributing to the property violations; (2) a slicing procedure that maps these observable behavior segments to the internal states and transitions of the Simulink model; and (3) a spectrum-based fault-localization method that combines the previous analysis from multiple tests to identify the internal states and/or transitions that are the most likely to explain the fault. We demonstrate the applicability of our approach on two Simulink models from the automotive and the avionics domain.","lang":"eng"}],"month":"04","scopus_import":"1","alternative_title":["HSCC Proceedings"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Bartocci, Ezio, et al. Localizing Faults in Simulink/Stateflow Models with STL. Association for Computing Machinery, Inc, 2018, pp. 197–206, doi:10.1145/3178126.3178131.","ieee":"E. Bartocci, T. Ferrere, N. Manjunath, and D. Nickovic, “Localizing faults in simulink/stateflow models with STL,” presented at the HSCC: Hybrid Systems: Computation and Control, Porto, Portugal, 2018, pp. 197–206.","short":"E. Bartocci, T. Ferrere, N. Manjunath, D. Nickovic, in:, Association for Computing Machinery, Inc, 2018, pp. 197–206.","ama":"Bartocci E, Ferrere T, Manjunath N, Nickovic D. Localizing faults in simulink/stateflow models with STL. In: Association for Computing Machinery, Inc; 2018:197-206. doi:10.1145/3178126.3178131","apa":"Bartocci, E., Ferrere, T., Manjunath, N., & Nickovic, D. (2018). Localizing faults in simulink/stateflow models with STL (pp. 197–206). Presented at the HSCC: Hybrid Systems: Computation and Control, Porto, Portugal: Association for Computing Machinery, Inc. https://doi.org/10.1145/3178126.3178131","chicago":"Bartocci, Ezio, Thomas Ferrere, Niveditha Manjunath, and Dejan Nickovic. “Localizing Faults in Simulink/Stateflow Models with STL,” 197–206. Association for Computing Machinery, Inc, 2018. https://doi.org/10.1145/3178126.3178131.","ista":"Bartocci E, Ferrere T, Manjunath N, Nickovic D. 2018. Localizing faults in simulink/stateflow models with STL. HSCC: Hybrid Systems: Computation and Control, HSCC Proceedings, , 197–206."},"title":"Localizing faults in simulink/stateflow models with STL","author":[{"first_name":"Ezio","last_name":"Bartocci","full_name":"Bartocci, Ezio"},{"first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere","full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143"},{"full_name":"Manjunath, Niveditha","last_name":"Manjunath","first_name":"Niveditha"},{"last_name":"Nickovic","full_name":"Nickovic, Dejan","first_name":"Dejan"}],"publist_id":"7738","article_processing_charge":"No","external_id":{"isi":["000474781600022"]},"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"day":"11","isi":1,"year":"2018","doi":"10.1145/3178126.3178131","date_published":"2018-04-11T00:00:00Z","date_created":"2018-12-11T11:45:04Z","page":"197 - 206","acknowledgement":"This work was partially supported by the Austrian Science Fund (FWF) under grants S11402-N23 and S11405-N23 (RiSE/SHiNE), the CPS/IoT project (HRSM), the EU ICT COST Action IC1402 on Run-time Verification beyond Monitoring (ARVI), the AMASS project (ECSEL 692474), and the ENABLE-S3 project (ECSEL 692455). The CPS/IoT project receives support from the Austrian government through the Federal Ministry of Science, Research and Economy (BMWFW) in the funding program Hochschulraum-Strukturmittel (HRSM) 2016. The ECSEL Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and Austria, Denmark, Germany, Finland, Czech Republic, Italy, Spain, Portugal, Poland, Ireland, Belgium, France, Netherlands, United Kingdom, Slovakia, Norway.","quality_controlled":"1","publisher":"Association for Computing Machinery, Inc"},{"date_updated":"2023-09-13T08:47:52Z","department":[{"_id":"LaEr"}],"_id":"566","type":"journal_article","article_type":"original","status":"public","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"issue":"1","related_material":{"record":[{"status":"public","id":"149","relation":"dissertation_contains"}]},"volume":28,"abstract":[{"lang":"eng","text":"We consider large random matrices X with centered, independent entries which have comparable but not necessarily identical variances. Girko's circular law asserts that the spectrum is supported in a disk and in case of identical variances, the limiting density is uniform. In this special case, the local circular law by Bourgade et. al. [11,12] shows that the empirical density converges even locally on scales slightly above the typical eigenvalue spacing. In the general case, the limiting density is typically inhomogeneous and it is obtained via solving a system of deterministic equations. Our main result is the local inhomogeneous circular law in the bulk spectrum on the optimal scale for a general variance profile of the entries of X. \r\n\r\n"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1612.07776 ","open_access":"1"}],"scopus_import":"1","intvolume":" 28","month":"03","citation":{"mla":"Alt, Johannes, et al. “Local Inhomogeneous Circular Law.” Annals Applied Probability , vol. 28, no. 1, Institute of Mathematical Statistics, 2018, pp. 148–203, doi:10.1214/17-AAP1302.","ama":"Alt J, Erdös L, Krüger TH. Local inhomogeneous circular law. Annals Applied Probability . 2018;28(1):148-203. doi:10.1214/17-AAP1302","apa":"Alt, J., Erdös, L., & Krüger, T. H. (2018). Local inhomogeneous circular law. Annals Applied Probability . Institute of Mathematical Statistics. https://doi.org/10.1214/17-AAP1302","ieee":"J. Alt, L. Erdös, and T. H. Krüger, “Local inhomogeneous circular law,” Annals Applied Probability , vol. 28, no. 1. Institute of Mathematical Statistics, pp. 148–203, 2018.","short":"J. Alt, L. Erdös, T.H. Krüger, Annals Applied Probability 28 (2018) 148–203.","chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “Local Inhomogeneous Circular Law.” Annals Applied Probability . Institute of Mathematical Statistics, 2018. https://doi.org/10.1214/17-AAP1302.","ista":"Alt J, Erdös L, Krüger TH. 2018. Local inhomogeneous circular law. Annals Applied Probability . 28(1), 148–203."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000431721800005"],"arxiv":["1612.07776 "]},"article_processing_charge":"No","author":[{"full_name":"Alt, Johannes","last_name":"Alt","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes"},{"last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H"}],"title":"Local inhomogeneous circular law","project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"}],"year":"2018","isi":1,"publication":"Annals Applied Probability ","day":"03","page":"148-203","date_created":"2018-12-11T11:47:13Z","date_published":"2018-03-03T00:00:00Z","doi":"10.1214/17-AAP1302","oa":1,"quality_controlled":"1","publisher":"Institute of Mathematical Statistics"},{"citation":{"mla":"Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” Mathematical Intelligencer, vol. 40, no. 3, Springer, 2018, pp. 26–31, doi:10.1007/s00283-018-9795-5.","ieee":"A. Akopyan and A. Petrunin, “Long geodesics on convex surfaces,” Mathematical Intelligencer, vol. 40, no. 3. Springer, pp. 26–31, 2018.","short":"A. Akopyan, A. Petrunin, Mathematical Intelligencer 40 (2018) 26–31.","apa":"Akopyan, A., & Petrunin, A. (2018). Long geodesics on convex surfaces. Mathematical Intelligencer. Springer. https://doi.org/10.1007/s00283-018-9795-5","ama":"Akopyan A, Petrunin A. Long geodesics on convex surfaces. Mathematical Intelligencer. 2018;40(3):26-31. doi:10.1007/s00283-018-9795-5","chicago":"Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” Mathematical Intelligencer. Springer, 2018. https://doi.org/10.1007/s00283-018-9795-5.","ista":"Akopyan A, Petrunin A. 2018. Long geodesics on convex surfaces. Mathematical Intelligencer. 40(3), 26–31."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7948","author":[{"first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X"},{"full_name":"Petrunin, Anton","last_name":"Petrunin","first_name":"Anton"}],"external_id":{"arxiv":["1702.05172"],"isi":["000444141200005"]},"article_processing_charge":"No","title":"Long geodesics on convex surfaces","isi":1,"year":"2018","day":"01","publication":"Mathematical Intelligencer","page":"26 - 31","doi":"10.1007/s00283-018-9795-5","date_published":"2018-09-01T00:00:00Z","date_created":"2018-12-11T11:44:40Z","quality_controlled":"1","publisher":"Springer","oa":1,"date_updated":"2023-09-13T08:49:16Z","department":[{"_id":"HeEd"}],"_id":"106","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"issue":"3","volume":40,"abstract":[{"text":"The goal of this article is to introduce the reader to the theory of intrinsic geometry of convex surfaces. We illustrate the power of the tools by proving a theorem on convex surfaces containing an arbitrarily long closed simple geodesic. Let us remind ourselves that a curve in a surface is called geodesic if every sufficiently short arc of the curve is length minimizing; if, in addition, it has no self-intersections, we call it simple geodesic. A tetrahedron with equal opposite edges is called isosceles. The axiomatic method of Alexandrov geometry allows us to work with the metrics of convex surfaces directly, without approximating it first by a smooth or polyhedral metric. Such approximations destroy the closed geodesics on the surface; therefore it is difficult (if at all possible) to apply approximations in the proof of our theorem. On the other hand, a proof in the smooth or polyhedral case usually admits a translation into Alexandrov’s language; such translation makes the result more general. In fact, our proof resembles a translation of the proof given by Protasov. Note that the main theorem implies in particular that a smooth convex surface does not have arbitrarily long simple closed geodesics. However we do not know a proof of this corollary that is essentially simpler than the one presented below.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1702.05172","open_access":"1"}],"month":"09","intvolume":" 40"},{"status":"public","type":"research_data_reference","_id":"9810","title":"Numerical data used in figures","department":[{"_id":"CaGu"}],"author":[{"last_name":"Chaudhry","full_name":"Chaudhry, Waqas","first_name":"Waqas"},{"first_name":"Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7460-7479","full_name":"Pleska, Maros","last_name":"Pleska"},{"full_name":"Shah, Nilang","last_name":"Shah","first_name":"Nilang"},{"first_name":"Howard","last_name":"Weiss","full_name":"Weiss, Howard"},{"first_name":"Ingrid","full_name":"Mccall, Ingrid","last_name":"Mccall"},{"first_name":"Justin","full_name":"Meyer, Justin","last_name":"Meyer"},{"full_name":"Gupta, Animesh","last_name":"Gupta","first_name":"Animesh"},{"last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Bruce","last_name":"Levin","full_name":"Levin, Bruce"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, (2018).","ieee":"W. Chaudhry et al., “Numerical data used in figures.” Public Library of Science, 2018.","apa":"Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin, B. (2018). Numerical data used in figures. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005971.s008","ama":"Chaudhry W, Pleska M, Shah N, et al. Numerical data used in figures. 2018. doi:10.1371/journal.pbio.2005971.s008","mla":"Chaudhry, Waqas, et al. Numerical Data Used in Figures. Public Library of Science, 2018, doi:10.1371/journal.pbio.2005971.s008.","ista":"Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC, Levin B. 2018. Numerical data used in figures, Public Library of Science, 10.1371/journal.pbio.2005971.s008.","chicago":"Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Numerical Data Used in Figures.” Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005971.s008."},"date_updated":"2023-09-13T08:45:41Z","month":"08","publisher":"Public Library of Science","oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"82","relation":"used_in_publication"}]},"doi":"10.1371/journal.pbio.2005971.s008","date_published":"2018-08-16T00:00:00Z","date_created":"2021-08-06T12:43:44Z","day":"16","year":"2018"},{"language":[{"iso":"eng"}],"file":[{"checksum":"9c7eba51a35c62da8c13f98120b64df4","file_id":"5704","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-17T12:50:07Z","file_name":"2018_JournalCellBiology_Brown.pdf","creator":"dernst","date_updated":"2020-07-14T12:45:45Z","file_size":2252043}],"publication_status":"published","ec_funded":1,"issue":"6","volume":217,"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Lymphatic endothelial cells (LECs) release extracellular chemokines to guide the migration of dendritic cells. In this study, we report that LECs also release basolateral exosome-rich endothelial vesicles (EEVs) that are secreted in greater numbers in the presence of inflammatory cytokines and accumulate in the perivascular stroma of small lymphatic vessels in human chronic inflammatory diseases. Proteomic analyses of EEV fractions identified > 1,700 cargo proteins and revealed a dominant motility-promoting protein signature. In vitro and ex vivo EEV fractions augmented cellular protrusion formation in a CX3CL1/fractalkine-dependent fashion and enhanced the directional migratory response of human dendritic cells along guidance cues. We conclude that perilymphatic LEC exosomes enhance exploratory behavior and thus promote directional migration of CX3CR1-expressing cells in complex tissue environments."}],"intvolume":" 217","month":"04","scopus_import":"1","ddc":["570"],"date_updated":"2023-09-13T08:51:29Z","department":[{"_id":"MiSi"},{"_id":"Bio"}],"file_date_updated":"2020-07-14T12:45:45Z","_id":"275","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","publication":"Journal of Cell Biology","day":"12","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:45:33Z","doi":"10.1083/jcb.201612051","date_published":"2018-04-12T00:00:00Z","page":"2205 - 2221","acknowledgement":"M. Brown was supported by the Cell Communication in Health and Disease Graduate Study Program of the Austrian Science Fund and Medizinische Universität Wien, M. Sixt by the European Research Council (ERC GA 281556) and an Austrian Science Fund START award, K.L. Bennett by the Austrian Academy of Sciences, D.G. Jackson and L.A. Johnson by Unit Funding (MC_UU_12010/2) and project grants from the Medical Research Council (G1100134 and MR/L008610/1), and M. Detmar by the Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung and Advanced European Research Council grant LYVICAM. K. Vaahtomeri was supported by an Academy of Finland postdoctoral research grant (287853). This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 668036 (RELENT).","oa":1,"publisher":"Rockefeller University Press","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Brown M, Johnson L, Leone D, et al. Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. 2018;217(6):2205-2221. doi:10.1083/jcb.201612051","apa":"Brown, M., Johnson, L., Leone, D., Májek, P., Vaahtomeri, K., Senfter, D., … Kerjaschki, D. (2018). Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201612051","ieee":"M. Brown et al., “Lymphatic exosomes promote dendritic cell migration along guidance cues,” Journal of Cell Biology, vol. 217, no. 6. Rockefeller University Press, pp. 2205–2221, 2018.","short":"M. Brown, L. Johnson, D. Leone, P. Májek, K. Vaahtomeri, D. Senfter, N. Bukosza, H. Schachner, G. Asfour, B. Langer, R. Hauschild, K. Parapatics, Y. Hong, K. Bennett, R. Kain, M. Detmar, M.K. Sixt, D. Jackson, D. Kerjaschki, Journal of Cell Biology 217 (2018) 2205–2221.","mla":"Brown, Markus, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” Journal of Cell Biology, vol. 217, no. 6, Rockefeller University Press, 2018, pp. 2205–21, doi:10.1083/jcb.201612051.","ista":"Brown M, Johnson L, Leone D, Májek P, Vaahtomeri K, Senfter D, Bukosza N, Schachner H, Asfour G, Langer B, Hauschild R, Parapatics K, Hong Y, Bennett K, Kain R, Detmar M, Sixt MK, Jackson D, Kerjaschki D. 2018. Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. 217(6), 2205–2221.","chicago":"Brown, Markus, Louise Johnson, Dario Leone, Peter Májek, Kari Vaahtomeri, Daniel Senfter, Nora Bukosza, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” Journal of Cell Biology. Rockefeller University Press, 2018. https://doi.org/10.1083/jcb.201612051."},"title":"Lymphatic exosomes promote dendritic cell migration along guidance cues","external_id":{"isi":["000438077800026"],"pmid":["29650776"]},"article_processing_charge":"No","publist_id":"7627","author":[{"id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","first_name":"Markus","full_name":"Brown, Markus","last_name":"Brown"},{"full_name":"Johnson, Louise","last_name":"Johnson","first_name":"Louise"},{"full_name":"Leone, Dario","last_name":"Leone","first_name":"Dario"},{"first_name":"Peter","full_name":"Májek, Peter","last_name":"Májek"},{"id":"368EE576-F248-11E8-B48F-1D18A9856A87","first_name":"Kari","last_name":"Vaahtomeri","orcid":"0000-0001-7829-3518","full_name":"Vaahtomeri, Kari"},{"full_name":"Senfter, Daniel","last_name":"Senfter","first_name":"Daniel"},{"last_name":"Bukosza","full_name":"Bukosza, Nora","first_name":"Nora"},{"last_name":"Schachner","full_name":"Schachner, Helga","first_name":"Helga"},{"full_name":"Asfour, Gabriele","last_name":"Asfour","first_name":"Gabriele"},{"full_name":"Langer, Brigitte","last_name":"Langer","first_name":"Brigitte"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Katja","last_name":"Parapatics","full_name":"Parapatics, Katja"},{"first_name":"Young","last_name":"Hong","full_name":"Hong, Young"},{"first_name":"Keiryn","full_name":"Bennett, Keiryn","last_name":"Bennett"},{"first_name":"Renate","last_name":"Kain","full_name":"Kain, Renate"},{"first_name":"Michael","last_name":"Detmar","full_name":"Detmar, Michael"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","full_name":"Jackson, David","last_name":"Jackson"},{"last_name":"Kerjaschki","full_name":"Kerjaschki, Dontscho","first_name":"Dontscho"}],"project":[{"name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","grant_number":"Y 564-B12","call_identifier":"FWF","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425"},{"grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}]},{"date_updated":"2023-09-13T08:53:28Z","department":[{"_id":"JiFr"}],"_id":"158","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"issue":"8","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/plant-mothers-talk-to-their-embryos-via-the-hormone-auxin/","description":"News on IST Homepage"}]},"volume":4,"pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","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."}],"intvolume":" 4","month":"07","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30013211","open_access":"1"}],"scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Robert, Hélène, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning in Arabidopsis.” Nature Plants, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 548–53, doi:10.1038/s41477-018-0204-z.","ieee":"H. Robert et al., “Maternal auxin supply contributes to early embryo patterning in Arabidopsis,” Nature Plants, vol. 4, no. 8. Nature Publishing Group, pp. 548–553, 2018.","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.","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. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/s41477-018-0204-z","ama":"Robert H, Park C, Gutièrrez C, et al. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. 2018;4(8):548-553. doi:10.1038/s41477-018-0204-z","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.” Nature Plants. Nature Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0204-z.","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."},"title":"Maternal auxin supply contributes to early embryo patterning in Arabidopsis","article_processing_charge":"No","external_id":{"pmid":["30013211"],"isi":["000443861300011"]},"author":[{"full_name":"Robert, Hélène","last_name":"Robert","first_name":"Hélène"},{"first_name":"Chulmin","full_name":"Park, Chulmin","last_name":"Park"},{"first_name":"Carla","last_name":"Gutièrrez","full_name":"Gutièrrez, Carla"},{"last_name":"Wójcikowska","full_name":"Wójcikowska, Barbara","first_name":"Barbara"},{"full_name":"Pěnčík, Aleš","last_name":"Pěnčík","first_name":"Aleš"},{"full_name":"Novák, Ondřej","last_name":"Novák","first_name":"Ondřej"},{"full_name":"Chen, Junyi","last_name":"Chen","first_name":"Junyi"},{"first_name":"Wim","full_name":"Grunewald, Wim","last_name":"Grunewald"},{"last_name":"Dresselhaus","full_name":"Dresselhaus, Thomas","first_name":"Thomas"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Laux","full_name":"Laux, Thomas","first_name":"Thomas"}],"publist_id":"7763","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"publication":"Nature Plants","day":"16","year":"2018","isi":1,"date_created":"2018-12-11T11:44:56Z","doi":"10.1038/s41477-018-0204-z","date_published":"2018-07-16T00:00:00Z","page":"548 - 553","acknowledgement":"This work was further supported by the Czech Science Foundation GACR (GA13-40637S) to J.F.;","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1"},{"title":"Mammalian mitochondrial complex I structure and disease causing mutations","publist_id":"7769","author":[{"full_name":"Fiedorczuk, Karol","last_name":"Fiedorczuk","id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0","first_name":"Karol"},{"orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000445118200007"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Fiedorczuk, Karol, and Leonid A. Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” Trends in Cell Biology, vol. 28, no. 10, Elsevier, 2018, pp. 835–67, doi:10.1016/j.tcb.2018.06.006.","short":"K. Fiedorczuk, L.A. Sazanov, Trends in Cell Biology 28 (2018) 835–867.","ieee":"K. Fiedorczuk and L. A. Sazanov, “Mammalian mitochondrial complex I structure and disease causing mutations,” Trends in Cell Biology, vol. 28, no. 10. Elsevier, pp. 835–867, 2018.","ama":"Fiedorczuk K, Sazanov LA. Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. 2018;28(10):835-867. doi:10.1016/j.tcb.2018.06.006","apa":"Fiedorczuk, K., & Sazanov, L. A. (2018). Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. Elsevier. https://doi.org/10.1016/j.tcb.2018.06.006","chicago":"Fiedorczuk, Karol, and Leonid A Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” Trends in Cell Biology. Elsevier, 2018. https://doi.org/10.1016/j.tcb.2018.06.006.","ista":"Fiedorczuk K, Sazanov LA. 2018. Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. 28(10), 835–867."},"doi":"10.1016/j.tcb.2018.06.006","date_published":"2018-07-26T00:00:00Z","date_created":"2018-12-11T11:44:54Z","page":"835 - 867","day":"26","publication":"Trends in Cell Biology","has_accepted_license":"1","isi":1,"year":"2018","publisher":"Elsevier","quality_controlled":"1","oa":1,"department":[{"_id":"LeSa"}],"file_date_updated":"2020-07-14T12:45:00Z","ddc":["572"],"date_updated":"2023-09-13T08:51:56Z","status":"public","type":"journal_article","article_type":"original","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"_id":"152","volume":28,"issue":"10","file":[{"file_size":2185385,"date_updated":"2020-07-14T12:45:00Z","creator":"lsazanov","file_name":"SasanovFinalMS+EdComments_LS_allacc_withFigs.pdf","date_created":"2019-11-07T12:55:20Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"ef6d2b4e1fd63948539639242610bfa6","file_id":"6994"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"07","intvolume":" 28","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"lang":"eng","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."}]},{"oa_version":"Preprint","abstract":[{"lang":"eng","text":"A model of computation that is widely used in the formal analysis of reactive systems is symbolic algorithms. In this model the access to the input graph is restricted to consist of symbolic operations, which are expensive in comparison to the standard RAM operations. We give lower bounds on the number of symbolic operations for basic graph problems such as the computation of the strongly connected components and of the approximate diameter as well as for fundamental problems in model checking such as safety, liveness, and coliveness. Our lower bounds are linear in the number of vertices of the graph, even for constant-diameter graphs. For none of these problems lower bounds on the number of symbolic operations were known before. The lower bounds show an interesting separation of these problems from the reachability problem, which can be solved with O(D) symbolic operations, where D is the diameter of the graph. Additionally we present an approximation algorithm for the graph diameter which requires Õ(n/D) symbolic steps to achieve a (1 +ϵ)-approximation for any constant > 0. This compares to O(n/D) symbolic steps for the (naive) exact algorithm and O(D) symbolic steps for a 2-approximation. Finally we also give a refined analysis of the strongly connected components algorithms of [15], showing that it uses an optimal number of symbolic steps that is proportional to the sum of the diameters of the strongly connected components."}],"month":"01","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1711.09148","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"_id":"310","status":"public","type":"conference","conference":{"location":"New Orleans, Louisiana, United States","end_date":"2018-01-10","start_date":"2018-01-07","name":"SODA: Symposium on Discrete Algorithms"},"date_updated":"2023-09-13T08:50:16Z","department":[{"_id":"KrCh"}],"quality_controlled":"1","publisher":"ACM","oa":1,"day":"01","isi":1,"year":"2018","doi":"10.1137/1.9781611975031.151","date_published":"2018-01-01T00:00:00Z","date_created":"2018-12-11T11:45:45Z","page":"2341 - 2356","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"K. Chatterjee, W. Dvorák, M.H. Henzinger, V. Loitzenbauer, in:, ACM, 2018, pp. 2341–2356.","ieee":"K. Chatterjee, W. Dvorák, M. H. Henzinger, and V. Loitzenbauer, “Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter,” presented at the SODA: Symposium on Discrete Algorithms, New Orleans, Louisiana, United States, 2018, pp. 2341–2356.","ama":"Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter. In: ACM; 2018:2341-2356. doi:10.1137/1.9781611975031.151","apa":"Chatterjee, K., Dvorák, W., Henzinger, M. H., & Loitzenbauer, V. (2018). Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter (pp. 2341–2356). Presented at the SODA: Symposium on Discrete Algorithms, New Orleans, Louisiana, United States: ACM. https://doi.org/10.1137/1.9781611975031.151","mla":"Chatterjee, Krishnendu, et al. Lower Bounds for Symbolic Computation on Graphs: Strongly Connected Components, Liveness, Safety, and Diameter. ACM, 2018, pp. 2341–56, doi:10.1137/1.9781611975031.151.","ista":"Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. 2018. Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter. SODA: Symposium on Discrete Algorithms, 2341–2356.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Veronika Loitzenbauer. “Lower Bounds for Symbolic Computation on Graphs: Strongly Connected Components, Liveness, Safety, and Diameter,” 2341–56. ACM, 2018. https://doi.org/10.1137/1.9781611975031.151."},"title":"Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Dvorák, Wolfgang","last_name":"Dvorák","first_name":"Wolfgang"},{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"first_name":"Veronika","last_name":"Loitzenbauer","full_name":"Loitzenbauer, Veronika"}],"publist_id":"7555","article_processing_charge":"No","external_id":{"arxiv":["1711.09148"],"isi":["000483921200152"]}},{"oa_version":"Preprint","abstract":[{"lang":"eng","text":"There has been significant interest recently in using complex quantum systems to create effective nonreciprocal dynamics. Proposals have been put forward for the realization of artificial magnetic fields for photons and phonons; experimental progress is fast making these proposals a reality. Much work has concentrated on the use of such systems for controlling the flow of signals, e.g., to create isolators or directional amplifiers for optical signals. In this Letter, we build on this work but move in a different direction. We develop the theory of and discuss a potential realization for the controllable flow of thermal noise in quantum systems. We demonstrate theoretically that the unidirectional flow of thermal noise is possible within quantum cascaded systems. Viewing an optomechanical platform as a cascaded system we show here that one can ultimately control the direction of the flow of thermal noise. By appropriately engineering the mechanical resonator, which acts as an artificial reservoir, the flow of thermal noise can be constrained to a desired direction, yielding a thermal rectifier. The proposed quantum thermal noise rectifier could potentially be used to develop devices such as a thermal modulator, a thermal router, and a thermal amplifier for nanoelectronic devices and superconducting circuits."}],"intvolume":" 120","month":"02","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.09051"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/interference-as-a-new-method-for-cooling-quantum-devices/","relation":"press_release","description":"News on IST Homepage"}]},"volume":120,"issue":"6","_id":"436","status":"public","type":"journal_article","date_updated":"2023-09-13T08:52:27Z","department":[{"_id":"JoFi"}],"oa":1,"publisher":"American Physical Society","quality_controlled":"1","publication":"Physical Review Letters","day":"07","year":"2018","isi":1,"date_created":"2018-12-11T11:46:28Z","doi":"10.1103/PhysRevLett.120.060601","date_published":"2018-02-07T00:00:00Z","article_number":"060601 ","project":[{"call_identifier":"H2020","_id":"257EB838-B435-11E9-9278-68D0E5697425","grant_number":"732894","name":"Hybrid Optomechanical Technologies"},{"call_identifier":"H2020","_id":"258047B6-B435-11E9-9278-68D0E5697425","grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Barzanjeh, Shabir, Matteo Aquilina, and André Xuereb. “Manipulating the Flow of Thermal Noise in Quantum Devices.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.120.060601.","ista":"Barzanjeh S, Aquilina M, Xuereb A. 2018. Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. 120(6), 060601.","mla":"Barzanjeh, Shabir, et al. “Manipulating the Flow of Thermal Noise in Quantum Devices.” Physical Review Letters, vol. 120, no. 6, 060601, American Physical Society, 2018, doi:10.1103/PhysRevLett.120.060601.","apa":"Barzanjeh, S., Aquilina, M., & Xuereb, A. (2018). Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.120.060601","ama":"Barzanjeh S, Aquilina M, Xuereb A. Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. 2018;120(6). doi:10.1103/PhysRevLett.120.060601","ieee":"S. Barzanjeh, M. Aquilina, and A. Xuereb, “Manipulating the flow of thermal noise in quantum devices,” Physical Review Letters, vol. 120, no. 6. American Physical Society, 2018.","short":"S. Barzanjeh, M. Aquilina, A. Xuereb, Physical Review Letters 120 (2018)."},"title":"Manipulating the flow of thermal noise in quantum devices","article_processing_charge":"No","external_id":{"isi":["000424382100004"],"arxiv":["1706.09051"]},"publist_id":"7387","author":[{"id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir","last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423"},{"full_name":"Aquilina, Matteo","last_name":"Aquilina","first_name":"Matteo"},{"first_name":"André","full_name":"Xuereb, André","last_name":"Xuereb"}]},{"citation":{"mla":"Hross, Sabrina, et al. “Mechanistic Description of Spatial Processes Using Integrative Modelling of Noise-Corrupted Imaging Data.” Journal of the Royal Society Interface, vol. 15, no. 149, 20180600, Royal Society Publishing, 2018, doi:10.1098/rsif.2018.0600.","ama":"Hross S, Theis FJ, Sixt MK, Hasenauer J. Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data. Journal of the Royal Society Interface. 2018;15(149). doi:10.1098/rsif.2018.0600","apa":"Hross, S., Theis, F. J., Sixt, M. K., & Hasenauer, J. (2018). Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data. Journal of the Royal Society Interface. Royal Society Publishing. https://doi.org/10.1098/rsif.2018.0600","short":"S. Hross, F.J. Theis, M.K. Sixt, J. Hasenauer, Journal of the Royal Society Interface 15 (2018).","ieee":"S. Hross, F. J. Theis, M. K. Sixt, and J. Hasenauer, “Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data,” Journal of the Royal Society Interface, vol. 15, no. 149. Royal Society Publishing, 2018.","chicago":"Hross, Sabrina, Fabian J. Theis, Michael K Sixt, and Jan Hasenauer. “Mechanistic Description of Spatial Processes Using Integrative Modelling of Noise-Corrupted Imaging Data.” Journal of the Royal Society Interface. Royal Society Publishing, 2018. https://doi.org/10.1098/rsif.2018.0600.","ista":"Hross S, Theis FJ, Sixt MK, Hasenauer J. 2018. Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data. Journal of the Royal Society Interface. 15(149), 20180600."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000456783800011"]},"author":[{"full_name":"Hross, Sabrina","last_name":"Hross","first_name":"Sabrina"},{"first_name":"Fabian J.","full_name":"Theis, Fabian J.","last_name":"Theis"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"},{"full_name":"Hasenauer, Jan","last_name":"Hasenauer","first_name":"Jan"}],"title":"Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data","article_number":"20180600","year":"2018","isi":1,"has_accepted_license":"1","publication":"Journal of the Royal Society Interface","day":"05","date_created":"2019-01-20T22:59:18Z","doi":"10.1098/rsif.2018.0600","date_published":"2018-12-05T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"Royal Society Publishing","date_updated":"2023-09-13T08:55:05Z","ddc":["570"],"file_date_updated":"2020-07-14T12:47:13Z","department":[{"_id":"MiSi"}],"_id":"5858","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"issn":["17425689"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2019-02-05T14:46:44Z","file_name":"2018_Interface_Hross.pdf","date_updated":"2020-07-14T12:47:13Z","file_size":1464288,"creator":"dernst","checksum":"56eb4308a15b7190bff938fab1f780e8","file_id":"5925","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"volume":15,"issue":"149","abstract":[{"text":"Spatial patterns are ubiquitous on the subcellular, cellular and tissue level, and can be studied using imaging techniques such as light and fluorescence microscopy. Imaging data provide quantitative information about biological systems; however, mechanisms causing spatial patterning often remain elusive. In recent years, spatio-temporal mathematical modelling has helped to overcome this problem. Yet, outliers and structured noise limit modelling of whole imaging data, and models often consider spatial summary statistics. Here, we introduce an integrated data-driven modelling approach that can cope with measurement artefacts and whole imaging data. Our approach combines mechanistic models of the biological processes with robust statistical models of the measurement process. The parameters of the integrated model are calibrated using a maximum-likelihood approach. We used this integrated modelling approach to study in vivo gradients of the chemokine (C-C motif) ligand 21 (CCL21). CCL21 gradients guide dendritic cells and are important in the adaptive immune response. Using artificial data, we verified that the integrated modelling approach provides reliable parameter estimates in the presence of measurement noise and that bias and variance of these estimates are reduced compared to conventional approaches. The application to experimental data allowed the parametrization and subsequent refinement of the model using additional mechanisms. Among other results, model-based hypothesis testing predicted lymphatic vessel-dependent concentration of heparan sulfate, the binding partner of CCL21. The selected model provided an accurate description of the experimental data and was partially validated using published data. Our findings demonstrate that integrated statistical modelling of whole imaging data is computationally feasible and can provide novel biological insights.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 15","month":"12"},{"volume":3,"issue":"10","ec_funded":1,"file":[{"file_id":"5043","checksum":"7fc0a2322214d1c04debef36d5bf2e8a","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:13:56Z","file_name":"IST-2018-1062-v1+1_PhysRevFluids.3.103303.pdf","creator":"system","date_updated":"2020-07-14T12:45:04Z","file_size":1838431}],"language":[{"iso":"eng"}],"publication_status":"published","month":"10","intvolume":" 3","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"We report quantitative evidence of mixing-layer elastic instability in a viscoelastic fluid flow between two widely spaced obstacles hindering a channel flow at Re 1 and Wi 1. Two mixing layers with nonuniform shear velocity profiles are formed in the region between the obstacles. The mixing-layer instability arises in the vicinity of an inflection point on the shear velocity profile with a steep variation in the elastic stress. The instability results in an intermittent appearance of small vortices in the mixing layers and an amplification of spatiotemporal averaged vorticity in the elastic turbulence regime. The latter is characterized through scaling of friction factor with Wi and both pressure and velocity spectra. Furthermore, the observations reported provide improved understanding of the stability of the mixing layer in a viscoelastic fluid at large elasticity, i.e., Wi 1 and Re 1 and oppose the current view of suppression of vorticity solely by polymer additives.","lang":"eng"}],"department":[{"_id":"BjHo"}],"file_date_updated":"2020-07-14T12:45:04Z","ddc":["532"],"date_updated":"2023-09-13T08:57:05Z","status":"public","pubrep_id":"1062","type":"journal_article","article_type":"original","_id":"16","doi":"10.1103/PhysRevFluids.3.103303","date_published":"2018-10-16T00:00:00Z","date_created":"2018-12-11T11:44:10Z","day":"16","publication":"Physical Review Fluids","has_accepted_license":"1","isi":1,"year":"2018","quality_controlled":"1","publisher":"American Physical Society","oa":1,"acknowledgement":"This work was partially supported by the Israel Science Foundation (ISF; Grant No. 882/15) and the Binational USA-Israel Foundation (BSF; Grant No. 2016145).","title":"Mixing layer instability and vorticity amplification in a creeping viscoelastic flow","author":[{"full_name":"Varshney, Atul","orcid":"0000-0002-3072-5999","last_name":"Varshney","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","first_name":"Atul"},{"first_name":"Victor","full_name":"Steinberg, Victor","last_name":"Steinberg"}],"publist_id":"8039","external_id":{"isi":["000447469200001"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Varshney A, Steinberg V. 2018. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. 3(10), 103303.","chicago":"Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” Physical Review Fluids. American Physical Society, 2018. https://doi.org/10.1103/PhysRevFluids.3.103303.","short":"A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).","ieee":"A. Varshney and V. Steinberg, “Mixing layer instability and vorticity amplification in a creeping viscoelastic flow,” Physical Review Fluids, vol. 3, no. 10. American Physical Society, 2018.","ama":"Varshney A, Steinberg V. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. 2018;3(10). doi:10.1103/PhysRevFluids.3.103303","apa":"Varshney, A., & Steinberg, V. (2018). Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.3.103303","mla":"Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” Physical Review Fluids, vol. 3, no. 10, 103303, American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.103303."},"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"103303"},{"_id":"43","pubrep_id":"1063","status":"public","type":"journal_article","ddc":["570","577"],"date_updated":"2023-09-13T08:57:38Z","department":[{"_id":"DaAl"}],"file_date_updated":"2020-07-14T12:46:26Z","oa_version":"Submitted Version","abstract":[{"text":"The initial amount of pathogens required to start an infection within a susceptible host is called the infective dose and is known to vary to a large extent between different pathogen species. We investigate the hypothesis that the differences in infective doses are explained by the mode of action in the underlying mechanism of pathogenesis: Pathogens with locally acting mechanisms tend to have smaller infective doses than pathogens with distantly acting mechanisms. While empirical evidence tends to support the hypothesis, a formal theoretical explanation has been lacking. We give simple analytical models to gain insight into this phenomenon and also investigate a stochastic, spatially explicit, mechanistic within-host model for toxin-dependent bacterial infections. The model shows that pathogens secreting locally acting toxins have smaller infective doses than pathogens secreting diffusive toxins, as hypothesized. While local pathogenetic mechanisms require smaller infective doses, pathogens with distantly acting toxins tend to spread faster and may cause more damage to the host. The proposed model can serve as a basis for the spatially explicit analysis of various virulence factors also in the context of other problems in infection dynamics.","lang":"eng"}],"intvolume":" 115","month":"10","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"df7ac544a587c06b75692653b9fabd18","file_id":"6258","creator":"dernst","file_size":4070777,"date_updated":"2020-07-14T12:46:26Z","file_name":"2018_PNAS_Rybicki.pdf","date_created":"2019-04-09T08:02:50Z"}],"publication_status":"published","ec_funded":1,"issue":"42","volume":115,"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Rybicki, Joel, et al. “Model of Bacterial Toxin-Dependent Pathogenesis Explains Infective Dose.” PNAS, vol. 115, no. 42, National Academy of Sciences, 2018, pp. 10690–95, doi:10.1073/pnas.1721061115.","short":"J. Rybicki, E. Kisdi, J. Anttila, PNAS 115 (2018) 10690–10695.","ieee":"J. Rybicki, E. Kisdi, and J. Anttila, “Model of bacterial toxin-dependent pathogenesis explains infective dose,” PNAS, vol. 115, no. 42. National Academy of Sciences, pp. 10690–10695, 2018.","apa":"Rybicki, J., Kisdi, E., & Anttila, J. (2018). Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1721061115","ama":"Rybicki J, Kisdi E, Anttila J. Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. 2018;115(42):10690-10695. doi:10.1073/pnas.1721061115","chicago":"Rybicki, Joel, Eva Kisdi, and Jani Anttila. “Model of Bacterial Toxin-Dependent Pathogenesis Explains Infective Dose.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1721061115.","ista":"Rybicki J, Kisdi E, Anttila J. 2018. Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. 115(42), 10690–10695."},"title":"Model of bacterial toxin-dependent pathogenesis explains infective dose","external_id":{"isi":["000447491300057"]},"article_processing_charge":"No","publist_id":"8011","author":[{"first_name":"Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6432-6646","full_name":"Rybicki, Joel","last_name":"Rybicki"},{"first_name":"Eva","full_name":"Kisdi, Eva","last_name":"Kisdi"},{"full_name":"Anttila, Jani","last_name":"Anttila","first_name":"Jani"}],"acknowledgement":"J.R. and J.V.A. were also supported by the Academy of Finland Grants 1273253 and 267541.","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","publication":"PNAS","day":"02","year":"2018","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:44:19Z","doi":"10.1073/pnas.1721061115","date_published":"2018-10-02T00:00:00Z","page":"10690 - 10695"},{"article_number":"136","project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Alderighi, Thomas, Luigi Malomo, Daniela Giorgi, Nico Pietroni, Bernd Bickel, and Paolo Cignoni. “Metamolds: Computational Design of Silicone Molds.” ACM Trans. Graph. ACM, 2018. https://doi.org/10.1145/3197517.3201381.","ista":"Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. 2018. Metamolds: Computational design of silicone molds. ACM Trans. Graph. 37(4), 136.","mla":"Alderighi, Thomas, et al. “Metamolds: Computational Design of Silicone Molds.” ACM Trans. Graph., vol. 37, no. 4, 136, ACM, 2018, doi:10.1145/3197517.3201381.","apa":"Alderighi, T., Malomo, L., Giorgi, D., Pietroni, N., Bickel, B., & Cignoni, P. (2018). Metamolds: Computational design of silicone molds. ACM Trans. Graph. ACM. https://doi.org/10.1145/3197517.3201381","ama":"Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. Metamolds: Computational design of silicone molds. ACM Trans Graph. 2018;37(4). doi:10.1145/3197517.3201381","ieee":"T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, and P. Cignoni, “Metamolds: Computational design of silicone molds,” ACM Trans. Graph., vol. 37, no. 4. ACM, 2018.","short":"T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, P. Cignoni, ACM Trans. Graph. 37 (2018)."},"title":"Metamolds: Computational design of silicone molds","external_id":{"isi":["000448185000097"]},"article_processing_charge":"No","author":[{"first_name":"Thomas","last_name":"Alderighi","full_name":"Alderighi, Thomas"},{"last_name":"Malomo","full_name":"Malomo, Luigi","first_name":"Luigi"},{"last_name":"Giorgi","full_name":"Giorgi, Daniela","first_name":"Daniela"},{"last_name":"Pietroni","full_name":"Pietroni, Nico","first_name":"Nico"},{"last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cignoni","full_name":"Cignoni, Paolo","first_name":"Paolo"}],"publist_id":"8043","oa":1,"publisher":"ACM","quality_controlled":"1","publication":"ACM Trans. Graph.","day":"04","year":"2018","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:44:09Z","doi":"10.1145/3197517.3201381","date_published":"2018-08-04T00:00:00Z","_id":"13","pubrep_id":"1038","status":"public","type":"journal_article","ddc":["004"],"date_updated":"2023-09-13T08:56:07Z","file_date_updated":"2020-07-14T12:44:43Z","department":[{"_id":"BeBi"}],"oa_version":"Submitted Version","abstract":[{"text":"We propose a new method for fabricating digital objects through reusable silicone molds. Molds are generated by casting liquid silicone into custom 3D printed containers called metamolds. Metamolds automatically define the cuts that are needed to extract the cast object from the silicone mold. The shape of metamolds is designed through a novel segmentation technique, which takes into account both geometric and topological constraints involved in the process of mold casting. Our technique is simple, does not require changing the shape or topology of the input objects, and only requires off-the- shelf materials and technologies. We successfully tested our method on a set of challenging examples with complex shapes and rich geometric detail. © 2018 Association for Computing Machinery.","lang":"eng"}],"intvolume":" 37","month":"08","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:44:43Z","file_size":91939066,"date_created":"2018-12-12T10:18:52Z","file_name":"IST-2018-1038-v1+1_metamolds_authorversion.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"61d46273dca4de626accef1d17a0aaad","file_id":"5374"}],"publication_status":"published","ec_funded":1,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/metamolds-molding-a-mold/","relation":"press_release","description":"News on IST Homepage"}]},"issue":"4","volume":37},{"project":[{"_id":"255BFFFA-B435-11E9-9278-68D0E5697425","grant_number":"RGY0084/2012","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)"}],"citation":{"apa":"Zhang, W., Herde, M., Mitchell, J., Whitfield, J., Wulff, A., Vongsouthi, V., … Henneberger, C. (2018). Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/s41589-018-0108-2","ama":"Zhang W, Herde M, Mitchell J, et al. Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. 2018;14(9):861-869. doi:10.1038/s41589-018-0108-2","ieee":"W. Zhang et al., “Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS,” Nature Chemical Biology, vol. 14, no. 9. Nature Publishing Group, pp. 861–869, 2018.","short":"W. Zhang, M. Herde, J. Mitchell, J. Whitfield, A. Wulff, V. Vongsouthi, I. Sanchez-Romero, P. Gulakova, D. Minge, B. Breithausen, S. Schoch, H.L. Janovjak, C. Jackson, C. Henneberger, Nature Chemical Biology 14 (2018) 861–869.","mla":"Zhang, William, et al. “Monitoring Hippocampal Glycine with the Computationally Designed Optical Sensor GlyFS.” Nature Chemical Biology, vol. 14, no. 9, Nature Publishing Group, 2018, pp. 861–69, doi:10.1038/s41589-018-0108-2.","ista":"Zhang W, Herde M, Mitchell J, Whitfield J, Wulff A, Vongsouthi V, Sanchez-Romero I, Gulakova P, Minge D, Breithausen B, Schoch S, Janovjak HL, Jackson C, Henneberger C. 2018. Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. 14(9), 861–869.","chicago":"Zhang, William, Michel Herde, Joshua Mitchell, Jason Whitfield, Andreas Wulff, Vanessa Vongsouthi, Inmaculada Sanchez-Romero, et al. “Monitoring Hippocampal Glycine with the Computationally Designed Optical Sensor GlyFS.” Nature Chemical Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41589-018-0108-2."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"pmid":["30061718 "],"isi":["000442174500013"]},"author":[{"first_name":"William","full_name":"Zhang, William","last_name":"Zhang"},{"first_name":"Michel","last_name":"Herde","full_name":"Herde, Michel"},{"first_name":"Joshua","full_name":"Mitchell, Joshua","last_name":"Mitchell"},{"first_name":"Jason","full_name":"Whitfield, Jason","last_name":"Whitfield"},{"last_name":"Wulff","full_name":"Wulff, Andreas","first_name":"Andreas"},{"last_name":"Vongsouthi","full_name":"Vongsouthi, Vanessa","first_name":"Vanessa"},{"last_name":"Sanchez Romero","full_name":"Sanchez Romero, Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","first_name":"Inmaculada"},{"full_name":"Gulakova, Polina","last_name":"Gulakova","first_name":"Polina"},{"first_name":"Daniel","full_name":"Minge, Daniel","last_name":"Minge"},{"first_name":"Björn","last_name":"Breithausen","full_name":"Breithausen, Björn"},{"full_name":"Schoch, Susanne","last_name":"Schoch","first_name":"Susanne"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak"},{"full_name":"Jackson, Colin","last_name":"Jackson","first_name":"Colin"},{"last_name":"Henneberger","full_name":"Henneberger, Christian","first_name":"Christian"}],"publist_id":"7786","title":"Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","year":"2018","isi":1,"publication":"Nature Chemical Biology","day":"30","page":"861 - 869","date_created":"2018-12-11T11:44:49Z","doi":"10.1038/s41589-018-0108-2","date_published":"2018-07-30T00:00:00Z","_id":"137","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-09-13T08:58:05Z","department":[{"_id":"HaJa"}],"abstract":[{"text":"Fluorescent sensors are an essential part of the experimental toolbox of the life sciences, where they are used ubiquitously to visualize intra- and extracellular signaling. In the brain, optical neurotransmitter sensors can shed light on temporal and spatial aspects of signal transmission by directly observing, for instance, neurotransmitter release and spread. Here we report the development and application of the first optical sensor for the amino acid glycine, which is both an inhibitory neurotransmitter and a co-agonist of the N-methyl-d-aspartate receptors (NMDARs) involved in synaptic plasticity. Computational design of a glycine-specific binding protein allowed us to produce the optical glycine FRET sensor (GlyFS), which can be used with single and two-photon excitation fluorescence microscopy. We took advantage of this newly developed sensor to test predictions about the uneven spatial distribution of glycine in extracellular space and to demonstrate that extracellular glycine levels are controlled by plasticity-inducing stimuli.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30061718","open_access":"1"}],"scopus_import":"1","intvolume":" 14","month":"07","publication_status":"published","language":[{"iso":"eng"}],"volume":14,"issue":"9"},{"oa_version":"None","pmid":1,"abstract":[{"lang":"eng","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."}],"month":"07","intvolume":" 147","scopus_import":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0091679X"]},"publication_status":"published","volume":147,"_id":"153","status":"public","type":"book_chapter","date_updated":"2023-09-13T08:56:35Z","department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"quality_controlled":"1","publisher":"Academic Press","day":"27","publication":"Methods in Cell Biology","isi":1,"year":"2018","doi":"10.1016/bs.mcb.2018.07.004","date_published":"2018-07-27T00:00:00Z","date_created":"2018-12-11T11:44:54Z","page":"79 - 91","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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 Methods in Cell Biology, 147:79–91. Academic Press, 2018. https://doi.org/10.1016/bs.mcb.2018.07.004.","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: Methods in Cell Biology. Vol 147. Academic Press; 2018:79-91. doi:10.1016/bs.mcb.2018.07.004","apa":"Renkawitz, J., Reversat, A., Leithner, A. F., Merrin, J., & Sixt, M. K. (2018). Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In Methods in Cell Biology (Vol. 147, pp. 79–91). Academic Press. https://doi.org/10.1016/bs.mcb.2018.07.004","short":"J. Renkawitz, A. Reversat, A.F. Leithner, J. Merrin, M.K. Sixt, in:, Methods in Cell Biology, Academic Press, 2018, pp. 79–91.","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 Methods in Cell Biology, vol. 147, Academic Press, 2018, pp. 79–91.","mla":"Renkawitz, Jörg, et al. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” Methods in Cell Biology, vol. 147, Academic Press, 2018, pp. 79–91, doi:10.1016/bs.mcb.2018.07.004."},"title":"Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments","author":[{"orcid":"0000-0003-2856-3369","full_name":"Renkawitz, Jörg","last_name":"Renkawitz","first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87"},{"id":"35B76592-F248-11E8-B48F-1D18A9856A87","first_name":"Anne","orcid":"0000-0003-0666-8928","full_name":"Reversat, Anne","last_name":"Reversat"},{"first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7768","external_id":{"pmid":["30165964"],"isi":["000452412300006"]},"article_processing_charge":"No"},{"quality_controlled":"1","publisher":"Cell Press","acknowledgement":"Research in the Bellaïche laboratory is supported by the European Research Council (ERC Advanced, TiMoprh, 340784), the Fondation ARC pour la Recherche sur le Cancer (SL220130607097), the Agence Nationale de la Recherche (ANR lLabex DEEP; 11-LBX-0044, ANR-10-IDEX-0001-02), the Centre National de la Recherche Scientifique, the Institut National de la Santé et de la Recherche Médicale, and Institut Curie and PSL Research University funding or grants.","date_created":"2018-12-11T11:44:23Z","date_published":"2018-10-08T00:00:00Z","doi":"10.1016/j.devcel.2018.09.014","page":"3 - 19","publication":"Developmental Cell","day":"08","year":"2018","isi":1,"title":"Mechanical force-driven adherents junction remodeling and epithelial dynamics","article_processing_charge":"No","external_id":{"isi":["000446579900002"]},"author":[{"id":"2E839F16-F248-11E8-B48F-1D18A9856A87","first_name":"Diana C","full_name":"Nunes Pinheiro, Diana C","orcid":"0000-0003-4333-7503","last_name":"Nunes Pinheiro"},{"full_name":"Bellaïche, Yohanns","last_name":"Bellaïche","first_name":"Yohanns"}],"publist_id":"8000","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Nunes Pinheiro, Diana C, and Yohanns Bellaïche. “Mechanical Force-Driven Adherents Junction Remodeling and Epithelial Dynamics.” Developmental Cell. Cell Press, 2018. https://doi.org/10.1016/j.devcel.2018.09.014.","ista":"Nunes Pinheiro DC, Bellaïche Y. 2018. Mechanical force-driven adherents junction remodeling and epithelial dynamics. Developmental Cell. 47(1), 3–19.","mla":"Nunes Pinheiro, Diana C., and Yohanns Bellaïche. “Mechanical Force-Driven Adherents Junction Remodeling and Epithelial Dynamics.” Developmental Cell, vol. 47, no. 1, Cell Press, 2018, pp. 3–19, doi:10.1016/j.devcel.2018.09.014.","ama":"Nunes Pinheiro DC, Bellaïche Y. Mechanical force-driven adherents junction remodeling and epithelial dynamics. Developmental Cell. 2018;47(1):3-19. doi:10.1016/j.devcel.2018.09.014","apa":"Nunes Pinheiro, D. C., & Bellaïche, Y. (2018). Mechanical force-driven adherents junction remodeling and epithelial dynamics. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2018.09.014","short":"D.C. Nunes Pinheiro, Y. Bellaïche, Developmental Cell 47 (2018) 3–19.","ieee":"D. C. Nunes Pinheiro and Y. Bellaïche, “Mechanical force-driven adherents junction remodeling and epithelial dynamics,” Developmental Cell, vol. 47, no. 1. Cell Press, pp. 3–19, 2018."},"intvolume":" 47","month":"10","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2018.09.014"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"During epithelial tissue development, repair, and homeostasis, adherens junctions (AJs) ensure intercellular adhesion and tissue integrity while allowing for cell and tissue dynamics. Mechanical forces play critical roles in AJs’ composition and dynamics. Recent findings highlight that beyond a well-established role in reinforcing cell-cell adhesion, AJ mechanosensitivity promotes junctional remodeling and polarization, thereby regulating critical processes such as cell intercalation, division, and collective migration. Here, we provide an integrated view of mechanosensing mechanisms that regulate cell-cell contact composition, geometry, and integrity under tension and highlight pivotal roles for mechanosensitive AJ remodeling in preserving epithelial integrity and sustaining tissue dynamics."}],"issue":"1","volume":47,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","article_type":"review","_id":"54","department":[{"_id":"CaHe"}],"date_updated":"2023-09-13T08:54:38Z"},{"title":"Nano-scale microfluidics to study 3D chemotaxis at the single cell level","external_id":{"isi":["000434384900031"]},"article_processing_charge":"No","publist_id":"7626","author":[{"last_name":"Frick","full_name":"Frick, Corina","first_name":"Corina"},{"last_name":"Dettinger","full_name":"Dettinger, Philip","first_name":"Philip"},{"first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","full_name":"Renkawitz, Jörg","orcid":"0000-0003-2856-3369","last_name":"Renkawitz"},{"full_name":"Jauch, Annaïse","last_name":"Jauch","first_name":"Annaïse"},{"full_name":"Berger, Christoph","last_name":"Berger","first_name":"Christoph"},{"last_name":"Recher","full_name":"Recher, Mike","first_name":"Mike"},{"full_name":"Schroeder, Timm","last_name":"Schroeder","first_name":"Timm"},{"first_name":"Matthias","full_name":"Mehling, Matthias","last_name":"Mehling"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Frick, Corina, et al. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the Single Cell Level.” PLoS One, vol. 13, no. 6, e0198330, Public Library of Science, 2018, doi:10.1371/journal.pone.0198330.","short":"C. Frick, P. Dettinger, J. Renkawitz, A. Jauch, C. Berger, M. Recher, T. Schroeder, M. Mehling, PLoS One 13 (2018).","ieee":"C. Frick et al., “Nano-scale microfluidics to study 3D chemotaxis at the single cell level,” PLoS One, vol. 13, no. 6. Public Library of Science, 2018.","ama":"Frick C, Dettinger P, Renkawitz J, et al. Nano-scale microfluidics to study 3D chemotaxis at the single cell level. PLoS One. 2018;13(6). doi:10.1371/journal.pone.0198330","apa":"Frick, C., Dettinger, P., Renkawitz, J., Jauch, A., Berger, C., Recher, M., … Mehling, M. (2018). Nano-scale microfluidics to study 3D chemotaxis at the single cell level. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0198330","chicago":"Frick, Corina, Philip Dettinger, Jörg Renkawitz, Annaïse Jauch, Christoph Berger, Mike Recher, Timm Schroeder, and Matthias Mehling. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the Single Cell Level.” PLoS One. Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0198330.","ista":"Frick C, Dettinger P, Renkawitz J, Jauch A, Berger C, Recher M, Schroeder T, Mehling M. 2018. Nano-scale microfluidics to study 3D chemotaxis at the single cell level. PLoS One. 13(6), e0198330."},"article_number":"e0198330","date_created":"2018-12-11T11:45:34Z","doi":"10.1371/journal.pone.0198330","date_published":"2018-06-07T00:00:00Z","publication":"PLoS One","day":"07","year":"2018","has_accepted_license":"1","isi":1,"oa":1,"publisher":"Public Library of Science","quality_controlled":"1","acknowledgement":"This work was supported by the Swiss National Science Foundation (MD-PhD fellowships, 323530_164221 to C.F.; and 323630_151483 to A.J.; grant PZ00P3_144863 to M.R, grant 31003A_156431 to T.S.; PZ00P3_148000 to C.T.B.; PZ00P3_154733 to M.M.), a Novartis “FreeNovation” grant to M.M. and T.S. and an EMBO long-term fellowship (ALTF 1396-2014) co-funded by the European Commission (LTFCOFUND2013, GA-2013-609409) to J.R.. M.R. was supported by the Gebert Rüf Foundation (GRS 058/14). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","department":[{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:45:45Z","ddc":["570"],"date_updated":"2023-09-13T09:00:15Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"276","issue":"6","volume":13,"language":[{"iso":"eng"}],"file":[{"file_name":"2018_Plos_Frick.pdf","date_created":"2018-12-17T14:10:32Z","creator":"dernst","file_size":7682167,"date_updated":"2020-07-14T12:45:45Z","checksum":"95fc5dc3938b3ad3b7697d10c83cc143","file_id":"5709","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","intvolume":" 13","month":"06","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Directed migration of cells relies on their ability to sense directional guidance cues and to interact with pericellular structures in order to transduce contractile cytoskeletal- into mechanical forces. These biomechanical processes depend highly on microenvironmental factors such as exposure to 2D surfaces or 3D matrices. In vivo, the majority of cells are exposed to 3D environments. Data on 3D cell migration are mostly derived from intravital microscopy or collagen-based in vitro assays. Both approaches offer only limited controlla-bility of experimental conditions. Here, we developed an automated microfluidic system that allows positioning of cells in 3D microenvironments containing highly controlled diffusion-based chemokine gradients. Tracking migration in such gradients was feasible in real time at the single cell level. Moreover, the setup allowed on-chip immunocytochemistry and thus linking of functional with phenotypical properties in individual cells. Spatially defined retrieval of cells from the device allows down-stream off-chip analysis. Using dendritic cells as a model, our setup specifically allowed us for the first time to quantitate key migration characteristics of cells exposed to identical gradients of the chemokine CCL19 yet placed on 2D vs in 3D environments. Migration properties between 2D and 3D migration were distinct. Morphological features of cells migrating in an in vitro 3D environment were similar to those of cells migrating in animal tissues, but different from cells migrating on a surface. Our system thus offers a highly controllable in vitro-mimic of a 3D environment that cells traffic in vivo."}]},{"department":[{"_id":"EvBe"}],"file_date_updated":"2020-07-14T12:45:49Z","date_updated":"2023-09-13T08:59:27Z","ddc":["570"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"283","issue":"1","volume":8,"publication_status":"published","file":[{"file_id":"5707","checksum":"9c3942d772f84f3df032ffde0ed9a8ea","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_ScientificReports_Ceinos.pdf","date_created":"2018-12-17T13:04:46Z","creator":"dernst","file_size":1855324,"date_updated":"2020-07-14T12:45:49Z"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"06","intvolume":" 8","abstract":[{"text":"Light represents the principal signal driving circadian clock entrainment. However, how light influences the evolution of the clock remains poorly understood. The cavefish Phreatichthys andruzzii represents a fascinating model to explore how evolution under extreme aphotic conditions shapes the circadian clock, since in this species the clock is unresponsive to light. We have previously demonstrated that loss-of-function mutations targeting non-visual opsins contribute in part to this blind clock phenotype. Here, we have compared orthologs of two core clock genes that play a key role in photic entrainment, cry1a and per2, in both zebrafish and P. andruzzii. We encountered aberrantly spliced variants for the P. andruzzii per2 transcript. The most abundant transcript encodes a truncated protein lacking the C-terminal Cry binding domain and incorporating an intronic, transposon-derived coding sequence. We demonstrate that the transposon insertion leads to a predominantly cytoplasmic localization of the cavefish Per2 protein in contrast to the zebrafish ortholog which is distributed in both the nucleus and cytoplasm. Thus, it seems that during evolution in complete darkness, the photic entrainment pathway of the circadian clock has been subject to mutation at multiple levels, extending from opsin photoreceptors to nuclear effectors.","lang":"eng"}],"oa_version":"Published Version","publist_id":"7616","author":[{"first_name":"Rosa Maria","last_name":"Ceinos","full_name":"Ceinos, Rosa Maria"},{"first_name":"Elena","last_name":"Frigato","full_name":"Frigato, Elena"},{"first_name":"Cristina","last_name":"Pagano","full_name":"Pagano, Cristina"},{"last_name":"Frohlich","full_name":"Frohlich, Nadine","first_name":"Nadine"},{"full_name":"Negrini, Pietro","last_name":"Negrini","first_name":"Pietro"},{"id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola","full_name":"Cavallari, Nicola","last_name":"Cavallari"},{"first_name":"Daniela","last_name":"Vallone","full_name":"Vallone, Daniela"},{"full_name":"Fuselli, Silvia","last_name":"Fuselli","first_name":"Silvia"},{"last_name":"Bertolucci","full_name":"Bertolucci, Cristiano","first_name":"Cristiano"},{"first_name":"Nicholas S","last_name":"Foulkes","full_name":"Foulkes, Nicholas S"}],"article_processing_charge":"No","external_id":{"isi":["000434640800008"]},"title":"Mutations in blind cavefish target the light regulated circadian clock gene period 2","citation":{"chicago":"Ceinos, Rosa Maria, Elena Frigato, Cristina Pagano, Nadine Frohlich, Pietro Negrini, Nicola Cavallari, Daniela Vallone, Silvia Fuselli, Cristiano Bertolucci, and Nicholas S Foulkes. “Mutations in Blind Cavefish Target the Light Regulated Circadian Clock Gene Period 2.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-27080-2.","ista":"Ceinos RM, Frigato E, Pagano C, Frohlich N, Negrini P, Cavallari N, Vallone D, Fuselli S, Bertolucci C, Foulkes NS. 2018. Mutations in blind cavefish target the light regulated circadian clock gene period 2. Scientific Reports. 8(1), 8754.","mla":"Ceinos, Rosa Maria, et al. “Mutations in Blind Cavefish Target the Light Regulated Circadian Clock Gene Period 2.” Scientific Reports, vol. 8, no. 1, 8754, Nature Publishing Group, 2018, doi:10.1038/s41598-018-27080-2.","apa":"Ceinos, R. M., Frigato, E., Pagano, C., Frohlich, N., Negrini, P., Cavallari, N., … Foulkes, N. S. (2018). Mutations in blind cavefish target the light regulated circadian clock gene period 2. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-27080-2","ama":"Ceinos RM, Frigato E, Pagano C, et al. Mutations in blind cavefish target the light regulated circadian clock gene period 2. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-27080-2","ieee":"R. M. Ceinos et al., “Mutations in blind cavefish target the light regulated circadian clock gene period 2,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018.","short":"R.M. Ceinos, E. Frigato, C. Pagano, N. Frohlich, P. Negrini, N. Cavallari, D. Vallone, S. Fuselli, C. Bertolucci, N.S. Foulkes, Scientific Reports 8 (2018)."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"8754","doi":"10.1038/s41598-018-27080-2","date_published":"2018-06-08T00:00:00Z","date_created":"2018-12-11T11:45:36Z","has_accepted_license":"1","isi":1,"year":"2018","day":"08","publication":"Scientific Reports","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1},{"volume":11022,"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"e5d81c9b50a6bd9d8a2c16953aad7e23","file_id":"8638","success":1,"date_updated":"2020-10-09T06:24:21Z","file_size":537219,"creator":"dernst","date_created":"2020-10-09T06:24:21Z","file_name":"2018_LNCS_Elgyuett.pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","alternative_title":["LNCS"],"month":"08","intvolume":" 11022","abstract":[{"lang":"eng","text":"We solve the offline monitoring problem for timed propositional temporal logic (TPTL), interpreted over dense-time Boolean signals. The variant of TPTL we consider extends linear temporal logic (LTL) with clock variables and reset quantifiers, providing a mechanism to specify real-time constraints. We first describe a general monitoring algorithm based on an exhaustive computation of the set of satisfying clock assignments as a finite union of zones. We then propose a specialized monitoring algorithm for the one-variable case using a partition of the time domain based on the notion of region equivalence, whose complexity is linear in the length of the signal, thereby generalizing a known result regarding the monitoring of metric temporal logic (MTL). The region and zone representations of time constraints are known from timed automata verification and can also be used in the discrete-time case. Our prototype implementation appears to outperform previous discrete-time implementations of TPTL monitoring,"}],"oa_version":"Submitted Version","file_date_updated":"2020-10-09T06:24:21Z","department":[{"_id":"ToHe"}],"date_updated":"2023-09-13T08:58:34Z","ddc":["000"],"type":"conference","conference":{"name":"FORMATS: Formal Modeling and Analysis of Timed Systems","start_date":"2018-09-04","location":"Beijing, China","end_date":"2018-09-06"},"status":"public","_id":"81","page":"53 - 70","doi":"10.1007/978-3-030-00151-3_4","date_published":"2018-08-26T00:00:00Z","date_created":"2018-12-11T11:44:31Z","has_accepted_license":"1","isi":1,"year":"2018","day":"26","quality_controlled":"1","publisher":"Springer","oa":1,"author":[{"full_name":"Elgyütt, Adrian","last_name":"Elgyütt","first_name":"Adrian","id":"4A2E9DBA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere","full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"}],"publist_id":"7973","article_processing_charge":"No","external_id":{"isi":["000884993200004"]},"title":"Monitoring temporal logic with clock variables","citation":{"mla":"Elgyütt, Adrian, et al. Monitoring Temporal Logic with Clock Variables. Vol. 11022, Springer, 2018, pp. 53–70, doi:10.1007/978-3-030-00151-3_4.","ieee":"A. Elgyütt, T. Ferrere, and T. A. Henzinger, “Monitoring temporal logic with clock variables,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Beijing, China, 2018, vol. 11022, pp. 53–70.","short":"A. Elgyütt, T. Ferrere, T.A. Henzinger, in:, Springer, 2018, pp. 53–70.","apa":"Elgyütt, A., Ferrere, T., & Henzinger, T. A. (2018). Monitoring temporal logic with clock variables (Vol. 11022, pp. 53–70). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Beijing, China: Springer. https://doi.org/10.1007/978-3-030-00151-3_4","ama":"Elgyütt A, Ferrere T, Henzinger TA. Monitoring temporal logic with clock variables. In: Vol 11022. Springer; 2018:53-70. doi:10.1007/978-3-030-00151-3_4","chicago":"Elgyütt, Adrian, Thomas Ferrere, and Thomas A Henzinger. “Monitoring Temporal Logic with Clock Variables,” 11022:53–70. Springer, 2018. https://doi.org/10.1007/978-3-030-00151-3_4.","ista":"Elgyütt A, Ferrere T, Henzinger TA. 2018. Monitoring temporal logic with clock variables. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11022, 53–70."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}]},{"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"citation":{"ista":"Lenzen C, Rybicki J. 2018. Near-optimal self-stabilising counting and firing squads. Distributed Computing.","chicago":"Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting and Firing Squads.” Distributed Computing. Springer, 2018. https://doi.org/10.1007/s00446-018-0342-6.","ama":"Lenzen C, Rybicki J. Near-optimal self-stabilising counting and firing squads. Distributed Computing. 2018. doi:10.1007/s00446-018-0342-6","apa":"Lenzen, C., & Rybicki, J. (2018). Near-optimal self-stabilising counting and firing squads. Distributed Computing. Springer. https://doi.org/10.1007/s00446-018-0342-6","ieee":"C. Lenzen and J. Rybicki, “Near-optimal self-stabilising counting and firing squads,” Distributed Computing. Springer, 2018.","short":"C. Lenzen, J. Rybicki, Distributed Computing (2018).","mla":"Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting and Firing Squads.” Distributed Computing, Springer, 2018, doi:10.1007/s00446-018-0342-6."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000475627800005"]},"publist_id":"7978","author":[{"full_name":"Lenzen, Christoph","last_name":"Lenzen","first_name":"Christoph"},{"id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","first_name":"Joel","last_name":"Rybicki","full_name":"Rybicki, Joel","orcid":"0000-0002-6432-6646"}],"title":"Near-optimal self-stabilising counting and firing squads","oa":1,"quality_controlled":"1","publisher":"Springer","year":"2018","isi":1,"has_accepted_license":"1","publication":"Distributed Computing","day":"12","date_created":"2018-12-11T11:44:30Z","doi":"10.1007/s00446-018-0342-6","date_published":"2018-09-12T00:00:00Z","_id":"76","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","date_updated":"2023-09-13T09:01:06Z","ddc":["000"],"department":[{"_id":"DaAl"}],"file_date_updated":"2020-07-14T12:48:01Z","abstract":[{"text":"Consider a fully-connected synchronous distributed system consisting of n nodes, where up to f nodes may be faulty and every node starts in an arbitrary initial state. In the synchronous C-counting problem, all nodes need to eventually agree on a counter that is increased by one modulo C in each round for given C>1. In the self-stabilising firing squad problem, the task is to eventually guarantee that all non-faulty nodes have simultaneous responses to external inputs: if a subset of the correct nodes receive an external “go” signal as input, then all correct nodes should agree on a round (in the not-too-distant future) in which to jointly output a “fire” signal. Moreover, no node should generate a “fire” signal without some correct node having previously received a “go” signal as input. We present a framework reducing both tasks to binary consensus at very small cost. For example, we obtain a deterministic algorithm for self-stabilising Byzantine firing squads with optimal resilience f<n/3, asymptotically optimal stabilisation and response time O(f), and message size O(log f). As our framework does not restrict the type of consensus routines used, we also obtain efficient randomised solutions.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"09","publication_status":"published","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5711","checksum":"872db70bba9b401500abe3c6ae2f1a61","file_size":799337,"date_updated":"2020-07-14T12:48:01Z","creator":"dernst","file_name":"2018_DistributedComputing_Lenzen.pdf","date_created":"2018-12-17T14:21:22Z"}]},{"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Inclusion–exclusion is an effective method for computing the volume of a union of measurable sets. We extend it to multiple coverings, proving short inclusion–exclusion formulas for the subset of Rn covered by at least k balls in a finite set. We implement two of the formulas in dimension n=3 and report on results obtained with our software."}],"intvolume":" 68","month":"03","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2019-02-12T06:47:52Z","file_name":"2018_Edelsbrunner.pdf","creator":"dernst","date_updated":"2020-07-14T12:46:38Z","file_size":708357,"checksum":"1c8d58cd489a66cd3e2064c1141c8c5e","file_id":"5953","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","ec_funded":1,"volume":68,"_id":"530","status":"public","type":"journal_article","ddc":["000"],"date_updated":"2023-09-13T08:59:00Z","department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:46:38Z","oa":1,"publisher":"Elsevier","quality_controlled":"1","publication":"Computational Geometry: Theory and Applications","day":"01","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:46:59Z","doi":"10.1016/j.comgeo.2017.06.014","date_published":"2018-03-01T00:00:00Z","page":"119 - 133","project":[{"grant_number":"318493","name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” Computational Geometry: Theory and Applications, vol. 68, Elsevier, 2018, pp. 119–33, doi:10.1016/j.comgeo.2017.06.014.","short":"H. Edelsbrunner, M. Iglesias Ham, Computational Geometry: Theory and Applications 68 (2018) 119–133.","ieee":"H. Edelsbrunner and M. Iglesias Ham, “Multiple covers with balls I: Inclusion–exclusion,” Computational Geometry: Theory and Applications, vol. 68. Elsevier, pp. 119–133, 2018.","ama":"Edelsbrunner H, Iglesias Ham M. Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. 2018;68:119-133. doi:10.1016/j.comgeo.2017.06.014","apa":"Edelsbrunner, H., & Iglesias Ham, M. (2018). Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2017.06.014","chicago":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” Computational Geometry: Theory and Applications. Elsevier, 2018. https://doi.org/10.1016/j.comgeo.2017.06.014.","ista":"Edelsbrunner H, Iglesias Ham M. 2018. Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. 68, 119–133."},"title":"Multiple covers with balls I: Inclusion–exclusion","external_id":{"isi":["000415778300010"]},"article_processing_charge":"No","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"first_name":"Mabel","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","full_name":"Iglesias Ham, Mabel","last_name":"Iglesias Ham"}],"publist_id":"7289"},{"main_file_link":[{"url":"https://arxiv.org/abs/1712.10127","open_access":"1"}],"scopus_import":"1","intvolume":" 97","month":"04","abstract":[{"text":"Spontaneous emission spectra of two initially excited closely spaced identical atoms are very sensitive to the strength and the direction of the applied magnetic field. We consider the relevant schemes that ensure the determination of the mutual spatial orientation of the atoms and the distance between them by entirely optical means. A corresponding theoretical description is given accounting for the dipole-dipole interaction between the two atoms in the presence of a magnetic field and for polarizations of the quantum field interacting with magnetic sublevels of the two-atom system. ","lang":"eng"}],"oa_version":"Submitted Version","issue":"4","volume":97,"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"307","department":[{"_id":"JoFi"}],"date_updated":"2023-09-13T09:00:41Z","oa":1,"quality_controlled":"1","publisher":"American Physical Society","acknowledgement":"The work was partially supported by Russian Foundation for Basic Research (Grant No. 15-02-05657a) and by the Basic research program of Higher School of Economics (HSE).","date_created":"2018-12-11T11:45:44Z","date_published":"2018-04-09T00:00:00Z","doi":"10.1103/PhysRevA.97.043812","year":"2018","isi":1,"publication":" Physical Review A - Atomic, Molecular, and Optical Physics","day":"09","article_number":" 043812 ","external_id":{"isi":["000429454000015"],"arxiv":["1712.10127"]},"article_processing_charge":"No","author":[{"first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","full_name":"Redchenko, Elena","last_name":"Redchenko"},{"last_name":"Makarov","full_name":"Makarov, Alexander","first_name":"Alexander"},{"first_name":"Vladimir","last_name":"Yudson","full_name":"Yudson, Vladimir"}],"publist_id":"7572","title":"Nanoscopy of pairs of atoms by fluorescence in a magnetic field","citation":{"ista":"Redchenko E, Makarov A, Yudson V. 2018. Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. 97(4), 043812.","chicago":"Redchenko, Elena, Alexander Makarov, and Vladimir Yudson. “Nanoscopy of Pairs of Atoms by Fluorescence in a Magnetic Field.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.043812.","apa":"Redchenko, E., Makarov, A., & Yudson, V. (2018). Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.043812","ama":"Redchenko E, Makarov A, Yudson V. Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. 2018;97(4). doi:10.1103/PhysRevA.97.043812","ieee":"E. Redchenko, A. Makarov, and V. Yudson, “Nanoscopy of pairs of atoms by fluorescence in a magnetic field,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4. American Physical Society, 2018.","short":"E. Redchenko, A. Makarov, V. Yudson, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018).","mla":"Redchenko, Elena, et al. “Nanoscopy of Pairs of Atoms by Fluorescence in a Magnetic Field.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4, 043812, American Physical Society, 2018, doi:10.1103/PhysRevA.97.043812."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"abstract":[{"lang":"eng","text":"Background: Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic mutations that affect essential tumor functions or specific domains remains a controversial topic. Results: Here, we analyze 7546 individual exomes from 26 tumor types from TCGA data to explore the portion of the cancer exome under negative selection. Although we find most of the genes neutrally evolving in a pan-cancer framework, we identify essential cancer genes and immune-exposed protein regions under significant negative selection. Moreover, our simulations suggest that the amount of negative selection is underestimated. We therefore choose an empirical approach to identify genes, functions, and protein regions under negative selection. We find that expression and mutation status of negatively selected genes is indicative of patient survival. Processes that are most strongly conserved are those that play fundamental cellular roles such as protein synthesis, glucose metabolism, and molecular transport. Intriguingly, we observe strong signals of selection in the immunopeptidome and proteins controlling peptide exposition, highlighting the importance of immune surveillance evasion. Additionally, tumor type-specific immune activity correlates with the strength of negative selection on human epitopes. Conclusions: In summary, our results show that negative selection is a hallmark of cell essentiality and immune response in cancer. The functional domains identified could be exploited therapeutically, ultimately allowing for the development of novel cancer treatments."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 19","month":"05","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_name":"2018_GenomeBiology_Zapata.pdf","date_created":"2018-12-17T14:05:01Z","creator":"dernst","file_size":1414722,"date_updated":"2020-07-14T12:45:47Z","checksum":"f3e4922486bd9bf1483271bdbed394a7","file_id":"5708","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"ec_funded":1,"volume":19,"related_material":{"record":[{"id":"9811","status":"public","relation":"research_data"},{"status":"public","id":"9812","relation":"research_data"}]},"_id":"279","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","date_updated":"2023-09-13T09:01:32Z","ddc":["570"],"department":[{"_id":"FyKo"}],"file_date_updated":"2020-07-14T12:45:47Z","oa":1,"publisher":"BioMed Central","quality_controlled":"1","year":"2018","has_accepted_license":"1","isi":1,"publication":"Genome Biology","day":"31","date_created":"2018-12-11T11:45:35Z","doi":"10.1186/s13059-018-1434-0","date_published":"2018-05-31T00:00:00Z","article_number":"67","project":[{"call_identifier":"FP7","_id":"26120F5C-B435-11E9-9278-68D0E5697425","name":"Systematic investigation of epistasis in molecular evolution","grant_number":"335980"}],"citation":{"mla":"Zapata, Luis, et al. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Genome Biology, vol. 19, 67, BioMed Central, 2018, doi:10.1186/s13059-018-1434-0.","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. BioMed Central. https://doi.org/10.1186/s13059-018-1434-0","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 2018;19. doi:10.1186/s13059-018-1434-0","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome,” Genome Biology, vol. 19. BioMed Central, 2018.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, Genome Biology 19 (2018).","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Genome Biology. BioMed Central, 2018. https://doi.org/10.1186/s13059-018-1434-0.","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 19, 67."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000433986200001"]},"author":[{"first_name":"Luis","full_name":"Zapata, Luis","last_name":"Zapata"},{"full_name":"Pich, Oriol","last_name":"Pich","first_name":"Oriol"},{"last_name":"Serrano","full_name":"Serrano, Luis","first_name":"Luis"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov"},{"last_name":"Ossowski","full_name":"Ossowski, Stephan","first_name":"Stephan"},{"full_name":"Schaefer, Martin","last_name":"Schaefer","first_name":"Martin"}],"publist_id":"7620","title":"Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome"},{"department":[{"_id":"JoDa"}],"file_date_updated":"2020-07-14T12:44:56Z","ddc":["570"],"date_updated":"2023-09-13T09:02:48Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"145","volume":37,"issue":"15","language":[{"iso":"eng"}],"file":[{"file_id":"5710","checksum":"a540feb6c9af6aefc78de531461a8835","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_EMBO_Truckenbrodt.pdf","date_created":"2018-12-17T14:17:29Z","file_size":2846470,"date_updated":"2020-07-14T12:44:56Z","creator":"dernst"}],"publication_status":"published","publication_identifier":{"issn":["0261-4189"]},"intvolume":" 37","month":"08","scopus_import":"1","oa_version":"Published Version","pmid":1,"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"}],"title":"Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission","article_processing_charge":"No","external_id":{"pmid":["29950309"],"isi":["000440416900005"]},"author":[{"full_name":"Truckenbrodt, Sven M","last_name":"Truckenbrodt","first_name":"Sven M","id":"45812BD4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Abhiyan","last_name":"Viplav","full_name":"Viplav, Abhiyan"},{"full_name":"Jähne, Sebsatian","last_name":"Jähne","first_name":"Sebsatian"},{"first_name":"Angela","last_name":"Vogts","full_name":"Vogts, Angela"},{"full_name":"Denker, Annette","last_name":"Denker","first_name":"Annette"},{"full_name":"Wildhagen, Hanna","last_name":"Wildhagen","first_name":"Hanna"},{"full_name":"Fornasiero, Eugenio","last_name":"Fornasiero","first_name":"Eugenio"},{"last_name":"Rizzoli","full_name":"Rizzoli, Silvio","first_name":"Silvio"}],"publist_id":"7778","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"S. M. Truckenbrodt et al., “Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission,” The EMBO Journal, vol. 37, no. 15. Wiley, 2018.","short":"S.M. Truckenbrodt, A. Viplav, S. Jähne, A. Vogts, A. Denker, H. Wildhagen, E. Fornasiero, S. Rizzoli, The EMBO Journal 37 (2018).","ama":"Truckenbrodt SM, Viplav A, Jähne S, et al. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. 2018;37(15). doi:10.15252/embj.201798044","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. The EMBO Journal. Wiley. https://doi.org/10.15252/embj.201798044","mla":"Truckenbrodt, Sven M., et al. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” The EMBO Journal, vol. 37, no. 15, e98044, Wiley, 2018, doi:10.15252/embj.201798044.","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.” The EMBO Journal. Wiley, 2018. https://doi.org/10.15252/embj.201798044."},"article_number":"e98044","date_created":"2018-12-11T11:44:52Z","doi":"10.15252/embj.201798044","date_published":"2018-08-01T00:00:00Z","publication":"The EMBO Journal","day":"01","year":"2018","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Wiley","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)."},{"_id":"462","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"article_type":"original","type":"journal_article","ddc":["580"],"date_updated":"2023-09-13T09:03:18Z","file_date_updated":"2020-07-14T12:46:32Z","department":[{"_id":"JiFr"}],"pmid":1,"oa_version":"Submitted Version","abstract":[{"text":"AtNHX5 and AtNHX6 are endosomal Na+,K+/H+ antiporters that are critical for growth and development in Arabidopsis, but the mechanism behind their action remains unknown. Here, we report that AtNHX5 and AtNHX6, functioning as H+ leak, control auxin homeostasis and auxin-mediated development. We found that nhx5 nhx6 exhibited growth variations of auxin-related defects. We further showed that nhx5 nhx6 was affected in auxin homeostasis. Genetic analysis showed that AtNHX5 and AtNHX6 were required for the function of the ER-localized auxin transporter PIN5. Although AtNHX5 and AtNHX6 were co-localized with PIN5 at ER, they did not interact directly. Instead, the conserved acidic residues in AtNHX5 and AtNHX6, which are essential for exchange activity, were required for PIN5 function. AtNHX5 and AtNHX6 regulated the pH in ER. Overall, AtNHX5 and AtNHX6 may regulate auxin transport across the ER via the pH gradient created by their transport activity. H+-leak pathway provides a fine-tuning mechanism that controls cellular auxin fluxes. ","lang":"eng"}],"intvolume":" 41","month":"05","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2019-11-18T16:22:22Z","file_name":"2018_PlantCellEnv_Fan.pdf","date_updated":"2020-07-14T12:46:32Z","file_size":1937976,"creator":"dernst","checksum":"6a20f843565f962cb20281cdf5e40914","file_id":"7042","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","license":"https://creativecommons.org/licenses/by-nc/4.0/","volume":41,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Fan, Ligang, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” Plant, Cell and Environment, vol. 41, Wiley-Blackwell, 2018, pp. 850–64, doi:10.1111/pce.13153.","apa":"Fan, L., Zhao, L., Hu, W., Li, W., Novák, O., Strnad, M., … Qiu, Q. (2018). NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. Wiley-Blackwell. https://doi.org/10.1111/pce.13153","ama":"Fan L, Zhao L, Hu W, et al. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. 2018;41:850-864. doi:10.1111/pce.13153","short":"L. Fan, L. Zhao, W. Hu, W. Li, O. Novák, M. Strnad, S. Simon, J. Friml, J. Shen, L. Jiang, Q. Qiu, Plant, Cell and Environment 41 (2018) 850–864.","ieee":"L. Fan et al., “NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development,” Plant, Cell and Environment, vol. 41. Wiley-Blackwell, pp. 850–864, 2018.","chicago":"Fan, Ligang, Lei Zhao, Wei Hu, Weina Li, Ondřej Novák, Miroslav Strnad, Sibu Simon, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” Plant, Cell and Environment. Wiley-Blackwell, 2018. https://doi.org/10.1111/pce.13153.","ista":"Fan L, Zhao L, Hu W, Li W, Novák O, Strnad M, Simon S, Friml J, Shen J, Jiang L, Qiu Q. 2018. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. 41, 850–864."},"title":"NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development","article_processing_charge":"No","external_id":{"pmid":["29360148"],"isi":["000426870500012"]},"publist_id":"7359","author":[{"last_name":"Fan","full_name":"Fan, Ligang","first_name":"Ligang"},{"first_name":"Lei","full_name":"Zhao, Lei","last_name":"Zhao"},{"first_name":"Wei","full_name":"Hu, Wei","last_name":"Hu"},{"first_name":"Weina","last_name":"Li","full_name":"Li, Weina"},{"last_name":"Novák","full_name":"Novák, Ondřej","first_name":"Ondřej"},{"full_name":"Strnad, Miroslav","last_name":"Strnad","first_name":"Miroslav"},{"id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","first_name":"Sibu","full_name":"Simon, Sibu","orcid":"0000-0002-1998-6741","last_name":"Simon"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"first_name":"Jinbo","last_name":"Shen","full_name":"Shen, Jinbo"},{"last_name":"Jiang","full_name":"Jiang, Liwen","first_name":"Liwen"},{"full_name":"Qiu, Quan","last_name":"Qiu","first_name":"Quan"}],"acknowledgement":"This work was supported by the National Natural Science Foundation of China (31571464, 31371438 and 31070222 to Q.S.Q.), the National Basic Research Program of China (973 project, 2013CB429904 to Q.S.Q.), the Research Fund for the Doctoral Program of Higher Education of China (20130211110001 to Q.S.Q.), the Ministry of Education, Youth and Sports of the Czech Republic (the National Program for Sustainability I, LO1204), and The Czech Science Foundation GAČR (GA13–40637S) to JF. We thank Dr. Tom J. Guilfoyle for DR5::GUS line and Dr. Jia Li for pBIB‐RFP vector and DR5::GFP line. We thank Liping Guan and Yang Zhao for their help with the confocal microscope assay. ","oa":1,"quality_controlled":"1","publisher":"Wiley-Blackwell","publication":"Plant, Cell and Environment","day":"01","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:46:36Z","date_published":"2018-05-01T00:00:00Z","doi":"10.1111/pce.13153","page":"850 - 864"},{"publication":"Journal of Magnetism and Magnetic Materials","day":"15","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:46:56Z","doi":"10.1016/j.jmmm.2017.12.073","date_published":"2018-04-15T00:00:00Z","page":"427 - 441","acknowledgement":"S.Altmeyer is a Serra Húnter Fellow","oa":1,"publisher":"Elsevier","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Altmeyer S. 2018. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. 452, 427–441.","chicago":"Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions in Ferrofluidic Taylor-Couette Flow.” Journal of Magnetism and Magnetic Materials. Elsevier, 2018. https://doi.org/10.1016/j.jmmm.2017.12.073.","short":"S. Altmeyer, Journal of Magnetism and Magnetic Materials 452 (2018) 427–441.","ieee":"S. Altmeyer, “Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow,” Journal of Magnetism and Magnetic Materials, vol. 452. Elsevier, pp. 427–441, 2018.","ama":"Altmeyer S. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. 2018;452:427-441. doi:10.1016/j.jmmm.2017.12.073","apa":"Altmeyer, S. (2018). Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. Elsevier. https://doi.org/10.1016/j.jmmm.2017.12.073","mla":"Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions in Ferrofluidic Taylor-Couette Flow.” Journal of Magnetism and Magnetic Materials, vol. 452, Elsevier, 2018, pp. 427–41, doi:10.1016/j.jmmm.2017.12.073."},"title":"Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow","external_id":{"isi":["000425547700061"]},"article_processing_charge":"No","author":[{"last_name":"Altmeyer","orcid":"0000-0001-5964-0203","full_name":"Altmeyer, Sebastian","first_name":"Sebastian","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7297","language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:46:37Z","file_size":17309535,"date_created":"2020-05-14T14:41:17Z","file_name":"2018_Magnetism_Altmeyer.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"431f5cd4a628d7ca21161f82b14ccb4f","file_id":"7838"}],"publication_status":"published","volume":452,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"This study treats with the influence of a symmetry-breaking transversal magnetic field on the nonlinear dynamics of ferrofluidic Taylor-Couette flow – flow confined between two concentric independently rotating cylinders. We detected alternating ‘flip’ solutions which are flow states featuring typical characteristics of slow-fast-dynamics in dynamical systems. The flip corresponds to a temporal change in the axial wavenumber and we find them to appear either as pure 2-fold axisymmetric (due to the symmetry-breaking nature of the applied transversal magnetic field) or involving non-axisymmetric, helical modes in its interim solution. The latter ones show features of typical ribbon solutions. In any case the flip solutions have a preferential first axial wavenumber which corresponds to the more stable state (slow dynamics) and second axial wavenumber, corresponding to the short appearing more unstable state (fast dynamics). However, in both cases the flip time grows exponential with increasing the magnetic field strength before the flip solutions, living on 2-tori invariant manifolds, cease to exist, with lifetime going to infinity. Further we show that ferrofluidic flow turbulence differ from the classical, ordinary (usually at high Reynolds number) turbulence. The applied magnetic field hinders the free motion of ferrofluid partials and therefore smoothen typical turbulent quantities and features so that speaking of mildly chaotic dynamics seems to be a more appropriate expression for the observed motion. "}],"intvolume":" 452","month":"04","scopus_import":"1","ddc":["530"],"date_updated":"2023-09-13T09:03:44Z","department":[{"_id":"BjHo"}],"file_date_updated":"2020-07-14T12:46:37Z","_id":"519","status":"public","type":"journal_article","article_type":"original"},{"editor":[{"last_name":"Ryu","full_name":"Ryu, Sukyoung","first_name":"Sukyoung"}],"title":"New approaches for almost-sure termination of probabilistic programs","author":[{"full_name":"Huang, Mingzhang","last_name":"Huang","first_name":"Mingzhang"},{"full_name":"Fu, Hongfei","last_name":"Fu","first_name":"Hongfei"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"arxiv":["1806.06683"],"isi":["000916310900011"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Huang, Mingzhang, et al. New Approaches for Almost-Sure Termination of Probabilistic Programs. Edited by Sukyoung Ryu, vol. 11275, Springer, 2018, pp. 181–201, doi:10.1007/978-3-030-02768-1_11.","ama":"Huang M, Fu H, Chatterjee K. New approaches for almost-sure termination of probabilistic programs. In: Ryu S, ed. Vol 11275. Springer; 2018:181-201. doi:10.1007/978-3-030-02768-1_11","apa":"Huang, M., Fu, H., & Chatterjee, K. (2018). New approaches for almost-sure termination of probabilistic programs. In S. Ryu (Ed.) (Vol. 11275, pp. 181–201). Presented at the 16th Asian Symposium on Programming Languages and Systems, APLAS, Wellington, New Zealand: Springer. https://doi.org/10.1007/978-3-030-02768-1_11","ieee":"M. Huang, H. Fu, and K. Chatterjee, “New approaches for almost-sure termination of probabilistic programs,” presented at the 16th Asian Symposium on Programming Languages and Systems, APLAS, Wellington, New Zealand, 2018, vol. 11275, pp. 181–201.","short":"M. Huang, H. Fu, K. Chatterjee, in:, S. Ryu (Ed.), Springer, 2018, pp. 181–201.","chicago":"Huang, Mingzhang, Hongfei Fu, and Krishnendu Chatterjee. “New Approaches for Almost-Sure Termination of Probabilistic Programs.” edited by Sukyoung Ryu, 11275:181–201. Springer, 2018. https://doi.org/10.1007/978-3-030-02768-1_11.","ista":"Huang M, Fu H, Chatterjee K. 2018. New approaches for almost-sure termination of probabilistic programs. 16th Asian Symposium on Programming Languages and Systems, APLAS, LNCS, vol. 11275, 181–201."},"project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"date_published":"2018-12-01T00:00:00Z","doi":"10.1007/978-3-030-02768-1_11","date_created":"2018-12-16T22:59:20Z","page":"181-201","day":"01","isi":1,"year":"2018","publisher":"Springer","quality_controlled":"1","oa":1,"department":[{"_id":"KrCh"}],"date_updated":"2023-09-13T09:02:22Z","status":"public","type":"conference","conference":{"location":"Wellington, New Zealand","end_date":"2018-12-06","start_date":"2018-12-02","name":"16th Asian Symposium on Programming Languages and Systems, APLAS"},"_id":"5679","volume":11275,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["03029743"],"isbn":["9783030027674"]},"month":"12","intvolume":" 11275","scopus_import":"1","alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1806.06683"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We study the almost-sure termination problem for probabilistic programs. First, we show that supermartingales with lower bounds on conditional absolute difference provide a sound approach for the almost-sure termination problem. Moreover, using this approach we can obtain explicit optimal bounds on tail probabilities of non-termination within a given number of steps. Second, we present a new approach based on Central Limit Theorem for the almost-sure termination problem, and show that this approach can establish almost-sure termination of programs which none of the existing approaches can handle. Finally, we discuss algorithmic approaches for the two above methods that lead to automated analysis techniques for almost-sure termination of probabilistic programs."}]},{"quality_controlled":"1","publisher":"Elsevier","date_created":"2018-12-11T11:47:06Z","doi":"10.1016/j.conb.2017.12.005","date_published":"2018-02-01T00:00:00Z","page":"131 - 138","publication":"Current Opinion in Neurobiology","day":"01","year":"2018","isi":1,"title":"Neural stem cells in neuropsychiatric disorders","article_processing_charge":"No","external_id":{"isi":["000427101600018"]},"author":[{"id":"42C9F57E-F248-11E8-B48F-1D18A9856A87","first_name":"Roberto","last_name":"Sacco","full_name":"Sacco, Roberto"},{"full_name":"Cacci, Emanuele","last_name":"Cacci","first_name":"Emanuele"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7268","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Sacco R, Cacci E, Novarino G. 2018. Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. 48(2), 131–138.","chicago":"Sacco, Roberto, Emanuele Cacci, and Gaia Novarino. “Neural Stem Cells in Neuropsychiatric Disorders.” Current Opinion in Neurobiology. Elsevier, 2018. https://doi.org/10.1016/j.conb.2017.12.005.","apa":"Sacco, R., Cacci, E., & Novarino, G. (2018). Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2017.12.005","ama":"Sacco R, Cacci E, Novarino G. Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. 2018;48(2):131-138. doi:10.1016/j.conb.2017.12.005","short":"R. Sacco, E. Cacci, G. Novarino, Current Opinion in Neurobiology 48 (2018) 131–138.","ieee":"R. Sacco, E. Cacci, and G. Novarino, “Neural stem cells in neuropsychiatric disorders,” Current Opinion in Neurobiology, vol. 48, no. 2. Elsevier, pp. 131–138, 2018.","mla":"Sacco, Roberto, et al. “Neural Stem Cells in Neuropsychiatric Disorders.” Current Opinion in Neurobiology, vol. 48, no. 2, Elsevier, 2018, pp. 131–38, doi:10.1016/j.conb.2017.12.005."},"intvolume":" 48","month":"02","scopus_import":"1","oa_version":"None","abstract":[{"lang":"eng","text":"The precise control of neural stem cell (NSC) proliferation and differentiation is crucial for the development and function of the human brain. Here, we review the emerging links between the alteration of embryonic and adult neurogenesis and the etiology of neuropsychiatric disorders (NPDs) such as autism spectrum disorders (ASDs) and schizophrenia (SCZ), as well as the advances in stem cell-based modeling and the novel therapeutic targets derived from these studies."}],"issue":"2","volume":48,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","_id":"546","department":[{"_id":"GaNo"}],"date_updated":"2023-09-13T09:01:56Z"},{"abstract":[{"text":"This document contains the full list of genes with their respective significance and dN/dS values. (TXT 4499Â kb)","lang":"eng"}],"oa_version":"Published Version","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.6401414.v1"}],"publisher":"Springer Nature","month":"05","year":"2018","day":"31","date_created":"2021-08-06T12:58:25Z","doi":"10.6084/m9.figshare.6401414.v1","related_material":{"record":[{"relation":"used_in_publication","id":"279","status":"public"}]},"date_published":"2018-05-31T00:00:00Z","_id":"9812","type":"research_data_reference","status":"public","date_updated":"2023-09-13T09:01:31Z","citation":{"ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018).","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401414.v1","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. https://doi.org/10.6084/m9.figshare.6401414.v1","mla":"Zapata, Luis, et al. Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401414.v1.","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401414.v1.","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.6401414.v1."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"first_name":"Luis","full_name":"Zapata, Luis","last_name":"Zapata"},{"first_name":"Oriol","full_name":"Pich, Oriol","last_name":"Pich"},{"first_name":"Luis","last_name":"Serrano","full_name":"Serrano, Luis"},{"last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"full_name":"Ossowski, Stephan","last_name":"Ossowski","first_name":"Stephan"},{"full_name":"Schaefer, Martin","last_name":"Schaefer","first_name":"Martin"}],"title":"Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","department":[{"_id":"FyKo"}]},{"date_updated":"2023-09-13T09:01:31Z","citation":{"chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.6401390.v1.","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401390.v1.","mla":"Zapata, Luis, et al. Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401390.v1.","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018).","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401390.v1","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. https://doi.org/10.6084/m9.figshare.6401390.v1"},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"last_name":"Zapata","full_name":"Zapata, Luis","first_name":"Luis"},{"full_name":"Pich, Oriol","last_name":"Pich","first_name":"Oriol"},{"last_name":"Serrano","full_name":"Serrano, Luis","first_name":"Luis"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"last_name":"Ossowski","full_name":"Ossowski, Stephan","first_name":"Stephan"},{"first_name":"Martin","last_name":"Schaefer","full_name":"Schaefer, Martin"}],"article_processing_charge":"No","title":"Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","department":[{"_id":"FyKo"}],"_id":"9811","type":"research_data_reference","status":"public","year":"2018","day":"31","date_published":"2018-05-31T00:00:00Z","related_material":{"record":[{"status":"public","id":"279","relation":"used_in_publication"}]},"doi":"10.6084/m9.figshare.6401390.v1","date_created":"2021-08-06T12:53:49Z","abstract":[{"lang":"eng","text":"This document contains additional supporting evidence presented as supplemental tables. (XLSX 50Â kb)"}],"oa_version":"Preprint","publisher":"Springer Nature","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.6401390.v1"}],"oa":1,"month":"05"},{"_id":"20","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-09-13T09:10:47Z","ddc":["570"],"department":[{"_id":"SiHi"}],"file_date_updated":"2020-07-14T12:45:23Z","abstract":[{"text":"Background: Norepinephrine (NE) signaling has a key role in white adipose tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under certain conditions, conversion of white into brite (brown-in-white) adipocytes. However, acute effects of NE stimulation have not been described at the transcriptional network level. Results: We used RNA-seq to uncover a broad transcriptional response. The inference of protein-protein and protein-DNA interaction networks allowed us to identify a set of immediate-early genes (IEGs) with high betweenness, validating our approach and suggesting a hierarchical control of transcriptional regulation. In addition, we identified a transcriptional regulatory network with IEGs as master regulators, including HSF1 and NFIL3 as novel NE-induced IEG candidates. Moreover, a functional enrichment analysis and gene clustering into functional modules suggest a crosstalk between metabolic, signaling, and immune responses. Conclusions: Altogether, our network biology approach explores for the first time the immediate-early systems level response of human adipocytes to acute sympathetic activation, thereby providing a first network basis of early cell fate programs and crosstalks between metabolic and transcriptional networks required for proper WAT function.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"11","intvolume":" 19","publication_identifier":{"issn":["1471-2164"]},"publication_status":"published","file":[{"date_created":"2018-12-17T14:52:57Z","file_name":"2018_BMCGenomics_Higareda.pdf","date_updated":"2020-07-14T12:45:23Z","file_size":4629784,"creator":"dernst","checksum":"a56516e734dab589dc7f3e1915973b4d","file_id":"5712","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"9807","status":"public","relation":"research_data"},{"relation":"research_data","status":"public","id":"9808"}]},"volume":19,"issue":"1","citation":{"ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 2018;19(1). doi:10.1186/s12864-018-5173-0","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. BioMed Central. https://doi.org/10.1186/s12864-018-5173-0","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, BMC Genomics 19 (2018).","ieee":"J. Higareda Almaraz et al., “Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes,” BMC Genomics, vol. 19, no. 1. BioMed Central, 2018.","mla":"Higareda Almaraz, Juan, et al. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics, vol. 19, no. 1, BioMed Central, 2018, doi:10.1186/s12864-018-5173-0.","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 19(1).","chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics. BioMed Central, 2018. https://doi.org/10.1186/s12864-018-5173-0."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Higareda Almaraz, Juan","last_name":"Higareda Almaraz","first_name":"Juan"},{"last_name":"Karbiener","full_name":"Karbiener, Michael","first_name":"Michael"},{"first_name":"Maude","last_name":"Giroud","full_name":"Giroud, Maude"},{"first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","last_name":"Pauler"},{"first_name":"Teresa","last_name":"Gerhalter","full_name":"Gerhalter, Teresa"},{"first_name":"Stephan","full_name":"Herzig, Stephan","last_name":"Herzig"},{"first_name":"Marcel","last_name":"Scheideler","full_name":"Scheideler, Marcel"}],"publist_id":"8035","article_processing_charge":"No","external_id":{"isi":["000450976700002"]},"title":"Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","acknowledgement":"This work was funded by the German Centre for Diabetes Research (DZD) and the Austrian Science Fund (FWF, P25729-B19).","publisher":"BioMed Central","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2018","day":"03","publication":"BMC Genomics","doi":"10.1186/s12864-018-5173-0","date_published":"2018-11-03T00:00:00Z","date_created":"2018-12-11T11:44:12Z"},{"citation":{"chicago":"Dziembowski, Stefan, Krzysztof Z Pietrzak, and Daniel Wichs. “Non-Malleable Codes.” Journal of the ACM. ACM, 2018. https://doi.org/10.1145/3178432.","ista":"Dziembowski S, Pietrzak KZ, Wichs D. 2018. Non-malleable codes. Journal of the ACM. 65(4), 20.","mla":"Dziembowski, Stefan, et al. “Non-Malleable Codes.” Journal of the ACM, vol. 65, no. 4, 20, ACM, 2018, doi:10.1145/3178432.","ama":"Dziembowski S, Pietrzak KZ, Wichs D. Non-malleable codes. Journal of the ACM. 2018;65(4). doi:10.1145/3178432","apa":"Dziembowski, S., Pietrzak, K. Z., & Wichs, D. (2018). Non-malleable codes. Journal of the ACM. ACM. https://doi.org/10.1145/3178432","short":"S. Dziembowski, K.Z. Pietrzak, D. Wichs, Journal of the ACM 65 (2018).","ieee":"S. Dziembowski, K. Z. Pietrzak, and D. Wichs, “Non-malleable codes,” Journal of the ACM, vol. 65, no. 4. ACM, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000442938200004"]},"publist_id":"7947","author":[{"first_name":"Stefan","full_name":"Dziembowski, Stefan","last_name":"Dziembowski"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak"},{"first_name":"Daniel","last_name":"Wichs","full_name":"Wichs, Daniel"}],"title":"Non-malleable codes","article_number":"20","project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks"},{"name":"Provable Security for Physical Cryptography","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"year":"2018","isi":1,"publication":"Journal of the ACM","day":"01","date_created":"2018-12-11T11:44:40Z","date_published":"2018-08-01T00:00:00Z","doi":"10.1145/3178432","oa":1,"publisher":"ACM","quality_controlled":"1","date_updated":"2023-09-13T09:05:17Z","department":[{"_id":"KrPi"}],"_id":"107","type":"journal_article","article_type":"original","status":"public","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":65,"issue":"4","abstract":[{"text":"We introduce the notion of “non-malleable codes” which relaxes the notion of error correction and error detection. Informally, a code is non-malleable if the message contained in a modified codeword is either the original message, or a completely unrelated value. In contrast to error correction and error detection, non-malleability can be achieved for very rich classes of modifications. We construct an efficient code that is non-malleable with respect to modifications that affect each bit of the codeword arbitrarily (i.e., leave it untouched, flip it, or set it to either 0 or 1), but independently of the value of the other bits of the codeword. Using the probabilistic method, we also show a very strong and general statement: there exists a non-malleable code for every “small enough” family F of functions via which codewords can be modified. Although this probabilistic method argument does not directly yield efficient constructions, it gives us efficient non-malleable codes in the random-oracle model for very general classes of tampering functions—e.g., functions where every bit in the tampered codeword can depend arbitrarily on any 99% of the bits in the original codeword. As an application of non-malleable codes, we show that they provide an elegant algorithmic solution to the task of protecting functionalities implemented in hardware (e.g., signature cards) against “tampering attacks.” In such attacks, the secret state of a physical system is tampered, in the hopes that future interaction with the modified system will reveal some secret information. This problem was previously studied in the work of Gennaro et al. in 2004 under the name “algorithmic tamper proof security” (ATP). We show that non-malleable codes can be used to achieve important improvements over the prior work. In particular, we show that any functionality can be made secure against a large class of tampering attacks, simply by encoding the secret state with a non-malleable code while it is stored in memory.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://eprint.iacr.org/2009/608","open_access":"1"}],"scopus_import":"1","intvolume":" 65","month":"08"},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00219525"]},"ec_funded":1,"volume":217,"issue":"12","pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"In epithelial tissues, cells tightly connect to each other through cell–cell junctions, but they also present the remarkable capacity of reorganizing themselves without compromising tissue integrity. Upon injury, simple epithelia efficiently resolve small lesions through the action of actin cytoskeleton contractile structures at the wound edge and cellular rearrangements. However, the underlying mechanisms and how they cooperate are still poorly understood. In this study, we combine live imaging and theoretical modeling to reveal a novel and indispensable role for occluding junctions (OJs) in this process. We demonstrate that OJ loss of function leads to defects in wound-closure dynamics: instead of contracting, wounds dramatically increase their area. OJ mutants exhibit phenotypes in cell shape, cellular rearrangements, and mechanical properties as well as in actin cytoskeleton dynamics at the wound edge. We propose that OJs are essential for wound closure by impacting on epithelial mechanics at the tissue level, which in turn is crucial for correct regulation of the cellular events occurring at the wound edge."}],"intvolume":" 217","month":"12","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30228162","open_access":"1"}],"scopus_import":"1","date_updated":"2023-09-13T09:11:17Z","department":[{"_id":"CaHe"}],"_id":"5676","status":"public","type":"journal_article","publication":"Journal of Cell Biology","day":"01","year":"2018","isi":1,"date_created":"2018-12-16T22:59:19Z","doi":"10.1083/jcb.201804048","date_published":"2018-12-01T00:00:00Z","page":"4267-4283","oa":1,"quality_controlled":"1","publisher":"Rockefeller University Press","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Carvalho, Lara, et al. “Occluding Junctions as Novel Regulators of Tissue Mechanics during Wound Repair.” Journal of Cell Biology, vol. 217, no. 12, Rockefeller University Press, 2018, pp. 4267–83, doi:10.1083/jcb.201804048.","apa":"Carvalho, L., Patricio, P., Ponte, S., Heisenberg, C.-P. J., Almeida, L., Nunes, A. S., … Jacinto, A. (2018). Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201804048","ama":"Carvalho L, Patricio P, Ponte S, et al. Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. 2018;217(12):4267-4283. doi:10.1083/jcb.201804048","ieee":"L. Carvalho et al., “Occluding junctions as novel regulators of tissue mechanics during wound repair,” Journal of Cell Biology, vol. 217, no. 12. Rockefeller University Press, pp. 4267–4283, 2018.","short":"L. Carvalho, P. Patricio, S. Ponte, C.-P.J. Heisenberg, L. Almeida, A.S. Nunes, N.A.M. Araújo, A. Jacinto, Journal of Cell Biology 217 (2018) 4267–4283.","chicago":"Carvalho, Lara, Pedro Patricio, Susana Ponte, Carl-Philipp J Heisenberg, Luis Almeida, André S. Nunes, Nuno A.M. Araújo, and Antonio Jacinto. “Occluding Junctions as Novel Regulators of Tissue Mechanics during Wound Repair.” Journal of Cell Biology. Rockefeller University Press, 2018. https://doi.org/10.1083/jcb.201804048.","ista":"Carvalho L, Patricio P, Ponte S, Heisenberg C-PJ, Almeida L, Nunes AS, Araújo NAM, Jacinto A. 2018. Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. 217(12), 4267–4283."},"title":"Occluding junctions as novel regulators of tissue mechanics during wound repair","article_processing_charge":"No","external_id":{"isi":["000451960800018"],"pmid":["30228162 "]},"author":[{"first_name":"Lara","last_name":"Carvalho","full_name":"Carvalho, Lara"},{"full_name":"Patricio, Pedro","last_name":"Patricio","first_name":"Pedro"},{"full_name":"Ponte, Susana","last_name":"Ponte","first_name":"Susana"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"last_name":"Almeida","full_name":"Almeida, Luis","first_name":"Luis"},{"first_name":"André S.","full_name":"Nunes, André S.","last_name":"Nunes"},{"full_name":"Araújo, Nuno A.M.","last_name":"Araújo","first_name":"Nuno A.M."},{"last_name":"Jacinto","full_name":"Jacinto, Antonio","first_name":"Antonio"}],"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}]},{"date_created":"2023-08-22T14:25:34Z","date_published":"2018-05-01T00:00:00Z","publication":"6th International Conference on Learning Representations","language":[{"iso":"eng"}],"day":"01","year":"2018","publication_status":"published","month":"05","main_file_link":[{"url":"https://arxiv.org/abs/1804.11130","open_access":"1"}],"oa":1,"quality_controlled":"1","scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","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."}],"title":"Clustering meets implicit generative models","department":[{"_id":"FrLo"}],"article_processing_charge":"No","external_id":{"arxiv":["1804.11130"]},"author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello"},{"full_name":"Vincent, Damien","last_name":"Vincent","first_name":"Damien"},{"full_name":"Tolstikhin, Ilya","last_name":"Tolstikhin","first_name":"Ilya"},{"full_name":"Ratsch, Gunnar","last_name":"Ratsch","first_name":"Gunnar"},{"first_name":"Sylvain","full_name":"Gelly, Sylvain","last_name":"Gelly"},{"last_name":"Scholkopf","full_name":"Scholkopf, Bernhard","first_name":"Bernhard"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"chicago":"Locatello, Francesco, Damien Vincent, Ilya Tolstikhin, Gunnar Ratsch, Sylvain Gelly, and Bernhard Scholkopf. “Clustering Meets Implicit Generative Models.” In 6th International Conference on Learning Representations, 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.","mla":"Locatello, Francesco, et al. “Clustering Meets Implicit Generative Models.” 6th International Conference on Learning Representations, 2018.","ieee":"F. Locatello, D. Vincent, I. Tolstikhin, G. Ratsch, S. Gelly, and B. Scholkopf, “Clustering meets implicit generative models,” in 6th International Conference on Learning Representations, Vancouver, Canada, 2018.","short":"F. Locatello, D. Vincent, I. Tolstikhin, G. Ratsch, S. Gelly, B. Scholkopf, in:, 6th International Conference on Learning Representations, 2018.","apa":"Locatello, F., Vincent, D., Tolstikhin, I., Ratsch, G., Gelly, S., & Scholkopf, B. (2018). Clustering meets implicit generative models. In 6th International Conference on Learning Representations. Vancouver, Canada.","ama":"Locatello F, Vincent D, Tolstikhin I, Ratsch G, Gelly S, Scholkopf B. Clustering meets implicit generative models. In: 6th International Conference on Learning Representations. ; 2018."},"date_updated":"2023-09-13T09:08:24Z","status":"public","conference":{"name":"International Conference on Machine Learning","start_date":"2018-04-30","location":"Vancouver, Canada","end_date":"2018-05-03"},"type":"conference","_id":"14224"},{"status":"public","type":"research_data_reference","_id":"9807","department":[{"_id":"SiHi"}],"title":"Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","article_processing_charge":"No","author":[{"last_name":"Higareda Almaraz","full_name":"Higareda Almaraz, Juan","first_name":"Juan"},{"full_name":"Karbiener, Michael","last_name":"Karbiener","first_name":"Michael"},{"last_name":"Giroud","full_name":"Giroud, Maude","first_name":"Maude"},{"last_name":"Pauler","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"full_name":"Gerhalter, Teresa","last_name":"Gerhalter","first_name":"Teresa"},{"first_name":"Stephan","last_name":"Herzig","full_name":"Herzig, Stephan"},{"first_name":"Marcel","last_name":"Scheideler","full_name":"Scheideler, Marcel"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-13T09:10:47Z","citation":{"chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 1: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295339.v1.","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes, Springer Nature, 10.6084/m9.figshare.7295339.v1.","mla":"Higareda Almaraz, Juan, et al. Additional File 1: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes. Springer Nature, 2018, doi:10.6084/m9.figshare.7295339.v1.","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295339.v1","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. 2018. doi:10.6084/m9.figshare.7295339.v1","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, (2018).","ieee":"J. Higareda Almaraz et al., “Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes.” Springer Nature, 2018."},"month":"11","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.7295339.v1","open_access":"1"}],"oa":1,"publisher":"Springer Nature","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Table S1. Genes with highest betweenness. Table S2. Local and Master regulators up-regulated. Table S3. Local and Master regulators down-regulated (XLSX 23 kb)."}],"date_created":"2021-08-06T12:26:53Z","date_published":"2018-11-03T00:00:00Z","doi":"10.6084/m9.figshare.7295339.v1","related_material":{"record":[{"status":"public","id":"20","relation":"used_in_publication"}]},"day":"03","year":"2018"},{"title":"Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","department":[{"_id":"SiHi"}],"article_processing_charge":"No","author":[{"first_name":"Juan","full_name":"Higareda Almaraz, Juan","last_name":"Higareda Almaraz"},{"last_name":"Karbiener","full_name":"Karbiener, Michael","first_name":"Michael"},{"first_name":"Maude","last_name":"Giroud","full_name":"Giroud, Maude"},{"last_name":"Pauler","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"full_name":"Gerhalter, Teresa","last_name":"Gerhalter","first_name":"Teresa"},{"first_name":"Stephan","full_name":"Herzig, Stephan","last_name":"Herzig"},{"last_name":"Scheideler","full_name":"Scheideler, Marcel","first_name":"Marcel"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 3: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295369.v1.","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes, Springer Nature, 10.6084/m9.figshare.7295369.v1.","mla":"Higareda Almaraz, Juan, et al. Additional File 3: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes. Springer Nature, 2018, doi:10.6084/m9.figshare.7295369.v1.","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, (2018).","ieee":"J. Higareda Almaraz et al., “Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes.” Springer Nature, 2018.","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295369.v1","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. 2018. doi:10.6084/m9.figshare.7295369.v1"},"date_updated":"2023-09-13T09:10:47Z","status":"public","type":"research_data_reference","_id":"9808","date_created":"2021-08-06T12:31:57Z","date_published":"2018-11-03T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"20","status":"public"}]},"doi":"10.6084/m9.figshare.7295369.v1","day":"03","year":"2018","month":"11","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.7295369.v1","open_access":"1"}],"oa":1,"publisher":"Springer Nature","oa_version":"Published Version","abstract":[{"text":"Table S4. Counts per Gene per Million Reads Mapped. (XLSX 2751 kb).","lang":"eng"}]}]