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Swoboda, V. Kolmogorov, in:, Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, IEEE, 2019.","chicago":"Swoboda, Paul, and Vladimir Kolmogorov. “Map Inference via Block-Coordinate Frank-Wolfe Algorithm.” In Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, Vol. 2019–June. IEEE, 2019. https://doi.org/10.1109/CVPR.2019.01140.","ama":"Swoboda P, Kolmogorov V. Map inference via block-coordinate Frank-Wolfe algorithm. In: Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. Vol 2019-June. IEEE; 2019. doi:10.1109/CVPR.2019.01140","ista":"Swoboda P, Kolmogorov V. 2019. Map inference via block-coordinate Frank-Wolfe algorithm. Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition vol. 2019–June, 11138–11147.","apa":"Swoboda, P., & Kolmogorov, V. (2019). 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Kolmogorov, “Map inference via block-coordinate Frank-Wolfe algorithm,” in Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, Long Beach, CA, United States, 2019, vol. 2019–June."},"publication":"Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition","date_published":"2019-06-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7468","status":"public","title":"Map inference via block-coordinate Frank-Wolfe algorithm","oa_version":"Preprint","type":"conference","abstract":[{"text":"We present a new proximal bundle method for Maximum-A-Posteriori (MAP) inference in structured energy minimization problems. The method optimizes a Lagrangean relaxation of the original energy minimization problem using a multi plane block-coordinate Frank-Wolfe method that takes advantage of the specific structure of the Lagrangean decomposition. We show empirically that our method outperforms state-of-the-art Lagrangean decomposition based algorithms on some challenging Markov Random Field, multi-label discrete tomography and graph matching problems.","lang":"eng"}]},{"type":"journal_article","issue":"Supplement 6","department":[{"_id":"GaNo"},{"_id":"LifeSc"}],"intvolume":" 29","publisher":"Elsevier","title":"S.16.05 Illuminating the role of the e3 ubiquitin ligase cullin3 in brain development and autism","status":"public","publication_status":"published","_id":"7415","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2019","oa_version":"None","volume":29,"date_updated":"2023-09-07T14:56:17Z","date_created":"2020-01-30T10:07:41Z","author":[{"full_name":"Morandell, Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87","last_name":"Morandell","first_name":"Jasmin"},{"id":"2A103192-F248-11E8-B48F-1D18A9856A87","last_name":"Nicolas","first_name":"Armel","full_name":"Nicolas, Armel"},{"last_name":"Schwarz","first_name":"Lena A","id":"29A8453C-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Lena A"},{"full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"}],"publication_identifier":{"issn":["0924-977X"]},"article_processing_charge":"No","month":"12","day":"13","page":"S11-S12","article_type":"original","isi":1,"quality_controlled":"1","external_id":{"isi":["000502657500021"]},"citation":{"ista":"Morandell J, Nicolas A, Schwarz LA, Novarino G. 2019. 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Editorial overview: Cell biology in the era of omics? Current Opinion in Plant Biology. 52(12), A1–A2.","ieee":"E. Benková and Y. Dagdas, “Editorial overview: Cell biology in the era of omics?,” Current Opinion in Plant Biology, vol. 52, no. 12. Elsevier, pp. A1–A2, 2019.","apa":"Benková, E., & Dagdas, Y. (2019). Editorial overview: Cell biology in the era of omics? Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2019.11.002","ama":"Benková E, Dagdas Y. Editorial overview: Cell biology in the era of omics? Current Opinion in Plant Biology. 2019;52(12):A1-A2. doi:10.1016/j.pbi.2019.11.002","chicago":"Benková, Eva, and Yasin Dagdas. “Editorial Overview: Cell Biology in the Era of Omics?” Current Opinion in Plant Biology. Elsevier, 2019. https://doi.org/10.1016/j.pbi.2019.11.002.","mla":"Benková, Eva, and Yasin Dagdas. “Editorial Overview: Cell Biology in the Era of Omics?” Current Opinion in Plant Biology, vol. 52, no. 12, Elsevier, 2019, pp. A1–2, doi:10.1016/j.pbi.2019.11.002.","short":"E. Benková, Y. Dagdas, Current Opinion in Plant Biology 52 (2019) A1–A2."},"article_type":"letter_note","page":"A1-A2","issue":"12","type":"journal_article","oa_version":"None","_id":"7394","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Editorial overview: Cell biology in the era of omics?","status":"public","intvolume":" 52"},{"date_published":"2019-10-01T00:00:00Z","publication":"IEEE International Conference on Computer Vision","citation":{"ista":"Phuong M, Lampert C. 2019. Distillation-based training for multi-exit architectures. IEEE International Conference on Computer Vision. ICCV: International Conference on Computer Vision vol. 2019–October, 1355–1364.","ieee":"M. Phuong and C. Lampert, “Distillation-based training for multi-exit architectures,” in IEEE International Conference on Computer Vision, Seoul, Korea, 2019, vol. 2019–October, pp. 1355–1364.","apa":"Phuong, M., & Lampert, C. (2019). Distillation-based training for multi-exit architectures. In IEEE International Conference on Computer Vision (Vol. 2019–October, pp. 1355–1364). Seoul, Korea: IEEE. https://doi.org/10.1109/ICCV.2019.00144","ama":"Phuong M, Lampert C. Distillation-based training for multi-exit architectures. In: IEEE International Conference on Computer Vision. Vol 2019-October. IEEE; 2019:1355-1364. doi:10.1109/ICCV.2019.00144","chicago":"Phuong, Mary, and Christoph Lampert. “Distillation-Based Training for Multi-Exit Architectures.” In IEEE International Conference on Computer Vision, 2019–October:1355–64. IEEE, 2019. https://doi.org/10.1109/ICCV.2019.00144.","mla":"Phuong, Mary, and Christoph Lampert. “Distillation-Based Training for Multi-Exit Architectures.” IEEE International Conference on Computer Vision, vol. 2019–October, IEEE, 2019, pp. 1355–64, doi:10.1109/ICCV.2019.00144.","short":"M. Phuong, C. 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In this work, we propose a new training procedure for multi-exit architectures based on the principle of knowledge distillation. The method encourage searly exits to mimic later, more accurate exits, by matching their output probabilities.\r\nExperiments on CIFAR100 and ImageNet show that distillation-based training significantly improves the accuracy of early exits while maintaining state-of-the-art accuracy for late ones. The method is particularly beneficial when training data is limited and it allows a straightforward extension to semi-supervised learning,i.e. making use of unlabeled data at training time. Moreover, it takes only afew lines to implement and incurs almost no computational overhead at training time, and none at all at test time.","lang":"eng"}],"type":"conference","conference":{"location":"Seoul, Korea","start_date":"2019-10-27","end_date":"2019-11-02","name":"ICCV: International Conference on Computer Vision"},"doi":"10.1109/ICCV.2019.00144","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000531438101047"]},"quality_controlled":"1","isi":1,"project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7"}],"month":"10","publication_identifier":{"isbn":["9781728148038"],"issn":["15505499"]},"author":[{"full_name":"Bui Thi Mai, Phuong","last_name":"Bui Thi Mai","first_name":"Phuong","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9418"}]},"date_created":"2020-02-11T09:06:57Z","date_updated":"2023-09-08T11:11:12Z","volume":"2019-October","year":"2019","publication_status":"published","department":[{"_id":"ChLa"}],"publisher":"IEEE","file_date_updated":"2020-07-14T12:47:59Z","ec_funded":1},{"language":[{"iso":"eng"}],"conference":{"name":"NIPS: Conference on Neural Information Processing Systems","end_date":"2019-12-14","start_date":"2019-12-08","location":"Vancouver, Canada"},"isi":1,"quality_controlled":"1","project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning"}],"external_id":{"arxiv":["1909.02253"],"isi":["000534424300084"]},"oa":1,"main_file_link":[{"url":"http://papers.nips.cc/paper/8379-powerset-convolutional-neural-networks","open_access":"1"}],"month":"12","publication_identifier":{"issn":["1049-5258"]},"date_created":"2020-02-28T10:03:24Z","date_updated":"2023-09-08T11:13:52Z","volume":32,"author":[{"full_name":"Wendler, Chris","first_name":"Chris","last_name":"Wendler"},{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Püschel","first_name":"Markus","full_name":"Püschel, Markus"}],"publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"Neural Information Processing Systems Foundation","year":"2019","ec_funded":1,"date_published":"2019-12-01T00:00:00Z","page":"927-938","citation":{"short":"C. Wendler, D.-A. Alistarh, M. Püschel, in:, Neural Information Processing Systems Foundation, 2019, pp. 927–938.","mla":"Wendler, Chris, et al. Powerset Convolutional Neural Networks. Vol. 32, Neural Information Processing Systems Foundation, 2019, pp. 927–38.","chicago":"Wendler, Chris, Dan-Adrian Alistarh, and Markus Püschel. “Powerset Convolutional Neural Networks,” 32:927–38. Neural Information Processing Systems Foundation, 2019.","ama":"Wendler C, Alistarh D-A, Püschel M. Powerset convolutional neural networks. In: Vol 32. Neural Information Processing Systems Foundation; 2019:927-938.","apa":"Wendler, C., Alistarh, D.-A., & Püschel, M. (2019). Powerset convolutional neural networks (Vol. 32, pp. 927–938). Presented at the NIPS: Conference on Neural Information Processing Systems, Vancouver, Canada: Neural Information Processing Systems Foundation.","ieee":"C. Wendler, D.-A. Alistarh, and M. Püschel, “Powerset convolutional neural networks,” presented at the NIPS: Conference on Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32, pp. 927–938.","ista":"Wendler C, Alistarh D-A, Püschel M. 2019. Powerset convolutional neural networks. NIPS: Conference on Neural Information Processing Systems vol. 32, 927–938."},"day":"01","article_processing_charge":"No","oa_version":"Published Version","title":"Powerset convolutional neural networks","status":"public","intvolume":" 32","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7542","abstract":[{"lang":"eng","text":"We present a novel class of convolutional neural networks (CNNs) for set functions,i.e., data indexed with the powerset of a finite set. The convolutions are derivedas linear, shift-equivariant functions for various notions of shifts on set functions.The framework is fundamentally different from graph convolutions based on theLaplacian, as it provides not one but several basic shifts, one for each element inthe ground set. Prototypical experiments with several set function classificationtasks on synthetic datasets and on datasets derived from real-world hypergraphsdemonstrate the potential of our new powerset CNNs."}],"type":"conference"},{"oa_version":"None","date_updated":"2023-09-08T11:12:04Z","date_created":"2020-02-23T23:00:36Z","edition":"2","author":[{"orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia","full_name":"Cremer, Sylvia"},{"id":"29D0B332-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8696-6978","first_name":"Megan","last_name":"Kutzer","full_name":"Kutzer, Megan"}],"editor":[{"first_name":"Jae","last_name":"Choe","full_name":"Choe, Jae"}],"department":[{"_id":"SyCr"}],"publisher":"Elsevier","title":"Social immunity","publication_status":"published","status":"public","year":"2019","_id":"7513","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"Social insects (i.e., ants, termites and the social bees and wasps) protect their colonies from disease using a combination of individual immunity and collectively performed defenses, termed social immunity. The first line of social immune defense is sanitary care, which is performed by colony members to protect their pathogen-exposed nestmates from developing an infection. If sanitary care fails and an infection becomes established, a second line of social immune defense is deployed to stop disease transmission within the colony and to protect the valuable queens, which together with the males are the reproductive individuals of the colony. Insect colonies are separated into these reproductive individuals and the sterile worker force, forming a superorganismal reproductive unit reminiscent of the differentiated germline and soma in a multicellular organism. Ultimately, the social immune response preserves the germline of the superorganism insect colony and increases overall fitness of the colony in case of disease. ","lang":"eng"}],"type":"book_chapter","language":[{"iso":"eng"}],"doi":"10.1016/B978-0-12-809633-8.90721-0","date_published":"2019-02-06T00:00:00Z","page":"747-755","isi":1,"quality_controlled":"1","external_id":{"isi":["000248989500026"]},"citation":{"ista":"Cremer S, Kutzer M. 2019.Social immunity. In: Encyclopedia of Animal Behavior. , 747–755.","ieee":"S. Cremer and M. Kutzer, “Social immunity,” in Encyclopedia of Animal Behavior, 2nd ed., J. Choe, Ed. Elsevier, 2019, pp. 747–755.","apa":"Cremer, S., & Kutzer, M. (2019). Social immunity. In J. Choe (Ed.), Encyclopedia of Animal Behavior (2nd ed., pp. 747–755). Elsevier. https://doi.org/10.1016/B978-0-12-809633-8.90721-0","ama":"Cremer S, Kutzer M. Social immunity. In: Choe J, ed. Encyclopedia of Animal Behavior. 2nd ed. Elsevier; 2019:747-755. doi:10.1016/B978-0-12-809633-8.90721-0","chicago":"Cremer, Sylvia, and Megan Kutzer. “Social Immunity.” In Encyclopedia of Animal Behavior, edited by Jae Choe, 2nd ed., 747–55. Elsevier, 2019. https://doi.org/10.1016/B978-0-12-809633-8.90721-0.","mla":"Cremer, Sylvia, and Megan Kutzer. “Social Immunity.” Encyclopedia of Animal Behavior, edited by Jae Choe, 2nd ed., Elsevier, 2019, pp. 747–55, doi:10.1016/B978-0-12-809633-8.90721-0.","short":"S. Cremer, M. Kutzer, in:, J. Choe (Ed.), Encyclopedia of Animal Behavior, 2nd ed., Elsevier, 2019, pp. 747–755."},"publication":"Encyclopedia of Animal Behavior","article_processing_charge":"No","publication_identifier":{"isbn":["9780128132517"],"eisbn":["9780128132524"]},"day":"06","month":"02","scopus_import":"1"},{"page":"509-515","quality_controlled":"1","isi":1,"external_id":{"isi":["000563497600059"]},"citation":{"mla":"Laccone, Francesco, et al. “FlexMaps Pavilion: A Twisted Arc Made of Mesostructured Flat Flexible Panels.” IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE, International Center for Numerical Methods in Engineering, 2019, pp. 509–15.","short":"F. Laccone, L. Malomo, J. Perez Rodriguez, N. Pietroni, F. Ponchio, B. Bickel, P. Cignoni, in:, IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE, International Center for Numerical Methods in Engineering, 2019, pp. 509–515.","chicago":"Laccone, Francesco, Luigi Malomo, Jesus Perez Rodriguez, Nico Pietroni, Federico Ponchio, Bernd Bickel, and Paolo Cignoni. “FlexMaps Pavilion: A Twisted Arc Made of Mesostructured Flat Flexible Panels.” In IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE, 509–15. International Center for Numerical Methods in Engineering, 2019.","ama":"Laccone F, Malomo L, Perez Rodriguez J, et al. FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels. In: IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE. International Center for Numerical Methods in Engineering; 2019:509-515.","ista":"Laccone F, Malomo L, Perez Rodriguez J, Pietroni N, Ponchio F, Bickel B, Cignoni P. 2019. FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels. IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE. IASS: International Association for Shell and Spatial Structures, 509–515.","ieee":"F. Laccone et al., “FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels,” in IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE, Barcelona, Spain, 2019, pp. 509–515.","apa":"Laccone, F., Malomo, L., Perez Rodriguez, J., Pietroni, N., Ponchio, F., Bickel, B., & Cignoni, P. (2019). FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels. In IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE (pp. 509–515). Barcelona, Spain: International Center for Numerical Methods in Engineering."},"publication":"IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE","language":[{"iso":"eng"}],"date_published":"2019-10-10T00:00:00Z","conference":{"start_date":"2019-10-07","location":"Barcelona, Spain","end_date":"2019-10-10","name":"IASS: International Association for Shell and Spatial Structures"},"scopus_import":"1","article_processing_charge":"No","publication_identifier":{"issn":["2518-6582"],"isbn":["9788412110104"]},"day":"10","month":"10","publisher":"International Center for Numerical Methods in Engineering","department":[{"_id":"BeBi"}],"publication_status":"published","title":"FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels","status":"public","_id":"9261","year":"2019","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"None","date_updated":"2023-09-08T11:21:54Z","date_created":"2021-03-21T23:01:21Z","author":[{"full_name":"Laccone, Francesco","first_name":"Francesco","last_name":"Laccone"},{"last_name":"Malomo","first_name":"Luigi","full_name":"Malomo, Luigi"},{"first_name":"Jesus","last_name":"Perez Rodriguez","id":"2DC83906-F248-11E8-B48F-1D18A9856A87","full_name":"Perez Rodriguez, Jesus"},{"full_name":"Pietroni, Nico","first_name":"Nico","last_name":"Pietroni"},{"full_name":"Ponchio, Federico","last_name":"Ponchio","first_name":"Federico"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd"},{"first_name":"Paolo","last_name":"Cignoni","full_name":"Cignoni, Paolo"}],"type":"conference","abstract":[{"lang":"eng","text":"Bending-active structures are able to efficiently produce complex curved shapes starting from flat panels. The desired deformation of the panels derives from the proper selection of their elastic properties. Optimized panels, called FlexMaps, are designed such that, once they are bent and assembled, the resulting static equilibrium configuration matches a desired input 3D shape. The FlexMaps elastic properties are controlled by locally varying spiraling geometric mesostructures, which are optimized in size and shape to match the global curvature (i.e., bending requests) of the target shape. The design pipeline starts from a quad mesh representing the input 3D shape, which defines the edge size and the total amount of spirals: every quad will embed one spiral. Then, an optimization algorithm tunes the geometry of the spirals by using a simplified pre-computed rod model. This rod model is derived from a non-linear regression algorithm which approximates the non-linear behavior of solid FEM spiral models subject to hundreds of load combinations. This innovative pipeline has been applied to the project of a lightweight plywood pavilion named FlexMaps Pavilion, which is a single-layer piecewise twisted arc that fits a bounding box of 3.90x3.96x3.25 meters."}]},{"abstract":[{"text":"We propose a new model for detecting visual relationships, such as \"person riding motorcycle\" or \"bottle on table\". This task is an important step towards comprehensive structured mage understanding, going beyond detecting individual objects. Our main novelty is a Box Attention mechanism that allows to model pairwise interactions between objects using standard object detection pipelines. The resulting model is conceptually clean, expressive and relies on well-justified training and prediction procedures. Moreover, unlike previously proposed approaches, our model does not introduce any additional complex components or hyperparameters on top of those already required by the underlying detection model. We conduct an experimental evaluation on two datasets, V-COCO and Open Images, demonstrating strong quantitative and qualitative results.","lang":"eng"}],"type":"conference","oa_version":"Preprint","_id":"7640","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Detecting visual relationships using box attention","status":"public","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-10-01T00:00:00Z","citation":{"chicago":"Kolesnikov, Alexander, Alina Kuznetsova, Christoph Lampert, and Vittorio Ferrari. “Detecting Visual Relationships Using Box Attention.” In Proceedings of the 2019 International Conference on Computer Vision Workshop. IEEE, 2019. https://doi.org/10.1109/ICCVW.2019.00217.","short":"A. Kolesnikov, A. Kuznetsova, C. Lampert, V. Ferrari, in:, Proceedings of the 2019 International Conference on Computer Vision Workshop, IEEE, 2019.","mla":"Kolesnikov, Alexander, et al. “Detecting Visual Relationships Using Box Attention.” Proceedings of the 2019 International Conference on Computer Vision Workshop, 1749–1753, IEEE, 2019, doi:10.1109/ICCVW.2019.00217.","ieee":"A. Kolesnikov, A. Kuznetsova, C. Lampert, and V. Ferrari, “Detecting visual relationships using box attention,” in Proceedings of the 2019 International Conference on Computer Vision Workshop, Seoul, South Korea, 2019.","apa":"Kolesnikov, A., Kuznetsova, A., Lampert, C., & Ferrari, V. (2019). Detecting visual relationships using box attention. In Proceedings of the 2019 International Conference on Computer Vision Workshop. Seoul, South Korea: IEEE. https://doi.org/10.1109/ICCVW.2019.00217","ista":"Kolesnikov A, Kuznetsova A, Lampert C, Ferrari V. 2019. Detecting visual relationships using box attention. Proceedings of the 2019 International Conference on Computer Vision Workshop. ICCVW: International Conference on Computer Vision Workshop, 1749–1753.","ama":"Kolesnikov A, Kuznetsova A, Lampert C, Ferrari V. Detecting visual relationships using box attention. In: Proceedings of the 2019 International Conference on Computer Vision Workshop. IEEE; 2019. doi:10.1109/ICCVW.2019.00217"},"publication":"Proceedings of the 2019 International Conference on Computer Vision Workshop","ec_funded":1,"article_number":"1749-1753","author":[{"id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","last_name":"Kolesnikov","first_name":"Alexander","full_name":"Kolesnikov, Alexander"},{"first_name":"Alina","last_name":"Kuznetsova","full_name":"Kuznetsova, Alina"},{"last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"},{"full_name":"Ferrari, Vittorio","last_name":"Ferrari","first_name":"Vittorio"}],"date_created":"2020-04-05T22:00:51Z","date_updated":"2023-09-08T11:18:37Z","year":"2019","department":[{"_id":"ChLa"}],"publisher":"IEEE","publication_status":"published","publication_identifier":{"isbn":["9781728150239"]},"month":"10","doi":"10.1109/ICCVW.2019.00217","conference":{"start_date":"2019-10-27","location":"Seoul, South Korea","end_date":"2019-10-28","name":"ICCVW: International Conference on Computer Vision Workshop"},"language":[{"iso":"eng"}],"external_id":{"isi":["000554591601098"],"arxiv":["1807.02136"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1807.02136"}],"project":[{"call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1"},{"scopus_import":"1","publication_identifier":{"isbn":["9781728150239"]},"article_processing_charge":"No","day":"01","month":"10","citation":{"ama":"Rannen-Triki A, Berman M, Kolmogorov V, Blaschko MB. Function norms for neural networks. In: Proceedings of the 2019 International Conference on Computer Vision Workshop. IEEE; 2019. doi:10.1109/ICCVW.2019.00097","ista":"Rannen-Triki A, Berman M, Kolmogorov V, Blaschko MB. 2019. Function norms for neural networks. Proceedings of the 2019 International Conference on Computer Vision Workshop. ICCVW: International Conference on Computer Vision Workshop, 748–752.","apa":"Rannen-Triki, A., Berman, M., Kolmogorov, V., & Blaschko, M. B. (2019). Function norms for neural networks. In Proceedings of the 2019 International Conference on Computer Vision Workshop. Seoul, South Korea: IEEE. https://doi.org/10.1109/ICCVW.2019.00097","ieee":"A. Rannen-Triki, M. Berman, V. Kolmogorov, and M. B. Blaschko, “Function norms for neural networks,” in Proceedings of the 2019 International Conference on Computer Vision Workshop, Seoul, South Korea, 2019.","mla":"Rannen-Triki, Amal, et al. “Function Norms for Neural Networks.” Proceedings of the 2019 International Conference on Computer Vision Workshop, 748–752, IEEE, 2019, doi:10.1109/ICCVW.2019.00097.","short":"A. Rannen-Triki, M. Berman, V. Kolmogorov, M.B. Blaschko, in:, Proceedings of the 2019 International Conference on Computer Vision Workshop, IEEE, 2019.","chicago":"Rannen-Triki, Amal, Maxim Berman, Vladimir Kolmogorov, and Matthew B. Blaschko. “Function Norms for Neural Networks.” In Proceedings of the 2019 International Conference on Computer Vision Workshop. IEEE, 2019. https://doi.org/10.1109/ICCVW.2019.00097."},"external_id":{"isi":["000554591600090"]},"publication":"Proceedings of the 2019 International Conference on Computer Vision Workshop","quality_controlled":"1","isi":1,"date_published":"2019-10-01T00:00:00Z","doi":"10.1109/ICCVW.2019.00097","conference":{"start_date":"2019-10-27","location":"Seoul, South Korea","end_date":"2019-10-28","name":"ICCVW: International Conference on Computer Vision Workshop"},"language":[{"iso":"eng"}],"type":"conference","article_number":"748-752","abstract":[{"text":"Deep neural networks (DNNs) have become increasingly important due to their excellent empirical performance on a wide range of problems. However, regularization is generally achieved by indirect means, largely due to the complex set of functions defined by a network and the difficulty in measuring function complexity. There exists no method in the literature for additive regularization based on a norm of the function, as is classically considered in statistical learning theory. In this work, we study the tractability of function norms for deep neural networks with ReLU activations. We provide, to the best of our knowledge, the first proof in the literature of the NP-hardness of computing function norms of DNNs of 3 or more layers. We also highlight a fundamental difference between shallow and deep networks. In the light on these results, we propose a new regularization strategy based on approximate function norms, and show its efficiency on a segmentation task with a DNN.","lang":"eng"}],"year":"2019","_id":"7639","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"IEEE","department":[{"_id":"VlKo"}],"status":"public","publication_status":"published","title":"Function norms for neural networks","author":[{"full_name":"Rannen-Triki, Amal","last_name":"Rannen-Triki","first_name":"Amal"},{"full_name":"Berman, Maxim","last_name":"Berman","first_name":"Maxim"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir"},{"first_name":"Matthew B.","last_name":"Blaschko","full_name":"Blaschko, Matthew B."}],"oa_version":"None","date_updated":"2023-09-08T11:19:12Z","date_created":"2020-04-05T22:00:50Z"},{"month":"07","publication_identifier":{"isbn":["9781119429142"]},"language":[{"iso":"eng"}],"doi":"10.1002/9781119487845.ch4","isi":1,"quality_controlled":"1","external_id":{"isi":["000261343000003"]},"date_updated":"2023-09-08T11:24:15Z","date_created":"2020-08-21T04:25:39Z","author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"full_name":"Etheridge, Alison","first_name":"Alison","last_name":"Etheridge"}],"edition":"4","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","editor":[{"full_name":"Balding, David","last_name":"Balding","first_name":"David"},{"last_name":"Moltke","first_name":"Ida","full_name":"Moltke, Ida"},{"last_name":"Marioni","first_name":"John","full_name":"Marioni, John"}],"year":"2019","day":"29","article_processing_charge":"No","date_published":"2019-07-29T00:00:00Z","page":"115-144","publication":"Handbook of statistical genomics","citation":{"short":"N.H. Barton, A. Etheridge, in:, D. Balding, I. Moltke, J. Marioni (Eds.), Handbook of Statistical Genomics, 4th ed., Wiley, 2019, pp. 115–144.","mla":"Barton, Nicholas H., and Alison Etheridge. “Mathematical Models in Population Genetics.” Handbook of Statistical Genomics, edited by David Balding et al., 4th ed., Wiley, 2019, pp. 115–44, doi:10.1002/9781119487845.ch4.","chicago":"Barton, Nicholas H, and Alison Etheridge. “Mathematical Models in Population Genetics.” In Handbook of Statistical Genomics, edited by David Balding, Ida Moltke, and John Marioni, 4th ed., 115–44. Wiley, 2019. https://doi.org/10.1002/9781119487845.ch4.","ama":"Barton NH, Etheridge A. Mathematical models in population genetics. In: Balding D, Moltke I, Marioni J, eds. Handbook of Statistical Genomics. 4th ed. Wiley; 2019:115-144. doi:10.1002/9781119487845.ch4","ieee":"N. H. Barton and A. Etheridge, “Mathematical models in population genetics,” in Handbook of statistical genomics, 4th ed., D. Balding, I. Moltke, and J. Marioni, Eds. Wiley, 2019, pp. 115–144.","apa":"Barton, N. H., & Etheridge, A. (2019). Mathematical models in population genetics. In D. Balding, I. Moltke, & J. Marioni (Eds.), Handbook of statistical genomics (4th ed., pp. 115–144). Wiley. https://doi.org/10.1002/9781119487845.ch4","ista":"Barton NH, Etheridge A. 2019.Mathematical models in population genetics. In: Handbook of statistical genomics. , 115–144."},"abstract":[{"text":"We review the history of population genetics, starting with its origins a century ago from the synthesis between Mendel and Darwin's ideas, through to the recent development of sophisticated schemes of inference from sequence data, based on the coalescent. We explain the close relation between the coalescent and a diffusion process, which we illustrate by their application to understand spatial structure. We summarise the powerful methods available for analysis of multiple loci, when linkage equilibrium can be assumed, and then discuss approaches to the more challenging case, where associations between alleles require that we follow genotype, rather than allele, frequencies. Though we can hardly cover the whole of population genetics, we give an overview of the current state of the subject, and future challenges to it.","lang":"eng"}],"type":"book_chapter","oa_version":"None","title":"Mathematical models in population genetics","ddc":["576"],"status":"public","_id":"8281","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"abstract":[{"lang":"eng","text":"Denote by ∆N the N-dimensional simplex. A map f : ∆N → Rd is an almost r-embedding if fσ1∩. . .∩fσr = ∅ whenever σ1, . . . , σr are pairwise disjoint faces. A counterexample to the topological Tverberg conjecture asserts that if r is not a prime power and d ≥ 2r + 1, then there is an almost r-embedding ∆(d+1)(r−1) → Rd. This was improved by Blagojevi´c–Frick–Ziegler using a simple construction of higher-dimensional counterexamples by taking k-fold join power of lower-dimensional ones. We improve this further (for d large compared to r): If r is not a prime power and N := (d+ 1)r−r l\r\nd + 2 r + 1 m−2, then there is an almost r-embedding ∆N → Rd. For the r-fold van Kampen–Flores conjecture we also produce counterexamples which are stronger than previously known. Our proof is based on generalizations of the Mabillard–Wagner theorem on construction of almost r-embeddings from equivariant maps, and of the Ozaydin theorem on existence of equivariant maps. "}],"type":"preprint","article_number":"1908.08731","oa_version":"Preprint","date_updated":"2023-09-08T11:20:02Z","date_created":"2020-07-30T10:45:34Z","related_material":{"record":[{"id":"8156","status":"public","relation":"dissertation_contains"}]},"author":[{"id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","last_name":"Avvakumov","first_name":"Sergey","full_name":"Avvakumov, Sergey"},{"full_name":"Karasev, R.","first_name":"R.","last_name":"Karasev"},{"full_name":"Skopenkov, A.","last_name":"Skopenkov","first_name":"A."}],"department":[{"_id":"UlWa"}],"publisher":"arXiv","status":"public","title":"Stronger counterexamples to the topological Tverberg conjecture","publication_status":"submitted","_id":"8184","year":"2019","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"We would like to thank F. Frick for helpful discussions","article_processing_charge":"No","day":"23","month":"08","language":[{"iso":"eng"}],"date_published":"2019-08-23T00:00:00Z","project":[{"_id":"26611F5C-B435-11E9-9278-68D0E5697425","grant_number":"P31312","call_identifier":"FWF","name":"Algorithms for Embeddings and Homotopy Theory"}],"isi":1,"external_id":{"arxiv":["1908.08731"],"isi":["000986519600004"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1908.08731"}],"citation":{"chicago":"Avvakumov, Sergey, R. Karasev, and A. Skopenkov. “Stronger Counterexamples to the Topological Tverberg Conjecture.” ArXiv. arXiv, n.d.","short":"S. Avvakumov, R. Karasev, A. Skopenkov, ArXiv (n.d.).","mla":"Avvakumov, Sergey, et al. “Stronger Counterexamples to the Topological Tverberg Conjecture.” ArXiv, 1908.08731, arXiv.","ieee":"S. Avvakumov, R. Karasev, and A. Skopenkov, “Stronger counterexamples to the topological Tverberg conjecture,” arXiv. arXiv.","apa":"Avvakumov, S., Karasev, R., & Skopenkov, A. (n.d.). Stronger counterexamples to the topological Tverberg conjecture. arXiv. arXiv.","ista":"Avvakumov S, Karasev R, Skopenkov A. Stronger counterexamples to the topological Tverberg conjecture. arXiv, 1908.08731.","ama":"Avvakumov S, Karasev R, Skopenkov A. Stronger counterexamples to the topological Tverberg conjecture. arXiv."},"publication":"arXiv"},{"language":[{"iso":"eng"}],"conference":{"name":"PKC: Public-Key Cryptograhy","location":"Beijing, China","start_date":"2019-04-14","end_date":"2019-04-17"},"doi":"10.1007/978-3-030-17259-6_11","quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"oa":1,"main_file_link":[{"url":"https://eprint.iacr.org/2018/426","open_access":"1"}],"month":"04","publication_identifier":{"isbn":["9783030172589"],"eissn":["16113349"],"issn":["03029743"]},"date_created":"2019-05-13T08:13:46Z","date_updated":"2023-09-08T11:33:20Z","volume":11443,"author":[{"full_name":"Fuchsbauer, Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","last_name":"Fuchsbauer","first_name":"Georg"},{"full_name":"Kamath Hosdurg, Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan","last_name":"Kamath Hosdurg"},{"full_name":"Klein, Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen","last_name":"Klein"},{"orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10035"}]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrPi"}],"year":"2019","ec_funded":1,"date_published":"2019-04-06T00:00:00Z","page":"317-346","citation":{"ista":"Fuchsbauer G, Kamath Hosdurg C, Klein K, Pietrzak KZ. 2019. Adaptively secure proxy re-encryption. PKC: Public-Key Cryptograhy, LNCS, vol. 11443, 317–346.","apa":"Fuchsbauer, G., Kamath Hosdurg, C., Klein, K., & Pietrzak, K. Z. (2019). Adaptively secure proxy re-encryption (Vol. 11443, pp. 317–346). Presented at the PKC: Public-Key Cryptograhy, Beijing, China: Springer Nature. https://doi.org/10.1007/978-3-030-17259-6_11","ieee":"G. Fuchsbauer, C. Kamath Hosdurg, K. Klein, and K. Z. Pietrzak, “Adaptively secure proxy re-encryption,” presented at the PKC: Public-Key Cryptograhy, Beijing, China, 2019, vol. 11443, pp. 317–346.","ama":"Fuchsbauer G, Kamath Hosdurg C, Klein K, Pietrzak KZ. Adaptively secure proxy re-encryption. In: Vol 11443. Springer Nature; 2019:317-346. doi:10.1007/978-3-030-17259-6_11","chicago":"Fuchsbauer, Georg, Chethan Kamath Hosdurg, Karen Klein, and Krzysztof Z Pietrzak. “Adaptively Secure Proxy Re-Encryption,” 11443:317–46. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-17259-6_11.","mla":"Fuchsbauer, Georg, et al. Adaptively Secure Proxy Re-Encryption. Vol. 11443, Springer Nature, 2019, pp. 317–46, doi:10.1007/978-3-030-17259-6_11.","short":"G. Fuchsbauer, C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, in:, Springer Nature, 2019, pp. 317–346."},"day":"06","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","title":"Adaptively secure proxy re-encryption","status":"public","intvolume":" 11443","_id":"6430","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"A proxy re-encryption (PRE) scheme is a public-key encryption scheme that allows the holder of a key pk to derive a re-encryption key for any other key 𝑝𝑘′. This re-encryption key lets anyone transform ciphertexts under pk into ciphertexts under 𝑝𝑘′ without having to know the underlying message, while transformations from 𝑝𝑘′ to pk should not be possible (unidirectional). Security is defined in a multi-user setting against an adversary that gets the users’ public keys and can ask for re-encryption keys and can corrupt users by requesting their secret keys. Any ciphertext that the adversary cannot trivially decrypt given the obtained secret and re-encryption keys should be secure.\r\n\r\nAll existing security proofs for PRE only show selective security, where the adversary must first declare the users it wants to corrupt. This can be lifted to more meaningful adaptive security by guessing the set of corrupted users among the n users, which loses a factor exponential in Open image in new window , rendering the result meaningless already for moderate Open image in new window .\r\n\r\nJafargholi et al. (CRYPTO’17) proposed a framework that in some cases allows to give adaptive security proofs for schemes which were previously only known to be selectively secure, while avoiding the exponential loss that results from guessing the adaptive choices made by an adversary. We apply their framework to PREs that satisfy some natural additional properties. Concretely, we give a more fine-grained reduction for several unidirectional PREs, proving adaptive security at a much smaller loss. The loss depends on the graph of users whose edges represent the re-encryption keys queried by the adversary. For trees and chains the loss is quasi-polynomial in the size and for general graphs it is exponential in their depth and indegree (instead of their size as for previous reductions). Fortunately, trees and low-depth graphs cover many, if not most, interesting applications.\r\n\r\nOur results apply e.g. to the bilinear-map based PRE schemes by Ateniese et al. (NDSS’05 and CT-RSA’09), Gentry’s FHE-based scheme (STOC’09) and the LWE-based scheme by Chandran et al. (PKC’14).","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference"},{"has_accepted_license":"1","article_processing_charge":"No","day":"26","scopus_import":"1","date_published":"2019-02-26T00:00:00Z","citation":{"chicago":"Mayzel, Jonathan, Victor Steinberg, and Atul Varshney. “Stokes Flow Analogous to Viscous Electron Current in Graphene.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-08916-5.","short":"J. Mayzel, V. Steinberg, A. Varshney, Nature Communications 10 (2019).","mla":"Mayzel, Jonathan, et al. “Stokes Flow Analogous to Viscous Electron Current in Graphene.” Nature Communications, vol. 10, 937, Springer Nature, 2019, doi:10.1038/s41467-019-08916-5.","apa":"Mayzel, J., Steinberg, V., & Varshney, A. (2019). Stokes flow analogous to viscous electron current in graphene. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-08916-5","ieee":"J. Mayzel, V. Steinberg, and A. Varshney, “Stokes flow analogous to viscous electron current in graphene,” Nature Communications, vol. 10. Springer Nature, 2019.","ista":"Mayzel J, Steinberg V, Varshney A. 2019. Stokes flow analogous to viscous electron current in graphene. Nature Communications. 10, 937.","ama":"Mayzel J, Steinberg V, Varshney A. Stokes flow analogous to viscous electron current in graphene. Nature Communications. 2019;10. doi:10.1038/s41467-019-08916-5"},"publication":"Nature Communications","abstract":[{"lang":"eng","text":"Electron transport in two-dimensional conducting materials such as graphene, with dominant electron–electron interaction, exhibits unusual vortex flow that leads to a nonlocal current-field relation (negative resistance), distinct from the classical Ohm’s law. The transport behavior of these materials is best described by low Reynolds number hydrodynamics, where the constitutive pressure–speed relation is Stoke’s law. Here we report evidence of such vortices observed in a viscous flow of Newtonian fluid in a microfluidic device consisting of a rectangular cavity—analogous to the electronic system. We extend our experimental observations to elliptic cavities of different eccentricities, and validate them by numerically solving bi-harmonic equation obtained for the viscous flow with no-slip boundary conditions. We verify the existence of a predicted threshold at which vortices appear. Strikingly, we find that a two-dimensional theoretical model captures the essential features of three-dimensional Stokes flow in experiments."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"6070","relation":"main_file","date_created":"2019-03-05T13:33:04Z","date_updated":"2020-07-14T12:47:18Z","checksum":"61192fc49e0d44907c2a4fe384e4b97f","file_name":"2019_NatureComm_Mayzel.pdf","access_level":"open_access","creator":"dernst","file_size":2646391,"content_type":"application/pdf"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6069","intvolume":" 10","ddc":["530","532"],"status":"public","title":"Stokes flow analogous to viscous electron current in graphene","publication_identifier":{"issn":["2041-1723"]},"month":"02","doi":"10.1038/s41467-019-08916-5","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000459704600001"]},"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","isi":1,"ec_funded":1,"file_date_updated":"2020-07-14T12:47:18Z","article_number":"937","author":[{"first_name":"Jonathan","last_name":"Mayzel","full_name":"Mayzel, Jonathan"},{"full_name":"Steinberg, Victor","last_name":"Steinberg","first_name":"Victor"},{"last_name":"Varshney","first_name":"Atul","orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","full_name":"Varshney, Atul"}],"volume":10,"date_created":"2019-03-05T13:18:30Z","date_updated":"2023-09-08T11:39:02Z","year":"2019","department":[{"_id":"BjHo"}],"publisher":"Springer Nature","publication_status":"published"},{"external_id":{"isi":["000458175300001"],"arxiv":["1902.03763"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"doi":"10.1038/s41467-019-08551-0","language":[{"iso":"eng"}],"month":"02","publication_identifier":{"issn":["2041-1723"]},"year":"2019","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"BjHo"}],"author":[{"full_name":"Varshney, Atul","last_name":"Varshney","first_name":"Atul","orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Steinberg","first_name":"Victor","full_name":"Steinberg, Victor"}],"date_created":"2019-02-15T07:10:46Z","date_updated":"2023-09-08T11:39:54Z","volume":10,"article_number":"652","file_date_updated":"2020-07-14T12:47:17Z","ec_funded":1,"publication":"Nature Communications","citation":{"ama":"Varshney A, Steinberg V. Elastic alfven waves in elastic turbulence. Nature Communications. 2019;10. doi:10.1038/s41467-019-08551-0","ieee":"A. Varshney and V. Steinberg, “Elastic alfven waves in elastic turbulence,” Nature Communications, vol. 10. Springer Nature, 2019.","apa":"Varshney, A., & Steinberg, V. (2019). Elastic alfven waves in elastic turbulence. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-08551-0","ista":"Varshney A, Steinberg V. 2019. Elastic alfven waves in elastic turbulence. Nature Communications. 10, 652.","short":"A. Varshney, V. Steinberg, Nature Communications 10 (2019).","mla":"Varshney, Atul, and Victor Steinberg. “Elastic Alfven Waves in Elastic Turbulence.” Nature Communications, vol. 10, 652, Springer Nature, 2019, doi:10.1038/s41467-019-08551-0.","chicago":"Varshney, Atul, and Victor Steinberg. “Elastic Alfven Waves in Elastic Turbulence.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-08551-0."},"article_type":"original","date_published":"2019-02-08T00:00:00Z","scopus_import":"1","day":"08","has_accepted_license":"1","article_processing_charge":"No","_id":"6014","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["530"],"title":"Elastic alfven waves in elastic turbulence","intvolume":" 10","file":[{"checksum":"d3acf07eaad95ec040d8e8565fc9ac37","date_created":"2019-02-15T07:15:00Z","date_updated":"2020-07-14T12:47:17Z","file_id":"6015","relation":"main_file","creator":"dernst","file_size":1331490,"content_type":"application/pdf","access_level":"open_access","file_name":"2019_NatureComm_Varshney.pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Speed of sound waves in gases and liquids are governed by the compressibility of the medium. There exists another type of non-dispersive wave where the wave speed depends on stress instead of elasticity of the medium. A well-known example is the Alfven wave, which propagates through plasma permeated by a magnetic field with the speed determined by magnetic tension. An elastic analogue of Alfven waves has been predicted in a flow of dilute polymer solution where the elastic stress of the stretching polymers determines the elastic wave speed. Here we present quantitative evidence of elastic Alfven waves in elastic turbulence of a viscoelastic creeping flow between two obstacles in channel flow. The key finding in the experimental proof is a nonlinear dependence of the elastic wave speed cel on the Weissenberg number Wi, which deviates from predictions based on a model of linear polymer elasticity."}]},{"file":[{"relation":"main_file","file_id":"6452","date_created":"2019-05-14T11:51:51Z","date_updated":"2020-07-14T12:47:30Z","checksum":"a9ad2296726c9474ad5860c9c2f53622","file_name":"2019_iScience_Amberg.pdf","access_level":"open_access","file_size":8365970,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6451","title":"EGFR controls hair shaft differentiation in a p53-independent manner","status":"public","ddc":["570"],"intvolume":" 15","abstract":[{"text":"Epidermal growth factor receptor (EGFR) signaling controls skin development and homeostasis inmice and humans, and its deficiency causes severe skin inflammation, which might affect epidermalstem cell behavior. Here, we describe the inflammation-independent effects of EGFR deficiency dur-ing skin morphogenesis and in adult hair follicle stem cells. Expression and alternative splicing analysisof RNA sequencing data from interfollicular epidermis and outer root sheath indicate that EGFR con-trols genes involved in epidermal differentiation and also in centrosome function, DNA damage, cellcycle, and apoptosis. Genetic experiments employingp53deletion in EGFR-deficient epidermis revealthat EGFR signaling exhibitsp53-dependent functions in proliferative epidermal compartments, aswell asp53-independent functions in differentiated hair shaft keratinocytes. Loss of EGFR leads toabsence of LEF1 protein specifically in the innermost epithelial hair layers, resulting in disorganizationof medulla cells. Thus, our results uncover important spatial and temporal features of cell-autonomousEGFR functions in the epidermis.","lang":"eng"}],"type":"journal_article","date_published":"2019-05-31T00:00:00Z","publication":"iScience","citation":{"ama":"Amberg N, Sotiropoulou PA, Heller G, et al. EGFR controls hair shaft differentiation in a p53-independent manner. iScience. 2019;15:243-256. doi:10.1016/j.isci.2019.04.018","apa":"Amberg, N., Sotiropoulou, P. A., Heller, G., Lichtenberger, B. M., Holcmann, M., Camurdanoglu, B., … Sibilia, M. (2019). EGFR controls hair shaft differentiation in a p53-independent manner. IScience. Elsevier. https://doi.org/10.1016/j.isci.2019.04.018","ieee":"N. Amberg et al., “EGFR controls hair shaft differentiation in a p53-independent manner,” iScience, vol. 15. Elsevier, pp. 243–256, 2019.","ista":"Amberg N, Sotiropoulou PA, Heller G, Lichtenberger BM, Holcmann M, Camurdanoglu B, Baykuscheva-Gentscheva T, Blanpain C, Sibilia M. 2019. EGFR controls hair shaft differentiation in a p53-independent manner. iScience. 15, 243–256.","short":"N. Amberg, P.A. Sotiropoulou, G. Heller, B.M. Lichtenberger, M. Holcmann, B. Camurdanoglu, T. Baykuscheva-Gentscheva, C. Blanpain, M. Sibilia, IScience 15 (2019) 243–256.","mla":"Amberg, Nicole, et al. “EGFR Controls Hair Shaft Differentiation in a P53-Independent Manner.” IScience, vol. 15, Elsevier, 2019, pp. 243–56, doi:10.1016/j.isci.2019.04.018.","chicago":"Amberg, Nicole, Panagiota A. Sotiropoulou, Gerwin Heller, Beate M. Lichtenberger, Martin Holcmann, Bahar Camurdanoglu, Temenuschka Baykuscheva-Gentscheva, Cedric Blanpain, and Maria Sibilia. “EGFR Controls Hair Shaft Differentiation in a P53-Independent Manner.” IScience. Elsevier, 2019. https://doi.org/10.1016/j.isci.2019.04.018."},"page":"243-256","day":"31","article_processing_charge":"No","has_accepted_license":"1","author":[{"last_name":"Amberg","first_name":"Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole"},{"last_name":"Sotiropoulou","first_name":"Panagiota A.","full_name":"Sotiropoulou, Panagiota A."},{"first_name":"Gerwin","last_name":"Heller","full_name":"Heller, Gerwin"},{"full_name":"Lichtenberger, Beate M.","last_name":"Lichtenberger","first_name":"Beate M."},{"first_name":"Martin","last_name":"Holcmann","full_name":"Holcmann, Martin"},{"full_name":"Camurdanoglu, Bahar","last_name":"Camurdanoglu","first_name":"Bahar"},{"full_name":"Baykuscheva-Gentscheva, Temenuschka","last_name":"Baykuscheva-Gentscheva","first_name":"Temenuschka"},{"full_name":"Blanpain, Cedric","last_name":"Blanpain","first_name":"Cedric"},{"first_name":"Maria","last_name":"Sibilia","full_name":"Sibilia, Maria"}],"date_created":"2019-05-14T11:47:40Z","date_updated":"2023-09-08T11:38:04Z","volume":15,"year":"2019","publication_status":"published","publisher":"Elsevier","department":[{"_id":"SiHi"}],"file_date_updated":"2020-07-14T12:47:30Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","doi":"10.1016/j.isci.2019.04.018","language":[{"iso":"eng"}],"tmp":{"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000470104600022"]},"oa":1,"isi":1,"quality_controlled":"1","month":"05","publication_identifier":{"issn":["2589-0042"]}},{"volume":9,"date_created":"2022-03-18T12:36:42Z","date_updated":"2023-09-08T11:35:31Z","author":[{"full_name":"Dietlein, Adrian M","first_name":"Adrian M","last_name":"Dietlein","id":"317CB464-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","last_name":"Gebert","full_name":"Gebert, Martin"},{"full_name":"Müller, Peter","first_name":"Peter","last_name":"Müller"}],"publisher":"European Mathematical Society Publishing House","department":[{"_id":"LaEr"}],"publication_status":"published","acknowledgement":"M.G. was supported by the DFG under grant GE 2871/1-1.","year":"2019","publication_identifier":{"issn":["1664-039X"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.4171/jst/267","quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1701.02956","open_access":"1"}],"external_id":{"isi":["000484709400006"],"arxiv":["1701.02956"]},"issue":"3","abstract":[{"lang":"eng","text":"We study effects of a bounded and compactly supported perturbation on multidimensional continuum random Schrödinger operators in the region of complete localisation. Our main emphasis is on Anderson orthogonality for random Schrödinger operators. Among others, we prove that Anderson orthogonality does occur for Fermi energies in the region of complete localisation with a non-zero probability. This partially confirms recent non-rigorous findings [V. Khemani et al., Nature Phys. 11 (2015), 560–565]. The spectral shift function plays an important role in our analysis of Anderson orthogonality. We identify it with the index of the corresponding pair of spectral projections and explore the consequences thereof. All our results rely on the main technical estimate of this paper which guarantees separate exponential decay of the disorder-averaged Schatten p-norm of χa(f(H)−f(Hτ))χb in a and b. Here, Hτ is a perturbation of the random Schrödinger operator H, χa is the multiplication operator corresponding to the indicator function of a unit cube centred about a∈Rd, and f is in a suitable class of functions of bounded variation with distributional derivative supported in the region of complete localisation for H."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 9","title":"Perturbations of continuum random Schrödinger operators with applications to Anderson orthogonality and the spectral shift function","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10879","article_processing_charge":"No","day":"01","keyword":["Random Schrödinger operators","spectral shift function","Anderson orthogonality"],"scopus_import":"1","date_published":"2019-03-01T00:00:00Z","page":"921-965","article_type":"original","citation":{"mla":"Dietlein, Adrian M., et al. “Perturbations of Continuum Random Schrödinger Operators with Applications to Anderson Orthogonality and the Spectral Shift Function.” Journal of Spectral Theory, vol. 9, no. 3, European Mathematical Society Publishing House, 2019, pp. 921–65, doi:10.4171/jst/267.","short":"A.M. Dietlein, M. Gebert, P. Müller, Journal of Spectral Theory 9 (2019) 921–965.","chicago":"Dietlein, Adrian M, Martin Gebert, and Peter Müller. “Perturbations of Continuum Random Schrödinger Operators with Applications to Anderson Orthogonality and the Spectral Shift Function.” Journal of Spectral Theory. European Mathematical Society Publishing House, 2019. https://doi.org/10.4171/jst/267.","ama":"Dietlein AM, Gebert M, Müller P. Perturbations of continuum random Schrödinger operators with applications to Anderson orthogonality and the spectral shift function. Journal of Spectral Theory. 2019;9(3):921-965. doi:10.4171/jst/267","ista":"Dietlein AM, Gebert M, Müller P. 2019. Perturbations of continuum random Schrödinger operators with applications to Anderson orthogonality and the spectral shift function. Journal of Spectral Theory. 9(3), 921–965.","ieee":"A. M. Dietlein, M. Gebert, and P. Müller, “Perturbations of continuum random Schrödinger operators with applications to Anderson orthogonality and the spectral shift function,” Journal of Spectral Theory, vol. 9, no. 3. European Mathematical Society Publishing House, pp. 921–965, 2019.","apa":"Dietlein, A. M., Gebert, M., & Müller, P. (2019). Perturbations of continuum random Schrödinger operators with applications to Anderson orthogonality and the spectral shift function. Journal of Spectral Theory. European Mathematical Society Publishing House. https://doi.org/10.4171/jst/267"},"publication":"Journal of Spectral Theory"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Starting from a microscopic model for a system of neurons evolving in time which individually follow a stochastic integrate-and-fire type model, we study a mean-field limit of the system. Our model is described by a system of SDEs with discontinuous coefficients for the action potential of each neuron and takes into account the (random) spatial configuration of neurons allowing the interaction to depend on it. In the limit as the number of particles tends to infinity, we obtain a nonlinear Fokker-Planck type PDE in two variables, with derivatives only with respect to one variable and discontinuous coefficients. We also study strong well-posedness of the system of SDEs and prove the existence and uniqueness of a weak measure-valued solution to the PDE, obtained as the limit of the laws of the empirical measures for the system of particles."}],"issue":"6","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10878","status":"public","title":"A mean-field model with discontinuous coefficients for neurons with spatial interaction","intvolume":" 39","oa_version":"Preprint","scopus_import":"1","keyword":["Applied Mathematics","Discrete Mathematics and Combinatorics","Analysis"],"day":"01","article_processing_charge":"No","publication":"Discrete and Continuous Dynamical Systems","citation":{"apa":"Flandoli, F., Priola, E., & Zanco, G. A. (2019). A mean-field model with discontinuous coefficients for neurons with spatial interaction. Discrete and Continuous Dynamical Systems. American Institute of Mathematical Sciences. https://doi.org/10.3934/dcds.2019126","ieee":"F. Flandoli, E. Priola, and G. A. Zanco, “A mean-field model with discontinuous coefficients for neurons with spatial interaction,” Discrete and Continuous Dynamical Systems, vol. 39, no. 6. American Institute of Mathematical Sciences, pp. 3037–3067, 2019.","ista":"Flandoli F, Priola E, Zanco GA. 2019. A mean-field model with discontinuous coefficients for neurons with spatial interaction. Discrete and Continuous Dynamical Systems. 39(6), 3037–3067.","ama":"Flandoli F, Priola E, Zanco GA. A mean-field model with discontinuous coefficients for neurons with spatial interaction. Discrete and Continuous Dynamical Systems. 2019;39(6):3037-3067. doi:10.3934/dcds.2019126","chicago":"Flandoli, Franco, Enrico Priola, and Giovanni A Zanco. “A Mean-Field Model with Discontinuous Coefficients for Neurons with Spatial Interaction.” Discrete and Continuous Dynamical Systems. American Institute of Mathematical Sciences, 2019. https://doi.org/10.3934/dcds.2019126.","short":"F. Flandoli, E. Priola, G.A. Zanco, Discrete and Continuous Dynamical Systems 39 (2019) 3037–3067.","mla":"Flandoli, Franco, et al. “A Mean-Field Model with Discontinuous Coefficients for Neurons with Spatial Interaction.” Discrete and Continuous Dynamical Systems, vol. 39, no. 6, American Institute of Mathematical Sciences, 2019, pp. 3037–67, doi:10.3934/dcds.2019126."},"article_type":"original","page":"3037-3067","date_published":"2019-06-01T00:00:00Z","year":"2019","acknowledgement":"The second author has been partially supported by INdAM through the GNAMPA Research\r\nProject (2017) “Sistemi stocastici singolari: buona posizione e problemi di controllo”. The third\r\nauthor was partly funded by the Austrian Science Fund (FWF) project F 65.","publication_status":"published","publisher":"American Institute of Mathematical Sciences","department":[{"_id":"JaMa"}],"author":[{"last_name":"Flandoli","first_name":"Franco","full_name":"Flandoli, Franco"},{"full_name":"Priola, Enrico","first_name":"Enrico","last_name":"Priola"},{"first_name":"Giovanni A","last_name":"Zanco","id":"47491882-F248-11E8-B48F-1D18A9856A87","full_name":"Zanco, Giovanni A"}],"date_created":"2022-03-18T12:33:34Z","date_updated":"2023-09-08T11:34:45Z","volume":39,"month":"06","publication_identifier":{"issn":["1553-5231"]},"main_file_link":[{"url":"https://arxiv.org/abs/1708.04156","open_access":"1"}],"external_id":{"arxiv":["1708.04156"],"isi":["000459954800003"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems"}],"doi":"10.3934/dcds.2019126","language":[{"iso":"eng"}]},{"month":"08","publication_identifier":{"isbn":["9781450362177"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"external_id":{"isi":["000570442000037"],"arxiv":["1905.03012"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.03012"}],"language":[{"iso":"eng"}],"conference":{"end_date":"2019-08-02","location":"Toronto, ON, Canada","start_date":"2019-07-29","name":"PODC: Symposium on Principles of Distributed Computing"},"doi":"10.1145/3293611.3331581","ec_funded":1,"publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"ACM","year":"2019","date_created":"2019-10-08T12:57:14Z","date_updated":"2023-09-08T11:37:22Z","author":[{"full_name":"Foerster, Klaus-Tycho","first_name":"Klaus-Tycho","last_name":"Foerster"},{"full_name":"Korhonen, Janne","id":"C5402D42-15BC-11E9-A202-CA2BE6697425","last_name":"Korhonen","first_name":"Janne"},{"first_name":"Joel","last_name":"Rybicki","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6432-6646","full_name":"Rybicki, Joel"},{"full_name":"Schmid, Stefan","first_name":"Stefan","last_name":"Schmid"}],"scopus_import":"1","day":"01","article_processing_charge":"No","page":"259-261","publication":"Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing","citation":{"ista":"Foerster K-T, Korhonen J, Rybicki J, Schmid S. 2019. Does preprocessing help under congestion? Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 259–261.","apa":"Foerster, K.-T., Korhonen, J., Rybicki, J., & Schmid, S. (2019). Does preprocessing help under congestion? In Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing (pp. 259–261). Toronto, ON, Canada: ACM. https://doi.org/10.1145/3293611.3331581","ieee":"K.-T. Foerster, J. Korhonen, J. Rybicki, and S. Schmid, “Does preprocessing help under congestion?,” in Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing, Toronto, ON, Canada, 2019, pp. 259–261.","ama":"Foerster K-T, Korhonen J, Rybicki J, Schmid S. Does preprocessing help under congestion? In: Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing. ACM; 2019:259-261. doi:10.1145/3293611.3331581","chicago":"Foerster, Klaus-Tycho, Janne Korhonen, Joel Rybicki, and Stefan Schmid. “Does Preprocessing Help under Congestion?” In Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing, 259–61. ACM, 2019. https://doi.org/10.1145/3293611.3331581.","mla":"Foerster, Klaus-Tycho, et al. “Does Preprocessing Help under Congestion?” Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing, ACM, 2019, pp. 259–61, doi:10.1145/3293611.3331581.","short":"K.-T. Foerster, J. Korhonen, J. Rybicki, S. Schmid, in:, Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing, ACM, 2019, pp. 259–261."},"date_published":"2019-08-01T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"This paper investigates the power of preprocessing in the CONGEST model. Schmid and Suomela (ACM HotSDN 2013) introduced the SUPPORTED CONGEST model to study the application of distributed algorithms in Software-Defined Networks (SDNs). In this paper, we show that a large class of lower bounds in the CONGEST model still hold in the SUPPORTED model, highlighting the robustness of these bounds. This also raises the question how much does\r\npreprocessing help in the CONGEST model."}],"status":"public","title":"Does preprocessing help under congestion?","_id":"6935","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint"},{"file_date_updated":"2020-07-14T12:44:47Z","publist_id":"7785","ec_funded":1,"publication_status":"published","department":[{"_id":"CaGu"}],"publisher":"Springer","year":"2019","date_updated":"2023-09-08T13:23:42Z","date_created":"2018-12-11T11:44:50Z","volume":65,"author":[{"full_name":"Nikolic, Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9068-6090","first_name":"Nela","last_name":"Nikolic"}],"month":"02","isi":1,"quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000456958800017"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00294-018-0879-8","type":"journal_article","abstract":[{"lang":"eng","text":"Autoregulation is the direct modulation of gene expression by the product of the corresponding gene. Autoregulation of bacterial gene expression has been mostly studied at the transcriptional level, when a protein acts as the cognate transcriptional repressor. A recent study investigating dynamics of the bacterial toxin–antitoxin MazEF system has shown how autoregulation at both the transcriptional and post-transcriptional levels affects the heterogeneity of Escherichia coli populations. Toxin–antitoxin systems hold a crucial but still elusive part in bacterial response to stress. This perspective highlights how these modules can also serve as a great model system for investigating basic concepts in gene regulation. However, as the genomic background and environmental conditions substantially influence toxin activation, it is important to study (auto)regulation of toxin–antitoxin systems in well-defined setups as well as in conditions that resemble the environmental niche."}],"issue":"1","status":"public","title":"Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system","ddc":["570"],"intvolume":" 65","_id":"138","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"date_updated":"2020-07-14T12:44:47Z","date_created":"2019-02-06T07:50:58Z","checksum":"6779708b0b632a1a6ed28c56f5161142","file_id":"5930","relation":"main_file","creator":"dernst","file_size":776399,"content_type":"application/pdf","file_name":"2019_CurrentGenetics_Nikolic.pdf","access_level":"open_access"}],"oa_version":"Published Version","scopus_import":"1","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","page":"133-138","publication":"Current Genetics","citation":{"ieee":"N. Nikolic, “Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system,” Current Genetics, vol. 65, no. 1. Springer, pp. 133–138, 2019.","apa":"Nikolic, N. (2019). Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. Current Genetics. Springer. https://doi.org/10.1007/s00294-018-0879-8","ista":"Nikolic N. 2019. Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. Current Genetics. 65(1), 133–138.","ama":"Nikolic N. Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. Current Genetics. 2019;65(1):133-138. doi:10.1007/s00294-018-0879-8","chicago":"Nikolic, Nela. “Autoregulation of Bacterial Gene Expression: Lessons from the MazEF Toxin–Antitoxin System.” Current Genetics. Springer, 2019. https://doi.org/10.1007/s00294-018-0879-8.","short":"N. Nikolic, Current Genetics 65 (2019) 133–138.","mla":"Nikolic, Nela. “Autoregulation of Bacterial Gene Expression: Lessons from the MazEF Toxin–Antitoxin System.” Current Genetics, vol. 65, no. 1, Springer, 2019, pp. 133–38, doi:10.1007/s00294-018-0879-8."},"date_published":"2019-02-01T00:00:00Z"},{"year":"2019","department":[{"_id":"JuFi"}],"publisher":"Elsevier","publication_status":"published","author":[{"full_name":"Fischer, Julian L","first_name":"Julian L","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X"},{"full_name":"Kneuss, Olivier","first_name":"Olivier","last_name":"Kneuss"}],"volume":266,"date_created":"2018-12-11T11:44:54Z","date_updated":"2023-09-08T13:25:35Z","publist_id":"7770","external_id":{"isi":["000449108500010"],"arxiv":["1408.1587"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1408.1587","open_access":"1"}],"quality_controlled":"1","isi":1,"doi":"10.1016/j.jde.2018.07.045","language":[{"iso":"eng"}],"month":"01","_id":"151","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 266","title":"Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity","status":"public","oa_version":"Preprint","type":"journal_article","issue":"1","abstract":[{"text":"We construct planar bi-Sobolev mappings whose local volume distortion is bounded from below by a given function f∈Lp with p>1. More precisely, for any 1<q<(p+1)/2 we construct W1,q-bi-Sobolev maps with identity boundary conditions; for f∈L∞, we provide bi-Lipschitz maps. The basic building block of our construction are bi-Lipschitz maps which stretch a given compact subset of the unit square by a given factor while preserving the boundary. The construction of these stretching maps relies on a slight strengthening of the celebrated covering result of Alberti, Csörnyei, and Preiss for measurable planar sets in the case of compact sets. We apply our result to a model functional in nonlinear elasticity, the integrand of which features fast blowup as the Jacobian determinant of the deformation becomes small. For such functionals, the derivation of the equilibrium equations for minimizers requires an additional regularization of test functions, which our maps provide.","lang":"eng"}],"citation":{"ista":"Fischer JL, Kneuss O. 2019. Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity. Journal of Differential Equations. 266(1), 257–311.","apa":"Fischer, J. L., & Kneuss, O. (2019). Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity. Journal of Differential Equations. Elsevier. https://doi.org/10.1016/j.jde.2018.07.045","ieee":"J. L. Fischer and O. Kneuss, “Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity,” Journal of Differential Equations, vol. 266, no. 1. Elsevier, pp. 257–311, 2019.","ama":"Fischer JL, Kneuss O. Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity. Journal of Differential Equations. 2019;266(1):257-311. doi:10.1016/j.jde.2018.07.045","chicago":"Fischer, Julian L, and Olivier Kneuss. “Bi-Sobolev Solutions to the Prescribed Jacobian Inequality in the Plane with L p Data and Applications to Nonlinear Elasticity.” Journal of Differential Equations. Elsevier, 2019. https://doi.org/10.1016/j.jde.2018.07.045.","mla":"Fischer, Julian L., and Olivier Kneuss. “Bi-Sobolev Solutions to the Prescribed Jacobian Inequality in the Plane with L p Data and Applications to Nonlinear Elasticity.” Journal of Differential Equations, vol. 266, no. 1, Elsevier, 2019, pp. 257–311, doi:10.1016/j.jde.2018.07.045.","short":"J.L. Fischer, O. Kneuss, Journal of Differential Equations 266 (2019) 257–311."},"publication":"Journal of Differential Equations","page":"257 - 311","date_published":"2019-01-05T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"05"},{"year":"2019","acknowledgement":" This work was supported by IST Austria institutional funds; NÖ Forschung und Bildung \r\nn[f+b] (C13-002) to SH; a program grant from the Human Frontiers Science Program (RGP0053/2014) to SH; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No 618444 to SH, and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 725780 LinPro)to SH.\r\n","publication_status":"published","publisher":"Wiley","department":[{"_id":"SiHi"}],"author":[{"full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg","first_name":"Nicole"},{"full_name":"Laukoter, Susanne","orcid":"0000-0002-7903-3010","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","last_name":"Laukoter","first_name":"Susanne"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"}],"date_created":"2018-12-11T11:44:14Z","date_updated":"2023-09-11T13:40:26Z","volume":149,"file_date_updated":"2020-07-14T12:45:45Z","ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000462680200002"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"LS13-002","_id":"25D92700-B435-11E9-9278-68D0E5697425","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain"},{"name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","_id":"25D7962E-B435-11E9-9278-68D0E5697425","grant_number":"RGP0053/2014"},{"name":"Molecular Mechanisms of Cerebral Cortex Development","call_identifier":"FP7","_id":"25D61E48-B435-11E9-9278-68D0E5697425","grant_number":"618444"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"doi":"10.1111/jnc.14601","language":[{"iso":"eng"}],"month":"04","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"27","status":"public","ddc":["570"],"title":"Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex","intvolume":" 149","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2019_Wiley_Amberg.pdf","creator":"kschuh","file_size":889709,"content_type":"application/pdf","file_id":"7239","relation":"main_file","checksum":"db027721a95d36f5de36aadcd0bdf7e6","date_created":"2020-01-07T13:35:52Z","date_updated":"2020-07-14T12:45:45Z"}],"type":"journal_article","abstract":[{"text":"The cerebral cortex is composed of a large variety of distinct cell-types including projection neurons, interneurons and glial cells which emerge from distinct neural stem cell (NSC) lineages. The vast majority of cortical projection neurons and certain classes of glial cells are generated by radial glial progenitor cells (RGPs) in a highly orchestrated manner. Recent studies employing single cell analysis and clonal lineage tracing suggest that NSC and RGP lineage progression are regulated in a profound deterministic manner. In this review we focus on recent advances based mainly on correlative phenotypic data emerging from functional genetic studies in mice. We establish hypotheses to test in future research and outline a conceptual framework how epigenetic cues modulate the generation of cell-type diversity during cortical development. This article is protected by copyright. All rights reserved.","lang":"eng"}],"issue":"1","publication":"Journal of Neurochemistry","citation":{"mla":"Amberg, Nicole, et al. “Epigenetic Cues Modulating the Generation of Cell Type Diversity in the Cerebral Cortex.” Journal of Neurochemistry, vol. 149, no. 1, Wiley, 2019, pp. 12–26, doi:10.1111/jnc.14601.","short":"N. Amberg, S. Laukoter, S. Hippenmeyer, Journal of Neurochemistry 149 (2019) 12–26.","chicago":"Amberg, Nicole, Susanne Laukoter, and Simon Hippenmeyer. “Epigenetic Cues Modulating the Generation of Cell Type Diversity in the Cerebral Cortex.” Journal of Neurochemistry. Wiley, 2019. https://doi.org/10.1111/jnc.14601.","ama":"Amberg N, Laukoter S, Hippenmeyer S. Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex. Journal of Neurochemistry. 2019;149(1):12-26. doi:10.1111/jnc.14601","ista":"Amberg N, Laukoter S, Hippenmeyer S. 2019. Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex. Journal of Neurochemistry. 149(1), 12–26.","ieee":"N. Amberg, S. Laukoter, and S. Hippenmeyer, “Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex,” Journal of Neurochemistry, vol. 149, no. 1. Wiley, pp. 12–26, 2019.","apa":"Amberg, N., Laukoter, S., & Hippenmeyer, S. (2019). Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex. Journal of Neurochemistry. Wiley. https://doi.org/10.1111/jnc.14601"},"article_type":"review","page":"12-26","date_published":"2019-04-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1"},{"month":"02","publication_identifier":{"issn":["14657392"]},"doi":"10.1038/s41556-018-0247-4","acknowledged_ssus":[{"_id":"Bio"}],"language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000457468300011"],"pmid":["30559456"]},"isi":1,"quality_controlled":"1","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020"},{"name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants (EMBO fellowship)","_id":"253E54C8-B435-11E9-9278-68D0E5697425","grant_number":"ALTF710-2016"}],"file_date_updated":"2020-10-21T07:18:35Z","ec_funded":1,"author":[{"full_name":"Petridou, Nicoletta","last_name":"Petridou","first_name":"Nicoletta","orcid":"0000-0002-8451-1195","id":"2A003F6C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Silvia","last_name":"Grigolon","full_name":"Grigolon, Silvia"},{"full_name":"Salbreux, Guillaume","last_name":"Salbreux","first_name":"Guillaume"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/when-a-fish-becomes-fluid/","description":"News on IST Homepage","relation":"press_release"}]},"date_created":"2018-12-30T22:59:15Z","date_updated":"2023-09-11T14:03:28Z","volume":21,"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"CaHe"},{"_id":"EdHa"}],"publisher":"Nature Publishing Group","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2019-02-01T00:00:00Z","publication":"Nature Cell Biology","citation":{"short":"N. Petridou, S. Grigolon, G. Salbreux, E.B. Hannezo, C.-P.J. Heisenberg, Nature Cell Biology 21 (2019) 169–178.","mla":"Petridou, Nicoletta, et al. “Fluidization-Mediated Tissue Spreading by Mitotic Cell Rounding and Non-Canonical Wnt Signalling.” Nature Cell Biology, vol. 21, Nature Publishing Group, 2019, pp. 169–178, doi:10.1038/s41556-018-0247-4.","chicago":"Petridou, Nicoletta, Silvia Grigolon, Guillaume Salbreux, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Fluidization-Mediated Tissue Spreading by Mitotic Cell Rounding and Non-Canonical Wnt Signalling.” Nature Cell Biology. Nature Publishing Group, 2019. https://doi.org/10.1038/s41556-018-0247-4.","ama":"Petridou N, Grigolon S, Salbreux G, Hannezo EB, Heisenberg C-PJ. Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. Nature Cell Biology. 2019;21:169–178. doi:10.1038/s41556-018-0247-4","ieee":"N. Petridou, S. Grigolon, G. Salbreux, E. B. Hannezo, and C.-P. J. Heisenberg, “Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling,” Nature Cell Biology, vol. 21. Nature Publishing Group, pp. 169–178, 2019.","apa":"Petridou, N., Grigolon, S., Salbreux, G., Hannezo, E. B., & Heisenberg, C.-P. J. (2019). Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/s41556-018-0247-4","ista":"Petridou N, Grigolon S, Salbreux G, Hannezo EB, Heisenberg C-PJ. 2019. Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. Nature Cell Biology. 21, 169–178."},"article_type":"original","page":"169–178","abstract":[{"text":"Tissue morphogenesis is driven by mechanical forces that elicit changes in cell size, shape and motion. The extent by which forces deform tissues critically depends on the rheological properties of the recipient tissue. Yet, whether and how dynamic changes in tissue rheology affect tissue morphogenesis and how they are regulated within the developing organism remain unclear. Here, we show that blastoderm spreading at the onset of zebrafish morphogenesis relies on a rapid, pronounced and spatially patterned tissue fluidization. Blastoderm fluidization is temporally controlled by mitotic cell rounding-dependent cell–cell contact disassembly during the last rounds of cell cleavages. Moreover, fluidization is spatially restricted to the central blastoderm by local activation of non-canonical Wnt signalling within the blastoderm margin, increasing cell cohesion and thereby counteracting the effect of mitotic rounding on contact disassembly. Overall, our results identify a fluidity transition mediated by loss of cell cohesion as a critical regulator of embryo morphogenesis.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","file":[{"file_id":"8685","relation":"main_file","success":1,"checksum":"e38523787b3bc84006f2793de99ad70f","date_created":"2020-10-21T07:18:35Z","date_updated":"2020-10-21T07:18:35Z","access_level":"open_access","file_name":"2018_NatureCellBio_Petridou_accepted.pdf","creator":"dernst","file_size":71590590,"content_type":"application/pdf"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5789","title":"Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling","status":"public","ddc":["570"],"intvolume":" 21"},{"volume":116,"date_created":"2018-12-11T11:45:08Z","date_updated":"2023-09-11T14:09:34Z","related_material":{"link":[{"description":"News on IST Webpage","relation":"press_release","url":"https://ist.ac.at/en/news/famous-sandpile-model-shown-to-move-like-a-traveling-sand-dune/"}]},"author":[{"last_name":"Lang","first_name":"Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","full_name":"Lang, Moritz"},{"orcid":"0000-0002-4310-178X","id":"35084A62-F248-11E8-B48F-1D18A9856A87","last_name":"Shkolnikov","first_name":"Mikhail","full_name":"Shkolnikov, Mikhail"}],"publisher":"National Academy of Sciences","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"TaHa"}],"publication_status":"published","pmid":1,"acknowledgement":"M.L. is grateful to the members of the C Guet and G Tkacik groups for valuable comments and support. M.S. is grateful to Nikita Kalinin for inspiring communications.\r\n","year":"2019","publication_identifier":{"eissn":["1091-6490"]},"month":"02","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1812015116","isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1812015116","open_access":"1"}],"external_id":{"arxiv":["1806.10823"],"pmid":[" 30728300"],"isi":["000459074400013"]},"issue":"8","abstract":[{"lang":"eng","text":"The abelian sandpile serves as a model to study self-organized criticality, a phenomenon occurring in biological, physical and social processes. The identity of the abelian group is a fractal composed of self-similar patches, and its limit is subject of extensive collaborative research. Here, we analyze the evolution of the sandpile identity under harmonic fields of different orders. We show that this evolution corresponds to periodic cycles through the abelian group characterized by the smooth transformation and apparent conservation of the patches constituting the identity. The dynamics induced by second and third order harmonics resemble smooth stretchings, respectively translations, of the identity, while the ones induced by fourth order harmonics resemble magnifications and rotations. Starting with order three, the dynamics pass through extended regions of seemingly random configurations which spontaneously reassemble into accentuated patterns. We show that the space of harmonic functions projects to the extended analogue of the sandpile group, thus providing a set of universal coordinates identifying configurations between different domains. Since the original sandpile group is a subgroup of the extended one, this directly implies that it admits a natural renormalization. Furthermore, we show that the harmonic fields can be induced by simple Markov processes, and that the corresponding stochastic dynamics show remarkable robustness over hundreds of periods. Finally, we encode information into seemingly random configurations, and decode this information with an algorithm requiring minimal prior knowledge. Our results suggest that harmonic fields might split the sandpile group into sub-sets showing different critical coefficients, and that it might be possible to extend the fractal structure of the identity beyond the boundaries of its domain. "}],"type":"journal_article","oa_version":"Published Version","intvolume":" 116","title":"Harmonic dynamics of the Abelian sandpile","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"196","article_processing_charge":"No","day":"19","scopus_import":"1","date_published":"2019-02-19T00:00:00Z","page":"2821-2830","article_type":"original","citation":{"short":"M. Lang, M. Shkolnikov, Proceedings of the National Academy of Sciences 116 (2019) 2821–2830.","mla":"Lang, Moritz, and Mikhail Shkolnikov. “Harmonic Dynamics of the Abelian Sandpile.” Proceedings of the National Academy of Sciences, vol. 116, no. 8, National Academy of Sciences, 2019, pp. 2821–30, doi:10.1073/pnas.1812015116.","chicago":"Lang, Moritz, and Mikhail Shkolnikov. “Harmonic Dynamics of the Abelian Sandpile.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1812015116.","ama":"Lang M, Shkolnikov M. Harmonic dynamics of the Abelian sandpile. Proceedings of the National Academy of Sciences. 2019;116(8):2821-2830. doi:10.1073/pnas.1812015116","ieee":"M. Lang and M. Shkolnikov, “Harmonic dynamics of the Abelian sandpile,” Proceedings of the National Academy of Sciences, vol. 116, no. 8. National Academy of Sciences, pp. 2821–2830, 2019.","apa":"Lang, M., & Shkolnikov, M. (2019). Harmonic dynamics of the Abelian sandpile. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1812015116","ista":"Lang M, Shkolnikov M. 2019. Harmonic dynamics of the Abelian sandpile. Proceedings of the National Academy of Sciences. 116(8), 2821–2830."},"publication":"Proceedings of the National Academy of Sciences"},{"author":[{"full_name":"Kavcic, Bor","last_name":"Kavcic","first_name":"Bor","orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"A.","last_name":"Sakashita","full_name":"Sakashita, A."},{"last_name":"Noguchi","first_name":"H.","full_name":"Noguchi, H."},{"first_name":"P.","last_name":"Ziherl","full_name":"Ziherl, P."}],"date_created":"2019-01-11T07:37:47Z","date_updated":"2023-09-13T08:47:16Z","volume":15,"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"Royal Society of Chemistry","file_date_updated":"2020-10-09T11:00:05Z","license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","doi":"10.1039/c8sm01956h","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode","short":"CC BY-NC-ND (3.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"isi":["000457329700003"],"pmid":["30629082"]},"isi":1,"quality_controlled":"1","month":"01","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"8641","date_created":"2020-10-09T11:00:05Z","date_updated":"2020-10-09T11:00:05Z","checksum":"614c337d6424ccd3d48d1b1f9513510d","success":1,"file_name":"lmt_sftmtr_V8.pdf","access_level":"open_access","content_type":"application/pdf","file_size":5370762,"creator":"bkavcic"}],"_id":"5817","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Limiting shapes of confined lipid vesicles","ddc":["530"],"status":"public","intvolume":" 15","abstract":[{"text":"We theoretically study the shapes of lipid vesicles confined to a spherical cavity, elaborating a framework based on the so-called limiting shapes constructed from geometrically simple structural elements such as double-membrane walls and edges. Partly inspired by numerical results, the proposed non-compartmentalized and compartmentalized limiting shapes are arranged in the bilayer-couple phase diagram which is then compared to its free-vesicle counterpart. We also compute the area-difference-elasticity phase diagram of the limiting shapes and we use it to interpret shape transitions experimentally observed in vesicles confined within another vesicle. The limiting-shape framework may be generalized to theoretically investigate the structure of certain cell organelles such as the mitochondrion.","lang":"eng"}],"issue":"4","type":"journal_article","date_published":"2019-01-10T00:00:00Z","publication":"Soft Matter","citation":{"chicago":"Kavcic, Bor, A. Sakashita, H. Noguchi, and P. Ziherl. “Limiting Shapes of Confined Lipid Vesicles.” Soft Matter. Royal Society of Chemistry, 2019. https://doi.org/10.1039/c8sm01956h.","short":"B. Kavcic, A. Sakashita, H. Noguchi, P. Ziherl, Soft Matter 15 (2019) 602–614.","mla":"Kavcic, Bor, et al. “Limiting Shapes of Confined Lipid Vesicles.” Soft Matter, vol. 15, no. 4, Royal Society of Chemistry, 2019, pp. 602–14, doi:10.1039/c8sm01956h.","apa":"Kavcic, B., Sakashita, A., Noguchi, H., & Ziherl, P. (2019). Limiting shapes of confined lipid vesicles. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c8sm01956h","ieee":"B. Kavcic, A. Sakashita, H. Noguchi, and P. Ziherl, “Limiting shapes of confined lipid vesicles,” Soft Matter, vol. 15, no. 4. Royal Society of Chemistry, pp. 602–614, 2019.","ista":"Kavcic B, Sakashita A, Noguchi H, Ziherl P. 2019. Limiting shapes of confined lipid vesicles. Soft Matter. 15(4), 602–614.","ama":"Kavcic B, Sakashita A, Noguchi H, Ziherl P. Limiting shapes of confined lipid vesicles. Soft Matter. 2019;15(4):602-614. doi:10.1039/c8sm01956h"},"article_type":"original","page":"602-614","day":"10","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1"},{"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","article_type":"original","citation":{"ama":"Erbar M, Maas J, Wirth M. On the geometry of geodesics in discrete optimal transport. Calculus of Variations and Partial Differential Equations. 2019;58(1). doi:10.1007/s00526-018-1456-1","ista":"Erbar M, Maas J, Wirth M. 2019. On the geometry of geodesics in discrete optimal transport. Calculus of Variations and Partial Differential Equations. 58(1), 19.","apa":"Erbar, M., Maas, J., & Wirth, M. (2019). On the geometry of geodesics in discrete optimal transport. Calculus of Variations and Partial Differential Equations. Springer. https://doi.org/10.1007/s00526-018-1456-1","ieee":"M. Erbar, J. Maas, and M. Wirth, “On the geometry of geodesics in discrete optimal transport,” Calculus of Variations and Partial Differential Equations, vol. 58, no. 1. Springer, 2019.","mla":"Erbar, Matthias, et al. “On the Geometry of Geodesics in Discrete Optimal Transport.” Calculus of Variations and Partial Differential Equations, vol. 58, no. 1, 19, Springer, 2019, doi:10.1007/s00526-018-1456-1.","short":"M. Erbar, J. Maas, M. Wirth, Calculus of Variations and Partial Differential Equations 58 (2019).","chicago":"Erbar, Matthias, Jan Maas, and Melchior Wirth. “On the Geometry of Geodesics in Discrete Optimal Transport.” Calculus of Variations and Partial Differential Equations. Springer, 2019. https://doi.org/10.1007/s00526-018-1456-1."},"publication":"Calculus of Variations and Partial Differential Equations","date_published":"2019-02-01T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"We consider the space of probability measures on a discrete set X, endowed with a dynamical optimal transport metric. Given two probability measures supported in a subset Y⊆X, it is natural to ask whether they can be connected by a constant speed geodesic with support in Y at all times. Our main result answers this question affirmatively, under a suitable geometric condition on Y introduced in this paper. The proof relies on an extension result for subsolutions to discrete Hamilton-Jacobi equations, which is of independent interest."}],"intvolume":" 58","title":"On the geometry of geodesics in discrete optimal transport","ddc":["510"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"73","file":[{"date_updated":"2020-07-14T12:47:55Z","date_created":"2019-01-28T15:37:11Z","checksum":"ba05ac2d69de4c58d2cd338b63512798","relation":"main_file","file_id":"5895","file_size":645565,"content_type":"application/pdf","creator":"dernst","file_name":"2018_Calculus_Erbar.pdf","access_level":"open_access"}],"oa_version":"Published Version","publication_identifier":{"issn":["09442669"]},"month":"02","project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics"},{"_id":"260482E2-B435-11E9-9278-68D0E5697425","grant_number":" F06504","call_identifier":"FWF","name":"Taming Complexity in Partial Di erential Systems"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000452849400001"],"arxiv":["1805.06040"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00526-018-1456-1","article_number":"19","ec_funded":1,"file_date_updated":"2020-07-14T12:47:55Z","department":[{"_id":"JaMa"}],"publisher":"Springer","publication_status":"published","year":"2019","volume":58,"date_updated":"2023-09-13T09:12:35Z","date_created":"2018-12-11T11:44:29Z","author":[{"full_name":"Erbar, Matthias","last_name":"Erbar","first_name":"Matthias"},{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","first_name":"Jan","last_name":"Maas","full_name":"Maas, Jan"},{"last_name":"Wirth","first_name":"Melchior","full_name":"Wirth, Melchior"}]},{"scopus_import":1,"day":"01","article_type":"original","publication":"ACM Transactions on Algorithms","citation":{"ama":"Akitaya H, Fulek R, Tóth C. Recognizing weak embeddings of graphs. ACM Transactions on Algorithms. 2019;15(4). doi:10.1145/3344549","ieee":"H. Akitaya, R. Fulek, and C. Tóth, “Recognizing weak embeddings of graphs,” ACM Transactions on Algorithms, vol. 15, no. 4. ACM, 2019.","apa":"Akitaya, H., Fulek, R., & Tóth, C. (2019). Recognizing weak embeddings of graphs. ACM Transactions on Algorithms. ACM. https://doi.org/10.1145/3344549","ista":"Akitaya H, Fulek R, Tóth C. 2019. Recognizing weak embeddings of graphs. ACM Transactions on Algorithms. 15(4), 50.","short":"H. Akitaya, R. Fulek, C. Tóth, ACM Transactions on Algorithms 15 (2019).","mla":"Akitaya, Hugo, et al. “Recognizing Weak Embeddings of Graphs.” ACM Transactions on Algorithms, vol. 15, no. 4, 50, ACM, 2019, doi:10.1145/3344549.","chicago":"Akitaya, Hugo, Radoslav Fulek, and Csaba Tóth. “Recognizing Weak Embeddings of Graphs.” ACM Transactions on Algorithms. ACM, 2019. https://doi.org/10.1145/3344549."},"date_published":"2019-10-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We present an efficient algorithm for a problem in the interface between clustering and graph embeddings. An embedding ϕ : G → M of a graph G into a 2-manifold M maps the vertices in V(G) to distinct points and the edges in E(G) to interior-disjoint Jordan arcs between the corresponding vertices. In applications in clustering, cartography, and visualization, nearby vertices and edges are often bundled to the same point or overlapping arcs due to data compression or low resolution. This raises the computational problem of deciding whether a given map ϕ : G → M comes from an embedding. A map ϕ : G → M is a weak embedding if it can be perturbed into an embedding ψ ϵ : G → M with ‖ ϕ − ψ ϵ ‖ < ϵ for every ϵ > 0, where ‖.‖ is the unform norm.\r\nA polynomial-time algorithm for recognizing weak embeddings has recently been found by Fulek and Kynčl. It reduces the problem to solving a system of linear equations over Z2. It runs in O(n2ω)≤ O(n4.75) time, where ω ∈ [2,2.373) is the matrix multiplication exponent and n is the number of vertices and edges of G. We improve the running time to O(n log n). Our algorithm is also conceptually simpler: We perform a sequence of local operations that gradually “untangles” the image ϕ(G) into an embedding ψ(G) or reports that ϕ is not a weak embedding. It combines local constraints on the orientation of subgraphs directly, thereby eliminating the need for solving large systems of linear equations.\r\n"}],"issue":"4","title":"Recognizing weak embeddings of graphs","status":"public","intvolume":" 15","_id":"6982","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","month":"10","quality_controlled":"1","project":[{"name":"Eliminating intersections in drawings of graphs","call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425","grant_number":"M02281"}],"oa":1,"external_id":{"arxiv":["1709.09209"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.09209"}],"language":[{"iso":"eng"}],"doi":"10.1145/3344549","article_number":"50","publication_status":"published","publisher":"ACM","department":[{"_id":"UlWa"}],"year":"2019","date_created":"2019-11-04T15:45:17Z","date_updated":"2023-09-15T12:19:31Z","volume":15,"author":[{"last_name":"Akitaya","first_name":"Hugo","full_name":"Akitaya, Hugo"},{"full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","first_name":"Radoslav"},{"full_name":"Tóth, Csaba","last_name":"Tóth","first_name":"Csaba"}],"related_material":{"record":[{"id":"309","status":"public","relation":"earlier_version"}]}},{"file_date_updated":"2020-07-14T12:47:43Z","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Institute of Science and Technology Austria","year":"2019","date_updated":"2023-09-19T09:30:43Z","date_created":"2019-09-22T14:08:44Z","author":[{"full_name":"Giacobbe, Mirco","first_name":"Mirco","last_name":"Giacobbe","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8180-0904"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"631"},{"relation":"part_of_dissertation","status":"public","id":"647"},{"id":"140","relation":"part_of_dissertation","status":"public"}]},"month":"09","publication_identifier":{"eissn":["2663-337X"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"supervisor":[{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:6894","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Hybrid automata combine finite automata and dynamical systems, and model the interaction of digital with physical systems. Formal analysis that can guarantee the safety of all behaviors or rigorously witness failures, while unsolvable in general, has been tackled algorithmically using, e.g., abstraction, bounded model-checking, assisted theorem proving.\r\nNevertheless, very few methods have addressed the time-unbounded reachability analysis of hybrid automata and, for current sound and automatic tools, scalability remains critical. We develop methods for the polyhedral abstraction of hybrid automata, which construct coarse overapproximations and tightens them incrementally, in a CEGAR fashion. We use template polyhedra, i.e., polyhedra whose facets are normal to a given set of directions.\r\nWhile, previously, directions were given by the user, we introduce (1) the first method\r\nfor computing template directions from spurious counterexamples, so as to generalize and\r\neliminate them. The method applies naturally to convex hybrid automata, i.e., hybrid\r\nautomata with (possibly non-linear) convex constraints on derivatives only, while for linear\r\nODE requires further abstraction. Specifically, we introduce (2) the conic abstractions,\r\nwhich, partitioning the state space into appropriate (possibly non-uniform) cones, divide\r\ncurvy trajectories into relatively straight sections, suitable for polyhedral abstractions.\r\nFinally, we introduce (3) space-time interpolation, which, combining interval arithmetic\r\nand template refinement, computes appropriate (possibly non-uniform) time partitioning\r\nand template directions along spurious trajectories, so as to eliminate them.\r\nWe obtain sound and automatic methods for the reachability analysis over dense\r\nand unbounded time of convex hybrid automata and hybrid automata with linear ODE.\r\nWe build prototype tools and compare—favorably—our methods against the respective\r\nstate-of-the-art tools, on several benchmarks.","lang":"eng"}],"ddc":["000"],"status":"public","title":"Automatic time-unbounded reachability analysis of hybrid systems","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6894","oa_version":"Published Version","file":[{"checksum":"773beaf4a85dc2acc2c12b578fbe1965","date_created":"2019-09-27T14:15:05Z","date_updated":"2020-07-14T12:47:43Z","file_id":"6916","relation":"main_file","creator":"mgiacobbe","content_type":"application/pdf","file_size":4100685,"access_level":"open_access","file_name":"giacobbe_thesis.pdf"},{"relation":"source_file","file_id":"6917","checksum":"97f1c3da71feefd27e6e625d32b4c75b","date_created":"2019-09-27T14:22:04Z","date_updated":"2020-07-14T12:47:43Z","access_level":"closed","file_name":"giacobbe_thesis_src.tar.gz","file_size":7959732,"content_type":"application/gzip","creator":"mgiacobbe"}],"day":"30","has_accepted_license":"1","article_processing_charge":"No","page":"132","citation":{"ista":"Giacobbe M. 2019. Automatic time-unbounded reachability analysis of hybrid systems. Institute of Science and Technology Austria.","ieee":"M. Giacobbe, “Automatic time-unbounded reachability analysis of hybrid systems,” Institute of Science and Technology Austria, 2019.","apa":"Giacobbe, M. (2019). Automatic time-unbounded reachability analysis of hybrid systems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6894","ama":"Giacobbe M. Automatic time-unbounded reachability analysis of hybrid systems. 2019. doi:10.15479/AT:ISTA:6894","chicago":"Giacobbe, Mirco. “Automatic Time-Unbounded Reachability Analysis of Hybrid Systems.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6894.","mla":"Giacobbe, Mirco. Automatic Time-Unbounded Reachability Analysis of Hybrid Systems. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6894.","short":"M. Giacobbe, Automatic Time-Unbounded Reachability Analysis of Hybrid Systems, Institute of Science and Technology Austria, 2019."},"date_published":"2019-09-30T00:00:00Z"},{"date_published":"2019-01-09T00:00:00Z","doi":"10.5061/dryad.2kb6fh4","oa":1,"citation":{"ama":"Barton NH. Data from: The consequences of an introgression event. 2019. doi:10.5061/dryad.2kb6fh4","ieee":"N. H. Barton, “Data from: The consequences of an introgression event.” Dryad, 2019.","apa":"Barton, N. H. (2019). Data from: The consequences of an introgression event. Dryad. https://doi.org/10.5061/dryad.2kb6fh4","ista":"Barton NH. 2019. Data from: The consequences of an introgression event, Dryad, 10.5061/dryad.2kb6fh4.","short":"N.H. Barton, (2019).","mla":"Barton, Nicholas H. Data from: The Consequences of an Introgression Event. Dryad, 2019, doi:10.5061/dryad.2kb6fh4.","chicago":"Barton, Nicholas H. “Data from: The Consequences of an Introgression Event.” Dryad, 2019. https://doi.org/10.5061/dryad.2kb6fh4."},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.2kb6fh4","open_access":"1"}],"article_processing_charge":"No","month":"01","day":"09","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"40"}]},"author":[{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"oa_version":"Published Version","date_created":"2021-08-06T12:03:50Z","date_updated":"2023-09-19T10:06:07Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9805","year":"2019","publisher":"Dryad","department":[{"_id":"NiBa"}],"title":"Data from: The consequences of an introgression event","status":"public","abstract":[{"text":"The spread of adaptive alleles is fundamental to evolution, and in theory, this process is well‐understood. However, only rarely can we follow this process—whether it originates from the spread of a new mutation, or by introgression from another population. In this issue of Molecular Ecology, Hanemaaijer et al. (2018) report on a 25‐year long study of the mosquitoes Anopheles gambiae (Figure 1) and Anopheles coluzzi in Mali, based on genotypes at 15 single‐nucleotide polymorphism (SNP). The species are usually reproductively isolated from each other, but in 2002 and 2006, bursts of hybridization were observed, when F1 hybrids became abundant. Alleles backcrossed from A. gambiae into A. coluzzi, but after the first event, these declined over the following years. In contrast, after 2006, an insecticide resistance allele that had established in A. gambiae spread into A. coluzzi, and rose to high frequency there, over 6 years (~75 generations). Whole genome sequences of 74 individuals showed that A. gambiae SNP from across the genome had become common in the A. coluzzi population, but that most of these were clustered in 34 genes around the resistance locus. A new set of SNP from 25 of these genes were assayed over time; over the 4 years since near‐fixation of the resistance allele; some remained common, whereas others declined. What do these patterns tell us about this introgression event?","lang":"eng"}],"type":"research_data_reference"},{"date_published":"2019-01-09T00:00:00Z","article_type":"original","page":"238-255","publication":"Journal of Neuroscience","citation":{"mla":"Trébuchet, Guillaume, et al. “The Repo Homeodomain Transcription Factor Suppresses Hematopoiesis in Drosophila and Preserves the Glial Fate.” Journal of Neuroscience, vol. 39, no. 2, Society for Neuroscience, 2019, pp. 238–55, doi:10.1523/JNEUROSCI.1059-18.2018.","short":"G. Trébuchet, P.B. Cattenoz, J. Zsámboki, D. Mazaud, D.E. Siekhaus, M. Fanto, A. Giangrande, Journal of Neuroscience 39 (2019) 238–255.","chicago":"Trébuchet, Guillaume, Pierre B Cattenoz, János Zsámboki, David Mazaud, Daria E Siekhaus, Manolis Fanto, and Angela Giangrande. “The Repo Homeodomain Transcription Factor Suppresses Hematopoiesis in Drosophila and Preserves the Glial Fate.” Journal of Neuroscience. Society for Neuroscience, 2019. https://doi.org/10.1523/JNEUROSCI.1059-18.2018.","ama":"Trébuchet G, Cattenoz PB, Zsámboki J, et al. The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate. Journal of Neuroscience. 2019;39(2):238-255. doi:10.1523/JNEUROSCI.1059-18.2018","ista":"Trébuchet G, Cattenoz PB, Zsámboki J, Mazaud D, Siekhaus DE, Fanto M, Giangrande A. 2019. The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate. Journal of Neuroscience. 39(2), 238–255.","ieee":"G. Trébuchet et al., “The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate,” Journal of Neuroscience, vol. 39, no. 2. Society for Neuroscience, pp. 238–255, 2019.","apa":"Trébuchet, G., Cattenoz, P. B., Zsámboki, J., Mazaud, D., Siekhaus, D. E., Fanto, M., & Giangrande, A. (2019). The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1059-18.2018"},"day":"09","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","file":[{"relation":"main_file","file_id":"8596","date_created":"2020-10-02T09:33:28Z","date_updated":"2020-10-02T09:33:28Z","checksum":"8f6925eb4cd1e8747d8ea25929c68de6","success":1,"file_name":"2019_JournNeuroscience_Trebuchet.pdf","access_level":"open_access","file_size":9455414,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","title":"The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate","status":"public","ddc":["570"],"intvolume":" 39","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8","abstract":[{"lang":"eng","text":"Despite their different origins, Drosophila glia and hemocytes are related cell populations that provide an immune function. Drosophila hemocytes patrol the body cavity and act as macrophages outside the nervous system whereas glia originate from the neuroepithelium and provide the scavenger population of the nervous system. Drosophila glia are hence the functional orthologs of vertebrate microglia, even though the latter are cells of immune origin that subsequently move into the brain during development. Interestingly, the Drosophila immune cells within (glia) and outside the nervous system (hemocytes) require the same transcription factor Glide/Gcm for their development. This raises the issue of how do glia specifically differentiate in the nervous system and hemocytes in the procephalic mesoderm. The Repo homeodomain transcription factor and pan-glial direct target of Glide/Gcm is known to ensure glial terminal differentiation. Here we show that Repo also takes center stage in the process that discriminates between glia and hemocytes. First, Repo expression is repressed in the hemocyte anlagen by mesoderm-specific factors. Second, Repo ectopic activation in the procephalic mesoderm is sufficient to repress the expression of hemocyte-specific genes. Third, the lack of Repo triggers the expression of hemocyte markers in glia. Thus, a complex network of tissue-specific cues biases the potential of Glide/Gcm. These data allow us to revise the concept of fate determinants and help us understand the bases of cell specification. Both sexes were analyzed.SIGNIFICANCE STATEMENTDistinct cell types often require the same pioneer transcription factor, raising the issue of how does one factor trigger different fates. In Drosophila, glia and hemocytes provide a scavenger activity within and outside the nervous system, respectively. While they both require the Glide/Gcm transcription factor, glia originate from the ectoderm, hemocytes from the mesoderm. Here we show that tissue-specific factors inhibit the gliogenic potential of Glide/Gcm in the mesoderm by repressing the expression of the homeodomain protein Repo, a major glial-specific target of Glide/Gcm. Repo expression in turn inhibits the expression of hemocyte-specific genes in the nervous system. These cell-specific networks secure the establishment of the glial fate only in the nervous system and allow cell diversification."}],"issue":"2","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1523/JNEUROSCI.1059-18.2018","quality_controlled":"1","isi":1,"project":[{"grant_number":"334077","_id":"2536F660-B435-11E9-9278-68D0E5697425","name":"Investigating the role of transporters in invasive migration through junctions","call_identifier":"FP7"}],"oa":1,"external_id":{"pmid":["30504274"],"isi":["000455189900006"]},"month":"01","date_updated":"2023-09-19T10:10:55Z","date_created":"2018-12-11T11:44:07Z","volume":39,"author":[{"full_name":"Trébuchet, Guillaume","first_name":"Guillaume","last_name":"Trébuchet"},{"first_name":"Pierre B","last_name":"Cattenoz","full_name":"Cattenoz, Pierre B"},{"last_name":"Zsámboki","first_name":"János","full_name":"Zsámboki, János"},{"last_name":"Mazaud","first_name":"David","full_name":"Mazaud, David"},{"first_name":"Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E"},{"full_name":"Fanto, Manolis","first_name":"Manolis","last_name":"Fanto"},{"first_name":"Angela","last_name":"Giangrande","full_name":"Giangrande, Angela"}],"publication_status":"published","department":[{"_id":"DaSi"}],"publisher":"Society for Neuroscience","acknowledgement":"This work was supported by INSERM, CNRS, UDS, Ligue Régionale contre le Cancer, Hôpital de Strasbourg, Association pour la Recherche sur le Cancer (ARC) and Agence Nationale de la Recherche (ANR) grants. P.B.C. was funded by the ANR and by the ARSEP (Fondation pour l'Aide à la Recherche sur la Sclérose en Plaques), and G.T. by governmental and ARC fellowships. This work was also supported by grants from the Ataxia UK (2491) and the NC3R (NC/L000199/1) awarded to M.F. The Institut de Génétique et de Biologie Moléculaire et Cellulaire was also supported by a French state fund through the ANR labex. D.E.S. was funded by Marie Curie Grant CIG 334077/IRTIM. We thank B. Altenhein, K. Brückner, M. Crozatier, L. Waltzer, M. Logan, E. Kurant, R. Reuter, E. Kurucz, J.L Dimarcq, J. Hoffmann, C. Goodman, the DHSB, and the BDSC for reagents and flies. We also thank all of the laboratory members for comments on the manuscript; C. Diebold, C. Delaporte, M. Pezze, the fly, and imaging and antibody facilities for technical assistance; and D. Dembele for help with statistics. In addition, we thank Alison Brewer for help with Luciferase assays.","year":"2019","pmid":1,"file_date_updated":"2020-10-02T09:33:28Z","ec_funded":1,"publist_id":"8048"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5","ddc":["510"],"title":"The wonderful compactification for quantum groups","status":"public","intvolume":" 99","oa_version":"Published Version","file":[{"date_created":"2020-01-07T13:31:53Z","date_updated":"2020-07-14T12:46:35Z","checksum":"1be56239b2cd740a0e9a084f773c22f6","file_id":"7238","relation":"main_file","creator":"kschuh","content_type":"application/pdf","file_size":431754,"file_name":"2019_Wiley_Ganev.pdf","access_level":"open_access"}],"type":"journal_article","abstract":[{"lang":"eng","text":"In this paper, we introduce a quantum version of the wonderful compactification of a group as a certain noncommutative projective scheme. Our approach stems from the fact that the wonderful compactification encodes the asymptotics of matrix coefficients, and from its realization as a GIT quotient of the Vinberg semigroup. In order to define the wonderful compactification for a quantum group, we adopt a generalized formalism of Proj categories in the spirit of Artin and Zhang. Key to our construction is a quantum version of the Vinberg semigroup, which we define as a q-deformation of a certain Rees algebra, compatible with a standard Poisson structure. Furthermore, we discuss quantum analogues of the stratification of the wonderful compactification by orbits for a certain group action, and provide explicit computations in the case of SL2."}],"issue":"3","publication":"Journal of the London Mathematical Society","citation":{"ama":"Ganev IV. The wonderful compactification for quantum groups. Journal of the London Mathematical Society. 2019;99(3):778-806. doi:10.1112/jlms.12193","ieee":"I. V. Ganev, “The wonderful compactification for quantum groups,” Journal of the London Mathematical Society, vol. 99, no. 3. Wiley, pp. 778–806, 2019.","apa":"Ganev, I. V. (2019). The wonderful compactification for quantum groups. Journal of the London Mathematical Society. Wiley. https://doi.org/10.1112/jlms.12193","ista":"Ganev IV. 2019. The wonderful compactification for quantum groups. Journal of the London Mathematical Society. 99(3), 778–806.","short":"I.V. Ganev, Journal of the London Mathematical Society 99 (2019) 778–806.","mla":"Ganev, Iordan V. “The Wonderful Compactification for Quantum Groups.” Journal of the London Mathematical Society, vol. 99, no. 3, Wiley, 2019, pp. 778–806, doi:10.1112/jlms.12193.","chicago":"Ganev, Iordan V. “The Wonderful Compactification for Quantum Groups.” Journal of the London Mathematical Society. Wiley, 2019. https://doi.org/10.1112/jlms.12193."},"page":"778-806","date_published":"2019-06-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","year":"2019","publication_status":"published","department":[{"_id":"TaHa"}],"publisher":"Wiley","author":[{"full_name":"Ganev, Iordan V","last_name":"Ganev","first_name":"Iordan V","id":"447491B8-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:44:06Z","date_updated":"2023-09-19T10:13:08Z","volume":99,"file_date_updated":"2020-07-14T12:46:35Z","publist_id":"8052","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000470025900008"]},"isi":1,"quality_controlled":"1","doi":"10.1112/jlms.12193","language":[{"iso":"eng"}],"month":"06"},{"file_date_updated":"2020-07-14T12:47:51Z","year":"2019","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JiFr"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1346"},{"status":"public","relation":"part_of_dissertation","id":"6377"},{"id":"449","relation":"part_of_dissertation","status":"public"}]},"author":[{"full_name":"Vasileva, Mina K","first_name":"Mina K","last_name":"Vasileva","id":"3407EB18-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-19T10:39:33Z","date_created":"2019-12-11T21:24:39Z","publication_identifier":{"eissn":["2663-337X"]},"month":"12","oa":1,"doi":"10.15479/AT:ISTA:7172","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"The development and growth of Arabidopsis thaliana is regulated by a combination of genetic programing and also by the environmental influences. An important role in these processes play the phytohormones and among them, auxin is crucial as it controls many important functions. It is transported through the whole plant body by creating local and temporal concentration maxima and minima, which have an impact on the cell status, tissue and organ identity. Auxin has the property to undergo a directional and finely regulated cell-to-cell transport, which is enabled by the transport proteins, localized on the plasma membrane. An important role in this process have the PIN auxin efflux proteins, which have an asymmetric/polar subcellular localization and determine the directionality of the auxin transport. During the last years, there were significant advances in understanding how the trafficking molecular machineries function, including studies on molecular interactions, function, subcellular localization and intracellular distribution. However, there is still a lack of detailed characterization on the steps of endocytosis, exocytosis, endocytic recycling and degradation. Due to this fact, I focused on the identification of novel trafficking factors and better characterization of the intracellular trafficking pathways. My PhD thesis consists of an introductory chapter, three experimental chapters, a chapter containing general discussion, conclusions and perspectives and also an appendix chapter with published collaborative papers.\r\nThe first chapter is separated in two different parts: I start by a general introduction to auxin biology and then I introduce the trafficking pathways in the model plant Arabidopsis thaliana. Then, I explain also the phosphorylation-signals for polar targeting and also the roles of the phytohormone strigolactone.\r\nThe second chapter includes the characterization of bar1/sacsin mutant, which was identified in a forward genetic screen for novel trafficking components in Arabidopsis thaliana, where by the implementation of an EMS-treated pPIN1::PIN1-GFP marker line and by using the established inhibitor of ARF-GEFs, Brefeldin A (BFA) as a tool to study trafficking processes, we identified a novel factor, which is mediating the adaptation of the plant cell to ARF-GEF inhibition. The mutation is in a previously uncharacterized gene, encoding a very big protein that we, based on its homologies, called SACSIN with domains suggesting roles as a molecular chaperon or as a component of the ubiquitin-proteasome system. Our physiology and imaging studies revealed that SACSIN is a crucial plant cell component of the adaptation to the ARF-GEF inhibition.\r\nThe third chapter includes six subchapters, where I focus on the role of the phytohormone strigolactone, which interferes with auxin feedback on PIN internalization. Strigolactone moderates the polar auxin transport by increasing the internalization of the PIN auxin efflux carriers, which reduces the canalization related growth responses. In addition, I also studied the role of phosphorylation in the strigolactone regulation of auxin feedback on PIN internalization. In this chapter I also present my results on the MAX2-dependence of strigolactone-mediated root growth inhibition and I also share my results on the auxin metabolomics profiling after application of GR24.\r\nIn the fourth chapter I studied the effect of two small molecules ES-9 and ES9-17, which were identified from a collection of small molecules with the property to impair the clathrin-mediated endocytosis.\r\nIn the fifth chapter, I discuss all my observations and experimental findings and suggest alternative hypothesis to interpret my results.\r\nIn the appendix there are three collaborative published projects. In the first, I participated in the characterization of the role of ES9 as a small molecule, which is inhibitor of clathrin- mediated endocytosis in different model organisms. In the second paper, I contributed to the characterization of another small molecule ES9-17, which is a non-protonophoric analog of ES9 and also impairs the clathrin-mediated endocytosis not only in plant cells, but also in mammalian HeLa cells. Last but not least, I also attach another paper, where I tried to establish the grafting method as a technique in our lab to study canalization related processes."}],"_id":"7172","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana","ddc":["570"],"oa_version":"Published Version","file":[{"relation":"source_file","file_id":"7175","checksum":"ef981c1a3b1d9da0edcbedcff4970d37","date_updated":"2020-07-14T12:47:51Z","date_created":"2019-12-12T09:32:36Z","access_level":"closed","file_name":"Thesis_Mina_final_upload_7.docx","file_size":20454014,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"mvasilev"},{"file_name":"Thesis_Mina_final_upload_7.pdf","access_level":"open_access","creator":"mvasilev","file_size":11565025,"content_type":"application/pdf","file_id":"7176","relation":"main_file","date_updated":"2020-07-14T12:47:51Z","date_created":"2019-12-12T09:33:10Z","checksum":"3882c4585e46c9cfb486e4225cad54ab"}],"article_processing_charge":"No","has_accepted_license":"1","day":"12","citation":{"apa":"Vasileva, M. K. (2019). Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7172","ieee":"M. K. Vasileva, “Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2019.","ista":"Vasileva MK. 2019. Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria.","ama":"Vasileva MK. Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana. 2019. doi:10.15479/AT:ISTA:7172","chicago":"Vasileva, Mina K. “Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7172.","short":"M.K. Vasileva, Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2019.","mla":"Vasileva, Mina K. Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7172."},"page":"192","date_published":"2019-12-12T00:00:00Z"},{"file_date_updated":"2020-07-14T12:47:19Z","article_number":"e0212699","author":[{"id":"3384113A-F248-11E8-B48F-1D18A9856A87","last_name":"Goudarzi","first_name":"Mohammad","full_name":"Goudarzi, Mohammad"},{"first_name":"Aleix","last_name":"Boquet-Pujadas","full_name":"Boquet-Pujadas, Aleix"},{"first_name":"Jean Christophe","last_name":"Olivo-Marin","full_name":"Olivo-Marin, Jean Christophe"},{"first_name":"Erez","last_name":"Raz","full_name":"Raz, Erez"}],"volume":14,"date_updated":"2023-09-19T14:46:47Z","date_created":"2019-03-10T22:59:21Z","year":"2019","publisher":"Public Library of Science","department":[{"_id":"Bio"}],"publication_status":"published","month":"02","doi":"10.1371/journal.pone.0212699","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000459712100022"]},"isi":1,"quality_controlled":"1","issue":"2","abstract":[{"text":"Blebs are cellular protrusions observed in migrating cells and in cells undergoing spreading, cytokinesis, and apoptosis. Here we investigate the flow of cytoplasm during bleb formation and the concurrent changes in cell volume using zebrafish primordial germ cells (PGCs) as an in vivo model. We show that bleb inflation occurs concomitantly with cytoplasmic inflow into it and that during this process the total cell volume does not change. We thus show that bleb formation in primordial germ cells results primarily from redistribution of material within the cell rather than being driven by flow of water from an external source.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"creator":"dernst","file_size":2967731,"content_type":"application/pdf","file_name":"2019_PLoSOne_Goudarzi.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:19Z","date_created":"2019-03-11T16:09:23Z","checksum":"b885de050ed4bb3c86f706487a47197f","file_id":"6096","relation":"main_file"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6093","intvolume":" 14","status":"public","ddc":["570"],"title":"Fluid dynamics during bleb formation in migrating cells in vivo","article_processing_charge":"No","has_accepted_license":"1","day":"26","scopus_import":"1","date_published":"2019-02-26T00:00:00Z","citation":{"ama":"Goudarzi M, Boquet-Pujadas A, Olivo-Marin JC, Raz E. Fluid dynamics during bleb formation in migrating cells in vivo. PLOS ONE. 2019;14(2). doi:10.1371/journal.pone.0212699","apa":"Goudarzi, M., Boquet-Pujadas, A., Olivo-Marin, J. C., & Raz, E. (2019). Fluid dynamics during bleb formation in migrating cells in vivo. PLOS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0212699","ieee":"M. Goudarzi, A. Boquet-Pujadas, J. C. Olivo-Marin, and E. Raz, “Fluid dynamics during bleb formation in migrating cells in vivo,” PLOS ONE, vol. 14, no. 2. Public Library of Science, 2019.","ista":"Goudarzi M, Boquet-Pujadas A, Olivo-Marin JC, Raz E. 2019. Fluid dynamics during bleb formation in migrating cells in vivo. PLOS ONE. 14(2), e0212699.","short":"M. Goudarzi, A. Boquet-Pujadas, J.C. Olivo-Marin, E. Raz, PLOS ONE 14 (2019).","mla":"Goudarzi, Mohammad, et al. “Fluid Dynamics during Bleb Formation in Migrating Cells in Vivo.” PLOS ONE, vol. 14, no. 2, e0212699, Public Library of Science, 2019, doi:10.1371/journal.pone.0212699.","chicago":"Goudarzi, Mohammad, Aleix Boquet-Pujadas, Jean Christophe Olivo-Marin, and Erez Raz. “Fluid Dynamics during Bleb Formation in Migrating Cells in Vivo.” PLOS ONE. Public Library of Science, 2019. https://doi.org/10.1371/journal.pone.0212699."},"publication":"PLOS ONE"},{"date_published":"2019-05-23T00:00:00Z","citation":{"short":"S.A. Cepeda Humerez, Estimating Information Flow in Single Cells, Institute of Science and Technology Austria, 2019.","mla":"Cepeda Humerez, Sarah A. Estimating Information Flow in Single Cells. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6473.","chicago":"Cepeda Humerez, Sarah A. “Estimating Information Flow in Single Cells.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6473.","ama":"Cepeda Humerez SA. Estimating information flow in single cells. 2019. doi:10.15479/AT:ISTA:6473","apa":"Cepeda Humerez, S. A. (2019). Estimating information flow in single cells. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6473","ieee":"S. A. Cepeda Humerez, “Estimating information flow in single cells,” Institute of Science and Technology Austria, 2019.","ista":"Cepeda Humerez SA. 2019. Estimating information flow in single cells. Institute of Science and Technology Austria."},"page":"135","has_accepted_license":"1","article_processing_charge":"No","day":"23","keyword":["Information estimation","Time-series","data analysis"],"oa_version":"Published Version","file":[{"date_created":"2019-05-23T11:18:16Z","date_updated":"2020-07-14T12:47:31Z","checksum":"75f9184c1346e10a5de5f9cc7338309a","relation":"source_file","file_id":"6480","file_size":23937464,"content_type":"application/zip","creator":"scepeda","file_name":"Thesis_Cepeda.zip","access_level":"closed"},{"date_created":"2019-05-23T11:18:13Z","date_updated":"2020-07-14T12:47:31Z","checksum":"afdc0633ddbd71d5b13550d7fb4f4454","file_id":"6481","relation":"main_file","creator":"scepeda","file_size":16646985,"content_type":"application/pdf","file_name":"CepedaThesis.pdf","access_level":"open_access"}],"_id":"6473","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["004"],"title":"Estimating information flow in single cells","abstract":[{"lang":"eng","text":"Single cells are constantly interacting with their environment and each other, more importantly, the accurate perception of environmental cues is crucial for growth, survival, and reproduction. This communication between cells and their environment can be formalized in mathematical terms and be quantified as the information flow between them, as prescribed by information theory. \r\nThe recent availability of real–time dynamical patterns of signaling molecules in single cells has allowed us to identify encoding about the identity of the environment in the time–series. However, efficient estimation of the information transmitted by these signals has been a data–analysis challenge due to the high dimensionality of the trajectories and the limited number of samples. In the first part of this thesis, we develop and evaluate decoding–based estimation methods to lower bound the mutual information and derive model–based precise information estimates for biological reaction networks governed by the chemical master equation. This is followed by applying the decoding-based methods to study the intracellular representation of extracellular changes in budding yeast, by observing the transient dynamics of nuclear translocation of 10 transcription factors in response to 3 stress conditions. Additionally, we apply these estimators to previously published data on ERK and Ca2+ signaling and yeast stress response. We argue that this single cell decoding-based measure of information provides an unbiased, quantitative and interpretable measure for the fidelity of biological signaling processes. \r\nFinally, in the last section, we deal with gene regulation which is primarily controlled by transcription factors (TFs) that bind to the DNA to activate gene expression. The possibility that non-cognate TFs activate transcription diminishes the accuracy of regulation with potentially disastrous effects for the cell. This ’crosstalk’ acts as a previously unexplored source of noise in biochemical networks and puts a strong constraint on their performance. To mitigate erroneous initiation we propose an out of equilibrium scheme that implements kinetic proofreading. We show that such architectures are favored over their equilibrium counterparts for complex organisms despite introducing noise in gene expression. "}],"type":"dissertation","alternative_title":["ISTA Thesis"],"doi":"10.15479/AT:ISTA:6473","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Tkačik, Gašper","first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"}],"degree_awarded":"PhD","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"05","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1576"},{"relation":"dissertation_contains","status":"public","id":"6900"},{"id":"281","relation":"dissertation_contains","status":"public"},{"id":"2016","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Cepeda Humerez, Sarah A","first_name":"Sarah A","last_name":"Cepeda Humerez","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2019-05-21T00:11:23Z","date_updated":"2023-09-19T15:13:26Z","year":"2019","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"}],"publication_status":"published","file_date_updated":"2020-07-14T12:47:31Z"},{"page":"189","citation":{"apa":"Prizak, R. (2019). Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th6071","ieee":"R. Prizak, “Coevolution of transcription factors and their binding sites in sequence space,” Institute of Science and Technology Austria, 2019.","ista":"Prizak R. 2019. Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria.","ama":"Prizak R. Coevolution of transcription factors and their binding sites in sequence space. 2019. doi:10.15479/at:ista:th6071","chicago":"Prizak, Roshan. “Coevolution of Transcription Factors and Their Binding Sites in Sequence Space.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:th6071.","short":"R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in Sequence Space, Institute of Science and Technology Austria, 2019.","mla":"Prizak, Roshan. Coevolution of Transcription Factors and Their Binding Sites in Sequence Space. Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:th6071."},"date_published":"2019-03-11T00:00:00Z","day":"11","article_processing_charge":"No","has_accepted_license":"1","ddc":["576"],"status":"public","title":"Coevolution of transcription factors and their binding sites in sequence space","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6071","oa_version":"Published Version","file":[{"creator":"rprizak","file_size":20995465,"content_type":"application/pdf","access_level":"open_access","file_name":"Thesis_final_PDFA_RoshanPrizak.pdf","checksum":"e60a72de35d270b31f1a23d50f224ec0","date_updated":"2020-07-14T12:47:18Z","date_created":"2019-03-06T16:05:07Z","file_id":"6072","relation":"main_file"},{"access_level":"closed","file_name":"thesis_v2_merge.zip","content_type":"application/zip","file_size":85705272,"creator":"rprizak","relation":"source_file","file_id":"6073","title":"Latex files","checksum":"67c2630333d05ebafef5f018863a8465","date_created":"2019-03-06T16:09:39Z","date_updated":"2020-07-14T12:47:18Z"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Transcription factors, by binding to specific sequences on the DNA, control the precise spatio-temporal expression of genes inside a cell. However, this specificity is limited, leading to frequent incorrect binding of transcription factors that might have deleterious consequences on the cell. By constructing a biophysical model of TF-DNA binding in the context of gene regulation, I will first explore how regulatory constraints can strongly shape the distribution of a population in sequence space. Then, by directly linking this to a picture of multiple types of transcription factors performing their functions simultaneously inside the cell, I will explore the extent of regulatory crosstalk -- incorrect binding interactions between transcription factors and binding sites that lead to erroneous regulatory states -- and understand the constraints this places on the design of regulatory systems. I will then develop a generic theoretical framework to investigate the coevolution of multiple transcription factors and multiple binding sites, in the context of a gene regulatory network that performs a certain function. As a particular tractable version of this problem, I will consider the evolution of two transcription factors when they transmit upstream signals to downstream target genes. Specifically, I will describe the evolutionary steady states and the evolutionary pathways involved, along with their timescales, of a system that initially undergoes a transcription factor duplication event. To connect this important theoretical model to the prominent biological event of transcription factor duplication giving rise to paralogous families, I will then describe a bioinformatics analysis of C2H2 Zn-finger transcription factors, a major family in humans, and focus on the patterns of evolution that paralogs have undergone in their various protein domains in the recent past. "}],"project":[{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"oa":1,"supervisor":[{"last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:th6071","month":"03","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","year":"2019","date_updated":"2023-09-22T10:00:48Z","date_created":"2019-03-06T16:16:10Z","author":[{"id":"4456104E-F248-11E8-B48F-1D18A9856A87","first_name":"Roshan","last_name":"Prizak","full_name":"Prizak, Roshan"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1358"},{"id":"955","status":"public","relation":"part_of_dissertation"}]},"file_date_updated":"2020-07-14T12:47:18Z"},{"date_published":"2019-05-20T00:00:00Z","publication":"Documenta Mathematica","citation":{"ama":"Srivastava TK. On derived equivalences of k3 surfaces in positive characteristic. Documenta Mathematica. 2019;24:1135-1177. doi:10.25537/dm.2019v24.1135-1177","ieee":"T. K. Srivastava, “On derived equivalences of k3 surfaces in positive characteristic,” Documenta Mathematica, vol. 24. EMS Press, pp. 1135–1177, 2019.","apa":"Srivastava, T. K. (2019). On derived equivalences of k3 surfaces in positive characteristic. Documenta Mathematica. EMS Press. https://doi.org/10.25537/dm.2019v24.1135-1177","ista":"Srivastava TK. 2019. On derived equivalences of k3 surfaces in positive characteristic. Documenta Mathematica. 24, 1135–1177.","short":"T.K. Srivastava, Documenta Mathematica 24 (2019) 1135–1177.","mla":"Srivastava, Tanya K. “On Derived Equivalences of K3 Surfaces in Positive Characteristic.” Documenta Mathematica, vol. 24, EMS Press, 2019, pp. 1135–77, doi:10.25537/dm.2019v24.1135-1177.","chicago":"Srivastava, Tanya K. “On Derived Equivalences of K3 Surfaces in Positive Characteristic.” Documenta Mathematica. EMS Press, 2019. https://doi.org/10.25537/dm.2019v24.1135-1177."},"article_type":"original","page":"1135-1177","day":"20","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","file":[{"checksum":"9a1a64bd49ab03fa4f738fb250fc4f90","date_created":"2020-02-03T06:26:12Z","date_updated":"2020-07-14T12:47:58Z","relation":"main_file","file_id":"7438","content_type":"application/pdf","file_size":469730,"creator":"dernst","access_level":"open_access","file_name":"2019_DocumMath_Srivastava.pdf"}],"oa_version":"Published Version","_id":"7436","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["510"],"status":"public","title":"On derived equivalences of k3 surfaces in positive characteristic","intvolume":" 24","abstract":[{"text":"For an ordinary K3 surface over an algebraically closed field of positive characteristic we show that every automorphism lifts to characteristic zero. Moreover, we show that the Fourier-Mukai partners of an ordinary K3 surface are in one-to-one correspondence with the Fourier-Mukai partners of the geometric generic fiber of its canonical lift. We also prove that the explicit counting formula for Fourier-Mukai partners of the K3 surfaces with Picard rank two and with discriminant equal to minus of a prime number, in terms of the class number of the prime, holds over a field of positive characteristic as well. We show that the image of the derived autoequivalence group of a K3 surface of finite height in the group of isometries of its crystalline cohomology has index at least two. Moreover, we provide a conditional upper bound on the kernel of this natural cohomological descent map. Further, we give an extended remark in the appendix on the possibility of an F-crystal structure on the crystalline cohomology of a K3 surface over an algebraically closed field of positive characteristic and show that the naive F-crystal structure fails in being compatible with inner product. ","lang":"eng"}],"type":"journal_article","doi":"10.25537/dm.2019v24.1135-1177","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000517806400019"],"arxiv":["1809.08970"]},"isi":1,"quality_controlled":"1","month":"05","publication_identifier":{"issn":["1431-0635"],"eissn":["1431-0643"]},"author":[{"id":"4D046628-F248-11E8-B48F-1D18A9856A87","last_name":"Srivastava","first_name":"Tanya K","full_name":"Srivastava, Tanya K"}],"date_created":"2020-02-02T23:01:06Z","date_updated":"2023-10-17T07:42:21Z","volume":24,"year":"2019","publication_status":"published","publisher":"EMS Press","department":[{"_id":"TaHa"}],"file_date_updated":"2020-07-14T12:47:58Z"},{"publication_identifier":{"issn":["0246-0203"]},"month":"09","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1710.02323"}],"external_id":{"isi":["000487763200001"],"arxiv":["1710.02323"]},"project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"},{"call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"doi":"10.1214/18-AIHP916","language":[{"iso":"eng"}],"ec_funded":1,"year":"2019","publisher":"Institute of Mathematical Statistics","department":[{"_id":"LaEr"},{"_id":"JaMa"}],"publication_status":"published","author":[{"full_name":"Ferrari, Patrick","last_name":"Ferrari","first_name":"Patrick"},{"full_name":"Ghosal, Promit","first_name":"Promit","last_name":"Ghosal"},{"full_name":"Nejjar, Peter","first_name":"Peter","last_name":"Nejjar","id":"4BF426E2-F248-11E8-B48F-1D18A9856A87"}],"volume":55,"date_created":"2018-12-11T11:44:29Z","date_updated":"2023-10-17T08:53:45Z","scopus_import":"1","article_processing_charge":"No","day":"25","citation":{"chicago":"Ferrari, Patrick, Promit Ghosal, and Peter Nejjar. “Limit Law of a Second Class Particle in TASEP with Non-Random Initial Condition.” Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-AIHP916.","mla":"Ferrari, Patrick, et al. “Limit Law of a Second Class Particle in TASEP with Non-Random Initial Condition.” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 55, no. 3, Institute of Mathematical Statistics, 2019, pp. 1203–25, doi:10.1214/18-AIHP916.","short":"P. Ferrari, P. Ghosal, P. Nejjar, Annales de l’institut Henri Poincare (B) Probability and Statistics 55 (2019) 1203–1225.","ista":"Ferrari P, Ghosal P, Nejjar P. 2019. Limit law of a second class particle in TASEP with non-random initial condition. Annales de l’institut Henri Poincare (B) Probability and Statistics. 55(3), 1203–1225.","ieee":"P. Ferrari, P. Ghosal, and P. Nejjar, “Limit law of a second class particle in TASEP with non-random initial condition,” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 55, no. 3. Institute of Mathematical Statistics, pp. 1203–1225, 2019.","apa":"Ferrari, P., Ghosal, P., & Nejjar, P. (2019). Limit law of a second class particle in TASEP with non-random initial condition. Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AIHP916","ama":"Ferrari P, Ghosal P, Nejjar P. Limit law of a second class particle in TASEP with non-random initial condition. Annales de l’institut Henri Poincare (B) Probability and Statistics. 2019;55(3):1203-1225. doi:10.1214/18-AIHP916"},"publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","page":"1203-1225","article_type":"original","date_published":"2019-09-25T00:00:00Z","type":"journal_article","issue":"3","abstract":[{"text":"We consider the totally asymmetric simple exclusion process (TASEP) with non-random initial condition having density ρ on ℤ− and λ on ℤ+, and a second class particle initially at the origin. For ρ<λ, there is a shock and the second class particle moves with speed 1−λ−ρ. For large time t, we show that the position of the second class particle fluctuates on a t1/3 scale and determine its limiting law. We also obtain the limiting distribution of the number of steps made by the second class particle until time t.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"72","intvolume":" 55","status":"public","title":"Limit law of a second class particle in TASEP with non-random initial condition","oa_version":"Preprint"},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.31263/voebm.v72i1.2276","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1022-2588"]},"month":"05","year":"2019","publisher":"Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","department":[{"_id":"E-Lib"}],"publication_status":"published","related_material":{"record":[{"id":"5686","relation":"earlier_version","status":"public"}]},"author":[{"full_name":"Danowski, Patrick","first_name":"Patrick","last_name":"Danowski","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6026-4409"}],"volume":72,"date_created":"2019-07-21T21:59:15Z","date_updated":"2023-10-17T11:33:58Z","file_date_updated":"2020-07-14T12:47:35Z","citation":{"apa":"Danowski, P. (2019). An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors. Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v72i1.2276","ieee":"P. Danowski, “An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 72, no. 1. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, pp. 59–65, 2019.","ista":"Danowski P. 2019. An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 72(1), 59–65.","ama":"Danowski P. An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 2019;72(1):59-65. doi:10.31263/voebm.v72i1.2276","chicago":"Danowski, Patrick. “An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2019. https://doi.org/10.31263/voebm.v72i1.2276.","short":"P. Danowski, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare 72 (2019) 59–65.","mla":"Danowski, Patrick. “An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare, vol. 72, no. 1, Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2019, pp. 59–65, doi:10.31263/voebm.v72i1.2276."},"publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","page":"59-65","article_type":"original","date_published":"2019-05-17T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"17","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6657","intvolume":" 72","status":"public","title":"An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors","ddc":["020"],"file":[{"date_created":"2019-07-22T08:45:03Z","date_updated":"2020-07-14T12:47:35Z","checksum":"c0d2695d6d0d34e62ba06fb3f0ebaaed","file_id":"6661","relation":"main_file","creator":"apreinsp","content_type":"application/pdf","file_size":468558,"file_name":"2019_MitteilungenDerVOEB_Danowski.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"text":"In this article a model is described how Open Access definitions can be formed on the basis of objective criteria. The common Open Access definitions such as \"gold\" and \"green\" are not exactly defined. This becomes a problem as soon as one begins to measure Open Access, for example if the development of the Open Access share should be monitored. This was discussed in the working group on Open Access Monitoring of the AT2OA project and the present model was developed, which is based on 5 critics with 4 characteristics: location, licence, version, embargo and conditions of the Open Access publication are taken into account. In the meantime, the model has also been tested in practice using R scripts, and the initial results are quite promising.","lang":"eng"}]},{"scopus_import":"1","publication_identifier":{"isbn":["9781943580576"]},"article_processing_charge":"No","month":"05","day":"01","quality_controlled":"1","citation":{"chicago":"Khatoniar, Mandeep, Nicholas Yama, Areg Ghazaryan, Sriram Guddala, Pouyan Ghaemi, and Vinod Menon. “Room Temperature Control of Valley Coherence in Bilayer WS2 Exciton Polaritons.” In CLEO: Applications and Technology. Optica Publishing Group, 2019. https://doi.org/10.1364/cleo_at.2019.jtu2a.52.","mla":"Khatoniar, Mandeep, et al. “Room Temperature Control of Valley Coherence in Bilayer WS2 Exciton Polaritons.” CLEO: Applications and Technology, paper JTu2A.52, Optica Publishing Group, 2019, doi:10.1364/cleo_at.2019.jtu2a.52.","short":"M. Khatoniar, N. Yama, A. Ghazaryan, S. Guddala, P. Ghaemi, V. Menon, in:, CLEO: Applications and Technology, Optica Publishing Group, 2019.","ista":"Khatoniar M, Yama N, Ghazaryan A, Guddala S, Ghaemi P, Menon V. 2019. Room temperature control of valley coherence in bilayer WS2 exciton polaritons. CLEO: Applications and Technology. CLEO: Conference on Lasers and Electro-Optics, paper JTu2A.52.","ieee":"M. Khatoniar, N. Yama, A. Ghazaryan, S. Guddala, P. Ghaemi, and V. Menon, “Room temperature control of valley coherence in bilayer WS2 exciton polaritons,” in CLEO: Applications and Technology, San Jose, CA, United States, 2019.","apa":"Khatoniar, M., Yama, N., Ghazaryan, A., Guddala, S., Ghaemi, P., & Menon, V. (2019). Room temperature control of valley coherence in bilayer WS2 exciton polaritons. In CLEO: Applications and Technology. San Jose, CA, United States: Optica Publishing Group. https://doi.org/10.1364/cleo_at.2019.jtu2a.52","ama":"Khatoniar M, Yama N, Ghazaryan A, Guddala S, Ghaemi P, Menon V. Room temperature control of valley coherence in bilayer WS2 exciton polaritons. In: CLEO: Applications and Technology. Optica Publishing Group; 2019. doi:10.1364/cleo_at.2019.jtu2a.52"},"publication":"CLEO: Applications and Technology","language":[{"iso":"eng"}],"date_published":"2019-05-01T00:00:00Z","doi":"10.1364/cleo_at.2019.jtu2a.52","conference":{"name":"CLEO: Conference on Lasers and Electro-Optics","start_date":"2019-05-05","location":"San Jose, CA, United States","end_date":"2019-05-10"},"type":"conference","article_number":"paper JTu2A.52","abstract":[{"lang":"eng","text":"We demonstrate robust retention of valley coherence and its control via polariton pseudospin precession through the optical TE-TM splitting in bilayer WS2 microcavity exciton polaritons at room temperature."}],"department":[{"_id":"MiLe"}],"publisher":"Optica Publishing Group","title":"Room temperature control of valley coherence in bilayer WS2 exciton polaritons","status":"public","publication_status":"published","year":"2019","_id":"6646","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","date_updated":"2023-10-17T12:14:29Z","date_created":"2019-07-17T09:40:44Z","author":[{"first_name":"Mandeep","last_name":"Khatoniar","full_name":"Khatoniar, Mandeep"},{"full_name":"Yama, Nicholas","last_name":"Yama","first_name":"Nicholas"},{"orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","first_name":"Areg","full_name":"Ghazaryan, Areg"},{"full_name":"Guddala, Sriram","first_name":"Sriram","last_name":"Guddala"},{"full_name":"Ghaemi, Pouyan","first_name":"Pouyan","last_name":"Ghaemi"},{"last_name":"Menon","first_name":"Vinod","full_name":"Menon, Vinod"}]},{"language":[{"iso":"eng"}],"doi":"10.1364/NLO.2019.NM2A.5","date_published":"2019-07-15T00:00:00Z","conference":{"end_date":"2019-07-19","start_date":"2019-07-15","location":"Waikoloa Beach, Hawaii (HI), United States","name":"NLO: Nonlinear Optics"},"quality_controlled":"1","citation":{"chicago":"Rueda Sanchez, Alfredo R, Florian Sedlmeir, Gerd Leuchs, Madhuri Kumari, and Harald G.L. Schwefel. “Resonant Electro-Optic Frequency Comb Generation in Lithium Niobate Disk Resonator inside a Microwave Cavity.” In Nonlinear Optics, OSA Technical Digest. Optica Publishing Group, 2019. https://doi.org/10.1364/NLO.2019.NM2A.5.","short":"A.R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kumari, H.G.L. Schwefel, in:, Nonlinear Optics, OSA Technical Digest, Optica Publishing Group, 2019.","mla":"Rueda Sanchez, Alfredo R., et al. “Resonant Electro-Optic Frequency Comb Generation in Lithium Niobate Disk Resonator inside a Microwave Cavity.” Nonlinear Optics, OSA Technical Digest, NM2A.5, Optica Publishing Group, 2019, doi:10.1364/NLO.2019.NM2A.5.","ieee":"A. R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kumari, and H. G. L. Schwefel, “Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity,” in Nonlinear Optics, OSA Technical Digest, Waikoloa Beach, Hawaii (HI), United States, 2019.","apa":"Rueda Sanchez, A. R., Sedlmeir, F., Leuchs, G., Kumari, M., & Schwefel, H. G. L. (2019). Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity. In Nonlinear Optics, OSA Technical Digest. Waikoloa Beach, Hawaii (HI), United States: Optica Publishing Group. https://doi.org/10.1364/NLO.2019.NM2A.5","ista":"Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kumari M, Schwefel HGL. 2019. Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity. Nonlinear Optics, OSA Technical Digest. NLO: Nonlinear Optics, NM2A.5.","ama":"Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kumari M, Schwefel HGL. Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity. In: Nonlinear Optics, OSA Technical Digest. Optica Publishing Group; 2019. doi:10.1364/NLO.2019.NM2A.5"},"publication":"Nonlinear Optics, OSA Technical Digest","article_processing_charge":"No","publication_identifier":{"isbn":["9781557528209"]},"day":"15","month":"07","scopus_import":"1","oa_version":"None","date_created":"2020-01-05T23:00:48Z","date_updated":"2023-10-17T12:14:46Z","author":[{"full_name":"Rueda Sanchez, Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860","first_name":"Alfredo R","last_name":"Rueda Sanchez"},{"first_name":"Florian","last_name":"Sedlmeir","full_name":"Sedlmeir, Florian"},{"full_name":"Leuchs, Gerd","last_name":"Leuchs","first_name":"Gerd"},{"last_name":"Kumari","first_name":"Madhuri","full_name":"Kumari, Madhuri"},{"full_name":"Schwefel, Harald G.L.","first_name":"Harald G.L.","last_name":"Schwefel"}],"department":[{"_id":"JoFi"}],"publisher":"Optica Publishing Group","publication_status":"published","title":"Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity","status":"public","year":"2019","_id":"7233","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We demonstrate electro-optic frequency comb generation using a doubly resonant system comprising a whispering gallery mode disk resonator made of lithium niobate mounted inside a three dimensional copper cavity. We observe 180 sidebands centred at 1550 nm."}],"type":"conference","article_number":"NM2A.5"},{"language":[{"iso":"eng"}],"doi":"10.1214/18-AIHP894","isi":1,"quality_controlled":"1","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"}],"external_id":{"isi":["000467793600003"],"arxiv":["1706.08343"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.08343"}],"month":"05","publication_identifier":{"issn":["0246-0203"]},"date_updated":"2023-10-17T12:20:20Z","date_created":"2019-04-08T14:05:04Z","volume":55,"author":[{"first_name":"Johannes","last_name":"Alt","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","full_name":"Alt, Johannes"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös","full_name":"Erdös, László"},{"first_name":"Torben H","last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H"},{"first_name":"Yuriy","last_name":"Nemish","id":"4D902E6A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7327-856X","full_name":"Nemish, Yuriy"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"149"}]},"publication_status":"published","publisher":"Institut Henri Poincaré","department":[{"_id":"LaEr"}],"year":"2019","ec_funded":1,"date_published":"2019-05-01T00:00:00Z","page":"661-696","publication":"Annales de l'institut Henri Poincare","citation":{"short":"J. Alt, L. Erdös, T.H. Krüger, Y. Nemish, Annales de l’institut Henri Poincare 55 (2019) 661–696.","mla":"Alt, Johannes, et al. “Location of the Spectrum of Kronecker Random Matrices.” Annales de l’institut Henri Poincare, vol. 55, no. 2, Institut Henri Poincaré, 2019, pp. 661–96, doi:10.1214/18-AIHP894.","chicago":"Alt, Johannes, László Erdös, Torben H Krüger, and Yuriy Nemish. “Location of the Spectrum of Kronecker Random Matrices.” Annales de l’institut Henri Poincare. Institut Henri Poincaré, 2019. https://doi.org/10.1214/18-AIHP894.","ama":"Alt J, Erdös L, Krüger TH, Nemish Y. Location of the spectrum of Kronecker random matrices. Annales de l’institut Henri Poincare. 2019;55(2):661-696. doi:10.1214/18-AIHP894","apa":"Alt, J., Erdös, L., Krüger, T. H., & Nemish, Y. (2019). Location of the spectrum of Kronecker random matrices. Annales de l’institut Henri Poincare. Institut Henri Poincaré. https://doi.org/10.1214/18-AIHP894","ieee":"J. Alt, L. Erdös, T. H. Krüger, and Y. Nemish, “Location of the spectrum of Kronecker random matrices,” Annales de l’institut Henri Poincare, vol. 55, no. 2. Institut Henri Poincaré, pp. 661–696, 2019.","ista":"Alt J, Erdös L, Krüger TH, Nemish Y. 2019. Location of the spectrum of Kronecker random matrices. Annales de l’institut Henri Poincare. 55(2), 661–696."},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","status":"public","title":"Location of the spectrum of Kronecker random matrices","intvolume":" 55","_id":"6240","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"For a general class of large non-Hermitian random block matrices X we prove that there are no eigenvalues away from a deterministic set with very high probability. This set is obtained from the Dyson equation of the Hermitization of X as the self-consistent approximation of the pseudospectrum. We demonstrate that the analysis of the matrix Dyson equation from (Probab. Theory Related Fields (2018)) offers a unified treatment of many structured matrix ensembles."}],"issue":"2","type":"journal_article"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"22","citation":{"chicago":"Andergassen, Daniel, Markus Muckenhuber, Philipp C. Bammer, Tomasz M. Kulinski, Hans-Christian Theussl, Takahiko Shimizu, Josef M. Penninger, Florian Pauler, and Quanah J. Hudson. “The Airn LncRNA Does Not Require Any DNA Elements within Its Locus to Silence Distant Imprinted Genes.” PLoS Genetics. Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008268.","short":"D. Andergassen, M. Muckenhuber, P.C. Bammer, T.M. Kulinski, H.-C. Theussl, T. Shimizu, J.M. Penninger, F. Pauler, Q.J. Hudson, PLoS Genetics 15 (2019).","mla":"Andergassen, Daniel, et al. “The Airn LncRNA Does Not Require Any DNA Elements within Its Locus to Silence Distant Imprinted Genes.” PLoS Genetics, vol. 15, no. 7, e1008268, Public Library of Science, 2019, doi:10.1371/journal.pgen.1008268.","apa":"Andergassen, D., Muckenhuber, M., Bammer, P. C., Kulinski, T. M., Theussl, H.-C., Shimizu, T., … Hudson, Q. J. (2019). The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008268","ieee":"D. Andergassen et al., “The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes,” PLoS Genetics, vol. 15, no. 7. Public Library of Science, 2019.","ista":"Andergassen D, Muckenhuber M, Bammer PC, Kulinski TM, Theussl H-C, Shimizu T, Penninger JM, Pauler F, Hudson QJ. 2019. The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes. PLoS Genetics. 15(7), e1008268.","ama":"Andergassen D, Muckenhuber M, Bammer PC, et al. The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes. PLoS Genetics. 2019;15(7). doi:10.1371/journal.pgen.1008268"},"publication":"PLoS Genetics","article_type":"original","date_published":"2019-07-22T00:00:00Z","type":"journal_article","issue":"7","abstract":[{"text":"Long non-coding (lnc) RNAs are numerous and found throughout the mammalian genome, and many are thought to be involved in the regulation of gene expression. However, the majority remain relatively uncharacterised and of uncertain function making the use of model systems to uncover their mode of action valuable. Imprinted lncRNAs target and recruit epigenetic silencing factors to a cluster of imprinted genes on the same chromosome, making them one of the best characterized lncRNAs for silencing distant genes in cis. In this study we examined silencing of the distant imprinted gene Slc22a3 by the lncRNA Airn in the Igf2r imprinted cluster in mouse. Previously we proposed that imprinted lncRNAs may silence distant imprinted genes by disrupting promoter-enhancer interactions by being transcribed through the enhancer, which we called the enhancer interference hypothesis. Here we tested this hypothesis by first using allele-specific chromosome conformation capture (3C) to detect interactions between the Slc22a3 promoter and the locus of the Airn lncRNA that silences it on the paternal chromosome. In agreement with the model, we found interactions enriched on the maternal allele across the entire Airn gene consistent with multiple enhancer-promoter interactions. Therefore, to test the enhancer interference hypothesis we devised an approach to delete the entire Airn gene. However, the deletion showed that there are no essential enhancers for Slc22a2, Pde10a and Slc22a3 within the Airn gene, strongly indicating that the Airn RNA rather than its transcription is responsible for silencing distant imprinted genes. Furthermore, we found that silent imprinted genes were covered with large blocks of H3K27me3 on the repressed paternal allele. Therefore we propose an alternative hypothesis whereby the chromosome interactions may initially guide the lncRNA to target imprinted promoters and recruit repressive chromatin, and that these interactions are lost once silencing is established.","lang":"eng"}],"_id":"7399","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 15","status":"public","ddc":["570"],"title":"The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes","file":[{"file_size":2302307,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2019_PlosGenetics_Andergassen.pdf","checksum":"2f51fc91e4a4199827adc51d432ad864","date_created":"2020-02-04T10:11:55Z","date_updated":"2020-07-14T12:47:57Z","relation":"main_file","file_id":"7446"}],"oa_version":"Published Version","publication_identifier":{"issn":["1553-7404"]},"month":"07","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000478689100025"],"pmid":["31329595"]},"isi":1,"quality_controlled":"1","doi":"10.1371/journal.pgen.1008268","language":[{"iso":"eng"}],"article_number":"e1008268","file_date_updated":"2020-07-14T12:47:57Z","pmid":1,"year":"2019","department":[{"_id":"SiHi"}],"publisher":"Public Library of Science","publication_status":"published","author":[{"full_name":"Andergassen, Daniel","last_name":"Andergassen","first_name":"Daniel"},{"last_name":"Muckenhuber","first_name":"Markus","full_name":"Muckenhuber, Markus"},{"full_name":"Bammer, Philipp C.","last_name":"Bammer","first_name":"Philipp C."},{"first_name":"Tomasz M.","last_name":"Kulinski","full_name":"Kulinski, Tomasz M."},{"last_name":"Theussl","first_name":"Hans-Christian","full_name":"Theussl, Hans-Christian"},{"first_name":"Takahiko","last_name":"Shimizu","full_name":"Shimizu, Takahiko"},{"full_name":"Penninger, Josef M.","last_name":"Penninger","first_name":"Josef M."},{"full_name":"Pauler, Florian","first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048"},{"full_name":"Hudson, Quanah J.","last_name":"Hudson","first_name":"Quanah J."}],"volume":15,"date_updated":"2023-10-17T12:30:27Z","date_created":"2020-01-29T16:14:07Z"},{"file_date_updated":"2020-07-14T12:47:49Z","ec_funded":1,"article_number":"e1007268","date_created":"2019-11-25T08:20:47Z","date_updated":"2023-10-17T12:30:07Z","volume":15,"author":[{"full_name":"Wang, Jilin W. J. L.","first_name":"Jilin W. J. L.","last_name":"Wang"},{"id":"A057D288-3E88-11E9-986D-0CF4E5697425","orcid":"0000-0003-2623-5249","first_name":"Fabrizio","last_name":"Lombardi","full_name":"Lombardi, Fabrizio"},{"last_name":"Zhang","first_name":"Xiyun","full_name":"Zhang, Xiyun"},{"full_name":"Anaclet, Christelle","last_name":"Anaclet","first_name":"Christelle"},{"last_name":"Ivanov","first_name":"Plamen Ch.","full_name":"Ivanov, Plamen Ch."}],"publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","year":"2019","pmid":1,"month":"11","publication_identifier":{"issn":["1553-7358"]},"language":[{"iso":"eng"}],"doi":"10.1371/journal.pcbi.1007268","quality_controlled":"1","isi":1,"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["31725712"],"isi":["000500976100014"]},"abstract":[{"text":"Origin and functions of intermittent transitions among sleep stages, including short awakenings and arousals, constitute a challenge to the current homeostatic framework for sleep regulation, focusing on factors modulating sleep over large time scales. Here we propose that the complex micro-architecture characterizing the sleep-wake cycle results from an underlying non-equilibrium critical dynamics, bridging collective behaviors across spatio-temporal scales. We investigate θ and δ wave dynamics in control rats and in rats with lesions of sleep-promoting neurons in the parafacial zone. We demonstrate that intermittent bursts in θ and δ rhythms exhibit a complex temporal organization, with long-range power-law correlations and a robust duality of power law (θ-bursts, active phase) and exponential-like (δ-bursts, quiescent phase) duration distributions, typical features of non-equilibrium systems self-organizing at criticality. Crucially, such temporal organization relates to anti-correlated coupling between θ- and δ-bursts, and is independent of the dominant physiologic state and lesions, a solid indication of a basic principle in sleep dynamics.","lang":"eng"}],"issue":"11","type":"journal_article","oa_version":"Published Version","file":[{"checksum":"2a096a9c6dcc6eaa94077b2603bc6c12","date_updated":"2020-07-14T12:47:49Z","date_created":"2019-11-25T08:24:01Z","relation":"main_file","file_id":"7104","content_type":"application/pdf","file_size":3982516,"creator":"dernst","access_level":"open_access","file_name":"2019_PLOSComBio_Wang.pdf"}],"ddc":["570","000"],"title":"Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture","status":"public","intvolume":" 15","_id":"7103","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2019-11-01T00:00:00Z","article_type":"original","publication":"PLoS Computational Biology","citation":{"short":"J.W.J.L. Wang, F. Lombardi, X. Zhang, C. Anaclet, P.C. Ivanov, PLoS Computational Biology 15 (2019).","mla":"Wang, Jilin W. J. L., et al. “Non-Equilibrium Critical Dynamics of Bursts in θ and δ Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.” PLoS Computational Biology, vol. 15, no. 11, e1007268, Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007268.","chicago":"Wang, Jilin W. J. L., Fabrizio Lombardi, Xiyun Zhang, Christelle Anaclet, and Plamen Ch. Ivanov. “Non-Equilibrium Critical Dynamics of Bursts in θ and δ Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.” PLoS Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007268.","ama":"Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. PLoS Computational Biology. 2019;15(11). doi:10.1371/journal.pcbi.1007268","ieee":"J. W. J. L. Wang, F. Lombardi, X. Zhang, C. Anaclet, and P. C. Ivanov, “Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture,” PLoS Computational Biology, vol. 15, no. 11. Public Library of Science, 2019.","apa":"Wang, J. W. J. L., Lombardi, F., Zhang, X., Anaclet, C., & Ivanov, P. C. (2019). Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007268","ista":"Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. 2019. Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. PLoS Computational Biology. 15(11), e1007268."}},{"type":"conference","abstract":[{"lang":"eng","text":"Knowledge distillation, i.e. one classifier being trained on the outputs of another classifier, is an empirically very successful technique for knowledge transfer between classifiers. It has even been observed that classifiers learn much faster and more reliably if trained with the outputs of another classifier as soft labels, instead of from ground truth data. So far, however, there is no satisfactory theoretical explanation of this phenomenon. In this work, we provide the first insights into the working mechanisms of distillation by studying the special case of linear and deep linear classifiers. Specifically, we prove a generalization bound that establishes fast convergence of the expected risk of a distillation-trained linear classifier. From the bound and its proof we extract three keyfactors that determine the success of distillation: data geometry – geometric properties of the datadistribution, in particular class separation, has an immediate influence on the convergence speed of the risk; optimization bias– gradient descentoptimization finds a very favorable minimum of the distillation objective; and strong monotonicity– the expected risk of the student classifier always decreases when the size of the training set grows."}],"ddc":["000"],"status":"public","title":"Towards understanding knowledge distillation","intvolume":" 97","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6569","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"6570","checksum":"a66d00e2694d749250f8507f301320ca","date_updated":"2020-07-14T12:47:33Z","date_created":"2019-06-20T18:22:56Z","access_level":"open_access","file_name":"paper.pdf","file_size":686432,"content_type":"application/pdf","creator":"bphuong"}],"scopus_import":"1","day":"13","article_processing_charge":"No","has_accepted_license":"1","page":"5142-5151","publication":"Proceedings of the 36th International Conference on Machine Learning","citation":{"chicago":"Phuong, Mary, and Christoph Lampert. “Towards Understanding Knowledge Distillation.” In Proceedings of the 36th International Conference on Machine Learning, 97:5142–51. ML Research Press, 2019.","short":"M. Phuong, C. Lampert, in:, Proceedings of the 36th International Conference on Machine Learning, ML Research Press, 2019, pp. 5142–5151.","mla":"Phuong, Mary, and Christoph Lampert. “Towards Understanding Knowledge Distillation.” Proceedings of the 36th International Conference on Machine Learning, vol. 97, ML Research Press, 2019, pp. 5142–51.","apa":"Phuong, M., & Lampert, C. (2019). Towards understanding knowledge distillation. In Proceedings of the 36th International Conference on Machine Learning (Vol. 97, pp. 5142–5151). Long Beach, CA, United States: ML Research Press.","ieee":"M. Phuong and C. Lampert, “Towards understanding knowledge distillation,” in Proceedings of the 36th International Conference on Machine Learning, Long Beach, CA, United States, 2019, vol. 97, pp. 5142–5151.","ista":"Phuong M, Lampert C. 2019. Towards understanding knowledge distillation. Proceedings of the 36th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 97, 5142–5151.","ama":"Phuong M, Lampert C. Towards understanding knowledge distillation. In: Proceedings of the 36th International Conference on Machine Learning. Vol 97. ML Research Press; 2019:5142-5151."},"date_published":"2019-06-13T00:00:00Z","file_date_updated":"2020-07-14T12:47:33Z","publication_status":"published","department":[{"_id":"ChLa"}],"publisher":"ML Research Press","year":"2019","date_updated":"2023-10-17T12:31:38Z","date_created":"2019-06-20T18:23:03Z","volume":97,"author":[{"last_name":"Bui Thi Mai","first_name":"Phuong","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","full_name":"Bui Thi Mai, Phuong"},{"last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"}],"month":"06","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"conference":{"name":"ICML: International Conference on Machine Learning","end_date":"2019-06-15","start_date":"2019-06-10","location":"Long Beach, CA, United States"}},{"publication_status":"published","department":[{"_id":"ChLa"}],"publisher":"ML Research Press","year":"2019","date_updated":"2023-10-17T12:31:55Z","date_created":"2019-06-27T14:18:23Z","volume":97,"author":[{"full_name":"Konstantinov, Nikola H","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","last_name":"Konstantinov","first_name":"Nikola H"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph"}],"related_material":{"record":[{"id":"10799","relation":"dissertation_contains","status":"public"}]},"ec_funded":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding","_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"oa":1,"external_id":{"arxiv":["1901.10310"]},"main_file_link":[{"url":"https://arxiv.org/abs/1901.10310","open_access":"1"}],"language":[{"iso":"eng"}],"conference":{"end_date":"2919-06-15","start_date":"2019-06-10","location":"Long Beach, CA, USA","name":"ICML: International Conference on Machine Learning"},"month":"06","title":"Robust learning from untrusted sources","status":"public","intvolume":" 97","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6590","oa_version":"Preprint","type":"conference","abstract":[{"lang":"eng","text":"Modern machine learning methods often require more data for training than a single expert can provide. Therefore, it has become a standard procedure to collect data from external sources, e.g. via crowdsourcing. Unfortunately, the quality of these sources is not always guaranteed. As additional complications, the data might be stored in a distributed way, or might even have to remain private. In this work, we address the question of how to learn robustly in such scenarios. Studying the problem through the lens of statistical learning theory, we derive a procedure that allows for learning from all available sources, yet automatically suppresses irrelevant or corrupted data. We show by extensive experiments that our method provides significant improvements over alternative approaches from robust statistics and distributed optimization. "}],"page":"3488-3498","publication":"Proceedings of the 36th International Conference on Machine Learning","citation":{"chicago":"Konstantinov, Nikola H, and Christoph Lampert. “Robust Learning from Untrusted Sources.” In Proceedings of the 36th International Conference on Machine Learning, 97:3488–98. ML Research Press, 2019.","short":"N.H. Konstantinov, C. Lampert, in:, Proceedings of the 36th International Conference on Machine Learning, ML Research Press, 2019, pp. 3488–3498.","mla":"Konstantinov, Nikola H., and Christoph Lampert. “Robust Learning from Untrusted Sources.” Proceedings of the 36th International Conference on Machine Learning, vol. 97, ML Research Press, 2019, pp. 3488–98.","ieee":"N. H. Konstantinov and C. Lampert, “Robust learning from untrusted sources,” in Proceedings of the 36th International Conference on Machine Learning, Long Beach, CA, USA, 2019, vol. 97, pp. 3488–3498.","apa":"Konstantinov, N. H., & Lampert, C. (2019). Robust learning from untrusted sources. In Proceedings of the 36th International Conference on Machine Learning (Vol. 97, pp. 3488–3498). Long Beach, CA, USA: ML Research Press.","ista":"Konstantinov NH, Lampert C. 2019. Robust learning from untrusted sources. Proceedings of the 36th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 97, 3488–3498.","ama":"Konstantinov NH, Lampert C. Robust learning from untrusted sources. In: Proceedings of the 36th International Conference on Machine Learning. Vol 97. ML Research Press; 2019:3488-3498."},"date_published":"2019-06-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No"},{"file_date_updated":"2020-07-14T12:47:46Z","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Proceedings of the National Academy of Sciences","year":"2019","pmid":1,"date_created":"2019-11-12T11:42:05Z","date_updated":"2023-10-17T12:32:37Z","volume":116,"author":[{"first_name":"D","last_name":"Huang","full_name":"Huang, D"},{"full_name":"Sun, Y","first_name":"Y","last_name":"Sun"},{"full_name":"Ma, Z","first_name":"Z","last_name":"Ma"},{"last_name":"Ke","first_name":"M","full_name":"Ke, M"},{"last_name":"Cui","first_name":"Y","full_name":"Cui, Y"},{"full_name":"Chen, Z","first_name":"Z","last_name":"Chen"},{"full_name":"Chen, C","first_name":"C","last_name":"Chen"},{"full_name":"Ji, C","last_name":"Ji","first_name":"C"},{"full_name":"Tran, TM","first_name":"TM","last_name":"Tran"},{"first_name":"L","last_name":"Yang","full_name":"Yang, L"},{"full_name":"Lam, SM","first_name":"SM","last_name":"Lam"},{"first_name":"Y","last_name":"Han","full_name":"Han, Y"},{"full_name":"Shu, G","first_name":"G","last_name":"Shu"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"},{"first_name":"Y","last_name":"Miao","full_name":"Miao, Y"},{"first_name":"L","last_name":"Jiang","full_name":"Jiang, L"},{"full_name":"Chen, X","last_name":"Chen","first_name":"X"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1073/pnas.2004738117"}]},"month":"10","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"isi":1,"quality_controlled":"1","oa":1,"tmp":{"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["31575745"],"isi":["000490183000068"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1911892116","type":"journal_article","abstract":[{"text":"Plasmodesmata (PD) are plant-specific membrane-lined channels that create cytoplasmic and membrane continuities between adjacent cells, thereby facilitating cell–cell communication and virus movement. Plant cells have evolved diverse mechanisms to regulate PD plasticity in response to numerous environmental stimuli. In particular, during defense against plant pathogens, the defense hormone, salicylic acid (SA), plays a crucial role in the regulation of PD permeability in a callose-dependent manner. Here, we uncover a mechanism by which plants restrict the spreading of virus and PD cargoes using SA signaling by increasing lipid order and closure of PD. We showed that exogenous SA application triggered the compartmentalization of lipid raft nanodomains through a modulation of the lipid raft-regulatory protein, Remorin (REM). Genetic studies, superresolution imaging, and transmission electron microscopy observation together demonstrated that Arabidopsis REM1.2 and REM1.3 are crucial for plasma membrane nanodomain assembly to control PD aperture and functionality. In addition, we also found that a 14-3-3 epsilon protein modulates REM clustering and membrane nanodomain compartmentalization through its direct interaction with REM proteins. This study unveils a molecular mechanism by which the key plant defense hormone, SA, triggers membrane lipid nanodomain reorganization, thereby regulating PD closure to impede virus spreading.","lang":"eng"}],"issue":"42","title":"Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization","status":"public","ddc":["580"],"intvolume":" 116","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6999","oa_version":"Published Version","file":[{"file_name":"2019_PNAS_Huang.pdf","access_level":"open_access","content_type":"application/pdf","file_size":3287466,"creator":"dernst","relation":"main_file","file_id":"7012","date_created":"2019-11-13T08:22:28Z","date_updated":"2020-07-14T12:47:46Z","checksum":"258c666bc6253eab81961f61169eefae"}],"scopus_import":"1","day":"15","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","page":"21274-21284","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"chicago":"Huang, D, Y Sun, Z Ma, M Ke, Y Cui, Z Chen, C Chen, et al. “Salicylic Acid-Mediated Plasmodesmal Closure via Remorin-Dependent Lipid Organization.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1911892116.","short":"D. Huang, Y. Sun, Z. Ma, M. Ke, Y. Cui, Z. Chen, C. Chen, C. Ji, T. Tran, L. Yang, S. Lam, Y. Han, G. Shu, J. Friml, Y. Miao, L. Jiang, X. Chen, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 21274–21284.","mla":"Huang, D., et al. “Salicylic Acid-Mediated Plasmodesmal Closure via Remorin-Dependent Lipid Organization.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 42, Proceedings of the National Academy of Sciences, 2019, pp. 21274–84, doi:10.1073/pnas.1911892116.","ieee":"D. Huang et al., “Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization,” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 42. Proceedings of the National Academy of Sciences, pp. 21274–21284, 2019.","apa":"Huang, D., Sun, Y., Ma, Z., Ke, M., Cui, Y., Chen, Z., … Chen, X. (2019). Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1911892116","ista":"Huang D, Sun Y, Ma Z, Ke M, Cui Y, Chen Z, Chen C, Ji C, Tran T, Yang L, Lam S, Han Y, Shu G, Friml J, Miao Y, Jiang L, Chen X. 2019. Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization. Proceedings of the National Academy of Sciences of the United States of America. 116(42), 21274–21284.","ama":"Huang D, Sun Y, Ma Z, et al. Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(42):21274-21284. doi:10.1073/pnas.1911892116"},"date_published":"2019-10-15T00:00:00Z"},{"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1905555116","quality_controlled":"1","isi":1,"external_id":{"isi":["000472719100010"],"pmid":["31213531"]},"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1905555116","open_access":"1"}],"oa":1,"month":"06","date_created":"2019-07-07T21:59:25Z","date_updated":"2023-10-17T12:44:15Z","volume":116,"author":[{"full_name":"Wright, Alison E.","last_name":"Wright","first_name":"Alison E."},{"last_name":"Darolti","first_name":"Iulia","full_name":"Darolti, Iulia"},{"first_name":"Natasha I.","last_name":"Bloch","full_name":"Bloch, Natasha I."},{"full_name":"Oostra, Vicencio","last_name":"Oostra","first_name":"Vicencio"},{"first_name":"Benjamin A.","last_name":"Sandkam","full_name":"Sandkam, Benjamin A."},{"full_name":"Buechel, Séverine D.","first_name":"Séverine D.","last_name":"Buechel"},{"full_name":"Kolm, Niclas","first_name":"Niclas","last_name":"Kolm"},{"first_name":"Felix","last_name":"Breden","full_name":"Breden, Felix"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz"},{"full_name":"Mank, Judith E.","first_name":"Judith E.","last_name":"Mank"}],"publication_status":"published","publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"BeVi"}],"year":"2019","pmid":1,"date_published":"2019-06-25T00:00:00Z","article_type":"letter_note","page":"12607-12608","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"ama":"Wright AE, Darolti I, Bloch NI, et al. On the power to detect rare recombination events. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(26):12607-12608. doi:10.1073/pnas.1905555116","ieee":"A. E. Wright et al., “On the power to detect rare recombination events,” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 26. Proceedings of the National Academy of Sciences, pp. 12607–12608, 2019.","apa":"Wright, A. E., Darolti, I., Bloch, N. I., Oostra, V., Sandkam, B. A., Buechel, S. D., … Mank, J. E. (2019). On the power to detect rare recombination events. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1905555116","ista":"Wright AE, Darolti I, Bloch NI, Oostra V, Sandkam BA, Buechel SD, Kolm N, Breden F, Vicoso B, Mank JE. 2019. On the power to detect rare recombination events. Proceedings of the National Academy of Sciences of the United States of America. 116(26), 12607–12608.","short":"A.E. Wright, I. Darolti, N.I. Bloch, V. Oostra, B.A. Sandkam, S.D. Buechel, N. Kolm, F. Breden, B. Vicoso, J.E. Mank, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 12607–12608.","mla":"Wright, Alison E., et al. “On the Power to Detect Rare Recombination Events.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 26, Proceedings of the National Academy of Sciences, 2019, pp. 12607–08, doi:10.1073/pnas.1905555116.","chicago":"Wright, Alison E., Iulia Darolti, Natasha I. Bloch, Vicencio Oostra, Benjamin A. Sandkam, Séverine D. Buechel, Niclas Kolm, Felix Breden, Beatriz Vicoso, and Judith E. Mank. “On the Power to Detect Rare Recombination Events.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1905555116."},"day":"25","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","title":"On the power to detect rare recombination events","status":"public","intvolume":" 116","_id":"6621","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We read with great interest the recent work in PNAS by Bergero et al. (1) describing differences in male and female recombination patterns on the guppy (Poecilia reticulata) sex chromosome. We fully agree that recombination in males is largely confined to the ends of the sex chromosome. Bergero et al. interpret these results to suggest that our previous findings of population-level variation in the degree of sex chromosome differentiation in this species (2) are incorrect. However, we suggest that their results are entirely consistent with our previous report, and that their interpretation presents a false controversy.","lang":"eng"}],"issue":"26","type":"journal_article"},{"publication_identifier":{"issn":["0028-646X"],"eissn":["1469-8137"]},"month":"11","doi":"10.1111/nph.16180","language":[{"iso":"eng"}],"external_id":{"pmid":["31505037"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"329960","_id":"25B36484-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Mating system and the evolutionary dynamics of hybrid zones"},{"call_identifier":"FWF","name":"Sex chromosomes and species barriers","grant_number":"M02463","_id":"2662AADE-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","ec_funded":1,"file_date_updated":"2020-07-14T12:47:42Z","author":[{"orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","first_name":"Melinda","full_name":"Pickup, Melinda"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"full_name":"Brandvain, Yaniv","last_name":"Brandvain","first_name":"Yaniv"},{"orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle","full_name":"Fraisse, Christelle"},{"first_name":"Sarah","last_name":"Yakimowski","full_name":"Yakimowski, Sarah"},{"full_name":"Dixit, Tanmay","last_name":"Dixit","first_name":"Tanmay"},{"last_name":"Lexer","first_name":"Christian","full_name":"Lexer, Christian"},{"last_name":"Cereghetti","first_name":"Eva","id":"71AA91B4-05ED-11EA-8BEB-F5833E63BD63","full_name":"Cereghetti, Eva"},{"orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David","full_name":"Field, David"}],"volume":224,"date_updated":"2023-10-18T08:47:08Z","date_created":"2019-09-07T14:35:40Z","pmid":1,"year":"2019","department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2019-11-01T00:00:00Z","citation":{"ama":"Pickup M, Barton NH, Brandvain Y, et al. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. 2019;224(3):1035-1047. doi:10.1111/nph.16180","apa":"Pickup, M., Barton, N. H., Brandvain, Y., Fraisse, C., Yakimowski, S., Dixit, T., … Field, D. (2019). Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. Wiley. https://doi.org/10.1111/nph.16180","ieee":"M. Pickup et al., “Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow,” New Phytologist, vol. 224, no. 3. Wiley, pp. 1035–1047, 2019.","ista":"Pickup M, Barton NH, Brandvain Y, Fraisse C, Yakimowski S, Dixit T, Lexer C, Cereghetti E, Field D. 2019. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. 224(3), 1035–1047.","short":"M. Pickup, N.H. Barton, Y. Brandvain, C. Fraisse, S. Yakimowski, T. Dixit, C. Lexer, E. Cereghetti, D. Field, New Phytologist 224 (2019) 1035–1047.","mla":"Pickup, Melinda, et al. “Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries to Gene Flow.” New Phytologist, vol. 224, no. 3, Wiley, 2019, pp. 1035–47, doi:10.1111/nph.16180.","chicago":"Pickup, Melinda, Nicholas H Barton, Yaniv Brandvain, Christelle Fraisse, Sarah Yakimowski, Tanmay Dixit, Christian Lexer, Eva Cereghetti, and David Field. “Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries to Gene Flow.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.16180."},"publication":"New Phytologist","page":"1035-1047","article_type":"original","issue":"3","abstract":[{"lang":"eng","text":"Plant mating systems play a key role in structuring genetic variation both within and between species. In hybrid zones, the outcomes and dynamics of hybridization are usually interpreted as the balance between gene flow and selection against hybrids. Yet, mating systems can introduce selective forces that alter these expectations; with diverse outcomes for the level and direction of gene flow depending on variation in outcrossing and whether the mating systems of the species pair are the same or divergent. We present a survey of hybridization in 133 species pairs from 41 plant families and examine how patterns of hybridization vary with mating system. We examine if hybrid zone mode, level of gene flow, asymmetries in gene flow and the frequency of reproductive isolating barriers vary in relation to mating system/s of the species pair. We combine these results with a simulation model and examples from the literature to address two general themes: (i) the two‐way interaction between introgression and the evolution of reproductive systems, and (ii) how mating system can facilitate or restrict interspecific gene flow. We conclude that examining mating system with hybridization provides unique opportunities to understand divergence and the processes underlying reproductive isolation."}],"type":"journal_article","file":[{"file_id":"7011","relation":"main_file","checksum":"21e4c95599bbcaf7c483b89954658672","date_created":"2019-11-13T08:15:05Z","date_updated":"2020-07-14T12:47:42Z","access_level":"open_access","file_name":"2019_NewPhytologist_Pickup.pdf","creator":"dernst","content_type":"application/pdf","file_size":1511958}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6856","intvolume":" 224","ddc":["570"],"status":"public","title":"Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow"},{"citation":{"chicago":"Fulek, Radoslav, Bernd Gärtner, Andrey Kupavskii, Pavel Valtr, and Uli Wagner. “The Crossing Tverberg Theorem.” In 35th International Symposium on Computational Geometry, 129:38:1-38:13. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.SOCG.2019.38.","mla":"Fulek, Radoslav, et al. “The Crossing Tverberg Theorem.” 35th International Symposium on Computational Geometry, vol. 129, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 38:1-38:13, doi:10.4230/LIPICS.SOCG.2019.38.","short":"R. Fulek, B. Gärtner, A. Kupavskii, P. Valtr, U. Wagner, in:, 35th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 38:1-38:13.","ista":"Fulek R, Gärtner B, Kupavskii A, Valtr P, Wagner U. 2019. The crossing Tverberg theorem. 35th International Symposium on Computational Geometry. SoCG 2019: Symposium on Computational Geometry, LIPIcs, vol. 129, 38:1-38:13.","apa":"Fulek, R., Gärtner, B., Kupavskii, A., Valtr, P., & Wagner, U. (2019). The crossing Tverberg theorem. In 35th International Symposium on Computational Geometry (Vol. 129, p. 38:1-38:13). Portland, OR, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.SOCG.2019.38","ieee":"R. Fulek, B. Gärtner, A. Kupavskii, P. Valtr, and U. Wagner, “The crossing Tverberg theorem,” in 35th International Symposium on Computational Geometry, Portland, OR, United States, 2019, vol. 129, p. 38:1-38:13.","ama":"Fulek R, Gärtner B, Kupavskii A, Valtr P, Wagner U. The crossing Tverberg theorem. In: 35th International Symposium on Computational Geometry. Vol 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:38:1-38:13. doi:10.4230/LIPICS.SOCG.2019.38"},"publication":"35th International Symposium on Computational Geometry","page":"38:1-38:13","date_published":"2019-06-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01","_id":"6647","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 129","status":"public","title":"The crossing Tverberg theorem","ddc":["000","510"],"oa_version":"Published Version","file":[{"date_created":"2019-07-24T06:54:52Z","date_updated":"2020-07-14T12:47:35Z","checksum":"d6d017f8b41291b94d102294fa96ae9c","file_id":"6667","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":559837,"file_name":"2019_LIPICS_Fulek.pdf","access_level":"open_access"}],"type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","text":"The Tverberg theorem is one of the cornerstones of discrete geometry. It states that, given a set X of at least (d+1)(r-1)+1 points in R^d, one can find a partition X=X_1 cup ... cup X_r of X, such that the convex hulls of the X_i, i=1,...,r, all share a common point. In this paper, we prove a strengthening of this theorem that guarantees a partition which, in addition to the above, has the property that the boundaries of full-dimensional convex hulls have pairwise nonempty intersections. Possible generalizations and algorithmic aspects are also discussed. As a concrete application, we show that any n points in the plane in general position span floor[n/3] vertex-disjoint triangles that are pairwise crossing, meaning that their boundaries have pairwise nonempty intersections; this number is clearly best possible. A previous result of Alvarez-Rebollar et al. guarantees floor[n/6] pairwise crossing triangles. Our result generalizes to a result about simplices in R^d,d >=2."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1812.04911"]},"oa":1,"project":[{"call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs","_id":"261FA626-B435-11E9-9278-68D0E5697425","grant_number":"M02281"}],"quality_controlled":"1","doi":"10.4230/LIPICS.SOCG.2019.38","conference":{"name":"SoCG 2019: Symposium on Computational Geometry","start_date":"2019-06-18","location":"Portland, OR, United States","end_date":"2019-06-21"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783959771047"],"issn":["1868-8969"]},"month":"06","year":"2019","department":[{"_id":"UlWa"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","related_material":{"record":[{"id":"13974","status":"public","relation":"later_version"}]},"author":[{"full_name":"Fulek, Radoslav","last_name":"Fulek","first_name":"Radoslav","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gärtner, Bernd","last_name":"Gärtner","first_name":"Bernd"},{"full_name":"Kupavskii, Andrey","last_name":"Kupavskii","first_name":"Andrey"},{"full_name":"Valtr, Pavel","first_name":"Pavel","last_name":"Valtr"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","first_name":"Uli","last_name":"Wagner","full_name":"Wagner, Uli"}],"volume":129,"date_created":"2019-07-17T10:35:04Z","date_updated":"2023-12-13T12:03:35Z","file_date_updated":"2020-07-14T12:47:35Z"},{"date_published":"2019-06-01T00:00:00Z","page":"986-996","publication":"Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing","citation":{"chicago":"Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and Leqi Zhu. “Why Extension-Based Proofs Fail.” In Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, 986–96. ACM Press, 2019. https://doi.org/10.1145/3313276.3316407.","short":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, in:, Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, ACM Press, 2019, pp. 986–996.","mla":"Alistarh, Dan-Adrian, et al. “Why Extension-Based Proofs Fail.” Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, ACM Press, 2019, pp. 986–96, doi:10.1145/3313276.3316407.","ieee":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, and L. Zhu, “Why extension-based proofs fail,” in Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, Phoenix, AZ, United States, 2019, pp. 986–996.","apa":"Alistarh, D.-A., Aspnes, J., Ellen, F., Gelashvili, R., & Zhu, L. (2019). Why extension-based proofs fail. In Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing (pp. 986–996). Phoenix, AZ, United States: ACM Press. https://doi.org/10.1145/3313276.3316407","ista":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. 2019. Why extension-based proofs fail. Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 986–996.","ama":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. Why extension-based proofs fail. In: Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing. ACM Press; 2019:986-996. doi:10.1145/3313276.3316407"},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","status":"public","title":"Why extension-based proofs fail","_id":"6676","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"It is impossible to deterministically solve wait-free consensus in an asynchronous system. The classic proof uses a valency argument, which constructs an infinite execution by repeatedly extending a finite execution. We introduce extension-based proofs, a class of impossibility proofs that are modelled as an interaction between a prover and a protocol and that include valency arguments.\r\n\r\nUsing proofs based on combinatorial topology, it has been shown that it is impossible to deterministically solve k-set agreement among n > k ≥ 2 processes in a wait-free manner. However, it was unknown whether proofs based on simpler techniques were possible. We show that this impossibility result cannot be obtained by an extension-based proof and, hence, extension-based proofs are limited in power."}],"type":"conference","language":[{"iso":"eng"}],"conference":{"name":"STOC: Symposium on Theory of Computing","location":"Phoenix, AZ, United States","start_date":"2019-06-23","end_date":"2019-06-26"},"doi":"10.1145/3313276.3316407","quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/1811.01421","open_access":"1"}],"external_id":{"arxiv":["1811.01421"],"isi":["000523199100089"]},"oa":1,"month":"06","publication_identifier":{"isbn":["9781450367059"]},"date_created":"2019-07-24T09:13:05Z","date_updated":"2023-12-13T12:28:28Z","author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Aspnes, James","last_name":"Aspnes","first_name":"James"},{"full_name":"Ellen, Faith","first_name":"Faith","last_name":"Ellen"},{"last_name":"Gelashvili","first_name":"Rati","full_name":"Gelashvili, Rati"},{"full_name":"Zhu, Leqi","last_name":"Zhu","first_name":"Leqi"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"14364"}]},"publication_status":"published","publisher":"ACM Press","department":[{"_id":"DaAl"}],"year":"2019"}]