[{"type":"journal_article","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"}],"issue":"1","status":"public","title":"Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity","intvolume":" 266","_id":"151","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","scopus_import":"1","day":"05","article_processing_charge":"No","page":"257 - 311","publication":"Journal of Differential Equations","citation":{"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.","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"},"date_published":"2019-01-05T00:00:00Z","publist_id":"7770","publication_status":"published","publisher":"Elsevier","department":[{"_id":"JuFi"}],"year":"2019","date_updated":"2023-09-08T13:25:35Z","date_created":"2018-12-11T11:44:54Z","volume":266,"author":[{"orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer","first_name":"Julian L","full_name":"Fischer, Julian L"},{"full_name":"Kneuss, Olivier","last_name":"Kneuss","first_name":"Olivier"}],"month":"01","quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000449108500010"],"arxiv":["1408.1587"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1408.1587"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.jde.2018.07.045"},{"doi":"10.1111/jnc.14601","language":[{"iso":"eng"}],"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":["000462680200002"]},"oa":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","grant_number":"RGP0053/2014","_id":"25D7962E-B435-11E9-9278-68D0E5697425"},{"grant_number":"618444","_id":"25D61E48-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Molecular Mechanisms of Cerebral Cortex Development"},{"call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"month":"04","author":[{"full_name":"Amberg, Nicole","last_name":"Amberg","first_name":"Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Laukoter","first_name":"Susanne","orcid":"0000-0002-7903-3010","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","full_name":"Laukoter, Susanne"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"volume":149,"date_created":"2018-12-11T11:44:14Z","date_updated":"2023-09-11T13:40:26Z","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","publisher":"Wiley","department":[{"_id":"SiHi"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-14T12:45:45Z","date_published":"2019-04-01T00:00:00Z","citation":{"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.","short":"N. Amberg, S. Laukoter, S. Hippenmeyer, Journal of Neurochemistry 149 (2019) 12–26.","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.","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","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.","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"},"publication":"Journal of Neurochemistry","page":"12-26","article_type":"review","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":889709,"creator":"kschuh","file_name":"2019_Wiley_Amberg.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:45Z","date_created":"2020-01-07T13:35:52Z","checksum":"db027721a95d36f5de36aadcd0bdf7e6","relation":"main_file","file_id":"7239"}],"_id":"27","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 149","title":"Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex","status":"public","ddc":["570"],"issue":"1","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"}],"type":"journal_article"},{"author":[{"id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8451-1195","first_name":"Nicoletta","last_name":"Petridou","full_name":"Petridou, Nicoletta"},{"full_name":"Grigolon, Silvia","first_name":"Silvia","last_name":"Grigolon"},{"first_name":"Guillaume","last_name":"Salbreux","full_name":"Salbreux, Guillaume"},{"last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/when-a-fish-becomes-fluid/","relation":"press_release","description":"News on IST Homepage"}]},"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","file_date_updated":"2020-10-21T07:18:35Z","ec_funded":1,"doi":"10.1038/s41556-018-0247-4","acknowledged_ssus":[{"_id":"Bio"}],"language":[{"iso":"eng"}],"external_id":{"isi":["000457468300011"],"pmid":["30559456"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"},{"grant_number":"ALTF710-2016","_id":"253E54C8-B435-11E9-9278-68D0E5697425","name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants (EMBO fellowship)"}],"month":"02","publication_identifier":{"issn":["14657392"]},"file":[{"file_name":"2018_NatureCellBio_Petridou_accepted.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":71590590,"file_id":"8685","relation":"main_file","date_created":"2020-10-21T07:18:35Z","date_updated":"2020-10-21T07:18:35Z","success":1,"checksum":"e38523787b3bc84006f2793de99ad70f"}],"oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5789","status":"public","title":"Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling","ddc":["570"],"intvolume":" 21","abstract":[{"lang":"eng","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."}],"type":"journal_article","date_published":"2019-02-01T00:00:00Z","publication":"Nature Cell Biology","citation":{"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.","short":"N. Petridou, S. Grigolon, G. Salbreux, E.B. Hannezo, C.-P.J. Heisenberg, Nature Cell Biology 21 (2019) 169–178.","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","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.","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","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."},"article_type":"original","page":"169–178","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1"},{"publication_identifier":{"eissn":["1091-6490"]},"month":"02","isi":1,"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1806.10823"],"isi":["000459074400013"],"pmid":[" 30728300"]},"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1812015116","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1812015116","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","volume":116,"date_created":"2018-12-11T11:45:08Z","date_updated":"2023-09-11T14:09:34Z","related_material":{"link":[{"relation":"press_release","description":"News on IST Webpage","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"},{"id":"35084A62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4310-178X","first_name":"Mikhail","last_name":"Shkolnikov","full_name":"Shkolnikov, Mikhail"}],"scopus_import":"1","article_processing_charge":"No","day":"19","page":"2821-2830","article_type":"original","citation":{"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.","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."},"publication":"Proceedings of the National Academy of Sciences","date_published":"2019-02-19T00:00:00Z","type":"journal_article","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. "}],"intvolume":" 116","status":"public","title":"Harmonic dynamics of the Abelian sandpile","_id":"196","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version"},{"quality_controlled":"1","publication":"8th International Conference on Learning Representations","citation":{"mla":"Locatello, Francesco, et al. “Disentangling Factors of Variation Using Few Labels.” 8th International Conference on Learning Representations, 2019.","short":"F. Locatello, M. Tschannen, S. Bauer, G. Rätsch, B. Schölkopf, O. Bachem, in:, 8th International Conference on Learning Representations, 2019.","chicago":"Locatello, Francesco, Michael Tschannen, Stefan Bauer, Gunnar Rätsch, Bernhard Schölkopf, and Olivier Bachem. “Disentangling Factors of Variation Using Few Labels.” In 8th International Conference on Learning Representations, 2019.","ama":"Locatello F, Tschannen M, Bauer S, Rätsch G, Schölkopf B, Bachem O. Disentangling factors of variation using few labels. In: 8th International Conference on Learning Representations. ; 2019.","ista":"Locatello F, Tschannen M, Bauer S, Rätsch G, Schölkopf B, Bachem O. 2019. Disentangling factors of variation using few labels. 8th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","apa":"Locatello, F., Tschannen, M., Bauer, S., Rätsch, G., Schölkopf, B., & Bachem, O. (2019). Disentangling factors of variation using few labels. In 8th International Conference on Learning Representations. Virtual.","ieee":"F. Locatello, M. Tschannen, S. Bauer, G. Rätsch, B. Schölkopf, and O. Bachem, “Disentangling factors of variation using few labels,” in 8th International Conference on Learning Representations, Virtual, 2019."},"main_file_link":[{"url":"https://arxiv.org/abs/1905.01258","open_access":"1"}],"external_id":{"arxiv":["1905.01258"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"ICLR: International Conference on Learning Representations","end_date":"2020-05-01","start_date":"2020-04-26","location":"Virtual"},"date_published":"2019-12-20T00:00:00Z","scopus_import":"1","day":"20","month":"12","article_processing_charge":"No","title":"Disentangling factors of variation using few labels","status":"public","publication_status":"published","department":[{"_id":"FrLo"}],"_id":"14184","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-08-22T14:06:37Z","date_updated":"2023-09-12T07:01:34Z","oa_version":"Preprint","author":[{"first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"full_name":"Tschannen, Michael","first_name":"Michael","last_name":"Tschannen"},{"first_name":"Stefan","last_name":"Bauer","full_name":"Bauer, Stefan"},{"full_name":"Rätsch, Gunnar","first_name":"Gunnar","last_name":"Rätsch"},{"full_name":"Schölkopf, Bernhard","last_name":"Schölkopf","first_name":"Bernhard"},{"first_name":"Olivier","last_name":"Bachem","full_name":"Bachem, Olivier"}],"type":"conference","extern":"1","abstract":[{"text":"Learning disentangled representations is considered a cornerstone problem in\r\nrepresentation learning. Recently, Locatello et al. (2019) demonstrated that\r\nunsupervised disentanglement learning without inductive biases is theoretically\r\nimpossible and that existing inductive biases and unsupervised methods do not\r\nallow to consistently learn disentangled representations. However, in many\r\npractical settings, one might have access to a limited amount of supervision,\r\nfor example through manual labeling of (some) factors of variation in a few\r\ntraining examples. In this paper, we investigate the impact of such supervision\r\non state-of-the-art disentanglement methods and perform a large scale study,\r\ntraining over 52000 models under well-defined and reproducible experimental\r\nconditions. We observe that a small number of labeled examples (0.01--0.5\\% of\r\nthe data set), with potentially imprecise and incomplete labels, is sufficient\r\nto perform model selection on state-of-the-art unsupervised models. Further, we\r\ninvestigate the benefit of incorporating supervision into the training process.\r\nOverall, we empirically validate that with little and imprecise supervision it\r\nis possible to reliably learn disentangled representations.","lang":"eng"}]},{"oa_version":"Preprint","intvolume":" 115","title":"The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14189","abstract":[{"lang":"eng","text":"We consider the problem of recovering a common latent source with independent\r\ncomponents from multiple views. This applies to settings in which a variable is\r\nmeasured with multiple experimental modalities, and where the goal is to\r\nsynthesize the disparate measurements into a single unified representation. We\r\nconsider the case that the observed views are a nonlinear mixing of\r\ncomponent-wise corruptions of the sources. When the views are considered\r\nseparately, this reduces to nonlinear Independent Component Analysis (ICA) for\r\nwhich it is provably impossible to undo the mixing. We present novel\r\nidentifiability proofs that this is possible when the multiple views are\r\nconsidered jointly, showing that the mixing can theoretically be undone using\r\nfunction approximators such as deep neural networks. In contrast to known\r\nidentifiability results for nonlinear ICA, we prove that independent latent\r\nsources with arbitrary mixing can be recovered as long as multiple,\r\nsufficiently different noisy views are available."}],"alternative_title":["PMLR"],"type":"conference","date_published":"2019-05-16T00:00:00Z","page":"217-227","citation":{"chicago":"Gresele, Luigi, Paul K. Rubenstein, Arash Mehrjou, Francesco Locatello, and Bernhard Schölkopf. “The Incomplete Rosetta Stone Problem: Identifiability Results for Multi-View Nonlinear ICA.” In Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence, 115:217–27. ML Research Press, 2019.","short":"L. Gresele, P.K. Rubenstein, A. Mehrjou, F. Locatello, B. Schölkopf, in:, Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence, ML Research Press, 2019, pp. 217–227.","mla":"Gresele, Luigi, et al. “The Incomplete Rosetta Stone Problem: Identifiability Results for Multi-View Nonlinear ICA.” Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence, vol. 115, ML Research Press, 2019, pp. 217–27.","apa":"Gresele, L., Rubenstein, P. K., Mehrjou, A., Locatello, F., & Schölkopf, B. (2019). The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA. In Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence (Vol. 115, pp. 217–227). Tel Aviv, Israel: ML Research Press.","ieee":"L. Gresele, P. K. Rubenstein, A. Mehrjou, F. Locatello, and B. Schölkopf, “The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA,” in Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence, Tel Aviv, Israel, 2019, vol. 115, pp. 217–227.","ista":"Gresele L, Rubenstein PK, Mehrjou A, Locatello F, Schölkopf B. 2019. The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA. Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence. UAI: Uncertainty in Artificial Intelligence, PMLR, vol. 115, 217–227.","ama":"Gresele L, Rubenstein PK, Mehrjou A, Locatello F, Schölkopf B. The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA. In: Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence. Vol 115. ML Research Press; 2019:217-227."},"publication":"Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence","article_processing_charge":"No","day":"16","scopus_import":"1","volume":115,"date_updated":"2023-09-12T08:07:38Z","date_created":"2023-08-22T14:08:35Z","author":[{"full_name":"Gresele, Luigi","first_name":"Luigi","last_name":"Gresele"},{"full_name":"Rubenstein, Paul K.","last_name":"Rubenstein","first_name":"Paul K."},{"first_name":"Arash","last_name":"Mehrjou","full_name":"Mehrjou, Arash"},{"full_name":"Locatello, Francesco","last_name":"Locatello","first_name":"Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"full_name":"Schölkopf, Bernhard","first_name":"Bernhard","last_name":"Schölkopf"}],"publisher":"ML Research Press","department":[{"_id":"FrLo"}],"publication_status":"published","year":"2019","extern":"1","language":[{"iso":"eng"}],"conference":{"start_date":"2019-07-22","location":"Tel Aviv, Israel","end_date":"2019-07-25","name":"UAI: Uncertainty in Artificial Intelligence"},"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1905.06642","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1905.06642"]},"month":"05"},{"date_published":"2019-12-08T00:00:00Z","citation":{"mla":"Locatello, Francesco, et al. “On the Fairness of Disentangled Representations.” Advances in Neural Information Processing Systems, vol. 32, 2019, pp. 14611–14624.","short":"F. Locatello, G. Abbati, T. Rainforth, S. Bauer, B. Schölkopf, O. Bachem, in:, Advances in Neural Information Processing Systems, 2019, pp. 14611–14624.","chicago":"Locatello, Francesco, Gabriele Abbati, Tom Rainforth, Stefan Bauer, Bernhard Schölkopf, and Olivier Bachem. “On the Fairness of Disentangled Representations.” In Advances in Neural Information Processing Systems, 32:14611–14624, 2019.","ama":"Locatello F, Abbati G, Rainforth T, Bauer S, Schölkopf B, Bachem O. On the fairness of disentangled representations. In: Advances in Neural Information Processing Systems. Vol 32. ; 2019:14611–14624.","ista":"Locatello F, Abbati G, Rainforth T, Bauer S, Schölkopf B, Bachem O. 2019. On the fairness of disentangled representations. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32, 14611–14624.","ieee":"F. Locatello, G. Abbati, T. Rainforth, S. Bauer, B. Schölkopf, and O. Bachem, “On the fairness of disentangled representations,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32, pp. 14611–14624.","apa":"Locatello, F., Abbati, G., Rainforth, T., Bauer, S., Schölkopf, B., & Bachem, O. (2019). On the fairness of disentangled representations. In Advances in Neural Information Processing Systems (Vol. 32, pp. 14611–14624). Vancouver, Canada."},"publication":"Advances in Neural Information Processing Systems","page":"14611–14624","article_processing_charge":"No","day":"08","scopus_import":"1","oa_version":"Preprint","_id":"14197","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 32","title":"On the fairness of disentangled representations","status":"public","abstract":[{"text":"Recently there has been a significant interest in learning disentangled\r\nrepresentations, as they promise increased interpretability, generalization to\r\nunseen scenarios and faster learning on downstream tasks. In this paper, we\r\ninvestigate the usefulness of different notions of disentanglement for\r\nimproving the fairness of downstream prediction tasks based on representations.\r\nWe consider the setting where the goal is to predict a target variable based on\r\nthe learned representation of high-dimensional observations (such as images)\r\nthat depend on both the target variable and an \\emph{unobserved} sensitive\r\nvariable. We show that in this setting both the optimal and empirical\r\npredictions can be unfair, even if the target variable and the sensitive\r\nvariable are independent. Analyzing the representations of more than\r\n\\num{12600} trained state-of-the-art disentangled models, we observe that\r\nseveral disentanglement scores are consistently correlated with increased\r\nfairness, suggesting that disentanglement may be a useful property to encourage\r\nfairness when sensitive variables are not observed.","lang":"eng"}],"type":"conference","conference":{"name":"NeurIPS: Neural Information Processing Systems","end_date":"2019-12-14","location":"Vancouver, Canada","start_date":"2019-12-08"},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1905.13662","open_access":"1"}],"external_id":{"arxiv":["1905.13662"]},"oa":1,"quality_controlled":"1","publication_identifier":{"isbn":["9781713807933"]},"month":"12","author":[{"full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco"},{"last_name":"Abbati","first_name":"Gabriele","full_name":"Abbati, Gabriele"},{"full_name":"Rainforth, Tom","last_name":"Rainforth","first_name":"Tom"},{"first_name":"Stefan","last_name":"Bauer","full_name":"Bauer, Stefan"},{"full_name":"Schölkopf, Bernhard","last_name":"Schölkopf","first_name":"Bernhard"},{"full_name":"Bachem, Olivier","last_name":"Bachem","first_name":"Olivier"}],"volume":32,"date_created":"2023-08-22T14:12:28Z","date_updated":"2023-09-12T09:37:22Z","year":"2019","department":[{"_id":"FrLo"}],"publication_status":"published","extern":"1"},{"date_published":"2019-12-29T00:00:00Z","citation":{"ama":"Locatello F, Yurtsever A, Fercoq O, Cevher V. Stochastic Frank-Wolfe for composite convex minimization. In: Advances in Neural Information Processing Systems. Vol 32. ; 2019:14291–14301.","ista":"Locatello F, Yurtsever A, Fercoq O, Cevher V. 2019. Stochastic Frank-Wolfe for composite convex minimization. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32, 14291–14301.","ieee":"F. Locatello, A. Yurtsever, O. Fercoq, and V. Cevher, “Stochastic Frank-Wolfe for composite convex minimization,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32, pp. 14291–14301.","apa":"Locatello, F., Yurtsever, A., Fercoq, O., & Cevher, V. (2019). Stochastic Frank-Wolfe for composite convex minimization. In Advances in Neural Information Processing Systems (Vol. 32, pp. 14291–14301). Vancouver, Canada.","mla":"Locatello, Francesco, et al. “Stochastic Frank-Wolfe for Composite Convex Minimization.” Advances in Neural Information Processing Systems, vol. 32, 2019, pp. 14291–14301.","short":"F. Locatello, A. Yurtsever, O. Fercoq, V. Cevher, in:, Advances in Neural Information Processing Systems, 2019, pp. 14291–14301.","chicago":"Locatello, Francesco, Alp Yurtsever, Olivier Fercoq, and Volkan Cevher. “Stochastic Frank-Wolfe for Composite Convex Minimization.” In Advances in Neural Information Processing Systems, 32:14291–14301, 2019."},"publication":"Advances in Neural Information Processing Systems","page":"14291–14301","article_processing_charge":"No","day":"29","scopus_import":"1","oa_version":"Preprint","_id":"14191","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 32","status":"public","title":"Stochastic Frank-Wolfe for composite convex minimization","abstract":[{"lang":"eng","text":"A broad class of convex optimization problems can be formulated as a semidefinite program (SDP), minimization of a convex function over the positive-semidefinite cone subject to some affine constraints. The majority of classical SDP solvers are designed for the deterministic setting where problem data is readily available. In this setting, generalized conditional gradient methods (aka Frank-Wolfe-type methods) provide scalable solutions by leveraging the so-called linear minimization oracle instead of the projection onto the semidefinite cone. Most problems in machine learning and modern engineering applications, however, contain some degree of stochasticity. In this work, we propose the first conditional-gradient-type method for solving stochastic optimization problems under affine constraints. Our method guarantees O(k−1/3) convergence rate in expectation on the objective residual and O(k−5/12) on the feasibility gap."}],"type":"conference","conference":{"name":"NeurIPS: Neural Information Processing Systems","end_date":"2019-12-14","start_date":"2019-12-08","location":"Vancouver, Canada"},"language":[{"iso":"eng"}],"external_id":{"arxiv":["1901.10348"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1901.10348"}],"quality_controlled":"1","publication_identifier":{"isbn":["9781713807933"]},"month":"12","author":[{"first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"last_name":"Yurtsever","first_name":"Alp","full_name":"Yurtsever, Alp"},{"full_name":"Fercoq, Olivier","last_name":"Fercoq","first_name":"Olivier"},{"full_name":"Cevher, Volkan","last_name":"Cevher","first_name":"Volkan"}],"volume":32,"date_created":"2023-08-22T14:09:35Z","date_updated":"2023-09-12T08:48:45Z","year":"2019","department":[{"_id":"FrLo"}],"publication_status":"published","extern":"1"},{"quality_controlled":"1","publication":"Advances in Neural Information Processing Systems","oa":1,"external_id":{"arxiv":["1905.12506"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1905.12506","open_access":"1"}],"citation":{"apa":"Steenkiste, S. van, Locatello, F., Schmidhuber, J., & Bachem, O. (2019). Are disentangled representations helpful for abstract visual reasoning? In Advances in Neural Information Processing Systems (Vol. 32). Vancouver, Canada.","ieee":"S. van Steenkiste, F. Locatello, J. Schmidhuber, and O. Bachem, “Are disentangled representations helpful for abstract visual reasoning?,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32.","ista":"Steenkiste S van, Locatello F, Schmidhuber J, Bachem O. 2019. Are disentangled representations helpful for abstract visual reasoning? Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32.","ama":"Steenkiste S van, Locatello F, Schmidhuber J, Bachem O. Are disentangled representations helpful for abstract visual reasoning? In: Advances in Neural Information Processing Systems. Vol 32. ; 2019.","chicago":"Steenkiste, Sjoerd van, Francesco Locatello, Jürgen Schmidhuber, and Olivier Bachem. “Are Disentangled Representations Helpful for Abstract Visual Reasoning?” In Advances in Neural Information Processing Systems, Vol. 32, 2019.","short":"S. van Steenkiste, F. Locatello, J. Schmidhuber, O. Bachem, in:, Advances in Neural Information Processing Systems, 2019.","mla":"Steenkiste, Sjoerd van, et al. “Are Disentangled Representations Helpful for Abstract Visual Reasoning?” Advances in Neural Information Processing Systems, vol. 32, 2019."},"language":[{"iso":"eng"}],"conference":{"name":"NeurIPS: Neural Information Processing Systems","start_date":"2019-12-08","location":"Vancouver, Canada","end_date":"2019-12-14"},"date_published":"2019-05-29T00:00:00Z","day":"29","month":"05","publication_identifier":{"isbn":["9781713807933"]},"article_processing_charge":"No","publication_status":"published","status":"public","title":"Are disentangled representations helpful for abstract visual reasoning?","intvolume":" 32","department":[{"_id":"FrLo"}],"_id":"14193","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-08-22T14:09:53Z","date_updated":"2023-09-12T09:02:43Z","oa_version":"Preprint","volume":32,"author":[{"full_name":"Steenkiste, Sjoerd van","last_name":"Steenkiste","first_name":"Sjoerd van"},{"full_name":"Locatello, Francesco","first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683"},{"full_name":"Schmidhuber, Jürgen","last_name":"Schmidhuber","first_name":"Jürgen"},{"first_name":"Olivier","last_name":"Bachem","full_name":"Bachem, Olivier"}],"type":"conference","extern":"1","abstract":[{"lang":"eng","text":"A disentangled representation encodes information about the salient factors\r\nof variation in the data independently. Although it is often argued that this\r\nrepresentational format is useful in learning to solve many real-world\r\ndown-stream tasks, there is little empirical evidence that supports this claim.\r\nIn this paper, we conduct a large-scale study that investigates whether\r\ndisentangled representations are more suitable for abstract reasoning tasks.\r\nUsing two new tasks similar to Raven's Progressive Matrices, we evaluate the\r\nusefulness of the representations learned by 360 state-of-the-art unsupervised\r\ndisentanglement models. Based on these representations, we train 3600 abstract\r\nreasoning models and observe that disentangled representations do in fact lead\r\nto better down-stream performance. In particular, they enable quicker learning\r\nusing fewer samples."}]},{"extern":"1","publisher":"ML Research Press","department":[{"_id":"FrLo"}],"publication_status":"published","year":"2019","volume":97,"date_created":"2023-08-22T14:13:08Z","date_updated":"2023-09-13T07:45:30Z","author":[{"full_name":"Locatello, Francesco","first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683"},{"first_name":"Stefan","last_name":"Bauer","full_name":"Bauer, Stefan"},{"full_name":"Lucic, Mario","first_name":"Mario","last_name":"Lucic"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"},{"full_name":"Gelly, Sylvain","first_name":"Sylvain","last_name":"Gelly"},{"full_name":"Schölkopf, Bernhard","last_name":"Schölkopf","first_name":"Bernhard"},{"full_name":"Bachem, Olivier","first_name":"Olivier","last_name":"Bachem"}],"month":"06","quality_controlled":"1","external_id":{"arxiv":["1811.12359"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.12359"}],"language":[{"iso":"eng"}],"conference":{"end_date":"2019-06-15","location":"Long Beach, CA, United States","start_date":"2019-06-10","name":"International Conference on Machine Learning"},"type":"conference","abstract":[{"text":"The key idea behind the unsupervised learning of disentangled representations\r\nis that real-world data is generated by a few explanatory factors of variation\r\nwhich can be recovered by unsupervised learning algorithms. In this paper, we\r\nprovide a sober look at recent progress in the field and challenge some common\r\nassumptions. We first theoretically show that the unsupervised learning of\r\ndisentangled representations is fundamentally impossible without inductive\r\nbiases on both the models and the data. Then, we train more than 12000 models\r\ncovering most prominent methods and evaluation metrics in a reproducible\r\nlarge-scale experimental study on seven different data sets. We observe that\r\nwhile the different methods successfully enforce properties ``encouraged'' by\r\nthe corresponding losses, well-disentangled models seemingly cannot be\r\nidentified without supervision. Furthermore, increased disentanglement does not\r\nseem to lead to a decreased sample complexity of learning for downstream tasks.\r\nOur results suggest that future work on disentanglement learning should be\r\nexplicit about the role of inductive biases and (implicit) supervision,\r\ninvestigate concrete benefits of enforcing disentanglement of the learned\r\nrepresentations, and consider a reproducible experimental setup covering\r\nseveral data sets.","lang":"eng"}],"intvolume":" 97","status":"public","title":"Challenging common assumptions in the unsupervised learning of disentangled representations","_id":"14200","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"09","page":"4114-4124","citation":{"mla":"Locatello, Francesco, et al. “Challenging Common Assumptions in the Unsupervised Learning of Disentangled Representations.” Proceedings of the 36th International Conference on Machine Learning, vol. 97, ML Research Press, 2019, pp. 4114–24.","short":"F. Locatello, S. Bauer, M. Lucic, G. Rätsch, S. Gelly, B. Schölkopf, O. Bachem, in:, Proceedings of the 36th International Conference on Machine Learning, ML Research Press, 2019, pp. 4114–4124.","chicago":"Locatello, Francesco, Stefan Bauer, Mario Lucic, Gunnar Rätsch, Sylvain Gelly, Bernhard Schölkopf, and Olivier Bachem. “Challenging Common Assumptions in the Unsupervised Learning of Disentangled Representations.” In Proceedings of the 36th International Conference on Machine Learning, 97:4114–24. ML Research Press, 2019.","ama":"Locatello F, Bauer S, Lucic M, et al. Challenging common assumptions in the unsupervised learning of disentangled representations. In: Proceedings of the 36th International Conference on Machine Learning. Vol 97. ML Research Press; 2019:4114-4124.","ista":"Locatello F, Bauer S, Lucic M, Rätsch G, Gelly S, Schölkopf B, Bachem O. 2019. Challenging common assumptions in the unsupervised learning of disentangled representations. Proceedings of the 36th International Conference on Machine Learning. International Conference on Machine Learning vol. 97, 4114–4124.","ieee":"F. Locatello et al., “Challenging common assumptions in the unsupervised learning of disentangled representations,” in Proceedings of the 36th International Conference on Machine Learning, Long Beach, CA, United States, 2019, vol. 97, pp. 4114–4124.","apa":"Locatello, F., Bauer, S., Lucic, M., Rätsch, G., Gelly, S., Schölkopf, B., & Bachem, O. (2019). Challenging common assumptions in the unsupervised learning of disentangled representations. In Proceedings of the 36th International Conference on Machine Learning (Vol. 97, pp. 4114–4124). Long Beach, CA, United States: ML Research Press."},"publication":"Proceedings of the 36th International Conference on Machine Learning","date_published":"2019-06-09T00:00:00Z"},{"date_created":"2019-01-11T07:37:47Z","date_updated":"2023-09-13T08:47:16Z","volume":15,"author":[{"full_name":"Kavcic, Bor","first_name":"Bor","last_name":"Kavcic","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X"},{"first_name":"A.","last_name":"Sakashita","full_name":"Sakashita, A."},{"first_name":"H.","last_name":"Noguchi","full_name":"Noguchi, H."},{"full_name":"Ziherl, P.","last_name":"Ziherl","first_name":"P."}],"publication_status":"published","publisher":"Royal Society of Chemistry","department":[{"_id":"GaTk"}],"year":"2019","pmid":1,"license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","file_date_updated":"2020-10-09T11:00:05Z","language":[{"iso":"eng"}],"doi":"10.1039/c8sm01956h","quality_controlled":"1","isi":1,"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":{"pmid":["30629082"],"isi":["000457329700003"]},"month":"01","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"file":[{"file_name":"lmt_sftmtr_V8.pdf","access_level":"open_access","creator":"bkavcic","file_size":5370762,"content_type":"application/pdf","file_id":"8641","relation":"main_file","date_updated":"2020-10-09T11:00:05Z","date_created":"2020-10-09T11:00:05Z","success":1,"checksum":"614c337d6424ccd3d48d1b1f9513510d"}],"oa_version":"Submitted Version","ddc":["530"],"status":"public","title":"Limiting shapes of confined lipid vesicles","intvolume":" 15","_id":"5817","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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","article_type":"original","page":"602-614","publication":"Soft Matter","citation":{"ista":"Kavcic B, Sakashita A, Noguchi H, Ziherl P. 2019. Limiting shapes of confined lipid vesicles. Soft Matter. 15(4), 602–614.","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.","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","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","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.","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.","short":"B. Kavcic, A. Sakashita, H. Noguchi, P. Ziherl, Soft Matter 15 (2019) 602–614."},"day":"10","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1"},{"publication_identifier":{"issn":["09442669"]},"month":"02","doi":"10.1007/s00526-018-1456-1","language":[{"iso":"eng"}],"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":["1805.06040"],"isi":["000452849400001"]},"oa":1,"project":[{"grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"},{"_id":"260482E2-B435-11E9-9278-68D0E5697425","grant_number":" F06504","name":"Taming Complexity in Partial Di erential Systems","call_identifier":"FWF"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"isi":1,"quality_controlled":"1","ec_funded":1,"file_date_updated":"2020-07-14T12:47:55Z","article_number":"19","author":[{"last_name":"Erbar","first_name":"Matthias","full_name":"Erbar, Matthias"},{"full_name":"Maas, Jan","first_name":"Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338"},{"last_name":"Wirth","first_name":"Melchior","full_name":"Wirth, Melchior"}],"volume":58,"date_created":"2018-12-11T11:44:29Z","date_updated":"2023-09-13T09:12:35Z","year":"2019","department":[{"_id":"JaMa"}],"publisher":"Springer","publication_status":"published","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1","date_published":"2019-02-01T00:00:00Z","citation":{"short":"M. Erbar, J. Maas, M. Wirth, Calculus of Variations and Partial Differential Equations 58 (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.","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.","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","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.","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."},"publication":"Calculus of Variations and Partial Differential Equations","article_type":"original","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."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_size":645565,"content_type":"application/pdf","creator":"dernst","file_name":"2018_Calculus_Erbar.pdf","access_level":"open_access","date_created":"2019-01-28T15:37:11Z","date_updated":"2020-07-14T12:47:55Z","checksum":"ba05ac2d69de4c58d2cd338b63512798","relation":"main_file","file_id":"5895"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"73","intvolume":" 58","title":"On the geometry of geodesics in discrete optimal transport","status":"public","ddc":["510"]},{"abstract":[{"text":"Learning meaningful and compact representations with disentangled semantic\r\naspects is considered to be of key importance in representation learning. Since\r\nreal-world data is notoriously costly to collect, many recent state-of-the-art\r\ndisentanglement models have heavily relied on synthetic toy data-sets. In this\r\npaper, we propose a novel data-set which consists of over one million images of\r\nphysical 3D objects with seven factors of variation, such as object color,\r\nshape, size and position. In order to be able to control all the factors of\r\nvariation precisely, we built an experimental platform where the objects are\r\nbeing moved by a robotic arm. In addition, we provide two more datasets which\r\nconsist of simulations of the experimental setup. These datasets provide for\r\nthe first time the possibility to systematically investigate how well different\r\ndisentanglement methods perform on real data in comparison to simulation, and\r\nhow simulated data can be leveraged to build better representations of the real\r\nworld. We provide a first experimental study of these questions and our results\r\nindicate that learned models transfer poorly, but that model and hyperparameter\r\nselection is an effective means of transferring information to the real world.","lang":"eng"}],"extern":"1","type":"conference","author":[{"last_name":"Gondal","first_name":"Muhammad Waleed","full_name":"Gondal, Muhammad Waleed"},{"full_name":"Wüthrich, Manuel","first_name":"Manuel","last_name":"Wüthrich"},{"last_name":"Miladinović","first_name":"Đorđe","full_name":"Miladinović, Đorđe"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","first_name":"Francesco","last_name":"Locatello","full_name":"Locatello, Francesco"},{"full_name":"Breidt, Martin","last_name":"Breidt","first_name":"Martin"},{"full_name":"Volchkov, Valentin","first_name":"Valentin","last_name":"Volchkov"},{"first_name":"Joel","last_name":"Akpo","full_name":"Akpo, Joel"},{"first_name":"Olivier","last_name":"Bachem","full_name":"Bachem, Olivier"},{"first_name":"Bernhard","last_name":"Schölkopf","full_name":"Schölkopf, Bernhard"},{"full_name":"Bauer, Stefan","first_name":"Stefan","last_name":"Bauer"}],"oa_version":"Preprint","volume":32,"date_created":"2023-08-22T14:09:13Z","date_updated":"2023-09-13T09:46:38Z","_id":"14190","year":"2019","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 32","department":[{"_id":"FrLo"}],"publication_status":"published","title":"On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset","status":"public","publication_identifier":{"isbn":["9781713807933"]},"article_processing_charge":"No","month":"06","day":"07","date_published":"2019-06-07T00:00:00Z","conference":{"name":"NeurIPS: Neural Information Processing Systems","end_date":"2019-12-14","start_date":"2019-12-08","location":"Vancouver, Canada"},"language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1906.03292"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1906.03292"}],"citation":{"chicago":"Gondal, Muhammad Waleed, Manuel Wüthrich, Đorđe Miladinović, Francesco Locatello, Martin Breidt, Valentin Volchkov, Joel Akpo, Olivier Bachem, Bernhard Schölkopf, and Stefan Bauer. “On the Transfer of Inductive Bias from Simulation to the Real World: A New Disentanglement Dataset.” In Advances in Neural Information Processing Systems, Vol. 32, 2019.","mla":"Gondal, Muhammad Waleed, et al. “On the Transfer of Inductive Bias from Simulation to the Real World: A New Disentanglement Dataset.” Advances in Neural Information Processing Systems, vol. 32, 2019.","short":"M.W. Gondal, M. Wüthrich, Đ. Miladinović, F. Locatello, M. Breidt, V. Volchkov, J. Akpo, O. Bachem, B. Schölkopf, S. Bauer, in:, Advances in Neural Information Processing Systems, 2019.","ista":"Gondal MW, Wüthrich M, Miladinović Đ, Locatello F, Breidt M, Volchkov V, Akpo J, Bachem O, Schölkopf B, Bauer S. 2019. On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32.","apa":"Gondal, M. W., Wüthrich, M., Miladinović, Đ., Locatello, F., Breidt, M., Volchkov, V., … Bauer, S. (2019). On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset. In Advances in Neural Information Processing Systems (Vol. 32). Vancouver, Canada.","ieee":"M. W. Gondal et al., “On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32.","ama":"Gondal MW, Wüthrich M, Miladinović Đ, et al. On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset. In: Advances in Neural Information Processing Systems. Vol 32. ; 2019."},"publication":"Advances in Neural Information Processing Systems","quality_controlled":"1"},{"issue":"4","abstract":[{"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","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6982","intvolume":" 15","title":"Recognizing weak embeddings of graphs","status":"public","day":"01","scopus_import":1,"date_published":"2019-10-01T00:00:00Z","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."},"publication":"ACM Transactions on Algorithms","article_type":"original","article_number":"50","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"309"}]},"author":[{"full_name":"Akitaya, Hugo","last_name":"Akitaya","first_name":"Hugo"},{"full_name":"Fulek, Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","first_name":"Radoslav","last_name":"Fulek"},{"last_name":"Tóth","first_name":"Csaba","full_name":"Tóth, Csaba"}],"volume":15,"date_updated":"2023-09-15T12:19:31Z","date_created":"2019-11-04T15:45:17Z","year":"2019","department":[{"_id":"UlWa"}],"publisher":"ACM","publication_status":"published","month":"10","doi":"10.1145/3344549","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1709.09209"]},"main_file_link":[{"url":"https://arxiv.org/abs/1709.09209","open_access":"1"}],"project":[{"call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs","_id":"261FA626-B435-11E9-9278-68D0E5697425","grant_number":"M02281"}],"quality_controlled":"1"},{"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"},"supervisor":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:6894","month":"09","publication_identifier":{"eissn":["2663-337X"]},"publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Institute of Science and Technology Austria","year":"2019","date_created":"2019-09-22T14:08:44Z","date_updated":"2023-09-19T09:30:43Z","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":[{"relation":"part_of_dissertation","status":"public","id":"631"},{"id":"647","relation":"part_of_dissertation","status":"public"},{"id":"140","relation":"part_of_dissertation","status":"public"}]},"file_date_updated":"2020-07-14T12:47:43Z","page":"132","citation":{"ama":"Giacobbe M. Automatic time-unbounded reachability analysis of hybrid systems. 2019. doi:10.15479/AT:ISTA:6894","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","ieee":"M. Giacobbe, “Automatic time-unbounded reachability analysis of hybrid systems,” Institute of Science and Technology Austria, 2019.","ista":"Giacobbe M. 2019. Automatic time-unbounded reachability analysis of hybrid systems. Institute of Science and Technology Austria.","short":"M. Giacobbe, Automatic Time-Unbounded Reachability Analysis of Hybrid Systems, Institute of Science and Technology Austria, 2019.","mla":"Giacobbe, Mirco. Automatic Time-Unbounded Reachability Analysis of Hybrid Systems. Institute of Science and Technology Austria, 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."},"date_published":"2019-09-30T00:00:00Z","day":"30","article_processing_charge":"No","has_accepted_license":"1","ddc":["000"],"status":"public","title":"Automatic time-unbounded reachability analysis of hybrid systems","_id":"6894","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"relation":"main_file","file_id":"6916","date_created":"2019-09-27T14:15:05Z","date_updated":"2020-07-14T12:47:43Z","checksum":"773beaf4a85dc2acc2c12b578fbe1965","file_name":"giacobbe_thesis.pdf","access_level":"open_access","content_type":"application/pdf","file_size":4100685,"creator":"mgiacobbe"},{"relation":"source_file","file_id":"6917","checksum":"97f1c3da71feefd27e6e625d32b4c75b","date_updated":"2020-07-14T12:47:43Z","date_created":"2019-09-27T14:22:04Z","access_level":"closed","file_name":"giacobbe_thesis_src.tar.gz","file_size":7959732,"content_type":"application/gzip","creator":"mgiacobbe"}],"oa_version":"Published Version","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"}]},{"date_published":"2019-01-09T00:00:00Z","doi":"10.5061/dryad.2kb6fh4","citation":{"chicago":"Barton, Nicholas H. “Data from: The Consequences of an Introgression Event.” Dryad, 2019. https://doi.org/10.5061/dryad.2kb6fh4.","mla":"Barton, Nicholas H. Data from: The Consequences of an Introgression Event. Dryad, 2019, doi:10.5061/dryad.2kb6fh4.","short":"N.H. Barton, (2019).","ista":"Barton NH. 2019. Data from: The consequences of an introgression event, Dryad, 10.5061/dryad.2kb6fh4.","apa":"Barton, N. H. (2019). Data from: The consequences of an introgression event. Dryad. https://doi.org/10.5061/dryad.2kb6fh4","ieee":"N. H. Barton, “Data from: The consequences of an introgression event.” Dryad, 2019.","ama":"Barton NH. Data from: The consequences of an introgression event. 2019. doi:10.5061/dryad.2kb6fh4"},"oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.2kb6fh4","open_access":"1"}],"day":"09","month":"01","article_processing_charge":"No","author":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"40"}]},"date_created":"2021-08-06T12:03:50Z","date_updated":"2023-09-19T10:06:07Z","oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9805","year":"2019","status":"public","title":"Data from: The consequences of an introgression event","department":[{"_id":"NiBa"}],"publisher":"Dryad","abstract":[{"lang":"eng","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?"}],"type":"research_data_reference"},{"type":"journal_article","issue":"2","abstract":[{"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.","lang":"eng"}],"intvolume":" 39","ddc":["570"],"status":"public","title":"The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate","_id":"8","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"file_name":"2019_JournNeuroscience_Trebuchet.pdf","access_level":"open_access","file_size":9455414,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8596","date_created":"2020-10-02T09:33:28Z","date_updated":"2020-10-02T09:33:28Z","checksum":"8f6925eb4cd1e8747d8ea25929c68de6","success":1}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"09","page":"238-255","article_type":"original","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"},"publication":"Journal of Neuroscience","date_published":"2019-01-09T00:00:00Z","publist_id":"8048","ec_funded":1,"file_date_updated":"2020-10-02T09:33:28Z","department":[{"_id":"DaSi"}],"publisher":"Society for Neuroscience","publication_status":"published","pmid":1,"year":"2019","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.","volume":39,"date_updated":"2023-09-19T10:10:55Z","date_created":"2018-12-11T11:44:07Z","author":[{"first_name":"Guillaume","last_name":"Trébuchet","full_name":"Trébuchet, Guillaume"},{"full_name":"Cattenoz, Pierre B","first_name":"Pierre B","last_name":"Cattenoz"},{"full_name":"Zsámboki, János","last_name":"Zsámboki","first_name":"János"},{"full_name":"Mazaud, David","first_name":"David","last_name":"Mazaud"},{"first_name":"Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E"},{"first_name":"Manolis","last_name":"Fanto","full_name":"Fanto, Manolis"},{"full_name":"Giangrande, Angela","first_name":"Angela","last_name":"Giangrande"}],"month":"01","project":[{"grant_number":"334077","_id":"2536F660-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Investigating the role of transporters in invasive migration through junctions"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000455189900006"],"pmid":["30504274"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1523/JNEUROSCI.1059-18.2018"},{"publist_id":"8052","file_date_updated":"2020-07-14T12:46:35Z","author":[{"full_name":"Ganev, Iordan V","id":"447491B8-F248-11E8-B48F-1D18A9856A87","last_name":"Ganev","first_name":"Iordan V"}],"volume":99,"date_created":"2018-12-11T11:44:06Z","date_updated":"2023-09-19T10:13:08Z","year":"2019","department":[{"_id":"TaHa"}],"publisher":"Wiley","publication_status":"published","month":"06","doi":"10.1112/jlms.12193","language":[{"iso":"eng"}],"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":["000470025900008"]},"oa":1,"quality_controlled":"1","isi":1,"issue":"3","abstract":[{"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.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"7238","relation":"main_file","checksum":"1be56239b2cd740a0e9a084f773c22f6","date_created":"2020-01-07T13:31:53Z","date_updated":"2020-07-14T12:46:35Z","access_level":"open_access","file_name":"2019_Wiley_Ganev.pdf","creator":"kschuh","file_size":431754,"content_type":"application/pdf"}],"_id":"5","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 99","status":"public","ddc":["510"],"title":"The wonderful compactification for quantum groups","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2019-06-01T00:00:00Z","citation":{"ista":"Ganev IV. 2019. The wonderful compactification for quantum groups. Journal of the London Mathematical Society. 99(3), 778–806.","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","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.","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","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.","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.","short":"I.V. Ganev, Journal of the London Mathematical Society 99 (2019) 778–806."},"publication":"Journal of the London Mathematical Society","page":"778-806"},{"doi":"10.15479/AT:ISTA:7172","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"supervisor":[{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"degree_awarded":"PhD","oa":1,"publication_identifier":{"eissn":["2663-337X"]},"month":"12","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1346"},{"relation":"part_of_dissertation","status":"public","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","year":"2019","department":[{"_id":"JiFr"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","file_date_updated":"2020-07-14T12:47:51Z","date_published":"2019-12-12T00:00:00Z","citation":{"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.","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.","short":"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.","ieee":"M. K. Vasileva, “Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2019.","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","ama":"Vasileva MK. Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana. 2019. doi:10.15479/AT:ISTA:7172"},"page":"192","has_accepted_license":"1","article_processing_charge":"No","day":"12","oa_version":"Published Version","file":[{"file_id":"7175","relation":"source_file","date_updated":"2020-07-14T12:47:51Z","date_created":"2019-12-12T09:32:36Z","checksum":"ef981c1a3b1d9da0edcbedcff4970d37","file_name":"Thesis_Mina_final_upload_7.docx","access_level":"closed","creator":"mvasilev","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":20454014},{"file_id":"7176","relation":"main_file","date_created":"2019-12-12T09:33:10Z","date_updated":"2020-07-14T12:47:51Z","checksum":"3882c4585e46c9cfb486e4225cad54ab","file_name":"Thesis_Mina_final_upload_7.pdf","access_level":"open_access","creator":"mvasilev","content_type":"application/pdf","file_size":11565025}],"_id":"7172","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana","ddc":["570"],"abstract":[{"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.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"]},{"type":"journal_article","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"}],"_id":"6093","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 14","title":"Fluid dynamics during bleb formation in migrating cells in vivo","ddc":["570"],"status":"public","oa_version":"Published Version","file":[{"checksum":"b885de050ed4bb3c86f706487a47197f","date_updated":"2020-07-14T12:47:19Z","date_created":"2019-03-11T16:09:23Z","relation":"main_file","file_id":"6096","content_type":"application/pdf","file_size":2967731,"creator":"dernst","access_level":"open_access","file_name":"2019_PLoSOne_Goudarzi.pdf"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"26","citation":{"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.","short":"M. Goudarzi, A. Boquet-Pujadas, J.C. Olivo-Marin, E. Raz, PLOS ONE 14 (2019).","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.","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","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.","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.","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"},"publication":"PLOS ONE","date_published":"2019-02-26T00:00:00Z","article_number":"e0212699","file_date_updated":"2020-07-14T12:47:19Z","year":"2019","department":[{"_id":"Bio"}],"publisher":"Public Library of Science","publication_status":"published","author":[{"id":"3384113A-F248-11E8-B48F-1D18A9856A87","last_name":"Goudarzi","first_name":"Mohammad","full_name":"Goudarzi, Mohammad"},{"last_name":"Boquet-Pujadas","first_name":"Aleix","full_name":"Boquet-Pujadas, Aleix"},{"full_name":"Olivo-Marin, Jean Christophe","last_name":"Olivo-Marin","first_name":"Jean Christophe"},{"full_name":"Raz, Erez","last_name":"Raz","first_name":"Erez"}],"volume":14,"date_updated":"2023-09-19T14:46:47Z","date_created":"2019-03-10T22:59:21Z","month":"02","external_id":{"isi":["000459712100022"]},"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,"quality_controlled":"1","isi":1,"doi":"10.1371/journal.pone.0212699","language":[{"iso":"eng"}]},{"has_accepted_license":"1","article_processing_charge":"No","day":"23","keyword":["Information estimation","Time-series","data analysis"],"date_published":"2019-05-23T00:00:00Z","page":"135","citation":{"ista":"Cepeda Humerez SA. 2019. Estimating information flow in single cells. Institute of Science and Technology Austria.","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.","ama":"Cepeda Humerez SA. Estimating information flow in single cells. 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.","mla":"Cepeda Humerez, Sarah A. Estimating Information Flow in Single Cells. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6473.","short":"S.A. Cepeda Humerez, Estimating Information Flow in Single Cells, Institute of Science and Technology Austria, 2019."},"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. "}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"relation":"source_file","file_id":"6480","checksum":"75f9184c1346e10a5de5f9cc7338309a","date_created":"2019-05-23T11:18:16Z","date_updated":"2020-07-14T12:47:31Z","access_level":"closed","file_name":"Thesis_Cepeda.zip","content_type":"application/zip","file_size":23937464,"creator":"scepeda"},{"date_updated":"2020-07-14T12:47:31Z","date_created":"2019-05-23T11:18:13Z","checksum":"afdc0633ddbd71d5b13550d7fb4f4454","relation":"main_file","file_id":"6481","content_type":"application/pdf","file_size":16646985,"creator":"scepeda","file_name":"CepedaThesis.pdf","access_level":"open_access"}],"ddc":["004"],"title":"Estimating information flow in single cells","status":"public","_id":"6473","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["2663-337X"]},"month":"05","language":[{"iso":"eng"}],"supervisor":[{"first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:6473","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,"file_date_updated":"2020-07-14T12:47:31Z","date_created":"2019-05-21T00:11:23Z","date_updated":"2023-09-19T15:13:26Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1576"},{"id":"6900","status":"public","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"281"},{"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"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"}],"publication_status":"published","year":"2019"},{"month":"03","publication_identifier":{"issn":["2663-337X"]},"oa":1,"project":[{"name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27"}],"doi":"10.15479/at:ista:th6071","degree_awarded":"PhD","supervisor":[{"last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:18Z","year":"2019","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"author":[{"full_name":"Prizak, Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","first_name":"Roshan","last_name":"Prizak"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1358"},{"id":"955","status":"public","relation":"part_of_dissertation"}]},"date_updated":"2023-09-22T10:00:48Z","date_created":"2019-03-06T16:16:10Z","day":"11","has_accepted_license":"1","article_processing_charge":"No","citation":{"ama":"Prizak R. Coevolution of transcription factors and their binding sites in sequence space. 2019. doi:10.15479/at:ista:th6071","ista":"Prizak R. 2019. Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria.","ieee":"R. Prizak, “Coevolution of transcription factors and their binding sites in sequence space,” Institute of Science and Technology Austria, 2019.","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","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.","short":"R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in Sequence Space, Institute of Science and Technology Austria, 2019.","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."},"page":"189","date_published":"2019-03-11T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"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. ","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6071","title":"Coevolution of transcription factors and their binding sites in sequence space","status":"public","ddc":["576"],"file":[{"date_updated":"2020-07-14T12:47:18Z","date_created":"2019-03-06T16:05:07Z","checksum":"e60a72de35d270b31f1a23d50f224ec0","relation":"main_file","file_id":"6072","content_type":"application/pdf","file_size":20995465,"creator":"rprizak","file_name":"Thesis_final_PDFA_RoshanPrizak.pdf","access_level":"open_access"},{"date_updated":"2020-07-14T12:47:18Z","date_created":"2019-03-06T16:09:39Z","checksum":"67c2630333d05ebafef5f018863a8465","relation":"source_file","title":"Latex files","file_id":"6073","file_size":85705272,"content_type":"application/zip","creator":"rprizak","file_name":"thesis_v2_merge.zip","access_level":"closed"}],"oa_version":"Published Version"},{"page":"1135-1177","article_type":"original","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","ista":"Srivastava TK. 2019. On derived equivalences of k3 surfaces in positive characteristic. Documenta Mathematica. 24, 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","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.","short":"T.K. Srivastava, Documenta Mathematica 24 (2019) 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."},"publication":"Documenta Mathematica","date_published":"2019-05-20T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"20","intvolume":" 24","status":"public","ddc":["510"],"title":"On derived equivalences of k3 surfaces in positive characteristic","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7436","oa_version":"Published Version","file":[{"checksum":"9a1a64bd49ab03fa4f738fb250fc4f90","date_created":"2020-02-03T06:26:12Z","date_updated":"2020-07-14T12:47:58Z","relation":"main_file","file_id":"7438","file_size":469730,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2019_DocumMath_Srivastava.pdf"}],"type":"journal_article","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"}],"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":["000517806400019"],"arxiv":["1809.08970"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.25537/dm.2019v24.1135-1177","publication_identifier":{"eissn":["1431-0643"],"issn":["1431-0635"]},"month":"05","publisher":"EMS Press","department":[{"_id":"TaHa"}],"publication_status":"published","year":"2019","volume":24,"date_updated":"2023-10-17T07:42:21Z","date_created":"2020-02-02T23:01:06Z","author":[{"full_name":"Srivastava, Tanya K","id":"4D046628-F248-11E8-B48F-1D18A9856A87","last_name":"Srivastava","first_name":"Tanya K"}],"file_date_updated":"2020-07-14T12:47:58Z"},{"abstract":[{"lang":"eng","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."}],"issue":"3","type":"journal_article","oa_version":"Preprint","title":"Limit law of a second class particle in TASEP with non-random initial condition","status":"public","intvolume":" 55","_id":"72","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"25","article_processing_charge":"No","scopus_import":"1","date_published":"2019-09-25T00:00:00Z","article_type":"original","page":"1203-1225","publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","citation":{"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","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.","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","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.","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.","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."},"ec_funded":1,"date_updated":"2023-10-17T08:53:45Z","date_created":"2018-12-11T11:44:29Z","volume":55,"author":[{"first_name":"Patrick","last_name":"Ferrari","full_name":"Ferrari, Patrick"},{"full_name":"Ghosal, Promit","last_name":"Ghosal","first_name":"Promit"},{"full_name":"Nejjar, Peter","id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Nejjar"}],"publication_status":"published","publisher":"Institute of Mathematical Statistics","department":[{"_id":"LaEr"},{"_id":"JaMa"}],"year":"2019","month":"09","publication_identifier":{"issn":["0246-0203"]},"language":[{"iso":"eng"}],"doi":"10.1214/18-AIHP916","isi":1,"quality_controlled":"1","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"},{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1710.02323","open_access":"1"}],"external_id":{"arxiv":["1710.02323"],"isi":["000487763200001"]}},{"file_date_updated":"2020-07-14T12:47:35Z","date_updated":"2023-10-17T11:33:58Z","date_created":"2019-07-21T21:59:15Z","volume":72,"author":[{"full_name":"Danowski, Patrick","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6026-4409","first_name":"Patrick","last_name":"Danowski"}],"related_material":{"record":[{"id":"5686","status":"public","relation":"earlier_version"}]},"publication_status":"published","publisher":"Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","department":[{"_id":"E-Lib"}],"year":"2019","month":"05","publication_identifier":{"eissn":["1022-2588"]},"language":[{"iso":"eng"}],"doi":"10.31263/voebm.v72i1.2276","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"},"oa":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"}],"issue":"1","type":"journal_article","file":[{"file_id":"6661","relation":"main_file","checksum":"c0d2695d6d0d34e62ba06fb3f0ebaaed","date_created":"2019-07-22T08:45:03Z","date_updated":"2020-07-14T12:47:35Z","access_level":"open_access","file_name":"2019_MitteilungenDerVOEB_Danowski.pdf","creator":"apreinsp","file_size":468558,"content_type":"application/pdf"}],"oa_version":"Published Version","ddc":["020"],"title":"An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors","status":"public","intvolume":" 72","_id":"6657","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"17","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2019-05-17T00:00:00Z","article_type":"original","page":"59-65","publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","citation":{"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.","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","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."}},{"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","publication_status":"published","status":"public","_id":"6646","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","oa_version":"None","date_updated":"2023-10-17T12:14:29Z","date_created":"2019-07-17T09:40:44Z","author":[{"last_name":"Khatoniar","first_name":"Mandeep","full_name":"Khatoniar, Mandeep"},{"full_name":"Yama, Nicholas","first_name":"Nicholas","last_name":"Yama"},{"full_name":"Ghazaryan, Areg","first_name":"Areg","last_name":"Ghazaryan","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543"},{"last_name":"Guddala","first_name":"Sriram","full_name":"Guddala, Sriram"},{"full_name":"Ghaemi, Pouyan","first_name":"Pouyan","last_name":"Ghaemi"},{"last_name":"Menon","first_name":"Vinod","full_name":"Menon, Vinod"}],"scopus_import":"1","article_processing_charge":"No","publication_identifier":{"isbn":["9781943580576"]},"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. 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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","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.","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.","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."},"publication":"Nonlinear Optics, OSA Technical Digest","quality_controlled":"1","doi":"10.1364/NLO.2019.NM2A.5","date_published":"2019-07-15T00:00:00Z","conference":{"location":"Waikoloa Beach, Hawaii (HI), United States","start_date":"2019-07-15","end_date":"2019-07-19","name":"NLO: Nonlinear Optics"},"language":[{"iso":"eng"}],"scopus_import":"1","publication_identifier":{"isbn":["9781557528209"]},"article_processing_charge":"No","month":"07","day":"15","_id":"7233","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","publisher":"Optica Publishing Group","department":[{"_id":"JoFi"}],"title":"Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity","publication_status":"published","status":"public","author":[{"full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez","first_name":"Alfredo R"},{"full_name":"Sedlmeir, Florian","last_name":"Sedlmeir","first_name":"Florian"},{"first_name":"Gerd","last_name":"Leuchs","full_name":"Leuchs, Gerd"},{"last_name":"Kumari","first_name":"Madhuri","full_name":"Kumari, Madhuri"},{"full_name":"Schwefel, Harald G.L.","last_name":"Schwefel","first_name":"Harald G.L."}],"oa_version":"None","date_created":"2020-01-05T23:00:48Z","date_updated":"2023-10-17T12:14:46Z","type":"conference","article_number":"NM2A.5","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."}]},{"oa_version":"Preprint","_id":"6240","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 55","title":"Location of the spectrum of Kronecker random matrices","status":"public","issue":"2","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."}],"type":"journal_article","date_published":"2019-05-01T00:00:00Z","citation":{"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.","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.","short":"J. Alt, L. Erdös, T.H. Krüger, Y. Nemish, Annales de l’institut Henri Poincare 55 (2019) 661–696.","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.","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.","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"},"publication":"Annales de l'institut Henri Poincare","page":"661-696","article_processing_charge":"No","day":"01","scopus_import":"1","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"149"}]},"author":[{"id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","last_name":"Alt","full_name":"Alt, Johannes"},{"full_name":"Erdös, László","first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297","first_name":"Torben H","last_name":"Krüger","full_name":"Krüger, Torben H"},{"full_name":"Nemish, Yuriy","first_name":"Yuriy","last_name":"Nemish","id":"4D902E6A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7327-856X"}],"volume":55,"date_created":"2019-04-08T14:05:04Z","date_updated":"2023-10-17T12:20:20Z","year":"2019","publisher":"Institut Henri Poincaré","department":[{"_id":"LaEr"}],"publication_status":"published","ec_funded":1,"doi":"10.1214/18-AIHP894","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000467793600003"],"arxiv":["1706.08343"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.08343"}],"project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["0246-0203"]},"month":"05"},{"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":["31329595"],"isi":["000478689100025"]},"quality_controlled":"1","isi":1,"doi":"10.1371/journal.pgen.1008268","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"issn":["1553-7404"]},"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"SiHi"}],"publisher":"Public Library of Science","author":[{"full_name":"Andergassen, Daniel","first_name":"Daniel","last_name":"Andergassen"},{"full_name":"Muckenhuber, Markus","first_name":"Markus","last_name":"Muckenhuber"},{"full_name":"Bammer, Philipp C.","first_name":"Philipp C.","last_name":"Bammer"},{"full_name":"Kulinski, Tomasz M.","first_name":"Tomasz M.","last_name":"Kulinski"},{"last_name":"Theussl","first_name":"Hans-Christian","full_name":"Theussl, Hans-Christian"},{"full_name":"Shimizu, Takahiko","last_name":"Shimizu","first_name":"Takahiko"},{"last_name":"Penninger","first_name":"Josef M.","full_name":"Penninger, Josef M."},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","first_name":"Florian","last_name":"Pauler","full_name":"Pauler, Florian"},{"full_name":"Hudson, Quanah J.","last_name":"Hudson","first_name":"Quanah J."}],"date_updated":"2023-10-17T12:30:27Z","date_created":"2020-01-29T16:14:07Z","volume":15,"article_number":"e1008268","file_date_updated":"2020-07-14T12:47:57Z","publication":"PLoS Genetics","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"},"article_type":"original","date_published":"2019-07-22T00:00:00Z","scopus_import":"1","day":"22","has_accepted_license":"1","article_processing_charge":"No","_id":"7399","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"title":"The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes","status":"public","intvolume":" 15","file":[{"date_created":"2020-02-04T10:11:55Z","date_updated":"2020-07-14T12:47:57Z","checksum":"2f51fc91e4a4199827adc51d432ad864","file_id":"7446","relation":"main_file","creator":"dernst","file_size":2302307,"content_type":"application/pdf","file_name":"2019_PlosGenetics_Andergassen.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","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"}],"issue":"7"},{"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","publication":"PLoS Computational Biology","citation":{"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.","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","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.","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","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.","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.","short":"J.W.J.L. Wang, F. Lombardi, X. Zhang, C. Anaclet, P.C. Ivanov, PLoS Computational Biology 15 (2019)."},"date_published":"2019-11-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","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."}],"issue":"11","title":"Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture","ddc":["570","000"],"status":"public","intvolume":" 15","_id":"7103","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"creator":"dernst","file_size":3982516,"content_type":"application/pdf","file_name":"2019_PLOSComBio_Wang.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:49Z","date_created":"2019-11-25T08:24:01Z","checksum":"2a096a9c6dcc6eaa94077b2603bc6c12","file_id":"7104","relation":"main_file"}],"month":"11","publication_identifier":{"issn":["1553-7358"]},"isi":1,"quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"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":{"pmid":["31725712"],"isi":["000500976100014"]},"language":[{"iso":"eng"}],"doi":"10.1371/journal.pcbi.1007268","article_number":"e1007268","file_date_updated":"2020-07-14T12:47:49Z","ec_funded":1,"publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","year":"2019","pmid":1,"date_updated":"2023-10-17T12:30:07Z","date_created":"2019-11-25T08:20:47Z","volume":15,"author":[{"full_name":"Wang, Jilin W. J. L.","last_name":"Wang","first_name":"Jilin W. J. L."},{"full_name":"Lombardi, Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425","orcid":"0000-0003-2623-5249","first_name":"Fabrizio","last_name":"Lombardi"},{"last_name":"Zhang","first_name":"Xiyun","full_name":"Zhang, Xiyun"},{"full_name":"Anaclet, Christelle","last_name":"Anaclet","first_name":"Christelle"},{"full_name":"Ivanov, Plamen Ch.","last_name":"Ivanov","first_name":"Plamen Ch."}]},{"ddc":["000"],"status":"public","title":"Towards understanding knowledge distillation","intvolume":" 97","_id":"6569","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-07-14T12:47:33Z","date_created":"2019-06-20T18:22:56Z","checksum":"a66d00e2694d749250f8507f301320ca","file_id":"6570","relation":"main_file","creator":"bphuong","content_type":"application/pdf","file_size":686432,"file_name":"paper.pdf","access_level":"open_access"}],"oa_version":"Published Version","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."}],"page":"5142-5151","publication":"Proceedings of the 36th International Conference on Machine Learning","citation":{"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.","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.","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.","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.","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.","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."},"date_published":"2019-06-13T00:00:00Z","scopus_import":"1","day":"13","has_accepted_license":"1","article_processing_charge":"No","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":[{"first_name":"Phuong","last_name":"Bui Thi Mai","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","full_name":"Bui Thi Mai, Phuong"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"}],"file_date_updated":"2020-07-14T12:47:33Z","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"conference":{"name":"ICML: International Conference on Machine Learning","start_date":"2019-06-10","location":"Long Beach, CA, United States","end_date":"2019-06-15"},"month":"06"},{"oa":1,"external_id":{"arxiv":["1901.10310"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1901.10310"}],"quality_controlled":"1","project":[{"name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036"},{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"conference":{"start_date":"2019-06-10","location":"Long Beach, CA, USA","end_date":"2919-06-15","name":"ICML: International Conference on Machine Learning"},"language":[{"iso":"eng"}],"month":"06","year":"2019","publication_status":"published","publisher":"ML Research Press","department":[{"_id":"ChLa"}],"author":[{"last_name":"Konstantinov","first_name":"Nikola H","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","full_name":"Konstantinov, Nikola H"},{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10799"}]},"date_created":"2019-06-27T14:18:23Z","date_updated":"2023-10-17T12:31:55Z","volume":97,"ec_funded":1,"publication":"Proceedings of the 36th International Conference on Machine Learning","citation":{"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.","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.","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.","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.","short":"N.H. Konstantinov, C. Lampert, in:, Proceedings of the 36th International Conference on Machine Learning, ML Research Press, 2019, pp. 3488–3498.","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."},"page":"3488-3498","date_published":"2019-06-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6590","title":"Robust learning from untrusted sources","status":"public","intvolume":" 97","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. "}]},{"citation":{"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.","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.","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.","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","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.","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"},"publication":"Proceedings of the National Academy of Sciences of the United States of America","page":"21274-21284","article_type":"original","date_published":"2019-10-15T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"15","_id":"6999","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 116","status":"public","title":"Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization","ddc":["580"],"oa_version":"Published Version","file":[{"file_name":"2019_PNAS_Huang.pdf","access_level":"open_access","creator":"dernst","file_size":3287466,"content_type":"application/pdf","file_id":"7012","relation":"main_file","date_created":"2019-11-13T08:22:28Z","date_updated":"2020-07-14T12:47:46Z","checksum":"258c666bc6253eab81961f61169eefae"}],"type":"journal_article","issue":"42","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"}],"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"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1073/pnas.1911892116","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"month":"10","pmid":1,"year":"2019","publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"JiFr"}],"publication_status":"published","related_material":{"link":[{"url":"https://doi.org/10.1073/pnas.2004738117","relation":"erratum"}]},"author":[{"full_name":"Huang, D","last_name":"Huang","first_name":"D"},{"first_name":"Y","last_name":"Sun","full_name":"Sun, Y"},{"full_name":"Ma, Z","last_name":"Ma","first_name":"Z"},{"first_name":"M","last_name":"Ke","full_name":"Ke, M"},{"first_name":"Y","last_name":"Cui","full_name":"Cui, Y"},{"first_name":"Z","last_name":"Chen","full_name":"Chen, Z"},{"full_name":"Chen, C","last_name":"Chen","first_name":"C"},{"first_name":"C","last_name":"Ji","full_name":"Ji, C"},{"full_name":"Tran, TM","first_name":"TM","last_name":"Tran"},{"last_name":"Yang","first_name":"L","full_name":"Yang, L"},{"last_name":"Lam","first_name":"SM","full_name":"Lam, SM"},{"last_name":"Han","first_name":"Y","full_name":"Han, Y"},{"first_name":"G","last_name":"Shu","full_name":"Shu, G"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří"},{"full_name":"Miao, Y","last_name":"Miao","first_name":"Y"},{"full_name":"Jiang, L","first_name":"L","last_name":"Jiang"},{"first_name":"X","last_name":"Chen","full_name":"Chen, X"}],"volume":116,"date_updated":"2023-10-17T12:32:37Z","date_created":"2019-11-12T11:42:05Z","file_date_updated":"2020-07-14T12:47:46Z"},{"article_processing_charge":"No","day":"25","scopus_import":"1","date_published":"2019-06-25T00:00:00Z","page":"12607-12608","article_type":"letter_note","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."},"publication":"Proceedings of the National Academy of Sciences of the United States of America","issue":"26","abstract":[{"lang":"eng","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."}],"type":"journal_article","oa_version":"Published Version","intvolume":" 116","title":"On the power to detect rare recombination events","status":"public","_id":"6621","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1905555116","isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1905555116","open_access":"1"}],"external_id":{"isi":["000472719100010"],"pmid":["31213531"]},"oa":1,"volume":116,"date_created":"2019-07-07T21:59:25Z","date_updated":"2023-10-17T12:44:15Z","author":[{"last_name":"Wright","first_name":"Alison E.","full_name":"Wright, Alison E."},{"first_name":"Iulia","last_name":"Darolti","full_name":"Darolti, Iulia"},{"last_name":"Bloch","first_name":"Natasha I.","full_name":"Bloch, Natasha I."},{"full_name":"Oostra, Vicencio","first_name":"Vicencio","last_name":"Oostra"},{"first_name":"Benjamin A.","last_name":"Sandkam","full_name":"Sandkam, Benjamin A."},{"first_name":"Séverine D.","last_name":"Buechel","full_name":"Buechel, Séverine D."},{"first_name":"Niclas","last_name":"Kolm","full_name":"Kolm, Niclas"},{"full_name":"Breden, Felix","last_name":"Breden","first_name":"Felix"},{"first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"},{"full_name":"Mank, Judith E.","first_name":"Judith E.","last_name":"Mank"}],"publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"BeVi"}],"publication_status":"published","pmid":1,"year":"2019"},{"date_published":"2019-11-01T00:00:00Z","article_type":"original","page":"1035-1047","publication":"New Phytologist","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","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.","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","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."},"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"date_created":"2019-11-13T08:15:05Z","date_updated":"2020-07-14T12:47:42Z","checksum":"21e4c95599bbcaf7c483b89954658672","relation":"main_file","file_id":"7011","file_size":1511958,"content_type":"application/pdf","creator":"dernst","file_name":"2019_NewPhytologist_Pickup.pdf","access_level":"open_access"}],"ddc":["570"],"status":"public","title":"Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow","intvolume":" 224","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6856","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."}],"issue":"3","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1111/nph.16180","quality_controlled":"1","project":[{"grant_number":"329960","_id":"25B36484-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Mating system and the evolutionary dynamics of hybrid zones"},{"_id":"2662AADE-B435-11E9-9278-68D0E5697425","grant_number":"M02463","call_identifier":"FWF","name":"Sex chromosomes and species barriers"}],"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,"month":"11","publication_identifier":{"issn":["0028-646X"],"eissn":["1469-8137"]},"date_created":"2019-09-07T14:35:40Z","date_updated":"2023-10-18T08:47:08Z","volume":224,"author":[{"orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","first_name":"Melinda","full_name":"Pickup, Melinda"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"last_name":"Brandvain","first_name":"Yaniv","full_name":"Brandvain, Yaniv"},{"full_name":"Fraisse, Christelle","first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075"},{"last_name":"Yakimowski","first_name":"Sarah","full_name":"Yakimowski, Sarah"},{"first_name":"Tanmay","last_name":"Dixit","full_name":"Dixit, Tanmay"},{"full_name":"Lexer, Christian","last_name":"Lexer","first_name":"Christian"},{"id":"71AA91B4-05ED-11EA-8BEB-F5833E63BD63","first_name":"Eva","last_name":"Cereghetti","full_name":"Cereghetti, Eva"},{"full_name":"Field, David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David"}],"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","year":"2019","pmid":1,"file_date_updated":"2020-07-14T12:47:42Z","ec_funded":1},{"language":[{"iso":"eng"}],"doi":"10.1021/acsnano.9b01025","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1021/acsnano.9b01025","open_access":"1"}],"oa":1,"external_id":{"pmid":["30990672"]},"month":"04","publication_identifier":{"eissn":["1936-086x"],"issn":["1936-0851"]},"date_created":"2023-09-06T12:48:47Z","date_updated":"2023-11-07T12:17:31Z","volume":13,"author":[{"first_name":"Engelhardt","last_name":"FAS","full_name":"FAS, Engelhardt"},{"last_name":"Praetorius","first_name":"Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","full_name":"Praetorius, Florian M"},{"last_name":"Wachauf","first_name":"CH","full_name":"Wachauf, CH"},{"full_name":"Brüggenthies, G","last_name":"Brüggenthies","first_name":"G"},{"full_name":"Kohler, F","last_name":"Kohler","first_name":"F"},{"last_name":"Kick","first_name":"B","full_name":"Kick, B"},{"first_name":"KL","last_name":"Kadletz","full_name":"Kadletz, KL"},{"last_name":"Pham","first_name":"PN","full_name":"Pham, PN"},{"first_name":"KL","last_name":"Behler","full_name":"Behler, KL"},{"full_name":"Gerling, T","last_name":"Gerling","first_name":"T"},{"full_name":"Dietz, H","last_name":"Dietz","first_name":"H"}],"publication_status":"published","publisher":"ACS Publications","year":"2019","pmid":1,"extern":"1","date_published":"2019-04-16T00:00:00Z","article_type":"original","page":"5015-5027","publication":"ACS Nano","citation":{"short":"E. FAS, F.M. Praetorius, C. Wachauf, G. Brüggenthies, F. Kohler, B. Kick, K. Kadletz, P. Pham, K. Behler, T. Gerling, H. Dietz, ACS Nano 13 (2019) 5015–5027.","mla":"FAS, Engelhardt, et al. “Custom-Size, Functional, and Durable DNA Origami with Design-Specific Scaffolds.” ACS Nano, vol. 13, no. 5, ACS Publications, 2019, pp. 5015–27, doi:10.1021/acsnano.9b01025.","chicago":"FAS, Engelhardt, Florian M Praetorius, CH Wachauf, G Brüggenthies, F Kohler, B Kick, KL Kadletz, et al. “Custom-Size, Functional, and Durable DNA Origami with Design-Specific Scaffolds.” ACS Nano. ACS Publications, 2019. https://doi.org/10.1021/acsnano.9b01025.","ama":"FAS E, Praetorius FM, Wachauf C, et al. Custom-size, functional, and durable DNA origami with design-specific scaffolds. ACS Nano. 2019;13(5):5015-5027. doi:10.1021/acsnano.9b01025","ieee":"E. FAS et al., “Custom-size, functional, and durable DNA origami with design-specific scaffolds,” ACS Nano, vol. 13, no. 5. ACS Publications, pp. 5015–5027, 2019.","apa":"FAS, E., Praetorius, F. M., Wachauf, C., Brüggenthies, G., Kohler, F., Kick, B., … Dietz, H. (2019). Custom-size, functional, and durable DNA origami with design-specific scaffolds. ACS Nano. ACS Publications. https://doi.org/10.1021/acsnano.9b01025","ista":"FAS E, Praetorius FM, Wachauf C, Brüggenthies G, Kohler F, Kick B, Kadletz K, Pham P, Behler K, Gerling T, Dietz H. 2019. Custom-size, functional, and durable DNA origami with design-specific scaffolds. ACS Nano. 13(5), 5015–5027."},"day":"16","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","status":"public","title":"Custom-size, functional, and durable DNA origami with design-specific scaffolds","intvolume":" 13","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14299","abstract":[{"text":"DNA origami nano-objects are usually designed around generic single-stranded “scaffolds”. Many properties of the target object are determined by details of those generic scaffold sequences. Here, we enable designers to fully specify the target structure not only in terms of desired 3D shape but also in terms of the sequences used. To this end, we built design tools to construct scaffold sequences de novo based on strand diagrams, and we developed scalable production methods for creating design-specific scaffold strands with fully user-defined sequences. We used 17 custom scaffolds having different lengths and sequence properties to study the influence of sequence redundancy and sequence composition on multilayer DNA origami assembly and to realize efficient one-pot assembly of multiscaffold DNA origami objects. Furthermore, as examples for functionalized scaffolds, we created a scaffold that enables direct, covalent cross-linking of DNA origami via UV irradiation, and we built DNAzyme-containing scaffolds that allow postfolding DNA origami domain separation.","lang":"eng"}],"issue":"5","type":"journal_article"},{"scopus_import":1,"day":"01","has_accepted_license":"1","page":"38:1-38:13","publication":"35th International Symposium on Computational Geometry","citation":{"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.","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.","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","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.","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.","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."},"date_published":"2019-06-01T00:00:00Z","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"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.","lang":"eng"}],"ddc":["000","510"],"status":"public","title":"The crossing Tverberg theorem","intvolume":" 129","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6647","oa_version":"Published Version","file":[{"file_name":"2019_LIPICS_Fulek.pdf","access_level":"open_access","file_size":559837,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"6667","date_updated":"2020-07-14T12:47:35Z","date_created":"2019-07-24T06:54:52Z","checksum":"d6d017f8b41291b94d102294fa96ae9c"}],"month":"06","publication_identifier":{"isbn":["9783959771047"],"issn":["1868-8969"]},"quality_controlled":"1","project":[{"grant_number":"M02281","_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs"}],"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,"language":[{"iso":"eng"}],"conference":{"location":"Portland, OR, United States","start_date":"2019-06-18","end_date":"2019-06-21","name":"SoCG 2019: Symposium on Computational Geometry"},"doi":"10.4230/LIPICS.SOCG.2019.38","file_date_updated":"2020-07-14T12:47:35Z","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"UlWa"}],"year":"2019","date_created":"2019-07-17T10:35:04Z","date_updated":"2023-12-13T12:03:35Z","volume":129,"author":[{"last_name":"Fulek","first_name":"Radoslav","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","full_name":"Fulek, Radoslav"},{"full_name":"Gärtner, Bernd","first_name":"Bernd","last_name":"Gärtner"},{"full_name":"Kupavskii, Andrey","last_name":"Kupavskii","first_name":"Andrey"},{"full_name":"Valtr, Pavel","last_name":"Valtr","first_name":"Pavel"},{"full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","first_name":"Uli","last_name":"Wagner"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"13974"}]}},{"author":[{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Aspnes","first_name":"James","full_name":"Aspnes, James"},{"last_name":"Ellen","first_name":"Faith","full_name":"Ellen, Faith"},{"first_name":"Rati","last_name":"Gelashvili","full_name":"Gelashvili, Rati"},{"first_name":"Leqi","last_name":"Zhu","full_name":"Zhu, Leqi"}],"related_material":{"record":[{"id":"14364","relation":"later_version","status":"public"}]},"date_created":"2019-07-24T09:13:05Z","date_updated":"2023-12-13T12:28:28Z","year":"2019","publication_status":"published","publisher":"ACM Press","department":[{"_id":"DaAl"}],"month":"06","publication_identifier":{"isbn":["9781450367059"]},"conference":{"location":"Phoenix, AZ, United States","start_date":"2019-06-23","end_date":"2019-06-26","name":"STOC: Symposium on Theory of Computing"},"doi":"10.1145/3313276.3316407","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.01421"}],"external_id":{"isi":["000523199100089"],"arxiv":["1811.01421"]},"oa":1,"quality_controlled":"1","isi":1,"abstract":[{"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.","lang":"eng"}],"type":"conference","oa_version":"Preprint","_id":"6676","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Why extension-based proofs fail","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-06-01T00:00:00Z","publication":"Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing","citation":{"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","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."},"page":"986-996"},{"type":"preprint","article_number":"1903.06981","abstract":[{"text":"The input to the token swapping problem is a graph with vertices v1, v2, . . . , vn, and n tokens with labels 1,2, . . . , n, one on each vertex. The goal is to get token i to vertex vi for all i= 1, . . . , n using a minimum number of swaps, where a swap exchanges the tokens on the endpoints of an edge.Token swapping on a tree, also known as “sorting with a transposition tree,” is not known to be in P nor NP-complete. We present some partial results:\r\n1. An optimum swap sequence may need to perform a swap on a leaf vertex that has the correct token (a “happy leaf”), disproving a conjecture of Vaughan.\r\n2. Any algorithm that fixes happy leaves—as all known approximation algorithms for the problem do—has approximation factor at least 4/3. Furthermore, the two best-known 2-approximation algorithms have approximation factor exactly 2.\r\n3. A generalized problem—weighted coloured token swapping—is NP-complete on trees, but solvable in polynomial time on paths and stars. In this version, tokens and vertices have colours, and colours have weights. The goal is to get every token to a vertex of the same colour, and the cost of a swap is the sum of the weights of the two tokens involved.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7950","year":"2019","department":[{"_id":"HeEd"},{"_id":"UlWa"},{"_id":"KrCh"}],"status":"public","title":"Token swapping on trees","publication_status":"submitted","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"7944"},{"relation":"later_version","status":"public","id":"12833"}]},"author":[{"full_name":"Biniaz, Ahmad","last_name":"Biniaz","first_name":"Ahmad"},{"full_name":"Jain, Kshitij","last_name":"Jain","first_name":"Kshitij"},{"full_name":"Lubiw, Anna","first_name":"Anna","last_name":"Lubiw"},{"orcid":"0000-0002-6660-1322","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","last_name":"Masárová","first_name":"Zuzana","full_name":"Masárová, Zuzana"},{"full_name":"Miltzow, Tillmann","last_name":"Miltzow","first_name":"Tillmann"},{"last_name":"Mondal","first_name":"Debajyoti","full_name":"Mondal, Debajyoti"},{"full_name":"Naredla, Anurag Murty","first_name":"Anurag Murty","last_name":"Naredla"},{"id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684","first_name":"Josef","last_name":"Tkadlec","full_name":"Tkadlec, Josef"},{"last_name":"Turcotte","first_name":"Alexi","full_name":"Turcotte, Alexi"}],"oa_version":"Preprint","date_created":"2020-06-08T12:25:25Z","date_updated":"2024-01-04T12:42:08Z","article_processing_charge":"No","month":"03","day":"16","citation":{"short":"A. Biniaz, K. Jain, A. Lubiw, Z. Masárová, T. Miltzow, D. Mondal, A.M. Naredla, J. Tkadlec, A. Turcotte, ArXiv (n.d.).","mla":"Biniaz, Ahmad, et al. “Token Swapping on Trees.” ArXiv, 1903.06981.","chicago":"Biniaz, Ahmad, Kshitij Jain, Anna Lubiw, Zuzana Masárová, Tillmann Miltzow, Debajyoti Mondal, Anurag Murty Naredla, Josef Tkadlec, and Alexi Turcotte. “Token Swapping on Trees.” ArXiv, n.d.","ama":"Biniaz A, Jain K, Lubiw A, et al. Token swapping on trees. arXiv.","ieee":"A. Biniaz et al., “Token swapping on trees,” arXiv. .","apa":"Biniaz, A., Jain, K., Lubiw, A., Masárová, Z., Miltzow, T., Mondal, D., … Turcotte, A. (n.d.). Token swapping on trees. arXiv.","ista":"Biniaz A, Jain K, Lubiw A, Masárová Z, Miltzow T, Mondal D, Naredla AM, Tkadlec J, Turcotte A. Token swapping on trees. arXiv, 1903.06981."},"external_id":{"arxiv":["1903.06981"]},"main_file_link":[{"url":"https://arxiv.org/abs/1903.06981","open_access":"1"}],"oa":1,"publication":"arXiv","date_published":"2019-03-16T00:00:00Z","language":[{"iso":"eng"}]},{"abstract":[{"lang":"eng","text":"Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lower genomic coverage in female than in male samples, and regions that harbor an excess of female-specific SNPs. We detect many Z-specific genes, which no longer have homologs on the W, but also Z-linked genes that appear to have diverged very recently from their existing W-linked homolog. We assess patterns of male and female expression in two tissues with extensive morphological dimorphism, gonads, and heads. In agreement with their morphology, sex-biased expression is common in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased genes, and seems to in fact have a mechanism of dosage compensation that leads to equal expression in males and in females. Both of these patterns are contrary to most ZW systems studied so far, making A. franciscana an excellent model for investigating the interplay between the evolution of sexual dimorphism and dosage compensation, as well as Z chromosome evolution in general."}],"issue":"4","type":"journal_article","file":[{"creator":"dernst","file_size":1256303,"content_type":"application/pdf","file_name":"2019_GBE_Huylmans.pdf","access_level":"open_access","date_created":"2019-05-14T08:29:38Z","date_updated":"2020-07-14T12:47:29Z","checksum":"7d0ede297b6741f3dc89cd59017c7642","file_id":"6446","relation":"main_file"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6418","title":"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome","status":"public","ddc":["570"],"intvolume":" 11","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2019-04-01T00:00:00Z","publication":"Genome biology and evolution","citation":{"ama":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome biology and evolution. 2019;11(4):1033-1044. doi:10.1093/gbe/evz053","apa":"Huylmans, A. K., Toups, M. A., Macon, A., Gammerdinger, W. J., & Vicoso, B. (2019). Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evz053","ieee":"A. K. Huylmans, M. A. Toups, A. Macon, W. J. Gammerdinger, and B. Vicoso, “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome,” Genome biology and evolution, vol. 11, no. 4. Oxford University Press, pp. 1033–1044, 2019.","ista":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. 2019. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome biology and evolution. 11(4), 1033–1044.","short":"A.K. Huylmans, M.A. Toups, A. Macon, W.J. Gammerdinger, B. Vicoso, Genome Biology and Evolution 11 (2019) 1033–1044.","mla":"Huylmans, Ann K., et al. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” Genome Biology and Evolution, vol. 11, no. 4, Oxford University Press, 2019, pp. 1033–44, doi:10.1093/gbe/evz053.","chicago":"Huylmans, Ann K, Melissa A Toups, Ariana Macon, William J Gammerdinger, and Beatriz Vicoso. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” Genome Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/gbe/evz053."},"page":"1033-1044","file_date_updated":"2020-07-14T12:47:29Z","ec_funded":1,"author":[{"full_name":"Huylmans, Ann K","first_name":"Ann K","last_name":"Huylmans","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8871-4961"},{"first_name":"Melissa A","last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","last_name":"Macon","full_name":"Macon, Ariana"},{"full_name":"Gammerdinger, William J","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9638-1220","first_name":"William J","last_name":"Gammerdinger"},{"first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"related_material":{"record":[{"relation":"popular_science","status":"public","id":"6060"}]},"date_created":"2019-05-13T07:58:38Z","date_updated":"2024-02-21T12:45:41Z","volume":11,"year":"2019","publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"BeVi"}],"month":"04","publication_identifier":{"eissn":["1759-6653"]},"doi":"10.1093/gbe/evz053","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"external_id":{"isi":["000476569800003"]},"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,"quality_controlled":"1","isi":1,"project":[{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020"}]},{"publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaGu"}],"status":"public","ddc":["576"],"title":"Data for the paper \"Gene amplification as a form of population-level gene expression regulation\"","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7016","year":"2019","file":[{"file_id":"7017","title":"Locus1_amplified","relation":"main_file","checksum":"72441055043eda4cbf1398a422e2c118","date_created":"2019-11-13T08:52:21Z","date_updated":"2020-07-14T12:47:47Z","access_level":"open_access","description":"Illumina whole genome sequence data for Locus 1 - 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see read_me_FACS"},{"date_created":"2020-01-22T15:44:16Z","date_updated":"2020-07-14T12:47:47Z","checksum":"a85caf092ae4b17668f70af2d93fad00","relation":"main_file","file_id":"7352","content_type":"text/rtf","file_size":4996,"creator":"itomanek","file_name":"read_me_FACS.rtf","access_level":"open_access"},{"creator":"itomanek","content_type":"text/rtf","file_size":868,"access_level":"open_access","file_name":"read_me_microfluidics.rtf","checksum":"fd8ba5d75d24e47ddf7e70bfdadb40d4","date_created":"2020-01-22T15:44:16Z","date_updated":"2020-07-14T12:47:47Z","file_id":"7353","relation":"main_file"},{"file_size":8141727,"content_type":"application/zip","creator":"itomanek","access_level":"open_access","file_name":"microfuidics_data.zip","description":"microfluidics time trace data - see read_me_microfluidics","checksum":"69c5dc5ca5c069a138183c934acc1778","date_created":"2020-01-22T15:44:17Z","date_updated":"2020-07-14T12:47:47Z","relation":"main_file","file_id":"7354","title":"microfluidics data"}],"oa_version":"Published Version","date_updated":"2024-02-21T12:45:25Z","date_created":"2019-11-13T09:07:31Z","related_material":{"record":[{"id":"7652","relation":"used_in_publication","status":"public"}]},"contributor":[{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","contributor_type":"project_leader","first_name":"Calin C"}],"author":[{"full_name":"Tomanek, Isabella","first_name":"Isabella","last_name":"Tomanek","id":"3981F020-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6197-363X"}],"type":"research_data","file_date_updated":"2020-07-14T12:47:47Z","abstract":[{"text":"Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature.","lang":"eng"}],"oa":1,"citation":{"ista":"Tomanek I. 2019. Data for the paper ‘Gene amplification as a form of population-level gene expression regulation’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7016.","apa":"Tomanek, I. (2019). Data for the paper “Gene amplification as a form of population-level gene expression regulation.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7016","ieee":"I. Tomanek, “Data for the paper ‘Gene amplification as a form of population-level gene expression regulation.’” Institute of Science and Technology Austria, 2019.","ama":"Tomanek I. Data for the paper “Gene amplification as a form of population-level gene expression regulation.” 2019. doi:10.15479/AT:ISTA:7016","chicago":"Tomanek, Isabella. “Data for the Paper ‘Gene Amplification as a Form of Population-Level Gene Expression Regulation.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7016.","mla":"Tomanek, Isabella. Data for the Paper “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7016.","short":"I. Tomanek, (2019)."},"date_published":"2019-11-13T00:00:00Z","doi":"10.15479/AT:ISTA:7016","keyword":["Escherichia coli","gene amplification","galactose","DOG","experimental evolution","Illumina sequence data","FACS data","microfluidics data"],"article_processing_charge":"No","has_accepted_license":"1","day":"13","month":"11"},{"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"chicago":"Guseinov, Ruslan. “Supplementary Data for ‘Programming Temporal Morphing of Self-Actuated Shells.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7154.","mla":"Guseinov, Ruslan. Supplementary Data for “Programming Temporal Morphing of Self-Actuated Shells.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7154.","short":"R. Guseinov, (2019).","ista":"Guseinov R. 2019. Supplementary data for ‘Programming temporal morphing of self-actuated shells’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7154.","ieee":"R. Guseinov, “Supplementary data for ‘Programming temporal morphing of self-actuated shells.’” Institute of Science and Technology Austria, 2019.","apa":"Guseinov, R. (2019). Supplementary data for “Programming temporal morphing of self-actuated shells.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7154","ama":"Guseinov R. Supplementary data for “Programming temporal morphing of self-actuated shells.” 2019. doi:10.15479/AT:ISTA:7154"},"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"date_published":"2019-12-06T00:00:00Z","doi":"10.15479/AT:ISTA:7154","has_accepted_license":"1","article_processing_charge":"No","month":"12","day":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7154","year":"2019","department":[{"_id":"BeBi"}],"publisher":"Institute of Science and Technology Austria","title":"Supplementary data for \"Programming temporal morphing of self-actuated shells\"","status":"public","ddc":["000"],"related_material":{"record":[{"relation":"used_in_publication","status":"deleted","id":"8433"},{"id":"7262","status":"public","relation":"used_in_publication"}]},"contributor":[{"first_name":"Ruslan","last_name":"Guseinov","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9819-5077"},{"first_name":"Connor","last_name":"McMahan"},{"id":"2DC83906-F248-11E8-B48F-1D18A9856A87","last_name":"Perez Rodriguez","first_name":"Jesus"},{"last_name":"Daraio","first_name":"Chiara"},{"orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd"}],"author":[{"last_name":"Guseinov","first_name":"Ruslan","orcid":"0000-0001-9819-5077","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","full_name":"Guseinov, Ruslan"}],"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"7155","date_created":"2019-12-09T07:52:17Z","date_updated":"2020-07-14T12:47:50Z","checksum":"155133e6e188e85b3c0676a5e70b9341","file_name":"temporal_morphing_supp_data.zip","access_level":"open_access","content_type":"application/x-zip-compressed","file_size":65307107,"creator":"dernst"}],"date_updated":"2024-02-21T12:45:03Z","date_created":"2019-12-09T07:52:46Z","type":"research_data","ec_funded":1,"file_date_updated":"2020-07-14T12:47:50Z","license":"https://creativecommons.org/publicdomain/zero/1.0/"},{"day":"28","month":"02","has_accepted_license":"1","article_processing_charge":"No","oa":1,"citation":{"mla":"Vicoso, Beatriz. Supplementary Data for “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome” (Huylman, Toups et Al., 2019). . Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6060.","short":"B. Vicoso, (2019).","chicago":"Vicoso, Beatriz. “Supplementary Data for ‘Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome’ (Huylman, Toups et Al., 2019). .” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6060.","ama":"Vicoso B. Supplementary data for “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . 2019. doi:10.15479/AT:ISTA:6060","ista":"Vicoso B. 2019. Supplementary data for ‘Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al., 2019). , Institute of Science and Technology Austria, 10.15479/AT:ISTA:6060.","apa":"Vicoso, B. (2019). Supplementary data for “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6060","ieee":"B. Vicoso, “Supplementary data for ‘Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al., 2019). .” Institute of Science and Technology Austria, 2019."},"doi":"10.15479/AT:ISTA:6060","date_published":"2019-02-28T00:00:00Z","type":"research_data","file_date_updated":"2020-07-14T12:47:17Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6060","year":"2019","status":"public","title":"Supplementary data for \"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome\" (Huylman, Toups et al., 2019). ","publisher":"Institute of Science and Technology Austria","department":[{"_id":"BeVi"}],"author":[{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz"}],"related_material":{"record":[{"id":"6418","relation":"research_paper","status":"public"}]},"date_updated":"2024-02-21T12:45:42Z","date_created":"2019-02-28T10:55:15Z","oa_version":"Published Version","file":[{"creator":"bvicoso","content_type":"application/zip","file_size":36646050,"file_name":"SupData.zip","access_level":"open_access","date_updated":"2020-07-14T12:47:17Z","date_created":"2019-02-28T10:54:27Z","checksum":"a338a622d728af0e3199cb07e6dd64d3","file_id":"6061","relation":"main_file"}]},{"day":"09","month":"01","has_accepted_license":"1","article_processing_charge":"No","doi":"10.15479/AT:ISTA:6074","date_published":"2019-01-09T00:00:00Z","oa":1,"citation":{"chicago":"Dotter, Christoph, and Gaia Novarino. “Supplementary Data for the Research Paper ‘Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6074.","short":"C. Dotter, G. Novarino, (2019).","mla":"Dotter, Christoph, and Gaia Novarino. Supplementary Data for the Research Paper “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental Gene Expression and Cognition.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6074.","ieee":"C. Dotter and G. Novarino, “Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.’” Institute of Science and Technology Austria, 2019.","apa":"Dotter, C., & Novarino, G. (2019). Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6074","ista":"Dotter C, Novarino G. 2019. Supplementary data for the research paper ‘Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:6074.","ama":"Dotter C, Novarino G. Supplementary data for the research paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition.” 2019. doi:10.15479/AT:ISTA:6074"},"file_date_updated":"2020-07-14T12:47:18Z","abstract":[{"text":"This dataset contains the supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\".\r\n\r\nThe contained files have the following content:\r\n'Supplementary Figures.pdf'\r\n\tAdditional figures (as referenced in the paper).\r\n'Supplementary Table 1. Statistics.xlsx'\r\n\tDetails on statistical tests performed in the paper.\r\n'Supplementary Table 2. Differentially expressed gene analysis.xlsx'\r\n\tResults for the differential gene expression analysis for embryonic (E9.5; analysis with edgeR) and in vitro (ESCs, EBs, NPCs; analysis with DESeq2) samples.\r\n'Supplementary Table 3. Gene Ontology (GO) term enrichment analysis.xlsx'\r\n\tResults for the GO term enrichment analysis for differentially expressed genes in embryonic (GO E9.5) and in vitro (GO ESC, GO EBs, GO NPCs) samples. Differentially expressed genes for in vitro samples were split into upregulated and downregulated genes (up/down) and the analysis was performed on each subset (e.g. GO ESC up / GO ESC down).\r\n'Supplementary Table 4. Differentially expressed gene analysis for CFC samples.xlsx'\r\n\tResults for the differential gene expression analysis for samples from adult mice before (HC - Homecage) and 1h and 3h after contextual fear conditioning (1h and 3h, respectively). Each sheet shows the results for a different comparison. Sheets 1-3 show results for comparisons between timepoints for wild type (WT) samples only and sheets 4-6 for the same comparisons in mutant (Het) samples. Sheets 7-9 show results for comparisons between genotypes at each time point and sheet 10 contains the results for the analysis of differential expression trajectories between wild type and mutant.\r\n'Supplementary Table 5. Cluster identification.xlsx'\r\n\tResults for k-means clustering of genes by expression. Sheet 1 shows clustering of just the genes with significantly different expression trajectories between genotypes. Sheet 2 shows clustering of all genes that are significantly differentially expressed in any of the comparisons (includes also genes with same trajectories).\r\n'Supplementary Table 6. GO term cluster analysis.xlsx'\r\n\tResults for the GO term enrichment analysis and EWCE analysis for enrichment of cell type specific genes for each cluster identified by clustering genes with different expression trajectories (see Table S5, sheet 1).\r\n'Supplementary Table 7. Setd5 mass spectrometry results.xlsx'\r\n\tResults showing proteins interacting with Setd5 as identified by mass spectrometry. Sheet 1 shows protein protein interaction data generated from these results (combined with data from the STRING database. Sheet 2 shows the results of the statistical analysis with limma.\r\n'Supplementary Table 8. PolII ChIP-seq analysis.xlsx'\r\n\tResults for the Chip-Seq analysis for binding of RNA polymerase II (PolII). Sheet 1 shows results for differential binding of PolII at the transcription start site (TSS) between genotypes and sheets 2+3 show the corresponding GO enrichment analysis for these differentially bound genes. Sheet 4 shows RNAseq counts for genes with increased binding of PolII at the TSS.","lang":"eng"}],"type":"research_data","date_created":"2019-03-07T13:32:35Z","date_updated":"2024-02-21T13:41:01Z","file":[{"date_created":"2019-03-07T13:37:19Z","date_updated":"2020-07-14T12:47:18Z","checksum":"bc1b285edca9e98a2c63d153c79bb75b","relation":"supplementary_material","file_id":"6084","file_size":33202743,"content_type":"application/zip","creator":"dernst","file_name":"Setd5_paper.zip","access_level":"open_access"}],"oa_version":"Published Version","author":[{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9033-9096","first_name":"Christoph","last_name":"Dotter","full_name":"Dotter, Christoph"},{"full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"}],"related_material":{"record":[{"id":"3","relation":"research_paper","status":"public"}]},"title":"Supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\"","ddc":["570"],"status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaNo"}],"_id":"6074","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_published":"2019-03-29T00:00:00Z","doi":"10.15479/AT:ISTA:6062","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"oa":1,"citation":{"ama":"Nardin M. Supplementary Code and Data for the paper “The Entorhinal Cognitive Map is Attracted to Goals.” 2019. doi:10.15479/AT:ISTA:6062","ieee":"M. Nardin, “Supplementary Code and Data for the paper ‘The Entorhinal Cognitive Map is Attracted to Goals.’” Institute of Science and Technology Austria, 2019.","apa":"Nardin, M. (2019). Supplementary Code and Data for the paper “The Entorhinal Cognitive Map is Attracted to Goals.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6062","ista":"Nardin M. 2019. Supplementary Code and Data for the paper ‘The Entorhinal Cognitive Map is Attracted to Goals’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:6062.","short":"M. Nardin, (2019).","mla":"Nardin, Michele. Supplementary Code and Data for the Paper “The Entorhinal Cognitive Map Is Attracted to Goals.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6062.","chicago":"Nardin, Michele. “Supplementary Code and Data for the Paper ‘The Entorhinal Cognitive Map Is Attracted to Goals.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6062."},"has_accepted_license":"1","article_processing_charge":"No","day":"29","month":"03","oa_version":"Published Version","file":[{"checksum":"48e7b9a02939b763417733239522a236","date_updated":"2020-07-14T12:47:18Z","date_created":"2019-03-05T09:29:37Z","title":"Data for the paper \"The Entorhinal Cognitive Map is Attracted to Goals\"","file_id":"6068","relation":"main_file","creator":"mnardin","file_size":37002186,"content_type":"application/zip","access_level":"open_access","file_name":"Online_data.zip"}],"date_created":"2019-03-04T14:20:58Z","date_updated":"2024-02-21T12:46:04Z","related_material":{"record":[{"id":"6194","relation":"research_paper","status":"public"}]},"author":[{"full_name":"Nardin, Michele","last_name":"Nardin","first_name":"Michele","orcid":"0000-0001-8849-6570","id":"30BD0376-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"JoCs"}],"title":"Supplementary Code and Data for the paper \"The Entorhinal Cognitive Map is Attracted to Goals\"","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6062","year":"2019","license":"https://creativecommons.org/licenses/by-sa/4.0/","abstract":[{"text":"Open the files in Jupyter Notebook (reccomended https://www.anaconda.com/distribution/#download-section with Python 3.7).","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:18Z","type":"research_data"},{"date_published":"2019-03-01T00:00:00Z","citation":{"ama":"Fraisse C, Puixeu Sala G, Vicoso B. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular biology and evolution. 2019;36(3):500-515. doi:10.1093/molbev/msy246","apa":"Fraisse, C., Puixeu Sala, G., & Vicoso, B. (2019). Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msy246","ieee":"C. Fraisse, G. Puixeu Sala, and B. Vicoso, “Pleiotropy modulates the efficacy of selection in drosophila melanogaster,” Molecular biology and evolution, vol. 36, no. 3. Oxford University Press, pp. 500–515, 2019.","ista":"Fraisse C, Puixeu Sala G, Vicoso B. 2019. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular biology and evolution. 36(3), 500–515.","short":"C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36 (2019) 500–515.","mla":"Fraisse, Christelle, et al. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular Biology and Evolution, vol. 36, no. 3, Oxford University Press, 2019, pp. 500–15, doi:10.1093/molbev/msy246.","chicago":"Fraisse, Christelle, Gemma Puixeu Sala, and Beatriz Vicoso. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/molbev/msy246."},"publication":"Molecular biology and evolution","page":"500-515","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Submitted Version","_id":"6089","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 36","title":"Pleiotropy modulates the efficacy of selection in drosophila melanogaster","status":"public","issue":"3","abstract":[{"text":"Pleiotropy is the well-established idea that a single mutation affects multiple phenotypes. If a mutation has opposite effects on fitness when expressed in different contexts, then genetic conflict arises. Pleiotropic conflict is expected to reduce the efficacy of selection by limiting the fixation of beneficial mutations through adaptation, and the removal of deleterious mutations through purifying selection. Although this has been widely discussed, in particular in the context of a putative “gender load,” it has yet to be systematically quantified. In this work, we empirically estimate to which extent different pleiotropic regimes impede the efficacy of selection in Drosophila melanogaster. We use whole-genome polymorphism data from a single African population and divergence data from D. simulans to estimate the fraction of adaptive fixations (α), the rate of adaptation (ωA), and the direction of selection (DoS). After controlling for confounding covariates, we find that the different pleiotropic regimes have a relatively small, but significant, effect on selection efficacy. Specifically, our results suggest that pleiotropic sexual antagonism may restrict the efficacy of selection, but that this conflict can be resolved by limiting the expression of genes to the sex where they are beneficial. Intermediate levels of pleiotropy across tissues and life stages can also lead to maladaptation in D. melanogaster, due to inefficient purifying selection combined with low frequency of mutations that confer a selective advantage. Thus, our study highlights the need to consider the efficacy of selection in the context of antagonistic pleiotropy, and of genetic conflict in general.","lang":"eng"}],"type":"journal_article","doi":"10.1093/molbev/msy246","language":[{"iso":"eng"}],"external_id":{"pmid":["30590559"],"isi":["000462585100006"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30590559","open_access":"1"}],"oa":1,"project":[{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"month":"03","related_material":{"record":[{"id":"5757","status":"public","relation":"popular_science"}]},"author":[{"full_name":"Fraisse, Christelle","first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075"},{"last_name":"Puixeu Sala","first_name":"Gemma","orcid":"0000-0001-8330-1754","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","full_name":"Puixeu Sala, Gemma"},{"first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"volume":36,"date_updated":"2024-02-21T13:59:17Z","date_created":"2019-03-10T22:59:19Z","pmid":1,"year":"2019","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"Oxford University Press","publication_status":"published"},{"page":"375","citation":{"ama":"Schröder DJ. From Dyson to Pearcey: Universal statistics in random matrix theory. 2019. doi:10.15479/AT:ISTA:th6179","ista":"Schröder DJ. 2019. From Dyson to Pearcey: Universal statistics in random matrix theory. Institute of Science and Technology Austria.","ieee":"D. J. Schröder, “From Dyson to Pearcey: Universal statistics in random matrix theory,” Institute of Science and Technology Austria, 2019.","apa":"Schröder, D. J. (2019). From Dyson to Pearcey: Universal statistics in random matrix theory. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th6179","mla":"Schröder, Dominik J. From Dyson to Pearcey: Universal Statistics in Random Matrix Theory. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:th6179.","short":"D.J. Schröder, From Dyson to Pearcey: Universal Statistics in Random Matrix Theory, Institute of Science and Technology Austria, 2019.","chicago":"Schröder, Dominik J. “From Dyson to Pearcey: Universal Statistics in Random Matrix Theory.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:th6179."},"date_published":"2019-03-18T00:00:00Z","day":"18","has_accepted_license":"1","article_processing_charge":"No","status":"public","ddc":["515","519"],"title":"From Dyson to Pearcey: Universal statistics in random matrix theory","_id":"6179","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"file_id":"6180","relation":"source_file","checksum":"6926f66f28079a81c4937e3764be00fc","date_created":"2019-03-28T08:53:52Z","date_updated":"2020-07-14T12:47:21Z","access_level":"closed","file_name":"2019_Schroeder_Thesis.tar.gz","creator":"dernst","content_type":"application/x-gzip","file_size":7104482},{"file_name":"2019_Schroeder_Thesis.pdf","access_level":"open_access","content_type":"application/pdf","file_size":4228794,"creator":"dernst","relation":"main_file","file_id":"6181","date_updated":"2020-07-14T12:47:21Z","date_created":"2019-03-28T08:53:52Z","checksum":"7d0ebb8d1207e89768cdd497a5bf80fb"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"In the first part of this thesis we consider large random matrices with arbitrary expectation and a general slowly decaying correlation among its entries. We prove universality of the local eigenvalue statistics and optimal local laws for the resolvent in the bulk and edge regime. The main novel tool is a systematic diagrammatic control of a multivariate cumulant expansion.\r\nIn the second part we consider Wigner-type matrices and show that at any cusp singularity of the limiting eigenvalue distribution the local eigenvalue statistics are uni- versal and form a Pearcey process. Since the density of states typically exhibits only square root or cubic root cusp singularities, our work complements previous results on the bulk and edge universality and it thus completes the resolution of the Wigner- Dyson-Mehta universality conjecture for the last remaining universality type. Our analysis holds not only for exact cusps, but approximate cusps as well, where an ex- tended Pearcey process emerges. As a main technical ingredient we prove an optimal local law at the cusp, and extend the fast relaxation to equilibrium of the Dyson Brow- nian motion to the cusp regime.\r\nIn the third and final part we explore the entrywise linear statistics of Wigner ma- trices and identify the fluctuations for a large class of test functions with little regularity. This enables us to study the rectangular Young diagram obtained from the interlacing eigenvalues of the random matrix and its minor, and we find that, despite having the same limit, the fluctuations differ from those of the algebraic Young tableaux equipped with the Plancharel measure.","lang":"eng"}],"project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"}],"oa":1,"degree_awarded":"PhD","supervisor":[{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:th6179","month":"03","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"LaEr"}],"year":"2019","date_updated":"2024-02-22T14:34:33Z","date_created":"2019-03-28T08:58:59Z","author":[{"first_name":"Dominik J","last_name":"Schröder","id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1144"},{"relation":"part_of_dissertation","status":"public","id":"6186"},{"id":"6185","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6182"},{"status":"public","relation":"part_of_dissertation","id":"1012"},{"id":"6184","status":"public","relation":"part_of_dissertation"}]},"file_date_updated":"2020-07-14T12:47:21Z","ec_funded":1},{"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783030129385","9783030129392"],"issn":["0302-9743"]},"month":"02","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1804.04171","open_access":"1"}],"external_id":{"arxiv":["1804.04171"]},"project":[{"call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding","_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036"}],"quality_controlled":"1","doi":"10.1007/978-3-030-12939-2_18","conference":{"name":"GCPR: Conference on Pattern Recognition","end_date":"2018-10-12","location":"Stuttgart, Germany","start_date":"2018-10-09"},"language":[{"iso":"eng"}],"ec_funded":1,"year":"2019","publisher":"Springer Nature","department":[{"_id":"ChLa"}],"publication_status":"published","related_material":{"record":[{"id":"6944","status":"public","relation":"later_version"}]},"author":[{"first_name":"Rémy","last_name":"Sun","full_name":"Sun, Rémy"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"}],"volume":11269,"date_updated":"2024-02-22T14:57:29Z","date_created":"2019-05-24T09:48:36Z","scopus_import":"1","article_processing_charge":"No","day":"14","citation":{"short":"R. Sun, C. Lampert, in:, Springer Nature, 2019, pp. 244–259.","mla":"Sun, Rémy, and Christoph Lampert. KS(Conf): A Light-Weight Test If a ConvNet Operates Outside of Its Specifications. Vol. 11269, Springer Nature, 2019, pp. 244–59, doi:10.1007/978-3-030-12939-2_18.","chicago":"Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a ConvNet Operates Outside of Its Specifications,” 11269:244–59. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-12939-2_18.","ama":"Sun R, Lampert C. KS(conf): A light-weight test if a ConvNet operates outside of Its specifications. In: Vol 11269. Springer Nature; 2019:244-259. doi:10.1007/978-3-030-12939-2_18","apa":"Sun, R., & Lampert, C. (2019). KS(conf): A light-weight test if a ConvNet operates outside of Its specifications (Vol. 11269, pp. 244–259). Presented at the GCPR: Conference on Pattern Recognition, Stuttgart, Germany: Springer Nature. https://doi.org/10.1007/978-3-030-12939-2_18","ieee":"R. Sun and C. Lampert, “KS(conf): A light-weight test if a ConvNet operates outside of Its specifications,” presented at the GCPR: Conference on Pattern Recognition, Stuttgart, Germany, 2019, vol. 11269, pp. 244–259.","ista":"Sun R, Lampert C. 2019. KS(conf): A light-weight test if a ConvNet operates outside of Its specifications. GCPR: Conference on Pattern Recognition, LNCS, vol. 11269, 244–259."},"page":"244-259","date_published":"2019-02-14T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Computer vision systems for automatic image categorization have become accurate and reliable enough that they can run continuously for days or even years as components of real-world commercial applications. A major open problem in this context, however, is quality control. Good classification performance can only be expected if systems run under the specific conditions, in particular data distributions, that they were trained for. Surprisingly, none of the currently used deep network architectures have a built-in functionality that could detect if a network operates on data from a distribution it was not trained for, such that potentially a warning to the human users could be triggered. In this work, we describe KS(conf), a procedure for detecting such outside of specifications (out-of-specs) operation, based on statistical testing of the network outputs. We show by extensive experiments using the ImageNet, AwA2 and DAVIS datasets on a variety of ConvNets architectures that KS(conf) reliably detects out-of-specs situations. It furthermore has a number of properties that make it a promising candidate for practical deployment: it is easy to implement, adds almost no overhead to the system, works with all networks, including pretrained ones, and requires no a priori knowledge of how the data distribution could change. "}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6482","intvolume":" 11269","title":"KS(conf): A light-weight test if a ConvNet operates outside of Its specifications","status":"public","oa_version":"Preprint"},{"scopus_import":"1","day":"21","article_processing_charge":"No","publication":"AIP Conference Proceedings","citation":{"ista":"Dostalík M, Pruša V, Skrivan T. 2019. On diffusive variants of some classical viscoelastic rate-type models. AIP Conference Proceedings. 8th International Conference on Novel Trends in Rheology vol. 2107, 020002.","ieee":"M. Dostalík, V. Pruša, and T. Skrivan, “On diffusive variants of some classical viscoelastic rate-type models,” in AIP Conference Proceedings, Zlin, Czech Republic, 2019, vol. 2107.","apa":"Dostalík, M., Pruša, V., & Skrivan, T. (2019). On diffusive variants of some classical viscoelastic rate-type models. In AIP Conference Proceedings (Vol. 2107). Zlin, Czech Republic: AIP Publishing. https://doi.org/10.1063/1.5109493","ama":"Dostalík M, Pruša V, Skrivan T. On diffusive variants of some classical viscoelastic rate-type models. In: AIP Conference Proceedings. Vol 2107. AIP Publishing; 2019. doi:10.1063/1.5109493","chicago":"Dostalík, Mark, Vít Pruša, and Tomas Skrivan. “On Diffusive Variants of Some Classical Viscoelastic Rate-Type Models.” In AIP Conference Proceedings, Vol. 2107. AIP Publishing, 2019. https://doi.org/10.1063/1.5109493.","mla":"Dostalík, Mark, et al. “On Diffusive Variants of Some Classical Viscoelastic Rate-Type Models.” AIP Conference Proceedings, vol. 2107, 020002, AIP Publishing, 2019, doi:10.1063/1.5109493.","short":"M. Dostalík, V. Pruša, T. Skrivan, in:, AIP Conference Proceedings, AIP Publishing, 2019."},"date_published":"2019-05-21T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"We present a thermodynamically based approach to the design of models for viscoelastic fluids with stress diffusion effect. In particular, we show how to add a stress diffusion term to some standard viscoelastic rate-type models (Giesekus, FENE-P, Johnson–Segalman, Phan-Thien–Tanner and Bautista–Manero–Puig) so that the resulting models with the added stress diffusion term are thermodynamically consistent in the sense that they obey the first and the second law of thermodynamics. We point out the potential applications of the provided thermodynamical background in the study of flows of fluids described by the proposed models."}],"status":"public","title":"On diffusive variants of some classical viscoelastic rate-type models","intvolume":" 2107","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6642","oa_version":"Preprint","month":"05","isi":1,"quality_controlled":"1","external_id":{"arxiv":["1902.07983"],"isi":["000479303100002"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.07983"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"location":"Zlin, Czech Republic","start_date":"2019-07-30","end_date":"2019-07-31","name":"8th International Conference on Novel Trends in Rheology"},"doi":"10.1063/1.5109493","article_number":"020002","publication_status":"published","publisher":"AIP Publishing","department":[{"_id":"ChWo"}],"year":"2019","date_created":"2019-07-15T10:07:09Z","date_updated":"2024-02-28T13:01:28Z","volume":2107,"author":[{"full_name":"Dostalík, Mark","last_name":"Dostalík","first_name":"Mark"},{"first_name":"Vít","last_name":"Pruša","full_name":"Pruša, Vít"},{"last_name":"Skrivan","first_name":"Tomas","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","full_name":"Skrivan, Tomas"}]},{"oa":1,"external_id":{"isi":["000505529800002"]},"isi":1,"quality_controlled":"1","doi":"10.1063/1.5138135","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00222488"]},"month":"12","year":"2019","department":[{"_id":"RoSe"}],"publisher":"AIP Publishing","publication_status":"published","author":[{"full_name":"Jaksic, Vojkan","last_name":"Jaksic","first_name":"Vojkan"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert"}],"volume":60,"date_updated":"2024-02-28T13:01:45Z","date_created":"2020-01-05T23:00:46Z","article_number":"123504","file_date_updated":"2020-07-14T12:47:54Z","citation":{"ama":"Jaksic V, Seiringer R. Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics. 2019;60(12). doi:10.1063/1.5138135","ista":"Jaksic V, Seiringer R. 2019. Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics. 60(12), 123504.","apa":"Jaksic, V., & Seiringer, R. (2019). Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/1.5138135","ieee":"V. Jaksic and R. Seiringer, “Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018,” Journal of Mathematical Physics, vol. 60, no. 12. AIP Publishing, 2019.","mla":"Jaksic, Vojkan, and Robert Seiringer. “Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018.” Journal of Mathematical Physics, vol. 60, no. 12, 123504, AIP Publishing, 2019, doi:10.1063/1.5138135.","short":"V. Jaksic, R. Seiringer, Journal of Mathematical Physics 60 (2019).","chicago":"Jaksic, Vojkan, and Robert Seiringer. “Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018.” Journal of Mathematical Physics. AIP Publishing, 2019. https://doi.org/10.1063/1.5138135."},"publication":"Journal of Mathematical Physics","article_type":"letter_note","date_published":"2019-12-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7226","intvolume":" 60","ddc":["500"],"title":"Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018","status":"public","file":[{"file_size":1025015,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2019_JournalMathPhysics_Jaksic.pdf","checksum":"bbd12ad1999a9ad7ba4d3c6f2e579c22","date_updated":"2020-07-14T12:47:54Z","date_created":"2020-01-07T14:59:13Z","relation":"main_file","file_id":"7244"}],"oa_version":"Published Version","type":"journal_article","issue":"12"}]