[{"month":"04","language":[{"iso":"eng"}],"doi":"10.1111/jnc.14601","isi":1,"quality_controlled":"1","project":[{"name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain","_id":"25D92700-B435-11E9-9278-68D0E5697425","grant_number":"LS13-002"},{"name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","_id":"25D7962E-B435-11E9-9278-68D0E5697425","grant_number":"RGP0053/2014"},{"_id":"25D61E48-B435-11E9-9278-68D0E5697425","grant_number":"618444","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","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000462680200002"]},"file_date_updated":"2020-07-14T12:45:45Z","ec_funded":1,"date_updated":"2023-09-11T13:40:26Z","date_created":"2018-12-11T11:44:14Z","volume":149,"author":[{"last_name":"Amberg","first_name":"Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole"},{"full_name":"Laukoter, Susanne","orcid":"0000-0002-7903-3010","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","last_name":"Laukoter","first_name":"Susanne"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"}],"publication_status":"published","publisher":"Wiley","department":[{"_id":"SiHi"}],"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","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_published":"2019-04-01T00:00:00Z","article_type":"review","page":"12-26","publication":"Journal of Neurochemistry","citation":{"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","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","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.","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.","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.","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."},"abstract":[{"text":"The cerebral cortex is composed of a large variety of distinct cell-types including projection neurons, interneurons and glial cells which emerge from distinct neural stem cell (NSC) lineages. The vast majority of cortical projection neurons and certain classes of glial cells are generated by radial glial progenitor cells (RGPs) in a highly orchestrated manner. Recent studies employing single cell analysis and clonal lineage tracing suggest that NSC and RGP lineage progression are regulated in a profound deterministic manner. In this review we focus on recent advances based mainly on correlative phenotypic data emerging from functional genetic studies in mice. We establish hypotheses to test in future research and outline a conceptual framework how epigenetic cues modulate the generation of cell-type diversity during cortical development. This article is protected by copyright. All rights reserved.","lang":"eng"}],"issue":"1","type":"journal_article","oa_version":"Published Version","file":[{"date_created":"2020-01-07T13:35:52Z","date_updated":"2020-07-14T12:45:45Z","checksum":"db027721a95d36f5de36aadcd0bdf7e6","relation":"main_file","file_id":"7239","content_type":"application/pdf","file_size":889709,"creator":"kschuh","file_name":"2019_Wiley_Amberg.pdf","access_level":"open_access"}],"status":"public","title":"Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex","ddc":["570"],"intvolume":" 149","_id":"27","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"oa_version":"Submitted Version","file":[{"file_id":"8685","relation":"main_file","date_updated":"2020-10-21T07:18:35Z","date_created":"2020-10-21T07:18:35Z","success":1,"checksum":"e38523787b3bc84006f2793de99ad70f","file_name":"2018_NatureCellBio_Petridou_accepted.pdf","access_level":"open_access","creator":"dernst","file_size":71590590,"content_type":"application/pdf"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5789","intvolume":" 21","status":"public","ddc":["570"],"title":"Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling","abstract":[{"text":"Tissue morphogenesis is driven by mechanical forces that elicit changes in cell size, shape and motion. The extent by which forces deform tissues critically depends on the rheological properties of the recipient tissue. Yet, whether and how dynamic changes in tissue rheology affect tissue morphogenesis and how they are regulated within the developing organism remain unclear. Here, we show that blastoderm spreading at the onset of zebrafish morphogenesis relies on a rapid, pronounced and spatially patterned tissue fluidization. Blastoderm fluidization is temporally controlled by mitotic cell rounding-dependent cell–cell contact disassembly during the last rounds of cell cleavages. Moreover, fluidization is spatially restricted to the central blastoderm by local activation of non-canonical Wnt signalling within the blastoderm margin, increasing cell cohesion and thereby counteracting the effect of mitotic rounding on contact disassembly. Overall, our results identify a fluidity transition mediated by loss of cell cohesion as a critical regulator of embryo morphogenesis.","lang":"eng"}],"type":"journal_article","date_published":"2019-02-01T00:00:00Z","citation":{"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.","ieee":"N. Petridou, S. Grigolon, G. Salbreux, E. B. Hannezo, and C.-P. J. Heisenberg, “Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling,” Nature Cell Biology, vol. 21. Nature Publishing Group, pp. 169–178, 2019.","apa":"Petridou, N., Grigolon, S., Salbreux, G., Hannezo, E. B., & Heisenberg, C.-P. J. (2019). Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/s41556-018-0247-4","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."},"publication":"Nature Cell Biology","page":"169–178","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/when-a-fish-becomes-fluid/"}]},"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","last_name":"Grigolon","first_name":"Silvia"},{"full_name":"Salbreux, Guillaume","first_name":"Guillaume","last_name":"Salbreux"},{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"volume":21,"date_updated":"2023-09-11T14:03:28Z","date_created":"2018-12-30T22:59:15Z","pmid":1,"year":"2019","publisher":"Nature Publishing Group","department":[{"_id":"CaHe"},{"_id":"EdHa"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2020-10-21T07:18:35Z","doi":"10.1038/s41556-018-0247-4","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"external_id":{"isi":["000457468300011"],"pmid":["30559456"]},"oa":1,"project":[{"grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020"},{"name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants (EMBO fellowship)","_id":"253E54C8-B435-11E9-9278-68D0E5697425","grant_number":"ALTF710-2016"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["14657392"]},"month":"02"},{"publication":"Proceedings of the National Academy of Sciences","citation":{"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.","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.","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","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.","ista":"Lang M, Shkolnikov M. 2019. Harmonic dynamics of the Abelian sandpile. Proceedings of the National Academy of Sciences. 116(8), 2821–2830.","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"},"article_type":"original","page":"2821-2830","date_published":"2019-02-19T00:00:00Z","scopus_import":"1","day":"19","article_processing_charge":"No","_id":"196","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Harmonic dynamics of the Abelian sandpile","status":"public","intvolume":" 116","oa_version":"Published Version","type":"journal_article","abstract":[{"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. ","lang":"eng"}],"issue":"8","external_id":{"pmid":[" 30728300"],"isi":["000459074400013"],"arxiv":["1806.10823"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1812015116","open_access":"1"}],"isi":1,"quality_controlled":"1","doi":"10.1073/pnas.1812015116","language":[{"iso":"eng"}],"month":"02","publication_identifier":{"eissn":["1091-6490"]},"year":"2019","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","pmid":1,"publication_status":"published","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"TaHa"}],"publisher":"National Academy of Sciences","author":[{"full_name":"Lang, Moritz","first_name":"Moritz","last_name":"Lang","id":"29E0800A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Shkolnikov, Mikhail","last_name":"Shkolnikov","first_name":"Mikhail","orcid":"0000-0002-4310-178X","id":"35084A62-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/famous-sandpile-model-shown-to-move-like-a-traveling-sand-dune/","description":"News on IST Webpage","relation":"press_release"}]},"date_updated":"2023-09-11T14:09:34Z","date_created":"2018-12-11T11:45:08Z","volume":116},{"scopus_import":"1","day":"20","month":"12","article_processing_charge":"No","quality_controlled":"1","publication":"8th International Conference on Learning Representations","main_file_link":[{"url":"https://arxiv.org/abs/1905.01258","open_access":"1"}],"external_id":{"arxiv":["1905.01258"]},"citation":{"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.","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.","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.","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.","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.","short":"F. Locatello, M. Tschannen, S. Bauer, G. Rätsch, B. Schölkopf, O. Bachem, in:, 8th International Conference on Learning Representations, 2019.","mla":"Locatello, Francesco, et al. “Disentangling Factors of Variation Using Few Labels.” 8th International Conference on Learning Representations, 2019."},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"ICLR: International Conference on Learning Representations","location":"Virtual","start_date":"2020-04-26","end_date":"2020-05-01"},"date_published":"2019-12-20T00:00:00Z","type":"conference","extern":"1","abstract":[{"lang":"eng","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."}],"status":"public","title":"Disentangling factors of variation using few labels","publication_status":"published","department":[{"_id":"FrLo"}],"year":"2019","_id":"14184","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":[{"last_name":"Locatello","first_name":"Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco"},{"first_name":"Michael","last_name":"Tschannen","full_name":"Tschannen, Michael"},{"full_name":"Bauer, Stefan","last_name":"Bauer","first_name":"Stefan"},{"full_name":"Rätsch, Gunnar","last_name":"Rätsch","first_name":"Gunnar"},{"last_name":"Schölkopf","first_name":"Bernhard","full_name":"Schölkopf, Bernhard"},{"full_name":"Bachem, Olivier","last_name":"Bachem","first_name":"Olivier"}]},{"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","oa_version":"Preprint","intvolume":" 115","status":"public","title":"The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA","_id":"14189","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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","language":[{"iso":"eng"}],"conference":{"name":"UAI: Uncertainty in Artificial Intelligence","start_date":"2019-07-22","location":"Tel Aviv, Israel","end_date":"2019-07-25"},"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1905.06642","open_access":"1"}],"external_id":{"arxiv":["1905.06642"]},"month":"05","volume":115,"date_updated":"2023-09-12T08:07:38Z","date_created":"2023-08-22T14:08:35Z","author":[{"last_name":"Gresele","first_name":"Luigi","full_name":"Gresele, Luigi"},{"full_name":"Rubenstein, Paul K.","last_name":"Rubenstein","first_name":"Paul K."},{"last_name":"Mehrjou","first_name":"Arash","full_name":"Mehrjou, Arash"},{"full_name":"Locatello, Francesco","first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683"},{"first_name":"Bernhard","last_name":"Schölkopf","full_name":"Schölkopf, Bernhard"}],"department":[{"_id":"FrLo"}],"publisher":"ML Research Press","publication_status":"published","year":"2019","extern":"1"},{"quality_controlled":"1","external_id":{"arxiv":["1905.13662"]},"main_file_link":[{"url":"https://arxiv.org/abs/1905.13662","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"start_date":"2019-12-08","location":"Vancouver, Canada","end_date":"2019-12-14","name":"NeurIPS: Neural Information Processing Systems"},"publication_identifier":{"isbn":["9781713807933"]},"month":"12","department":[{"_id":"FrLo"}],"publication_status":"published","year":"2019","volume":32,"date_created":"2023-08-22T14:12:28Z","date_updated":"2023-09-12T09:37:22Z","author":[{"first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"first_name":"Gabriele","last_name":"Abbati","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"},{"first_name":"Olivier","last_name":"Bachem","full_name":"Bachem, Olivier"}],"extern":"1","page":"14611–14624","citation":{"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.","short":"F. Locatello, G. Abbati, T. Rainforth, S. Bauer, B. Schölkopf, O. Bachem, in:, Advances in Neural Information Processing Systems, 2019, pp. 14611–14624.","mla":"Locatello, Francesco, et al. “On the Fairness of Disentangled Representations.” Advances in Neural Information Processing Systems, vol. 32, 2019, 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.","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.","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.","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."},"publication":"Advances in Neural Information Processing Systems","date_published":"2019-12-08T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"08","intvolume":" 32","status":"public","title":"On the fairness of disentangled representations","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14197","oa_version":"Preprint","type":"conference","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"}]},{"month":"12","publication_identifier":{"isbn":["9781713807933"]},"oa":1,"external_id":{"arxiv":["1901.10348"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1901.10348"}],"quality_controlled":"1","conference":{"name":"NeurIPS: Neural Information Processing Systems","end_date":"2019-12-14","start_date":"2019-12-08","location":"Vancouver, Canada"},"language":[{"iso":"eng"}],"extern":"1","year":"2019","publication_status":"published","department":[{"_id":"FrLo"}],"author":[{"full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco"},{"last_name":"Yurtsever","first_name":"Alp","full_name":"Yurtsever, Alp"},{"last_name":"Fercoq","first_name":"Olivier","full_name":"Fercoq, Olivier"},{"last_name":"Cevher","first_name":"Volkan","full_name":"Cevher, Volkan"}],"date_created":"2023-08-22T14:09:35Z","date_updated":"2023-09-12T08:48:45Z","volume":32,"scopus_import":"1","day":"29","article_processing_charge":"No","publication":"Advances in Neural Information Processing Systems","citation":{"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.","short":"F. Locatello, A. Yurtsever, O. Fercoq, V. Cevher, in:, Advances in Neural Information Processing Systems, 2019, pp. 14291–14301.","mla":"Locatello, Francesco, et al. “Stochastic Frank-Wolfe for Composite Convex Minimization.” Advances in Neural Information Processing Systems, vol. 32, 2019, 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.","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.","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.","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."},"page":"14291–14301","date_published":"2019-12-29T00:00:00Z","type":"conference","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."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14191","status":"public","title":"Stochastic Frank-Wolfe for composite convex minimization","intvolume":" 32","oa_version":"Preprint"},{"quality_controlled":"1","publication":"Advances in Neural Information Processing Systems","external_id":{"arxiv":["1905.12506"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1905.12506"}],"oa":1,"citation":{"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.","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.","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","article_processing_charge":"No","publication_identifier":{"isbn":["9781713807933"]},"status":"public","title":"Are disentangled representations helpful for abstract visual reasoning?","publication_status":"published","department":[{"_id":"FrLo"}],"intvolume":" 32","_id":"14193","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-12T09:02:43Z","date_created":"2023-08-22T14:09:53Z","volume":32,"oa_version":"Preprint","author":[{"last_name":"Steenkiste","first_name":"Sjoerd van","full_name":"Steenkiste, Sjoerd van"},{"full_name":"Locatello, Francesco","last_name":"Locatello","first_name":"Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"full_name":"Schmidhuber, Jürgen","last_name":"Schmidhuber","first_name":"Jürgen"},{"full_name":"Bachem, Olivier","last_name":"Bachem","first_name":"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."}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14200","status":"public","title":"Challenging common assumptions in the unsupervised learning of disentangled representations","intvolume":" 97","oa_version":"Preprint","type":"conference","abstract":[{"lang":"eng","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."}],"publication":"Proceedings of the 36th International Conference on Machine Learning","citation":{"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.","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.","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.","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.","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.","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.","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."},"page":"4114-4124","date_published":"2019-06-09T00:00:00Z","scopus_import":"1","day":"09","article_processing_charge":"No","year":"2019","publication_status":"published","publisher":"ML Research Press","department":[{"_id":"FrLo"}],"author":[{"full_name":"Locatello, Francesco","last_name":"Locatello","first_name":"Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"first_name":"Stefan","last_name":"Bauer","full_name":"Bauer, Stefan"},{"full_name":"Lucic, Mario","last_name":"Lucic","first_name":"Mario"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"},{"last_name":"Gelly","first_name":"Sylvain","full_name":"Gelly, Sylvain"},{"full_name":"Schölkopf, Bernhard","first_name":"Bernhard","last_name":"Schölkopf"},{"full_name":"Bachem, Olivier","last_name":"Bachem","first_name":"Olivier"}],"date_created":"2023-08-22T14:13:08Z","date_updated":"2023-09-13T07:45:30Z","volume":97,"extern":"1","external_id":{"arxiv":["1811.12359"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1811.12359","open_access":"1"}],"quality_controlled":"1","conference":{"name":"International Conference on Machine Learning","start_date":"2019-06-10","location":"Long Beach, CA, United States","end_date":"2019-06-15"},"language":[{"iso":"eng"}],"month":"06"},{"_id":"5817","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Limiting shapes of confined lipid vesicles","ddc":["530"],"status":"public","intvolume":" 15","file":[{"date_created":"2020-10-09T11:00:05Z","date_updated":"2020-10-09T11:00:05Z","checksum":"614c337d6424ccd3d48d1b1f9513510d","success":1,"relation":"main_file","file_id":"8641","content_type":"application/pdf","file_size":5370762,"creator":"bkavcic","file_name":"lmt_sftmtr_V8.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","type":"journal_article","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","publication":"Soft Matter","citation":{"short":"B. Kavcic, A. Sakashita, H. Noguchi, P. Ziherl, Soft Matter 15 (2019) 602–614.","mla":"Kavcic, Bor, et al. “Limiting Shapes of Confined Lipid Vesicles.” Soft Matter, vol. 15, no. 4, Royal Society of Chemistry, 2019, pp. 602–14, doi:10.1039/c8sm01956h.","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.","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","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","ista":"Kavcic B, Sakashita A, Noguchi H, Ziherl P. 2019. Limiting shapes of confined lipid vesicles. Soft Matter. 15(4), 602–614."},"article_type":"original","page":"602-614","date_published":"2019-01-10T00:00:00Z","scopus_import":"1","day":"10","article_processing_charge":"No","has_accepted_license":"1","year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"Royal Society of Chemistry","author":[{"full_name":"Kavcic, Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X","first_name":"Bor","last_name":"Kavcic"},{"last_name":"Sakashita","first_name":"A.","full_name":"Sakashita, A."},{"full_name":"Noguchi, H.","last_name":"Noguchi","first_name":"H."},{"full_name":"Ziherl, P.","first_name":"P.","last_name":"Ziherl"}],"date_created":"2019-01-11T07:37:47Z","date_updated":"2023-09-13T08:47:16Z","volume":15,"file_date_updated":"2020-10-09T11:00:05Z","license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode","short":"CC BY-NC-ND (3.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"isi":["000457329700003"],"pmid":["30629082"]},"isi":1,"quality_controlled":"1","doi":"10.1039/c8sm01956h","language":[{"iso":"eng"}],"month":"01","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]}},{"year":"2019","department":[{"_id":"JaMa"}],"publisher":"Springer","publication_status":"published","author":[{"last_name":"Erbar","first_name":"Matthias","full_name":"Erbar, Matthias"},{"full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","first_name":"Jan"},{"first_name":"Melchior","last_name":"Wirth","full_name":"Wirth, Melchior"}],"volume":58,"date_updated":"2023-09-13T09:12:35Z","date_created":"2018-12-11T11:44:29Z","article_number":"19","ec_funded":1,"file_date_updated":"2020-07-14T12:47:55Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000452849400001"],"arxiv":["1805.06040"]},"oa":1,"project":[{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"name":"Taming Complexity in Partial Di erential Systems","call_identifier":"FWF","_id":"260482E2-B435-11E9-9278-68D0E5697425","grant_number":" F06504"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"quality_controlled":"1","isi":1,"doi":"10.1007/s00526-018-1456-1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["09442669"]},"month":"02","_id":"73","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 58","ddc":["510"],"title":"On the geometry of geodesics in discrete optimal transport","status":"public","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":645565,"creator":"dernst","file_name":"2018_Calculus_Erbar.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:55Z","date_created":"2019-01-28T15:37:11Z","checksum":"ba05ac2d69de4c58d2cd338b63512798","relation":"main_file","file_id":"5895"}],"type":"journal_article","issue":"1","abstract":[{"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.","lang":"eng"}],"citation":{"ama":"Erbar M, Maas J, Wirth M. On the geometry of geodesics in discrete optimal transport. Calculus of Variations and Partial Differential Equations. 2019;58(1). doi:10.1007/s00526-018-1456-1","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.","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","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.","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."},"publication":"Calculus of Variations and Partial Differential Equations","article_type":"original","date_published":"2019-02-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01"},{"_id":"14190","year":"2019","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 32","department":[{"_id":"FrLo"}],"title":"On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset","publication_status":"published","status":"public","author":[{"full_name":"Gondal, Muhammad Waleed","first_name":"Muhammad Waleed","last_name":"Gondal"},{"last_name":"Wüthrich","first_name":"Manuel","full_name":"Wüthrich, Manuel"},{"full_name":"Miladinović, Đorđe","first_name":"Đorđe","last_name":"Miladinović"},{"full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","first_name":"Francesco","last_name":"Locatello"},{"last_name":"Breidt","first_name":"Martin","full_name":"Breidt, Martin"},{"last_name":"Volchkov","first_name":"Valentin","full_name":"Volchkov, Valentin"},{"full_name":"Akpo, Joel","first_name":"Joel","last_name":"Akpo"},{"full_name":"Bachem, Olivier","first_name":"Olivier","last_name":"Bachem"},{"last_name":"Schölkopf","first_name":"Bernhard","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","type":"conference","abstract":[{"lang":"eng","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."}],"extern":"1","oa":1,"external_id":{"arxiv":["1906.03292"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1906.03292"}],"citation":{"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.","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.","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.","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.","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.","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.","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."},"publication":"Advances in Neural Information Processing Systems","quality_controlled":"1","date_published":"2019-06-07T00:00:00Z","conference":{"name":"NeurIPS: Neural Information Processing Systems","end_date":"2019-12-14","location":"Vancouver, Canada","start_date":"2019-12-08"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781713807933"]},"article_processing_charge":"No","day":"07","month":"06"},{"date_created":"2019-11-04T15:45:17Z","date_updated":"2023-09-15T12:19:31Z","volume":15,"author":[{"last_name":"Akitaya","first_name":"Hugo","full_name":"Akitaya, Hugo"},{"full_name":"Fulek, Radoslav","first_name":"Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774"},{"full_name":"Tóth, Csaba","first_name":"Csaba","last_name":"Tóth"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"309"}]},"publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"ACM","year":"2019","article_number":"50","language":[{"iso":"eng"}],"doi":"10.1145/3344549","quality_controlled":"1","project":[{"name":"Eliminating intersections in drawings of graphs","call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425","grant_number":"M02281"}],"oa":1,"external_id":{"arxiv":["1709.09209"]},"main_file_link":[{"url":"https://arxiv.org/abs/1709.09209","open_access":"1"}],"month":"10","oa_version":"Preprint","title":"Recognizing weak embeddings of graphs","status":"public","intvolume":" 15","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6982","abstract":[{"lang":"eng","text":"We present an efficient algorithm for a problem in the interface between clustering and graph embeddings. An embedding ϕ : G → M of a graph G into a 2-manifold M maps the vertices in V(G) to distinct points and the edges in E(G) to interior-disjoint Jordan arcs between the corresponding vertices. In applications in clustering, cartography, and visualization, nearby vertices and edges are often bundled to the same point or overlapping arcs due to data compression or low resolution. This raises the computational problem of deciding whether a given map ϕ : G → M comes from an embedding. A map ϕ : G → M is a weak embedding if it can be perturbed into an embedding ψ ϵ : G → M with ‖ ϕ − ψ ϵ ‖ < ϵ for every ϵ > 0, where ‖.‖ is the unform norm.\r\nA polynomial-time algorithm for recognizing weak embeddings has recently been found by Fulek and Kynčl. It reduces the problem to solving a system of linear equations over Z2. It runs in O(n2ω)≤ O(n4.75) time, where ω ∈ [2,2.373) is the matrix multiplication exponent and n is the number of vertices and edges of G. We improve the running time to O(n log n). Our algorithm is also conceptually simpler: We perform a sequence of local operations that gradually “untangles” the image ϕ(G) into an embedding ψ(G) or reports that ϕ is not a weak embedding. It combines local constraints on the orientation of subgraphs directly, thereby eliminating the need for solving large systems of linear equations.\r\n"}],"issue":"4","type":"journal_article","date_published":"2019-10-01T00:00:00Z","article_type":"original","publication":"ACM Transactions on Algorithms","citation":{"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.","ama":"Akitaya H, Fulek R, Tóth C. Recognizing weak embeddings of graphs. ACM Transactions on Algorithms. 2019;15(4). 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.","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."},"day":"01","scopus_import":1},{"publication_identifier":{"eissn":["2663-337X"]},"month":"09","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"},"doi":"10.15479/AT:ISTA:6894","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"}],"degree_awarded":"PhD","file_date_updated":"2020-07-14T12:47:43Z","year":"2019","publisher":"Institute of Science and Technology Austria","department":[{"_id":"ToHe"}],"publication_status":"published","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"631"},{"id":"647","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"140"}]},"author":[{"last_name":"Giacobbe","first_name":"Mirco","orcid":"0000-0001-8180-0904","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","full_name":"Giacobbe, Mirco"}],"date_created":"2019-09-22T14:08:44Z","date_updated":"2023-09-19T09:30:43Z","has_accepted_license":"1","article_processing_charge":"No","day":"30","citation":{"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.","ama":"Giacobbe M. Automatic time-unbounded reachability analysis of hybrid systems. 2019. doi:10.15479/AT:ISTA:6894","chicago":"Giacobbe, Mirco. “Automatic Time-Unbounded Reachability Analysis of Hybrid Systems.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6894.","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."},"page":"132","date_published":"2019-09-30T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","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."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6894","title":"Automatic time-unbounded reachability analysis of hybrid systems","ddc":["000"],"status":"public","oa_version":"Published Version","file":[{"checksum":"773beaf4a85dc2acc2c12b578fbe1965","date_created":"2019-09-27T14:15:05Z","date_updated":"2020-07-14T12:47:43Z","relation":"main_file","file_id":"6916","file_size":4100685,"content_type":"application/pdf","creator":"mgiacobbe","access_level":"open_access","file_name":"giacobbe_thesis.pdf"},{"content_type":"application/gzip","file_size":7959732,"creator":"mgiacobbe","file_name":"giacobbe_thesis_src.tar.gz","access_level":"closed","date_updated":"2020-07-14T12:47:43Z","date_created":"2019-09-27T14:22:04Z","checksum":"97f1c3da71feefd27e6e625d32b4c75b","relation":"source_file","file_id":"6917"}]},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9805","year":"2019","status":"public","title":"Data from: The consequences of an introgression event","publisher":"Dryad","department":[{"_id":"NiBa"}],"author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"40"}]},"date_updated":"2023-09-19T10:06:07Z","date_created":"2021-08-06T12:03:50Z","oa_version":"Published Version","type":"research_data_reference","abstract":[{"text":"The spread of adaptive alleles is fundamental to evolution, and in theory, this process is well‐understood. However, only rarely can we follow this process—whether it originates from the spread of a new mutation, or by introgression from another population. In this issue of Molecular Ecology, Hanemaaijer et al. (2018) report on a 25‐year long study of the mosquitoes Anopheles gambiae (Figure 1) and Anopheles coluzzi in Mali, based on genotypes at 15 single‐nucleotide polymorphism (SNP). The species are usually reproductively isolated from each other, but in 2002 and 2006, bursts of hybridization were observed, when F1 hybrids became abundant. Alleles backcrossed from A. gambiae into A. coluzzi, but after the first event, these declined over the following years. In contrast, after 2006, an insecticide resistance allele that had established in A. gambiae spread into A. coluzzi, and rose to high frequency there, over 6 years (~75 generations). Whole genome sequences of 74 individuals showed that A. gambiae SNP from across the genome had become common in the A. coluzzi population, but that most of these were clustered in 34 genes around the resistance locus. A new set of SNP from 25 of these genes were assayed over time; over the 4 years since near‐fixation of the resistance allele; some remained common, whereas others declined. What do these patterns tell us about this introgression event?","lang":"eng"}],"oa":1,"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"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.2kb6fh4"}],"doi":"10.5061/dryad.2kb6fh4","date_published":"2019-01-09T00:00:00Z","month":"01","day":"09","article_processing_charge":"No"},{"isi":1,"quality_controlled":"1","project":[{"name":"Investigating the role of transporters in invasive migration through junctions","call_identifier":"FP7","grant_number":"334077","_id":"2536F660-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"pmid":["30504274"],"isi":["000455189900006"]},"language":[{"iso":"eng"}],"doi":"10.1523/JNEUROSCI.1059-18.2018","month":"01","publication_status":"published","department":[{"_id":"DaSi"}],"publisher":"Society for Neuroscience","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.","pmid":1,"date_created":"2018-12-11T11:44:07Z","date_updated":"2023-09-19T10:10:55Z","volume":39,"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","last_name":"Mazaud","first_name":"David"},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","first_name":"Daria E","last_name":"Siekhaus","full_name":"Siekhaus, Daria E"},{"full_name":"Fanto, Manolis","first_name":"Manolis","last_name":"Fanto"},{"full_name":"Giangrande, Angela","last_name":"Giangrande","first_name":"Angela"}],"file_date_updated":"2020-10-02T09:33:28Z","ec_funded":1,"publist_id":"8048","article_type":"original","page":"238-255","publication":"Journal of Neuroscience","citation":{"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","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."},"date_published":"2019-01-09T00:00:00Z","scopus_import":"1","day":"09","has_accepted_license":"1","article_processing_charge":"No","status":"public","title":"The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate","ddc":["570"],"intvolume":" 39","_id":"8","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"8596","checksum":"8f6925eb4cd1e8747d8ea25929c68de6","success":1,"date_updated":"2020-10-02T09:33:28Z","date_created":"2020-10-02T09:33:28Z","access_level":"open_access","file_name":"2019_JournNeuroscience_Trebuchet.pdf","file_size":9455414,"content_type":"application/pdf","creator":"dernst"}],"type":"journal_article","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"}],"issue":"2"},{"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"}],"issue":"3","type":"journal_article","file":[{"checksum":"1be56239b2cd740a0e9a084f773c22f6","date_created":"2020-01-07T13:31:53Z","date_updated":"2020-07-14T12:46:35Z","file_id":"7238","relation":"main_file","creator":"kschuh","content_type":"application/pdf","file_size":431754,"access_level":"open_access","file_name":"2019_Wiley_Ganev.pdf"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5","title":"The wonderful compactification for quantum groups","ddc":["510"],"status":"public","intvolume":" 99","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","date_published":"2019-06-01T00:00:00Z","publication":"Journal of the London Mathematical Society","citation":{"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.","short":"I.V. Ganev, Journal of the London Mathematical Society 99 (2019) 778–806.","mla":"Ganev, Iordan V. “The Wonderful Compactification for Quantum Groups.” Journal of the London Mathematical Society, vol. 99, no. 3, Wiley, 2019, pp. 778–806, doi:10.1112/jlms.12193.","ieee":"I. V. Ganev, “The wonderful compactification for quantum groups,” Journal of the London Mathematical Society, vol. 99, no. 3. Wiley, pp. 778–806, 2019.","apa":"Ganev, I. V. (2019). The wonderful compactification for quantum groups. Journal of the London Mathematical Society. Wiley. https://doi.org/10.1112/jlms.12193","ista":"Ganev IV. 2019. The wonderful compactification for quantum groups. Journal of the London Mathematical Society. 99(3), 778–806.","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"},"page":"778-806","file_date_updated":"2020-07-14T12:46:35Z","publist_id":"8052","author":[{"id":"447491B8-F248-11E8-B48F-1D18A9856A87","first_name":"Iordan V","last_name":"Ganev","full_name":"Ganev, Iordan V"}],"date_updated":"2023-09-19T10:13:08Z","date_created":"2018-12-11T11:44:06Z","volume":99,"year":"2019","publication_status":"published","publisher":"Wiley","department":[{"_id":"TaHa"}],"month":"06","doi":"10.1112/jlms.12193","language":[{"iso":"eng"}],"external_id":{"isi":["000470025900008"]},"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},{"file_date_updated":"2020-07-14T12:47:51Z","year":"2019","department":[{"_id":"JiFr"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1346"},{"relation":"part_of_dissertation","status":"public","id":"6377"},{"id":"449","status":"public","relation":"part_of_dissertation"}]},"author":[{"id":"3407EB18-F248-11E8-B48F-1D18A9856A87","last_name":"Vasileva","first_name":"Mina K","full_name":"Vasileva, Mina K"}],"date_created":"2019-12-11T21:24:39Z","date_updated":"2023-09-19T10:39:33Z","publication_identifier":{"eissn":["2663-337X"]},"month":"12","oa":1,"doi":"10.15479/AT:ISTA:7172","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"supervisor":[{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"degree_awarded":"PhD","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"The development and growth of Arabidopsis thaliana is regulated by a combination of genetic programing and also by the environmental influences. An important role in these processes play the phytohormones and among them, auxin is crucial as it controls many important functions. It is transported through the whole plant body by creating local and temporal concentration maxima and minima, which have an impact on the cell status, tissue and organ identity. Auxin has the property to undergo a directional and finely regulated cell-to-cell transport, which is enabled by the transport proteins, localized on the plasma membrane. An important role in this process have the PIN auxin efflux proteins, which have an asymmetric/polar subcellular localization and determine the directionality of the auxin transport. During the last years, there were significant advances in understanding how the trafficking molecular machineries function, including studies on molecular interactions, function, subcellular localization and intracellular distribution. However, there is still a lack of detailed characterization on the steps of endocytosis, exocytosis, endocytic recycling and degradation. Due to this fact, I focused on the identification of novel trafficking factors and better characterization of the intracellular trafficking pathways. My PhD thesis consists of an introductory chapter, three experimental chapters, a chapter containing general discussion, conclusions and perspectives and also an appendix chapter with published collaborative papers.\r\nThe first chapter is separated in two different parts: I start by a general introduction to auxin biology and then I introduce the trafficking pathways in the model plant Arabidopsis thaliana. Then, I explain also the phosphorylation-signals for polar targeting and also the roles of the phytohormone strigolactone.\r\nThe second chapter includes the characterization of bar1/sacsin mutant, which was identified in a forward genetic screen for novel trafficking components in Arabidopsis thaliana, where by the implementation of an EMS-treated pPIN1::PIN1-GFP marker line and by using the established inhibitor of ARF-GEFs, Brefeldin A (BFA) as a tool to study trafficking processes, we identified a novel factor, which is mediating the adaptation of the plant cell to ARF-GEF inhibition. The mutation is in a previously uncharacterized gene, encoding a very big protein that we, based on its homologies, called SACSIN with domains suggesting roles as a molecular chaperon or as a component of the ubiquitin-proteasome system. Our physiology and imaging studies revealed that SACSIN is a crucial plant cell component of the adaptation to the ARF-GEF inhibition.\r\nThe third chapter includes six subchapters, where I focus on the role of the phytohormone strigolactone, which interferes with auxin feedback on PIN internalization. Strigolactone moderates the polar auxin transport by increasing the internalization of the PIN auxin efflux carriers, which reduces the canalization related growth responses. In addition, I also studied the role of phosphorylation in the strigolactone regulation of auxin feedback on PIN internalization. In this chapter I also present my results on the MAX2-dependence of strigolactone-mediated root growth inhibition and I also share my results on the auxin metabolomics profiling after application of GR24.\r\nIn the fourth chapter I studied the effect of two small molecules ES-9 and ES9-17, which were identified from a collection of small molecules with the property to impair the clathrin-mediated endocytosis.\r\nIn the fifth chapter, I discuss all my observations and experimental findings and suggest alternative hypothesis to interpret my results.\r\nIn the appendix there are three collaborative published projects. In the first, I participated in the characterization of the role of ES9 as a small molecule, which is inhibitor of clathrin- mediated endocytosis in different model organisms. In the second paper, I contributed to the characterization of another small molecule ES9-17, which is a non-protonophoric analog of ES9 and also impairs the clathrin-mediated endocytosis not only in plant cells, but also in mammalian HeLa cells. Last but not least, I also attach another paper, where I tried to establish the grafting method as a technique in our lab to study canalization related processes."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7172","ddc":["570"],"status":"public","title":"Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana","file":[{"access_level":"closed","file_name":"Thesis_Mina_final_upload_7.docx","file_size":20454014,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"mvasilev","relation":"source_file","file_id":"7175","checksum":"ef981c1a3b1d9da0edcbedcff4970d37","date_created":"2019-12-12T09:32:36Z","date_updated":"2020-07-14T12:47:51Z"},{"date_updated":"2020-07-14T12:47:51Z","date_created":"2019-12-12T09:33:10Z","checksum":"3882c4585e46c9cfb486e4225cad54ab","relation":"main_file","file_id":"7176","content_type":"application/pdf","file_size":11565025,"creator":"mvasilev","file_name":"Thesis_Mina_final_upload_7.pdf","access_level":"open_access"}],"oa_version":"Published Version","article_processing_charge":"No","has_accepted_license":"1","day":"12","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.","short":"M.K. Vasileva, Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2019.","mla":"Vasileva, Mina K. Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7172.","apa":"Vasileva, M. K. (2019). Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7172","ieee":"M. K. Vasileva, “Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2019.","ista":"Vasileva MK. 2019. Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria.","ama":"Vasileva MK. Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana. 2019. doi:10.15479/AT:ISTA:7172"},"page":"192","date_published":"2019-12-12T00:00:00Z"},{"month":"05","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:6473","supervisor":[{"full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file_date_updated":"2020-07-14T12:47:31Z","author":[{"full_name":"Cepeda Humerez, Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","last_name":"Cepeda Humerez","first_name":"Sarah A"}],"related_material":{"record":[{"id":"1576","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"6900"},{"status":"public","relation":"dissertation_contains","id":"281"},{"id":"2016","relation":"dissertation_contains","status":"public"}]},"date_created":"2019-05-21T00:11:23Z","date_updated":"2023-09-19T15:13:26Z","year":"2019","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"}],"day":"23","article_processing_charge":"No","has_accepted_license":"1","keyword":["Information estimation","Time-series","data analysis"],"date_published":"2019-05-23T00:00:00Z","citation":{"ieee":"S. A. Cepeda Humerez, “Estimating information flow in single cells,” Institute of Science and Technology Austria, 2019.","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","ista":"Cepeda Humerez SA. 2019. Estimating information flow in single cells. Institute of Science and Technology Austria.","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.","short":"S.A. Cepeda Humerez, Estimating Information Flow in Single Cells, Institute of Science and Technology Austria, 2019.","mla":"Cepeda Humerez, Sarah A. Estimating Information Flow in Single Cells. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6473."},"page":"135","abstract":[{"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. ","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"date_created":"2019-05-23T11:18:16Z","date_updated":"2020-07-14T12:47:31Z","checksum":"75f9184c1346e10a5de5f9cc7338309a","file_id":"6480","relation":"source_file","creator":"scepeda","file_size":23937464,"content_type":"application/zip","file_name":"Thesis_Cepeda.zip","access_level":"closed"},{"date_created":"2019-05-23T11:18:13Z","date_updated":"2020-07-14T12:47:31Z","checksum":"afdc0633ddbd71d5b13550d7fb4f4454","relation":"main_file","file_id":"6481","file_size":16646985,"content_type":"application/pdf","creator":"scepeda","file_name":"CepedaThesis.pdf","access_level":"open_access"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6473","status":"public","ddc":["004"],"title":"Estimating information flow in single cells"},{"day":"11","article_processing_charge":"No","has_accepted_license":"1","citation":{"ista":"Prizak R. 2019. Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria.","apa":"Prizak, R. (2019). Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th6071","ieee":"R. Prizak, “Coevolution of transcription factors and their binding sites in sequence space,” Institute of Science and Technology Austria, 2019.","ama":"Prizak R. Coevolution of transcription factors and their binding sites in sequence space. 2019. doi:10.15479/at:ista:th6071","chicago":"Prizak, Roshan. “Coevolution of Transcription Factors and Their Binding Sites in Sequence Space.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:th6071.","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."},"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"],"oa_version":"Published Version","file":[{"file_id":"6072","relation":"main_file","checksum":"e60a72de35d270b31f1a23d50f224ec0","date_created":"2019-03-06T16:05:07Z","date_updated":"2020-07-14T12:47:18Z","access_level":"open_access","file_name":"Thesis_final_PDFA_RoshanPrizak.pdf","creator":"rprizak","content_type":"application/pdf","file_size":20995465},{"creator":"rprizak","file_size":85705272,"content_type":"application/zip","file_name":"thesis_v2_merge.zip","access_level":"closed","date_created":"2019-03-06T16:09:39Z","date_updated":"2020-07-14T12:47:18Z","checksum":"67c2630333d05ebafef5f018863a8465","title":"Latex files","file_id":"6073","relation":"source_file"}],"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":[{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik"}],"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":[{"id":"1358","relation":"part_of_dissertation","status":"public"},{"id":"955","relation":"part_of_dissertation","status":"public"}]},"date_updated":"2023-09-22T10:00:48Z","date_created":"2019-03-06T16:16:10Z"},{"date_published":"2019-05-20T00:00:00Z","publication":"Documenta Mathematica","citation":{"ama":"Srivastava TK. On derived equivalences of k3 surfaces in positive characteristic. Documenta Mathematica. 2019;24:1135-1177. doi:10.25537/dm.2019v24.1135-1177","ieee":"T. K. Srivastava, “On derived equivalences of k3 surfaces in positive characteristic,” Documenta Mathematica, vol. 24. EMS Press, pp. 1135–1177, 2019.","apa":"Srivastava, T. K. (2019). On derived equivalences of k3 surfaces in positive characteristic. Documenta Mathematica. EMS Press. https://doi.org/10.25537/dm.2019v24.1135-1177","ista":"Srivastava TK. 2019. On derived equivalences of k3 surfaces in positive characteristic. Documenta Mathematica. 24, 1135–1177.","short":"T.K. Srivastava, Documenta Mathematica 24 (2019) 1135–1177.","mla":"Srivastava, Tanya K. “On Derived Equivalences of K3 Surfaces in Positive Characteristic.” Documenta Mathematica, vol. 24, EMS Press, 2019, pp. 1135–77, doi:10.25537/dm.2019v24.1135-1177.","chicago":"Srivastava, Tanya K. “On Derived Equivalences of K3 Surfaces in Positive Characteristic.” Documenta Mathematica. EMS Press, 2019. https://doi.org/10.25537/dm.2019v24.1135-1177."},"article_type":"original","page":"1135-1177","day":"20","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"7438","date_created":"2020-02-03T06:26:12Z","date_updated":"2020-07-14T12:47:58Z","checksum":"9a1a64bd49ab03fa4f738fb250fc4f90","file_name":"2019_DocumMath_Srivastava.pdf","access_level":"open_access","file_size":469730,"content_type":"application/pdf","creator":"dernst"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7436","ddc":["510"],"title":"On derived equivalences of k3 surfaces in positive characteristic","status":"public","intvolume":" 24","abstract":[{"lang":"eng","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. "}],"type":"journal_article","doi":"10.25537/dm.2019v24.1135-1177","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":["1809.08970"],"isi":["000517806400019"]},"oa":1,"quality_controlled":"1","isi":1,"month":"05","publication_identifier":{"eissn":["1431-0643"],"issn":["1431-0635"]},"author":[{"full_name":"Srivastava, Tanya K","last_name":"Srivastava","first_name":"Tanya K","id":"4D046628-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2020-02-02T23:01:06Z","date_updated":"2023-10-17T07:42:21Z","volume":24,"year":"2019","publication_status":"published","publisher":"EMS Press","department":[{"_id":"TaHa"}],"file_date_updated":"2020-07-14T12:47:58Z"},{"ec_funded":1,"year":"2019","publication_status":"published","department":[{"_id":"LaEr"},{"_id":"JaMa"}],"publisher":"Institute of Mathematical Statistics","author":[{"first_name":"Patrick","last_name":"Ferrari","full_name":"Ferrari, Patrick"},{"full_name":"Ghosal, Promit","last_name":"Ghosal","first_name":"Promit"},{"id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Nejjar","full_name":"Nejjar, Peter"}],"date_created":"2018-12-11T11:44:29Z","date_updated":"2023-10-17T08:53:45Z","volume":55,"month":"09","publication_identifier":{"issn":["0246-0203"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1710.02323"}],"external_id":{"arxiv":["1710.02323"],"isi":["000487763200001"]},"quality_controlled":"1","isi":1,"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"},{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"}],"doi":"10.1214/18-AIHP916","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"We consider the totally asymmetric simple exclusion process (TASEP) with non-random initial condition having density ρ on ℤ− and λ on ℤ+, and a second class particle initially at the origin. For ρ<λ, there is a shock and the second class particle moves with speed 1−λ−ρ. For large time t, we show that the position of the second class particle fluctuates on a t1/3 scale and determine its limiting law. We also obtain the limiting distribution of the number of steps made by the second class particle until time t.","lang":"eng"}],"issue":"3","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"72","status":"public","title":"Limit law of a second class particle in TASEP with non-random initial condition","intvolume":" 55","oa_version":"Preprint","scopus_import":"1","day":"25","article_processing_charge":"No","publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","citation":{"chicago":"Ferrari, Patrick, Promit Ghosal, and Peter Nejjar. “Limit Law of a Second Class Particle in TASEP with Non-Random Initial Condition.” Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-AIHP916.","mla":"Ferrari, Patrick, et al. “Limit Law of a Second Class Particle in TASEP with Non-Random Initial Condition.” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 55, no. 3, Institute of Mathematical Statistics, 2019, pp. 1203–25, doi:10.1214/18-AIHP916.","short":"P. Ferrari, P. Ghosal, P. Nejjar, Annales de l’institut Henri Poincare (B) Probability and Statistics 55 (2019) 1203–1225.","ista":"Ferrari P, Ghosal P, Nejjar P. 2019. Limit law of a second class particle in TASEP with non-random initial condition. Annales de l’institut Henri Poincare (B) Probability and Statistics. 55(3), 1203–1225.","ieee":"P. Ferrari, P. Ghosal, and P. Nejjar, “Limit law of a second class particle in TASEP with non-random initial condition,” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 55, no. 3. Institute of Mathematical Statistics, pp. 1203–1225, 2019.","apa":"Ferrari, P., Ghosal, P., & Nejjar, P. (2019). Limit law of a second class particle in TASEP with non-random initial condition. Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AIHP916","ama":"Ferrari P, Ghosal P, Nejjar P. Limit law of a second class particle in TASEP with non-random initial condition. Annales de l’institut Henri Poincare (B) Probability and Statistics. 2019;55(3):1203-1225. doi:10.1214/18-AIHP916"},"article_type":"original","page":"1203-1225","date_published":"2019-09-25T00:00:00Z"},{"day":"01","month":"05","publication_identifier":{"isbn":["9781943580576"]},"article_processing_charge":"No","scopus_import":"1","conference":{"end_date":"2019-05-10","location":"San Jose, CA, United States","start_date":"2019-05-05","name":"CLEO: Conference on Lasers and Electro-Optics"},"doi":"10.1364/cleo_at.2019.jtu2a.52","date_published":"2019-05-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"CLEO: Applications and Technology","citation":{"ama":"Khatoniar M, Yama N, Ghazaryan A, Guddala S, Ghaemi P, Menon V. Room temperature control of valley coherence in bilayer WS2 exciton polaritons. In: CLEO: Applications and Technology. Optica Publishing Group; 2019. doi:10.1364/cleo_at.2019.jtu2a.52","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","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.","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."},"quality_controlled":"1","abstract":[{"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.","lang":"eng"}],"article_number":"paper JTu2A.52","type":"conference","author":[{"first_name":"Mandeep","last_name":"Khatoniar","full_name":"Khatoniar, Mandeep"},{"last_name":"Yama","first_name":"Nicholas","full_name":"Yama, Nicholas"},{"first_name":"Areg","last_name":"Ghazaryan","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg"},{"first_name":"Sriram","last_name":"Guddala","full_name":"Guddala, Sriram"},{"first_name":"Pouyan","last_name":"Ghaemi","full_name":"Ghaemi, Pouyan"},{"full_name":"Menon, Vinod","first_name":"Vinod","last_name":"Menon"}],"date_created":"2019-07-17T09:40:44Z","date_updated":"2023-10-17T12:14:29Z","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6646","year":"2019","title":"Room temperature control of valley coherence in bilayer WS2 exciton polaritons","publication_status":"published","status":"public","publisher":"Optica Publishing Group","department":[{"_id":"MiLe"}]},{"oa_version":"None","date_updated":"2023-10-17T12:14:46Z","date_created":"2020-01-05T23:00:48Z","author":[{"full_name":"Rueda Sanchez, Alfredo R","last_name":"Rueda Sanchez","first_name":"Alfredo R","orcid":"0000-0001-6249-5860","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Florian","last_name":"Sedlmeir","full_name":"Sedlmeir, Florian"},{"last_name":"Leuchs","first_name":"Gerd","full_name":"Leuchs, Gerd"},{"last_name":"Kumari","first_name":"Madhuri","full_name":"Kumari, Madhuri"},{"full_name":"Schwefel, Harald G.L.","first_name":"Harald G.L.","last_name":"Schwefel"}],"publisher":"Optica Publishing Group","department":[{"_id":"JoFi"}],"publication_status":"published","title":"Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7233","year":"2019","abstract":[{"lang":"eng","text":"We demonstrate electro-optic frequency comb generation using a doubly resonant system comprising a whispering gallery mode disk resonator made of lithium niobate mounted inside a three dimensional copper cavity. We observe 180 sidebands centred at 1550 nm."}],"type":"conference","article_number":"NM2A.5","language":[{"iso":"eng"}],"doi":"10.1364/NLO.2019.NM2A.5","date_published":"2019-07-15T00:00:00Z","conference":{"start_date":"2019-07-15","location":"Waikoloa Beach, Hawaii (HI), United States","end_date":"2019-07-19","name":"NLO: Nonlinear Optics"},"quality_controlled":"1","citation":{"short":"A.R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kumari, H.G.L. Schwefel, in:, Nonlinear Optics, OSA Technical Digest, Optica Publishing Group, 2019.","mla":"Rueda Sanchez, Alfredo R., et al. “Resonant Electro-Optic Frequency Comb Generation in Lithium Niobate Disk Resonator inside a Microwave Cavity.” Nonlinear Optics, OSA Technical Digest, NM2A.5, Optica Publishing Group, 2019, doi:10.1364/NLO.2019.NM2A.5.","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.","ama":"Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kumari M, Schwefel HGL. Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity. In: Nonlinear Optics, OSA Technical Digest. Optica Publishing Group; 2019. doi:10.1364/NLO.2019.NM2A.5","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","ieee":"A. R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kumari, and H. G. L. Schwefel, “Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity,” in Nonlinear Optics, OSA Technical Digest, Waikoloa Beach, Hawaii (HI), United States, 2019.","ista":"Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kumari M, Schwefel HGL. 2019. Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity. Nonlinear Optics, OSA Technical Digest. NLO: Nonlinear Optics, NM2A.5."},"publication":"Nonlinear Optics, OSA Technical Digest","article_processing_charge":"No","publication_identifier":{"isbn":["9781557528209"]},"month":"07","day":"15","scopus_import":"1"},{"date_published":"2019-05-01T00:00:00Z","page":"661-696","publication":"Annales de l'institut Henri Poincare","citation":{"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","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.","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.","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."},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","status":"public","title":"Location of the spectrum of Kronecker random matrices","intvolume":" 55","_id":"6240","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"For a general class of large non-Hermitian random block matrices X we prove that there are no eigenvalues away from a deterministic set with very high probability. This set is obtained from the Dyson equation of the Hermitization of X as the self-consistent approximation of the pseudospectrum. We demonstrate that the analysis of the matrix Dyson equation from (Probab. Theory Related Fields (2018)) offers a unified treatment of many structured matrix ensembles."}],"issue":"2","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1214/18-AIHP894","isi":1,"quality_controlled":"1","project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"isi":["000467793600003"],"arxiv":["1706.08343"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.08343"}],"month":"05","publication_identifier":{"issn":["0246-0203"]},"date_updated":"2023-10-17T12:20:20Z","date_created":"2019-04-08T14:05:04Z","volume":55,"author":[{"id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","last_name":"Alt","first_name":"Johannes","full_name":"Alt, Johannes"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös","full_name":"Erdös, László"},{"full_name":"Krüger, Torben H","first_name":"Torben H","last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297"},{"full_name":"Nemish, Yuriy","orcid":"0000-0002-7327-856X","id":"4D902E6A-F248-11E8-B48F-1D18A9856A87","last_name":"Nemish","first_name":"Yuriy"}],"related_material":{"record":[{"id":"149","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"Institut Henri Poincaré","year":"2019","ec_funded":1},{"publication":"PLoS Genetics","citation":{"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.","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.","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","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.","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","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."},"article_type":"original","date_published":"2019-07-22T00:00:00Z","scopus_import":"1","day":"22","article_processing_charge":"No","has_accepted_license":"1","_id":"7399","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes","ddc":["570"],"intvolume":" 15","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2019_PlosGenetics_Andergassen.pdf","creator":"dernst","content_type":"application/pdf","file_size":2302307,"file_id":"7446","relation":"main_file","checksum":"2f51fc91e4a4199827adc51d432ad864","date_updated":"2020-07-14T12:47:57Z","date_created":"2020-02-04T10:11:55Z"}],"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","external_id":{"isi":["000478689100025"],"pmid":["31329595"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","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":[{"last_name":"Andergassen","first_name":"Daniel","full_name":"Andergassen, Daniel"},{"full_name":"Muckenhuber, Markus","last_name":"Muckenhuber","first_name":"Markus"},{"first_name":"Philipp C.","last_name":"Bammer","full_name":"Bammer, Philipp C."},{"first_name":"Tomasz M.","last_name":"Kulinski","full_name":"Kulinski, Tomasz M."},{"full_name":"Theussl, Hans-Christian","last_name":"Theussl","first_name":"Hans-Christian"},{"full_name":"Shimizu, Takahiko","last_name":"Shimizu","first_name":"Takahiko"},{"first_name":"Josef M.","last_name":"Penninger","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.","first_name":"Quanah J.","last_name":"Hudson"}],"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"},{"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2019-11-01T00:00:00Z","publication":"PLoS Computational Biology","citation":{"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).","chicago":"Wang, Jilin W. J. L., Fabrizio Lombardi, Xiyun Zhang, Christelle Anaclet, and Plamen Ch. Ivanov. “Non-Equilibrium Critical Dynamics of Bursts in θ and δ Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.” PLoS Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007268.","ama":"Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. PLoS Computational Biology. 2019;15(11). doi:10.1371/journal.pcbi.1007268","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."},"article_type":"original","abstract":[{"text":"Origin and functions of intermittent transitions among sleep stages, including short awakenings and arousals, constitute a challenge to the current homeostatic framework for sleep regulation, focusing on factors modulating sleep over large time scales. Here we propose that the complex micro-architecture characterizing the sleep-wake cycle results from an underlying non-equilibrium critical dynamics, bridging collective behaviors across spatio-temporal scales. We investigate θ and δ wave dynamics in control rats and in rats with lesions of sleep-promoting neurons in the parafacial zone. We demonstrate that intermittent bursts in θ and δ rhythms exhibit a complex temporal organization, with long-range power-law correlations and a robust duality of power law (θ-bursts, active phase) and exponential-like (δ-bursts, quiescent phase) duration distributions, typical features of non-equilibrium systems self-organizing at criticality. Crucially, such temporal organization relates to anti-correlated coupling between θ- and δ-bursts, and is independent of the dominant physiologic state and lesions, a solid indication of a basic principle in sleep dynamics.","lang":"eng"}],"issue":"11","type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"7104","checksum":"2a096a9c6dcc6eaa94077b2603bc6c12","date_updated":"2020-07-14T12:47:49Z","date_created":"2019-11-25T08:24:01Z","access_level":"open_access","file_name":"2019_PLOSComBio_Wang.pdf","content_type":"application/pdf","file_size":3982516,"creator":"dernst"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7103","status":"public","ddc":["570","000"],"title":"Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture","intvolume":" 15","month":"11","publication_identifier":{"issn":["1553-7358"]},"doi":"10.1371/journal.pcbi.1007268","language":[{"iso":"eng"}],"external_id":{"isi":["000500976100014"],"pmid":["31725712"]},"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":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2020-07-14T12:47:49Z","ec_funded":1,"article_number":"e1007268","author":[{"first_name":"Jilin W. J. L.","last_name":"Wang","full_name":"Wang, Jilin W. J. L."},{"first_name":"Fabrizio","last_name":"Lombardi","id":"A057D288-3E88-11E9-986D-0CF4E5697425","orcid":"0000-0003-2623-5249","full_name":"Lombardi, Fabrizio"},{"first_name":"Xiyun","last_name":"Zhang","full_name":"Zhang, Xiyun"},{"last_name":"Anaclet","first_name":"Christelle","full_name":"Anaclet, Christelle"},{"first_name":"Plamen Ch.","last_name":"Ivanov","full_name":"Ivanov, Plamen Ch."}],"date_created":"2019-11-25T08:20:47Z","date_updated":"2023-10-17T12:30:07Z","volume":15,"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science"},{"date_created":"2019-06-20T18:23:03Z","date_updated":"2023-10-17T12:31:38Z","volume":97,"author":[{"full_name":"Bui Thi Mai, Phuong","first_name":"Phuong","last_name":"Bui Thi Mai","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph"}],"publication_status":"published","publisher":"ML Research Press","department":[{"_id":"ChLa"}],"year":"2019","file_date_updated":"2020-07-14T12:47:33Z","language":[{"iso":"eng"}],"conference":{"location":"Long Beach, CA, United States","start_date":"2019-06-10","end_date":"2019-06-15","name":"ICML: International Conference on Machine Learning"},"quality_controlled":"1","oa":1,"month":"06","oa_version":"Published Version","file":[{"file_id":"6570","relation":"main_file","checksum":"a66d00e2694d749250f8507f301320ca","date_updated":"2020-07-14T12:47:33Z","date_created":"2019-06-20T18:22:56Z","access_level":"open_access","file_name":"paper.pdf","creator":"bphuong","content_type":"application/pdf","file_size":686432}],"status":"public","ddc":["000"],"title":"Towards understanding knowledge distillation","intvolume":" 97","_id":"6569","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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."}],"type":"conference","date_published":"2019-06-13T00:00:00Z","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.","apa":"Phuong, M., & Lampert, C. (2019). Towards understanding knowledge distillation. In Proceedings of the 36th International Conference on Machine Learning (Vol. 97, pp. 5142–5151). Long Beach, CA, United States: ML Research Press.","ieee":"M. Phuong and C. Lampert, “Towards understanding knowledge distillation,” in Proceedings of the 36th International Conference on Machine Learning, Long Beach, CA, United States, 2019, vol. 97, pp. 5142–5151.","ista":"Phuong M, Lampert C. 2019. Towards understanding knowledge distillation. Proceedings of the 36th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 97, 5142–5151."},"day":"13","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"month":"06","conference":{"name":"ICML: International Conference on Machine Learning","location":"Long Beach, CA, USA","start_date":"2019-06-10","end_date":"2919-06-15"},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1901.10310","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1901.10310"]},"project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"quality_controlled":"1","ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10799"}]},"author":[{"id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","last_name":"Konstantinov","first_name":"Nikola H","full_name":"Konstantinov, Nikola H"},{"full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"volume":97,"date_created":"2019-06-27T14:18:23Z","date_updated":"2023-10-17T12:31:55Z","year":"2019","department":[{"_id":"ChLa"}],"publisher":"ML Research Press","publication_status":"published","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-06-01T00:00:00Z","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."},"publication":"Proceedings of the 36th International Conference on Machine Learning","page":"3488-3498","abstract":[{"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. ","lang":"eng"}],"type":"conference","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6590","intvolume":" 97","title":"Robust learning from untrusted sources","status":"public"},{"title":"Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization","status":"public","ddc":["580"],"intvolume":" 116","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6999","file":[{"file_id":"7012","relation":"main_file","checksum":"258c666bc6253eab81961f61169eefae","date_created":"2019-11-13T08:22:28Z","date_updated":"2020-07-14T12:47:46Z","access_level":"open_access","file_name":"2019_PNAS_Huang.pdf","creator":"dernst","file_size":3287466,"content_type":"application/pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Plasmodesmata (PD) are plant-specific membrane-lined channels that create cytoplasmic and membrane continuities between adjacent cells, thereby facilitating cell–cell communication and virus movement. Plant cells have evolved diverse mechanisms to regulate PD plasticity in response to numerous environmental stimuli. In particular, during defense against plant pathogens, the defense hormone, salicylic acid (SA), plays a crucial role in the regulation of PD permeability in a callose-dependent manner. Here, we uncover a mechanism by which plants restrict the spreading of virus and PD cargoes using SA signaling by increasing lipid order and closure of PD. We showed that exogenous SA application triggered the compartmentalization of lipid raft nanodomains through a modulation of the lipid raft-regulatory protein, Remorin (REM). Genetic studies, superresolution imaging, and transmission electron microscopy observation together demonstrated that Arabidopsis REM1.2 and REM1.3 are crucial for plasma membrane nanodomain assembly to control PD aperture and functionality. In addition, we also found that a 14-3-3 epsilon protein modulates REM clustering and membrane nanodomain compartmentalization through its direct interaction with REM proteins. This study unveils a molecular mechanism by which the key plant defense hormone, SA, triggers membrane lipid nanodomain reorganization, thereby regulating PD closure to impede virus spreading.","lang":"eng"}],"issue":"42","article_type":"original","page":"21274-21284","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"chicago":"Huang, D, Y Sun, Z Ma, M Ke, Y Cui, Z Chen, C Chen, et al. “Salicylic Acid-Mediated Plasmodesmal Closure via Remorin-Dependent Lipid Organization.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1911892116.","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.","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","ama":"Huang D, Sun Y, Ma Z, et al. Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(42):21274-21284. doi:10.1073/pnas.1911892116"},"date_published":"2019-10-15T00:00:00Z","scopus_import":"1","day":"15","article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"JiFr"}],"year":"2019","pmid":1,"date_updated":"2023-10-17T12:32:37Z","date_created":"2019-11-12T11:42:05Z","volume":116,"author":[{"last_name":"Huang","first_name":"D","full_name":"Huang, D"},{"first_name":"Y","last_name":"Sun","full_name":"Sun, Y"},{"last_name":"Ma","first_name":"Z","full_name":"Ma, Z"},{"first_name":"M","last_name":"Ke","full_name":"Ke, M"},{"full_name":"Cui, Y","last_name":"Cui","first_name":"Y"},{"first_name":"Z","last_name":"Chen","full_name":"Chen, Z"},{"first_name":"C","last_name":"Chen","full_name":"Chen, C"},{"last_name":"Ji","first_name":"C","full_name":"Ji, C"},{"full_name":"Tran, TM","first_name":"TM","last_name":"Tran"},{"full_name":"Yang, L","first_name":"L","last_name":"Yang"},{"first_name":"SM","last_name":"Lam","full_name":"Lam, SM"},{"full_name":"Han, Y","first_name":"Y","last_name":"Han"},{"last_name":"Shu","first_name":"G","full_name":"Shu, G"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Miao","first_name":"Y","full_name":"Miao, Y"},{"full_name":"Jiang, L","first_name":"L","last_name":"Jiang"},{"last_name":"Chen","first_name":"X","full_name":"Chen, X"}],"related_material":{"link":[{"url":"https://doi.org/10.1073/pnas.2004738117","relation":"erratum"}]},"file_date_updated":"2020-07-14T12:47:46Z","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000490183000068"],"pmid":["31575745"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1911892116","month":"10","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]}},{"month":"06","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1905555116","quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1905555116","open_access":"1"}],"external_id":{"pmid":["31213531"],"isi":["000472719100010"]},"oa":1,"date_created":"2019-07-07T21:59:25Z","date_updated":"2023-10-17T12:44:15Z","volume":116,"author":[{"full_name":"Wright, Alison E.","last_name":"Wright","first_name":"Alison E."},{"full_name":"Darolti, Iulia","first_name":"Iulia","last_name":"Darolti"},{"full_name":"Bloch, Natasha I.","first_name":"Natasha I.","last_name":"Bloch"},{"last_name":"Oostra","first_name":"Vicencio","full_name":"Oostra, Vicencio"},{"first_name":"Benjamin A.","last_name":"Sandkam","full_name":"Sandkam, Benjamin A."},{"first_name":"Séverine D.","last_name":"Buechel","full_name":"Buechel, Séverine D."},{"full_name":"Kolm, Niclas","first_name":"Niclas","last_name":"Kolm"},{"full_name":"Breden, Felix","first_name":"Felix","last_name":"Breden"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz"},{"last_name":"Mank","first_name":"Judith E.","full_name":"Mank, Judith E."}],"publication_status":"published","publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"BeVi"}],"year":"2019","pmid":1,"day":"25","article_processing_charge":"No","scopus_import":"1","date_published":"2019-06-25T00:00:00Z","article_type":"letter_note","page":"12607-12608","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"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.","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","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.","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."},"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."}],"issue":"26","type":"journal_article","oa_version":"Published Version","status":"public","title":"On the power to detect rare recombination events","intvolume":" 116","_id":"6621","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"quality_controlled":"1","project":[{"name":"Mating system and the evolutionary dynamics of hybrid zones","call_identifier":"FP7","grant_number":"329960","_id":"25B36484-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Sex chromosomes and species barriers","grant_number":"M02463","_id":"2662AADE-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["31505037"]},"language":[{"iso":"eng"}],"doi":"10.1111/nph.16180","month":"11","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","year":"2019","pmid":1,"date_updated":"2023-10-18T08:47:08Z","date_created":"2019-09-07T14:35:40Z","volume":224,"author":[{"full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","first_name":"Melinda"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"full_name":"Brandvain, Yaniv","last_name":"Brandvain","first_name":"Yaniv"},{"full_name":"Fraisse, Christelle","last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yakimowski, Sarah","last_name":"Yakimowski","first_name":"Sarah"},{"first_name":"Tanmay","last_name":"Dixit","full_name":"Dixit, Tanmay"},{"full_name":"Lexer, Christian","last_name":"Lexer","first_name":"Christian"},{"first_name":"Eva","last_name":"Cereghetti","id":"71AA91B4-05ED-11EA-8BEB-F5833E63BD63","full_name":"Cereghetti, Eva"},{"full_name":"Field, David","first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"}],"file_date_updated":"2020-07-14T12:47:42Z","ec_funded":1,"article_type":"original","page":"1035-1047","publication":"New Phytologist","citation":{"apa":"Pickup, M., Barton, N. H., Brandvain, Y., Fraisse, C., Yakimowski, S., Dixit, T., … Field, D. (2019). Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. Wiley. https://doi.org/10.1111/nph.16180","ieee":"M. Pickup et al., “Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow,” New Phytologist, vol. 224, no. 3. Wiley, pp. 1035–1047, 2019.","ista":"Pickup M, Barton NH, Brandvain Y, Fraisse C, Yakimowski S, Dixit T, Lexer C, Cereghetti E, Field D. 2019. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. 224(3), 1035–1047.","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","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.","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."},"date_published":"2019-11-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","ddc":["570"],"title":"Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow","status":"public","intvolume":" 224","_id":"6856","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"7011","relation":"main_file","checksum":"21e4c95599bbcaf7c483b89954658672","date_created":"2019-11-13T08:15:05Z","date_updated":"2020-07-14T12:47:42Z","access_level":"open_access","file_name":"2019_NewPhytologist_Pickup.pdf","creator":"dernst","file_size":1511958,"content_type":"application/pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"3"},{"publication_identifier":{"isbn":["9783959771047"],"issn":["1868-8969"]},"month":"06","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":{"arxiv":["1812.04911"]},"project":[{"name":"Eliminating intersections in drawings of graphs","call_identifier":"FWF","grant_number":"M02281","_id":"261FA626-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.4230/LIPICS.SOCG.2019.38","conference":{"end_date":"2019-06-21","start_date":"2019-06-18","location":"Portland, OR, United States","name":"SoCG 2019: Symposium on Computational Geometry"},"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:35Z","year":"2019","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"UlWa"}],"publication_status":"published","related_material":{"record":[{"relation":"later_version","status":"public","id":"13974"}]},"author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","first_name":"Radoslav","last_name":"Fulek","full_name":"Fulek, Radoslav"},{"full_name":"Gärtner, Bernd","first_name":"Bernd","last_name":"Gärtner"},{"first_name":"Andrey","last_name":"Kupavskii","full_name":"Kupavskii, Andrey"},{"full_name":"Valtr, Pavel","last_name":"Valtr","first_name":"Pavel"},{"orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli","full_name":"Wagner, Uli"}],"volume":129,"date_updated":"2023-12-13T12:03:35Z","date_created":"2019-07-17T10:35:04Z","scopus_import":1,"has_accepted_license":"1","day":"01","citation":{"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.","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.","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","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.","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","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."},"publication":"35th International Symposium on Computational Geometry","page":"38:1-38:13","date_published":"2019-06-01T00:00:00Z","type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","text":"The Tverberg theorem is one of the cornerstones of discrete geometry. It states that, given a set X of at least (d+1)(r-1)+1 points in R^d, one can find a partition X=X_1 cup ... cup X_r of X, such that the convex hulls of the X_i, i=1,...,r, all share a common point. In this paper, we prove a strengthening of this theorem that guarantees a partition which, in addition to the above, has the property that the boundaries of full-dimensional convex hulls have pairwise nonempty intersections. Possible generalizations and algorithmic aspects are also discussed. As a concrete application, we show that any n points in the plane in general position span floor[n/3] vertex-disjoint triangles that are pairwise crossing, meaning that their boundaries have pairwise nonempty intersections; this number is clearly best possible. A previous result of Alvarez-Rebollar et al. guarantees floor[n/6] pairwise crossing triangles. Our result generalizes to a result about simplices in R^d,d >=2."}],"_id":"6647","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 129","title":"The crossing Tverberg theorem","ddc":["000","510"],"status":"public","file":[{"access_level":"open_access","file_name":"2019_LIPICS_Fulek.pdf","content_type":"application/pdf","file_size":559837,"creator":"dernst","relation":"main_file","file_id":"6667","checksum":"d6d017f8b41291b94d102294fa96ae9c","date_updated":"2020-07-14T12:47:35Z","date_created":"2019-07-24T06:54:52Z"}],"oa_version":"Published Version"},{"month":"06","publication_identifier":{"isbn":["9781450367059"]},"conference":{"name":"STOC: Symposium on Theory of Computing","location":"Phoenix, AZ, United States","start_date":"2019-06-23","end_date":"2019-06-26"},"doi":"10.1145/3313276.3316407","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,"author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Aspnes, James","first_name":"James","last_name":"Aspnes"},{"last_name":"Ellen","first_name":"Faith","full_name":"Ellen, Faith"},{"last_name":"Gelashvili","first_name":"Rati","full_name":"Gelashvili, Rati"},{"full_name":"Zhu, Leqi","first_name":"Leqi","last_name":"Zhu"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"14364"}]},"date_updated":"2023-12-13T12:28:28Z","date_created":"2019-07-24T09:13:05Z","year":"2019","publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"ACM Press","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":{"chicago":"Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and Leqi Zhu. “Why Extension-Based Proofs Fail.” In Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, 986–96. ACM Press, 2019. https://doi.org/10.1145/3313276.3316407.","short":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, in:, Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, ACM Press, 2019, pp. 986–996.","mla":"Alistarh, Dan-Adrian, et al. “Why Extension-Based Proofs Fail.” Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, ACM Press, 2019, pp. 986–96, doi:10.1145/3313276.3316407.","ieee":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, and L. Zhu, “Why extension-based proofs fail,” in Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing, Phoenix, AZ, United States, 2019, pp. 986–996.","apa":"Alistarh, D.-A., Aspnes, J., Ellen, F., Gelashvili, R., & Zhu, L. (2019). Why extension-based proofs fail. In Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing (pp. 986–996). Phoenix, AZ, United States: ACM Press. https://doi.org/10.1145/3313276.3316407","ista":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. 2019. Why extension-based proofs fail. Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 986–996.","ama":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. Why extension-based proofs fail. In: Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing. ACM Press; 2019:986-996. doi:10.1145/3313276.3316407"},"page":"986-996","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"},{"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"7944"},{"id":"12833","status":"public","relation":"later_version"}]},"author":[{"full_name":"Biniaz, Ahmad","last_name":"Biniaz","first_name":"Ahmad"},{"full_name":"Jain, Kshitij","last_name":"Jain","first_name":"Kshitij"},{"first_name":"Anna","last_name":"Lubiw","full_name":"Lubiw, Anna"},{"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"},{"last_name":"Naredla","first_name":"Anurag Murty","full_name":"Naredla, Anurag Murty"},{"last_name":"Tkadlec","first_name":"Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef"},{"first_name":"Alexi","last_name":"Turcotte","full_name":"Turcotte, Alexi"}],"oa_version":"Preprint","date_created":"2020-06-08T12:25:25Z","date_updated":"2024-01-04T12:42:08Z","year":"2019","_id":"7950","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"},{"_id":"UlWa"},{"_id":"KrCh"}],"status":"public","title":"Token swapping on trees","publication_status":"submitted","abstract":[{"lang":"eng","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."}],"type":"preprint","article_number":"1903.06981","date_published":"2019-03-16T00:00:00Z","language":[{"iso":"eng"}],"citation":{"mla":"Biniaz, Ahmad, et al. “Token Swapping on Trees.” ArXiv, 1903.06981.","short":"A. Biniaz, K. Jain, A. Lubiw, Z. Masárová, T. Miltzow, D. Mondal, A.M. Naredla, J. Tkadlec, A. Turcotte, ArXiv (n.d.).","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.","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.","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."},"oa":1,"external_id":{"arxiv":["1903.06981"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1903.06981"}],"publication":"arXiv","article_processing_charge":"No","day":"16","month":"03"},{"month":"04","publication_identifier":{"eissn":["1759-6653"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257"}],"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":["000476569800003"]},"oa":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.1093/gbe/evz053","file_date_updated":"2020-07-14T12:47:29Z","ec_funded":1,"publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"BeVi"}],"year":"2019","date_updated":"2024-02-21T12:45:41Z","date_created":"2019-05-13T07:58:38Z","volume":11,"author":[{"first_name":"Ann K","last_name":"Huylmans","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8871-4961","full_name":"Huylmans, Ann K"},{"last_name":"Toups","first_name":"Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","full_name":"Toups, Melissa A"},{"full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","last_name":"Macon"},{"id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9638-1220","first_name":"William J","last_name":"Gammerdinger","full_name":"Gammerdinger, William J"},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso"}],"related_material":{"record":[{"relation":"popular_science","status":"public","id":"6060"}]},"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","page":"1033-1044","publication":"Genome biology and evolution","citation":{"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.","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.","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","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.","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.","short":"A.K. Huylmans, M.A. Toups, A. Macon, W.J. Gammerdinger, B. Vicoso, Genome Biology and Evolution 11 (2019) 1033–1044."},"date_published":"2019-04-01T00:00:00Z","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"4","ddc":["570"],"status":"public","title":"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome","intvolume":" 11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6418","oa_version":"Published Version","file":[{"checksum":"7d0ede297b6741f3dc89cd59017c7642","date_created":"2019-05-14T08:29:38Z","date_updated":"2020-07-14T12:47:29Z","file_id":"6446","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1256303,"access_level":"open_access","file_name":"2019_GBE_Huylmans.pdf"}]},{"keyword":["Escherichia coli","gene amplification","galactose","DOG","experimental evolution","Illumina sequence data","FACS data","microfluidics data"],"month":"11","day":"13","article_processing_charge":"No","has_accepted_license":"1","citation":{"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.","short":"I. Tomanek, (2019).","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.","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.","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.","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"},"oa":1,"doi":"10.15479/AT:ISTA:7016","date_published":"2019-11-13T00:00:00Z","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"}],"status":"public","title":"Data for the paper \"Gene amplification as a form of population-level gene expression regulation\"","ddc":["576"],"department":[{"_id":"CaGu"}],"publisher":"Institute of Science and Technology Austria","_id":"7016","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","date_created":"2019-11-13T09:07:31Z","date_updated":"2024-02-21T12:45:25Z","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:47Z","date_created":"2019-11-13T08:52:21Z","checksum":"72441055043eda4cbf1398a422e2c118","file_id":"7017","title":"Locus1_amplified","relation":"main_file","creator":"itomanek","file_size":2456192500,"content_type":"application/octet-stream","file_name":"D8_S35_R2_001.fastq","description":"Illumina whole genome sequence data for Locus 1 - 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Supplementary Data for “Programming Temporal Morphing of Self-Actuated Shells.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7154."},"doi":"10.15479/AT:ISTA:7154","date_published":"2019-12-06T00:00:00Z","month":"12","day":"06","article_processing_charge":"No","has_accepted_license":"1"},{"type":"research_data","file_date_updated":"2020-07-14T12:47:17Z","_id":"6060","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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). ","department":[{"_id":"BeVi"}],"publisher":"Institute of Science and Technology Austria","author":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"related_material":{"record":[{"id":"6418","status":"public","relation":"research_paper"}]},"date_created":"2019-02-28T10:55:15Z","date_updated":"2024-02-21T12:45:42Z","oa_version":"Published Version","file":[{"content_type":"application/zip","file_size":36646050,"creator":"bvicoso","access_level":"open_access","file_name":"SupData.zip","checksum":"a338a622d728af0e3199cb07e6dd64d3","date_updated":"2020-07-14T12:47:17Z","date_created":"2019-02-28T10:54:27Z","relation":"main_file","file_id":"6061"}],"month":"02","day":"28","has_accepted_license":"1","article_processing_charge":"No","citation":{"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.","short":"B. Vicoso, (2019).","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.","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.","ista":"Vicoso B. 2019. 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Novarino, (2019).","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.","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","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.","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","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."},"oa":1,"date_published":"2019-01-09T00:00:00Z","doi":"10.15479/AT:ISTA:6074","type":"research_data","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"}],"file_date_updated":"2020-07-14T12:47:18Z","year":"2019","_id":"6074","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"status":"public","title":"Supplementary data for the research paper \"Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition\"","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaNo"}],"author":[{"full_name":"Dotter, Christoph","last_name":"Dotter","first_name":"Christoph","orcid":"0000-0002-9033-9096","id":"4C66542E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"}],"related_material":{"record":[{"relation":"research_paper","status":"public","id":"3"}]},"date_updated":"2024-02-21T13:41:01Z","date_created":"2019-03-07T13:32:35Z","oa_version":"Published Version","file":[{"file_name":"Setd5_paper.zip","access_level":"open_access","content_type":"application/zip","file_size":33202743,"creator":"dernst","relation":"supplementary_material","file_id":"6084","date_updated":"2020-07-14T12:47:18Z","date_created":"2019-03-07T13:37:19Z","checksum":"bc1b285edca9e98a2c63d153c79bb75b"}]},{"article_processing_charge":"No","has_accepted_license":"1","day":"29","month":"03","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."},"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,"doi":"10.15479/AT:ISTA:6062","date_published":"2019-03-29T00:00:00Z","type":"research_data","license":"https://creativecommons.org/licenses/by-sa/4.0/","abstract":[{"lang":"eng","text":"Open the files in Jupyter Notebook (reccomended https://www.anaconda.com/distribution/#download-section with Python 3.7)."}],"file_date_updated":"2020-07-14T12:47:18Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JoCs"}],"status":"public","title":"Supplementary Code and Data for the paper \"The Entorhinal Cognitive Map is Attracted to Goals\"","_id":"6062","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","file":[{"creator":"mnardin","content_type":"application/zip","file_size":37002186,"access_level":"open_access","file_name":"Online_data.zip","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"}],"oa_version":"Published Version","date_created":"2019-03-04T14:20:58Z","date_updated":"2024-02-21T12:46:04Z","related_material":{"record":[{"id":"6194","status":"public","relation":"research_paper"}]},"author":[{"full_name":"Nardin, Michele","last_name":"Nardin","first_name":"Michele","orcid":"0000-0001-8849-6570","id":"30BD0376-F248-11E8-B48F-1D18A9856A87"}]},{"scopus_import":"1","day":"01","article_processing_charge":"No","page":"500-515","publication":"Molecular biology and evolution","citation":{"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.","short":"C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36 (2019) 500–515.","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.","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","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.","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."},"date_published":"2019-03-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","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."}],"issue":"3","status":"public","title":"Pleiotropy modulates the efficacy of selection in drosophila melanogaster","intvolume":" 36","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6089","oa_version":"Submitted Version","month":"03","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30590559","open_access":"1"}],"oa":1,"external_id":{"isi":["000462585100006"],"pmid":["30590559"]},"language":[{"iso":"eng"}],"doi":"10.1093/molbev/msy246","publication_status":"published","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"Oxford University Press","year":"2019","pmid":1,"date_created":"2019-03-10T22:59:19Z","date_updated":"2024-02-21T13:59:17Z","volume":36,"author":[{"first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"},{"full_name":"Puixeu Sala, Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754","first_name":"Gemma","last_name":"Puixeu Sala"},{"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":"5757","relation":"popular_science","status":"public"}]}},{"day":"18","has_accepted_license":"1","article_processing_charge":"No","page":"375","citation":{"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.","short":"D.J. Schröder, From Dyson to Pearcey: Universal Statistics in Random Matrix Theory, Institute of Science and Technology Austria, 2019.","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.","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","ieee":"D. J. Schröder, “From Dyson to Pearcey: Universal statistics in random matrix theory,” Institute of Science and Technology Austria, 2019.","ista":"Schröder DJ. 2019. From Dyson to Pearcey: Universal statistics in random matrix theory. Institute of Science and Technology Austria.","ama":"Schröder DJ. From Dyson to Pearcey: Universal statistics in random matrix theory. 2019. doi:10.15479/AT:ISTA:th6179"},"date_published":"2019-03-18T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","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."}],"status":"public","ddc":["515","519"],"title":"From Dyson to Pearcey: Universal statistics in random matrix theory","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6179","oa_version":"Published Version","file":[{"file_id":"6180","relation":"source_file","date_created":"2019-03-28T08:53:52Z","date_updated":"2020-07-14T12:47:21Z","checksum":"6926f66f28079a81c4937e3764be00fc","file_name":"2019_Schroeder_Thesis.tar.gz","access_level":"closed","creator":"dernst","file_size":7104482,"content_type":"application/x-gzip"},{"access_level":"open_access","file_name":"2019_Schroeder_Thesis.pdf","creator":"dernst","content_type":"application/pdf","file_size":4228794,"file_id":"6181","relation":"main_file","checksum":"7d0ebb8d1207e89768cdd497a5bf80fb","date_updated":"2020-07-14T12:47:21Z","date_created":"2019-03-28T08:53:52Z"}],"month":"03","publication_identifier":{"issn":["2663-337X"]},"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"oa":1,"degree_awarded":"PhD","supervisor":[{"first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:th6179","file_date_updated":"2020-07-14T12:47:21Z","ec_funded":1,"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"LaEr"}],"year":"2019","date_created":"2019-03-28T08:58:59Z","date_updated":"2024-02-22T14:34:33Z","author":[{"last_name":"Schröder","first_name":"Dominik J","orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87","full_name":"Schröder, Dominik J"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1144"},{"id":"6186","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"6185"},{"relation":"part_of_dissertation","status":"public","id":"6182"},{"id":"1012","relation":"part_of_dissertation","status":"public"},{"id":"6184","status":"public","relation":"part_of_dissertation"}]}},{"article_processing_charge":"No","day":"14","scopus_import":"1","date_published":"2019-02-14T00:00:00Z","page":"244-259","citation":{"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.","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","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.","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","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.","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."},"abstract":[{"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. ","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Preprint","intvolume":" 11269","title":"KS(conf): A light-weight test if a ConvNet operates outside of Its specifications","status":"public","_id":"6482","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["0302-9743"],"isbn":["9783030129385","9783030129392"],"eissn":["1611-3349"]},"month":"02","language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-12939-2_18","conference":{"name":"GCPR: Conference on Pattern Recognition","location":"Stuttgart, Germany","start_date":"2018-10-09","end_date":"2018-10-12"},"project":[{"grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding"}],"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1804.04171"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.04171"}],"ec_funded":1,"volume":11269,"date_updated":"2024-02-22T14:57:29Z","date_created":"2019-05-24T09:48:36Z","related_material":{"record":[{"id":"6944","status":"public","relation":"later_version"}]},"author":[{"first_name":"Rémy","last_name":"Sun","full_name":"Sun, Rémy"},{"first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"publisher":"Springer Nature","department":[{"_id":"ChLa"}],"publication_status":"published","year":"2019"},{"citation":{"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","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.","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.","short":"M. Dostalík, V. Pruša, T. Skrivan, in:, AIP Conference Proceedings, AIP Publishing, 2019.","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."},"publication":"AIP Conference Proceedings","date_published":"2019-05-21T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"21","_id":"6642","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 2107","status":"public","title":"On diffusive variants of some classical viscoelastic rate-type models","oa_version":"Preprint","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."}],"external_id":{"arxiv":["1902.07983"],"isi":["000479303100002"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.07983"}],"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1063/1.5109493","conference":{"end_date":"2019-07-31","start_date":"2019-07-30","location":"Zlin, Czech Republic","name":"8th International Conference on Novel Trends in Rheology"},"language":[{"iso":"eng"}],"month":"05","year":"2019","department":[{"_id":"ChWo"}],"publisher":"AIP Publishing","publication_status":"published","author":[{"full_name":"Dostalík, Mark","last_name":"Dostalík","first_name":"Mark"},{"full_name":"Pruša, Vít","first_name":"Vít","last_name":"Pruša"},{"full_name":"Skrivan, Tomas","first_name":"Tomas","last_name":"Skrivan","id":"486A5A46-F248-11E8-B48F-1D18A9856A87"}],"volume":2107,"date_created":"2019-07-15T10:07:09Z","date_updated":"2024-02-28T13:01:28Z","article_number":"020002"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7226","intvolume":" 60","title":"Introduction to the Special Collection: International Congress on Mathematical Physics (ICMP) 2018","ddc":["500"],"status":"public","oa_version":"Published Version","file":[{"file_name":"2019_JournalMathPhysics_Jaksic.pdf","access_level":"open_access","file_size":1025015,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7244","date_created":"2020-01-07T14:59:13Z","date_updated":"2020-07-14T12:47:54Z","checksum":"bbd12ad1999a9ad7ba4d3c6f2e579c22"}],"type":"journal_article","issue":"12","citation":{"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.","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.","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","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","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.","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)."},"publication":"Journal of Mathematical Physics","article_type":"letter_note","date_published":"2019-12-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","year":"2019","publisher":"AIP Publishing","department":[{"_id":"RoSe"}],"publication_status":"published","author":[{"first_name":"Vojkan","last_name":"Jaksic","full_name":"Jaksic, Vojkan"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, 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","oa":1,"external_id":{"isi":["000505529800002"]},"quality_controlled":"1","isi":1,"doi":"10.1063/1.5138135","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00222488"]},"month":"12"},{"intvolume":" 1","ddc":["530"],"status":"public","title":"In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7190","file":[{"date_updated":"2020-07-14T12:47:52Z","date_created":"2019-12-18T07:13:14Z","checksum":"382eb67e62a77052a23887332d363f96","relation":"main_file","file_id":"7193","file_size":1370022,"content_type":"application/pdf","creator":"dernst","file_name":"2019_PhysRevResearch_Huber.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"We investigate the ground-state energy of a one-dimensional Fermi gas with two bosonic impurities. We consider spinless fermions with no fermion-fermion interactions. The fermion-impurity and impurity-impurity interactions are modeled with Dirac delta functions. First, we study the case where impurity and fermion have equal masses, and the impurity-impurity two-body interaction is identical to the fermion-impurity interaction, such that the system is solvable with the Bethe ansatz. For attractive interactions, we find that the energy of the impurity-impurity subsystem is below the energy of the bound state that exists without the Fermi gas. We interpret this as a manifestation of attractive boson-boson interactions induced by the fermionic medium, and refer to the impurity-impurity subsystem as an in-medium bound state. For repulsive interactions, we find no in-medium bound states. Second, we construct an effective model to describe these interactions, and compare its predictions to the exact solution. We use this effective model to study nonintegrable systems with unequal masses and/or potentials. We discuss parameter regimes for which impurity-impurity attraction induced by the Fermi gas can lead to the formation of in-medium bound states made of bosons that repel each other in the absence of the Fermi gas."}],"article_type":"original","citation":{"chicago":"Huber, D., H.-W. Hammer, and Artem Volosniev. “In-Medium Bound States of Two Bosonic Impurities in a One-Dimensional Fermi Gas.” Physical Review Research. American Physical Society, 2019. https://doi.org/10.1103/physrevresearch.1.033177.","short":"D. Huber, H.-W. Hammer, A. Volosniev, Physical Review Research 1 (2019).","mla":"Huber, D., et al. “In-Medium Bound States of Two Bosonic Impurities in a One-Dimensional Fermi Gas.” Physical Review Research, vol. 1, no. 3, 033177, American Physical Society, 2019, doi:10.1103/physrevresearch.1.033177.","apa":"Huber, D., Hammer, H.-W., & Volosniev, A. (2019). In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.1.033177","ieee":"D. Huber, H.-W. Hammer, and A. Volosniev, “In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas,” Physical Review Research, vol. 1, no. 3. American Physical Society, 2019.","ista":"Huber D, Hammer H-W, Volosniev A. 2019. In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas. Physical Review Research. 1(3), 033177.","ama":"Huber D, Hammer H-W, Volosniev A. In-medium bound states of two bosonic impurities in a one-dimensional Fermi gas. Physical Review Research. 2019;1(3). doi:10.1103/physrevresearch.1.033177"},"publication":"Physical Review Research","date_published":"2019-12-16T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"16","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"publication_status":"published","year":"2019","volume":1,"date_updated":"2024-02-28T13:11:40Z","date_created":"2019-12-17T13:03:41Z","author":[{"first_name":"D.","last_name":"Huber","full_name":"Huber, D."},{"full_name":"Hammer, H.-W.","last_name":"Hammer","first_name":"H.-W."},{"last_name":"Volosniev","first_name":"Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem"}],"article_number":"033177","ec_funded":1,"file_date_updated":"2020-07-14T12:47:52Z","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"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"},"external_id":{"arxiv":["1908.02483"]},"language":[{"iso":"eng"}],"doi":"10.1103/physrevresearch.1.033177","publication_identifier":{"issn":["2643-1564"]},"month":"12"},{"article_number":"220603","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MaSe"}],"year":"2019","date_created":"2019-06-23T21:59:13Z","date_updated":"2024-02-28T13:12:22Z","volume":122,"author":[{"first_name":"Soonwon","last_name":"Choi","full_name":"Choi, Soonwon"},{"first_name":"Christopher J.","last_name":"Turner","full_name":"Turner, Christopher J."},{"last_name":"Pichler","first_name":"Hannes","full_name":"Pichler, Hannes"},{"first_name":"Wen Wei","last_name":"Ho","full_name":"Ho, Wen Wei"},{"orcid":"0000-0002-8443-1064","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","last_name":"Michailidis","first_name":"Alexios","full_name":"Michailidis, Alexios"},{"first_name":"Zlatko","last_name":"Papić","full_name":"Papić, Zlatko"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn","full_name":"Serbyn, Maksym"},{"full_name":"Lukin, Mikhail D.","last_name":"Lukin","first_name":"Mikhail D."},{"full_name":"Abanin, Dmitry A.","first_name":"Dmitry A.","last_name":"Abanin"}],"month":"06","publication_identifier":{"issn":["00319007"],"eissn":["10797114"]},"quality_controlled":"1","isi":1,"external_id":{"isi":["000470885800005"],"arxiv":["1812.05561"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1812.05561","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.122.220603","type":"journal_article","abstract":[{"lang":"eng","text":"Motivated by recent experimental observations of coherent many-body revivals in a constrained Rydbergatom chain, we construct a weak quasilocal deformation of the Rydberg-blockaded Hamiltonian, whichmakes the revivals virtually perfect. Our analysis suggests the existence of an underlying nonintegrableHamiltonian which supports an emergent SU(2)-spin dynamics within a small subspace of the many-bodyHilbert space. We show that such perfect dynamics necessitates the existence of atypical, nonergodicenergy eigenstates—quantum many-body scars. Furthermore, using these insights, we construct a toymodel that hosts exact quantum many-body scars, providing an intuitive explanation of their origin. Ourresults offer specific routes to enhancing coherent many-body revivals and provide a step towardestablishing the stability of quantum many-body scars in the thermodynamic limit."}],"issue":"22","title":"Emergent SU(2) dynamics and perfect quantum many-body scars","status":"public","intvolume":" 122","_id":"6575","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","scopus_import":"1","day":"07","article_processing_charge":"No","article_type":"original","publication":"Physical Review Letters","citation":{"short":"S. Choi, C.J. Turner, H. Pichler, W.W. Ho, A. Michailidis, Z. Papić, M. Serbyn, M.D. Lukin, D.A. Abanin, Physical Review Letters 122 (2019).","mla":"Choi, Soonwon, et al. “Emergent SU(2) Dynamics and Perfect Quantum Many-Body Scars.” Physical Review Letters, vol. 122, no. 22, 220603, American Physical Society, 2019, doi:10.1103/PhysRevLett.122.220603.","chicago":"Choi, Soonwon, Christopher J. Turner, Hannes Pichler, Wen Wei Ho, Alexios Michailidis, Zlatko Papić, Maksym Serbyn, Mikhail D. Lukin, and Dmitry A. Abanin. “Emergent SU(2) Dynamics and Perfect Quantum Many-Body Scars.” Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/PhysRevLett.122.220603.","ama":"Choi S, Turner CJ, Pichler H, et al. Emergent SU(2) dynamics and perfect quantum many-body scars. Physical Review Letters. 2019;122(22). doi:10.1103/PhysRevLett.122.220603","apa":"Choi, S., Turner, C. J., Pichler, H., Ho, W. W., Michailidis, A., Papić, Z., … Abanin, D. A. (2019). Emergent SU(2) dynamics and perfect quantum many-body scars. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.122.220603","ieee":"S. Choi et al., “Emergent SU(2) dynamics and perfect quantum many-body scars,” Physical Review Letters, vol. 122, no. 22. American Physical Society, 2019.","ista":"Choi S, Turner CJ, Pichler H, Ho WW, Michailidis A, Papić Z, Serbyn M, Lukin MD, Abanin DA. 2019. Emergent SU(2) dynamics and perfect quantum many-body scars. Physical Review Letters. 122(22), 220603."},"date_published":"2019-06-07T00:00:00Z"},{"author":[{"full_name":"Mentink, Johann H","last_name":"Mentink","first_name":"Johann H"},{"last_name":"Katsnelson","first_name":"Mikhail","full_name":"Katsnelson, Mikhail"},{"orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail"}],"volume":99,"date_updated":"2024-02-28T13:11:54Z","date_created":"2019-03-10T22:59:20Z","year":"2019","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"publication_status":"published","article_number":"064428","doi":"10.1103/PhysRevB.99.064428","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.01638"}],"oa":1,"external_id":{"arxiv":["1802.01638"],"isi":["000459223400004"]},"project":[{"name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"month":"02","oa_version":"Preprint","_id":"6092","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 99","title":"Quantum many-body dynamics of the Einstein-de Haas effect","status":"public","issue":"6","abstract":[{"text":"In 1915, Einstein and de Haas and Barnett demonstrated that changing the magnetization of a magnetic material results in mechanical rotation and vice versa. At the microscopic level, this effect governs the transfer between electron spin and orbital angular momentum, and lattice degrees of freedom, understanding which is key for molecular magnets, nano-magneto-mechanics, spintronics, and ultrafast magnetism. Until now, the timescales of electron-to-lattice angular momentum transfer remain unclear, since modeling this process on a microscopic level requires the addition of an infinite amount of quantum angular momenta. We show that this problem can be solved by reformulating it in terms of the recently discovered angulon quasiparticles, which results in a rotationally invariant quantum many-body theory. In particular, we demonstrate that nonperturbative effects take place even if the electron-phonon coupling is weak and give rise to angular momentum transfer on femtosecond timescales.","lang":"eng"}],"type":"journal_article","date_published":"2019-02-01T00:00:00Z","citation":{"ama":"Mentink JH, Katsnelson M, Lemeshko M. Quantum many-body dynamics of the Einstein-de Haas effect. Physical Review B. 2019;99(6). doi:10.1103/PhysRevB.99.064428","apa":"Mentink, J. H., Katsnelson, M., & Lemeshko, M. (2019). Quantum many-body dynamics of the Einstein-de Haas effect. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.99.064428","ieee":"J. H. Mentink, M. Katsnelson, and M. Lemeshko, “Quantum many-body dynamics of the Einstein-de Haas effect,” Physical Review B, vol. 99, no. 6. American Physical Society, 2019.","ista":"Mentink JH, Katsnelson M, Lemeshko M. 2019. Quantum many-body dynamics of the Einstein-de Haas effect. Physical Review B. 99(6), 064428.","short":"J.H. Mentink, M. Katsnelson, M. Lemeshko, Physical Review B 99 (2019).","mla":"Mentink, Johann H., et al. “Quantum Many-Body Dynamics of the Einstein-de Haas Effect.” Physical Review B, vol. 99, no. 6, 064428, American Physical Society, 2019, doi:10.1103/PhysRevB.99.064428.","chicago":"Mentink, Johann H, Mikhail Katsnelson, and Mikhail Lemeshko. “Quantum Many-Body Dynamics of the Einstein-de Haas Effect.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/PhysRevB.99.064428."},"publication":"Physical Review B","article_processing_charge":"No","day":"01","scopus_import":"1"},{"date_published":"2019-02-26T00:00:00Z","publication":"Physical Review E","citation":{"chicago":"Carballo-Pacheco, Martín, Jonathan Desponds, Tatyana Gavrilchenko, Andreas Mayer, Roshan Prizak, Gautam Reddy, Ilya Nemenman, and Thierry Mora. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review E. American Physical Society, 2019. https://doi.org/10.1103/PhysRevE.99.022423.","mla":"Carballo-Pacheco, Martín, et al. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review E, vol. 99, no. 2, 022423, American Physical Society, 2019, doi:10.1103/PhysRevE.99.022423.","short":"M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G. Reddy, I. Nemenman, T. Mora, Physical Review E 99 (2019).","ista":"Carballo-Pacheco M, Desponds J, Gavrilchenko T, Mayer A, Prizak R, Reddy G, Nemenman I, Mora T. 2019. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 99(2), 022423.","ieee":"M. Carballo-Pacheco et al., “Receptor crosstalk improves concentration sensing of multiple ligands,” Physical Review E, vol. 99, no. 2. American Physical Society, 2019.","apa":"Carballo-Pacheco, M., Desponds, J., Gavrilchenko, T., Mayer, A., Prizak, R., Reddy, G., … Mora, T. (2019). Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.99.022423","ama":"Carballo-Pacheco M, Desponds J, Gavrilchenko T, et al. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 2019;99(2). doi:10.1103/PhysRevE.99.022423"},"day":"26","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","_id":"6090","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Receptor crosstalk improves concentration sensing of multiple ligands","status":"public","intvolume":" 99","abstract":[{"text":"Cells need to reliably sense external ligand concentrations to achieve various biological functions such as chemotaxis or signaling. The molecular recognition of ligands by surface receptors is degenerate in many systems, leading to crosstalk between ligand-receptor pairs. Crosstalk is often thought of as a deviation from optimal specific recognition, as the binding of noncognate ligands can interfere with the detection of the receptor's cognate ligand, possibly leading to a false triggering of a downstream signaling pathway. Here we quantify the optimal precision of sensing the concentrations of multiple ligands by a collection of promiscuous receptors. We demonstrate that crosstalk can improve precision in concentration sensing and discrimination tasks. To achieve superior precision, the additional information about ligand concentrations contained in short binding events of the noncognate ligand should be exploited. We present a proofreading scheme to realize an approximate estimation of multiple ligand concentrations that reaches a precision close to the derived optimal bounds. Our results help rationalize the observed ubiquity of receptor crosstalk in molecular sensing.","lang":"eng"}],"issue":"2","type":"journal_article","doi":"10.1103/PhysRevE.99.022423","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/448118v1.abstract","open_access":"1"}],"external_id":{"isi":["000459916500007"]},"isi":1,"quality_controlled":"1","month":"02","author":[{"full_name":"Carballo-Pacheco, Martín","first_name":"Martín","last_name":"Carballo-Pacheco"},{"full_name":"Desponds, Jonathan","first_name":"Jonathan","last_name":"Desponds"},{"first_name":"Tatyana","last_name":"Gavrilchenko","full_name":"Gavrilchenko, Tatyana"},{"full_name":"Mayer, Andreas","last_name":"Mayer","first_name":"Andreas"},{"full_name":"Prizak, Roshan","last_name":"Prizak","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Reddy","first_name":"Gautam","full_name":"Reddy, Gautam"},{"full_name":"Nemenman, Ilya","last_name":"Nemenman","first_name":"Ilya"},{"first_name":"Thierry","last_name":"Mora","full_name":"Mora, Thierry"}],"date_created":"2019-03-10T22:59:20Z","date_updated":"2024-02-28T13:12:06Z","volume":99,"year":"2019","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"article_number":"022423"},{"issue":"2","abstract":[{"text":"Dipolar coupling plays a fundamental role in the interaction between electrically or magnetically polarized species such as magnetic atoms and dipolar molecules in a gas or dipolar excitons in the solid state. Unlike Coulomb or contactlike interactions found in many atomic, molecular, and condensed-matter systems, this interaction is long-ranged and highly anisotropic, as it changes from repulsive to attractive depending on the relative positions and orientation of the dipoles. Because of this unique property, many exotic, symmetry-breaking collective states have been recently predicted for cold dipolar gases, but only a few have been experimentally detected and only in dilute atomic dipolar Bose-Einstein condensates. Here, we report on the first observation of attractive dipolar coupling between excitonic dipoles using a new design of stacked semiconductor bilayers. We show that the presence of a dipolar exciton fluid in one bilayer modifies the spatial distribution and increases the binding energy of excitonic dipoles in a vertically remote layer. The binding energy changes are explained using a many-body polaron model describing the deformation of the exciton cloud due to its interaction with a remote dipolar exciton. The surprising nonmonotonic dependence on the cloud density indicates the important role of dipolar correlations, which is unique to dense, strongly interacting dipolar solid-state systems. Our concept provides a route for the realization of dipolar lattices with strong anisotropic interactions in semiconductor systems, which open the way for the observation of theoretically predicted new and exotic collective phases, as well as for engineering and sensing their collective excitations.","lang":"eng"}],"type":"journal_article","file":[{"file_name":"2019_PhysReviewX_Hubert.pdf","access_level":"open_access","creator":"dernst","file_size":1193550,"content_type":"application/pdf","file_id":"6802","relation":"main_file","date_updated":"2020-07-14T12:47:40Z","date_created":"2019-08-12T12:14:18Z","checksum":"065ff82ee4a1d2c3773ce4b76ff4213c"}],"oa_version":"Published Version","_id":"6786","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 9","title":"Attractive dipolar coupling between stacked exciton fluids","status":"public","ddc":["530"],"has_accepted_license":"1","article_processing_charge":"No","day":"08","scopus_import":"1","date_published":"2019-05-08T00:00:00Z","citation":{"ama":"Hubert C, Baruchi Y, Mazuz-Harpaz Y, et al. Attractive dipolar coupling between stacked exciton fluids. Physical Review X. 2019;9(2). doi:10.1103/PhysRevX.9.021026","ista":"Hubert C, Baruchi Y, Mazuz-Harpaz Y, Cohen K, Biermann K, Lemeshko M, West K, Pfeiffer L, Rapaport R, Santos P. 2019. Attractive dipolar coupling between stacked exciton fluids. Physical Review X. 9(2), 021026.","apa":"Hubert, C., Baruchi, Y., Mazuz-Harpaz, Y., Cohen, K., Biermann, K., Lemeshko, M., … Santos, P. (2019). Attractive dipolar coupling between stacked exciton fluids. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.9.021026","ieee":"C. Hubert et al., “Attractive dipolar coupling between stacked exciton fluids,” Physical Review X, vol. 9, no. 2. American Physical Society, 2019.","mla":"Hubert, Colin, et al. “Attractive Dipolar Coupling between Stacked Exciton Fluids.” Physical Review X, vol. 9, no. 2, 021026, American Physical Society, 2019, doi:10.1103/PhysRevX.9.021026.","short":"C. Hubert, Y. Baruchi, Y. Mazuz-Harpaz, K. Cohen, K. Biermann, M. Lemeshko, K. West, L. Pfeiffer, R. Rapaport, P. Santos, Physical Review X 9 (2019).","chicago":"Hubert, Colin, Yifat Baruchi, Yotam Mazuz-Harpaz, Kobi Cohen, Klaus Biermann, Mikhail Lemeshko, Ken West, Loren Pfeiffer, Ronen Rapaport, and Paulo Santos. “Attractive Dipolar Coupling between Stacked Exciton Fluids.” Physical Review X. American Physical Society, 2019. https://doi.org/10.1103/PhysRevX.9.021026."},"publication":"Physical Review X","article_type":"original","file_date_updated":"2020-07-14T12:47:40Z","article_number":"021026","author":[{"full_name":"Hubert, Colin","last_name":"Hubert","first_name":"Colin"},{"first_name":"Yifat","last_name":"Baruchi","full_name":"Baruchi, Yifat"},{"full_name":"Mazuz-Harpaz, Yotam","first_name":"Yotam","last_name":"Mazuz-Harpaz"},{"full_name":"Cohen, Kobi","last_name":"Cohen","first_name":"Kobi"},{"last_name":"Biermann","first_name":"Klaus","full_name":"Biermann, Klaus"},{"first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"},{"full_name":"West, Ken","last_name":"West","first_name":"Ken"},{"full_name":"Pfeiffer, Loren","last_name":"Pfeiffer","first_name":"Loren"},{"full_name":"Rapaport, Ronen","first_name":"Ronen","last_name":"Rapaport"},{"first_name":"Paulo","last_name":"Santos","full_name":"Santos, Paulo"}],"volume":9,"date_updated":"2024-02-28T13:12:48Z","date_created":"2019-08-11T21:59:20Z","year":"2019","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","publication_status":"published","publication_identifier":{"eissn":["2160-3308"]},"month":"05","doi":"10.1103/PhysRevX.9.021026","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"},"oa":1,"external_id":{"isi":["000467402900001"],"arxiv":["1807.11238"]},"project":[{"name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902"}],"quality_controlled":"1","isi":1},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.04043"}],"oa":1,"external_id":{"arxiv":["1907.04043"],"isi":["000489036500004"]},"isi":1,"quality_controlled":"1","doi":"10.1103/physrevb.100.134504","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"year":"2019","publication_status":"published","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","author":[{"first_name":"Tuure","last_name":"Orell","full_name":"Orell, Tuure"},{"full_name":"Michailidis, Alexios","first_name":"Alexios","last_name":"Michailidis","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8443-1064"},{"first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"},{"last_name":"Silveri","first_name":"Matti","full_name":"Silveri, Matti"}],"date_created":"2019-11-13T08:25:48Z","date_updated":"2024-02-28T13:13:13Z","volume":100,"article_number":"134504","publication":"Physical Review B","citation":{"ieee":"T. Orell, A. Michailidis, M. Serbyn, and M. Silveri, “Probing the many-body localization phase transition with superconducting circuits,” Physical Review B, vol. 100, no. 13. American Physical Society, 2019.","apa":"Orell, T., Michailidis, A., Serbyn, M., & Silveri, M. (2019). Probing the many-body localization phase transition with superconducting circuits. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.100.134504","ista":"Orell T, Michailidis A, Serbyn M, Silveri M. 2019. Probing the many-body localization phase transition with superconducting circuits. Physical Review B. 100(13), 134504.","ama":"Orell T, Michailidis A, Serbyn M, Silveri M. Probing the many-body localization phase transition with superconducting circuits. Physical Review B. 2019;100(13). doi:10.1103/physrevb.100.134504","chicago":"Orell, Tuure, Alexios Michailidis, Maksym Serbyn, and Matti Silveri. “Probing the Many-Body Localization Phase Transition with Superconducting Circuits.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.100.134504.","short":"T. Orell, A. Michailidis, M. Serbyn, M. Silveri, Physical Review B 100 (2019).","mla":"Orell, Tuure, et al. “Probing the Many-Body Localization Phase Transition with Superconducting Circuits.” Physical Review B, vol. 100, no. 13, 134504, American Physical Society, 2019, doi:10.1103/physrevb.100.134504."},"article_type":"original","date_published":"2019-10-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7013","status":"public","title":"Probing the many-body localization phase transition with superconducting circuits","intvolume":" 100","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"Chains of superconducting circuit devices provide a natural platform for studies of synthetic bosonic quantum matter. Motivated by the recent experimental progress in realizing disordered and interacting chains of superconducting transmon devices, we study the bosonic many-body localization phase transition using the methods of exact diagonalization as well as matrix product state dynamics. We estimate the location of transition separating the ergodic and the many-body localized phases as a function of the disorder strength and the many-body on-site interaction strength. The main difference between the bosonic model realized by superconducting circuits and similar fermionic model is that the effect of the on-site interaction is stronger due to the possibility of multiple excitations occupying the same site. The phase transition is found to be robust upon including longer-range hopping and interaction terms present in the experiments. Furthermore, we calculate experimentally relevant local observables and show that their temporal fluctuations can be used to distinguish between the dynamics of Anderson insulator, many-body localization, and delocalized phases. While we consider unitary dynamics, neglecting the effects of dissipation, decoherence, and measurement back action, the timescales on which the dynamics is unitary are sufficient for observation of characteristic dynamics in the many-body localized phase. Moreover, the experimentally available disorder strength and interactions allow for tuning the many-body localization phase transition, thus making the arrays of superconducting circuit devices a promising platform for exploring localization physics and phase transition."}],"issue":"13"},{"doi":"10.1103/PhysRevB.100.174518","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.13579"}],"oa":1,"external_id":{"arxiv":["1907.13579"],"isi":["000498845700006"]},"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"month":"11","author":[{"full_name":"Brighi, Pietro","orcid":"0000-0002-7969-2729","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","last_name":"Brighi","first_name":"Pietro"},{"full_name":"Grilli, Marco","first_name":"Marco","last_name":"Grilli"},{"full_name":"Leridon, Brigitte","last_name":"Leridon","first_name":"Brigitte"},{"full_name":"Caprara, Sergio","first_name":"Sergio","last_name":"Caprara"}],"volume":100,"date_updated":"2024-02-28T13:14:08Z","date_created":"2019-12-22T23:00:41Z","year":"2019","publisher":"American Physical Society","department":[{"_id":"MaSe"}],"publication_status":"published","article_number":"174518","date_published":"2019-11-25T00:00:00Z","citation":{"short":"P. Brighi, M. Grilli, B. Leridon, S. Caprara, Physical Review B 100 (2019).","mla":"Brighi, Pietro, et al. “Effect of Anomalous Diffusion of Fluctuating Cooper Pairs on the Density of States of Superconducting NbN Thin Films.” Physical Review B, vol. 100, no. 17, 174518, American Physical Society, 2019, doi:10.1103/PhysRevB.100.174518.","chicago":"Brighi, Pietro, Marco Grilli, Brigitte Leridon, and Sergio Caprara. “Effect of Anomalous Diffusion of Fluctuating Cooper Pairs on the Density of States of Superconducting NbN Thin Films.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/PhysRevB.100.174518.","ama":"Brighi P, Grilli M, Leridon B, Caprara S. Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films. Physical Review B. 2019;100(17). doi:10.1103/PhysRevB.100.174518","apa":"Brighi, P., Grilli, M., Leridon, B., & Caprara, S. (2019). Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.100.174518","ieee":"P. Brighi, M. Grilli, B. Leridon, and S. Caprara, “Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films,” Physical Review B, vol. 100, no. 17. American Physical Society, 2019.","ista":"Brighi P, Grilli M, Leridon B, Caprara S. 2019. Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films. Physical Review B. 100(17), 174518."},"publication":"Physical Review B","article_type":"original","article_processing_charge":"No","day":"25","scopus_import":"1","oa_version":"Preprint","_id":"7200","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 100","title":"Effect of anomalous diffusion of fluctuating Cooper pairs on the density of states of superconducting NbN thin films","status":"public","issue":"17","abstract":[{"lang":"eng","text":"Recent scanning tunneling microscopy experiments in NbN thin disordered superconducting films found an emergent inhomogeneity at the scale of tens of nanometers. This inhomogeneity is mirrored by an apparent dimensional crossover in the paraconductivity measured in transport above the superconducting critical temperature Tc. This behavior was interpreted in terms of an anomalous diffusion of fluctuating Cooper pairs that display a quasiconfinement (i.e., a slowing down of their diffusive dynamics) on length scales shorter than the inhomogeneity identified by tunneling experiments. Here, we assume this anomalous diffusive behavior of fluctuating Cooper pairs and calculate the effect of these fluctuations on the electron density of states above Tc. We find that the density of states is substantially suppressed up to temperatures well above Tc. This behavior, which is closely reminiscent of a pseudogap, only arises from the anomalous diffusion of fluctuating Cooper pairs in the absence of stable preformed pairs, setting the stage for an intermediate behavior between the two common paradigms in the superconducting-insulator transition, namely, the localization of Cooper pairs (the so-called bosonic scenario) and the breaking of Cooper pairs into unpaired electrons due to strong disorder (the so-called fermionic scenario)."}],"type":"journal_article"},{"date_published":"2019-07-25T00:00:00Z","citation":{"ama":"Suri B, Pallantla RK, Schatz MF, Grigoriev RO. Heteroclinic and homoclinic connections in a Kolmogorov-like flow. Physical Review E. 2019;100(1). doi:10.1103/physreve.100.013112","ieee":"B. Suri, R. K. Pallantla, M. F. Schatz, and R. O. Grigoriev, “Heteroclinic and homoclinic connections in a Kolmogorov-like flow,” Physical Review E, vol. 100, no. 1. American Physical Society, 2019.","apa":"Suri, B., Pallantla, R. K., Schatz, M. F., & Grigoriev, R. O. (2019). Heteroclinic and homoclinic connections in a Kolmogorov-like flow. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.100.013112","ista":"Suri B, Pallantla RK, Schatz MF, Grigoriev RO. 2019. Heteroclinic and homoclinic connections in a Kolmogorov-like flow. Physical Review E. 100(1), 013112.","short":"B. Suri, R.K. Pallantla, M.F. Schatz, R.O. Grigoriev, Physical Review E 100 (2019).","mla":"Suri, Balachandra, et al. “Heteroclinic and Homoclinic Connections in a Kolmogorov-like Flow.” Physical Review E, vol. 100, no. 1, 013112, American Physical Society, 2019, doi:10.1103/physreve.100.013112.","chicago":"Suri, Balachandra, Ravi Kumar Pallantla, Michael F. Schatz, and Roman O. Grigoriev. “Heteroclinic and Homoclinic Connections in a Kolmogorov-like Flow.” Physical Review E. American Physical Society, 2019. https://doi.org/10.1103/physreve.100.013112."},"publication":"Physical Review E","article_type":"original","article_processing_charge":"No","day":"25","scopus_import":"1","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6779","intvolume":" 100","ddc":["532"],"status":"public","title":"Heteroclinic and homoclinic connections in a Kolmogorov-like flow","issue":"1","abstract":[{"lang":"eng","text":"Recent studies suggest that unstable recurrent solutions of the Navier-Stokes equation provide new insights\r\ninto dynamics of turbulent flows. In this study, we compute an extensive network of dynamical connections\r\nbetween such solutions in a weakly turbulent quasi-two-dimensional Kolmogorov flow that lies in the inversion symmetric subspace. In particular, we find numerous isolated heteroclinic connections between different\r\ntypes of solutions—equilibria, periodic, and quasiperiodic orbits—as well as continua of connections forming\r\nhigher-dimensional connecting manifolds. We also compute a homoclinic connection of a periodic orbit and\r\nprovide strong evidence that the associated homoclinic tangle forms the chaotic repeller that underpins transient\r\nturbulence in the symmetric subspace."}],"type":"journal_article","doi":"10.1103/physreve.100.013112","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1907.05860"],"isi":["000477911800012"]},"main_file_link":[{"url":"https://arxiv.org/abs/1907.05860","open_access":"1"}],"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"month":"07","author":[{"full_name":"Suri, Balachandra","id":"47A5E706-F248-11E8-B48F-1D18A9856A87","first_name":"Balachandra","last_name":"Suri"},{"full_name":"Pallantla, Ravi Kumar","last_name":"Pallantla","first_name":"Ravi Kumar"},{"first_name":"Michael F.","last_name":"Schatz","full_name":"Schatz, Michael F."},{"last_name":"Grigoriev","first_name":"Roman O.","full_name":"Grigoriev, Roman O."}],"volume":100,"date_updated":"2024-02-28T13:13:00Z","date_created":"2019-08-09T09:40:41Z","year":"2019","department":[{"_id":"BjHo"}],"publisher":"American Physical Society","publication_status":"published","ec_funded":1,"article_number":"013112"},{"language":[{"iso":"eng"}],"doi":"10.1103/physrevb.100.035127","project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000477888200001"],"arxiv":["1905.09138"]},"main_file_link":[{"url":"https://arxiv.org/abs/1905.09138","open_access":"1"}],"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"month":"07","volume":100,"date_updated":"2024-02-28T13:13:23Z","date_created":"2019-11-13T08:41:48Z","author":[{"first_name":"Mathieu","last_name":"Lewin","full_name":"Lewin, Mathieu"},{"last_name":"Lieb","first_name":"Elliott H.","full_name":"Lieb, Elliott H."},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert","full_name":"Seiringer, Robert"}],"department":[{"_id":"RoSe"}],"publisher":"American Physical Society","publication_status":"published","year":"2019","ec_funded":1,"article_number":"035127","date_published":"2019-07-25T00:00:00Z","article_type":"original","citation":{"ama":"Lewin M, Lieb EH, Seiringer R. Floating Wigner crystal with no boundary charge fluctuations. Physical Review B. 2019;100(3). doi:10.1103/physrevb.100.035127","ista":"Lewin M, Lieb EH, Seiringer R. 2019. Floating Wigner crystal with no boundary charge fluctuations. Physical Review B. 100(3), 035127.","ieee":"M. Lewin, E. H. Lieb, and R. Seiringer, “Floating Wigner crystal with no boundary charge fluctuations,” Physical Review B, vol. 100, no. 3. American Physical Society, 2019.","apa":"Lewin, M., Lieb, E. H., & Seiringer, R. (2019). Floating Wigner crystal with no boundary charge fluctuations. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.100.035127","mla":"Lewin, Mathieu, et al. “Floating Wigner Crystal with No Boundary Charge Fluctuations.” Physical Review B, vol. 100, no. 3, 035127, American Physical Society, 2019, doi:10.1103/physrevb.100.035127.","short":"M. Lewin, E.H. Lieb, R. Seiringer, Physical Review B 100 (2019).","chicago":"Lewin, Mathieu, Elliott H. Lieb, and Robert Seiringer. “Floating Wigner Crystal with No Boundary Charge Fluctuations.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.100.035127."},"publication":"Physical Review B","article_processing_charge":"No","day":"25","scopus_import":"1","oa_version":"Preprint","intvolume":" 100","status":"public","title":"Floating Wigner crystal with no boundary charge fluctuations","_id":"7015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","abstract":[{"lang":"eng","text":"We modify the \"floating crystal\" trial state for the classical homogeneous electron gas (also known as jellium), in order to suppress the boundary charge fluctuations that are known to lead to a macroscopic increase of the energy. The argument is to melt a thin layer of the crystal close to the boundary and consequently replace it by an incompressible fluid. With the aid of this trial state we show that three different definitions of the ground-state energy of jellium coincide. In the first point of view the electrons are placed in a neutralizing uniform background. In the second definition there is no background but the electrons are submitted to the constraint that their density is constant, as is appropriate in density functional theory. Finally, in the third system each electron interacts with a periodic image of itself; that is, periodic boundary conditions are imposed on the interaction potential."}],"type":"journal_article"},{"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"month":"11","doi":"10.1103/physrevb.100.205412","language":[{"iso":"eng"}],"external_id":{"isi":["000495967500006"],"arxiv":["1908.05549"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1908.05549","open_access":"1"}],"quality_controlled":"1","isi":1,"article_number":"205412","author":[{"last_name":"Anselmetti","first_name":"G. L. R.","full_name":"Anselmetti, G. L. R."},{"full_name":"Martinez, E. A.","last_name":"Martinez","first_name":"E. A."},{"first_name":"G. C.","last_name":"Ménard","full_name":"Ménard, G. C."},{"full_name":"Puglia, D.","last_name":"Puglia","first_name":"D."},{"first_name":"F. K.","last_name":"Malinowski","full_name":"Malinowski, F. K."},{"full_name":"Lee, J. S.","last_name":"Lee","first_name":"J. S."},{"full_name":"Choi, S.","first_name":"S.","last_name":"Choi"},{"last_name":"Pendharkar","first_name":"M.","full_name":"Pendharkar, M."},{"first_name":"C. J.","last_name":"Palmstrøm","full_name":"Palmstrøm, C. J."},{"last_name":"Marcus","first_name":"C. M.","full_name":"Marcus, C. M."},{"full_name":"Casparis, L.","first_name":"L.","last_name":"Casparis"},{"full_name":"Higginbotham, Andrew P","orcid":"0000-0003-2607-2363","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","first_name":"Andrew P"}],"volume":100,"date_created":"2019-12-04T16:02:25Z","date_updated":"2024-02-28T13:13:51Z","year":"2019","department":[{"_id":"AnHi"}],"publisher":"American Physical Society","publication_status":"published","article_processing_charge":"No","day":"15","scopus_import":"1","date_published":"2019-11-15T00:00:00Z","citation":{"ama":"Anselmetti GLR, Martinez EA, Ménard GC, et al. End-to-end correlated subgap states in hybrid nanowires. Physical Review B. 2019;100(20). doi:10.1103/physrevb.100.205412","apa":"Anselmetti, G. L. R., Martinez, E. A., Ménard, G. C., Puglia, D., Malinowski, F. K., Lee, J. S., … Higginbotham, A. P. (2019). End-to-end correlated subgap states in hybrid nanowires. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.100.205412","ieee":"G. L. R. Anselmetti et al., “End-to-end correlated subgap states in hybrid nanowires,” Physical Review B, vol. 100, no. 20. American Physical Society, 2019.","ista":"Anselmetti GLR, Martinez EA, Ménard GC, Puglia D, Malinowski FK, Lee JS, Choi S, Pendharkar M, Palmstrøm CJ, Marcus CM, Casparis L, Higginbotham AP. 2019. End-to-end correlated subgap states in hybrid nanowires. Physical Review B. 100(20), 205412.","short":"G.L.R. Anselmetti, E.A. Martinez, G.C. Ménard, D. Puglia, F.K. Malinowski, J.S. Lee, S. Choi, M. Pendharkar, C.J. Palmstrøm, C.M. Marcus, L. Casparis, A.P. Higginbotham, Physical Review B 100 (2019).","mla":"Anselmetti, G. L. R., et al. “End-to-End Correlated Subgap States in Hybrid Nanowires.” Physical Review B, vol. 100, no. 20, 205412, American Physical Society, 2019, doi:10.1103/physrevb.100.205412.","chicago":"Anselmetti, G. L. R., E. A. Martinez, G. C. Ménard, D. Puglia, F. K. Malinowski, J. S. Lee, S. Choi, et al. “End-to-End Correlated Subgap States in Hybrid Nanowires.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.100.205412."},"publication":"Physical Review B","article_type":"original","issue":"20","abstract":[{"lang":"eng","text":"End-to-end correlated bound states are investigated in superconductor-semiconductor hybrid nanowires at zero magnetic field. Peaks in subgap conductance are independently identified from each wire end, and a cross-correlation function is computed that counts end-to-end coincidences, averaging over thousands of subgap features. Strong correlations in a short, 300-nm device are reduced by a factor of 4 in a long, 900-nm device. In addition, subgap conductance distributions are investigated, and correlations between the left and right distributions are identified based on their mutual information."}],"type":"journal_article","oa_version":"Preprint","_id":"7145","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 100","title":"End-to-end correlated subgap states in hybrid nanowires","status":"public"},{"scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"ama":"Goremykina A, Vasseur R, Serbyn M. Analytically solvable renormalization group for the many-body localization transition. Physical Review Letters. 2019;122(4). doi:10.1103/physrevlett.122.040601","ieee":"A. Goremykina, R. Vasseur, and M. Serbyn, “Analytically solvable renormalization group for the many-body localization transition,” Physical Review Letters, vol. 122, no. 4. American Physical Society, 2019.","apa":"Goremykina, A., Vasseur, R., & Serbyn, M. (2019). Analytically solvable renormalization group for the many-body localization transition. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.122.040601","ista":"Goremykina A, Vasseur R, Serbyn M. 2019. Analytically solvable renormalization group for the many-body localization transition. Physical Review Letters. 122(4), 040601.","short":"A. Goremykina, R. Vasseur, M. Serbyn, Physical Review Letters 122 (2019).","mla":"Goremykina, Anna, et al. “Analytically Solvable Renormalization Group for the Many-Body Localization Transition.” Physical Review Letters, vol. 122, no. 4, 040601, American Physical Society, 2019, doi:10.1103/physrevlett.122.040601.","chicago":"Goremykina, Anna, Romain Vasseur, and Maksym Serbyn. “Analytically Solvable Renormalization Group for the Many-Body Localization Transition.” Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/physrevlett.122.040601."},"publication":"Physical Review Letters","article_type":"original","date_published":"2019-02-01T00:00:00Z","type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"We introduce a simple, exactly solvable strong-randomness renormalization group (RG) model for the many-body localization (MBL) transition in one dimension. Our approach relies on a family of RG flows parametrized by the asymmetry between thermal and localized phases. We identify the physical MBL transition in the limit of maximal asymmetry, reflecting the instability of MBL against rare thermal inclusions. We find a critical point that is localized with power-law distributed thermal inclusions. The typical size of critical inclusions remains finite at the transition, while the average size is logarithmically diverging. We propose a two-parameter scaling theory for the many-body localization transition that falls into the Kosterlitz-Thouless universality class, with the MBL phase corresponding to a stable line of fixed points with multifractal behavior."}],"_id":"5906","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 122","title":"Analytically solvable renormalization group for the many-body localization transition","status":"public","oa_version":"Preprint","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"month":"02","main_file_link":[{"url":"https://arxiv.org/abs/1807.04285","open_access":"1"}],"oa":1,"external_id":{"isi":["000456783700001"],"arxiv":["1807.04285"]},"quality_controlled":"1","isi":1,"doi":"10.1103/physrevlett.122.040601","language":[{"iso":"eng"}],"article_number":"040601","year":"2019","publisher":"American Physical Society","department":[{"_id":"MaSe"}],"publication_status":"published","author":[{"full_name":"Goremykina, Anna","last_name":"Goremykina","first_name":"Anna"},{"last_name":"Vasseur","first_name":"Romain","full_name":"Vasseur, Romain"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn","full_name":"Serbyn, Maksym"}],"volume":122,"date_updated":"2024-02-28T13:13:38Z","date_created":"2019-02-01T08:22:28Z"},{"article_number":"063627","year":"2019","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","publication_status":"published","author":[{"full_name":"Karle, Volker","last_name":"Karle","first_name":"Volker"},{"last_name":"Defenu","first_name":"Nicolò","full_name":"Defenu, Nicolò"},{"full_name":"Enss, Tilman","last_name":"Enss","first_name":"Tilman"}],"volume":99,"date_updated":"2024-02-28T13:12:34Z","date_created":"2019-07-14T21:59:17Z","publication_identifier":{"eissn":["24699934"],"issn":["24699926"]},"month":"06","main_file_link":[{"url":"https://arxiv.org/abs/1903.06759","open_access":"1"}],"oa":1,"external_id":{"isi":["000473133600007"],"arxiv":["1903.06759"]},"isi":1,"quality_controlled":"1","doi":"10.1103/PhysRevA.99.063627","language":[{"iso":"eng"}],"type":"journal_article","issue":"6","abstract":[{"text":"We consider a two-component Bose gas in two dimensions at a low temperature with short-range repulsive interaction. In the coexistence phase where both components are superfluid, interspecies interactions induce a nondissipative drag between the two superfluid flows (Andreev-Bashkin effect). We show that this behavior leads to a modification of the usual Berezinskii-Kosterlitz-Thouless (BKT) transition in two dimensions. We extend the renormalization of the superfluid densities at finite temperature using the renormalization-group approach and find that the vortices of one component have a large influence on the superfluid properties of the other, mediated by the nondissipative drag. The extended BKT flow equations indicate that the occurrence of the vortex unbinding transition in one of the components can induce the breakdown of superfluidity also in the other, leading to a locking phenomenon for the critical temperatures of the two gases.","lang":"eng"}],"_id":"6632","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 99","status":"public","title":"Coupled superfluidity of binary Bose mixtures in two dimensions","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"28","citation":{"ama":"Karle V, Defenu N, Enss T. Coupled superfluidity of binary Bose mixtures in two dimensions. Physical Review A. 2019;99(6). doi:10.1103/PhysRevA.99.063627","ista":"Karle V, Defenu N, Enss T. 2019. Coupled superfluidity of binary Bose mixtures in two dimensions. Physical Review A. 99(6), 063627.","apa":"Karle, V., Defenu, N., & Enss, T. (2019). Coupled superfluidity of binary Bose mixtures in two dimensions. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.99.063627","ieee":"V. Karle, N. Defenu, and T. Enss, “Coupled superfluidity of binary Bose mixtures in two dimensions,” Physical Review A, vol. 99, no. 6. American Physical Society, 2019.","mla":"Karle, Volker, et al. “Coupled Superfluidity of Binary Bose Mixtures in Two Dimensions.” Physical Review A, vol. 99, no. 6, 063627, American Physical Society, 2019, doi:10.1103/PhysRevA.99.063627.","short":"V. Karle, N. Defenu, T. Enss, Physical Review A 99 (2019).","chicago":"Karle, Volker, Nicolò Defenu, and Tilman Enss. “Coupled Superfluidity of Binary Bose Mixtures in Two Dimensions.” Physical Review A. American Physical Society, 2019. https://doi.org/10.1103/PhysRevA.99.063627."},"publication":"Physical Review A","date_published":"2019-06-28T00:00:00Z"},{"abstract":[{"text":"The angular momentum of molecules, or, equivalently, their rotation in three-dimensional space, is ideally suited for quantum control. Molecular angular momentum is naturally quantized, time evolution is governed by a well-known Hamiltonian with only a few accurately known parameters, and transitions between rotational levels can be driven by external fields from various parts of the electromagnetic spectrum. Control over the rotational motion can be exerted in one-, two-, and many-body scenarios, thereby allowing one to probe Anderson localization, target stereoselectivity of bimolecular reactions, or encode quantum information to name just a few examples. The corresponding approaches to quantum control are pursued within separate, and typically disjoint, subfields of physics, including ultrafast science, cold collisions, ultracold gases, quantum information science, and condensed-matter physics. It is the purpose of this review to present the various control phenomena, which all rely on the same underlying physics, within a unified framework. To this end, recall the Hamiltonian for free rotations, assuming the rigid rotor approximation to be valid, and summarize the different ways for a rotor to interact with external electromagnetic fields. These interactions can be exploited for control—from achieving alignment, orientation, or laser cooling in a one-body framework, steering bimolecular collisions, or realizing a quantum computer or quantum simulator in the many-body setting.","lang":"eng"}],"issue":"3","type":"journal_article","oa_version":"Preprint","_id":"7396","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Quantum control of molecular rotation","intvolume":" 91","day":"18","article_processing_charge":"No","scopus_import":"1","date_published":"2019-09-18T00:00:00Z","publication":"Reviews of Modern Physics","citation":{"ama":"Koch CP, Lemeshko M, Sugny D. Quantum control of molecular rotation. Reviews of Modern Physics. 2019;91(3). doi:10.1103/revmodphys.91.035005","apa":"Koch, C. P., Lemeshko, M., & Sugny, D. (2019). Quantum control of molecular rotation. Reviews of Modern Physics. American Physical Society. https://doi.org/10.1103/revmodphys.91.035005","ieee":"C. P. Koch, M. Lemeshko, and D. Sugny, “Quantum control of molecular rotation,” Reviews of Modern Physics, vol. 91, no. 3. American Physical Society, 2019.","ista":"Koch CP, Lemeshko M, Sugny D. 2019. Quantum control of molecular rotation. Reviews of Modern Physics. 91(3), 035005.","short":"C.P. Koch, M. Lemeshko, D. Sugny, Reviews of Modern Physics 91 (2019).","mla":"Koch, Christiane P., et al. “Quantum Control of Molecular Rotation.” Reviews of Modern Physics, vol. 91, no. 3, 035005, American Physical Society, 2019, doi:10.1103/revmodphys.91.035005.","chicago":"Koch, Christiane P., Mikhail Lemeshko, and Dominique Sugny. “Quantum Control of Molecular Rotation.” Reviews of Modern Physics. American Physical Society, 2019. https://doi.org/10.1103/revmodphys.91.035005."},"article_type":"original","article_number":"035005 ","author":[{"full_name":"Koch, Christiane P.","last_name":"Koch","first_name":"Christiane P."},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail"},{"last_name":"Sugny","first_name":"Dominique","full_name":"Sugny, Dominique"}],"date_updated":"2024-02-28T13:15:33Z","date_created":"2020-01-29T16:04:19Z","volume":91,"year":"2019","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","month":"09","publication_identifier":{"eissn":["1539-0756"],"issn":["0034-6861"]},"doi":"10.1103/revmodphys.91.035005","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1810.11338"}],"oa":1,"external_id":{"arxiv":["1810.11338"],"isi":["000486661700001"]},"isi":1,"quality_controlled":"1","project":[{"name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902"}]},{"article_number":"8989292","ec_funded":1,"publication_status":"published","publisher":"IEEE","department":[{"_id":"GaTk"}],"year":"2019","date_created":"2020-03-22T23:00:47Z","date_updated":"2024-03-06T14:22:51Z","author":[{"full_name":"Hledik, Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87","last_name":"Hledik","first_name":"Michal"},{"full_name":"Sokolowski, Thomas R","last_name":"Sokolowski","first_name":"Thomas R","orcid":"0000-0002-1287-3779","id":"3E999752-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"15020"}]},"month":"08","publication_identifier":{"isbn":["9781538669006"]},"isi":1,"quality_controlled":"1","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"external_id":{"arxiv":["1812.01475"],"isi":["000540384500015"]},"main_file_link":[{"url":"https://arxiv.org/abs/1812.01475","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"Information Theory Workshop","location":"Visby, Sweden","start_date":"2019-08-25","end_date":"2019-08-28"},"doi":"10.1109/ITW44776.2019.8989292","type":"conference","abstract":[{"text":"We derive a tight lower bound on equivocation (conditional entropy), or equivalently a tight upper bound on mutual information between a signal variable and channel outputs. The bound is in terms of the joint distribution of the signals and maximum a posteriori decodes (most probable signals given channel output). As part of our derivation, we describe the key properties of the distribution of signals, channel outputs and decodes, that minimizes equivocation and maximizes mutual information. This work addresses a problem in data analysis, where mutual information between signals and decodes is sometimes used to lower bound the mutual information between signals and channel outputs. Our result provides a corresponding upper bound.","lang":"eng"}],"status":"public","title":"A tight upper bound on mutual information","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7606","oa_version":"Preprint","scopus_import":"1","day":"01","article_processing_charge":"No","publication":"IEEE Information Theory Workshop, ITW 2019","citation":{"chicago":"Hledik, Michal, Thomas R Sokolowski, and Gašper Tkačik. “A Tight Upper Bound on Mutual Information.” In IEEE Information Theory Workshop, ITW 2019. IEEE, 2019. https://doi.org/10.1109/ITW44776.2019.8989292.","short":"M. Hledik, T.R. Sokolowski, G. Tkačik, in:, IEEE Information Theory Workshop, ITW 2019, IEEE, 2019.","mla":"Hledik, Michal, et al. “A Tight Upper Bound on Mutual Information.” IEEE Information Theory Workshop, ITW 2019, 8989292, IEEE, 2019, doi:10.1109/ITW44776.2019.8989292.","ieee":"M. Hledik, T. R. Sokolowski, and G. Tkačik, “A tight upper bound on mutual information,” in IEEE Information Theory Workshop, ITW 2019, Visby, Sweden, 2019.","apa":"Hledik, M., Sokolowski, T. R., & Tkačik, G. (2019). A tight upper bound on mutual information. In IEEE Information Theory Workshop, ITW 2019. Visby, Sweden: IEEE. https://doi.org/10.1109/ITW44776.2019.8989292","ista":"Hledik M, Sokolowski TR, Tkačik G. 2019. A tight upper bound on mutual information. IEEE Information Theory Workshop, ITW 2019. Information Theory Workshop, 8989292.","ama":"Hledik M, Sokolowski TR, Tkačik G. A tight upper bound on mutual information. In: IEEE Information Theory Workshop, ITW 2019. IEEE; 2019. doi:10.1109/ITW44776.2019.8989292"},"date_published":"2019-08-01T00:00:00Z"},{"doi":"10.1145/3293611.3331633","conference":{"start_date":"2019-07-29","location":"Toronto, ON, Canada","end_date":"2019-08-02","name":"PODC: Symposium on Principles of Distributed Computing"},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1903.05956","open_access":"1"}],"oa":1,"external_id":{"isi":["000570442000011"],"arxiv":["1903.05956"]},"quality_controlled":"1","isi":1,"publication_identifier":{"isbn":["9781450362177"]},"month":"08","related_material":{"record":[{"status":"public","relation":"later_version","id":"7939"}]},"author":[{"first_name":"Keren","last_name":"Censor-Hillel","full_name":"Censor-Hillel, Keren"},{"full_name":"Dory, Michal","last_name":"Dory","first_name":"Michal"},{"full_name":"Korhonen, Janne","last_name":"Korhonen","first_name":"Janne","id":"C5402D42-15BC-11E9-A202-CA2BE6697425"},{"full_name":"Leitersdorf, Dean","last_name":"Leitersdorf","first_name":"Dean"}],"date_updated":"2024-03-07T14:43:38Z","date_created":"2019-10-08T12:48:42Z","year":"2019","publisher":"ACM","department":[{"_id":"DaAl"}],"publication_status":"published","date_published":"2019-08-01T00:00:00Z","citation":{"short":"K. Censor-Hillel, M. Dory, J. Korhonen, D. Leitersdorf, in:, Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin, ACM, 2019, pp. 74–83.","mla":"Censor-Hillel, Keren, et al. “Fast Approximate Shortest Paths in the Congested Clique.” Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin, ACM, 2019, pp. 74–83, doi:10.1145/3293611.3331633.","chicago":"Censor-Hillel, Keren, Michal Dory, Janne Korhonen, and Dean Leitersdorf. “Fast Approximate Shortest Paths in the Congested Clique.” In Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin, 74–83. ACM, 2019. https://doi.org/10.1145/3293611.3331633.","ama":"Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. Fast approximate shortest paths in the congested clique. In: Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin. ACM; 2019:74-83. doi:10.1145/3293611.3331633","apa":"Censor-Hillel, K., Dory, M., Korhonen, J., & Leitersdorf, D. (2019). Fast approximate shortest paths in the congested clique. In Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin (pp. 74–83). Toronto, ON, Canada: ACM. https://doi.org/10.1145/3293611.3331633","ieee":"K. Censor-Hillel, M. Dory, J. Korhonen, and D. Leitersdorf, “Fast approximate shortest paths in the congested clique,” in Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin, Toronto, ON, Canada, 2019, pp. 74–83.","ista":"Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. 2019. Fast approximate shortest paths in the congested clique. Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin. PODC: Symposium on Principles of Distributed Computing, 74–83."},"publication":"Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin","page":"74-83","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Preprint","_id":"6933","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Fast approximate shortest paths in the congested clique","abstract":[{"lang":"eng","text":"We design fast deterministic algorithms for distance computation in the CONGESTED CLIQUE model. Our key contributions include:\r\n\r\n - A (2+ε)-approximation for all-pairs shortest paths problem in O(log²n / ε) rounds on unweighted undirected graphs. With a small additional additive factor, this also applies for weighted graphs. This is the first sub-polynomial constant-factor approximation for APSP in this model.\r\n - A (1+ε)-approximation for multi-source shortest paths problem from O(√n) sources in O(log² n / ε) rounds on weighted undirected graphs. This is the first sub-polynomial algorithm obtaining this approximation for a set of sources of polynomial size.\r\n\r\nOur main techniques are new distance tools that are obtained via improved algorithms for sparse matrix multiplication, which we leverage to construct efficient hopsets and shortest paths. Furthermore, our techniques extend to additional distance problems for which we improve upon the state-of-the-art, including diameter approximation, and an exact single-source shortest paths algorithm for weighted undirected graphs in Õ(n^{1/6}) rounds."}],"type":"conference"},{"oa_version":"Published Version","file":[{"file_size":43740796,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"mlukacisin","embargo_to":"open_access","file_name":"Thesis_Draft_v3.4Final.docx","access_level":"closed","date_updated":"2020-07-14T12:47:29Z","date_created":"2019-05-10T13:51:49Z","checksum":"829bda074444857c7935171237bb7c0c","relation":"hidden","file_id":"6409"},{"access_level":"open_access","file_name":"Thesis_Draft_v3.4FinalA.pdf","file_size":35228388,"content_type":"application/pdf","creator":"mlukacisin","relation":"main_file","embargo":"2020-04-17","file_id":"6410","checksum":"56cb5e97f5f8fc41692401b53832d8e0","date_updated":"2021-02-11T11:17:16Z","date_created":"2019-05-10T14:13:42Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6392","title":"Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory","ddc":["570"],"status":"public","abstract":[{"lang":"eng","text":"The regulation of gene expression is one of the most fundamental processes in living systems. In recent years, thanks to advances in sequencing technology and automation, it has become possible to study gene expression quantitatively, genome-wide and in high-throughput. This leads to the possibility of exploring changes in gene expression in the context of many external perturbations and their combinations, and thus of characterising the basic principles governing gene regulation. In this thesis, I present quantitative experimental approaches to studying transcriptional and protein level changes in response to combinatorial drug treatment, as well as a theoretical data-driven approach to analysing thermodynamic principles guiding transcription of protein coding genes. \r\nIn the first part of this work, I present a novel methodological framework for quantifying gene expression changes in drug combinations, termed isogrowth profiling. External perturbations through small molecule drugs influence the growth rate of the cell, leading to wide-ranging changes in cellular physiology and gene expression. This confounds the gene expression changes specifically elicited by the particular drug. Combinatorial perturbations, owing to the increased stress they exert, influence the growth rate even more strongly and hence suffer the convolution problem to a greater extent when measuring gene expression changes. Isogrowth profiling is a way to experimentally abstract non-specific, growth rate related changes, by performing the measurement using varying ratios of two drugs at such concentrations that the overall inhibition rate is constant. Using a robotic setup for automated high-throughput re-dilution culture of Saccharomyces cerevisiae, the budding yeast, I investigate all pairwise interactions of four small molecule drugs through sequencing RNA along a growth isobole. Through principal component analysis, I demonstrate here that isogrowth profiling can uncover drug-specific as well as drug-interaction-specific gene expression changes. I show that drug-interaction-specific gene expression changes can be used for prediction of higher-order drug interactions. I propose a simplified generalised framework of isogrowth profiling, with few measurements needed for each drug pair, enabling the broad application of isogrowth profiling to high-throughput screening of inhibitors of cellular growth and beyond. Such high-throughput screenings of gene expression changes specific to pairwise drug interactions will be instrumental for predicting the higher-order interactions of the drugs.\r\n\r\nIn the second part of this work, I extend isogrowth profiling to single-cell measurements of gene expression, characterising population heterogeneity in the budding yeast in response to combinatorial drug perturbation while controlling for non-specific growth rate effects. Through flow cytometry of strains with protein products fused to green fluorescent protein, I discover multiple proteins with bi-modally distributed expression levels in the population in response to drug treatment. I characterize more closely the effect of an ionic stressor, lithium chloride, and find that it inhibits the splicing of mRNA, most strongly affecting ribosomal protein transcripts and leading to a bi-stable behaviour of a small ribosomal subunit protein Rps22B. Time-lapse microscopy of a microfluidic culture system revealed that the induced Rps22B heterogeneity leads to preferential survival of Rps22B-low cells after long starvation, but to preferential proliferation of Rps22B-high cells after short starvation. Overall, this suggests that yeast cells might use splicing of ribosomal genes for bet-hedging in fluctuating environments. I give specific examples of how further exploration of cellular heterogeneity in yeast in response to external perturbation has the potential to reveal yet-undiscovered gene regulation circuitry.\r\n\r\nIn the last part of this thesis, a re-analysis of a published sequencing dataset of nascent elongating transcripts is used to characterise the thermodynamic constraints for RNA polymerase II (RNAP) elongation. Population-level data on RNAP position throughout the transcribed genome with single nucleotide resolution are used to infer the sequence specific thermodynamic determinants of RNAP pausing and backtracking. This analysis reveals that the basepairing strength of the eight nucleotide-long RNA:DNA duplex relative to the basepairing strength of the same sequence when in DNA:DNA duplex, and the change in this quantity during RNA polymerase movement, is the key determinant of RNAP pausing. This is true for RNAP pausing while elongating, but also of RNAP pausing while backtracking and of the backtracking length. The quantitative dependence of RNAP pausing on basepairing energetics is used to infer the increase in pausing due to transcriptional mismatches, leading to a hypothesis that pervasive RNA polymerase II pausing is due to basepairing energetics, as an evolutionary cost for increased RNA polymerase II fidelity.\r\n\r\nThis work advances our understanding of the general principles governing gene expression, with the goal of making computational predictions of single-cell gene expression responses to combinatorial perturbations based on the individual perturbations possible. This ability would substantially facilitate the design of drug combination treatments and, in the long term, lead to our increased ability to more generally design targeted manipulations to any biological system. "}],"type":"dissertation","alternative_title":["IST Austria Thesis"],"date_published":"2019-05-09T00:00:00Z","citation":{"chicago":"Lukacisin, Martin. “Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory.” IST Austria, 2019. https://doi.org/10.15479/AT:ISTA:6392.","short":"M. Lukacisin, Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory, IST Austria, 2019.","mla":"Lukacisin, Martin. Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory. IST Austria, 2019, doi:10.15479/AT:ISTA:6392.","ieee":"M. Lukacisin, “Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory,” IST Austria, 2019.","apa":"Lukacisin, M. (2019). Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. IST Austria. https://doi.org/10.15479/AT:ISTA:6392","ista":"Lukacisin M. 2019. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. IST Austria.","ama":"Lukacisin M. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. 2019. doi:10.15479/AT:ISTA:6392"},"page":"103","has_accepted_license":"1","day":"09","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1029"}]},"author":[{"full_name":"Lukacisin, Martin","last_name":"Lukacisin","first_name":"Martin","orcid":"0000-0001-6549-4177","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2019-05-09T19:53:00Z","date_updated":"2023-09-22T09:19:41Z","year":"2019","department":[{"_id":"ToBo"}],"publisher":"IST Austria","publication_status":"published","file_date_updated":"2021-02-11T11:17:16Z","extern":"1","doi":"10.15479/AT:ISTA:6392","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"oa":1,"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-001-5"]},"month":"05"},{"status":"public","ddc":["570","006","578","592"],"title":"Collective defenses of garden ants against a fungal pathogen","_id":"6435","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"relation":"main_file","embargo":"2020-05-08","file_id":"6438","checksum":"6daf2d2086111aa8fd3fbc919a3e2833","date_created":"2019-05-13T09:16:20Z","date_updated":"2021-02-11T11:17:15Z","access_level":"open_access","file_name":"tesisDoctoradoBC.pdf","content_type":"application/pdf","file_size":3895187,"creator":"casillas"},{"date_updated":"2020-07-14T12:47:30Z","date_created":"2019-05-13T09:16:20Z","checksum":"3d221aaff7559a7060230a1ff610594f","relation":"source_file","file_id":"6439","content_type":"application/zip","file_size":7365118,"creator":"casillas","embargo_to":"open_access","file_name":"tesisDoctoradoBC.zip","access_level":"closed"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Social insect colonies tend to have numerous members which function together like a single organism in such harmony that the term ``super-organism'' is often used. In this analogy the reproductive caste is analogous to the primordial germ\r\ncells of a metazoan, while the sterile worker caste corresponds to somatic cells. The worker castes, like tissues, are\r\nin charge of all functions of a living being, besides reproduction. The establishment of new super-organismal units\r\n(i.e. new colonies) is accomplished by the co-dependent castes. The term oftentimes goes beyond a metaphor. We invoke it when we speak about the metabolic rate, thermoregulation, nutrient regulation and gas exchange of a social insect colony. Furthermore, we assert that the super-organism has an immune system, and benefits from ``social immunity''.\r\n\r\nSocial immunity was first summoned by evolutionary biologists to resolve the apparent discrepancy between the expected high frequency of disease outbreak amongst numerous, closely related tightly-interacting hosts, living in stable and microbially-rich environments, against the exceptionally scarce epidemic accounts in natural populations. Social\r\nimmunity comprises a multi-layer assembly of behaviours which have evolved to effectively keep the pathogenic enemies of a colony at bay. The field of social immunity has drawn interest, as it becomes increasingly urgent to stop\r\nthe collapse of pollinator species and curb the growth of invasive pests. In the past decade, several mechanisms of\r\nsocial immune responses have been dissected, but many more questions remain open.\r\n\r\nI present my work in two experimental chapters. In the first, I use invasive garden ants (*Lasius neglectus*) to study how pathogen load and its distribution among nestmates affect the grooming response of the group. Any given group of ants will carry out the same total grooming work, but will direct their grooming effort towards individuals\r\ncarrying a relatively higher spore load. Contrary to expectation, the highest risk of transmission does not stem from grooming highly contaminated ants, but instead, we suggest that the grooming response likely minimizes spore loss to the environment, reducing contamination from inadvertent pickup from the substrate.\r\n\r\nThe second is a comparative developmental approach. I follow black garden ant queens (*Lasius niger*) and their colonies from mating flight, through hibernation for a year. Colonies which grow fast from the start, have a lower chance of survival through hibernation, and those which survive grow at a lower pace later. This is true for colonies of naive\r\nand challenged queens. Early pathogen exposure of the queens changes colony dynamics in an unexpected way: colonies from exposed queens are more likely to grow slowly and recover in numbers only after they survive hibernation.\r\n\r\nIn addition to the two experimental chapters, this thesis includes a co-authored published review on organisational\r\nimmunity, where we enlist the experimental evidence and theoretical framework on which this hypothesis is built,\r\nidentify the caveats and underline how the field is ripe to overcome them. In a final chapter, I describe my part in\r\ntwo collaborative efforts, one to develop an image-based tracker, and the second to develop a classifier for ant\r\nbehaviour."}],"page":"183","citation":{"ama":"Casillas Perez BE. Collective defenses of garden ants against a fungal pathogen. 2019. doi:10.15479/AT:ISTA:6435","apa":"Casillas Perez, B. E. (2019). Collective defenses of garden ants against a fungal pathogen. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6435","ieee":"B. E. Casillas Perez, “Collective defenses of garden ants against a fungal pathogen,” Institute of Science and Technology Austria, 2019.","ista":"Casillas Perez BE. 2019. Collective defenses of garden ants against a fungal pathogen. Institute of Science and Technology Austria.","short":"B.E. Casillas Perez, Collective Defenses of Garden Ants against a Fungal Pathogen, Institute of Science and Technology Austria, 2019.","mla":"Casillas Perez, Barbara E. Collective Defenses of Garden Ants against a Fungal Pathogen. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6435.","chicago":"Casillas Perez, Barbara E. “Collective Defenses of Garden Ants against a Fungal Pathogen.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6435."},"date_published":"2019-05-07T00:00:00Z","keyword":["Social Immunity","Sanitary care","Social Insects","Organisational Immunity","Colony development","Multi-target tracking"],"day":"07","has_accepted_license":"1","article_processing_charge":"No","publication_status":"published","department":[{"_id":"SyCr"}],"publisher":"Institute of Science and Technology Austria","year":"2019","date_created":"2019-05-13T08:58:35Z","date_updated":"2023-09-07T12:57:04Z","author":[{"full_name":"Casillas Perez, Barbara E","last_name":"Casillas Perez","first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"1999","relation":"part_of_dissertation","status":"public"}]},"file_date_updated":"2021-02-11T11:17:15Z","ec_funded":1,"project":[{"call_identifier":"H2020","name":"Epidemics in ant societies on a chip","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","grant_number":"771402"}],"oa":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"LifeSc"}],"supervisor":[{"full_name":"Cremer, Sylvia M","first_name":"Sylvia M","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:6435","month":"05","publication_identifier":{"issn":["2663-337X"]}},{"month":"02","publication_identifier":{"issn":["2663-337X"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"doi":"10.15479/at:ista:th1075","supervisor":[{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"file_date_updated":"2021-02-11T23:30:15Z","year":"2019","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Narasimhan, Madhumitha","last_name":"Narasimhan","first_name":"Madhumitha","orcid":"0000-0002-8600-0671","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"412"}]},"date_updated":"2023-09-08T11:43:03Z","date_created":"2019-04-09T14:37:06Z","day":"04","has_accepted_license":"1","article_processing_charge":"No","citation":{"short":"M. Narasimhan, Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants , Institute of Science and Technology Austria, 2019.","mla":"Narasimhan, Madhumitha. Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants . Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:th1075.","chicago":"Narasimhan, Madhumitha. “Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants .” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:th1075.","ama":"Narasimhan M. Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . 2019. doi:10.15479/at:ista:th1075","ieee":"M. Narasimhan, “Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants ,” Institute of Science and Technology Austria, 2019.","apa":"Narasimhan, M. (2019). Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th1075","ista":"Narasimhan M. 2019. Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . Institute of Science and Technology Austria."},"page":"138","date_published":"2019-02-04T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Clathrin-Mediated Endocytosis (CME) is an aspect of cellular trafficking that is constantly regulated for mediating developmental and physiological responses. The main aim of my thesis is to decipher the basic mechanisms of CME and post-endocytic trafficking in the whole multicellular organ systems of Arabidopsis. The first chapter of my thesis describes the search for new components involved in CME. Tandem affinity purification was conducted using CLC and its interacting partners were identified. Amongst the identified proteins were the Auxilin-likes1 and 2 (Axl1/2), putative uncoating factors, for which we made a full functional analysis. Over-expression of Axl1/2 causes extreme modifications in the dynamics of the machinery proteins and inhibition of endocytosis altogether. However the loss of function of the axl1/2 did not present any cellular or physiological phenotype, meaning Auxilin-likes do not form the major uncoating machinery. The second chapter of my thesis describes the establishment/utilisation of techniques to capture the dynamicity and the complexity of CME and post-endocytic trafficking. We have studied the development of endocytic pits at the PM – specifically, the mode of membrane remodeling during pit development and the role of actin in it, given plant cells possess high turgor pressure. Utilizing the improved z-resolution of TIRF and VAEM techniques, we captured the time-lapse of the endocytic events at the plasma membrane; and using particle detection software, we quantitatively analysed all the endocytic trajectories in an unbiased way to obtain the endocytic rate of the system. This together with the direct analysis of cargo internalisation from the PM provided an estimate on the endocytic potential of the cell. We also developed a methodology for ultrastructural analysis of different populations of Clathrin-Coated Structures (CCSs) in both PM and endomembranes in unroofed protoplasts. Structural analysis, together with the intensity profile of CCSs at the PM show that the mode of CCP development at the PM follows ‘Constant curvature model’; meaning that clathrin polymerisation energy is a major contributing factor of membrane remodeling. In addition, other analyses clearly show that actin is not required for membrane remodeling during invagination or any other step of CCP development, despite the prevalent high turgor pressure. However, actin is essential in orchestrating the post-endocytic trafficking of CCVs facilitating the EE formation. We also observed that the uncoating process post-endocytosis is not immediate; an alternative mechanism of uncoating – Sequential multi-step process – functions in the cell. Finally we also looked at one of the important physiological stimuli modulating the process – hormone, auxin. auxin has been known to influence CME before. We have made a detailed study on the concentration-time based effect of auxin on the machinery proteins, CCP development, and the specificity of cargoes endocytosed. To this end, we saw no general effect of auxin on CME at earlier time points. However, very low concentration of IAA, such as 50nM, accelerates endocytosis of specifically PIN2 through CME. Such a tight regulatory control with high specificity to PIN2 could be essential in modulating its polarity. 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work was supported by the ERC and EU Horizon 2020 (ERC 692692; MSC-IF 708497) and FWF Z 312-B27 Wittgenstein award; W 1205-B09).","year":"2019","publication_status":"published","department":[{"_id":"PeJo"}],"publisher":"Austrian Pharmacological Society","author":[{"last_name":"Kim","first_name":"Olena","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","full_name":"Kim, Olena"},{"orcid":"0000-0003-0005-401X","id":"4305C450-F248-11E8-B48F-1D18A9856A87","last_name":"Borges Merjane","first_name":"Carolina","full_name":"Borges Merjane, Carolina"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter 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Suppl. 1, A3.27, Austrian Pharmacological Society, 2019, doi:10.25006/ia.7.s1-a3.27.","short":"O. Kim, C. Borges Merjane, P.M. Jonas, in:, Intrinsic Activity, Austrian Pharmacological Society, 2019.","chicago":"Kim, Olena, Carolina Borges Merjane, and Peter M Jonas. “Functional Analysis of the Docked Vesicle Pool in Hippocampal Mossy Fiber Terminals by Electron Microscopy.” In Intrinsic Activity, Vol. 7. Austrian Pharmacological Society, 2019. https://doi.org/10.25006/ia.7.s1-a3.27.","ama":"Kim O, Borges Merjane C, Jonas PM. Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy. In: Intrinsic Activity. Vol 7. Austrian Pharmacological Society; 2019. doi:10.25006/ia.7.s1-a3.27","ista":"Kim O, Borges Merjane C, Jonas PM. 2019. Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy. Intrinsic Activity. ANA: Austrian Neuroscience Association ; APHAR: Austrian Pharmacological Society vol. 7, A3.27.","apa":"Kim, O., Borges Merjane, C., & Jonas, P. M. (2019). Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy. In Intrinsic Activity (Vol. 7). Innsbruck, Austria: Austrian Pharmacological Society. https://doi.org/10.25006/ia.7.s1-a3.27","ieee":"O. Kim, C. Borges Merjane, and P. M. Jonas, “Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy,” in Intrinsic Activity, Innsbruck, Austria, 2019, vol. 7, no. Suppl. 1."},"date_published":"2019-09-11T00:00:00Z","keyword":["hippocampus","mossy fibers","readily releasable pool","electron microscopy"],"day":"11","article_processing_charge":"No"},{"oa":1,"doi":"10.15479/AT:ISTA:6947","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"supervisor":[{"full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"}],"language":[{"iso":"eng"}],"month":"10","publication_identifier":{"issn":["2663-337X"]},"year":"2019","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"MiSi"}],"author":[{"last_name":"Assen","first_name":"Frank P","orcid":"0000-0003-3470-6119","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","full_name":"Assen, Frank P"}],"related_material":{"record":[{"id":"664","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"402"}]},"date_created":"2019-10-14T16:54:52Z","date_updated":"2023-09-13T08:50:57Z","file_date_updated":"2020-11-07T23:30:03Z","citation":{"chicago":"Assen, Frank P. “Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6947.","mla":"Assen, Frank P. Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6947.","short":"F.P. Assen, Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking, Institute of Science and Technology Austria, 2019.","ista":"Assen FP. 2019. Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. Institute of Science and Technology Austria.","apa":"Assen, F. P. (2019). Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6947","ieee":"F. P. Assen, “Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking,” Institute of Science and Technology Austria, 2019.","ama":"Assen FP. Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. 2019. doi:10.15479/AT:ISTA:6947"},"page":"142","date_published":"2019-10-09T00:00:00Z","day":"9","has_accepted_license":"1","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6947","ddc":["570"],"title":"Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking","status":"public","oa_version":"Published Version","file":[{"relation":"source_file","file_id":"6990","date_created":"2019-11-06T12:30:02Z","date_updated":"2020-11-07T23:30:03Z","checksum":"53a739752a500f84d0f8ec953cbbd0b6","embargo_to":"open_access","file_name":"PhDthesis_FrankAssen_revised2.docx","access_level":"closed","file_size":214172667,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"fassen"},{"access_level":"open_access","file_name":"PhDthesis_FrankAssen_revised2.pdf","content_type":"application/pdf","file_size":83637532,"creator":"fassen","relation":"main_file","file_id":"6991","embargo":"2020-11-06","checksum":"8c156b65d9347bb599623a4b09f15d15","date_updated":"2020-11-07T23:30:03Z","date_created":"2019-11-06T12:30:57Z"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Lymph nodes are es s ential organs of the immune s ys tem where adaptive immune responses originate, and consist of various leukocyte populations and a stromal backbone. Fibroblastic reticular cells (FRCs) are the main stromal cells and form a sponge-like extracellular matrix network, called conduits , which they thems elves enwrap and contract. Lymph, containing s oluble antigens , arrive in lymph nodes via afferent lymphatic vessels that connect to the s ubcaps ular s inus and conduit network. According to the current paradigm, the conduit network dis tributes afferent lymph through lymph nodes and thus provides acces s for immune cells to lymph-borne antigens. An elas tic caps ule s urrounds the organ and confines the immune cells and FRC network. Lymph nodes are completely packed with lymphocytes and lymphocyte numbers directly dictates the size of the organ. Although lymphocytes cons tantly enter and leave the lymph node, its s ize remains remarkedly s table under homeostatic conditions. It is only partly known how the cellularity and s ize of the lymph node is regulated and how the lymph node is able to swell in inflammation. The role of the FRC network in lymph node s welling and trans fer of fluids are inves tigated in this thes is. Furthermore, we s tudied what trafficking routes are us ed by cancer cells in lymph nodes to form distal metastases.We examined the role of a mechanical feedback in regulation of lymph node swelling. Using parallel plate compression and UV-las er cutting experiments we dis s ected the mechanical force dynamics of the whole lymph node, and individually for FRCs and the caps ule. Physical forces generated by packed lymphocytes directly affect the tens ion on the FRC network and capsule, which increases its resistance to swelling. This implies a feedback mechanism between tis s ue pres s ure and ability of lymphocytes to enter the organ. Following inflammation, the lymph node swells ∼10 fold in two weeks . Yet, what is the role for tens ion on the FRC network and caps ule, and how are lymphocytes able to enter in conditions that resist swelling remain open ques tions . We s how that tens ion on the FRC network is important to limit the swelling rate of the organ so that the FRC network can grow in a coordinated fashion. This is illustrated by interfering with FRC contractility, which leads to faster swelling rates and a dis organized FRC network in the inflamed lymph node. Growth of the FRC network in turn is expected to releas e tens ion on thes e s tructures and lowers the res is tance to swelling, thereby allowing more lymphocytes to enter the organ and drive more swelling. Halt of swelling coincides with a thickening of the caps ule, which forms a thick res is tant band around the organ and lowers tens ion on the FRC network to form a new force equilibrium.The FRC and conduit network are further believed to be a privileged s ite of s oluble information within the lymph node, although many details remain uns olved. We s how by 3D ultra-recons truction that FRCs and antigen pres enting cells cover the s urface of conduit s ys tem for more than 99% and we dis cus s the implications for s oluble information exchangeat the conduit level.Finally, there is an ongoing debate in the cancer field whether and how cancer cells in lymph nodes s eed dis tal metas tas es . We s how that cancer cells infus ed into the lymph node can utilize trafficking routes of immune cells and rapidly migrate to blood vessels. Once in the blood circulation, these cells are able to form metastases in distal tissues.","lang":"eng"}]},{"title":"The role of CCK-interneurons in regulating hippocampal network dynamics","status":"public","ddc":["570"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6849","file":[{"creator":"drangel","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":18253100,"file_name":"Thesis_Damaris_Rangel_source.docx","embargo_to":"open_access","access_level":"closed","date_created":"2019-09-09T13:09:45Z","date_updated":"2021-02-10T23:30:09Z","checksum":"244dc4f74dbfc94f414156092298831f","file_id":"6865","relation":"source_file"},{"relation":"main_file","file_id":"6866","embargo":"2020-09-10","checksum":"59c73be40eeaa1c4db24067270151555","date_created":"2019-09-09T13:09:52Z","date_updated":"2020-09-11T22:30:04Z","access_level":"open_access","file_name":"Thesis_Damaris_Rangel_pdfa.pdf","request_a_copy":0,"content_type":"application/pdf","file_size":2160109,"creator":"drangel"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Brain function is mediated by complex dynamical interactions between excitatory and inhibitory cell types. The Cholecystokinin-expressing inhibitory cells (CCK-interneurons) are one of the least studied types, despite being suspected to play important roles in cognitive processes. We studied the network effects of optogenetic silencing of CCK-interneurons in the CA1 hippocampal area during exploration and sleep states. The cell firing pattern in response to light pulses allowed us to classify the recorded neurons in 5 classes, including disinhibited and non-responsive pyramidal cell and interneurons, and the inhibited interneurons corresponding to the CCK group. The light application, which inhibited the activity of CCK interneurons triggered wider changes in the firing dynamics of cells. We observed rate changes (i.e. remapping) of pyramidal cells during the exploration session in which the light was applied relative to the previous control session that was not restricted neither in time nor space to the light delivery. Also, the disinhibited pyramidal cells had higher increase in bursting than in single spike firing rate as a result of CCK silencing. In addition, the firing activity patterns during exploratory periods were more weakly reactivated in sleep for those periods in which CCK-interneuron were silenced than in the unaffected periods. Furthermore, light pulses during sleep disrupted the reactivation of recent waking patterns. Hence, silencing CCK neurons during exploration suppressed the reactivation of waking firing patterns in sleep and CCK interneuron activity was also required during sleep for the normal reactivation of waking patterns. These findings demonstrate the involvement of CCK cells in reactivation-related memory consolidation. An important part of our analysis was to test the relationship of the identified CCKinterneurons to brain oscillations. Our findings showed that these cells exhibited different oscillatory behaviour during anaesthesia and natural waking and sleep conditions. We showed that: 1) Contrary to the past studies performed under anaesthesia, the identified CCKinterneurons fired on the descending portion of the theta phase in waking exploration. 2) CCKinterneuron preferred phases around the trough of gamma oscillations. 3) Contrary to anaesthesia conditions, the average firing rate of the CCK-interneurons increased around the peak activity of the sharp-wave ripple (SWR) events in natural sleep, which is congruent with new reports about their functional connectivity. We also found that light driven CCK-interneuron silencing altered the dynamics on the CA1 network oscillatory activity: 1) Pyramidal cells negatively shifted their preferred theta phases when the light was applied, while interneurons responses were less consistent. 2) As a population, pyramidal cells negatively shifted their preferred activity during gamma oscillations, albeit we did not find gamma modulation differences related to the light application when pyramidal cells were subdivided into the disinhibited and unaffected groups. 3) During the peak of SWR events, all but the CCK-interneurons had a reduction in their relative firing rate change during the light application as compared to the change observed at SWR initiation. Finally, regarding to the place field activity of the recorded pyramidal neurons, we showed that the disinhibited pyramidal cells had reduced place field similarity, coherence and spatial information, but only during the light application. The mechanisms behind such observed behaviours might involve eCB signalling and plastic changes in CCK-interneuron synapses. In conclusion, the observed changes related to the light-mediated silencing of CCKinterneurons have unravelled characteristics of this interneuron subpopulation that might change the understanding not only of their particular network interactions, but also of the current theories about the emergence of certain cognitive processes such as place coding needed for navigation or hippocampus-dependent memory consolidation. "}],"page":"97","citation":{"chicago":"Rangel Guerrero, Dámaris K. “The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6849.","mla":"Rangel Guerrero, Dámaris K. The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6849.","short":"D.K. Rangel Guerrero, The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics, Institute of Science and Technology Austria, 2019.","ista":"Rangel Guerrero DK. 2019. The role of CCK-interneurons in regulating hippocampal network dynamics. Institute of Science and Technology Austria.","apa":"Rangel Guerrero, D. K. (2019). The role of CCK-interneurons in regulating hippocampal network dynamics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6849","ieee":"D. K. Rangel Guerrero, “The role of CCK-interneurons in regulating hippocampal network dynamics,” Institute of Science and Technology Austria, 2019.","ama":"Rangel Guerrero DK. The role of CCK-interneurons in regulating hippocampal network dynamics. 2019. doi:10.15479/AT:ISTA:6849"},"date_published":"2019-09-09T00:00:00Z","day":"09","has_accepted_license":"1","article_processing_charge":"No","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JoCs"}],"year":"2019","date_created":"2019-09-06T06:54:16Z","date_updated":"2023-09-19T10:01:12Z","author":[{"full_name":"Rangel Guerrero, Dámaris K","first_name":"Dámaris K","last_name":"Rangel Guerrero","id":"4871BCE6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8602-4374"}],"related_material":{"record":[{"id":"5914","status":"public","relation":"part_of_dissertation"}]},"file_date_updated":"2021-02-10T23:30:09Z","oa":1,"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"M-Shop"}],"supervisor":[{"first_name":"Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:6849","month":"09","publication_identifier":{"isbn":["9783990780039"],"issn":["2663-337X"]}},{"publication_identifier":{"issn":["00928674"],"eissn":["10974172"]},"month":"05","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"doi":"10.1016/j.cell.2019.04.015","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"quality_controlled":"1","isi":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"},"external_id":{"isi":["000466843000015"],"pmid":["31051107"]},"ec_funded":1,"file_date_updated":"2020-07-14T12:47:28Z","volume":177,"date_updated":"2024-03-28T23:30:10Z","date_created":"2019-04-28T21:59:14Z","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/specialized-plant-cells-regain-stem-cell-features-to-heal-wounds/"}],"record":[{"id":"9992","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Marhavá, Petra","id":"44E59624-F248-11E8-B48F-1D18A9856A87","first_name":"Petra","last_name":"Marhavá"},{"full_name":"Hörmayer, Lukas","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Hörmayer","first_name":"Lukas"},{"full_name":"Yoshida, Saiko","first_name":"Saiko","last_name":"Yoshida","id":"2E46069C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Marhavy, Peter","last_name":"Marhavy","first_name":"Peter","orcid":"0000-0001-5227-5741","id":"3F45B078-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"publisher":"Elsevier","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"publication_status":"published","pmid":1,"year":"2019","has_accepted_license":"1","article_processing_charge":"No","day":"02","scopus_import":"1","date_published":"2019-05-02T00:00:00Z","page":"957-969.e13","citation":{"chicago":"Marhavá, Petra, Lukas Hörmayer, Saiko Yoshida, Peter Marhavý, Eva Benková, and Jiří Friml. “Re-Activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.04.015.","mla":"Marhavá, Petra, et al. “Re-Activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing.” Cell, vol. 177, no. 4, Elsevier, 2019, p. 957–969.e13, doi:10.1016/j.cell.2019.04.015.","short":"P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, J. Friml, Cell 177 (2019) 957–969.e13.","ista":"Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. 2019. Re-activation of stem cell pathways for pattern restoration in plant wound healing. Cell. 177(4), 957–969.e13.","ieee":"P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, and J. Friml, “Re-activation of stem cell pathways for pattern restoration in plant wound healing,” Cell, vol. 177, no. 4. Elsevier, p. 957–969.e13, 2019.","apa":"Marhavá, P., Hörmayer, L., Yoshida, S., Marhavý, P., Benková, E., & Friml, J. (2019). Re-activation of stem cell pathways for pattern restoration in plant wound healing. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.04.015","ama":"Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. Re-activation of stem cell pathways for pattern restoration in plant wound healing. Cell. 2019;177(4):957-969.e13. doi:10.1016/j.cell.2019.04.015"},"publication":"Cell","issue":"4","abstract":[{"lang":"eng","text":"A process of restorative patterning in plant roots correctly replaces eliminated cells to heal local injuries despite the absence of cell migration, which underpins wound healing in animals. \r\n\r\nPatterning in plants relies on oriented cell divisions and acquisition of specific cell identities. Plants regularly endure wounds caused by abiotic or biotic environmental stimuli and have developed extraordinary abilities to restore their tissues after injuries. Here, we provide insight into a mechanism of restorative patterning that repairs tissues after wounding. Laser-assisted elimination of different cells in Arabidopsis root combined with live-imaging tracking during vertical growth allowed analysis of the regeneration processes in vivo. Specifically, the cells adjacent to the inner side of the injury re-activated their stem cell transcriptional programs. They accelerated their progression through cell cycle, coordinately changed the cell division orientation, and ultimately acquired de novo the correct cell fates to replace missing cells. These observations highlight existence of unknown intercellular positional signaling and demonstrate the capability of specified cells to re-acquire stem cell programs as a crucial part of the plant-specific mechanism of wound healing."}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"2019_Cell_Marhava.pdf","content_type":"application/pdf","file_size":10272032,"creator":"dernst","relation":"main_file","file_id":"6411","checksum":"4ceba04a96a74f5092ec3ce2c579a0c7","date_created":"2019-05-13T06:12:45Z","date_updated":"2020-07-14T12:47:28Z"}],"oa_version":"Published Version","intvolume":" 177","status":"public","title":"Re-activation of stem cell pathways for pattern restoration in plant wound healing","ddc":["570"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6351"},{"_id":"6943","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 52","title":"Targeted cell ablation-based insights into wound healing and restorative patterning","status":"public","ddc":["580"],"oa_version":"Published Version","file":[{"checksum":"d6fd68a6e965f1efe3f0bf2d2070a616","date_created":"2019-10-14T14:48:21Z","date_updated":"2020-07-14T12:47:45Z","file_id":"6946","relation":"main_file","creator":"dernst","file_size":1659288,"content_type":"application/pdf","access_level":"open_access","file_name":"2019_CurrentOpinionPlant_Hoermayer.pdf"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Plants as sessile organisms are constantly under attack by herbivores, rough environmental situations, or mechanical pressure. These challenges often lead to the induction of wounds or destruction of already specified and developed tissues. Additionally, wounding makes plants vulnerable to invasion by pathogens, which is why wound signalling often triggers specific defence responses. To stay competitive or, eventually, survive under these circumstances, plants need to regenerate efficiently, which in rigid, tissue migration-incompatible plant tissues requires post-embryonic patterning and organogenesis. Now, several studies used laser-assisted single cell ablation in the Arabidopsis root tip as a minimal wounding proxy. Here, we discuss their findings and put them into context of a broader spectrum of wound signalling, pathogen responses and tissue as well as organ regeneration."}],"citation":{"apa":"Hörmayer, L., & Friml, J. (2019). Targeted cell ablation-based insights into wound healing and restorative patterning. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2019.08.006","ieee":"L. Hörmayer and J. Friml, “Targeted cell ablation-based insights into wound healing and restorative patterning,” Current Opinion in Plant Biology, vol. 52. Elsevier, pp. 124–130, 2019.","ista":"Hörmayer L, Friml J. 2019. Targeted cell ablation-based insights into wound healing and restorative patterning. Current Opinion in Plant Biology. 52, 124–130.","ama":"Hörmayer L, Friml J. Targeted cell ablation-based insights into wound healing and restorative patterning. Current Opinion in Plant Biology. 2019;52:124-130. doi:10.1016/j.pbi.2019.08.006","chicago":"Hörmayer, Lukas, and Jiří Friml. “Targeted Cell Ablation-Based Insights into Wound Healing and Restorative Patterning.” Current Opinion in Plant Biology. Elsevier, 2019. https://doi.org/10.1016/j.pbi.2019.08.006.","short":"L. Hörmayer, J. Friml, Current Opinion in Plant Biology 52 (2019) 124–130.","mla":"Hörmayer, Lukas, and Jiří Friml. “Targeted Cell Ablation-Based Insights into Wound Healing and Restorative Patterning.” Current Opinion in Plant Biology, vol. 52, Elsevier, 2019, pp. 124–30, doi:10.1016/j.pbi.2019.08.006."},"publication":"Current Opinion in Plant Biology","page":"124-130","article_type":"original","date_published":"2019-12-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","pmid":1,"year":"2019","publisher":"Elsevier","department":[{"_id":"JiFr"}],"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9992"}]},"author":[{"full_name":"Hörmayer, Lukas","first_name":"Lukas","last_name":"Hörmayer","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8295-2926"},{"first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"volume":52,"date_created":"2019-10-14T07:00:24Z","date_updated":"2024-03-28T23:30:10Z","ec_funded":1,"file_date_updated":"2020-07-14T12:47:45Z","external_id":{"pmid":["31585333"],"isi":["000502890600017"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"doi":"10.1016/j.pbi.2019.08.006","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1369-5266"]},"month":"12"},{"file":[{"relation":"main_file","file_id":"7448","checksum":"f3e90056a49f09b205b1c4f8c739ffd1","date_created":"2020-02-04T10:48:36Z","date_updated":"2020-07-14T12:47:57Z","access_level":"open_access","file_name":"2019_iScience_Tabata.pdf","content_type":"application/pdf","file_size":7197776,"creator":"dernst"}],"oa_version":"Published Version","intvolume":" 22","ddc":["570"],"title":"Electron microscopic detection of single membrane proteins by a specific chemical labeling","status":"public","_id":"7391","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"12","abstract":[{"lang":"eng","text":"Electron microscopy (EM) is a technology that enables visualization of single proteins at a nanometer resolution. However, current protein analysis by EM mainly relies on immunolabeling with gold-particle-conjugated antibodies, which is compromised by large size of antibody, precluding precise detection of protein location in biological samples. Here, we develop a specific chemical labeling method for EM detection of proteins at single-molecular level. Rational design of α-helical peptide tag and probe structure provided a complementary reaction pair that enabled specific cysteine conjugation of the tag. The developed chemical labeling with gold-nanoparticle-conjugated probe showed significantly higher labeling efficiency and detectability of high-density clusters of tag-fused G protein-coupled receptors in freeze-fracture replicas compared with immunogold labeling. Furthermore, in ultrathin sections, the spatial resolution of the chemical labeling was significantly higher than that of antibody-mediated labeling. These results demonstrate substantial advantages of the chemical labeling approach for single protein visualization by EM."}],"type":"journal_article","date_published":"2019-12-20T00:00:00Z","page":"256-268","article_type":"original","citation":{"ama":"Tabata S, Jevtic M, Kurashige N, et al. Electron microscopic detection of single membrane proteins by a specific chemical labeling. iScience. 2019;22(12):256-268. doi:10.1016/j.isci.2019.11.025","ista":"Tabata S, Jevtic M, Kurashige N, Fuchida H, Kido M, Tani K, Zenmyo N, Uchinomiya S, Harada H, Itakura M, Hamachi I, Shigemoto R, Ojida A. 2019. Electron microscopic detection of single membrane proteins by a specific chemical labeling. iScience. 22(12), 256–268.","apa":"Tabata, S., Jevtic, M., Kurashige, N., Fuchida, H., Kido, M., Tani, K., … Ojida, A. (2019). Electron microscopic detection of single membrane proteins by a specific chemical labeling. IScience. Elsevier. https://doi.org/10.1016/j.isci.2019.11.025","ieee":"S. Tabata et al., “Electron microscopic detection of single membrane proteins by a specific chemical labeling,” iScience, vol. 22, no. 12. Elsevier, pp. 256–268, 2019.","mla":"Tabata, Shigekazu, et al. “Electron Microscopic Detection of Single Membrane Proteins by a Specific Chemical Labeling.” IScience, vol. 22, no. 12, Elsevier, 2019, pp. 256–68, doi:10.1016/j.isci.2019.11.025.","short":"S. Tabata, M. Jevtic, N. Kurashige, H. Fuchida, M. Kido, K. Tani, N. Zenmyo, S. Uchinomiya, H. Harada, M. Itakura, I. Hamachi, R. Shigemoto, A. Ojida, IScience 22 (2019) 256–268.","chicago":"Tabata, Shigekazu, Marijo Jevtic, Nobutaka Kurashige, Hirokazu Fuchida, Munetsugu Kido, Kazushi Tani, Naoki Zenmyo, et al. “Electron Microscopic Detection of Single Membrane Proteins by a Specific Chemical Labeling.” IScience. Elsevier, 2019. https://doi.org/10.1016/j.isci.2019.11.025."},"publication":"iScience","has_accepted_license":"1","article_processing_charge":"No","day":"20","scopus_import":"1","volume":22,"date_updated":"2024-03-28T23:30:12Z","date_created":"2020-01-29T15:56:56Z","related_material":{"record":[{"id":"11393","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Tabata, Shigekazu","id":"4427179E-F248-11E8-B48F-1D18A9856A87","last_name":"Tabata","first_name":"Shigekazu"},{"full_name":"Jevtic, Marijo","last_name":"Jevtic","first_name":"Marijo","id":"4BE3BC94-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kurashige, Nobutaka","last_name":"Kurashige","first_name":"Nobutaka"},{"full_name":"Fuchida, Hirokazu","first_name":"Hirokazu","last_name":"Fuchida"},{"last_name":"Kido","first_name":"Munetsugu","full_name":"Kido, Munetsugu"},{"full_name":"Tani, Kazushi","last_name":"Tani","first_name":"Kazushi"},{"last_name":"Zenmyo","first_name":"Naoki","full_name":"Zenmyo, Naoki"},{"full_name":"Uchinomiya, Shohei","last_name":"Uchinomiya","first_name":"Shohei"},{"full_name":"Harada, Harumi","first_name":"Harumi","last_name":"Harada","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7429-7896"},{"full_name":"Itakura, Makoto","first_name":"Makoto","last_name":"Itakura"},{"last_name":"Hamachi","first_name":"Itaru","full_name":"Hamachi, Itaru"},{"last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"},{"last_name":"Ojida","first_name":"Akio","full_name":"Ojida, Akio"}],"department":[{"_id":"RySh"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"year":"2019","ec_funded":1,"file_date_updated":"2020-07-14T12:47:57Z","language":[{"iso":"eng"}],"doi":"10.1016/j.isci.2019.11.025","project":[{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","grant_number":"694539"},{"call_identifier":"H2020","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","_id":"25CBA828-B435-11E9-9278-68D0E5697425","grant_number":"720270"}],"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"},"external_id":{"isi":[":000504652000020"],"pmid":["31786521"]},"publication_identifier":{"issn":["2589-0042"]},"month":"12"},{"type":"journal_article","abstract":[{"text":"Proton-translocating transhydrogenase (also known as nicotinamide nucleotide transhydrogenase (NNT)) is found in the plasma membranes of bacteria and the inner mitochondrial membranes of eukaryotes. NNT catalyses the transfer of a hydride between NADH and NADP+, coupled to the translocation of one proton across the membrane. Its main physiological function is the generation of NADPH, which is a substrate in anabolic reactions and a regulator of oxidative status; however, NNT may also fine-tune the Krebs cycle1,2. NNT deficiency causes familial glucocorticoid deficiency in humans and metabolic abnormalities in mice, similar to those observed in type II diabetes3,4. The catalytic mechanism of NNT has been proposed to involve a rotation of around 180° of the entire NADP(H)-binding domain that alternately participates in hydride transfer and proton-channel gating. However, owing to the lack of high-resolution structures of intact NNT, the details of this process remain unclear5,6. Here we present the cryo-electron microscopy structure of intact mammalian NNT in different conformational states. We show how the NADP(H)-binding domain opens the proton channel to the opposite sides of the membrane, and we provide structures of these two states. We also describe the catalytically important interfaces and linkers between the membrane and the soluble domains and their roles in nucleotide exchange. These structures enable us to propose a revised mechanism for a coupling process in NNT that is consistent with a large body of previous biochemical work. Our results are relevant to the development of currently unavailable NNT inhibitors, which may have therapeutic potential in ischaemia reperfusion injury, metabolic syndrome and some cancers7,8,9.","lang":"eng"}],"issue":"7773","_id":"6848","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Structure and mechanism of mitochondrial proton-translocating transhydrogenase","status":"public","ddc":["572"],"intvolume":" 573","file":[{"file_id":"8821","relation":"main_file","success":1,"checksum":"52728cda5210a3e9b74cc204e8aed3d5","date_created":"2020-11-26T16:33:44Z","date_updated":"2020-11-26T16:33:44Z","access_level":"open_access","file_name":"Manuscript_final_acc_withFigs_SI_opt_red.pdf","creator":"lsazanov","file_size":3066206,"content_type":"application/pdf"}],"oa_version":"Submitted Version","scopus_import":"1","day":"12","article_processing_charge":"No","has_accepted_license":"1","publication":"Nature","citation":{"ama":"Kampjut D, Sazanov LA. Structure and mechanism of mitochondrial proton-translocating transhydrogenase. Nature. 2019;573(7773):291–295. doi:10.1038/s41586-019-1519-2","ista":"Kampjut D, Sazanov LA. 2019. Structure and mechanism of mitochondrial proton-translocating transhydrogenase. Nature. 573(7773), 291–295.","apa":"Kampjut, D., & Sazanov, L. A. (2019). Structure and mechanism of mitochondrial proton-translocating transhydrogenase. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1519-2","ieee":"D. Kampjut and L. A. Sazanov, “Structure and mechanism of mitochondrial proton-translocating transhydrogenase,” Nature, vol. 573, no. 7773. Springer Nature, pp. 291–295, 2019.","mla":"Kampjut, Domen, and Leonid A. Sazanov. “Structure and Mechanism of Mitochondrial Proton-Translocating Transhydrogenase.” Nature, vol. 573, no. 7773, Springer Nature, 2019, pp. 291–295, doi:10.1038/s41586-019-1519-2.","short":"D. Kampjut, L.A. Sazanov, Nature 573 (2019) 291–295.","chicago":"Kampjut, Domen, and Leonid A Sazanov. “Structure and Mechanism of Mitochondrial Proton-Translocating Transhydrogenase.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1519-2."},"article_type":"letter_note","page":"291–295","date_published":"2019-09-12T00:00:00Z","file_date_updated":"2020-11-26T16:33:44Z","ec_funded":1,"acknowledgement":" We thank R. Thompson, G. Effantin and V.-V. Hodirnau for their assistance with collecting NADP+, NADPH and apo datasets, respectively. Data processing was performed at the IST high-performance computing cluster.\r\nThis project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement no. 665385.","year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"LeSa"}],"publisher":"Springer Nature","author":[{"full_name":"Kampjut, Domen","id":"37233050-F248-11E8-B48F-1D18A9856A87","last_name":"Kampjut","first_name":"Domen"},{"full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","first_name":"Leonid A","last_name":"Sazanov"}],"related_material":{"record":[{"id":"8340","relation":"dissertation_contains","status":"public"}],"link":[{"description":"News on IST Website","relation":"press_release","url":"https://ist.ac.at/en/news/high-end-microscopy-reveals-structure-and-function-of-crucial-metabolic-enzyme/"}]},"date_updated":"2024-03-28T23:30:15Z","date_created":"2019-09-04T06:21:41Z","volume":573,"month":"09","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"oa":1,"external_id":{"pmid":["31462775"],"isi":["000485415400061"]},"isi":1,"quality_controlled":"1","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"}],"doi":"10.1038/s41586-019-1519-2","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}]},{"oa":1,"external_id":{"isi":["000462738000034"]},"quality_controlled":"1","isi":1,"project":[{"name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","call_identifier":"FP7","grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"doi":"10.1126/science.aav4837","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"year":"2019","publication_status":"published","publisher":"American Association for the Advancement of Science","department":[{"_id":"JoCs"}],"author":[{"first_name":"Charlotte N.","last_name":"Boccara","id":"3FC06552-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7237-5109","full_name":"Boccara, Charlotte N."},{"orcid":"0000-0001-8849-6570","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","last_name":"Nardin","first_name":"Michele","full_name":"Nardin, Michele"},{"full_name":"Stella, Federico","last_name":"Stella","first_name":"Federico","orcid":"0000-0001-9439-3148","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87"},{"full_name":"O'Neill, Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87","first_name":"Joseph","last_name":"O'Neill"},{"full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"popular_science","id":"6062"},{"relation":"dissertation_contains","status":"public","id":"11932"}],"link":[{"url":"https://ist.ac.at/en/news/grid-cells-create-treasure-map-in-rat-brain/","description":"News on IST Homepage","relation":"press_release"}]},"date_updated":"2024-03-28T23:30:16Z","date_created":"2019-04-04T08:39:30Z","volume":363,"file_date_updated":"2020-07-14T12:47:23Z","ec_funded":1,"publication":"Science","citation":{"ieee":"C. N. Boccara, M. Nardin, F. Stella, J. O’Neill, and J. L. Csicsvari, “The entorhinal cognitive map is attracted to goals,” Science, vol. 363, no. 6434. American Association for the Advancement of Science, pp. 1443–1447, 2019.","apa":"Boccara, C. N., Nardin, M., Stella, F., O’Neill, J., & Csicsvari, J. L. (2019). The entorhinal cognitive map is attracted to goals. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aav4837","ista":"Boccara CN, Nardin M, Stella F, O’Neill J, Csicsvari JL. 2019. The entorhinal cognitive map is attracted to goals. Science. 363(6434), 1443–1447.","ama":"Boccara CN, Nardin M, Stella F, O’Neill J, Csicsvari JL. The entorhinal cognitive map is attracted to goals. Science. 2019;363(6434):1443-1447. doi:10.1126/science.aav4837","chicago":"Boccara, Charlotte N., Michele Nardin, Federico Stella, Joseph O’Neill, and Jozsef L Csicsvari. “The Entorhinal Cognitive Map Is Attracted to Goals.” Science. American Association for the Advancement of Science, 2019. https://doi.org/10.1126/science.aav4837.","short":"C.N. Boccara, M. Nardin, F. Stella, J. O’Neill, J.L. Csicsvari, Science 363 (2019) 1443–1447.","mla":"Boccara, Charlotte N., et al. “The Entorhinal Cognitive Map Is Attracted to Goals.” Science, vol. 363, no. 6434, American Association for the Advancement of Science, 2019, pp. 1443–47, doi:10.1126/science.aav4837."},"article_type":"original","page":"1443-1447","date_published":"2019-03-29T00:00:00Z","scopus_import":"1","day":"29","article_processing_charge":"No","has_accepted_license":"1","_id":"6194","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["570"],"status":"public","title":"The entorhinal cognitive map is attracted to goals","intvolume":" 363","file":[{"relation":"main_file","file_id":"7826","date_created":"2020-05-14T09:11:10Z","date_updated":"2020-07-14T12:47:23Z","checksum":"5e6b16742cde10a560cfaf2130764da1","file_name":"2019_Science_Boccara.pdf","access_level":"open_access","content_type":"application/pdf","file_size":9045923,"creator":"dernst"}],"oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"Grid cells with their rigid hexagonal firing fields are thought to provide an invariant metric to the hippocampal cognitive map, yet environmental geometrical features have recently been shown to distort the grid structure. Given that the hippocampal role goes beyond space, we tested the influence of nonspatial information on the grid organization. We trained rats to daily learn three new reward locations on a cheeseboard maze while recording from the medial entorhinal cortex and the hippocampal CA1 region. Many grid fields moved toward goal location, leading to long-lasting deformations of the entorhinal map. Therefore, distortions in the grid structure contribute to goal representation during both learning and recall, which demonstrates that grid cells participate in mnemonic coding and do not merely provide a simple metric of space."}],"issue":"6434"},{"file_date_updated":"2020-07-14T12:47:50Z","date_updated":"2024-03-28T23:30:21Z","date_created":"2019-11-27T09:07:14Z","related_material":{"record":[{"id":"6266","relation":"old_edition","status":"public"}]},"author":[{"full_name":"Mckenzie, Catherine","last_name":"Mckenzie","first_name":"Catherine","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"HaJa"}],"publication_status":"published","year":"2019","publication_identifier":{"issn":["2663-337X"]},"month":"06","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","first_name":"Harald L"}],"doi":"10.15479/at:ista:7132","oa":1,"abstract":[{"lang":"eng","text":"A major challenge in neuroscience research is to dissect the circuits that orchestrate behavior in health and disease. Proteins from a wide range of non-mammalian species, such as microbial opsins, have been successfully transplanted to specific neuronal targets to override their natural communication patterns. The goal of our work is to manipulate synaptic communication in a manner that closely incorporates the functional intricacies of synapses by preserving temporal encoding (i.e. the firing pattern of the presynaptic neuron) and connectivity (i.e. target specific synapses rather than specific neurons). Our strategy to achieve this goal builds on the use of non-mammalian transplants to create a synthetic synapse. The mode of modulation comes from pre-synaptic uptake of a synthetic neurotransmitter (SN) into synaptic vesicles by means of a genetically targeted transporter selective for the SN. Upon natural vesicular release, exposure of the SN to the synaptic cleft will modify the post-synaptic potential through an orthogonal ligand gated ion channel. To achieve this goal we have functionally characterized a mixed cationic methionine-gated ion channel from Arabidopsis thaliana, designed a method to functionally characterize a synthetic transporter in isolated synaptic vesicles without the need for transgenic animals, identified and extracted multiple prokaryotic uptake systems that are substrate specific for methionine (Met), and established a primary/cell line co-culture system that would allow future combinatorial testing of this orthogonal transmitter-transporter-channel trifecta.\r\nSynthetic synapses will provide a unique opportunity to manipulate synaptic communication while maintaining the electrophysiological integrity of the pre-synaptic cell. In this way, information may be preserved that was generated in upstream circuits and that could be essential for concerted function and information processing."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"file_size":5054633,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"dernst","file_name":"McKenzie PhD Thesis August 2018 - Corrected Final.docx","access_level":"closed","date_updated":"2020-07-14T12:47:50Z","date_created":"2019-11-27T09:06:10Z","checksum":"34d0fe0f6e0af97b5937205a3e350423","relation":"source_file","file_id":"7133"},{"access_level":"open_access","file_name":"McKenzie PhD Thesis August 2018 - Corrected Final.pdf","creator":"dernst","file_size":3231837,"content_type":"application/pdf","file_id":"7134","relation":"main_file","checksum":"140dfb5e3df7edca34f4b6fcc55d876f","date_updated":"2020-07-14T12:47:50Z","date_created":"2019-11-27T09:06:10Z"}],"oa_version":"Published Version","title":"Design and characterization of methods and biological components to realize synthetic neurotransmission","status":"public","ddc":["571","573"],"_id":"7132","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","article_processing_charge":"No","day":"27","date_published":"2019-06-27T00:00:00Z","page":"95","citation":{"chicago":"Mckenzie, Catherine. “Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:7132.","mla":"Mckenzie, Catherine. Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission. Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:7132.","short":"C. Mckenzie, Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission, Institute of Science and Technology Austria, 2019.","ista":"Mckenzie C. 2019. Design and characterization of methods and biological components to realize synthetic neurotransmission. Institute of Science and Technology Austria.","ieee":"C. Mckenzie, “Design and characterization of methods and biological components to realize synthetic neurotransmission,” Institute of Science and Technology Austria, 2019.","apa":"Mckenzie, C. (2019). Design and characterization of methods and biological components to realize synthetic neurotransmission. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:7132","ama":"Mckenzie C. Design and characterization of methods and biological components to realize synthetic neurotransmission. 2019. doi:10.15479/at:ista:7132"}},{"article_type":"original","page":"802-816","publication":"Hippocampus","citation":{"ama":"Käfer K, Malagon-Vina H, Dickerson D, et al. Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization. Hippocampus. 2019;29(9):802-816. doi:10.1002/hipo.23076","ista":"Käfer K, Malagon-Vina H, Dickerson D, O’Neill J, Trossbach SV, Korth C, Csicsvari JL. 2019. Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization. Hippocampus. 29(9), 802–816.","apa":"Käfer, K., Malagon-Vina, H., Dickerson, D., O’Neill, J., Trossbach, S. V., Korth, C., & Csicsvari, J. L. (2019). Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization. Hippocampus. Wiley. https://doi.org/10.1002/hipo.23076","ieee":"K. Käfer et al., “Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization,” Hippocampus, vol. 29, no. 9. Wiley, pp. 802–816, 2019.","mla":"Käfer, Karola, et al. “Disrupted-in-Schizophrenia 1 Overexpression Disrupts Hippocampal Coding and Oscillatory Synchronization.” Hippocampus, vol. 29, no. 9, Wiley, 2019, pp. 802–16, doi:10.1002/hipo.23076.","short":"K. Käfer, H. Malagon-Vina, D. Dickerson, J. O’Neill, S.V. Trossbach, C. Korth, J.L. Csicsvari, Hippocampus 29 (2019) 802–816.","chicago":"Käfer, Karola, Hugo Malagon-Vina, Desiree Dickerson, Joseph O’Neill, Svenja V. Trossbach, Carsten Korth, and Jozsef L Csicsvari. “Disrupted-in-Schizophrenia 1 Overexpression Disrupts Hippocampal Coding and Oscillatory Synchronization.” Hippocampus. Wiley, 2019. https://doi.org/10.1002/hipo.23076."},"date_published":"2019-09-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","status":"public","title":"Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization","ddc":["570"],"intvolume":" 29","_id":"5949","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5950","date_created":"2019-02-11T10:42:51Z","date_updated":"2020-07-14T12:47:13Z","checksum":"5e8de271ca04aef92a5de42d6aac4404","file_name":"2019_Hippocampus_Kaefer.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2132893,"creator":"dernst"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Aberrant proteostasis of protein aggregation may lead to behavior disorders including chronic mental illnesses (CMI). Furthermore, the neuronal activity alterations that underlie CMI are not well understood. We recorded the local field potential and single-unit activity of the hippocampal CA1 region in vivo in rats transgenically overexpressing the Disrupted-in-Schizophrenia 1 (DISC1) gene (tgDISC1), modeling sporadic CMI. These tgDISC1 rats have previously been shown to exhibit DISC1 protein aggregation, disturbances in the dopaminergic system and attention-related deficits. Recordings were performed during exploration of familiar and novel open field environments and during sleep, allowing investigation of neuronal abnormalities in unconstrained behavior. Compared to controls, tgDISC1 place cells exhibited smaller place fields and decreased speed-modulation of their firing rates, demonstrating altered spatial coding and deficits in encoding location-independent sensory inputs. Oscillation analyses showed that tgDISC1 pyramidal neurons had higher theta phase locking strength during novelty, limiting their phase coding ability. However, their mean theta phases were more variable at the population level, reducing oscillatory network synchronization. Finally, tgDISC1 pyramidal neurons showed a lack of novelty-induced shift in their preferred theta and gamma firing phases, indicating deficits in coding of novel environments with oscillatory firing. By combining single cell and neuronal population analyses, we link DISC1 protein pathology with abnormal hippocampal neural coding and network synchrony, and thereby gain a more comprehensive understanding of CMI mechanisms."}],"issue":"9","quality_controlled":"1","isi":1,"project":[{"_id":"257BBB4C-B435-11E9-9278-68D0E5697425","grant_number":"607616","name":"Inter-and intracellular signalling in schizophrenia","call_identifier":"FP7"}],"external_id":{"isi":["000480635400003"]},"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,"language":[{"iso":"eng"}],"doi":"10.1002/hipo.23076","month":"09","publication_status":"published","department":[{"_id":"JoCs"}],"publisher":"Wiley","year":"2019","date_updated":"2024-03-28T23:30:22Z","date_created":"2019-02-10T22:59:18Z","volume":29,"author":[{"last_name":"Käfer","first_name":"Karola","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","full_name":"Käfer, Karola"},{"full_name":"Malagon-Vina, Hugo","last_name":"Malagon-Vina","first_name":"Hugo"},{"id":"444EB89E-F248-11E8-B48F-1D18A9856A87","last_name":"Dickerson","first_name":"Desiree","full_name":"Dickerson, Desiree"},{"full_name":"O'Neill, Joseph","last_name":"O'Neill","first_name":"Joseph"},{"last_name":"Trossbach","first_name":"Svenja V.","full_name":"Trossbach, Svenja V."},{"first_name":"Carsten","last_name":"Korth","full_name":"Korth, Carsten"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L"}],"related_material":{"record":[{"id":"6825","relation":"dissertation_contains","status":"public"}]},"file_date_updated":"2020-07-14T12:47:13Z","ec_funded":1},{"day":"24","article_processing_charge":"No","has_accepted_license":"1","citation":{"ama":"Käfer K. The hippocampus and medial prefrontal cortex during flexible behavior. 2019. doi:10.15479/AT:ISTA:6825","ista":"Käfer K. 2019. The hippocampus and medial prefrontal cortex during flexible behavior. Institute of Science and Technology Austria.","apa":"Käfer, K. (2019). The hippocampus and medial prefrontal cortex during flexible behavior. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6825","ieee":"K. Käfer, “The hippocampus and medial prefrontal cortex during flexible behavior,” Institute of Science and Technology Austria, 2019.","mla":"Käfer, Karola. The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6825.","short":"K. Käfer, The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior, Institute of Science and Technology Austria, 2019.","chicago":"Käfer, Karola. “The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6825."},"page":"89","date_published":"2019-08-24T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"The solving of complex tasks requires the functions of more than one brain area and their interaction. Whilst spatial navigation and memory is dependent on the hippocampus, flexible behavior relies on the medial prefrontal cortex (mPFC). To further examine the roles of the hippocampus and mPFC, we recorded their neural activity during a task that depends on both of these brain regions.\r\nWith tetrodes, we recorded the extracellular activity of dorsal hippocampal CA1 (HPC) and mPFC neurons in Long-Evans rats performing a rule-switching task on the plus-maze. The plus-maze task had a spatial component since it required navigation along one of the two start arms and at the maze center a choice between one of the two goal arms. Which goal contained a reward depended on the rule currently in place. After an uncued rule change the animal had to abandon the old strategy and switch to the new rule, testing cognitive flexibility. Investigating the coordination of activity between the HPC and mPFC allows determination during which task stages their interaction is required. Additionally, comparing neural activity patterns in these two brain regions allows delineation of the specialized functions of the HPC and mPFC in this task. We analyzed neural activity in the HPC and mPFC in terms of oscillatory interactions, rule coding and replay.\r\nWe found that theta coherence between the HPC and mPFC is increased at the center and goals of the maze, both when the rule was stable or has changed. Similar results were found for locking of HPC and mPFC neurons to HPC theta oscillations. However, no differences in HPC-mPFC theta coordination were observed between the spatially- and cue-guided rule. Phase locking of HPC and mPFC neurons to HPC gamma oscillations was not modulated by\r\nmaze position or rule type. We found that the HPC coded for the two different rules with cofiring relationships between\r\ncell pairs. However, we could not find conclusive evidence for rule coding in the mPFC. Spatially-selective firing in the mPFC generalized between the two start and two goal arms. With Bayesian positional decoding, we found that the mPFC reactivated non-local positions during awake immobility periods. Replay of these non-local positions could represent entire behavioral trajectories resembling trajectory replay of the HPC. Furthermore, mPFC\r\ntrajectory-replay at the goal positively correlated with rule-switching performance. \r\nFinally, HPC and mPFC trajectory replay occurred independently of each other. These results show that the mPFC can replay ordered patterns of activity during awake immobility, possibly underlying its role in flexible behavior. "}],"_id":"6825","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"The hippocampus and medial prefrontal cortex during flexible behavior","status":"public","ddc":["570"],"file":[{"file_size":3205202,"content_type":"application/pdf","request_a_copy":0,"creator":"kkaefer","access_level":"open_access","file_name":"Thesis_Kaefer_PDFA.pdf","checksum":"2664420e332a33338568f4f3bfc59287","date_created":"2019-09-03T08:07:13Z","date_updated":"2020-09-06T22:30:03Z","relation":"main_file","file_id":"6846","embargo":"2020-09-05"},{"checksum":"9a154eab6f07aa590a3d2651dc0d926a","date_created":"2019-09-03T08:07:17Z","date_updated":"2020-09-15T22:30:05Z","relation":"main_file","file_id":"6847","file_size":2506835,"content_type":"application/zip","creator":"kkaefer","access_level":"closed","embargo_to":"open_access","file_name":"Thesis_Kaefer.zip"}],"oa_version":"Published Version","month":"08","publication_identifier":{"issn":["2663-337X"]},"oa":1,"doi":"10.15479/AT:ISTA:6825","supervisor":[{"first_name":"Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"file_date_updated":"2020-09-15T22:30:05Z","year":"2019","publication_status":"published","department":[{"_id":"JoCs"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Käfer, Karola","first_name":"Karola","last_name":"Käfer","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"5949"}]},"date_created":"2019-08-21T15:00:57Z","date_updated":"2023-09-07T13:01:42Z"},{"file":[{"access_level":"open_access","file_name":"2019_eLife_Castro.pdf","file_size":6748249,"content_type":"application/pdf","creator":"apreinsp","relation":"main_file","file_id":"6721","checksum":"fa0936fe58f0d9e3f8e75038570e5a17","date_created":"2019-07-29T07:41:18Z","date_updated":"2020-07-14T12:47:38Z"}],"oa_version":"Published Version","intvolume":" 8","status":"public","ddc":["576"],"title":"An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice","_id":"6713","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response."}],"type":"journal_article","date_published":"2019-06-06T00:00:00Z","citation":{"ama":"Castro JP, Yancoskie MN, Marchini M, et al. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. eLife. 2019;8. doi:10.7554/eLife.42014","ista":"Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. eLife. 8, e42014.","ieee":"J. P. Castro et al., “An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice,” eLife, vol. 8. eLife Sciences Publications, 2019.","apa":"Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L., Kučka, M., … Chan, Y. F. (2019). An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.42014","mla":"Castro, João Pl, et al. “An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” ELife, vol. 8, e42014, eLife Sciences Publications, 2019, doi:10.7554/eLife.42014.","short":"J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M. Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F. Chan, ELife 8 (2019).","chicago":"Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.42014."},"publication":"eLife","has_accepted_license":"1","article_processing_charge":"No","day":"06","scopus_import":"1","volume":8,"date_created":"2019-07-28T21:59:17Z","date_updated":"2024-03-28T23:30:23Z","related_material":{"record":[{"id":"9804","relation":"research_data","status":"public"},{"id":"11388","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Castro, João Pl","first_name":"João Pl","last_name":"Castro"},{"last_name":"Yancoskie","first_name":"Michelle N.","full_name":"Yancoskie, Michelle N."},{"full_name":"Marchini, Marta","last_name":"Marchini","first_name":"Marta"},{"full_name":"Belohlavy, Stefanie","orcid":"0000-0002-9849-498X","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","last_name":"Belohlavy","first_name":"Stefanie"},{"full_name":"Hiramatsu, Layla","last_name":"Hiramatsu","first_name":"Layla"},{"first_name":"Marek","last_name":"Kučka","full_name":"Kučka, Marek"},{"full_name":"Beluch, William H.","first_name":"William H.","last_name":"Beluch"},{"first_name":"Ronald","last_name":"Naumann","full_name":"Naumann, Ronald"},{"last_name":"Skuplik","first_name":"Isabella","full_name":"Skuplik, Isabella"},{"full_name":"Cobb, John","last_name":"Cobb","first_name":"John"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"first_name":"Campbell","last_name":"Rolian","full_name":"Rolian, Campbell"},{"first_name":"Yingguang Frank","last_name":"Chan","full_name":"Chan, Yingguang Frank"}],"department":[{"_id":"NiBa"}],"publisher":"eLife Sciences Publications","publication_status":"published","pmid":1,"year":"2019","file_date_updated":"2020-07-14T12:47:38Z","article_number":"e42014","language":[{"iso":"eng"}],"doi":"10.7554/eLife.42014","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"},"oa":1,"external_id":{"pmid":["31169497"],"isi":["000473588700001"]},"month":"06"},{"article_number":"1910.05841","type":"preprint","abstract":[{"lang":"eng","text":"We study double quantum dots in a Ge/SiGe heterostructure and test their maturity towards singlet-triplet ($S-T_0$) qubits. We demonstrate a large range of tunability, from two single quantum dots to a double quantum dot. We measure Pauli spin blockade and study the anisotropy of the $g$-factor. We use an adjacent quantum dot for sensing charge transitions in the double quantum dot at interest. In conclusion, Ge/SiGe possesses all ingredients necessary for building a singlet-triplet qubit."}],"ec_funded":1,"status":"public","title":"Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits","publication_status":"submitted","department":[{"_id":"GeKa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10065","acknowledgement":"We thank Matthias Brauns for helpful discussions and careful proofreading of the manuscript. This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 844511 and from the FWF project P30207. The research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA machine shop and the nanofabrication\r\nfacility.","year":"2019","date_created":"2021-10-01T12:14:51Z","date_updated":"2024-03-28T23:30:27Z","oa_version":"Preprint","author":[{"full_name":"Hofmann, Andrea C","last_name":"Hofmann","first_name":"Andrea C","id":"340F461A-F248-11E8-B48F-1D18A9856A87"},{"id":"4C473F58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7197-4801","first_name":"Daniel","last_name":"Jirovec","full_name":"Jirovec, Daniel"},{"last_name":"Borovkov","first_name":"Maxim","full_name":"Borovkov, Maxim"},{"orcid":"0000-0002-7370-5357","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Prieto Gonzalez","first_name":"Ivan","full_name":"Prieto Gonzalez, Ivan"},{"full_name":"Ballabio, Andrea","first_name":"Andrea","last_name":"Ballabio"},{"full_name":"Frigerio, Jacopo","first_name":"Jacopo","last_name":"Frigerio"},{"first_name":"Daniel","last_name":"Chrastina","full_name":"Chrastina, Daniel"},{"first_name":"Giovanni","last_name":"Isella","full_name":"Isella, Giovanni"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","first_name":"Georgios","last_name":"Katsaros","full_name":"Katsaros, Georgios"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10058"}]},"day":"13","month":"10","article_processing_charge":"No","project":[{"_id":"26A151DA-B435-11E9-9278-68D0E5697425","grant_number":"844511","name":"Majorana bound states in Ge/SiGe heterostructures","call_identifier":"H2020"},{"call_identifier":"FWF","name":"Hole spin orbit qubits in Ge quantum wells","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","grant_number":"P30207"}],"publication":"arXiv","main_file_link":[{"url":"https://arxiv.org/abs/1910.05841","open_access":"1"}],"oa":1,"citation":{"mla":"Hofmann, Andrea C., et al. “Assessing the Potential of Ge/SiGe Quantum Dots as Hosts for Singlet-Triplet Qubits.” ArXiv, 1910.05841, doi:10.48550/arXiv.1910.05841.","short":"A.C. Hofmann, D. Jirovec, M. Borovkov, I. Prieto Gonzalez, A. Ballabio, J. Frigerio, D. Chrastina, G. Isella, G. Katsaros, ArXiv (n.d.).","chicago":"Hofmann, Andrea C, Daniel Jirovec, Maxim Borovkov, Ivan Prieto Gonzalez, Andrea Ballabio, Jacopo Frigerio, Daniel Chrastina, Giovanni Isella, and Georgios Katsaros. “Assessing the Potential of Ge/SiGe Quantum Dots as Hosts for Singlet-Triplet Qubits.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1910.05841.","ama":"Hofmann AC, Jirovec D, Borovkov M, et al. Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits. arXiv. doi:10.48550/arXiv.1910.05841","ista":"Hofmann AC, Jirovec D, Borovkov M, Prieto Gonzalez I, Ballabio A, Frigerio J, Chrastina D, Isella G, Katsaros G. Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits. arXiv, 1910.05841.","apa":"Hofmann, A. C., Jirovec, D., Borovkov, M., Prieto Gonzalez, I., Ballabio, A., Frigerio, J., … Katsaros, G. (n.d.). Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits. arXiv. https://doi.org/10.48550/arXiv.1910.05841","ieee":"A. C. Hofmann et al., “Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits,” arXiv. ."},"external_id":{"arxiv":["1910.05841"]},"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"doi":"10.48550/arXiv.1910.05841","date_published":"2019-10-13T00:00:00Z"},{"publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"DaSi"}],"year":"2019","date_created":"2019-03-28T13:37:45Z","date_updated":"2024-03-28T23:30:30Z","volume":8,"author":[{"full_name":"Valosková, Katarina","last_name":"Valosková","first_name":"Katarina","id":"46F146FC-F248-11E8-B48F-1D18A9856A87"},{"id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87","last_name":"Biebl","first_name":"Julia","full_name":"Biebl, Julia"},{"full_name":"Roblek, Marko","id":"3047D808-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9588-1389","first_name":"Marko","last_name":"Roblek"},{"full_name":"Emtenani, Shamsi","id":"49D32318-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6981-6938","first_name":"Shamsi","last_name":"Emtenani"},{"orcid":"0000-0002-1819-198X","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","last_name":"György","first_name":"Attila","full_name":"György, Attila"},{"last_name":"Misova","first_name":"Michaela","orcid":"0000-0003-2427-6856","id":"495A3C32-F248-11E8-B48F-1D18A9856A87","full_name":"Misova, Michaela"},{"full_name":"Ratheesh, Aparna","orcid":"0000-0001-7190-0776","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87","last_name":"Ratheesh","first_name":"Aparna"},{"full_name":"Rodrigues, Patricia","last_name":"Rodrigues","first_name":"Patricia","id":"2CE4065A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Shkarina, Katerina","last_name":"Shkarina","first_name":"Katerina"},{"last_name":"Larsen","first_name":"Ida Signe Bohse","full_name":"Larsen, Ida Signe Bohse"},{"full_name":"Vakhrushev, Sergey Y","first_name":"Sergey Y","last_name":"Vakhrushev"},{"first_name":"Henrik","last_name":"Clausen","full_name":"Clausen, Henrik"},{"full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","first_name":"Daria E","last_name":"Siekhaus"}],"related_material":{"record":[{"id":"6530","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"8983"},{"status":"public","relation":"dissertation_contains","id":"6546"}],"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-gene-potentially-involved-in-metastasis-identified/"}]},"article_number":"e41801","file_date_updated":"2020-07-14T12:47:23Z","ec_funded":1,"quality_controlled":"1","isi":1,"project":[{"name":"Examination of the role of a MFS transporter in the migration of Drosophila immune cells","_id":"253CDE40-B435-11E9-9278-68D0E5697425","grant_number":"24283"},{"grant_number":"P29638","_id":"253B6E48-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The role of Drosophila TNF alpha in immune cell invasion"},{"grant_number":"334077","_id":"2536F660-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Investigating the role of transporters in invasive migration through junctions"},{"name":"Breaking barriers: Investigating the junctional and mechanobiological changes underlying the ability of Drosophila immune cells to invade an epithelium","call_identifier":"FP7","_id":"25388084-B435-11E9-9278-68D0E5697425","grant_number":"329540"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000462530200001"]},"acknowledged_ssus":[{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"doi":"10.7554/elife.41801","month":"03","publication_identifier":{"issn":["2050-084X"]},"ddc":["570"],"status":"public","title":"A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion","intvolume":" 8","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6187","file":[{"file_id":"6188","relation":"main_file","checksum":"cc0d1a512559d52e7e7cb0e9b9854b40","date_updated":"2020-07-14T12:47:23Z","date_created":"2019-03-28T14:00:41Z","access_level":"open_access","file_name":"2019_eLife_Valoskova.pdf","creator":"dernst","file_size":4496017,"content_type":"application/pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Aberrant display of the truncated core1 O-glycan T-antigen is a common feature of human cancer cells that correlates with metastasis. Here we show that T-antigen in Drosophila melanogaster macrophages is involved in their developmentally programmed tissue invasion. Higher macrophage T-antigen levels require an atypical major facilitator superfamily (MFS) member that we named Minerva which enables macrophage dissemination and invasion. We characterize for the first time the T and Tn glycoform O-glycoproteome of the Drosophila melanogaster embryo, and determine that Minerva increases the presence of T-antigen on proteins in pathways previously linked to cancer, most strongly on the sulfhydryl oxidase Qsox1 which we show is required for macrophage tissue entry. Minerva’s vertebrate ortholog, MFSD1, rescues the minerva mutant’s migration and T-antigen glycosylation defects. We thus identify a key conserved regulator that orchestrates O-glycosylation on a protein subset to activate a program governing migration steps important for both development and cancer metastasis.","lang":"eng"}],"publication":"eLife","citation":{"mla":"Valosková, Katarina, et al. “A Conserved Major Facilitator Superfamily Member Orchestrates a Subset of O-Glycosylation to Aid Macrophage Tissue Invasion.” ELife, vol. 8, e41801, eLife Sciences Publications, 2019, doi:10.7554/elife.41801.","short":"K. Valosková, J. Bicher, M. Roblek, S. Emtenani, A. György, M. Misova, A. Ratheesh, P. Rodrigues, K. Shkarina, I.S.B. Larsen, S.Y. Vakhrushev, H. Clausen, D.E. Siekhaus, ELife 8 (2019).","chicago":"Valosková, Katarina, Julia Bicher, Marko Roblek, Shamsi Emtenani, Attila György, Michaela Misova, Aparna Ratheesh, et al. “A Conserved Major Facilitator Superfamily Member Orchestrates a Subset of O-Glycosylation to Aid Macrophage Tissue Invasion.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/elife.41801.","ama":"Valosková K, Bicher J, Roblek M, et al. A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion. eLife. 2019;8. doi:10.7554/elife.41801","ista":"Valosková K, Bicher J, Roblek M, Emtenani S, György A, Misova M, Ratheesh A, Rodrigues P, Shkarina K, Larsen ISB, Vakhrushev SY, Clausen H, Siekhaus DE. 2019. A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion. eLife. 8, e41801.","apa":"Valosková, K., Bicher, J., Roblek, M., Emtenani, S., György, A., Misova, M., … Siekhaus, D. E. (2019). A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.41801","ieee":"K. Valosková et al., “A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion,” eLife, vol. 8. eLife Sciences Publications, 2019."},"date_published":"2019-03-26T00:00:00Z","scopus_import":"1","day":"26","has_accepted_license":"1","article_processing_charge":"No"},{"project":[{"grant_number":"24283","_id":"253CDE40-B435-11E9-9278-68D0E5697425","name":"Examination of the role of a MFS transporter in the migration of Drosophila immune cells"}],"oa":1,"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"}],"supervisor":[{"full_name":"Siekhaus, Daria E","first_name":"Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:6546","month":"06","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"DaSi"}],"year":"2019","date_created":"2019-06-07T12:49:19Z","date_updated":"2023-09-19T10:15:54Z","author":[{"last_name":"Valosková","first_name":"Katarina","id":"46F146FC-F248-11E8-B48F-1D18A9856A87","full_name":"Valosková, Katarina"}],"related_material":{"record":[{"id":"6187","relation":"part_of_dissertation","status":"public"},{"id":"544","status":"public","relation":"part_of_dissertation"}]},"file_date_updated":"2021-02-11T11:17:14Z","page":"141","citation":{"ieee":"K. Valosková, “The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration,” Institute of Science and Technology Austria, 2019.","apa":"Valosková, K. (2019). The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6546","ista":"Valosková K. 2019. The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration. Institute of Science and Technology Austria.","ama":"Valosková K. The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration. 2019. doi:10.15479/AT:ISTA:6546","chicago":"Valosková, Katarina. “The Role of a Highly Conserved Major Facilitator Superfamily Member in Drosophila Embryonic Macrophage Migration.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6546.","short":"K. Valosková, The Role of a Highly Conserved Major Facilitator Superfamily Member in Drosophila Embryonic Macrophage Migration, Institute of Science and Technology Austria, 2019.","mla":"Valosková, Katarina. The Role of a Highly Conserved Major Facilitator Superfamily Member in Drosophila Embryonic Macrophage Migration. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6546."},"date_published":"2019-06-07T00:00:00Z","day":"07","article_processing_charge":"No","has_accepted_license":"1","title":"The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration","ddc":["570"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6546","file":[{"file_name":"Katarina Valoskova_PhD thesis_final version.docx","embargo_to":"open_access","access_level":"closed","creator":"khribikova","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":14110626,"file_id":"6549","relation":"source_file","date_updated":"2020-07-14T12:47:33Z","date_created":"2019-06-07T13:00:04Z","checksum":"68949c2d96210b45b981a23e9c9cd93c"},{"creator":"khribikova","file_size":10054156,"content_type":"application/pdf","access_level":"open_access","file_name":"Katarina Valoskova_PhD thesis_final version.pdf","checksum":"555329cd76e196c96f5278c480ee2e6e","date_updated":"2021-02-11T11:17:14Z","date_created":"2019-06-07T13:00:08Z","file_id":"6550","embargo":"2020-06-07","relation":"main_file"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Invasive migration plays a crucial role not only during development and homeostasis but also in pathological states, such as tumor metastasis. Drosophila macrophage migration into the extended germband is an interesting system to study invasive migration. It carries similarities to immune cell transmigration and cancer cell invasion, therefore studying this process could also bring new understanding of invasion in higher organisms. In our work, we uncover a highly conserved member of the major facilitator family that plays a role in tissue invasion through regulation of glycosylation on a subgroup of proteins and/or by aiding the precise timing of DN-Cadherin downregulation. \r\n\r\nAberrant display of the truncated core1 O-glycan T-antigen is a common feature of human cancer cells that correlates with metastasis. Here we show that T-antigen in Drosophila melanogaster macrophages is involved in their developmentally programmed tissue invasion. Higher macrophage T-antigen levels require an atypical major facilitator superfamily (MFS) member that we named Minerva which enables macrophage dissemination and invasion. We characterize for the first time the T and Tn glycoform O-glycoproteome of the Drosophila melanogaster embryo, and determine that Minerva increases the presence of T-antigen on proteins in pathways previously linked to cancer, most strongly on the sulfhydryl oxidase Qsox1 which we show is required for macrophage tissue entry. Minerva’s vertebrate ortholog, MFSD1, rescues the minerva mutant’s migration and T-antigen glycosylation defects. We thus identify \r\na key conserved regulator that orchestrates O-glycosylation on a protein subset to activate \r\na program governing migration steps important for both development and cancer metastasis. \r\n","lang":"eng"}]},{"month":"04","publication_identifier":{"isbn":["978-3-99078-000-8"],"issn":["2663-337X"]},"degree_awarded":"PhD","supervisor":[{"full_name":"Jonas, Peter M","last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:6363","oa":1,"file_date_updated":"2021-02-11T11:17:15Z","date_created":"2019-04-30T11:56:10Z","date_updated":"2023-09-15T12:03:48Z","author":[{"id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4710-2082","first_name":"Claudia ","last_name":"Espinoza Martinez","full_name":"Espinoza Martinez, Claudia "}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"21"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"PeJo"}],"year":"2019","day":"30","article_processing_charge":"No","has_accepted_license":"1","date_published":"2019-04-30T00:00:00Z","page":"140","citation":{"apa":"Espinoza Martinez, C. (2019). Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6363","ieee":"C. Espinoza Martinez, “Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits,” Institute of Science and Technology Austria, 2019.","ista":"Espinoza Martinez C. 2019. Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits. Institute of Science and Technology Austria.","ama":"Espinoza Martinez C. Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits. 2019. doi:10.15479/AT:ISTA:6363","chicago":"Espinoza Martinez, Claudia . “Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6363.","short":"C. Espinoza Martinez, Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits, Institute of Science and Technology Austria, 2019.","mla":"Espinoza Martinez, Claudia. Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6363."},"abstract":[{"text":"Distinguishing between similar experiences is achieved by the brain in a process called pattern separation. In the hippocampus, pattern separation reduces the interference of memories and increases the storage capacity by decorrelating similar inputs patterns of neuronal activity into non-overlapping output firing patterns. Winners-take-all (WTA) mechanism is a theoretical model for pattern separation in which a \"winner\" cell suppresses the activity of the neighboring neurons through feedback inhibition. However, if the network properties of the dentate gyrus support WTA as a biologically conceivable model remains unknown. Here, we showed that the connectivity rules of PV+interneurons and their synaptic properties are optimizedfor efficient pattern separation. We found using multiple whole-cell in vitrorecordings that PV+interneurons mainly connect to granule cells (GC) through lateral inhibition, a form of feedback inhibition in which a GC inhibits other GCs but not itself through the activation of PV+interneurons. Thus, lateral inhibition between GC–PV+interneurons was ~10 times more abundant than recurrent connections. Furthermore, the GC–PV+interneuron connectivity was more spatially confined but less abundant than PV+interneurons–GC connectivity, leading to an asymmetrical distribution of excitatory and inhibitory connectivity. Our network model of the dentate gyrus with incorporated real connectivity rules efficiently decorrelates neuronal activity patterns using WTA as the primary mechanism. This process relied on lateral inhibition, fast-signaling properties of PV+interneurons and the asymmetrical distribution of excitatory and inhibitory connectivity. Finally, we found that silencing the activity of PV+interneurons in vivoleads to acute deficits in discrimination between similar environments, suggesting that PV+interneuron networks are necessary for behavioral relevant computations. Our results demonstrate that PV+interneurons possess unique connectivity and fast signaling properties that confer to the dentate gyrus network properties that allow the emergence of pattern separation. Thus, our results contribute to the knowledge of how specific forms of network organization underlie sophisticated types of information processing. \r\n","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"embargo":"2020-05-09","file_id":"6389","relation":"main_file","checksum":"77c6c05cfe8b58c8abcf1b854375d084","date_updated":"2021-02-11T11:17:15Z","date_created":"2019-05-07T16:00:39Z","access_level":"open_access","file_name":"Espinozathesis_all2.pdf","creator":"cespinoza","content_type":"application/pdf","file_size":13966891},{"date_updated":"2020-07-14T12:47:28Z","date_created":"2019-05-07T16:00:48Z","checksum":"f6aa819f127691a2b0fc21c76eb09746","file_id":"6390","relation":"source_file","creator":"cespinoza","file_size":11159900,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Espinoza_Thesis.docx","embargo_to":"open_access","access_level":"closed"}],"status":"public","title":"Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits","ddc":["570"],"_id":"6363","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"article_number":"129","license":"https://creativecommons.org/licenses/by-nc/4.0/","ec_funded":1,"file_date_updated":"2020-07-14T12:47:40Z","publisher":"ACM","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2019","volume":3,"date_updated":"2024-03-28T23:30:34Z","date_created":"2019-08-09T09:54:20Z","related_material":{"record":[{"id":"8934","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Huang, Mingzhang","last_name":"Huang","first_name":"Mingzhang"},{"full_name":"Fu, Hongfei","first_name":"Hongfei","last_name":"Fu"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Amir Kafshdar","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar"}],"month":"10","project":[{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"arxiv":["1901.06087"]},"language":[{"iso":"eng"}],"doi":"10.1145/3360555","conference":{"end_date":"2019-10-25","start_date":"2019-10-23","location":"Athens, Greece","name":"OOPSLA: Object-oriented Programming, Systems, Languages and Applications"},"type":"conference","abstract":[{"lang":"eng","text":"In this work, we consider the almost-sure termination problem for probabilistic programs that asks whether a\r\ngiven probabilistic program terminates with probability 1. Scalable approaches for program analysis often\r\nrely on modularity as their theoretical basis. In non-probabilistic programs, the classical variant rule (V-rule)\r\nof Floyd-Hoare logic provides the foundation for modular analysis. Extension of this rule to almost-sure\r\ntermination of probabilistic programs is quite tricky, and a probabilistic variant was proposed in [16]. While the\r\nproposed probabilistic variant cautiously addresses the key issue of integrability, we show that the proposed\r\nmodular rule is still not sound for almost-sure termination of probabilistic programs.\r\nBesides establishing unsoundness of the previous rule, our contributions are as follows: First, we present a\r\nsound modular rule for almost-sure termination of probabilistic programs. Our approach is based on a novel\r\nnotion of descent supermartingales. Second, for algorithmic approaches, we consider descent supermartingales\r\nthat are linear and show that they can be synthesized in polynomial time. Finally, we present experimental\r\nresults on a variety of benchmarks and several natural examples that model various types of nested while\r\nloops in probabilistic programs and demonstrate that our approach is able to efficiently prove their almost-sure\r\ntermination property"}],"intvolume":" 3","status":"public","ddc":["000"],"title":"Modular verification for almost-sure termination of probabilistic programs","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"6780","oa_version":"Published Version","file":[{"checksum":"3482d8ace6fb4991eb7810e3b70f1b9f","date_updated":"2020-07-14T12:47:40Z","date_created":"2019-08-12T15:40:57Z","relation":"main_file","file_id":"6807","content_type":"application/pdf","file_size":1024643,"creator":"akafshda","access_level":"open_access","file_name":"oopsla-2019.pdf"},{"file_name":"2019_ACM_Huang.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":538579,"file_id":"7821","relation":"main_file","date_created":"2020-05-12T15:15:14Z","date_updated":"2020-07-14T12:47:40Z","checksum":"4e5a6fb2b59a75222a4e8335a5a60eac"}],"article_processing_charge":"No","has_accepted_license":"1","day":"01","citation":{"chicago":"Huang, Mingzhang, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Modular Verification for Almost-Sure Termination of Probabilistic Programs.” In Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications , Vol. 3. ACM, 2019. https://doi.org/10.1145/3360555.","short":"M. Huang, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications , ACM, 2019.","mla":"Huang, Mingzhang, et al. “Modular Verification for Almost-Sure Termination of Probabilistic Programs.” Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications , vol. 3, 129, ACM, 2019, doi:10.1145/3360555.","apa":"Huang, M., Fu, H., Chatterjee, K., & Goharshady, A. K. (2019). Modular verification for almost-sure termination of probabilistic programs. In Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications (Vol. 3). Athens, Greece: ACM. https://doi.org/10.1145/3360555","ieee":"M. Huang, H. Fu, K. Chatterjee, and A. K. Goharshady, “Modular verification for almost-sure termination of probabilistic programs,” in Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications , Athens, Greece, 2019, vol. 3.","ista":"Huang M, Fu H, Chatterjee K, Goharshady AK. 2019. Modular verification for almost-sure termination of probabilistic programs. Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications . OOPSLA: Object-oriented Programming, Systems, Languages and Applications vol. 3, 129.","ama":"Huang M, Fu H, Chatterjee K, Goharshady AK. Modular verification for almost-sure termination of probabilistic programs. In: Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications . Vol 3. ACM; 2019. doi:10.1145/3360555"},"publication":"Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications ","date_published":"2019-10-01T00:00:00Z"},{"article_number":"53","ec_funded":1,"file_date_updated":"2020-07-14T12:47:29Z","department":[{"_id":"KrCh"}],"publisher":"ACM","publication_status":"published","year":"2019","volume":3,"date_updated":"2024-03-28T23:30:33Z","date_created":"2019-05-06T12:18:17Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8934"}]},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Goharshady","first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir Kafshdar"},{"first_name":"Nastaran","last_name":"Okati","full_name":"Okati, Nastaran"},{"first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"}],"publication_identifier":{"issn":["2475-1421"]},"month":"01","project":[{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"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"},"language":[{"iso":"eng"}],"doi":"10.1145/3290366","type":"journal_article","issue":"POPL","abstract":[{"text":"There is a huge gap between the speeds of modern caches and main memories, and therefore cache misses account for a considerable loss of efficiency in programs. The predominant technique to address this issue has been Data Packing: data elements that are frequently accessed within time proximity are packed into the same cache block, thereby minimizing accesses to the main memory. We consider the algorithmic problem of Data Packing on a two-level memory system. Given a reference sequence R of accesses to data elements, the task is to partition the elements into cache blocks such that the number of cache misses on R is minimized. The problem is notoriously difficult: it is NP-hard even when the cache has size 1, and is hard to approximate for any cache size larger than 4. Therefore, all existing techniques for Data Packing are based on heuristics and lack theoretical guarantees. In this work, we present the first positive theoretical results for Data Packing, along with new and stronger negative results. We consider the problem under the lens of the underlying access hypergraphs, which are hypergraphs of affinities between the data elements, where the order of an access hypergraph corresponds to the size of the affinity group. We study the problem parameterized by the treewidth of access hypergraphs, which is a standard notion in graph theory to measure the closeness of a graph to a tree. Our main results are as follows: We show there is a number q* depending on the cache parameters such that (a) if the access hypergraph of order q* has constant treewidth, then there is a linear-time algorithm for Data Packing; (b)the Data Packing problem remains NP-hard even if the access hypergraph of order q*-1 has constant treewidth. Thus, we establish a fine-grained dichotomy depending on a single parameter, namely, the highest order among access hypegraphs that have constant treewidth; and establish the optimal value q* of this parameter. Finally, we present an experimental evaluation of a prototype implementation of our algorithm. Our results demonstrate that, in practice, access hypergraphs of many commonly-used algorithms have small treewidth. We compare our approach with several state-of-the-art heuristic-based algorithms and show that our algorithm leads to significantly fewer cache-misses. ","lang":"eng"}],"intvolume":" 3","ddc":["004"],"title":"Efficient parameterized algorithms for data packing","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6380","oa_version":"Published Version","file":[{"file_name":"2019_ACM_POPL_Chatterjee.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1294962,"creator":"dernst","relation":"main_file","file_id":"6381","date_created":"2019-05-06T12:23:11Z","date_updated":"2020-07-14T12:47:29Z","checksum":"c157752f96877b36685ad7063ada4524"}],"pubrep_id":"1056","has_accepted_license":"1","day":"01","citation":{"chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Nastaran Okati, and Andreas Pavlogiannis. “Efficient Parameterized Algorithms for Data Packing.” Proceedings of the ACM on Programming Languages. ACM, 2019. https://doi.org/10.1145/3290366.","mla":"Chatterjee, Krishnendu, et al. “Efficient Parameterized Algorithms for Data Packing.” Proceedings of the ACM on Programming Languages, vol. 3, no. POPL, 53, ACM, 2019, doi:10.1145/3290366.","short":"K. Chatterjee, A.K. Goharshady, N. Okati, A. Pavlogiannis, Proceedings of the ACM on Programming Languages 3 (2019).","ista":"Chatterjee K, Goharshady AK, Okati N, Pavlogiannis A. 2019. Efficient parameterized algorithms for data packing. Proceedings of the ACM on Programming Languages. 3(POPL), 53.","ieee":"K. Chatterjee, A. K. Goharshady, N. Okati, and A. Pavlogiannis, “Efficient parameterized algorithms for data packing,” Proceedings of the ACM on Programming Languages, vol. 3, no. POPL. ACM, 2019.","apa":"Chatterjee, K., Goharshady, A. K., Okati, N., & Pavlogiannis, A. (2019). Efficient parameterized algorithms for data packing. Proceedings of the ACM on Programming Languages. ACM. https://doi.org/10.1145/3290366","ama":"Chatterjee K, Goharshady AK, Okati N, Pavlogiannis A. Efficient parameterized algorithms for data packing. Proceedings of the ACM on Programming Languages. 2019;3(POPL). doi:10.1145/3290366"},"publication":"Proceedings of the ACM on Programming Languages","date_published":"2019-01-01T00:00:00Z"},{"month":"05","external_id":{"arxiv":["1902.07986"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1902.07986"}],"project":[{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"},{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"}],"quality_controlled":"1","doi":"10.1109/BLOC.2019.8751326","conference":{"name":"IEEE International Conference on Blockchain and Cryptocurrency","end_date":"2019-05-17","location":"Seoul, Korea","start_date":"2019-05-14"},"language":[{"iso":"eng"}],"article_number":"8751326","ec_funded":1,"year":"2019","department":[{"_id":"KrCh"}],"publisher":"IEEE","publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8934"}]},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar"},{"full_name":"Pourdamghani, Arash","first_name":"Arash","last_name":"Pourdamghani"}],"date_updated":"2024-03-28T23:30:33Z","date_created":"2019-02-26T09:03:15Z","scopus_import":1,"day":"01","citation":{"ama":"Chatterjee K, Goharshady AK, Pourdamghani A. Probabilistic smart contracts: Secure randomness on the blockchain. In: IEEE International Conference on Blockchain and Cryptocurrency. IEEE; 2019. doi:10.1109/BLOC.2019.8751326","ista":"Chatterjee K, Goharshady AK, Pourdamghani A. 2019. Probabilistic smart contracts: Secure randomness on the blockchain. IEEE International Conference on Blockchain and Cryptocurrency. IEEE International Conference on Blockchain and Cryptocurrency, 8751326.","ieee":"K. Chatterjee, A. K. Goharshady, and A. Pourdamghani, “Probabilistic smart contracts: Secure randomness on the blockchain,” in IEEE International Conference on Blockchain and Cryptocurrency, Seoul, Korea, 2019.","apa":"Chatterjee, K., Goharshady, A. K., & Pourdamghani, A. (2019). Probabilistic smart contracts: Secure randomness on the blockchain. In IEEE International Conference on Blockchain and Cryptocurrency. Seoul, Korea: IEEE. https://doi.org/10.1109/BLOC.2019.8751326","mla":"Chatterjee, Krishnendu, et al. “Probabilistic Smart Contracts: Secure Randomness on the Blockchain.” IEEE International Conference on Blockchain and Cryptocurrency, 8751326, IEEE, 2019, doi:10.1109/BLOC.2019.8751326.","short":"K. Chatterjee, A.K. Goharshady, A. Pourdamghani, in:, IEEE International Conference on Blockchain and Cryptocurrency, IEEE, 2019.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Arash Pourdamghani. “Probabilistic Smart Contracts: Secure Randomness on the Blockchain.” In IEEE International Conference on Blockchain and Cryptocurrency. IEEE, 2019. https://doi.org/10.1109/BLOC.2019.8751326."},"publication":"IEEE International Conference on Blockchain and Cryptocurrency","date_published":"2019-05-01T00:00:00Z","type":"conference","abstract":[{"text":"In today's programmable blockchains, smart contracts are limited to being deterministic and non-probabilistic. This lack of randomness is a consequential limitation, given that a wide variety of real-world financial contracts, such as casino games and lotteries, depend entirely on randomness. As a result, several ad-hoc random number generation approaches have been developed to be used in smart contracts. These include ideas such as using an oracle or relying on the block hash. However, these approaches are manipulatable, i.e. their output can be tampered with by parties who might not be neutral, such as the owner of the oracle or the miners.We propose a novel game-theoretic approach for generating provably unmanipulatable pseudorandom numbers on the blockchain. Our approach allows smart contracts to access a trustworthy source of randomness that does not rely on potentially compromised miners or oracles, hence enabling the creation of a new generation of smart contracts that are not limited to being non-probabilistic and can be drawn from the much more general class of probabilistic programs.","lang":"eng"}],"_id":"6056","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Probabilistic smart contracts: Secure randomness on the blockchain","status":"public","oa_version":"Preprint"},{"type":"conference","abstract":[{"text":"In today's cryptocurrencies, Hashcash proof of work is the most commonly-adopted approach to mining. In Hashcash, when a miner decides to add a block to the chain, she has to solve the difficult computational puzzle of inverting a hash function. While Hashcash has been successfully adopted in both Bitcoin and Ethereum, it has attracted significant and harsh criticism due to its massive waste of electricity, its carbon footprint and environmental effects, and the inherent lack of usefulness in inverting a hash function. Various other mining protocols have been suggested, including proof of stake, in which a miner's chance of adding the next block is proportional to her current balance. However, such protocols lead to a higher entry cost for new miners who might not still have any stake in the cryptocurrency, and can in the worst case lead to an oligopoly, where the rich have complete control over mining. In this paper, we propose Hybrid Mining: a new mining protocol that combines solving real-world useful problems with Hashcash. Our protocol allows new miners to join the network by taking part in Hashcash mining without having to own an initial stake. It also allows nodes of the network to submit hard computational problems whose solutions are of interest in the real world, e.g.~protein folding problems. Then, miners can choose to compete in solving these problems, in lieu of Hashcash, for adding a new block. Hence, Hybrid Mining incentivizes miners to solve useful problems, such as hard computational problems arising in biology, in a distributed manner. It also gives researchers in other areas an easy-to-use tool to outsource their hard computations to the blockchain network, which has enormous computational power, by paying a reward to the miner who solves the problem for them. Moreover, our protocol provides strong security guarantees and is at least as resilient to double spending as Bitcoin.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6378","title":"Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving","status":"public","ddc":["004"],"pubrep_id":"1069","oa_version":"Submitted Version","file":[{"file_size":1023934,"content_type":"application/pdf","creator":"dernst","file_name":"2019_ACM_Chatterjee.pdf","access_level":"open_access","date_created":"2019-05-06T12:09:27Z","date_updated":"2020-07-14T12:47:29Z","checksum":"fbfbcd5a0c7a743862bfc3045539a614","relation":"main_file","file_id":"6379"}],"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","publication":"Proceedings of the 34th ACM Symposium on Applied Computing","citation":{"mla":"Chatterjee, Krishnendu, et al. “Hybrid Mining: Exploiting Blockchain’s Computational Power for Distributed Problem Solving.” Proceedings of the 34th ACM Symposium on Applied Computing, vol. Part F147772, ACM, 2019, pp. 374–81, doi:10.1145/3297280.3297319.","short":"K. Chatterjee, A.K. Goharshady, A. Pourdamghani, in:, Proceedings of the 34th ACM Symposium on Applied Computing, ACM, 2019, pp. 374–381.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Arash Pourdamghani. “Hybrid Mining: Exploiting Blockchain’s Computational Power for Distributed Problem Solving.” In Proceedings of the 34th ACM Symposium on Applied Computing, Part F147772:374–81. ACM, 2019. https://doi.org/10.1145/3297280.3297319.","ama":"Chatterjee K, Goharshady AK, Pourdamghani A. Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving. In: Proceedings of the 34th ACM Symposium on Applied Computing. Vol Part F147772. ACM; 2019:374-381. doi:10.1145/3297280.3297319","ista":"Chatterjee K, Goharshady AK, Pourdamghani A. 2019. Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving. Proceedings of the 34th ACM Symposium on Applied Computing. ACM Symposium on Applied Computing vol. Part F147772, 374–381.","ieee":"K. Chatterjee, A. K. Goharshady, and A. Pourdamghani, “Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving,” in Proceedings of the 34th ACM Symposium on Applied Computing, Limassol, Cyprus, 2019, vol. Part F147772, pp. 374–381.","apa":"Chatterjee, K., Goharshady, A. K., & Pourdamghani, A. (2019). Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving. In Proceedings of the 34th ACM Symposium on Applied Computing (Vol. Part F147772, pp. 374–381). Limassol, Cyprus: ACM. https://doi.org/10.1145/3297280.3297319"},"page":"374-381","date_published":"2019-04-01T00:00:00Z","file_date_updated":"2020-07-14T12:47:29Z","ec_funded":1,"year":"2019","publication_status":"published","publisher":"ACM","department":[{"_id":"KrCh"}],"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar","last_name":"Goharshady","full_name":"Goharshady, Amir Kafshdar"},{"first_name":"Arash","last_name":"Pourdamghani","full_name":"Pourdamghani, Arash"}],"related_material":{"record":[{"id":"8934","relation":"dissertation_contains","status":"public"}]},"date_created":"2019-05-06T12:11:36Z","date_updated":"2024-03-28T23:30:34Z","volume":"Part F147772","month":"04","publication_identifier":{"isbn":["9781450359337"]},"external_id":{"isi":["000474685800049"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"conference":{"end_date":"2019-04-12","location":"Limassol, Cyprus","start_date":"2019-04-08","name":"ACM Symposium on Applied Computing"},"doi":"10.1145/3297280.3297319","language":[{"iso":"eng"}]},{"day":"08","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","keyword":["Program Cost Analysis","Program Termination","Probabilistic Programs","Martingales"],"date_published":"2019-06-08T00:00:00Z","publication":"PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation","citation":{"chicago":"Wang, Peixin, Hongfei Fu, Amir Kafshdar Goharshady, Krishnendu Chatterjee, Xudong Qin, and Wenjun Shi. “Cost Analysis of Nondeterministic Probabilistic Programs.” In PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation, 204–20. Association for Computing Machinery, 2019. https://doi.org/10.1145/3314221.3314581.","short":"P. Wang, H. Fu, A.K. Goharshady, K. Chatterjee, X. Qin, W. Shi, in:, PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2019, pp. 204–220.","mla":"Wang, Peixin, et al. “Cost Analysis of Nondeterministic Probabilistic Programs.” PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2019, pp. 204–20, doi:10.1145/3314221.3314581.","ieee":"P. Wang, H. Fu, A. K. Goharshady, K. Chatterjee, X. Qin, and W. Shi, “Cost analysis of nondeterministic probabilistic programs,” in PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation, Phoenix, AZ, United States, 2019, pp. 204–220.","apa":"Wang, P., Fu, H., Goharshady, A. K., Chatterjee, K., Qin, X., & Shi, W. (2019). Cost analysis of nondeterministic probabilistic programs. In PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation (pp. 204–220). Phoenix, AZ, United States: Association for Computing Machinery. https://doi.org/10.1145/3314221.3314581","ista":"Wang P, Fu H, Goharshady AK, Chatterjee K, Qin X, Shi W. 2019. Cost analysis of nondeterministic probabilistic programs. PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation. PLDI: Conference on Programming Language Design and Implementation, 204–220.","ama":"Wang P, Fu H, Goharshady AK, Chatterjee K, Qin X, Shi W. Cost analysis of nondeterministic probabilistic programs. In: PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2019:204-220. doi:10.1145/3314221.3314581"},"page":"204-220","abstract":[{"lang":"eng","text":"We consider the problem of expected cost analysis over nondeterministic probabilistic programs,\r\nwhich aims at automated methods for analyzing the resource-usage of such programs.\r\nPrevious approaches for this problem could only handle nonnegative bounded costs.\r\nHowever, in many scenarios, such as queuing networks or analysis of cryptocurrency protocols,\r\nboth positive and negative costs are necessary and the costs are unbounded as well.\r\n\r\nIn this work, we present a sound and efficient approach to obtain polynomial bounds on the\r\nexpected accumulated cost of nondeterministic probabilistic programs.\r\nOur approach can handle (a) general positive and negative costs with bounded updates in\r\nvariables; and (b) nonnegative costs with general updates to variables.\r\nWe show that several natural examples which could not be\r\nhandled by previous approaches are captured in our framework.\r\n\r\nMoreover, our approach leads to an efficient polynomial-time algorithm, while no\r\nprevious approach for cost analysis of probabilistic programs could guarantee polynomial runtime.\r\nFinally, we show the effectiveness of our approach using experimental results on a variety of programs for which we efficiently synthesize tight resource-usage bounds."}],"type":"conference","file":[{"file_name":"paper.pdf","access_level":"open_access","creator":"akafshda","file_size":4051066,"content_type":"application/pdf","file_id":"6176","relation":"main_file","date_created":"2019-03-25T10:11:22Z","date_updated":"2020-07-14T12:47:20Z","checksum":"703a5e9b8c8587f2a44085ffd9a4db64"}],"oa_version":"Submitted Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6175","ddc":["000"],"title":"Cost analysis of nondeterministic probabilistic programs","status":"public","month":"06","conference":{"name":"PLDI: Conference on Programming Language Design and Implementation","start_date":"2019-06-22","location":"Phoenix, AZ, United States","end_date":"2019-06-26"},"doi":"10.1145/3314221.3314581","language":[{"iso":"eng"}],"external_id":{"arxiv":["1902.04659"],"isi":["000523190300014"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"file_date_updated":"2020-07-14T12:47:20Z","ec_funded":1,"author":[{"full_name":"Wang, Peixin","last_name":"Wang","first_name":"Peixin"},{"full_name":"Fu, Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","last_name":"Fu","first_name":"Hongfei"},{"full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","first_name":"Amir Kafshdar"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Qin, Xudong","first_name":"Xudong","last_name":"Qin"},{"full_name":"Shi, Wenjun","last_name":"Shi","first_name":"Wenjun"}],"related_material":{"record":[{"id":"5457","status":"public","relation":"earlier_version"},{"id":"8934","relation":"dissertation_contains","status":"public"}]},"date_created":"2019-03-25T10:13:25Z","date_updated":"2024-03-28T23:30:34Z","year":"2019","publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"KrCh"}]},{"type":"conference","abstract":[{"text":"Smart contracts are programs that are stored and executed on the Blockchain and can receive, manage and transfer money (cryptocurrency units). Two important problems regarding smart contracts are formal analysis and compiler optimization. Formal analysis is extremely important, because smart contracts hold funds worth billions of dollars and their code is immutable after deployment. Hence, an undetected bug can cause significant financial losses. Compiler optimization is also crucial, because every action of a smart contract has to be executed by every node in the Blockchain network. Therefore, optimizations in compiling smart contracts can lead to significant savings in computation, time and energy.\r\n\r\nTwo classical approaches in program analysis and compiler optimization are intraprocedural and interprocedural analysis. In intraprocedural analysis, each function is analyzed separately, while interprocedural analysis considers the entire program. In both cases, the analyses are usually reduced to graph problems over the control flow graph (CFG) of the program. These graph problems are often computationally expensive. Hence, there has been ample research on exploiting structural properties of CFGs for efficient algorithms. One such well-studied property is the treewidth, which is a measure of tree-likeness of graphs. It is known that intraprocedural CFGs of structured programs have treewidth at most 6, whereas the interprocedural treewidth cannot be bounded. This result has been used as a basis for many efficient intraprocedural analyses.\r\n\r\nIn this paper, we explore the idea of exploiting the treewidth of smart contracts for formal analysis and compiler optimization. First, similar to classical programs, we show that the intraprocedural treewidth of structured Solidity and Vyper smart contracts is at most 9. Second, for global analysis, we prove that the interprocedural treewidth of structured smart contracts is bounded by 10 and, in sharp contrast with classical programs, treewidth-based algorithms can be easily applied for interprocedural analysis. Finally, we supplement our theoretical results with experiments using a tool we implemented for computing treewidth of smart contracts and show that the treewidth is much lower in practice. We use 36,764 real-world Ethereum smart contracts as benchmarks and find that they have an average treewidth of at most 3.35 for the intraprocedural case and 3.65 for the interprocedural case.\r\n","lang":"eng"}],"title":"The treewidth of smart contracts","status":"public","ddc":["000"],"_id":"6490","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Submitted Version","file":[{"file_name":"2019_ACM_Chatterjee.pdf","access_level":"open_access","file_size":6937138,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7827","date_updated":"2020-07-14T12:47:32Z","date_created":"2020-05-14T09:50:11Z","checksum":"dddc20f6d9881f23b8755eb720ec9d6f"}],"pubrep_id":"1070","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","page":"400-408","citation":{"short":"K. Chatterjee, A.K. Goharshady, E.K. Goharshady, in:, Proceedings of the 34th ACM Symposium on Applied Computing, ACM, n.d., pp. 400–408.","mla":"Chatterjee, Krishnendu, et al. “The Treewidth of Smart Contracts.” Proceedings of the 34th ACM Symposium on Applied Computing, vol. Part F147772, ACM, pp. 400–08, doi:10.1145/3297280.3297322.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Ehsan Kafshdar Goharshady. “The Treewidth of Smart Contracts.” In Proceedings of the 34th ACM Symposium on Applied Computing, Part F147772:400–408. ACM, n.d. https://doi.org/10.1145/3297280.3297322.","ama":"Chatterjee K, Goharshady AK, Goharshady EK. The treewidth of smart contracts. In: Proceedings of the 34th ACM Symposium on Applied Computing. Vol Part F147772. ACM; :400-408. doi:10.1145/3297280.3297322","ieee":"K. Chatterjee, A. K. Goharshady, and E. K. Goharshady, “The treewidth of smart contracts,” in Proceedings of the 34th ACM Symposium on Applied Computing, Limassol, Cyprus, vol. Part F147772, pp. 400–408.","apa":"Chatterjee, K., Goharshady, A. K., & Goharshady, E. K. (n.d.). The treewidth of smart contracts. In Proceedings of the 34th ACM Symposium on Applied Computing (Vol. Part F147772, pp. 400–408). Limassol, Cyprus: ACM. https://doi.org/10.1145/3297280.3297322","ista":"Chatterjee K, Goharshady AK, Goharshady EK. The treewidth of smart contracts. Proceedings of the 34th ACM Symposium on Applied Computing. SAC: Symposium on Applied Computing vol. Part F147772, 400–408."},"publication":"Proceedings of the 34th ACM Symposium on Applied Computing","date_published":"2019-04-01T00:00:00Z","file_date_updated":"2020-07-14T12:47:32Z","publisher":"ACM","department":[{"_id":"KrCh"}],"publication_status":"submitted","year":"2019","volume":"Part F147772","date_updated":"2024-03-28T23:30:34Z","date_created":"2019-05-26T21:59:15Z","related_material":{"record":[{"id":"8934","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Amir Kafshdar","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar"},{"last_name":"Goharshady","first_name":"Ehsan Kafshdar","full_name":"Goharshady, Ehsan Kafshdar"}],"publication_identifier":{"isbn":["9781450359337"]},"month":"04","isi":1,"quality_controlled":"1","external_id":{"isi":["000474685800052"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1145/3297280.3297322","conference":{"end_date":"2019-04-12","start_date":"2019-04-08","location":"Limassol, Cyprus","name":"SAC: Symposium on Applied Computing"}},{"publication":"ACM Transactions on Programming Languages and Systems","citation":{"chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Prateesh Goyal, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Faster Algorithms for Dynamic Algebraic Queries in Basic RSMs with Constant Treewidth.” ACM Transactions on Programming Languages and Systems. ACM, 2019. https://doi.org/10.1145/3363525.","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithms for Dynamic Algebraic Queries in Basic RSMs with Constant Treewidth.” ACM Transactions on Programming Languages and Systems, vol. 41, no. 4, 23, ACM, 2019, doi:10.1145/3363525.","short":"K. Chatterjee, A.K. Goharshady, P. Goyal, R. Ibsen-Jensen, A. Pavlogiannis, ACM Transactions on Programming Languages and Systems 41 (2019).","ista":"Chatterjee K, Goharshady AK, Goyal P, Ibsen-Jensen R, Pavlogiannis A. 2019. Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth. ACM Transactions on Programming Languages and Systems. 41(4), 23.","ieee":"K. Chatterjee, A. K. Goharshady, P. Goyal, R. Ibsen-Jensen, and A. Pavlogiannis, “Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth,” ACM Transactions on Programming Languages and Systems, vol. 41, no. 4. ACM, 2019.","apa":"Chatterjee, K., Goharshady, A. K., Goyal, P., Ibsen-Jensen, R., & Pavlogiannis, A. (2019). Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth. ACM Transactions on Programming Languages and Systems. ACM. https://doi.org/10.1145/3363525","ama":"Chatterjee K, Goharshady AK, Goyal P, Ibsen-Jensen R, Pavlogiannis A. Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth. ACM Transactions on Programming Languages and Systems. 2019;41(4). doi:10.1145/3363525"},"article_type":"original","date_published":"2019-11-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","_id":"7158","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth","status":"public","ddc":["000"],"intvolume":" 41","file":[{"content_type":"application/pdf","file_size":667357,"creator":"dernst","access_level":"open_access","file_name":"2019_ACMTransactions_Chatterjee.pdf","checksum":"291cc86a07bd010d4815e177dac57b70","success":1,"date_updated":"2020-10-08T12:58:10Z","date_created":"2020-10-08T12:58:10Z","relation":"main_file","file_id":"8632"}],"oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"Interprocedural analysis is at the heart of numerous applications in programming languages, such as alias analysis, constant propagation, and so on. Recursive state machines (RSMs) are standard models for interprocedural analysis. We consider a general framework with RSMs where the transitions are labeled from a semiring and path properties are algebraic with semiring operations. RSMs with algebraic path properties can model interprocedural dataflow analysis problems, the shortest path problem, the most probable path problem, and so on. The traditional algorithms for interprocedural analysis focus on path properties where the starting point is fixed as the entry point of a specific method. In this work, we consider possible multiple queries as required in many applications such as in alias analysis. The study of multiple queries allows us to bring in an important algorithmic distinction between the resource usage of the one-time preprocessing vs for each individual query. The second aspect we consider is that the control flow graphs for most programs have constant treewidth.\r\n\r\nOur main contributions are simple and implementable algorithms that support multiple queries for algebraic path properties for RSMs that have constant treewidth. Our theoretical results show that our algorithms have small additional one-time preprocessing but can answer subsequent queries significantly faster as compared to the current algorithmic solutions for interprocedural dataflow analysis. We have also implemented our algorithms and evaluated their performance for performing on-demand interprocedural dataflow analysis on various domains, such as for live variable analysis and reaching definitions, on a standard benchmark set. Our experimental results align with our theoretical statements and show that after a lightweight preprocessing, on-demand queries are answered much faster than the standard existing algorithmic approaches.\r\n","lang":"eng"}],"issue":"4","external_id":{"isi":["000564108400004"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"doi":"10.1145/3363525","language":[{"iso":"eng"}],"month":"11","publication_identifier":{"issn":["0164-0925"]},"year":"2019","publication_status":"published","publisher":"ACM","department":[{"_id":"KrCh"}],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Amir Kafshdar","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar"},{"full_name":"Goyal, Prateesh","last_name":"Goyal","first_name":"Prateesh"},{"full_name":"Ibsen-Jensen, Rasmus","first_name":"Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389"},{"full_name":"Pavlogiannis, Andreas","first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722"}],"related_material":{"record":[{"id":"8934","relation":"dissertation_contains","status":"public"}]},"date_updated":"2024-03-28T23:30:34Z","date_created":"2019-12-09T08:33:33Z","volume":41,"article_number":"23","file_date_updated":"2020-10-08T12:58:10Z","ec_funded":1},{"doi":"10.1145/3339984","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1705.00317","open_access":"1"}],"external_id":{"isi":["000564108400001"],"arxiv":["1705.00317"]},"project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"isi":1,"quality_controlled":"1","month":"10","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"639"},{"id":"8934","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Fu, Hongfei","last_name":"Fu","first_name":"Hongfei"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar","last_name":"Goharshady","full_name":"Goharshady, Amir Kafshdar"}],"volume":41,"date_created":"2019-11-13T08:33:43Z","date_updated":"2024-03-28T23:30:34Z","year":"2019","department":[{"_id":"KrCh"}],"publisher":"ACM","publication_status":"published","ec_funded":1,"article_number":"20","date_published":"2019-10-01T00:00:00Z","citation":{"ista":"Chatterjee K, Fu H, Goharshady AK. 2019. Non-polynomial worst-case analysis of recursive programs. ACM Transactions on Programming Languages and Systems. 41(4), 20.","apa":"Chatterjee, K., Fu, H., & Goharshady, A. K. (2019). Non-polynomial worst-case analysis of recursive programs. ACM Transactions on Programming Languages and Systems. ACM. https://doi.org/10.1145/3339984","ieee":"K. Chatterjee, H. Fu, and A. K. Goharshady, “Non-polynomial worst-case analysis of recursive programs,” ACM Transactions on Programming Languages and Systems, vol. 41, no. 4. ACM, 2019.","ama":"Chatterjee K, Fu H, Goharshady AK. Non-polynomial worst-case analysis of recursive programs. ACM Transactions on Programming Languages and Systems. 2019;41(4). doi:10.1145/3339984","chicago":"Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Non-Polynomial Worst-Case Analysis of Recursive Programs.” ACM Transactions on Programming Languages and Systems. ACM, 2019. https://doi.org/10.1145/3339984.","mla":"Chatterjee, Krishnendu, et al. “Non-Polynomial Worst-Case Analysis of Recursive Programs.” ACM Transactions on Programming Languages and Systems, vol. 41, no. 4, 20, ACM, 2019, doi:10.1145/3339984.","short":"K. Chatterjee, H. Fu, A.K. Goharshady, ACM Transactions on Programming Languages and Systems 41 (2019)."},"publication":"ACM Transactions on Programming Languages and Systems","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7014","intvolume":" 41","status":"public","title":"Non-polynomial worst-case analysis of recursive programs","issue":"4","abstract":[{"text":"We study the problem of developing efficient approaches for proving\r\nworst-case bounds of non-deterministic recursive programs. Ranking functions\r\nare sound and complete for proving termination and worst-case bounds of\r\nnonrecursive programs. First, we apply ranking functions to recursion,\r\nresulting in measure functions. We show that measure functions provide a sound\r\nand complete approach to prove worst-case bounds of non-deterministic recursive\r\nprograms. Our second contribution is the synthesis of measure functions in\r\nnonpolynomial forms. We show that non-polynomial measure functions with\r\nlogarithm and exponentiation can be synthesized through abstraction of\r\nlogarithmic or exponentiation terms, Farkas' Lemma, and Handelman's Theorem\r\nusing linear programming. While previous methods obtain worst-case polynomial\r\nbounds, our approach can synthesize bounds of the form $\\mathcal{O}(n\\log n)$\r\nas well as $\\mathcal{O}(n^r)$ where $r$ is not an integer. We present\r\nexperimental results to demonstrate that our approach can obtain efficiently\r\nworst-case bounds of classical recursive algorithms such as (i) Merge-Sort, the\r\ndivide-and-conquer algorithm for the Closest-Pair problem, where we obtain\r\n$\\mathcal{O}(n \\log n)$ worst-case bound, and (ii) Karatsuba's algorithm for\r\npolynomial multiplication and Strassen's algorithm for matrix multiplication,\r\nwhere we obtain $\\mathcal{O}(n^r)$ bound such that $r$ is not an integer and\r\nclose to the best-known bounds for the respective algorithms.","lang":"eng"}],"type":"journal_article"},{"author":[{"full_name":"Kühnen, Jakob","orcid":"0000-0003-4312-0179","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","last_name":"Kühnen","first_name":"Jakob"},{"orcid":"0000-0001-5227-4271","id":"40315C30-F248-11E8-B48F-1D18A9856A87","last_name":"Scarselli","first_name":"Davide","full_name":"Scarselli, Davide"},{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"}],"related_material":{"record":[{"id":"7258","relation":"dissertation_contains","status":"public"}]},"date_created":"2019-05-26T21:59:13Z","date_updated":"2024-03-28T23:30:36Z","volume":141,"year":"2019","publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"ASME","ec_funded":1,"article_number":"111105","doi":"10.1115/1.4043494","acknowledged_ssus":[{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"external_id":{"arxiv":["1809.07625"],"isi":["000487748600005"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1809.07625","open_access":"1"}],"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Decoding the complexity of turbulence at its origin","grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425"}],"month":"11","publication_identifier":{"eissn":["1528901X"],"issn":["00982202"]},"oa_version":"Preprint","_id":"6486","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Relaminarization of pipe flow by means of 3D-printed shaped honeycombs","status":"public","intvolume":" 141","abstract":[{"text":"Based on a novel control scheme, where a steady modification of the streamwise velocity profile leads to complete relaminarization of initially fully turbulent pipe flow, we investigate the applicability and usefulness of custom-shaped honeycombs for such control. The custom-shaped honeycombs are used as stationary flow management devices which generate specific modifications of the streamwise velocity profile. Stereoscopic particle image velocimetry and pressure drop measurements are used to investigate and capture the development of the relaminarizing flow downstream these devices. We compare the performance of straight (constant length across the radius of the pipe) honeycombs with custom-shaped ones (variable length across the radius) and try to determine the optimal shape for maximal relaminarization at minimal pressure loss. The optimally modified streamwise velocity profile is found to be M-shaped, and the maximum attainable Reynolds number for total relaminarization is found to be of the order of 10,000. Consequently, the respective reduction in skin friction downstream of the device is almost by a factor of 5. The break-even point, where the additional pressure drop caused by the device is balanced by the savings due to relaminarization and a net gain is obtained, corresponds to a downstream stretch of distances as low as approximately 100 pipe diameters of laminar flow.","lang":"eng"}],"issue":"11","type":"journal_article","date_published":"2019-11-01T00:00:00Z","publication":"Journal of Fluids Engineering","citation":{"chicago":"Kühnen, Jakob, Davide Scarselli, and Björn Hof. “Relaminarization of Pipe Flow by Means of 3D-Printed Shaped Honeycombs.” Journal of Fluids Engineering. ASME, 2019. https://doi.org/10.1115/1.4043494.","mla":"Kühnen, Jakob, et al. “Relaminarization of Pipe Flow by Means of 3D-Printed Shaped Honeycombs.” Journal of Fluids Engineering, vol. 141, no. 11, 111105, ASME, 2019, doi:10.1115/1.4043494.","short":"J. Kühnen, D. Scarselli, B. Hof, Journal of Fluids Engineering 141 (2019).","ista":"Kühnen J, Scarselli D, Hof B. 2019. Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. Journal of Fluids Engineering. 141(11), 111105.","ieee":"J. Kühnen, D. Scarselli, and B. Hof, “Relaminarization of pipe flow by means of 3D-printed shaped honeycombs,” Journal of Fluids Engineering, vol. 141, no. 11. ASME, 2019.","apa":"Kühnen, J., Scarselli, D., & Hof, B. (2019). Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. Journal of Fluids Engineering. ASME. https://doi.org/10.1115/1.4043494","ama":"Kühnen J, Scarselli D, Hof B. Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. Journal of Fluids Engineering. 2019;141(11). doi:10.1115/1.4043494"},"article_type":"original","day":"01","article_processing_charge":"No","scopus_import":"1"},{"type":"journal_article","abstract":[{"text":"Following the recent observation that turbulent pipe flow can be relaminarised bya relatively simple modification of the mean velocity profile, we here carry out aquantitative experimental investigation of this phenomenon. Our study confirms thata flat velocity profile leads to a collapse of turbulence and in order to achieve theblunted profile shape, we employ a moving pipe segment that is briefly and rapidlyshifted in the streamwise direction. The relaminarisation threshold and the minimumshift length and speeds are determined as a function of Reynolds number. Althoughturbulence is still active after the acceleration phase, the modulated profile possessesa severely decreased lift-up potential as measured by transient growth. As shown,this results in an exponential decay of fluctuations and the flow relaminarises. Whilethis method can be easily applied at low to moderate flow speeds, the minimumstreamwise length over which the acceleration needs to act increases linearly with theReynolds number.","lang":"eng"}],"intvolume":" 867","title":"Relaminarising pipe flow by wall movement","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6228","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"25","page":"934-948","citation":{"chicago":"Scarselli, Davide, Jakob Kühnen, and Björn Hof. “Relaminarising Pipe Flow by Wall Movement.” Journal of Fluid Mechanics. Cambridge University Press, 2019. https://doi.org/10.1017/jfm.2019.191.","mla":"Scarselli, Davide, et al. “Relaminarising Pipe Flow by Wall Movement.” Journal of Fluid Mechanics, vol. 867, Cambridge University Press, 2019, pp. 934–48, doi:10.1017/jfm.2019.191.","short":"D. Scarselli, J. Kühnen, B. Hof, Journal of Fluid Mechanics 867 (2019) 934–948.","ista":"Scarselli D, Kühnen J, Hof B. 2019. Relaminarising pipe flow by wall movement. Journal of Fluid Mechanics. 867, 934–948.","apa":"Scarselli, D., Kühnen, J., & Hof, B. (2019). Relaminarising pipe flow by wall movement. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2019.191","ieee":"D. Scarselli, J. Kühnen, and B. Hof, “Relaminarising pipe flow by wall movement,” Journal of Fluid Mechanics, vol. 867. Cambridge University Press, pp. 934–948, 2019.","ama":"Scarselli D, Kühnen J, Hof B. Relaminarising pipe flow by wall movement. Journal of Fluid Mechanics. 2019;867:934-948. doi:10.1017/jfm.2019.191"},"publication":"Journal of Fluid Mechanics","date_published":"2019-05-25T00:00:00Z","ec_funded":1,"publisher":"Cambridge University Press","department":[{"_id":"BjHo"}],"publication_status":"published","year":"2019","volume":867,"date_updated":"2024-03-28T23:30:36Z","date_created":"2019-04-07T21:59:14Z","related_material":{"link":[{"url":"https://doi.org/10.1017/jfm.2019.191","relation":"supplementary_material"}],"record":[{"id":"7258","relation":"dissertation_contains","status":"public"}]},"author":[{"id":"40315C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-4271","first_name":"Davide","last_name":"Scarselli","full_name":"Scarselli, Davide"},{"full_name":"Kühnen, Jakob","first_name":"Jakob","last_name":"Kühnen","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4312-0179"},{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"}],"publication_identifier":{"issn":["00221120"],"eissn":["14697645"]},"month":"05","project":[{"_id":"25152F3A-B435-11E9-9278-68D0E5697425","grant_number":"306589","name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7"},{"grant_number":"737549","_id":"25104D44-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Eliminating turbulence in oil pipelines"}],"isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1807.05357"}],"external_id":{"arxiv":["1807.05357"],"isi":["000462606100001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1017/jfm.2019.191"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1104/pp.19.00201"}],"oa":1,"external_id":{"isi":["000470086100045"],"pmid":["30936248"]},"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","doi":"10.1104/pp.19.00201","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"month":"06","pmid":1,"acknowledgement":"We thank Dr. H. Fukaki (University of Kobe), Dr. R. Offringa (Leiden University), Dr. Jianwei Pan (Zhejiang Normal University), and Dr. M. Estelle (University of California at San Diego) for providing mutants and transgenic line seeds.\r\nThis work was supported by the Ministry of Education, Culture, Sports, Science, and Technology (Grant-in-Aid for Scientific Research no. JP25114518 to K.H.), the Biotechnology and Biological Sciences Research Council (award no. BB/L009366/1 to R.N. and S.K.), and the European Union’s Horizon2020 program (European Research Council grant agreement no. 742985 to J.F.).","year":"2019","department":[{"_id":"JiFr"}],"publisher":"ASPB","publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"11626"},{"id":"8822","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Oochi, A","last_name":"Oochi","first_name":"A"},{"full_name":"Hajny, Jakub","first_name":"Jakub","last_name":"Hajny","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2140-7195"},{"last_name":"Fukui","first_name":"K","full_name":"Fukui, K"},{"full_name":"Nakao, Y","first_name":"Y","last_name":"Nakao"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368","first_name":"Michelle C","last_name":"Gallei","full_name":"Gallei, Michelle C"},{"full_name":"Quareshy, M","last_name":"Quareshy","first_name":"M"},{"last_name":"Takahashi","first_name":"K","full_name":"Takahashi, K"},{"first_name":"T","last_name":"Kinoshita","full_name":"Kinoshita, T"},{"last_name":"Harborough","first_name":"SR","full_name":"Harborough, SR"},{"full_name":"Kepinski, S","first_name":"S","last_name":"Kepinski"},{"last_name":"Kasahara","first_name":"H","full_name":"Kasahara, H"},{"first_name":"RM","last_name":"Napier","full_name":"Napier, RM"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"},{"first_name":"KI","last_name":"Hayashi","full_name":"Hayashi, KI"}],"volume":180,"date_created":"2019-04-09T08:38:20Z","date_updated":"2024-03-28T23:30:38Z","ec_funded":1,"citation":{"ista":"Oochi A, Hajny J, Fukui K, Nakao Y, Gallei MC, Quareshy M, Takahashi K, Kinoshita T, Harborough S, Kepinski S, Kasahara H, Napier R, Friml J, Hayashi K. 2019. Pinstatic acid promotes auxin transport by inhibiting PIN internalization. Plant Physiology. 180(2), 1152–1165.","apa":"Oochi, A., Hajny, J., Fukui, K., Nakao, Y., Gallei, M. C., Quareshy, M., … Hayashi, K. (2019). Pinstatic acid promotes auxin transport by inhibiting PIN internalization. Plant Physiology. ASPB. https://doi.org/10.1104/pp.19.00201","ieee":"A. Oochi et al., “Pinstatic acid promotes auxin transport by inhibiting PIN internalization,” Plant Physiology, vol. 180, no. 2. ASPB, pp. 1152–1165, 2019.","ama":"Oochi A, Hajny J, Fukui K, et al. Pinstatic acid promotes auxin transport by inhibiting PIN internalization. Plant Physiology. 2019;180(2):1152-1165. doi:10.1104/pp.19.00201","chicago":"Oochi, A, Jakub Hajny, K Fukui, Y Nakao, Michelle C Gallei, M Quareshy, K Takahashi, et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN Internalization.” Plant Physiology. ASPB, 2019. https://doi.org/10.1104/pp.19.00201.","mla":"Oochi, A., et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN Internalization.” Plant Physiology, vol. 180, no. 2, ASPB, 2019, pp. 1152–65, doi:10.1104/pp.19.00201.","short":"A. Oochi, J. Hajny, K. Fukui, Y. Nakao, M.C. Gallei, M. Quareshy, K. Takahashi, T. Kinoshita, S. Harborough, S. Kepinski, H. Kasahara, R. Napier, J. Friml, K. Hayashi, Plant Physiology 180 (2019) 1152–1165."},"publication":"Plant Physiology","page":"1152-1165","article_type":"original","date_published":"2019-06-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6260","intvolume":" 180","status":"public","title":"Pinstatic acid promotes auxin transport by inhibiting PIN internalization","oa_version":"Published Version","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"Polar auxin transport plays a pivotal role in plant growth and development. PIN auxin efflux carriers regulate directional auxin movement by establishing local auxin maxima, minima, and gradients that drive multiple developmental processes and responses to environmental signals. Auxin has been proposed to modulate its own transport by regulating subcellular PIN trafficking via processes such as clathrin-mediated PIN endocytosis and constitutive recycling. Here, we further investigated the mechanisms by which auxin affects PIN trafficking by screening auxin analogs and identified pinstatic acid (PISA) as a positive modulator of polar auxin transport in Arabidopsis thaliana. PISA had an auxin-like effect on hypocotyl elongation and adventitious root formation via positive regulation of auxin transport. PISA did not activate SCFTIR1/AFB signaling and yet induced PIN accumulation at the cell surface by inhibiting PIN internalization from the plasma membrane. This work demonstrates PISA to be a promising chemical tool to dissect the regulatory mechanisms behind subcellular PIN trafficking and auxin transport."}]},{"volume":177,"date_updated":"2024-03-28T23:30:39Z","date_created":"2019-06-02T21:59:12Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/how-the-cytoplasm-separates-from-the-yolk/","description":"News on IST Homepage","relation":"press_release"}],"record":[{"status":"public","relation":"dissertation_contains","id":"8350"}]},"author":[{"full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan","last_name":"Shamipour"},{"first_name":"Roland","last_name":"Kardos","id":"4039350E-F248-11E8-B48F-1D18A9856A87","full_name":"Kardos, Roland"},{"full_name":"Xue, Shi-lei","last_name":"Xue","first_name":"Shi-lei","id":"31D2C804-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"publisher":"Elsevier","department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"BjHo"}],"publication_status":"published","pmid":1,"acknowledgement":"We would like to thank Pierre Recho, Guillaume Salbreux, and Silvia Grigolon for advice on the theory, Lila Solnica-Krezel for kindly providing us with zebrafish dachsous mutants, members of the Heisenberg and Hannezo groups for fruitful discussions, and the Bioimaging and zebrafish facilities at IST Austria for their continuous support. This project has received funding from the European Union (European Research Council Advanced Grant 742573 to C.P.H.) and from the Austrian Science Fund (FWF) (P 31639 to E.H.).","year":"2019","ec_funded":1,"file_date_updated":"2020-10-21T07:22:34Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"doi":"10.1016/j.cell.2019.04.030","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425"},{"name":"Active mechano-chemical description of the cell cytoskeleton","call_identifier":"FWF","grant_number":"P31639","_id":"268294B6-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"pmid":["31080065"],"isi":["000469415100013"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.cell.2019.04.030","open_access":"1"}],"publication_identifier":{"eissn":["10974172"],"issn":["00928674"]},"month":"05","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":3356292,"creator":"dernst","file_name":"2019_Cell_Shamipour_accepted.pdf","access_level":"open_access","date_created":"2020-10-21T07:22:34Z","date_updated":"2020-10-21T07:22:34Z","checksum":"aea43726d80e35ce3885073a5f05c3e3","success":1,"relation":"main_file","file_id":"8686"}],"intvolume":" 177","title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes","status":"public","ddc":["570"],"_id":"6508","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"6","abstract":[{"text":"Segregation of maternal determinants within the oocyte constitutes the first step in embryo patterning. In zebrafish oocytes, extensive ooplasmic streaming leads to the segregation of ooplasm from yolk granules along the animal-vegetal axis of the oocyte. Here, we show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the oocyte. This wave functions in segregation by both pulling ooplasm animally and pushing yolk granules vegetally. Using biophysical experimentation and theory, we show that ooplasm pulling is mediated by bulk actin network flows exerting friction forces on the ooplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. Our study defines a novel role of cell-cycle-controlled bulk actin polymerization waves in oocyte polarization via ooplasmic segregation.","lang":"eng"}],"type":"journal_article","date_published":"2019-05-30T00:00:00Z","page":"1463-1479.e18","article_type":"original","citation":{"chicago":"Shamipour, Shayan, Roland Kardos, Shi-lei Xue, Björn Hof, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.04.030.","mla":"Shamipour, Shayan, et al. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes.” Cell, vol. 177, no. 6, Elsevier, 2019, p. 1463–1479.e18, doi:10.1016/j.cell.2019.04.030.","short":"S. Shamipour, R. Kardos, S. Xue, B. Hof, E.B. Hannezo, C.-P.J. Heisenberg, Cell 177 (2019) 1463–1479.e18.","ista":"Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. 2019. Bulk actin dynamics drive phase segregation in zebrafish oocytes. Cell. 177(6), 1463–1479.e18.","apa":"Shamipour, S., Kardos, R., Xue, S., Hof, B., Hannezo, E. B., & Heisenberg, C.-P. J. (2019). Bulk actin dynamics drive phase segregation in zebrafish oocytes. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.04.030","ieee":"S. Shamipour, R. Kardos, S. Xue, B. Hof, E. B. Hannezo, and C.-P. J. Heisenberg, “Bulk actin dynamics drive phase segregation in zebrafish oocytes,” Cell, vol. 177, no. 6. Elsevier, p. 1463–1479.e18, 2019.","ama":"Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. Bulk actin dynamics drive phase segregation in zebrafish oocytes. Cell. 2019;177(6):1463-1479.e18. doi:10.1016/j.cell.2019.04.030"},"publication":"Cell","article_processing_charge":"No","has_accepted_license":"1","day":"30","scopus_import":"1"},{"issue":"4","type":"journal_article","file":[{"file_name":"2019_Cell_Schwayer_accepted.pdf","access_level":"open_access","creator":"dernst","file_size":8805878,"content_type":"application/pdf","file_id":"8684","relation":"main_file","date_updated":"2020-10-21T07:09:45Z","date_created":"2020-10-21T07:09:45Z","success":1,"checksum":"33dac4bb77ee630e2666e936b4d57980"}],"oa_version":"Submitted Version","_id":"7001","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Mechanosensation of tight junctions depends on ZO-1 phase separation and flow","status":"public","ddc":["570"],"intvolume":" 179","day":"31","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2019-10-31T00:00:00Z","publication":"Cell","citation":{"short":"C. Schwayer, S. Shamipour, K. Pranjic-Ferscha, A. Schauer, M. Balda, M. Tada, K. Matter, C.-P.J. Heisenberg, Cell 179 (2019) 937–952.e18.","mla":"Schwayer, Cornelia, et al. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” Cell, vol. 179, no. 4, Cell Press, 2019, p. 937–952.e18, doi:10.1016/j.cell.2019.10.006.","chicago":"Schwayer, Cornelia, Shayan Shamipour, Kornelija Pranjic-Ferscha, Alexandra Schauer, M Balda, M Tada, K Matter, and Carl-Philipp J Heisenberg. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” Cell. Cell Press, 2019. https://doi.org/10.1016/j.cell.2019.10.006.","ama":"Schwayer C, Shamipour S, Pranjic-Ferscha K, et al. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. 2019;179(4):937-952.e18. doi:10.1016/j.cell.2019.10.006","ieee":"C. Schwayer et al., “Mechanosensation of tight junctions depends on ZO-1 phase separation and flow,” Cell, vol. 179, no. 4. Cell Press, p. 937–952.e18, 2019.","apa":"Schwayer, C., Shamipour, S., Pranjic-Ferscha, K., Schauer, A., Balda, M., Tada, M., … Heisenberg, C.-P. J. (2019). Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. Cell Press. https://doi.org/10.1016/j.cell.2019.10.006","ista":"Schwayer C, Shamipour S, Pranjic-Ferscha K, Schauer A, Balda M, Tada M, Matter K, Heisenberg C-PJ. 2019. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. 179(4), 937–952.e18."},"article_type":"original","page":"937-952.e18","file_date_updated":"2020-10-21T07:09:45Z","ec_funded":1,"author":[{"full_name":"Schwayer, Cornelia","first_name":"Cornelia","last_name":"Schwayer","id":"3436488C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5130-2226"},{"first_name":"Shayan","last_name":"Shamipour","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Shamipour, Shayan"},{"full_name":"Pranjic-Ferscha, Kornelija","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","last_name":"Pranjic-Ferscha","first_name":"Kornelija"},{"first_name":"Alexandra","last_name":"Schauer","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7659-9142","full_name":"Schauer, Alexandra"},{"last_name":"Balda","first_name":"M","full_name":"Balda, M"},{"full_name":"Tada, M","first_name":"M","last_name":"Tada"},{"full_name":"Matter, K","first_name":"K","last_name":"Matter"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"related_material":{"record":[{"id":"7186","status":"public","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"8350"}],"link":[{"url":"https://ist.ac.at/en/news/biochemistry-meets-mechanics-the-sensitive-nature-of-cell-cell-contact-formation-in-embryo-development/","description":"News auf IST Website","relation":"press_release"}]},"date_created":"2019-11-12T12:51:06Z","date_updated":"2024-03-28T23:30:39Z","volume":179,"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"CaHe"},{"_id":"BjHo"}],"publisher":"Cell Press","month":"10","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"doi":"10.1016/j.cell.2019.10.006","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000493898000012"],"pmid":["31675500"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425"}]},{"file_date_updated":"2020-10-17T22:30:03Z","year":"2019","department":[{"_id":"MiSi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"id":"6328","status":"public","relation":"part_of_dissertation"},{"id":"15","status":"public","relation":"part_of_dissertation"},{"id":"6877","relation":"part_of_dissertation","status":"public"}],"link":[{"url":"https://ist.ac.at/en/news/feeling-like-a-cell/","relation":"press_release"}]},"author":[{"first_name":"Aglaja","last_name":"Kopf","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2187-6656","full_name":"Kopf, Aglaja"}],"date_created":"2019-09-19T08:19:44Z","date_updated":"2023-10-18T08:49:17Z","publication_identifier":{"isbn":["978-3-99078-002-2"],"eissn":["2663-337X"]},"month":"07","oa":1,"project":[{"name":"Nano-Analytics of Cellular Systems","call_identifier":"FWF","grant_number":"W01250-B20","_id":"265E2996-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/AT:ISTA:6891","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"While cells of mesenchymal or epithelial origin perform their effector functions in a purely anchorage dependent manner, cells derived from the hematopoietic lineage are not committed to operate only within a specific niche. Instead, these cells are able to function autonomously of the molecular composition in a broad range of tissue compartments. By this means, cells of the hematopoietic lineage retain the capacity to disseminate into connective tissue and recirculate between organs, building the foundation for essential processes such as tissue regeneration or immune surveillance. \r\nCells of the immune system, specifically leukocytes, are extraordinarily good at performing this task. These cells are able to flexibly shift their mode of migration between an adhesion-mediated and an adhesion-independent manner, instantaneously accommodating for any changes in molecular composition of the external scaffold. The key component driving directed leukocyte migration is the chemokine receptor 7, which guides the cell along gradients of chemokine ligand. Therefore, the physical destination of migrating leukocytes is purely deterministic, i.e. given by global directional cues such as chemokine gradients. \r\nNevertheless, these cells typically reside in three-dimensional scaffolds of inhomogeneous complexity, raising the question whether cells are able to locally discriminate between multiple optional migration routes. Current literature provides evidence that leukocytes, specifically dendritic cells, do indeed probe their surrounding by virtue of multiple explorative protrusions. However, it remains enigmatic how these cells decide which one is the more favorable route to follow and what are the key players involved in performing this task. Due to the heterogeneous environment of most tissues, and the vast adaptability of migrating leukocytes, at this time it is not clear to what extent leukocytes are able to optimize their migratory strategy by adapting their level of adhesiveness. And, given the fact that leukocyte migration is characterized by branched cell shapes in combination with high migration velocities, it is reasonable to assume that these cells require fine tuned shape maintenance mechanisms that tightly coordinate protrusion and adhesion dynamics in a spatiotemporal manner. \r\nTherefore, this study aimed to elucidate how rapidly migrating leukocytes opt for an ideal migratory path while maintaining a continuous cell shape and balancing adhesive forces to efficiently navigate through complex microenvironments. \r\nThe results of this study unraveled a role for the microtubule cytoskeleton in promoting the decision making process during path finding and for the first time point towards a microtubule-mediated function in cell shape maintenance of highly ramified cells such as dendritic cells. Furthermore, we found that migrating low-adhesive leukocytes are able to instantaneously adapt to increased tensile load by engaging adhesion receptors. This response was only occurring tangential to the substrate while adhesive properties in the vertical direction were not increased. As leukocytes are primed for rapid migration velocities, these results demonstrate that leukocyte integrins are able to confer a high level of traction forces parallel to the cell membrane along the direction of migration without wasting energy in gluing the cell to the substrate. \r\nThus, the data in the here presented thesis provide new insights into the pivotal role of cytoskeletal dynamics and the mechanisms of force transduction during leukocyte migration. \r\nThereby the here presented results help to further define fundamental principles underlying leukocyte migration and open up potential therapeutic avenues of clinical relevance.\r\n"}],"_id":"6891","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"The implication of cytoskeletal dynamics on leukocyte migration","ddc":["570"],"oa_version":"Published Version","file":[{"file_size":74735267,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"akopf","access_level":"closed","embargo_to":"open_access","file_name":"Kopf_PhD_Thesis.docx","checksum":"00d100d6468e31e583051e0a006b640c","date_created":"2019-10-15T05:28:42Z","date_updated":"2020-10-17T22:30:03Z","relation":"source_file","file_id":"6950"},{"creator":"akopf","content_type":"application/pdf","file_size":52787224,"access_level":"open_access","file_name":"Kopf_PhD_Thesis1.pdf","checksum":"5d1baa899993ae6ca81aebebe1797000","date_created":"2019-10-15T05:28:47Z","date_updated":"2020-10-17T22:30:03Z","file_id":"6951","embargo":"2020-10-16","relation":"main_file"}],"keyword":["cell biology","immunology","leukocyte","migration","microfluidics"],"has_accepted_license":"1","article_processing_charge":"No","day":"24","citation":{"ama":"Kopf A. The implication of cytoskeletal dynamics on leukocyte migration. 2019. doi:10.15479/AT:ISTA:6891","apa":"Kopf, A. (2019). The implication of cytoskeletal dynamics on leukocyte migration. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6891","ieee":"A. Kopf, “The implication of cytoskeletal dynamics on leukocyte migration,” Institute of Science and Technology Austria, 2019.","ista":"Kopf A. 2019. The implication of cytoskeletal dynamics on leukocyte migration. Institute of Science and Technology Austria.","short":"A. Kopf, The Implication of Cytoskeletal Dynamics on Leukocyte Migration, Institute of Science and Technology Austria, 2019.","mla":"Kopf, Aglaja. The Implication of Cytoskeletal Dynamics on Leukocyte Migration. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6891.","chicago":"Kopf, Aglaja. “The Implication of Cytoskeletal Dynamics on Leukocyte Migration.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6891."},"page":"171","date_published":"2019-07-24T00:00:00Z"},{"ec_funded":1,"publication_status":"published","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"}],"publisher":"Springer Nature","year":"2019","pmid":1,"date_created":"2019-04-17T06:52:28Z","date_updated":"2024-03-28T23:30:40Z","volume":568,"author":[{"orcid":"0000-0003-2856-3369","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","last_name":"Renkawitz","first_name":"Jörg","full_name":"Renkawitz, Jörg"},{"full_name":"Kopf, Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2187-6656","first_name":"Aglaja","last_name":"Kopf"},{"id":"489E3F00-F248-11E8-B48F-1D18A9856A87","last_name":"Stopp","first_name":"Julian A","full_name":"Stopp, Julian A"},{"id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","first_name":"Ingrid","last_name":"de Vries","full_name":"de Vries, Ingrid"},{"first_name":"Meghan K.","last_name":"Driscoll","full_name":"Driscoll, Meghan K."},{"full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","first_name":"Jack","last_name":"Merrin"},{"last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert"},{"first_name":"Erik S.","last_name":"Welf","full_name":"Welf, Erik S."},{"full_name":"Danuser, Gaudenz","last_name":"Danuser","first_name":"Gaudenz"},{"full_name":"Fiolka, Reto","first_name":"Reto","last_name":"Fiolka"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14697"},{"relation":"dissertation_contains","status":"public","id":"6891"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/leukocytes-use-their-nucleus-as-a-ruler-to-choose-path-of-least-resistance/"}]},"month":"04","isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425"},{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373","call_identifier":"H2020","name":"Cellular navigation along spatial gradients"},{"_id":"265FAEBA-B435-11E9-9278-68D0E5697425","grant_number":"W01250-B20","name":"Nano-Analytics of Cellular Systems","call_identifier":"FWF"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"grant_number":"ALTF 1396-2014","_id":"25A48D24-B435-11E9-9278-68D0E5697425","name":"Molecular and system level view of immune cell migration"}],"external_id":{"isi":["000465594200050"],"pmid":["30944468"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217284/","open_access":"1"}],"oa":1,"acknowledged_ssus":[{"_id":"SSU"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41586-019-1087-5","type":"journal_article","abstract":[{"lang":"eng","text":"During metazoan development, immune surveillance and cancer dissemination, cells migrate in complex three-dimensional microenvironments1,2,3. These spaces are crowded by cells and extracellular matrix, generating mazes with differently sized gaps that are typically smaller than the diameter of the migrating cell4,5. Most mesenchymal and epithelial cells and some—but not all—cancer cells actively generate their migratory path using pericellular tissue proteolysis6. By contrast, amoeboid cells such as leukocytes use non-destructive strategies of locomotion7, raising the question how these extremely fast cells navigate through dense tissues. Here we reveal that leukocytes sample their immediate vicinity for large pore sizes, and are thereby able to choose the path of least resistance. This allows them to circumnavigate local obstacles while effectively following global directional cues such as chemotactic gradients. Pore-size discrimination is facilitated by frontward positioning of the nucleus, which enables the cells to use their bulkiest compartment as a mechanical gauge. Once the nucleus and the closely associated microtubule organizing centre pass the largest pore, cytoplasmic protrusions still lingering in smaller pores are retracted. These retractions are coordinated by dynamic microtubules; when microtubules are disrupted, migrating cells lose coherence and frequently fragment into migratory cytoplasmic pieces. As nuclear positioning in front of the microtubule organizing centre is a typical feature of amoeboid migration, our findings link the fundamental organization of cellular polarity to the strategy of locomotion."}],"title":"Nuclear positioning facilitates amoeboid migration along the path of least resistance","status":"public","intvolume":" 568","_id":"6328","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Submitted Version","scopus_import":"1","day":"25","article_processing_charge":"No","article_type":"letter_note","page":"546-550","publication":"Nature","citation":{"ama":"Renkawitz J, Kopf A, Stopp JA, et al. Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. 2019;568:546-550. doi:10.1038/s41586-019-1087-5","apa":"Renkawitz, J., Kopf, A., Stopp, J. A., de Vries, I., Driscoll, M. K., Merrin, J., … Sixt, M. K. (2019). Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1087-5","ieee":"J. Renkawitz et al., “Nuclear positioning facilitates amoeboid migration along the path of least resistance,” Nature, vol. 568. Springer Nature, pp. 546–550, 2019.","ista":"Renkawitz J, Kopf A, Stopp JA, de Vries I, Driscoll MK, Merrin J, Hauschild R, Welf ES, Danuser G, Fiolka R, Sixt MK. 2019. Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. 568, 546–550.","short":"J. Renkawitz, A. Kopf, J.A. Stopp, I. de Vries, M.K. Driscoll, J. Merrin, R. Hauschild, E.S. Welf, G. Danuser, R. Fiolka, M.K. Sixt, Nature 568 (2019) 546–550.","mla":"Renkawitz, Jörg, et al. “Nuclear Positioning Facilitates Amoeboid Migration along the Path of Least Resistance.” Nature, vol. 568, Springer Nature, 2019, pp. 546–50, doi:10.1038/s41586-019-1087-5.","chicago":"Renkawitz, Jörg, Aglaja Kopf, Julian A Stopp, Ingrid de Vries, Meghan K. Driscoll, Jack Merrin, Robert Hauschild, et al. “Nuclear Positioning Facilitates Amoeboid Migration along the Path of Least Resistance.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1087-5."},"date_published":"2019-04-25T00:00:00Z"},{"month":"09","publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.cell.2019.08.047","isi":1,"quality_controlled":"1","external_id":{"isi":["000486618500011"],"pmid":["31539498"]},"date_updated":"2024-03-28T23:30:40Z","date_created":"2019-09-15T22:00:46Z","volume":179,"author":[{"full_name":"Kopf, Aglaja","orcid":"0000-0002-2187-6656","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","last_name":"Kopf","first_name":"Aglaja"},{"last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6891"}]},"publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"Elsevier","year":"2019","pmid":1,"day":"19","article_processing_charge":"No","scopus_import":"1","date_published":"2019-09-19T00:00:00Z","article_type":"original","page":"51-53","publication":"Cell","citation":{"ista":"Kopf A, Sixt MK. 2019. The neural crest pitches in to remove apoptotic debris. Cell. 179(1), 51–53.","apa":"Kopf, A., & Sixt, M. K. (2019). The neural crest pitches in to remove apoptotic debris. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.08.047","ieee":"A. Kopf and M. K. Sixt, “The neural crest pitches in to remove apoptotic debris,” Cell, vol. 179, no. 1. Elsevier, pp. 51–53, 2019.","ama":"Kopf A, Sixt MK. The neural crest pitches in to remove apoptotic debris. Cell. 2019;179(1):51-53. doi:10.1016/j.cell.2019.08.047","chicago":"Kopf, Aglaja, and Michael K Sixt. “The Neural Crest Pitches in to Remove Apoptotic Debris.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.08.047.","mla":"Kopf, Aglaja, and Michael K. Sixt. “The Neural Crest Pitches in to Remove Apoptotic Debris.” Cell, vol. 179, no. 1, Elsevier, 2019, pp. 51–53, doi:10.1016/j.cell.2019.08.047.","short":"A. Kopf, M.K. Sixt, Cell 179 (2019) 51–53."},"issue":"1","type":"journal_article","oa_version":"None","status":"public","title":"The neural crest pitches in to remove apoptotic debris","intvolume":" 179","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6877"},{"doi":"10.1016/j.neuron.2019.08.021","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["31487522"],"isi":["000484400200002"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.neuron.2019.08.021"}],"quality_controlled":"1","isi":1,"month":"09","publication_identifier":{"eissn":["10974199"],"issn":["08966273"]},"author":[{"first_name":"Ximena","last_name":"Contreras","id":"475990FE-F248-11E8-B48F-1D18A9856A87","full_name":"Contreras, Ximena"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7902"}]},"date_updated":"2024-03-28T23:30:42Z","date_created":"2019-08-25T22:00:50Z","volume":103,"year":"2019","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"SiHi"}],"date_published":"2019-09-04T00:00:00Z","publication":"Neuron","citation":{"ista":"Contreras X, Hippenmeyer S. 2019. Memo1 tiles the radial glial cell grid. Neuron. 103(5), 750–752.","apa":"Contreras, X., & Hippenmeyer, S. (2019). Memo1 tiles the radial glial cell grid. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.08.021","ieee":"X. Contreras and S. Hippenmeyer, “Memo1 tiles the radial glial cell grid,” Neuron, vol. 103, no. 5. Elsevier, pp. 750–752, 2019.","ama":"Contreras X, Hippenmeyer S. Memo1 tiles the radial glial cell grid. Neuron. 2019;103(5):750-752. doi:10.1016/j.neuron.2019.08.021","chicago":"Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial Cell Grid.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.08.021.","mla":"Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial Cell Grid.” Neuron, vol. 103, no. 5, Elsevier, 2019, pp. 750–52, doi:10.1016/j.neuron.2019.08.021.","short":"X. Contreras, S. Hippenmeyer, Neuron 103 (2019) 750–752."},"article_type":"letter_note","page":"750-752","day":"04","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6830","title":"Memo1 tiles the radial glial cell grid","status":"public","intvolume":" 103","issue":"5","type":"journal_article"},{"issue":"13","abstract":[{"lang":"eng","text":"Cortical microtubule arrays in elongating epidermal cells in both the root and stem of plants have the propensity of dynamic reorientations that are correlated with the activation or inhibition of growth. Factors regulating plant growth, among them the hormone auxin, have been recognized as regulators of microtubule array orientations. Some previous work in the field has aimed at elucidating the causal relationship between cell growth, the signaling of auxin or other growth-regulating factors, and microtubule array reorientations, with various conclusions. Here, we revisit this problem of causality with a comprehensive set of experiments in Arabidopsis thaliana, using the now available pharmacological and genetic tools. We use isolated, auxin-depleted hypocotyls, an experimental system allowing for full control of both growth and auxin signaling. We demonstrate that reorientation of microtubules is not directly triggered by an auxin signal during growth activation. Instead, reorientation is triggered by the activation of the growth process itself and is auxin-independent in its nature. We discuss these findings in the context of previous relevant work, including that on the mechanical regulation of microtubule array orientation."}],"type":"journal_article","file":[{"file_name":"2019_JournalMolecularScience_Adamowski.pdf","access_level":"open_access","content_type":"application/pdf","file_size":3330291,"creator":"dernst","relation":"main_file","file_id":"6645","date_updated":"2020-07-14T12:47:34Z","date_created":"2019-07-17T06:17:15Z","checksum":"dd9d1cbb933a72ceb666c9667890ac51"}],"oa_version":"Published Version","intvolume":" 20","status":"public","title":"Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling","ddc":["580"],"_id":"6627","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","article_processing_charge":"Yes","day":"07","scopus_import":"1","date_published":"2019-07-07T00:00:00Z","article_type":"original","citation":{"chicago":"Adamowski, Maciek, Lanxin Li, and Jiří Friml. “Reorientation of Cortical Microtubule Arrays in the Hypocotyl of Arabidopsis Thaliana Is Induced by the Cell Growth Process and Independent of Auxin Signaling.” International Journal of Molecular Sciences. MDPI, 2019. https://doi.org/10.3390/ijms20133337.","short":"M. Adamowski, L. Li, J. Friml, International Journal of Molecular Sciences 20 (2019).","mla":"Adamowski, Maciek, et al. “Reorientation of Cortical Microtubule Arrays in the Hypocotyl of Arabidopsis Thaliana Is Induced by the Cell Growth Process and Independent of Auxin Signaling.” International Journal of Molecular Sciences, vol. 20, no. 13, 3337, MDPI, 2019, doi:10.3390/ijms20133337.","ieee":"M. Adamowski, L. Li, and J. Friml, “Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling,” International Journal of Molecular Sciences, vol. 20, no. 13. MDPI, 2019.","apa":"Adamowski, M., Li, L., & Friml, J. (2019). Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms20133337","ista":"Adamowski M, Li L, Friml J. 2019. Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. 20(13), 3337.","ama":"Adamowski M, Li L, Friml J. Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. 2019;20(13). doi:10.3390/ijms20133337"},"publication":"International Journal of Molecular Sciences","ec_funded":1,"file_date_updated":"2020-07-14T12:47:34Z","article_number":"3337","volume":20,"date_updated":"2024-03-28T23:30:44Z","date_created":"2019-07-11T12:00:32Z","related_material":{"record":[{"id":"10083","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Adamowski, Maciek","last_name":"Adamowski","first_name":"Maciek","orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Li, Lanxin","first_name":"Lanxin","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"}],"department":[{"_id":"JiFr"}],"publisher":"MDPI","publication_status":"published","pmid":1,"year":"2019","publication_identifier":{"eissn":["1422-0067"]},"month":"07","language":[{"iso":"eng"}],"doi":"10.3390/ijms20133337","project":[{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"},{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000477041100221"],"pmid":["31284661"]},"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":["0730-0301"]},"oa":1,"external_id":{"isi":["000498397300007"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"doi":"10.1145/3355089.3356576","language":[{"iso":"eng"}],"article_number":"157","file_date_updated":"2020-07-14T12:47:49Z","ec_funded":1,"year":"2019","publication_status":"published","department":[{"_id":"BeBi"}],"publisher":"ACM","author":[{"last_name":"Hafner","first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","full_name":"Hafner, Christian"},{"first_name":"Christian","last_name":"Schumacher","full_name":"Schumacher, Christian"},{"first_name":"Espen","last_name":"Knoop","full_name":"Knoop, Espen"},{"full_name":"Auzinger, Thomas","first_name":"Thomas","last_name":"Auzinger","id":"4718F954-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1546-3265"},{"last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd"},{"first_name":"Moritz","last_name":"Bächer","full_name":"Bächer, Moritz"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12897"}]},"date_created":"2019-11-26T14:22:09Z","date_updated":"2024-03-28T23:30:47Z","volume":38,"scopus_import":"1","day":"06","has_accepted_license":"1","article_processing_charge":"No","publication":"ACM Transactions on Graphics","citation":{"ama":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. 2019;38(6). doi:10.1145/3355089.3356576","ista":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. 2019. X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. 38(6), 157.","ieee":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, and M. Bächer, “X-CAD: Optimizing CAD Models with Extended Finite Elements,” ACM Transactions on Graphics, vol. 38, no. 6. ACM, 2019.","apa":"Hafner, C., Schumacher, C., Knoop, E., Auzinger, T., Bickel, B., & Bächer, M. (2019). X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3355089.3356576","mla":"Hafner, Christian, et al. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” ACM Transactions on Graphics, vol. 38, no. 6, 157, ACM, 2019, doi:10.1145/3355089.3356576.","short":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, M. Bächer, ACM Transactions on Graphics 38 (2019).","chicago":"Hafner, Christian, Christian Schumacher, Espen Knoop, Thomas Auzinger, Bernd Bickel, and Moritz Bächer. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3355089.3356576."},"article_type":"original","date_published":"2019-11-06T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We propose a novel generic shape optimization method for CAD models based on the eXtended Finite Element Method (XFEM). Our method works directly on the intersection between the model and a regular simulation grid, without the need to mesh or remesh, thus removing a bottleneck of classical shape optimization strategies. This is made possible by a novel hierarchical integration scheme that accurately integrates finite element quantities with sub-element precision. For optimization, we efficiently compute analytical shape derivatives of the entire framework, from model intersection to integration rule generation and XFEM simulation. Moreover, we describe a differentiable projection of shape parameters onto a constraint manifold spanned by user-specified shape preservation, consistency, and manufacturability constraints. We demonstrate the utility of our approach by optimizing mass distribution, strength-to-weight ratio, and inverse elastic shape design objectives directly on parameterized 3D CAD models."}],"issue":"6","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7117","title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","status":"public","ddc":["000"],"intvolume":" 38","oa_version":"Submitted Version","file":[{"relation":"supplementary_material","title":"X-CAD Supplemental Material","file_id":"7119","checksum":"56a2fb019adcb556d2b022f5e5acb68c","date_created":"2019-11-26T14:24:26Z","date_updated":"2020-07-14T12:47:49Z","access_level":"open_access","file_name":"xcad_sup_mat_siga19.pdf","file_size":1673176,"content_type":"application/pdf","creator":"bbickel"},{"checksum":"5f29d76aceb5102e766cbab9b17d776e","date_created":"2019-11-26T14:24:27Z","date_updated":"2020-07-14T12:47:49Z","relation":"main_file","title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","file_id":"7120","file_size":14563618,"content_type":"application/pdf","creator":"bbickel","access_level":"open_access","file_name":"XCAD_authors_version.pdf","description":"This is the author's version of the work."},{"file_name":"XCAD_video.mp4","access_level":"open_access","content_type":"video/mp4","file_size":259979129,"creator":"bbickel","relation":"main_file","file_id":"7121","date_created":"2019-11-26T14:27:37Z","date_updated":"2020-07-14T12:47:49Z","checksum":"0d31e123286cbec9e28b2001c2bb0d55"}]},{"volume":122,"date_created":"2019-03-31T21:59:12Z","date_updated":"2024-03-28T23:30:48Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9728"}]},"author":[{"last_name":"Agrawal","first_name":"Nishchal","id":"469E6004-F248-11E8-B48F-1D18A9856A87","full_name":"Agrawal, Nishchal"},{"full_name":"Choueiri, George H","first_name":"George H","last_name":"Choueiri","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"}],"department":[{"_id":"BjHo"}],"publisher":"American Physical Society","publication_status":"published","year":"2019","article_number":"114502","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.122.114502","isi":1,"quality_controlled":"1","external_id":{"isi":["000461922000006"],"arxiv":["1809.06358"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.06358"}],"publication_identifier":{"eissn":["10797114"],"issn":["00319007"]},"month":"03","oa_version":"Preprint","intvolume":" 122","title":"Transition to turbulence in particle laden flows","status":"public","_id":"6189","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"11","abstract":[{"text":"Suspended particles can alter the properties of fluids and in particular also affect the transition fromlaminar to turbulent flow. An earlier study [Mataset al.,Phys. Rev. Lett.90, 014501 (2003)] reported howthe subcritical (i.e., hysteretic) transition to turbulent puffs is affected by the addition of particles. Here weshow that in addition to this known transition, with increasing concentration a supercritical (i.e.,continuous) transition to a globally fluctuating state is found. At the same time the Newtonian-typetransition to puffs is delayed to larger Reynolds numbers. At even higher concentration only the globallyfluctuating state is found. The dynamics of particle laden flows are hence determined by two competinginstabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle inducedglobally fluctuating state at high, and a coexistence state at intermediate concentrations.","lang":"eng"}],"type":"journal_article","date_published":"2019-03-22T00:00:00Z","citation":{"mla":"Agrawal, Nishchal, et al. “Transition to Turbulence in Particle Laden Flows.” Physical Review Letters, vol. 122, no. 11, 114502, American Physical Society, 2019, doi:10.1103/PhysRevLett.122.114502.","short":"N. Agrawal, G.H. Choueiri, B. Hof, Physical Review Letters 122 (2019).","chicago":"Agrawal, Nishchal, George H Choueiri, and Björn Hof. “Transition to Turbulence in Particle Laden Flows.” Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/PhysRevLett.122.114502.","ama":"Agrawal N, Choueiri GH, Hof B. Transition to turbulence in particle laden flows. Physical Review Letters. 2019;122(11). doi:10.1103/PhysRevLett.122.114502","ista":"Agrawal N, Choueiri GH, Hof B. 2019. Transition to turbulence in particle laden flows. Physical Review Letters. 122(11), 114502.","ieee":"N. Agrawal, G. H. Choueiri, and B. Hof, “Transition to turbulence in particle laden flows,” Physical Review Letters, vol. 122, no. 11. American Physical Society, 2019.","apa":"Agrawal, N., Choueiri, G. H., & Hof, B. (2019). Transition to turbulence in particle laden flows. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.122.114502"},"publication":"Physical Review Letters","article_processing_charge":"No","day":"22","scopus_import":"1"}]