[{"file_date_updated":"2020-07-14T12:47:54Z","license":"https://creativecommons.org/licenses/by/4.0/","article_number":"641","author":[{"first_name":"Sergey","last_name":"Aganezov","full_name":"Aganezov, Sergey"},{"full_name":"Zban, Ilya","last_name":"Zban","first_name":"Ilya"},{"full_name":"Aksenov, Vitalii","id":"2980135A-F248-11E8-B48F-1D18A9856A87","first_name":"Vitalii","last_name":"Aksenov"},{"full_name":"Alexeev, Nikita","last_name":"Alexeev","first_name":"Nikita"},{"full_name":"Schatz, Michael C.","first_name":"Michael C.","last_name":"Schatz"}],"date_updated":"2023-09-06T14:51:06Z","date_created":"2019-12-29T23:00:46Z","volume":20,"year":"2019","publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"BMC","month":"12","publication_identifier":{"eissn":["14712105"]},"doi":"10.1186/s12859-019-3208-4","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000511618800007"]},"oa":1,"isi":1,"quality_controlled":"1","abstract":[{"text":"Background: Many cancer genomes are extensively rearranged with highly aberrant chromosomal karyotypes. Structural and copy number variations in cancer genomes can be determined via abnormal mapping of sequenced reads to the reference genome. Recently it became possible to reconcile both of these types of large-scale variations into a karyotype graph representation of the rearranged cancer genomes. Such a representation, however, does not directly describe the linear and/or circular structure of the underlying rearranged cancer chromosomes, thus limiting possible analysis of cancer genomes somatic evolutionary process as well as functional genomic changes brought by the large-scale genome rearrangements.\r\n\r\nResults: Here we address the aforementioned limitation by introducing a novel methodological framework for recovering rearranged cancer chromosomes from karyotype graphs. For a cancer karyotype graph we formulate an Eulerian Decomposition Problem (EDP) of finding a collection of linear and/or circular rearranged cancer chromosomes that are determined by the graph. We derive and prove computational complexities for several variations of the EDP. We then demonstrate that Eulerian decomposition of the cancer karyotype graphs is not always unique and present the Consistent Contig Covering Problem (CCCP) of recovering unambiguous cancer contigs from the cancer karyotype graph, and describe a novel algorithm CCR capable of solving CCCP in polynomial time. We apply CCR on a prostate cancer dataset and demonstrate that it is capable of consistently recovering large cancer contigs even when underlying cancer genomes are highly rearranged.\r\n\r\nConclusions: CCR can recover rearranged cancer contigs from karyotype graphs thereby addressing existing limitation in inferring chromosomal structures of rearranged cancer genomes and advancing our understanding of both patient/cancer-specific as well as the overall genetic instability in cancer.","lang":"eng"}],"type":"journal_article","file":[{"content_type":"application/pdf","file_size":1917374,"creator":"dernst","access_level":"open_access","file_name":"2019_BMCBioinfo_Aganezov.pdf","checksum":"7a30357efdcf8f66587ed495c0927724","date_updated":"2020-07-14T12:47:54Z","date_created":"2020-01-02T16:10:58Z","relation":"main_file","file_id":"7221"}],"oa_version":"Published Version","_id":"7214","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["570"],"status":"public","title":"Recovering rearranged cancer chromosomes from karyotype graphs","intvolume":" 20","day":"17","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2019-12-17T00:00:00Z","publication":"BMC Bioinformatics","citation":{"chicago":"Aganezov, Sergey, Ilya Zban, Vitalii Aksenov, Nikita Alexeev, and Michael C. Schatz. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” BMC Bioinformatics. BMC, 2019. https://doi.org/10.1186/s12859-019-3208-4.","mla":"Aganezov, Sergey, et al. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” BMC Bioinformatics, vol. 20, 641, BMC, 2019, doi:10.1186/s12859-019-3208-4.","short":"S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, M.C. Schatz, BMC Bioinformatics 20 (2019).","ista":"Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. 2019. Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. 20, 641.","ieee":"S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, and M. C. Schatz, “Recovering rearranged cancer chromosomes from karyotype graphs,” BMC Bioinformatics, vol. 20. BMC, 2019.","apa":"Aganezov, S., Zban, I., Aksenov, V., Alexeev, N., & Schatz, M. C. (2019). Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. BMC. https://doi.org/10.1186/s12859-019-3208-4","ama":"Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics. 2019;20. doi:10.1186/s12859-019-3208-4"},"article_type":"original"},{"scopus_import":"1","day":"13","article_processing_charge":"No","publication":"25th Anniversary of Euro-Par","citation":{"apa":"Koval, N., Alistarh, D.-A., & Elizarov, R. (2019). Scalable FIFO channels for programming via communicating sequential processes. In 25th Anniversary of Euro-Par (Vol. 11725, pp. 317–333). Göttingen, Germany: Springer Nature. https://doi.org/10.1007/978-3-030-29400-7_23","ieee":"N. Koval, D.-A. Alistarh, and R. Elizarov, “Scalable FIFO channels for programming via communicating sequential processes,” in 25th Anniversary of Euro-Par, Göttingen, Germany, 2019, vol. 11725, pp. 317–333.","ista":"Koval N, Alistarh D-A, Elizarov R. 2019. Scalable FIFO channels for programming via communicating sequential processes. 25th Anniversary of Euro-Par. Euro-Par: European Conference on Parallel Processing, LNCS, vol. 11725, 317–333.","ama":"Koval N, Alistarh D-A, Elizarov R. Scalable FIFO channels for programming via communicating sequential processes. In: 25th Anniversary of Euro-Par. Vol 11725. Springer Nature; 2019:317-333. doi:10.1007/978-3-030-29400-7_23","chicago":"Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. “Scalable FIFO Channels for Programming via Communicating Sequential Processes.” In 25th Anniversary of Euro-Par, 11725:317–33. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29400-7_23.","short":"N. Koval, D.-A. Alistarh, R. Elizarov, in:, 25th Anniversary of Euro-Par, Springer Nature, 2019, pp. 317–333.","mla":"Koval, Nikita, et al. “Scalable FIFO Channels for Programming via Communicating Sequential Processes.” 25th Anniversary of Euro-Par, vol. 11725, Springer Nature, 2019, pp. 317–33, doi:10.1007/978-3-030-29400-7_23."},"page":"317-333","date_published":"2019-08-13T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Traditional concurrent programming involves manipulating shared mutable state. Alternatives to this programming style are communicating sequential processes (CSP) and actor models, which share data via explicit communication. These models have been known for almost half a century, and have recently had started to gain significant traction among modern programming languages. The common abstraction for communication between several processes is the channel. Although channels are similar to producer-consumer data structures, they have different semantics and support additional operations, such as the select expression. Despite their growing popularity, most known implementations of channels use lock-based data structures and can be rather inefficient.\r\n\r\nIn this paper, we present the first efficient lock-free algorithm for implementing a communication channel for CSP programming. We provide implementations and experimental results in the Kotlin and Go programming languages. Our new algorithm outperforms existing implementations on many workloads, while providing non-blocking progress guarantee. Our design can serve as an example of how to construct general communication data structures for CSP and actor models. "}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7228","status":"public","title":"Scalable FIFO channels for programming via communicating sequential processes","intvolume":" 11725","oa_version":"None","month":"08","publication_identifier":{"issn":["0302-9743"],"isbn":["978-3-0302-9399-4"],"eissn":["1611-3349"]},"external_id":{"isi":["000851061400023"]},"isi":1,"quality_controlled":"1","conference":{"location":"Göttingen, Germany","start_date":"2019-08-26","end_date":"2019-08-30","name":"Euro-Par: European Conference on Parallel Processing"},"doi":"10.1007/978-3-030-29400-7_23","language":[{"iso":"eng"}],"year":"2019","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"DaAl"}],"author":[{"full_name":"Koval, Nikita","last_name":"Koval","first_name":"Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"},{"full_name":"Elizarov, Roman","first_name":"Roman","last_name":"Elizarov"}],"date_updated":"2023-09-06T14:53:59Z","date_created":"2020-01-05T23:00:46Z","volume":11725},{"article_processing_charge":"No","publication_identifier":{"isbn":["9781538670248"]},"day":"28","month":"11","scopus_import":"1","language":[{"iso":"eng"}],"date_published":"2019-11-28T00:00:00Z","doi":"10.1109/ITSC.2019.8917514","conference":{"name":"ITSC: Intelligent Transportation Systems Conference","end_date":"2019-10-30","start_date":"2019-10-27","location":"Auckland, New Zealand"},"isi":1,"quality_controlled":"1","citation":{"short":"G.F. Osang, J. Cook, A. Fabrikant, M. Gruteser, in:, 2019 IEEE Intelligent Transportation Systems Conference, IEEE, 2019.","mla":"Osang, Georg F., et al. “LiveTraVeL: Real-Time Matching of Transit Vehicle Trajectories to Transit Routes at Scale.” 2019 IEEE Intelligent Transportation Systems Conference, 8917514, IEEE, 2019, doi:10.1109/ITSC.2019.8917514.","chicago":"Osang, Georg F, James Cook, Alex Fabrikant, and Marco Gruteser. “LiveTraVeL: Real-Time Matching of Transit Vehicle Trajectories to Transit Routes at Scale.” In 2019 IEEE Intelligent Transportation Systems Conference. IEEE, 2019. https://doi.org/10.1109/ITSC.2019.8917514.","ama":"Osang GF, Cook J, Fabrikant A, Gruteser M. LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale. In: 2019 IEEE Intelligent Transportation Systems Conference. IEEE; 2019. doi:10.1109/ITSC.2019.8917514","ieee":"G. F. Osang, J. Cook, A. Fabrikant, and M. Gruteser, “LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale,” in 2019 IEEE Intelligent Transportation Systems Conference, Auckland, New Zealand, 2019.","apa":"Osang, G. F., Cook, J., Fabrikant, A., & Gruteser, M. (2019). LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale. In 2019 IEEE Intelligent Transportation Systems Conference. Auckland, New Zealand: IEEE. https://doi.org/10.1109/ITSC.2019.8917514","ista":"Osang GF, Cook J, Fabrikant A, Gruteser M. 2019. LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale. 2019 IEEE Intelligent Transportation Systems Conference. ITSC: Intelligent Transportation Systems Conference, 8917514."},"external_id":{"isi":["000521238102050"]},"publication":"2019 IEEE Intelligent Transportation Systems Conference","abstract":[{"text":"We present LiveTraVeL (Live Transit Vehicle Labeling), a real-time system to label a stream of noisy observations of transit vehicle trajectories with the transit routes they are serving (e.g., northbound bus #5). In order to scale efficiently to large transit networks, our system first retrieves a small set of candidate routes from a geometrically indexed data structure, then applies a fine-grained scoring step to choose the best match. Given that real-time data remains unavailable for the majority of the world’s transit agencies, these inferences can help feed a real-time map of a transit system’s trips, infer transit trip delays in real time, or measure and correct noisy transit tracking data. This system can run on vehicle observations from a variety of sources that don’t attach route information to vehicle observations, such as public imagery streams or user-contributed transit vehicle sightings.We abstract away the specifics of the sensing system and demonstrate the effectiveness of our system on a \"semisynthetic\" dataset of all New York City buses, where we simulate sensed trajectories by starting with fully labeled vehicle trajectories reported via the GTFS-Realtime protocol, removing the transit route IDs, and perturbing locations with synthetic noise. Using just the geometric shapes of the trajectories, we demonstrate that our system converges on the correct route ID within a few minutes, even after a vehicle switches from serving one trip to the next.","lang":"eng"}],"type":"conference","article_number":"8917514","oa_version":"None","date_created":"2019-12-29T23:00:47Z","date_updated":"2023-09-06T14:50:28Z","author":[{"id":"464B40D6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8882-5116","first_name":"Georg F","last_name":"Osang","full_name":"Osang, Georg F"},{"last_name":"Cook","first_name":"James","full_name":"Cook, James"},{"last_name":"Fabrikant","first_name":"Alex","full_name":"Fabrikant, Alex"},{"full_name":"Gruteser, Marco","last_name":"Gruteser","first_name":"Marco"}],"publisher":"IEEE","department":[{"_id":"HeEd"}],"publication_status":"published","title":"LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale","status":"public","_id":"7216","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2019"},{"language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-29662-9_8","conference":{"name":"FORMATS: Formal Modeling and Analysis of Timed Systems","start_date":"2019-08-27","location":"Amsterdam, The Netherlands","end_date":"2019-08-29"},"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1907.11514"],"isi":["000611677700008"]},"main_file_link":[{"url":"https://arxiv.org/abs/1907.11514","open_access":"1"}],"publication_identifier":{"issn":["0302-9743"],"isbn":["978-3-0302-9661-2"],"eissn":["1611-3349"]},"month":"08","volume":11750,"date_created":"2020-01-05T23:00:47Z","date_updated":"2023-09-06T14:55:15Z","author":[{"id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3066-6941","first_name":"Hui","last_name":"Kong","full_name":"Kong, Hui"},{"first_name":"Ezio","last_name":"Bartocci","full_name":"Bartocci, Ezio"},{"first_name":"Yu","last_name":"Jiang","full_name":"Jiang, Yu"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Springer Nature","department":[{"_id":"ToHe"}],"publication_status":"published","year":"2019","date_published":"2019-08-13T00:00:00Z","page":"123-141","citation":{"ieee":"H. Kong, E. Bartocci, Y. Jiang, and T. A. Henzinger, “Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty,” in 17th International Conference on Formal Modeling and Analysis of Timed Systems, Amsterdam, The Netherlands, 2019, vol. 11750, pp. 123–141.","apa":"Kong, H., Bartocci, E., Jiang, Y., & Henzinger, T. A. (2019). Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. In 17th International Conference on Formal Modeling and Analysis of Timed Systems (Vol. 11750, pp. 123–141). Amsterdam, The Netherlands: Springer Nature. https://doi.org/10.1007/978-3-030-29662-9_8","ista":"Kong H, Bartocci E, Jiang Y, Henzinger TA. 2019. Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. 17th International Conference on Formal Modeling and Analysis of Timed Systems. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11750, 123–141.","ama":"Kong H, Bartocci E, Jiang Y, Henzinger TA. Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty. In: 17th International Conference on Formal Modeling and Analysis of Timed Systems. Vol 11750. Springer Nature; 2019:123-141. doi:10.1007/978-3-030-29662-9_8","chicago":"Kong, Hui, Ezio Bartocci, Yu Jiang, and Thomas A Henzinger. “Piecewise Robust Barrier Tubes for Nonlinear Hybrid Systems with Uncertainty.” In 17th International Conference on Formal Modeling and Analysis of Timed Systems, 11750:123–41. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29662-9_8.","short":"H. Kong, E. Bartocci, Y. Jiang, T.A. Henzinger, in:, 17th International Conference on Formal Modeling and Analysis of Timed Systems, Springer Nature, 2019, pp. 123–141.","mla":"Kong, Hui, et al. “Piecewise Robust Barrier Tubes for Nonlinear Hybrid Systems with Uncertainty.” 17th International Conference on Formal Modeling and Analysis of Timed Systems, vol. 11750, Springer Nature, 2019, pp. 123–41, doi:10.1007/978-3-030-29662-9_8."},"publication":"17th International Conference on Formal Modeling and Analysis of Timed Systems","article_processing_charge":"No","day":"13","scopus_import":"1","oa_version":"Preprint","intvolume":" 11750","title":"Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7231","abstract":[{"lang":"eng","text":"Piecewise Barrier Tubes (PBT) is a new technique for flowpipe overapproximation for nonlinear systems with polynomial dynamics, which leverages a combination of barrier certificates. PBT has advantages over traditional time-step based methods in dealing with those nonlinear dynamical systems in which there is a large difference in speed between trajectories, producing an overapproximation that is time independent. However, the existing approach for PBT is not efficient due to the application of interval methods for enclosure-box computation, and it can only deal with continuous dynamical systems without uncertainty. In this paper, we extend the approach with the ability to handle both continuous and hybrid dynamical systems with uncertainty that can reside in parameters and/or noise. We also improve the efficiency of the method significantly, by avoiding the use of interval-based methods for the enclosure-box computation without loosing soundness. We have developed a C++ prototype implementing the proposed approach and we evaluate it on several benchmarks. The experiments show that our approach is more efficient and precise than other methods in the literature."}],"alternative_title":["LNCS"],"type":"conference"},{"file":[{"file_id":"8777","relation":"main_file","date_created":"2020-11-19T11:37:41Z","date_updated":"2020-11-19T11:37:41Z","success":1,"checksum":"29fcbcd8c1fc7f11a596ed7f14ea1c82","file_name":"2019_eLife_AminWetzel.pdf","access_level":"open_access","creator":"dernst","file_size":4817384,"content_type":"application/pdf"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7340","ddc":["570"],"status":"public","title":"Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR","intvolume":" 8","abstract":[{"text":"Coupling of endoplasmic reticulum stress to dimerisation‑dependent activation of the UPR transducer IRE1 is incompletely understood. Whilst the luminal co-chaperone ERdj4 promotes a complex between the Hsp70 BiP and IRE1's stress-sensing luminal domain (IRE1LD) that favours the latter's monomeric inactive state and loss of ERdj4 de-represses IRE1, evidence linking these cellular and in vitro observations is presently lacking. We report that enforced loading of endogenous BiP onto endogenous IRE1α repressed UPR signalling in CHO cells and deletions in the IRE1α locus that de-repressed the UPR in cells, encode flexible regions of IRE1LD that mediated BiP‑induced monomerisation in vitro. Changes in the hydrogen exchange mass spectrometry profile of IRE1LD induced by ERdj4 and BiP confirmed monomerisation and were consistent with active destabilisation of the IRE1LD dimer. Together, these observations support a competition model whereby waning ER stress passively partitions ERdj4 and BiP to IRE1LD to initiate active repression of UPR signalling.","lang":"eng"}],"type":"journal_article","date_published":"2019-12-24T00:00:00Z","publication":"eLife","citation":{"ista":"Amin-Wetzel NP, Neidhardt L, Yan Y, Mayer MP, Ron D. 2019. Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. eLife. 8, e50793.","ieee":"N. P. Amin-Wetzel, L. Neidhardt, Y. Yan, M. P. Mayer, and D. Ron, “Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR,” eLife, vol. 8. eLife Sciences Publications, 2019.","apa":"Amin-Wetzel, N. P., Neidhardt, L., Yan, Y., Mayer, M. P., & Ron, D. (2019). Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.50793","ama":"Amin-Wetzel NP, Neidhardt L, Yan Y, Mayer MP, Ron D. Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR. eLife. 2019;8. doi:10.7554/eLife.50793","chicago":"Amin-Wetzel, Niko Paresh, Lisa Neidhardt, Yahui Yan, Matthias P. Mayer, and David Ron. “Unstructured Regions in IRE1α Specify BiP-Mediated Destabilisation of the Luminal Domain Dimer and Repression of the UPR.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.50793.","mla":"Amin-Wetzel, Niko Paresh, et al. “Unstructured Regions in IRE1α Specify BiP-Mediated Destabilisation of the Luminal Domain Dimer and Repression of the UPR.” ELife, vol. 8, e50793, eLife Sciences Publications, 2019, doi:10.7554/eLife.50793.","short":"N.P. Amin-Wetzel, L. Neidhardt, Y. Yan, M.P. Mayer, D. Ron, ELife 8 (2019)."},"article_type":"original","day":"24","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","author":[{"first_name":"Niko Paresh","last_name":"Amin-Wetzel","id":"E95D3014-9D8C-11E9-9C80-D2F8E5697425","full_name":"Amin-Wetzel, Niko Paresh"},{"full_name":"Neidhardt, Lisa","first_name":"Lisa","last_name":"Neidhardt"},{"full_name":"Yan, Yahui","last_name":"Yan","first_name":"Yahui"},{"last_name":"Mayer","first_name":"Matthias P.","full_name":"Mayer, Matthias P."},{"full_name":"Ron, David","last_name":"Ron","first_name":"David"}],"date_created":"2020-01-19T23:00:39Z","date_updated":"2023-09-06T14:58:02Z","volume":8,"acknowledgement":"We thank the CIMR flow cytometry core facility team (Reiner Schulte, Chiara Cossetti and Gabriela Grondys-Kotarba) for assistance with FACS, the Huntington lab for access to the Octet machine, Steffen Preissler for advice on data interpretation, Roman Kityk and Nicole Luebbehusen for help and advice with HX-MS experiments.","year":"2019","pmid":1,"publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"MaDe"}],"file_date_updated":"2020-11-19T11:37:41Z","article_number":"e50793","doi":"10.7554/eLife.50793","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":{"pmid":["31873072"],"isi":["000512303700001"]},"isi":1,"quality_controlled":"1","month":"12","publication_identifier":{"eissn":["2050084X"]}},{"oa_version":"Preprint","_id":"7422","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"eGFRD in all dimensions","status":"public","intvolume":" 150","abstract":[{"lang":"eng","text":"Biochemical reactions often occur at low copy numbers but at once in crowded and diverse environments. Space and stochasticity therefore play an essential role in biochemical networks. Spatial-stochastic simulations have become a prominent tool for understanding how stochasticity at the microscopic level influences the macroscopic behavior of such systems. While particle-based models guarantee the level of detail necessary to accurately describe the microscopic dynamics at very low copy numbers, the algorithms used to simulate them typically imply trade-offs between computational efficiency and biochemical accuracy. eGFRD (enhanced Green’s Function Reaction Dynamics) is an exact algorithm that evades such trade-offs by partitioning the N-particle system into M ≤ N analytically tractable one- and two-particle systems; the analytical solutions (Green’s functions) then are used to implement an event-driven particle-based scheme that allows particles to make large jumps in time and space while retaining access to their state variables at arbitrary simulation times. Here we present “eGFRD2,” a new eGFRD version that implements the principle of eGFRD in all dimensions, thus enabling efficient particle-based simulation of biochemical reaction-diffusion processes in the 3D cytoplasm, on 2D planes representing membranes, and on 1D elongated cylinders representative of, e.g., cytoskeletal tracks or DNA; in 1D, it also incorporates convective motion used to model active transport. We find that, for low particle densities, eGFRD2 is up to 6 orders of magnitude faster than conventional Brownian dynamics. We exemplify the capabilities of eGFRD2 by simulating an idealized model of Pom1 gradient formation, which involves 3D diffusion, active transport on microtubules, and autophosphorylation on the membrane, confirming recent experimental and theoretical results on this system to hold under genuinely stochastic conditions."}],"issue":"5","type":"journal_article","date_published":"2019-02-07T00:00:00Z","publication":"The Journal of Chemical Physics","citation":{"ieee":"T. R. Sokolowski et al., “eGFRD in all dimensions,” The Journal of Chemical Physics, vol. 150, no. 5. AIP Publishing, 2019.","apa":"Sokolowski, T. R., Paijmans, J., Bossen, L., Miedema, T., Wehrens, M., Becker, N. B., … ten Wolde, P. R. (2019). eGFRD in all dimensions. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.5064867","ista":"Sokolowski TR, Paijmans J, Bossen L, Miedema T, Wehrens M, Becker NB, Kaizu K, Takahashi K, Dogterom M, ten Wolde PR. 2019. eGFRD in all dimensions. The Journal of Chemical Physics. 150(5), 054108.","ama":"Sokolowski TR, Paijmans J, Bossen L, et al. eGFRD in all dimensions. The Journal of Chemical Physics. 2019;150(5). doi:10.1063/1.5064867","chicago":"Sokolowski, Thomas R, Joris Paijmans, Laurens Bossen, Thomas Miedema, Martijn Wehrens, Nils B. Becker, Kazunari Kaizu, Koichi Takahashi, Marileen Dogterom, and Pieter Rein ten Wolde. “EGFRD in All Dimensions.” The Journal of Chemical Physics. AIP Publishing, 2019. https://doi.org/10.1063/1.5064867.","short":"T.R. Sokolowski, J. Paijmans, L. Bossen, T. Miedema, M. Wehrens, N.B. Becker, K. Kaizu, K. Takahashi, M. Dogterom, P.R. ten Wolde, The Journal of Chemical Physics 150 (2019).","mla":"Sokolowski, Thomas R., et al. “EGFRD in All Dimensions.” The Journal of Chemical Physics, vol. 150, no. 5, 054108, AIP Publishing, 2019, doi:10.1063/1.5064867."},"article_type":"original","day":"07","article_processing_charge":"No","author":[{"orcid":"0000-0002-1287-3779","id":"3E999752-F248-11E8-B48F-1D18A9856A87","last_name":"Sokolowski","first_name":"Thomas R","full_name":"Sokolowski, Thomas R"},{"last_name":"Paijmans","first_name":"Joris","full_name":"Paijmans, Joris"},{"last_name":"Bossen","first_name":"Laurens","full_name":"Bossen, Laurens"},{"last_name":"Miedema","first_name":"Thomas","full_name":"Miedema, Thomas"},{"first_name":"Martijn","last_name":"Wehrens","full_name":"Wehrens, Martijn"},{"full_name":"Becker, Nils B.","first_name":"Nils B.","last_name":"Becker"},{"full_name":"Kaizu, Kazunari","last_name":"Kaizu","first_name":"Kazunari"},{"first_name":"Koichi","last_name":"Takahashi","full_name":"Takahashi, Koichi"},{"first_name":"Marileen","last_name":"Dogterom","full_name":"Dogterom, Marileen"},{"full_name":"ten Wolde, Pieter Rein","first_name":"Pieter Rein","last_name":"ten Wolde"}],"date_created":"2020-01-30T10:34:36Z","date_updated":"2023-09-06T14:59:28Z","volume":150,"year":"2019","publication_status":"published","publisher":"AIP Publishing","department":[{"_id":"GaTk"}],"article_number":"054108","doi":"10.1063/1.5064867","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000458109300009"],"arxiv":["1708.09364"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.09364"}],"quality_controlled":"1","isi":1,"month":"02","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]}},{"oa_version":"Preprint","intvolume":" 11904","status":"public","title":"Extending simple drawings","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7230","abstract":[{"text":"Simple drawings of graphs are those in which each pair of edges share at most one point, either a common endpoint or a proper crossing. In this paper we study the problem of extending a simple drawing D(G) of a graph G by inserting a set of edges from the complement of G into D(G) such that the result is a simple drawing. In the context of rectilinear drawings, the problem is trivial. For pseudolinear drawings, the existence of such an extension follows from Levi’s enlargement lemma. In contrast, we prove that deciding if a given set of edges can be inserted into a simple drawing is NP-complete. Moreover, we show that the maximization version of the problem is APX-hard. We also present a polynomial-time algorithm for deciding whether one edge uv can be inserted into D(G) when {u,v} is a dominating set for the graph G.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","date_published":"2019-11-28T00:00:00Z","page":"230-243","citation":{"ieee":"A. M. Arroyo Guevara, M. Derka, and I. Parada, “Extending simple drawings,” in 27th International Symposium on Graph Drawing and Network Visualization, Prague, Czech Republic, 2019, vol. 11904, pp. 230–243.","apa":"Arroyo Guevara, A. M., Derka, M., & Parada, I. (2019). Extending simple drawings. In 27th International Symposium on Graph Drawing and Network Visualization (Vol. 11904, pp. 230–243). Prague, Czech Republic: Springer Nature. https://doi.org/10.1007/978-3-030-35802-0_18","ista":"Arroyo Guevara AM, Derka M, Parada I. 2019. Extending simple drawings. 27th International Symposium on Graph Drawing and Network Visualization. GD: Graph Drawing and Network Visualization, LNCS, vol. 11904, 230–243.","ama":"Arroyo Guevara AM, Derka M, Parada I. Extending simple drawings. In: 27th International Symposium on Graph Drawing and Network Visualization. Vol 11904. Springer Nature; 2019:230-243. doi:10.1007/978-3-030-35802-0_18","chicago":"Arroyo Guevara, Alan M, Martin Derka, and Irene Parada. “Extending Simple Drawings.” In 27th International Symposium on Graph Drawing and Network Visualization, 11904:230–43. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-35802-0_18.","short":"A.M. Arroyo Guevara, M. Derka, I. Parada, in:, 27th International Symposium on Graph Drawing and Network Visualization, Springer Nature, 2019, pp. 230–243.","mla":"Arroyo Guevara, Alan M., et al. “Extending Simple Drawings.” 27th International Symposium on Graph Drawing and Network Visualization, vol. 11904, Springer Nature, 2019, pp. 230–43, doi:10.1007/978-3-030-35802-0_18."},"publication":"27th International Symposium on Graph Drawing and Network Visualization","article_processing_charge":"No","day":"28","scopus_import":"1","volume":11904,"date_updated":"2023-09-06T14:56:00Z","date_created":"2020-01-05T23:00:47Z","author":[{"full_name":"Arroyo Guevara, Alan M","first_name":"Alan M","last_name":"Arroyo Guevara","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2401-8670"},{"full_name":"Derka, Martin","first_name":"Martin","last_name":"Derka"},{"full_name":"Parada, Irene","last_name":"Parada","first_name":"Irene"}],"department":[{"_id":"UlWa"}],"publisher":"Springer Nature","publication_status":"published","year":"2019","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-35802-0_18","conference":{"name":"GD: Graph Drawing and Network Visualization","end_date":"2019-09-20","start_date":"2019-09-17","location":"Prague, Czech Republic"},"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1908.08129","open_access":"1"}],"external_id":{"isi":["000612918800018"],"arxiv":["1908.08129"]},"publication_identifier":{"issn":["0302-9743"],"isbn":["978-3-0303-5801-3"],"eissn":["1611-3349"]},"month":"11"},{"volume":11750,"date_created":"2020-01-05T23:00:48Z","date_updated":"2023-09-06T14:57:17Z","author":[{"full_name":"Ferrere, Thomas","last_name":"Ferrere","first_name":"Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Oded","last_name":"Maler","full_name":"Maler, Oded"},{"id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","last_name":"Nickovic","first_name":"Dejan","full_name":"Nickovic, Dejan"}],"publisher":"Springer Nature","department":[{"_id":"ToHe"}],"publication_status":"published","year":"2019","language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-29662-9_4","conference":{"start_date":"2019-08-27","location":"Amsterdam, The Netherlands","end_date":"2019-08-29","name":"FORMATS: Formal Modeling and Anaysis of Timed Systems"},"project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000611677700004"]},"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["978-3-0302-9661-2"]},"month":"08","oa_version":"None","intvolume":" 11750","title":"Mixed-time signal temporal logic","status":"public","_id":"7232","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"We present Mixed-time Signal Temporal Logic (STL−MX), a specification formalism which extends STL by capturing the discrete/ continuous time duality found in many cyber-physical systems (CPS), as well as mixed-signal electronic designs. In STL−MX, properties of components with continuous dynamics are expressed in STL, while specifications of components with discrete dynamics are written in LTL. To combine the two layers, we evaluate formulas on two traces, discrete- and continuous-time, and introduce two interface operators that map signals, properties and their satisfaction signals across the two time domains. We show that STL-mx has the expressive power of STL supplemented with an implicit T-periodic clock signal. We develop and implement an algorithm for monitoring STL-mx formulas and illustrate the approach using a mixed-signal example. ","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","date_published":"2019-08-13T00:00:00Z","page":"59-75","citation":{"ista":"Ferrere T, Maler O, Nickovic D. 2019. Mixed-time signal temporal logic. 17th International Conference on Formal Modeling and Analysis of Timed Systems. FORMATS: Formal Modeling and Anaysis of Timed Systems, LNCS, vol. 11750, 59–75.","ieee":"T. Ferrere, O. Maler, and D. Nickovic, “Mixed-time signal temporal logic,” in 17th International Conference on Formal Modeling and Analysis of Timed Systems, Amsterdam, The Netherlands, 2019, vol. 11750, pp. 59–75.","apa":"Ferrere, T., Maler, O., & Nickovic, D. (2019). Mixed-time signal temporal logic. In 17th International Conference on Formal Modeling and Analysis of Timed Systems (Vol. 11750, pp. 59–75). Amsterdam, The Netherlands: Springer Nature. https://doi.org/10.1007/978-3-030-29662-9_4","ama":"Ferrere T, Maler O, Nickovic D. Mixed-time signal temporal logic. In: 17th International Conference on Formal Modeling and Analysis of Timed Systems. Vol 11750. Springer Nature; 2019:59-75. doi:10.1007/978-3-030-29662-9_4","chicago":"Ferrere, Thomas, Oded Maler, and Dejan Nickovic. “Mixed-Time Signal Temporal Logic.” In 17th International Conference on Formal Modeling and Analysis of Timed Systems, 11750:59–75. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29662-9_4.","mla":"Ferrere, Thomas, et al. “Mixed-Time Signal Temporal Logic.” 17th International Conference on Formal Modeling and Analysis of Timed Systems, vol. 11750, Springer Nature, 2019, pp. 59–75, doi:10.1007/978-3-030-29662-9_4.","short":"T. Ferrere, O. Maler, D. Nickovic, in:, 17th International Conference on Formal Modeling and Analysis of Timed Systems, Springer Nature, 2019, pp. 59–75."},"publication":"17th International Conference on Formal Modeling and Analysis of Timed Systems","article_processing_charge":"No","day":"13","scopus_import":"1"},{"article_processing_charge":"No","day":"07","citation":{"ama":"Sahgal P, Alanko JH, Icha J, et al. GGA2 and RAB13 promote activity-dependent β1-integrin recycling. Journal of Cell Science. 2019;132(11). doi:10.1242/jcs.233387","ista":"Sahgal P, Alanko JH, Icha J, Paatero I, Hamidi H, Arjonen A, Pietilä M, Rokka A, Ivaska J. 2019. GGA2 and RAB13 promote activity-dependent β1-integrin recycling. Journal of Cell Science. 132(11), jcs233387.","ieee":"P. Sahgal et al., “GGA2 and RAB13 promote activity-dependent β1-integrin recycling,” Journal of Cell Science, vol. 132, no. 11. The Company of Biologists, 2019.","apa":"Sahgal, P., Alanko, J. H., Icha, J., Paatero, I., Hamidi, H., Arjonen, A., … Ivaska, J. (2019). GGA2 and RAB13 promote activity-dependent β1-integrin recycling. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.233387","mla":"Sahgal, Pranshu, et al. “GGA2 and RAB13 Promote Activity-Dependent Β1-Integrin Recycling.” Journal of Cell Science, vol. 132, no. 11, jcs233387, The Company of Biologists, 2019, doi:10.1242/jcs.233387.","short":"P. Sahgal, J.H. Alanko, J. Icha, I. Paatero, H. Hamidi, A. Arjonen, M. Pietilä, A. Rokka, J. Ivaska, Journal of Cell Science 132 (2019).","chicago":"Sahgal, Pranshu, Jonna H Alanko, Jaroslav Icha, Ilkka Paatero, Hellyeh Hamidi, Antti Arjonen, Mika Pietilä, Anne Rokka, and Johanna Ivaska. “GGA2 and RAB13 Promote Activity-Dependent Β1-Integrin Recycling.” Journal of Cell Science. The Company of Biologists, 2019. https://doi.org/10.1242/jcs.233387."},"publication":"Journal of Cell Science","article_type":"original","date_published":"2019-06-07T00:00:00Z","type":"journal_article","issue":"11","abstract":[{"text":"β1-integrins mediate cell–matrix interactions and their trafficking is important in the dynamic regulation of cell adhesion, migration and malignant processes, including cancer cell invasion. Here, we employ an RNAi screen to characterize regulators of integrin traffic and identify the association of Golgi-localized gamma ear-containing Arf-binding protein 2 (GGA2) with β1-integrin, and its role in recycling of active but not inactive β1-integrin receptors. Silencing of GGA2 limits active β1-integrin levels in focal adhesions and decreases cancer cell migration and invasion, which is in agreement with its ability to regulate the dynamics of active integrins. By using the proximity-dependent biotin identification (BioID) method, we identified two RAB family small GTPases, i.e. RAB13 and RAB10, as novel interactors of GGA2. Functionally, RAB13 silencing triggers the intracellular accumulation of active β1-integrin, and reduces integrin activity in focal adhesions and cell migration similarly to GGA2 depletion, indicating that both facilitate active β1-integrin recycling to the plasma membrane. Thus, GGA2 and RAB13 are important specificity determinants for integrin activity-dependent traffic.","lang":"eng"}],"_id":"7420","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 132","status":"public","title":"GGA2 and RAB13 promote activity-dependent β1-integrin recycling","oa_version":"Published Version","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"month":"06","oa":1,"external_id":{"isi":["000473327900017"],"pmid":["31076515"]},"main_file_link":[{"url":"https://doi.org/10.1242/jcs.233387","open_access":"1"}],"quality_controlled":"1","isi":1,"doi":"10.1242/jcs.233387","language":[{"iso":"eng"}],"article_number":"jcs233387","pmid":1,"year":"2019","publisher":"The Company of Biologists","department":[{"_id":"MiSi"}],"publication_status":"published","author":[{"full_name":"Sahgal, Pranshu","last_name":"Sahgal","first_name":"Pranshu"},{"full_name":"Alanko, Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7698-3061","first_name":"Jonna H","last_name":"Alanko"},{"last_name":"Icha","first_name":"Jaroslav","full_name":"Icha, Jaroslav"},{"full_name":"Paatero, Ilkka","first_name":"Ilkka","last_name":"Paatero"},{"last_name":"Hamidi","first_name":"Hellyeh","full_name":"Hamidi, Hellyeh"},{"last_name":"Arjonen","first_name":"Antti","full_name":"Arjonen, Antti"},{"full_name":"Pietilä, Mika","last_name":"Pietilä","first_name":"Mika"},{"last_name":"Rokka","first_name":"Anne","full_name":"Rokka, Anne"},{"full_name":"Ivaska, Johanna","first_name":"Johanna","last_name":"Ivaska"}],"volume":132,"date_updated":"2023-09-06T15:01:00Z","date_created":"2020-01-30T10:31:42Z"},{"year":"2019","publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"Institute of Mathematical Statistics","author":[{"last_name":"Akemann","first_name":"Gernot","full_name":"Akemann, Gernot"},{"full_name":"Checinski, Tomasz","first_name":"Tomasz","last_name":"Checinski"},{"full_name":"Liu, Dangzheng","first_name":"Dangzheng","last_name":"Liu","id":"2F947E34-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Strahov, Eugene","last_name":"Strahov","first_name":"Eugene"}],"date_created":"2020-01-30T10:36:50Z","date_updated":"2023-09-06T14:58:39Z","volume":55,"month":"02","publication_identifier":{"issn":["0246-0203"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.05224"}],"oa":1,"external_id":{"isi":["000456070200013"],"arxiv":["1704.05224"]},"isi":1,"quality_controlled":"1","doi":"10.1214/18-aihp888","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"We compare finite rank perturbations of the following three ensembles of complex rectangular random matrices: First, a generalised Wishart ensemble with one random and two fixed correlation matrices introduced by Borodin and Péché, second, the product of two independent random matrices where one has correlated entries, and third, the case when the two random matrices become also coupled through a fixed matrix. The singular value statistics of all three ensembles is shown to be determinantal and we derive double contour integral representations for their respective kernels. Three different kernels are found in the limit of infinite matrix dimension at the origin of the spectrum. They depend on finite rank perturbations of the correlation and coupling matrices and are shown to be integrable. The first kernel (I) is found for two independent matrices from the second, and two weakly coupled matrices from the third ensemble. It generalises the Meijer G-kernel for two independent and uncorrelated matrices. The third kernel (III) is obtained for the generalised Wishart ensemble and for two strongly coupled matrices. It further generalises the perturbed Bessel kernel of Desrosiers and Forrester. Finally, kernel (II), found for the ensemble of two coupled matrices, provides an interpolation between the kernels (I) and (III), generalising previous findings of part of the authors.","lang":"eng"}],"issue":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7423","title":"Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles","status":"public","intvolume":" 55","oa_version":"Preprint","day":"01","article_processing_charge":"No","publication":"Annales de l'Institut Henri Poincaré, Probabilités et Statistiques","citation":{"short":"G. Akemann, T. Checinski, D. Liu, E. Strahov, Annales de l’Institut Henri Poincaré, Probabilités et Statistiques 55 (2019) 441–479.","mla":"Akemann, Gernot, et al. “Finite Rank Perturbations in Products of Coupled Random Matrices: From One Correlated to Two Wishart Ensembles.” Annales de l’Institut Henri Poincaré, Probabilités et Statistiques, vol. 55, no. 1, Institute of Mathematical Statistics, 2019, pp. 441–79, doi:10.1214/18-aihp888.","chicago":"Akemann, Gernot, Tomasz Checinski, Dangzheng Liu, and Eugene Strahov. “Finite Rank Perturbations in Products of Coupled Random Matrices: From One Correlated to Two Wishart Ensembles.” Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-aihp888.","ama":"Akemann G, Checinski T, Liu D, Strahov E. Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles. Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. 2019;55(1):441-479. doi:10.1214/18-aihp888","ieee":"G. Akemann, T. Checinski, D. Liu, and E. Strahov, “Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles,” Annales de l’Institut Henri Poincaré, Probabilités et Statistiques, vol. 55, no. 1. Institute of Mathematical Statistics, pp. 441–479, 2019.","apa":"Akemann, G., Checinski, T., Liu, D., & Strahov, E. (2019). Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles. Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. Institute of Mathematical Statistics. https://doi.org/10.1214/18-aihp888","ista":"Akemann G, Checinski T, Liu D, Strahov E. 2019. Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles. Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. 55(1), 441–479."},"article_type":"original","page":"441-479","date_published":"2019-02-01T00:00:00Z"},{"date_created":"2020-01-30T10:33:05Z","date_updated":"2023-09-06T15:00:13Z","volume":28,"author":[{"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":"Rodrigues, Nicolas","first_name":"Nicolas","last_name":"Rodrigues"},{"full_name":"Perrin, Nicolas","last_name":"Perrin","first_name":"Nicolas"},{"full_name":"Kirkpatrick, Mark","first_name":"Mark","last_name":"Kirkpatrick"}],"publication_status":"published","department":[{"_id":"BeVi"}],"publisher":"Wiley","year":"2019","pmid":1,"language":[{"iso":"eng"}],"doi":"10.1111/mec.14990","isi":1,"quality_controlled":"1","external_id":{"pmid":["30576024"],"isi":["000468200800004"]},"month":"04","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"oa_version":"None","status":"public","title":"A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog","intvolume":" 28","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7421","abstract":[{"lang":"eng","text":"X and Y chromosomes can diverge when rearrangements block recombination between them. Here we present the first genomic view of a reciprocal translocation that causes two physically unconnected pairs of chromosomes to be coinherited as sex chromosomes. In a population of the common frog (Rana temporaria), both pairs of X and Y chromosomes show extensive sequence differentiation, but not degeneration of the Y chromosomes. A new method based on gene trees shows both chromosomes are sex‐linked. Furthermore, the gene trees from the two Y chromosomes have identical topologies, showing they have been coinherited since the reciprocal translocation occurred. Reciprocal translocations can thus reshape sex linkage on a much greater scale compared with inversions, the type of rearrangement that is much better known in sex chromosome evolution, and they can greatly amplify the power of sexually antagonistic selection to drive genomic rearrangement. Two more populations show evidence of other rearrangements, suggesting that this species has unprecedented structural polymorphism in its sex chromosomes."}],"issue":"8","type":"journal_article","date_published":"2019-04-01T00:00:00Z","article_type":"original","page":"1877-1889","publication":"Molecular Ecology","citation":{"ama":"Toups MA, Rodrigues N, Perrin N, Kirkpatrick M. A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog. Molecular Ecology. 2019;28(8):1877-1889. doi:10.1111/mec.14990","apa":"Toups, M. A., Rodrigues, N., Perrin, N., & Kirkpatrick, M. (2019). A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.14990","ieee":"M. A. Toups, N. Rodrigues, N. Perrin, and M. Kirkpatrick, “A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog,” Molecular Ecology, vol. 28, no. 8. Wiley, pp. 1877–1889, 2019.","ista":"Toups MA, Rodrigues N, Perrin N, Kirkpatrick M. 2019. A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog. Molecular Ecology. 28(8), 1877–1889.","short":"M.A. Toups, N. Rodrigues, N. Perrin, M. Kirkpatrick, Molecular Ecology 28 (2019) 1877–1889.","mla":"Toups, Melissa A., et al. “A Reciprocal Translocation Radically Reshapes Sex‐linked Inheritance in the Common Frog.” Molecular Ecology, vol. 28, no. 8, Wiley, 2019, pp. 1877–89, doi:10.1111/mec.14990.","chicago":"Toups, Melissa A, Nicolas Rodrigues, Nicolas Perrin, and Mark Kirkpatrick. “A Reciprocal Translocation Radically Reshapes Sex‐linked Inheritance in the Common Frog.” Molecular Ecology. Wiley, 2019. https://doi.org/10.1111/mec.14990."},"day":"01","article_processing_charge":"No"},{"date_published":"2019-04-24T00:00:00Z","page":"277-291","publication":"Advances in Cryptology – EUROCRYPT 2019","citation":{"ieee":"H. M. Abusalah, C. Kamath Hosdurg, K. Klein, K. Z. Pietrzak, and M. Walter, “Reversible proofs of sequential work,” in Advances in Cryptology – EUROCRYPT 2019, Darmstadt, Germany, 2019, vol. 11477, pp. 277–291.","apa":"Abusalah, H. M., Kamath Hosdurg, C., Klein, K., Pietrzak, K. Z., & Walter, M. (2019). Reversible proofs of sequential work. In Advances in Cryptology – EUROCRYPT 2019 (Vol. 11477, pp. 277–291). Darmstadt, Germany: Springer International Publishing. https://doi.org/10.1007/978-3-030-17656-3_10","ista":"Abusalah HM, Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. 2019. Reversible proofs of sequential work. Advances in Cryptology – EUROCRYPT 2019. International Conference on the Theory and Applications of Cryptographic Techniques, LNCS, vol. 11477, 277–291.","ama":"Abusalah HM, Kamath Hosdurg C, Klein K, Pietrzak KZ, Walter M. Reversible proofs of sequential work. In: Advances in Cryptology – EUROCRYPT 2019. Vol 11477. Springer International Publishing; 2019:277-291. doi:10.1007/978-3-030-17656-3_10","chicago":"Abusalah, Hamza M, Chethan Kamath Hosdurg, Karen Klein, Krzysztof Z Pietrzak, and Michael Walter. “Reversible Proofs of Sequential Work.” In Advances in Cryptology – EUROCRYPT 2019, 11477:277–91. Springer International Publishing, 2019. https://doi.org/10.1007/978-3-030-17656-3_10.","short":"H.M. Abusalah, C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, M. Walter, in:, Advances in Cryptology – EUROCRYPT 2019, Springer International Publishing, 2019, pp. 277–291.","mla":"Abusalah, Hamza M., et al. “Reversible Proofs of Sequential Work.” Advances in Cryptology – EUROCRYPT 2019, vol. 11477, Springer International Publishing, 2019, pp. 277–91, doi:10.1007/978-3-030-17656-3_10."},"day":"24","article_processing_charge":"No","scopus_import":"1","oa_version":"Submitted Version","title":"Reversible proofs of sequential work","status":"public","intvolume":" 11477","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7411","abstract":[{"lang":"eng","text":"Proofs of sequential work (PoSW) are proof systems where a prover, upon receiving a statement χ and a time parameter T computes a proof ϕ(χ,T) which is efficiently and publicly verifiable. The proof can be computed in T sequential steps, but not much less, even by a malicious party having large parallelism. A PoSW thus serves as a proof that T units of time have passed since χ\r\n\r\nwas received.\r\n\r\nPoSW were introduced by Mahmoody, Moran and Vadhan [MMV11], a simple and practical construction was only recently proposed by Cohen and Pietrzak [CP18].\r\n\r\nIn this work we construct a new simple PoSW in the random permutation model which is almost as simple and efficient as [CP18] but conceptually very different. Whereas the structure underlying [CP18] is a hash tree, our construction is based on skip lists and has the interesting property that computing the PoSW is a reversible computation.\r\nThe fact that the construction is reversible can potentially be used for new applications like constructing proofs of replication. We also show how to “embed” the sloth function of Lenstra and Weselowski [LW17] into our PoSW to get a PoSW where one additionally can verify correctness of the output much more efficiently than recomputing it (though recent constructions of “verifiable delay functions” subsume most of the applications this construction was aiming at)."}],"alternative_title":["LNCS"],"type":"conference","language":[{"iso":"eng"}],"conference":{"name":"International Conference on the Theory and Applications of Cryptographic Techniques","start_date":"2019-05-19","location":"Darmstadt, Germany","end_date":"2019-05-23"},"doi":"10.1007/978-3-030-17656-3_10","isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"isi":["000483516200010"]},"main_file_link":[{"url":"https://eprint.iacr.org/2019/252","open_access":"1"}],"month":"04","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783030176556","9783030176563"]},"date_updated":"2023-09-06T15:26:06Z","date_created":"2020-01-30T09:26:14Z","volume":11477,"author":[{"last_name":"Abusalah","first_name":"Hamza M","id":"40297222-F248-11E8-B48F-1D18A9856A87","full_name":"Abusalah, Hamza M"},{"id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","last_name":"Kamath Hosdurg","first_name":"Chethan","full_name":"Kamath Hosdurg, Chethan"},{"full_name":"Klein, Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","last_name":"Klein","first_name":"Karen"},{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak"},{"first_name":"Michael","last_name":"Walter","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3186-2482","full_name":"Walter, Michael"}],"publication_status":"published","publisher":"Springer International Publishing","department":[{"_id":"KrPi"}],"year":"2019","ec_funded":1},{"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.jneumeth.2018.11.018","quality_controlled":"1","isi":1,"project":[{"grant_number":"303564","_id":"25548C20-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Microbial Ion Channels for Synthetic Neurobiology"},{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"},{"call_identifier":"FWF","name":"Molecular Drug Targets","grant_number":"W1232-B24","_id":"2548AE96-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000456220900013"],"pmid":["30496761"]},"month":"01","publication_identifier":{"issn":["0165-0270"]},"date_updated":"2023-09-06T15:27:29Z","date_created":"2020-01-30T09:12:19Z","volume":312,"author":[{"first_name":"Catherine","last_name":"Mckenzie","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","full_name":"Mckenzie, Catherine"},{"full_name":"Spanova, Miroslava","first_name":"Miroslava","last_name":"Spanova","id":"44A924DC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J"},{"first_name":"Stephanie","last_name":"Kainrath","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","full_name":"Kainrath, Stephanie"},{"last_name":"Zheden","first_name":"Vanessa","orcid":"0000-0002-9438-4783","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","full_name":"Zheden, Vanessa"},{"last_name":"Sitte","first_name":"Harald H.","full_name":"Sitte, Harald H."},{"full_name":"Janovjak, Harald L","first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315"}],"publication_status":"published","publisher":"Elsevier","department":[{"_id":"HaJa"},{"_id":"Bio"}],"year":"2019","pmid":1,"ec_funded":1,"date_published":"2019-01-15T00:00:00Z","article_type":"original","page":"114-121","publication":"Journal of Neuroscience Methods","citation":{"ama":"Mckenzie C, Spanova M, Johnson AJ, et al. Isolation of synaptic vesicles from genetically engineered cultured neurons. Journal of Neuroscience Methods. 2019;312:114-121. doi:10.1016/j.jneumeth.2018.11.018","apa":"Mckenzie, C., Spanova, M., Johnson, A. J., Kainrath, S., Zheden, V., Sitte, H. H., & Janovjak, H. L. (2019). Isolation of synaptic vesicles from genetically engineered cultured neurons. Journal of Neuroscience Methods. Elsevier. https://doi.org/10.1016/j.jneumeth.2018.11.018","ieee":"C. Mckenzie et al., “Isolation of synaptic vesicles from genetically engineered cultured neurons,” Journal of Neuroscience Methods, vol. 312. Elsevier, pp. 114–121, 2019.","ista":"Mckenzie C, Spanova M, Johnson AJ, Kainrath S, Zheden V, Sitte HH, Janovjak HL. 2019. Isolation of synaptic vesicles from genetically engineered cultured neurons. Journal of Neuroscience Methods. 312, 114–121.","short":"C. Mckenzie, M. Spanova, A.J. Johnson, S. Kainrath, V. Zheden, H.H. Sitte, H.L. Janovjak, Journal of Neuroscience Methods 312 (2019) 114–121.","mla":"Mckenzie, Catherine, et al. “Isolation of Synaptic Vesicles from Genetically Engineered Cultured Neurons.” Journal of Neuroscience Methods, vol. 312, Elsevier, 2019, pp. 114–21, doi:10.1016/j.jneumeth.2018.11.018.","chicago":"Mckenzie, Catherine, Miroslava Spanova, Alexander J Johnson, Stephanie Kainrath, Vanessa Zheden, Harald H. Sitte, and Harald L Janovjak. “Isolation of Synaptic Vesicles from Genetically Engineered Cultured Neurons.” Journal of Neuroscience Methods. Elsevier, 2019. https://doi.org/10.1016/j.jneumeth.2018.11.018."},"day":"15","article_processing_charge":"No","scopus_import":"1","oa_version":"None","status":"public","title":"Isolation of synaptic vesicles from genetically engineered cultured neurons","intvolume":" 312","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7406","abstract":[{"text":"Background\r\nSynaptic vesicles (SVs) are an integral part of the neurotransmission machinery, and isolation of SVs from their host neuron is necessary to reveal their most fundamental biochemical and functional properties in in vitro assays. Isolated SVs from neurons that have been genetically engineered, e.g. to introduce genetically encoded indicators, are not readily available but would permit new insights into SV structure and function. Furthermore, it is unclear if cultured neurons can provide sufficient starting material for SV isolation procedures.\r\n\r\nNew method\r\nHere, we demonstrate an efficient ex vivo procedure to obtain functional SVs from cultured rat cortical neurons after genetic engineering with a lentivirus.\r\n\r\nResults\r\nWe show that ∼108 plated cortical neurons allow isolation of suitable SV amounts for functional analysis and imaging. We found that SVs isolated from cultured neurons have neurotransmitter uptake comparable to that of SVs isolated from intact cortex. Using total internal reflection fluorescence (TIRF) microscopy, we visualized an exogenous SV-targeted marker protein and demonstrated the high efficiency of SV modification.\r\n\r\nComparison with existing methods\r\nObtaining SVs from genetically engineered neurons currently generally requires the availability of transgenic animals, which is constrained by technical (e.g. cost and time) and biological (e.g. developmental defects and lethality) limitations.\r\n\r\nConclusions\r\nThese results demonstrate the modification and isolation of functional SVs using cultured neurons and viral transduction. The ability to readily obtain SVs from genetically engineered neurons will permit linking in situ studies to in vitro experiments in a variety of genetic contexts.","lang":"eng"}],"type":"journal_article"},{"date_published":"2019-06-01T00:00:00Z","citation":{"ama":"Yu C, Tang H, Renggli C, et al. Distributed learning over unreliable networks. In: 36th International Conference on Machine Learning, ICML 2019. Vol 2019-June. IMLS; 2019:12481-12512.","ista":"Yu C, Tang H, Renggli C, Kassing S, Singla A, Alistarh D-A, Zhang C, Liu J. 2019. Distributed learning over unreliable networks. 36th International Conference on Machine Learning, ICML 2019. ICML: International Conference on Machine Learning vol. 2019–June, 12481–12512.","ieee":"C. Yu et al., “Distributed learning over unreliable networks,” in 36th International Conference on Machine Learning, ICML 2019, Long Beach, CA, United States, 2019, vol. 2019–June, pp. 12481–12512.","apa":"Yu, C., Tang, H., Renggli, C., Kassing, S., Singla, A., Alistarh, D.-A., … Liu, J. (2019). Distributed learning over unreliable networks. In 36th International Conference on Machine Learning, ICML 2019 (Vol. 2019–June, pp. 12481–12512). Long Beach, CA, United States: IMLS.","mla":"Yu, Chen, et al. “Distributed Learning over Unreliable Networks.” 36th International Conference on Machine Learning, ICML 2019, vol. 2019–June, IMLS, 2019, pp. 12481–512.","short":"C. Yu, H. Tang, C. Renggli, S. Kassing, A. Singla, D.-A. Alistarh, C. Zhang, J. Liu, in:, 36th International Conference on Machine Learning, ICML 2019, IMLS, 2019, pp. 12481–12512.","chicago":"Yu, Chen, Hanlin Tang, Cedric Renggli, Simon Kassing, Ankit Singla, Dan-Adrian Alistarh, Ce Zhang, and Ji Liu. “Distributed Learning over Unreliable Networks.” In 36th International Conference on Machine Learning, ICML 2019, 2019–June:12481–512. IMLS, 2019."},"publication":"36th International Conference on Machine Learning, ICML 2019","page":"12481-12512","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Preprint","_id":"7437","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Distributed learning over unreliable networks","status":"public","abstract":[{"text":"Most of today's distributed machine learning systems assume reliable networks: whenever two machines exchange information (e.g., gradients or models), the network should guarantee the delivery of the message. At the same time, recent work exhibits the impressive tolerance of machine learning algorithms to errors or noise arising from relaxed communication or synchronization. In this paper, we connect these two trends, and consider the following question: Can we design machine learning systems that are tolerant to network unreliability during training? With this motivation, we focus on a theoretical problem of independent interest-given a standard distributed parameter server architecture, if every communication between the worker and the server has a non-zero probability p of being dropped, does there exist an algorithm that still converges, and at what speed? The technical contribution of this paper is a novel theoretical analysis proving that distributed learning over unreliable network can achieve comparable convergence rate to centralized or distributed learning over reliable networks. Further, we prove that the influence of the packet drop rate diminishes with the growth of the number of parameter servers. We map this theoretical result onto a real-world scenario, training deep neural networks over an unreliable network layer, and conduct network simulation to validate the system improvement by allowing the networks to be unreliable.","lang":"eng"}],"type":"conference","conference":{"end_date":"2019-06-15","location":"Long Beach, CA, United States","start_date":"2019-06-10","name":"ICML: International Conference on Machine Learning"},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1810.07766","open_access":"1"}],"external_id":{"arxiv":["1810.07766"],"isi":["000684034307036"]},"oa":1,"quality_controlled":"1","isi":1,"publication_identifier":{"isbn":["9781510886988"]},"month":"06","author":[{"last_name":"Yu","first_name":"Chen","full_name":"Yu, Chen"},{"full_name":"Tang, Hanlin","first_name":"Hanlin","last_name":"Tang"},{"full_name":"Renggli, Cedric","first_name":"Cedric","last_name":"Renggli"},{"last_name":"Kassing","first_name":"Simon","full_name":"Kassing, Simon"},{"first_name":"Ankit","last_name":"Singla","full_name":"Singla, Ankit"},{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"},{"first_name":"Ce","last_name":"Zhang","full_name":"Zhang, Ce"},{"full_name":"Liu, Ji","first_name":"Ji","last_name":"Liu"}],"volume":"2019-June","date_updated":"2023-09-06T15:21:48Z","date_created":"2020-02-02T23:01:06Z","year":"2019","publisher":"IMLS","department":[{"_id":"DaAl"}],"publication_status":"published"},{"article_processing_charge":"No","day":"31","scopus_import":"1","date_published":"2019-10-31T00:00:00Z","citation":{"chicago":"Achlioptas, Dimitris, Fotis Iliopoulos, and Vladimir Kolmogorov. “A Local Lemma for Focused Stochastical Algorithms.” SIAM Journal on Computing. SIAM, 2019. https://doi.org/10.1137/16m109332x.","short":"D. Achlioptas, F. Iliopoulos, V. Kolmogorov, SIAM Journal on Computing 48 (2019) 1583–1602.","mla":"Achlioptas, Dimitris, et al. “A Local Lemma for Focused Stochastical Algorithms.” SIAM Journal on Computing, vol. 48, no. 5, SIAM, 2019, pp. 1583–602, doi:10.1137/16m109332x.","apa":"Achlioptas, D., Iliopoulos, F., & Kolmogorov, V. (2019). A local lemma for focused stochastical algorithms. SIAM Journal on Computing. SIAM. https://doi.org/10.1137/16m109332x","ieee":"D. Achlioptas, F. Iliopoulos, and V. Kolmogorov, “A local lemma for focused stochastical algorithms,” SIAM Journal on Computing, vol. 48, no. 5. SIAM, pp. 1583–1602, 2019.","ista":"Achlioptas D, Iliopoulos F, Kolmogorov V. 2019. A local lemma for focused stochastical algorithms. SIAM Journal on Computing. 48(5), 1583–1602.","ama":"Achlioptas D, Iliopoulos F, Kolmogorov V. A local lemma for focused stochastical algorithms. SIAM Journal on Computing. 2019;48(5):1583-1602. doi:10.1137/16m109332x"},"publication":"SIAM Journal on Computing","page":"1583-1602","article_type":"original","issue":"5","abstract":[{"text":"We develop a framework for the rigorous analysis of focused stochastic local search algorithms. These algorithms search a state space by repeatedly selecting some constraint that is violated in the current state and moving to a random nearby state that addresses the violation, while (we hope) not introducing many new violations. An important class of focused local search algorithms with provable performance guarantees has recently arisen from algorithmizations of the Lovász local lemma (LLL), a nonconstructive tool for proving the existence of satisfying states by introducing a background measure on the state space. While powerful, the state transitions of algorithms in this class must be, in a precise sense, perfectly compatible with the background measure. In many applications this is a very restrictive requirement, and one needs to step outside the class. Here we introduce the notion of measure distortion and develop a framework for analyzing arbitrary focused stochastic local search algorithms, recovering LLL algorithmizations as the special case of no distortion. Our framework takes as input an arbitrary algorithm of such type and an arbitrary probability measure and shows how to use the measure as a yardstick of algorithmic progress, even for algorithms designed independently of the measure.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7412","intvolume":" 48","title":"A local lemma for focused stochastical algorithms","status":"public","publication_identifier":{"issn":["0097-5397"],"eissn":["1095-7111"]},"month":"10","doi":"10.1137/16m109332x","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1809.01537","open_access":"1"}],"external_id":{"isi":["000493900200005"],"arxiv":["1809.01537"]},"project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"}],"quality_controlled":"1","isi":1,"ec_funded":1,"author":[{"full_name":"Achlioptas, Dimitris","first_name":"Dimitris","last_name":"Achlioptas"},{"last_name":"Iliopoulos","first_name":"Fotis","full_name":"Iliopoulos, Fotis"},{"full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov"}],"volume":48,"date_created":"2020-01-30T09:27:32Z","date_updated":"2023-09-06T15:25:29Z","year":"2019","department":[{"_id":"VlKo"}],"publisher":"SIAM","publication_status":"published"},{"article_number":"151","author":[{"last_name":"Karlík","first_name":"Ondřej","full_name":"Karlík, Ondřej"},{"full_name":"Šik, Martin","first_name":"Martin","last_name":"Šik"},{"full_name":"Vévoda, Petr","first_name":"Petr","last_name":"Vévoda"},{"full_name":"Skrivan, Tomas","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","last_name":"Skrivan","first_name":"Tomas"},{"full_name":"Křivánek, Jaroslav","first_name":"Jaroslav","last_name":"Křivánek"}],"volume":38,"date_updated":"2023-09-06T15:22:23Z","date_created":"2020-01-30T10:19:43Z","year":"2019","department":[{"_id":"ChWo"}],"publisher":"ACM","publication_status":"published","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"month":"11","doi":"10.1145/3355089.3356565","language":[{"iso":"eng"}],"external_id":{"isi":["000498397300001"]},"quality_controlled":"1","isi":1,"issue":"6","abstract":[{"text":"Multiple importance sampling (MIS) has become an indispensable tool in Monte Carlo rendering, widely accepted as a near-optimal solution for combining different sampling techniques. But an MIS combination, using the common balance or power heuristics, often results in an overly defensive estimator, leading to high variance. We show that by generalizing the MIS framework, variance can be substantially reduced. Specifically, we optimize one of the combined sampling techniques so as to decrease the overall variance of the resulting MIS estimator. We apply the approach to the computation of direct illumination due to an HDR environment map and to the computation of global illumination using a path guiding algorithm. The implementation can be as simple as subtracting a constant value from the tabulated sampling density done entirely in a preprocessing step. This produces a consistent noise reduction in all our tests with no negative influence on run time, no artifacts or bias, and no failure cases.","lang":"eng"}],"type":"journal_article","oa_version":"None","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7418","intvolume":" 38","status":"public","title":"MIS compensation: Optimizing sampling techniques in multiple importance sampling","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-11-01T00:00:00Z","citation":{"chicago":"Karlík, Ondřej, Martin Šik, Petr Vévoda, Tomas Skrivan, and Jaroslav Křivánek. “MIS Compensation: Optimizing Sampling Techniques in Multiple Importance Sampling.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3355089.3356565.","short":"O. Karlík, M. Šik, P. Vévoda, T. Skrivan, J. Křivánek, ACM Transactions on Graphics 38 (2019).","mla":"Karlík, Ondřej, et al. “MIS Compensation: Optimizing Sampling Techniques in Multiple Importance Sampling.” ACM Transactions on Graphics, vol. 38, no. 6, 151, ACM, 2019, doi:10.1145/3355089.3356565.","apa":"Karlík, O., Šik, M., Vévoda, P., Skrivan, T., & Křivánek, J. (2019). MIS compensation: Optimizing sampling techniques in multiple importance sampling. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3355089.3356565","ieee":"O. Karlík, M. Šik, P. Vévoda, T. Skrivan, and J. Křivánek, “MIS compensation: Optimizing sampling techniques in multiple importance sampling,” ACM Transactions on Graphics, vol. 38, no. 6. ACM, 2019.","ista":"Karlík O, Šik M, Vévoda P, Skrivan T, Křivánek J. 2019. MIS compensation: Optimizing sampling techniques in multiple importance sampling. ACM Transactions on Graphics. 38(6), 151.","ama":"Karlík O, Šik M, Vévoda P, Skrivan T, Křivánek J. MIS compensation: Optimizing sampling techniques in multiple importance sampling. ACM Transactions on Graphics. 2019;38(6). doi:10.1145/3355089.3356565"},"publication":"ACM Transactions on Graphics","article_type":"original"},{"scopus_import":"1","article_processing_charge":"No","day":"07","citation":{"ama":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. Bogoliubov theory in the Gross–Pitaevskii limit. Acta Mathematica. 2019;222(2):219-335. doi:10.4310/acta.2019.v222.n2.a1","ista":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. 2019. Bogoliubov theory in the Gross–Pitaevskii limit. Acta Mathematica. 222(2), 219–335.","apa":"Boccato, C., Brennecke, C., Cenatiempo, S., & Schlein, B. (2019). Bogoliubov theory in the Gross–Pitaevskii limit. Acta Mathematica. International Press of Boston. https://doi.org/10.4310/acta.2019.v222.n2.a1","ieee":"C. Boccato, C. Brennecke, S. Cenatiempo, and B. Schlein, “Bogoliubov theory in the Gross–Pitaevskii limit,” Acta Mathematica, vol. 222, no. 2. International Press of Boston, pp. 219–335, 2019.","mla":"Boccato, Chiara, et al. “Bogoliubov Theory in the Gross–Pitaevskii Limit.” Acta Mathematica, vol. 222, no. 2, International Press of Boston, 2019, pp. 219–335, doi:10.4310/acta.2019.v222.n2.a1.","short":"C. Boccato, C. Brennecke, S. Cenatiempo, B. Schlein, Acta Mathematica 222 (2019) 219–335.","chicago":"Boccato, Chiara, Christian Brennecke, Serena Cenatiempo, and Benjamin Schlein. “Bogoliubov Theory in the Gross–Pitaevskii Limit.” Acta Mathematica. International Press of Boston, 2019. https://doi.org/10.4310/acta.2019.v222.n2.a1."},"publication":"Acta Mathematica","page":"219-335","article_type":"original","date_published":"2019-06-07T00:00:00Z","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"We consider Bose gases consisting of N particles trapped in a box with volume one and interacting through a repulsive potential with scattering length of order N−1 (Gross–Pitaevskii regime). We determine the ground state energy and the low-energy excitation spectrum, up to errors vanishing as N→∞. Our results confirm Bogoliubov’s predictions."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7413","intvolume":" 222","title":"Bogoliubov theory in the Gross–Pitaevskii limit","status":"public","oa_version":"Preprint","publication_identifier":{"eissn":["1871-2509"],"issn":["0001-5962"]},"month":"06","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1801.01389","open_access":"1"}],"external_id":{"isi":["000495865300001"],"arxiv":["1801.01389"]},"isi":1,"quality_controlled":"1","doi":"10.4310/acta.2019.v222.n2.a1","language":[{"iso":"eng"}],"year":"2019","publisher":"International Press of Boston","department":[{"_id":"RoSe"}],"publication_status":"published","author":[{"full_name":"Boccato, Chiara","first_name":"Chiara","last_name":"Boccato","id":"342E7E22-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christian","last_name":"Brennecke","full_name":"Brennecke, Christian"},{"last_name":"Cenatiempo","first_name":"Serena","full_name":"Cenatiempo, Serena"},{"full_name":"Schlein, Benjamin","first_name":"Benjamin","last_name":"Schlein"}],"volume":222,"date_created":"2020-01-30T09:30:41Z","date_updated":"2023-09-06T15:24:31Z"},{"article_type":"original","citation":{"ama":"Morales HE, Faria R, Johannesson K, et al. Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. 2019;5(12). doi:10.1126/sciadv.aav9963","ieee":"H. E. Morales et al., “Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast,” Science Advances, vol. 5, no. 12. AAAS, 2019.","apa":"Morales, H. E., Faria, R., Johannesson, K., Larsson, T., Panova, M., Westram, A. M., & Butlin, R. K. (2019). Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. AAAS. https://doi.org/10.1126/sciadv.aav9963","ista":"Morales HE, Faria R, Johannesson K, Larsson T, Panova M, Westram AM, Butlin RK. 2019. Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. 5(12), eaav9963.","short":"H.E. Morales, R. Faria, K. Johannesson, T. Larsson, M. Panova, A.M. Westram, R.K. Butlin, Science Advances 5 (2019).","mla":"Morales, Hernán E., et al. “Genomic Architecture of Parallel Ecological Divergence: Beyond a Single Environmental Contrast.” Science Advances, vol. 5, no. 12, eaav9963, AAAS, 2019, doi:10.1126/sciadv.aav9963.","chicago":"Morales, Hernán E., Rui Faria, Kerstin Johannesson, Tomas Larsson, Marina Panova, Anja M Westram, and Roger K. Butlin. “Genomic Architecture of Parallel Ecological Divergence: Beyond a Single Environmental Contrast.” Science Advances. AAAS, 2019. https://doi.org/10.1126/sciadv.aav9963."},"publication":"Science Advances","date_published":"2019-12-04T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"04","intvolume":" 5","title":"Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast","ddc":["570"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7393","file":[{"file_id":"7442","relation":"main_file","date_created":"2020-02-03T13:33:25Z","date_updated":"2020-07-14T12:47:57Z","checksum":"af99a5dcdc66c6d6102051faf3be48d8","file_name":"2019_ScienceAdvances_Morales.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1869449}],"oa_version":"Published Version","type":"journal_article","issue":"12","abstract":[{"lang":"eng","text":"The study of parallel ecological divergence provides important clues to the operation of natural selection. Parallel divergence often occurs in heterogeneous environments with different kinds of environmental gradients in different locations, but the genomic basis underlying this process is unknown. We investigated the genomics of rapid parallel adaptation in the marine snail Littorina saxatilis in response to two independent environmental axes (crab-predation versus wave-action and low-shore versus high-shore). Using pooled whole-genome resequencing, we show that sharing of genomic regions of high differentiation between environments is generally low but increases at smaller spatial scales. We identify different shared genomic regions of divergence for each environmental axis and show that most of these regions overlap with candidate chromosomal inversions. Several inversion regions are divergent and polymorphic across many localities. We argue that chromosomal inversions could store shared variation that fuels rapid parallel adaptation to heterogeneous environments, possibly as balanced polymorphism shared by adaptive gene flow."}],"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Theoretical and empirical approaches to understanding Parallel Adaptation","call_identifier":"H2020","_id":"265B41B8-B435-11E9-9278-68D0E5697425","grant_number":"797747"}],"isi":1,"quality_controlled":"1","external_id":{"pmid":["31840052"],"isi":["000505069600008"]},"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)"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1126/sciadv.aav9963","publication_identifier":{"issn":["2375-2548"]},"month":"12","department":[{"_id":"NiBa"}],"publisher":"AAAS","publication_status":"published","pmid":1,"year":"2019","volume":5,"date_updated":"2023-09-06T15:35:56Z","date_created":"2020-01-29T15:58:27Z","author":[{"full_name":"Morales, Hernán E.","first_name":"Hernán E.","last_name":"Morales"},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"last_name":"Larsson","first_name":"Tomas","full_name":"Larsson, Tomas"},{"full_name":"Panova, Marina","last_name":"Panova","first_name":"Marina"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"article_number":"eaav9963","license":"https://creativecommons.org/licenses/by-nc/4.0/","ec_funded":1,"file_date_updated":"2020-07-14T12:47:57Z"},{"abstract":[{"text":"Polymer additives can substantially reduce the drag of turbulent flows and the upperlimit, the so called “maximum drag reduction” (MDR) asymptote is universal, i.e. inde-pendent of the type of polymer and solvent used. Until recently, the consensus was that,in this limit, flows are in a marginal state where only a minimal level of turbulence activ-ity persists. Observations in direct numerical simulations using minimal sized channelsappeared to support this view and reported long “hibernation” periods where turbu-lence is marginalized. In simulations of pipe flow we find that, indeed, with increasingWeissenberg number (Wi), turbulence expresses long periods of hibernation if the domainsize is small. However, with increasing pipe length, the temporal hibernation continuouslyalters to spatio-temporal intermittency and here the flow consists of turbulent puffs sur-rounded by laminar flow. Moreover, upon an increase in Wi, the flow fully relaminarises,in agreement with recent experiments. At even larger Wi, a different instability is en-countered causing a drag increase towards MDR. Our findings hence link earlier minimalflow unit simulations with recent experiments and confirm that the addition of polymersinitially suppresses Newtonian turbulence and leads to a reverse transition. The MDRstate on the other hand results from a separate instability and the underlying dynamicscorresponds to the recently proposed state of elasto-inertial-turbulence (EIT).","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","status":"public","title":"Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit","intvolume":" 874","_id":"7397","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"10","article_processing_charge":"No","scopus_import":"1","date_published":"2019-09-10T00:00:00Z","article_type":"original","page":"699-719","publication":"Journal of Fluid Mechanics","citation":{"short":"J.M. Lopez Alonso, G.H. Choueiri, B. Hof, Journal of Fluid Mechanics 874 (2019) 699–719.","mla":"Lopez Alonso, Jose M., et al. “Dynamics of Viscoelastic Pipe Flow at Low Reynolds Numbers in the Maximum Drag Reduction Limit.” Journal of Fluid Mechanics, vol. 874, CUP, 2019, pp. 699–719, doi:10.1017/jfm.2019.486.","chicago":"Lopez Alonso, Jose M, George H Choueiri, and Björn Hof. “Dynamics of Viscoelastic Pipe Flow at Low Reynolds Numbers in the Maximum Drag Reduction Limit.” Journal of Fluid Mechanics. CUP, 2019. https://doi.org/10.1017/jfm.2019.486.","ama":"Lopez Alonso JM, Choueiri GH, Hof B. Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit. Journal of Fluid Mechanics. 2019;874:699-719. doi:10.1017/jfm.2019.486","ieee":"J. M. Lopez Alonso, G. H. Choueiri, and B. Hof, “Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit,” Journal of Fluid Mechanics, vol. 874. CUP, pp. 699–719, 2019.","apa":"Lopez Alonso, J. M., Choueiri, G. H., & Hof, B. (2019). Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit. Journal of Fluid Mechanics. CUP. https://doi.org/10.1017/jfm.2019.486","ista":"Lopez Alonso JM, Choueiri GH, Hof B. 2019. Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit. Journal of Fluid Mechanics. 874, 699–719."},"date_updated":"2023-09-06T15:36:36Z","date_created":"2020-01-29T16:05:19Z","volume":874,"author":[{"full_name":"Lopez Alonso, Jose M","id":"40770848-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0384-2022","first_name":"Jose M","last_name":"Lopez Alonso"},{"id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","last_name":"Choueiri","first_name":"George H","full_name":"Choueiri, George H"},{"full_name":"Hof, Björn","first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754"}],"publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"CUP","year":"2019","month":"09","publication_identifier":{"eissn":["1469-7645"],"issn":["0022-1120"]},"language":[{"iso":"eng"}],"doi":"10.1017/jfm.2019.486","quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1808.04080","open_access":"1"}],"external_id":{"arxiv":["1808.04080"],"isi":["000475349900001"]}},{"date_updated":"2023-09-07T12:07:12Z","date_created":"2018-12-16T22:59:20Z","volume":62,"author":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert"},{"full_name":"Nikitenko, Anton","orcid":"0000-0002-0659-3201","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","last_name":"Nikitenko","first_name":"Anton"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6287"}]},"publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Springer","year":"2019","file_date_updated":"2020-07-14T12:47:10Z","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00454-018-0049-2","isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Alpha Shape Theory Extended","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"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":["000494042900008"],"arxiv":["1709.09380"]},"month":"12","publication_identifier":{"eissn":["14320444"],"issn":["01795376"]},"oa_version":"Published Version","file":[{"date_created":"2019-02-06T10:10:46Z","date_updated":"2020-07-14T12:47:10Z","checksum":"f9d00e166efaccb5a76bbcbb4dcea3b4","file_id":"5932","relation":"main_file","creator":"dernst","file_size":599339,"content_type":"application/pdf","file_name":"2018_DiscreteCompGeometry_Edelsbrunner.pdf","access_level":"open_access"}],"status":"public","title":"Poisson–Delaunay Mosaics of Order k","ddc":["516"],"intvolume":" 62","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"5678","abstract":[{"text":"The order-k Voronoi tessellation of a locally finite set 𝑋⊆ℝ𝑛 decomposes ℝ𝑛 into convex domains whose points have the same k nearest neighbors in X. Assuming X is a stationary Poisson point process, we give explicit formulas for the expected number and total area of faces of a given dimension per unit volume of space. We also develop a relaxed version of discrete Morse theory and generalize by counting only faces, for which the k nearest points in X are within a given distance threshold.","lang":"eng"}],"issue":"4","type":"journal_article","date_published":"2019-12-01T00:00:00Z","article_type":"original","page":"865–878","publication":"Discrete and Computational Geometry","citation":{"chicago":"Edelsbrunner, Herbert, and Anton Nikitenko. “Poisson–Delaunay Mosaics of Order K.” Discrete and Computational Geometry. Springer, 2019. https://doi.org/10.1007/s00454-018-0049-2.","short":"H. Edelsbrunner, A. Nikitenko, Discrete and Computational Geometry 62 (2019) 865–878.","mla":"Edelsbrunner, Herbert, and Anton Nikitenko. “Poisson–Delaunay Mosaics of Order K.” Discrete and Computational Geometry, vol. 62, no. 4, Springer, 2019, pp. 865–878, doi:10.1007/s00454-018-0049-2.","apa":"Edelsbrunner, H., & Nikitenko, A. (2019). Poisson–Delaunay Mosaics of Order k. Discrete and Computational Geometry. Springer. https://doi.org/10.1007/s00454-018-0049-2","ieee":"H. Edelsbrunner and A. Nikitenko, “Poisson–Delaunay Mosaics of Order k,” Discrete and Computational Geometry, vol. 62, no. 4. Springer, pp. 865–878, 2019.","ista":"Edelsbrunner H, Nikitenko A. 2019. Poisson–Delaunay Mosaics of Order k. Discrete and Computational Geometry. 62(4), 865–878.","ama":"Edelsbrunner H, Nikitenko A. Poisson–Delaunay Mosaics of Order k. Discrete and Computational Geometry. 2019;62(4):865–878. doi:10.1007/s00454-018-0049-2"},"day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1"},{"day":"02","article_processing_charge":"No","scopus_import":"1","date_published":"2019-01-02T00:00:00Z","article_type":"original","page":"119-132.e4","publication":"Neuron","citation":{"mla":"Xu, Haibing, et al. “Assembly Responses of Hippocampal CA1 Place Cells Predict Learned Behavior in Goal-Directed Spatial Tasks on the Radial Eight-Arm Maze.” Neuron, vol. 101, no. 1, Elsevier, 2019, p. 119–132.e4, doi:10.1016/j.neuron.2018.11.015.","short":"H. Xu, P. Baracskay, J. O’Neill, J.L. Csicsvari, Neuron 101 (2019) 119–132.e4.","chicago":"Xu, Haibing, Peter Baracskay, Joseph O’Neill, and Jozsef L Csicsvari. “Assembly Responses of Hippocampal CA1 Place Cells Predict Learned Behavior in Goal-Directed Spatial Tasks on the Radial Eight-Arm Maze.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2018.11.015.","ama":"Xu H, Baracskay P, O’Neill J, Csicsvari JL. Assembly responses of hippocampal CA1 place cells predict learned behavior in goal-directed spatial tasks on the radial eight-arm maze. Neuron. 2019;101(1):119-132.e4. doi:10.1016/j.neuron.2018.11.015","ista":"Xu H, Baracskay P, O’Neill J, Csicsvari JL. 2019. Assembly responses of hippocampal CA1 place cells predict learned behavior in goal-directed spatial tasks on the radial eight-arm maze. Neuron. 101(1), 119–132.e4.","apa":"Xu, H., Baracskay, P., O’Neill, J., & Csicsvari, J. L. (2019). Assembly responses of hippocampal CA1 place cells predict learned behavior in goal-directed spatial tasks on the radial eight-arm maze. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2018.11.015","ieee":"H. Xu, P. Baracskay, J. O’Neill, and J. L. Csicsvari, “Assembly responses of hippocampal CA1 place cells predict learned behavior in goal-directed spatial tasks on the radial eight-arm maze,” Neuron, vol. 101, no. 1. Elsevier, p. 119–132.e4, 2019."},"abstract":[{"lang":"eng","text":"Hippocampus is needed for both spatial working and reference memories. Here, using a radial eight-arm maze, we examined how the combined demand on these memories influenced CA1 place cell assemblies while reference memories were partially updated. This was contrasted with control tasks requiring only working memory or the update of reference memory. Reference memory update led to the reward-directed place field shifts at newly rewarded arms and to the gradual strengthening of firing in passes between newly rewarded arms but not between those passes that included a familiar-rewarded arm. At the maze center, transient network synchronization periods preferentially replayed trajectories of the next chosen arm in reference memory tasks but the previously visited arm in the working memory task. Hence, reference memory demand was uniquely associated with a gradual, goal novelty-related reorganization of place cell assemblies and with trajectory replay that reflected the animal's decision of which arm to visit next."}],"issue":"1","type":"journal_article","oa_version":"Published Version","title":"Assembly responses of hippocampal CA1 place cells predict learned behavior in goal-directed spatial tasks on the radial eight-arm maze","status":"public","intvolume":" 101","_id":"5828","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"01","publication_identifier":{"issn":["10974199"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2018.11.015","quality_controlled":"1","isi":1,"project":[{"call_identifier":"FP7","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"https://www.doi.org/10.1016/j.neuron.2018.11.015","open_access":"1"}],"external_id":{"isi":["000454791500014"]},"oa":1,"ec_funded":1,"date_created":"2019-01-13T22:59:10Z","date_updated":"2023-09-07T12:06:37Z","volume":101,"author":[{"first_name":"Haibing","last_name":"Xu","id":"310349D0-F248-11E8-B48F-1D18A9856A87","full_name":"Xu, Haibing"},{"full_name":"Baracskay, Peter","id":"361CC00E-F248-11E8-B48F-1D18A9856A87","last_name":"Baracskay","first_name":"Peter"},{"full_name":"O'Neill, Joseph","last_name":"O'Neill","first_name":"Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87"},{"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":[{"id":"837","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://ist.ac.at/en/news/reading-rats-minds/","description":"News on IST Homepage","relation":"press_release"}]},"publication_status":"published","publisher":"Elsevier","department":[{"_id":"JoCs"}],"year":"2019"},{"ec_funded":1,"file_date_updated":"2020-07-14T12:47:12Z","year":"2019","publisher":"Springer","department":[{"_id":"RoSe"}],"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"52"}]},"author":[{"id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","last_name":"Moser","first_name":"Thomas","full_name":"Moser, Thomas"},{"first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"volume":20,"date_created":"2019-01-20T22:59:17Z","date_updated":"2023-09-07T12:37:42Z","publication_identifier":{"issn":["14240637"]},"month":"04","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":["000462444300008"],"arxiv":["1807.00739"]},"project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"},{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"isi":1,"quality_controlled":"1","doi":"10.1007/s00023-018-00757-0","language":[{"iso":"eng"}],"type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"We give a bound on the ground-state energy of a system of N non-interacting fermions in a three-dimensional cubic box interacting with an impurity particle via point interactions. We show that the change in energy compared to the system in the absence of the impurity is bounded in terms of the gas density and the scattering length of the interaction, independently of N. Our bound holds as long as the ratio of the mass of the impurity to the one of the gas particles is larger than a critical value m∗ ∗≈ 0.36 , which is the same regime for which we recently showed stability of the system."}],"_id":"5856","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 20","status":"public","ddc":["530"],"title":"Energy contribution of a point-interacting impurity in a Fermi gas","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2019_Annales_Moser.pdf","creator":"dernst","file_size":859846,"content_type":"application/pdf","file_id":"5894","relation":"main_file","checksum":"255e42f957a8e2b10aad2499c750a8d6","date_created":"2019-01-28T15:27:17Z","date_updated":"2020-07-14T12:47:12Z"}],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","citation":{"apa":"Moser, T., & Seiringer, R. (2019). Energy contribution of a point-interacting impurity in a Fermi gas. Annales Henri Poincare. Springer. https://doi.org/10.1007/s00023-018-00757-0","ieee":"T. Moser and R. Seiringer, “Energy contribution of a point-interacting impurity in a Fermi gas,” Annales Henri Poincare, vol. 20, no. 4. Springer, pp. 1325–1365, 2019.","ista":"Moser T, Seiringer R. 2019. Energy contribution of a point-interacting impurity in a Fermi gas. Annales Henri Poincare. 20(4), 1325–1365.","ama":"Moser T, Seiringer R. Energy contribution of a point-interacting impurity in a Fermi gas. Annales Henri Poincare. 2019;20(4):1325–1365. doi:10.1007/s00023-018-00757-0","chicago":"Moser, Thomas, and Robert Seiringer. “Energy Contribution of a Point-Interacting Impurity in a Fermi Gas.” Annales Henri Poincare. Springer, 2019. https://doi.org/10.1007/s00023-018-00757-0.","short":"T. Moser, R. Seiringer, Annales Henri Poincare 20 (2019) 1325–1365.","mla":"Moser, Thomas, and Robert Seiringer. “Energy Contribution of a Point-Interacting Impurity in a Fermi Gas.” Annales Henri Poincare, vol. 20, no. 4, Springer, 2019, pp. 1325–1365, doi:10.1007/s00023-018-00757-0."},"publication":"Annales Henri Poincare","page":"1325–1365","article_type":"original","date_published":"2019-04-01T00:00:00Z"},{"publisher":"Institute of Science and Technology Austria","department":[{"_id":"BjHo"}],"publication_status":"published","year":"2019","date_updated":"2023-09-07T12:53:25Z","date_created":"2019-10-22T12:08:43Z","author":[{"full_name":"Paranjape, Chaitanya S","id":"3D85B7C4-F248-11E8-B48F-1D18A9856A87","first_name":"Chaitanya S","last_name":"Paranjape"}],"file_date_updated":"2020-07-14T12:47:46Z","oa":1,"language":[{"iso":"eng"}],"supervisor":[{"last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:6957","publication_identifier":{"eissn":["2663-337X"]},"month":"10","status":"public","ddc":["532"],"title":"Onset of turbulence in plane Poiseuille flow","_id":"6957","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"creator":"cparanjape","file_size":45828099,"content_type":"application/zip","access_level":"closed","file_name":"Chaitanya_Paranjape_source_files_tex_figures.zip","checksum":"7ba298ba0ce7e1d11691af6b8eaf0a0a","date_created":"2019-10-23T09:54:43Z","date_updated":"2020-07-14T12:47:46Z","file_id":"6962","relation":"source_file"},{"checksum":"642697618314e31ac31392da7909c2d9","date_updated":"2020-07-14T12:47:46Z","date_created":"2019-10-23T10:37:09Z","relation":"main_file","file_id":"6963","content_type":"application/pdf","file_size":19504197,"creator":"cparanjape","access_level":"open_access","file_name":"Chaitanya_Paranjape_Thesis.pdf"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"In many shear flows like pipe flow, plane Couette flow, plane Poiseuille flow, etc. turbulence emerges subcritically. Here, when subjected to strong enough perturbations, the flow becomes turbulent in spite of the laminar base flow being linearly stable. The nature of this instability has puzzled the scientific community for decades. At onset, turbulence appears in localized patches and flows are spatio-temporally intermittent. In pipe flow the localized turbulent structures are referred to as puffs and in planar flows like plane Couette and channel flow, patches arise in the form of localized oblique bands. In this thesis, we study the onset of turbulence in channel flow in direct numerical simulations from a dynamical system theory perspective, as well as by performing experiments in a large aspect ratio channel.\r\n\r\nThe aim of the experimental work is to determine the critical Reynolds number where turbulence first becomes sustained. Recently, the onset of turbulence has been described in analogy to absorbing state phase transition (i.e. directed percolation). In particular, it has been shown that the critical point can be estimated from the competition between spreading and decay processes. Here, by performing experiments, we identify the mechanisms underlying turbulence proliferation in channel flow and find the critical Reynolds number, above which turbulence becomes sustained. Above the critical point, the continuous growth at the tip of the stripes outweighs the stochastic shedding of turbulent patches at the tail and the stripes expand. For growing stripes, the probability to decay decreases while the probability of stripe splitting increases. Consequently, and unlike for the puffs in pipe flow, neither of these two processes is time-independent i.e. memoryless. Coupling between stripe expansion and creation of new stripes via splitting leads to a significantly lower critical point ($Re_c=670+/-10$) than most earlier studies suggest. \r\n\r\nWhile the above approach sheds light on how turbulence first becomes sustained, it provides no insight into the origin of the stripes themselves. In the numerical part of the thesis we investigate how turbulent stripes form from invariant solutions of the Navier-Stokes equations. The origin of these turbulent stripes can be identified by applying concepts from the dynamical system theory. In doing so, we identify the exact coherent structures underlying stripes and their bifurcations and how they give rise to the turbulent attractor in phase space. We first report a family of localized nonlinear traveling wave solutions of the Navier-Stokes equations in channel flow. These solutions show structural similarities with turbulent stripes in experiments like obliqueness, quasi-streamwise streaks and vortices, etc. A parametric study of these traveling wave solution is performed, with parameters like Reynolds number, stripe tilt angle and domain size, including the stability of the solutions. These solutions emerge through saddle-node bifurcations and form a phase space skeleton for the turbulent stripes observed in the experiments. The lower branches of these TW solutions at different tilt angles undergo Hopf bifurcation and new solutions branches of relative periodic orbits emerge. These RPO solutions do not belong to the same family and therefore the routes to chaos for different angles are different. \r\n\r\nIn shear flows, turbulence at onset is transient in nature. Consequently,turbulence can not be tracked to lower Reynolds numbers, where the dynamics may simplify. Before this happens, turbulence becomes short-lived and laminarizes. In the last part of the thesis, we show that using numerical simulations we can continue turbulent stripes in channel flow past the 'relaminarization barrier' all the way to their origin. Here, turbulent stripe dynamics simplifies and the fluctuations are no longer stochastic and the stripe settles down to a relative periodic orbit. This relative periodic orbit originates from the aforementioned traveling wave solutions. Starting from the relative periodic orbit, a small increase in speed i.e. Reynolds number gives rise to chaos and the attractor dimension sharply increases in contrast to the classical transition scenario where the instabilities affect the flow globally and give rise to much more gradual route to turbulence."}],"page":"138","citation":{"chicago":"Paranjape, Chaitanya S. “Onset of Turbulence in Plane Poiseuille Flow.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6957.","short":"C.S. Paranjape, Onset of Turbulence in Plane Poiseuille Flow, Institute of Science and Technology Austria, 2019.","mla":"Paranjape, Chaitanya S. Onset of Turbulence in Plane Poiseuille Flow. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6957.","ieee":"C. S. Paranjape, “Onset of turbulence in plane Poiseuille flow,” Institute of Science and Technology Austria, 2019.","apa":"Paranjape, C. S. (2019). Onset of turbulence in plane Poiseuille flow. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6957","ista":"Paranjape CS. 2019. Onset of turbulence in plane Poiseuille flow. Institute of Science and Technology Austria.","ama":"Paranjape CS. Onset of turbulence in plane Poiseuille flow. 2019. doi:10.15479/AT:ISTA:6957"},"date_published":"2019-10-24T00:00:00Z","keyword":["Instabilities","Turbulence","Nonlinear dynamics"],"has_accepted_license":"1","article_processing_charge":"No","day":"24"},{"type":"journal_article","abstract":[{"lang":"eng","text":"We consider large random matrices with a general slowly decaying correlation among its entries. We prove universality of the local eigenvalue statistics and optimal local laws for the resolvent away from the spectral edges, generalizing the recent result of Ajanki et al. [‘Stability of the matrix Dyson equation and random matrices with correlations’, Probab. Theory Related Fields 173(1–2) (2019), 293–373] to allow slow correlation decay and arbitrary expectation. The main novel tool is\r\na systematic diagrammatic control of a multivariate cumulant expansion."}],"_id":"6182","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 7","ddc":["510"],"status":"public","title":"Random matrices with slow correlation decay","file":[{"file_id":"6883","relation":"main_file","date_created":"2019-09-17T14:24:13Z","date_updated":"2020-07-14T12:47:22Z","checksum":"933a472568221c73b2c3ce8c87bf6d15","file_name":"2019_Forum_Erdoes.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1520344}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"26","citation":{"apa":"Erdös, L., Krüger, T. H., & Schröder, D. J. (2019). Random matrices with slow correlation decay. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2019.2","ieee":"L. Erdös, T. H. Krüger, and D. J. Schröder, “Random matrices with slow correlation decay,” Forum of Mathematics, Sigma, vol. 7. Cambridge University Press, 2019.","ista":"Erdös L, Krüger TH, Schröder DJ. 2019. Random matrices with slow correlation decay. Forum of Mathematics, Sigma. 7, e8.","ama":"Erdös L, Krüger TH, Schröder DJ. Random matrices with slow correlation decay. Forum of Mathematics, Sigma. 2019;7. doi:10.1017/fms.2019.2","chicago":"Erdös, László, Torben H Krüger, and Dominik J Schröder. “Random Matrices with Slow Correlation Decay.” Forum of Mathematics, Sigma. Cambridge University Press, 2019. https://doi.org/10.1017/fms.2019.2.","short":"L. Erdös, T.H. Krüger, D.J. Schröder, Forum of Mathematics, Sigma 7 (2019).","mla":"Erdös, László, et al. “Random Matrices with Slow Correlation Decay.” Forum of Mathematics, Sigma, vol. 7, e8, Cambridge University Press, 2019, doi:10.1017/fms.2019.2."},"publication":"Forum of Mathematics, Sigma","article_type":"original","date_published":"2019-03-26T00:00:00Z","article_number":"e8","ec_funded":1,"file_date_updated":"2020-07-14T12:47:22Z","year":"2019","department":[{"_id":"LaEr"}],"publisher":"Cambridge University Press","publication_status":"published","related_material":{"record":[{"id":"6179","status":"public","relation":"dissertation_contains"}]},"author":[{"first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","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"},{"id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","first_name":"Dominik J","last_name":"Schröder","full_name":"Schröder, Dominik J"}],"volume":7,"date_updated":"2023-09-07T12:54:12Z","date_created":"2019-03-28T09:05:23Z","publication_identifier":{"eissn":["20505094"]},"month":"03","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":["000488847100001"],"arxiv":["1705.10661"]},"project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","doi":"10.1017/fms.2019.2","language":[{"iso":"eng"}]},{"status":"public","title":"Cusp universality for random matrices, II: The real symmetric case","intvolume":" 1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6186","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We prove that the local eigenvalue statistics of real symmetric Wigner-type\r\nmatrices near the cusp points of the eigenvalue density are universal. Together\r\nwith the companion paper [arXiv:1809.03971], which proves the same result for\r\nthe complex Hermitian symmetry class, this completes the last remaining case of\r\nthe Wigner-Dyson-Mehta universality conjecture after bulk and edge\r\nuniversalities have been established in the last years. We extend the recent\r\nDyson Brownian motion analysis at the edge [arXiv:1712.03881] to the cusp\r\nregime using the optimal local law from [arXiv:1809.03971] and the accurate\r\nlocal shape analysis of the density from [arXiv:1506.05095, arXiv:1804.07752].\r\nWe also present a PDE-based method to improve the estimate on eigenvalue\r\nrigidity via the maximum principle of the heat flow related to the Dyson\r\nBrownian motion."}],"issue":"4","article_type":"original","page":"615–707","publication":"Pure and Applied Analysis ","citation":{"ieee":"G. Cipolloni, L. Erdös, T. H. Krüger, and D. J. Schröder, “Cusp universality for random matrices, II: The real symmetric case,” Pure and Applied Analysis , vol. 1, no. 4. MSP, pp. 615–707, 2019.","apa":"Cipolloni, G., Erdös, L., Krüger, T. H., & Schröder, D. J. (2019). Cusp universality for random matrices, II: The real symmetric case. Pure and Applied Analysis . MSP. https://doi.org/10.2140/paa.2019.1.615","ista":"Cipolloni G, Erdös L, Krüger TH, Schröder DJ. 2019. Cusp universality for random matrices, II: The real symmetric case. Pure and Applied Analysis . 1(4), 615–707.","ama":"Cipolloni G, Erdös L, Krüger TH, Schröder DJ. Cusp universality for random matrices, II: The real symmetric case. Pure and Applied Analysis . 2019;1(4):615–707. doi:10.2140/paa.2019.1.615","chicago":"Cipolloni, Giorgio, László Erdös, Torben H Krüger, and Dominik J Schröder. “Cusp Universality for Random Matrices, II: The Real Symmetric Case.” Pure and Applied Analysis . MSP, 2019. https://doi.org/10.2140/paa.2019.1.615.","short":"G. Cipolloni, L. Erdös, T.H. Krüger, D.J. Schröder, Pure and Applied Analysis 1 (2019) 615–707.","mla":"Cipolloni, Giorgio, et al. “Cusp Universality for Random Matrices, II: The Real Symmetric Case.” Pure and Applied Analysis , vol. 1, no. 4, MSP, 2019, pp. 615–707, doi:10.2140/paa.2019.1.615."},"date_published":"2019-10-12T00:00:00Z","day":"12","article_processing_charge":"No","publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"MSP","year":"2019","date_updated":"2023-09-07T12:54:12Z","date_created":"2019-03-28T10:21:17Z","volume":1,"author":[{"orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","last_name":"Cipolloni","first_name":"Giorgio","full_name":"Cipolloni, Giorgio"},{"last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"full_name":"Krüger, Torben H","last_name":"Krüger","first_name":"Torben H","orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87"},{"id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","first_name":"Dominik J","last_name":"Schröder","full_name":"Schröder, Dominik J"}],"related_material":{"record":[{"id":"6179","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"quality_controlled":"1","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"oa":1,"external_id":{"arxiv":["1811.04055"]},"main_file_link":[{"url":"https://arxiv.org/abs/1811.04055","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.2140/paa.2019.1.615","month":"10","publication_identifier":{"eissn":["2578-5885"],"issn":["2578-5893"]}},{"file_date_updated":"2020-07-14T12:47:44Z","publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","year":"2019","pmid":1,"date_updated":"2023-09-07T12:55:21Z","date_created":"2019-09-22T22:00:37Z","volume":15,"author":[{"last_name":"Cepeda Humerez","first_name":"Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","full_name":"Cepeda Humerez, Sarah A"},{"full_name":"Ruess, Jakob","orcid":"0000-0003-1615-3282","last_name":"Ruess","first_name":"Jakob"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper"}],"related_material":{"record":[{"id":"6473","status":"public","relation":"part_of_dissertation"}]},"month":"09","publication_identifier":{"eissn":["15537358"]},"quality_controlled":"1","isi":1,"project":[{"_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation"}],"external_id":{"isi":["000489741800021"],"pmid":["31479447"]},"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":"10.1371/journal.pcbi.1007290","type":"journal_article","abstract":[{"text":"Across diverse biological systems—ranging from neural networks to intracellular signaling and genetic regulatory networks—the information about changes in the environment is frequently encoded in the full temporal dynamics of the network nodes. A pressing data-analysis challenge has thus been to efficiently estimate the amount of information that these dynamics convey from experimental data. Here we develop and evaluate decoding-based estimation methods to lower bound the mutual information about a finite set of inputs, encoded in single-cell high-dimensional time series data. For biological reaction networks governed by the chemical Master equation, we derive model-based information approximations and analytical upper bounds, against which we benchmark our proposed model-free decoding estimators. In contrast to the frequently-used k-nearest-neighbor estimator, decoding-based estimators robustly extract a large fraction of the available information from high-dimensional trajectories with a realistic number of data samples. We apply these estimators to previously published data on Erk and Ca2+ signaling in mammalian cells and to yeast stress-response, and find that substantial amount of information about environmental state can be encoded by non-trivial response statistics even in stationary signals. We argue that these single-cell, decoding-based information estimates, rather than the commonly-used tests for significant differences between selected population response statistics, provide a proper and unbiased measure for the performance of biological signaling networks.","lang":"eng"}],"issue":"9","ddc":["570"],"status":"public","title":"Estimating information in time-varying signals","intvolume":" 15","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6900","file":[{"file_id":"6925","relation":"main_file","checksum":"81bdce1361c9aa8395d6fa635fb6ab47","date_updated":"2020-07-14T12:47:44Z","date_created":"2019-10-01T10:53:45Z","access_level":"open_access","file_name":"2019_PLoS_Cepeda-Humerez.pdf","creator":"kschuh","file_size":3081855,"content_type":"application/pdf"}],"oa_version":"Published Version","scopus_import":"1","day":"03","article_processing_charge":"No","has_accepted_license":"1","page":"e1007290","publication":"PLoS computational biology","citation":{"chicago":"Cepeda Humerez, Sarah A, Jakob Ruess, and Gašper Tkačik. “Estimating Information in Time-Varying Signals.” PLoS Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007290.","short":"S.A. Cepeda Humerez, J. Ruess, G. Tkačik, PLoS Computational Biology 15 (2019) e1007290.","mla":"Cepeda Humerez, Sarah A., et al. “Estimating Information in Time-Varying Signals.” PLoS Computational Biology, vol. 15, no. 9, Public Library of Science, 2019, p. e1007290, doi:10.1371/journal.pcbi.1007290.","ieee":"S. A. Cepeda Humerez, J. Ruess, and G. Tkačik, “Estimating information in time-varying signals,” PLoS computational biology, vol. 15, no. 9. Public Library of Science, p. e1007290, 2019.","apa":"Cepeda Humerez, S. A., Ruess, J., & Tkačik, G. (2019). Estimating information in time-varying signals. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007290","ista":"Cepeda Humerez SA, Ruess J, Tkačik G. 2019. Estimating information in time-varying signals. PLoS computational biology. 15(9), e1007290.","ama":"Cepeda Humerez SA, Ruess J, Tkačik G. Estimating information in time-varying signals. PLoS computational biology. 2019;15(9):e1007290. doi:10.1371/journal.pcbi.1007290"},"date_published":"2019-09-03T00:00:00Z"},{"status":"public","title":"Disruption of endocytosis through chemical inhibition of clathrin heavy chain function","intvolume":" 15","_id":"6377","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"None","type":"journal_article","abstract":[{"text":"Clathrin-mediated endocytosis (CME) is a highly conserved and essential cellular process in eukaryotic cells, but its dynamic and vital nature makes it challenging to study using classical genetics tools. In contrast, although small molecules can acutely and reversibly perturb CME, the few chemical CME inhibitors that have been applied to plants are either ineffective or show undesirable side effects. Here, we identify the previously described endosidin9 (ES9) as an inhibitor of clathrin heavy chain (CHC) function in both Arabidopsis and human cells through affinity-based target isolation, in vitro binding studies and X-ray crystallography. Moreover, we present a chemically improved ES9 analog, ES9-17, which lacks the undesirable side effects of ES9 while retaining the ability to target CHC. ES9 and ES9-17 have expanded the chemical toolbox used to probe CHC function, and present chemical scaffolds for further design of more specific and potent CHC inhibitors across different systems.","lang":"eng"}],"issue":"6","article_type":"original","page":"641–649","publication":"Nature Chemical Biology","citation":{"short":"W. Dejonghe, I. Sharma, B. Denoo, S. De Munck, Q. Lu, K. Mishev, H. Bulut, E. Mylle, R. De Rycke, M.K. Vasileva, D.V. Savatin, W. Nerinckx, A. Staes, A. Drozdzecki, D. Audenaert, K. Yperman, A. Madder, J. Friml, D. Van Damme, K. Gevaert, V. Haucke, S.N. Savvides, J. Winne, E. Russinova, Nature Chemical Biology 15 (2019) 641–649.","mla":"Dejonghe, Wim, et al. “Disruption of Endocytosis through Chemical Inhibition of Clathrin Heavy Chain Function.” Nature Chemical Biology, vol. 15, no. 6, Springer Nature, 2019, pp. 641–649, doi:10.1038/s41589-019-0262-1.","chicago":"Dejonghe, Wim, Isha Sharma, Bram Denoo, Steven De Munck, Qing Lu, Kiril Mishev, Haydar Bulut, et al. “Disruption of Endocytosis through Chemical Inhibition of Clathrin Heavy Chain Function.” Nature Chemical Biology. Springer Nature, 2019. https://doi.org/10.1038/s41589-019-0262-1.","ama":"Dejonghe W, Sharma I, Denoo B, et al. Disruption of endocytosis through chemical inhibition of clathrin heavy chain function. Nature Chemical Biology. 2019;15(6):641–649. doi:10.1038/s41589-019-0262-1","apa":"Dejonghe, W., Sharma, I., Denoo, B., De Munck, S., Lu, Q., Mishev, K., … Russinova, E. (2019). Disruption of endocytosis through chemical inhibition of clathrin heavy chain function. Nature Chemical Biology. Springer Nature. https://doi.org/10.1038/s41589-019-0262-1","ieee":"W. Dejonghe et al., “Disruption of endocytosis through chemical inhibition of clathrin heavy chain function,” Nature Chemical Biology, vol. 15, no. 6. Springer Nature, pp. 641–649, 2019.","ista":"Dejonghe W, Sharma I, Denoo B, De Munck S, Lu Q, Mishev K, Bulut H, Mylle E, De Rycke R, Vasileva MK, Savatin DV, Nerinckx W, Staes A, Drozdzecki A, Audenaert D, Yperman K, Madder A, Friml J, Van Damme D, Gevaert K, Haucke V, Savvides SN, Winne J, Russinova E. 2019. Disruption of endocytosis through chemical inhibition of clathrin heavy chain function. Nature Chemical Biology. 15(6), 641–649."},"date_published":"2019-06-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JiFr"}],"year":"2019","date_created":"2019-05-05T21:59:11Z","date_updated":"2023-09-07T12:54:35Z","volume":15,"author":[{"full_name":"Dejonghe, Wim","first_name":"Wim","last_name":"Dejonghe"},{"last_name":"Sharma","first_name":"Isha","full_name":"Sharma, Isha"},{"last_name":"Denoo","first_name":"Bram","full_name":"Denoo, Bram"},{"full_name":"De Munck, Steven","last_name":"De Munck","first_name":"Steven"},{"full_name":"Lu, Qing","first_name":"Qing","last_name":"Lu"},{"last_name":"Mishev","first_name":"Kiril","full_name":"Mishev, Kiril"},{"full_name":"Bulut, Haydar","last_name":"Bulut","first_name":"Haydar"},{"last_name":"Mylle","first_name":"Evelien","full_name":"Mylle, Evelien"},{"full_name":"De Rycke, Riet","last_name":"De Rycke","first_name":"Riet"},{"full_name":"Vasileva, Mina K","last_name":"Vasileva","first_name":"Mina K","id":"3407EB18-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Savatin","first_name":"Daniel V.","full_name":"Savatin, Daniel V."},{"full_name":"Nerinckx, Wim","last_name":"Nerinckx","first_name":"Wim"},{"first_name":"An","last_name":"Staes","full_name":"Staes, An"},{"full_name":"Drozdzecki, Andrzej","last_name":"Drozdzecki","first_name":"Andrzej"},{"last_name":"Audenaert","first_name":"Dominique","full_name":"Audenaert, Dominique"},{"first_name":"Klaas","last_name":"Yperman","full_name":"Yperman, Klaas"},{"full_name":"Madder, Annemieke","last_name":"Madder","first_name":"Annemieke"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"},{"full_name":"Van Damme, Daniël","first_name":"Daniël","last_name":"Van Damme"},{"full_name":"Gevaert, Kris","first_name":"Kris","last_name":"Gevaert"},{"first_name":"Volker","last_name":"Haucke","full_name":"Haucke, Volker"},{"full_name":"Savvides, Savvas N.","last_name":"Savvides","first_name":"Savvas N."},{"full_name":"Winne, Johan","first_name":"Johan","last_name":"Winne"},{"full_name":"Russinova, Eugenia","first_name":"Eugenia","last_name":"Russinova"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"7172"}]},"quality_controlled":"1","isi":1,"external_id":{"isi":["000468195600018"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41589-019-0262-1","month":"06","publication_identifier":{"issn":["15524450"],"eissn":["15524469"]}},{"publication_identifier":{"issn":["2663-337X"]},"month":"12","oa":1,"language":[{"iso":"eng"}],"supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"SSU"}],"doi":"10.15479/AT:ISTA:7186","file_date_updated":"2020-07-14T12:47:52Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaHe"}],"publication_status":"published","year":"2019","date_created":"2019-12-16T14:26:14Z","date_updated":"2023-09-07T12:56:42Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1096"},{"status":"public","relation":"part_of_dissertation","id":"7001"}]},"author":[{"last_name":"Schwayer","first_name":"Cornelia","orcid":"0000-0001-5130-2226","id":"3436488C-F248-11E8-B48F-1D18A9856A87","full_name":"Schwayer, Cornelia"}],"has_accepted_license":"1","article_processing_charge":"No","day":"16","page":"107","citation":{"chicago":"Schwayer, Cornelia. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7186.","short":"C. Schwayer, Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow, Institute of Science and Technology Austria, 2019.","mla":"Schwayer, Cornelia. Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7186.","ieee":"C. Schwayer, “Mechanosensation of tight junctions depends on ZO-1 phase separation and flow,” Institute of Science and Technology Austria, 2019.","apa":"Schwayer, C. (2019). Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7186","ista":"Schwayer C. 2019. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Institute of Science and Technology Austria.","ama":"Schwayer C. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. 2019. doi:10.15479/AT:ISTA:7186"},"date_published":"2019-12-16T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Tissue morphogenesis in developmental or physiological processes is regulated by molecular\r\nand mechanical signals. While the molecular signaling cascades are increasingly well\r\ndescribed, the mechanical signals affecting tissue shape changes have only recently been\r\nstudied in greater detail. To gain more insight into the mechanochemical and biophysical\r\nbasis of an epithelial spreading process (epiboly) in early zebrafish development, we studied\r\ncell-cell junction formation and actomyosin network dynamics at the boundary between\r\nsurface layer epithelial cells (EVL) and the yolk syncytial layer (YSL). During zebrafish epiboly,\r\nthe cell mass sitting on top of the yolk cell spreads to engulf the yolk cell by the end of\r\ngastrulation. It has been previously shown that an actomyosin ring residing within the YSL\r\npulls on the EVL tissue through a cable-constriction and a flow-friction motor, thereby\r\ndragging the tissue vegetal wards. Pulling forces are likely transmitted from the YSL\r\nactomyosin ring to EVL cells; however, the nature and formation of the junctional structure\r\nmediating this process has not been well described so far. Therefore, our main aim was to\r\ndetermine the nature, dynamics and potential function of the EVL-YSL junction during this\r\nepithelial tissue spreading. Specifically, we show that the EVL-YSL junction is a\r\nmechanosensitive structure, predominantly made of tight junction (TJ) proteins. The process\r\nof TJ mechanosensation depends on the retrograde flow of non-junctional, phase-separated\r\nZonula Occludens-1 (ZO-1) protein clusters towards the EVL-YSL boundary. Interestingly, we\r\ncould demonstrate that ZO-1 is present in a non-junctional pool on the surface of the yolk\r\ncell, and ZO-1 undergoes a phase separation process that likely renders the protein\r\nresponsive to flows. These flows are directed towards the junction and mediate proper\r\ntension-dependent recruitment of ZO-1. Upon reaching the EVL-YSL junction ZO-1 gets\r\nincorporated into the junctional pool mediated through its direct actin-binding domain.\r\nWhen the non-junctional pool and/or ZO-1 direct actin binding is absent, TJs fail in their\r\nproper mechanosensitive responses resulting in slower tissue spreading. We could further\r\ndemonstrate that depletion of ZO proteins within the YSL results in diminished actomyosin\r\nring formation. This suggests that a mechanochemical feedback loop is at work during\r\nzebrafish epiboly: ZO proteins help in proper actomyosin ring formation and actomyosin\r\ncontractility and flows positively influence ZO-1 junctional recruitment. Finally, such a\r\nmesoscale polarization process mediated through the flow of phase-separated protein\r\nclusters might have implications for other processes such as immunological synapse\r\nformation, C. elegans zygote polarization and wound healing.","lang":"eng"}],"ddc":["570"],"status":"public","title":"Mechanosensation of tight junctions depends on ZO-1 phase separation and flow","_id":"7186","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_id":"7194","relation":"source_file","date_created":"2019-12-19T15:18:11Z","date_updated":"2020-07-14T12:47:52Z","checksum":"585583c1c875c5d9525703a539668a7c","file_name":"DocumentSourceFiles.zip","access_level":"closed","creator":"cschwayer","file_size":19431292,"content_type":"application/zip"},{"relation":"main_file","file_id":"7195","date_updated":"2020-07-14T12:47:52Z","date_created":"2019-12-19T15:19:21Z","checksum":"9b9b24351514948d27cec659e632e2cd","file_name":"Thesis_CS_final.pdf","access_level":"open_access","content_type":"application/pdf","file_size":19226428,"creator":"cschwayer"}],"oa_version":"Published Version"},{"file_date_updated":"2020-07-14T12:47:37Z","date_created":"2019-07-26T11:14:34Z","date_updated":"2023-09-07T13:10:36Z","related_material":{"record":[{"id":"6774","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Zhechev, Stephan Y","first_name":"Stephan Y","last_name":"Zhechev","id":"3AA52972-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"UlWa"}],"publication_status":"published","year":"2019","publication_identifier":{"issn":["2663-337X"]},"month":"08","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","first_name":"Uli","last_name":"Wagner"}],"doi":"10.15479/AT:ISTA:6681","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"},"abstract":[{"lang":"eng","text":"The first part of the thesis considers the computational aspects of the homotopy groups πd(X) of a topological space X. It is well known that there is no algorithm to decide whether the fundamental group π1(X) of a given finite simplicial complex X is trivial. On the other hand, there are several algorithms that, given a finite simplicial complex X that is simply connected (i.e., with π1(X) trivial), compute the higher homotopy group πd(X) for any given d ≥ 2.\r\nHowever, these algorithms come with a caveat: They compute the isomorphism type of πd(X), d ≥ 2 as an abstract finitely generated abelian group given by generators and relations, but they work with very implicit representations of the elements of πd(X). We present an algorithm that, given a simply connected space X, computes πd(X) and represents its elements as simplicial maps from suitable triangulations of the d-sphere Sd to X. For fixed d, the algorithm runs in time exponential in size(X), the number of simplices of X. Moreover, we prove that this is optimal: For every fixed d ≥ 2,\r\nwe construct a family of simply connected spaces X such that for any simplicial map representing a generator of πd(X), the size of the triangulation of S d on which the map is defined, is exponential in size(X).\r\nIn the second part of the thesis, we prove that the following question is algorithmically undecidable for d < ⌊3(k+1)/2⌋, k ≥ 5 and (k, d) ̸= (5, 7), which covers essentially everything outside the meta-stable range: Given a finite simplicial complex K of dimension k, decide whether there exists a piecewise-linear (i.e., linear on an arbitrarily fine subdivision of K) embedding f : K ↪→ Rd of K into a d-dimensional Euclidean space."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"date_created":"2019-08-07T13:02:50Z","date_updated":"2020-07-14T12:47:37Z","checksum":"3231e7cbfca3b5687366f84f0a57a0c0","file_id":"6771","relation":"main_file","creator":"szhechev","file_size":1464227,"content_type":"application/pdf","file_name":"Stephan_Zhechev_thesis.pdf","access_level":"open_access"},{"file_name":"Stephan_Zhechev_thesis.tex","access_level":"closed","content_type":"application/octet-stream","file_size":303988,"creator":"szhechev","relation":"source_file","file_id":"6772","date_updated":"2020-07-14T12:47:37Z","date_created":"2019-08-07T13:03:22Z","checksum":"85d65eb27b4377a9e332ee37a70f08b6"},{"access_level":"closed","file_name":"supplementary_material.zip","content_type":"application/zip","file_size":1087004,"creator":"szhechev","relation":"supplementary_material","file_id":"6773","checksum":"86b374d264ca2dd53e712728e253ee75","date_updated":"2020-07-14T12:47:37Z","date_created":"2019-08-07T13:03:34Z"}],"ddc":["514"],"title":"Algorithmic aspects of homotopy theory and embeddability","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6681","has_accepted_license":"1","article_processing_charge":"No","day":"08","date_published":"2019-08-08T00:00:00Z","page":"104","citation":{"mla":"Zhechev, Stephan Y. Algorithmic Aspects of Homotopy Theory and Embeddability. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6681.","short":"S.Y. Zhechev, Algorithmic Aspects of Homotopy Theory and Embeddability, Institute of Science and Technology Austria, 2019.","chicago":"Zhechev, Stephan Y. “Algorithmic Aspects of Homotopy Theory and Embeddability.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6681.","ama":"Zhechev SY. Algorithmic aspects of homotopy theory and embeddability. 2019. doi:10.15479/AT:ISTA:6681","ista":"Zhechev SY. 2019. Algorithmic aspects of homotopy theory and embeddability. Institute of Science and Technology Austria.","apa":"Zhechev, S. Y. (2019). Algorithmic aspects of homotopy theory and embeddability. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6681","ieee":"S. Y. Zhechev, “Algorithmic aspects of homotopy theory and embeddability,” Institute of Science and Technology Austria, 2019."}},{"date_published":"2019-10-28T00:00:00Z","language":[{"iso":"eng"}],"publication":"arXiv","citation":{"ista":"Avvakumov S, Kudrya S. Vanishing of all equivariant obstructions and the mapping degree. arXiv, 1910.12628.","apa":"Avvakumov, S., & Kudrya, S. (n.d.). Vanishing of all equivariant obstructions and the mapping degree. arXiv. arXiv.","ieee":"S. Avvakumov and S. Kudrya, “Vanishing of all equivariant obstructions and the mapping degree,” arXiv. arXiv.","ama":"Avvakumov S, Kudrya S. Vanishing of all equivariant obstructions and the mapping degree. arXiv.","chicago":"Avvakumov, Sergey, and Sergey Kudrya. “Vanishing of All Equivariant Obstructions and the Mapping Degree.” ArXiv. arXiv, n.d.","mla":"Avvakumov, Sergey, and Sergey Kudrya. “Vanishing of All Equivariant Obstructions and the Mapping Degree.” ArXiv, 1910.12628, arXiv.","short":"S. Avvakumov, S. Kudrya, ArXiv (n.d.)."},"external_id":{"arxiv":["1910.12628"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1910.12628"}],"oa":1,"project":[{"_id":"26611F5C-B435-11E9-9278-68D0E5697425","grant_number":"P31312","name":"Algorithms for Embeddings and Homotopy Theory","call_identifier":"FWF"}],"day":"28","month":"10","article_processing_charge":"No","author":[{"full_name":"Avvakumov, Sergey","last_name":"Avvakumov","first_name":"Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87"},{"id":"ecf01965-d252-11ea-95a5-8ada5f6c6a67","last_name":"Kudrya","first_name":"Sergey","full_name":"Kudrya, Sergey"}],"related_material":{"record":[{"id":"11446","relation":"later_version","status":"public"},{"id":"8156","relation":"dissertation_contains","status":"public"}]},"date_created":"2020-07-30T10:45:08Z","date_updated":"2023-09-07T13:12:17Z","oa_version":"Preprint","_id":"8182","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"submitted","title":"Vanishing of all equivariant obstructions and the mapping degree","publisher":"arXiv","department":[{"_id":"UlWa"}],"abstract":[{"text":"Suppose that $n\\neq p^k$ and $n\\neq 2p^k$ for all $k$ and all primes $p$. We prove that for any Hausdorff compactum $X$ with a free action of the symmetric group $\\mathfrak S_n$ there exists an $\\mathfrak S_n$-equivariant map $X \\to\r\n{\\mathbb R}^n$ whose image avoids the diagonal $\\{(x,x\\dots,x)\\in {\\mathbb R}^n|x\\in {\\mathbb R}\\}$.\r\n Previously, the special cases of this statement for certain $X$ were usually proved using the equivartiant obstruction theory. Such calculations are difficult and may become infeasible past the first (primary) obstruction. We\r\ntake a different approach which allows us to prove the vanishing of all obstructions simultaneously. The essential step in the proof is classifying the possible degrees of $\\mathfrak S_n$-equivariant maps from the boundary\r\n$\\partial\\Delta^{n-1}$ of $(n-1)$-simplex to itself. Existence of equivariant maps between spaces is important for many questions arising from discrete mathematics and geometry, such as Kneser's conjecture, the Square Peg conjecture, the Splitting Necklace problem, and the Topological Tverberg conjecture, etc. We demonstrate the utility of our result applying it to one such question, a specific instance of envy-free division problem.","lang":"eng"}],"article_number":"1910.12628","type":"preprint"},{"oa_version":"Preprint","date_created":"2020-07-30T10:45:51Z","date_updated":"2023-09-07T13:12:17Z","related_material":{"link":[{"relation":"later_version","url":"https://doi.org/10.1112/mtk.12059"}],"record":[{"relation":"dissertation_contains","status":"public","id":"8156"}]},"author":[{"first_name":"Sergey","last_name":"Avvakumov","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","full_name":"Avvakumov, Sergey"},{"first_name":"Roman","last_name":"Karasev","full_name":"Karasev, Roman"}],"department":[{"_id":"UlWa"}],"status":"public","title":"Envy-free division using mapping degree","publication_status":"submitted","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8185","year":"2019","abstract":[{"lang":"eng","text":"In this paper we study envy-free division problems. The classical approach to some of such problems, used by David Gale, reduces to considering continuous maps of a simplex to itself and finding sufficient conditions when this map hits the center of the simplex. The mere continuity is not sufficient for such a conclusion, the usual assumption (for example, in the Knaster--Kuratowski--Mazurkiewicz and the Gale theorem) is a certain boundary condition.\r\n We follow Erel Segal-Halevi, Fr\\'ed\\'eric Meunier, and Shira Zerbib, and replace the boundary condition by another assumption, which has the economic meaning of possibility for a player to prefer an empty part in the segment\r\npartition problem. We solve the problem positively when $n$, the number of players that divide the segment, is a prime power, and we provide counterexamples for every $n$ which is not a prime power. We also provide counterexamples relevant to a wider class of fair or envy-free partition problems when $n$ is odd and not a prime power."}],"type":"preprint","article_number":"1907.11183","language":[{"iso":"eng"}],"doi":"10.48550/arXiv.1907.11183","date_published":"2019-07-25T00:00:00Z","project":[{"grant_number":"P31312","_id":"26611F5C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Algorithms for Embeddings and Homotopy Theory"}],"citation":{"ista":"Avvakumov S, Karasev R. Envy-free division using mapping degree. arXiv, 1907.11183.","ieee":"S. Avvakumov and R. Karasev, “Envy-free division using mapping degree,” arXiv. .","apa":"Avvakumov, S., & Karasev, R. (n.d.). Envy-free division using mapping degree. arXiv. https://doi.org/10.48550/arXiv.1907.11183","ama":"Avvakumov S, Karasev R. Envy-free division using mapping degree. arXiv. doi:10.48550/arXiv.1907.11183","chicago":"Avvakumov, Sergey, and Roman Karasev. “Envy-Free Division Using Mapping Degree.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1907.11183.","mla":"Avvakumov, Sergey, and Roman Karasev. “Envy-Free Division Using Mapping Degree.” ArXiv, 1907.11183, doi:10.48550/arXiv.1907.11183.","short":"S. Avvakumov, R. Karasev, ArXiv (n.d.)."},"oa":1,"external_id":{"arxiv":["1907.11183"]},"main_file_link":[{"url":"https://arxiv.org/abs/1907.11183","open_access":"1"}],"publication":"arXiv","article_processing_charge":"No","month":"07","day":"25"},{"page":"61","project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"publication":"arXiv:1910.03372","oa":1,"citation":{"ama":"Deuchert A, Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas. I. Lower bound. arXiv:191003372.","ieee":"A. Deuchert, S. Mayer, and R. Seiringer, “The free energy of the two-dimensional dilute Bose gas. I. Lower bound,” arXiv:1910.03372. ArXiv.","apa":"Deuchert, A., Mayer, S., & Seiringer, R. (n.d.). The free energy of the two-dimensional dilute Bose gas. I. Lower bound. arXiv:1910.03372. ArXiv.","ista":"Deuchert A, Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas. I. Lower bound. arXiv:1910.03372, .","short":"A. Deuchert, S. Mayer, R. Seiringer, ArXiv:1910.03372 (n.d.).","mla":"Deuchert, Andreas, et al. “The Free Energy of the Two-Dimensional Dilute Bose Gas. I. Lower Bound.” ArXiv:1910.03372, ArXiv.","chicago":"Deuchert, Andreas, Simon Mayer, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. I. Lower Bound.” ArXiv:1910.03372. ArXiv, n.d."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1910.03372"}],"language":[{"iso":"eng"}],"date_published":"2019-10-08T00:00:00Z","scopus_import":1,"day":"08","month":"10","article_processing_charge":"No","publication_status":"draft","status":"public","title":"The free energy of the two-dimensional dilute Bose gas. I. Lower bound","publisher":"ArXiv","department":[{"_id":"RoSe"}],"year":"2019","_id":"7524","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-07T13:12:41Z","date_created":"2020-02-26T08:46:40Z","oa_version":"Preprint","author":[{"orcid":"0000-0003-3146-6746","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","last_name":"Deuchert","first_name":"Andreas","full_name":"Deuchert, Andreas"},{"full_name":"Mayer, Simon","id":"30C4630A-F248-11E8-B48F-1D18A9856A87","last_name":"Mayer","first_name":"Simon"},{"full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"7790"},{"status":"public","relation":"dissertation_contains","id":"7514"}]},"type":"preprint","abstract":[{"lang":"eng","text":"We prove a lower bound for the free energy (per unit volume) of the two-dimensional Bose gas in the thermodynamic limit. We show that the free energy at density $\\rho$ and inverse temperature $\\beta$ differs from the one of the non-interacting system by the correction term $4 \\pi \\rho^2 |\\ln a^2 \\rho|^{-1} (2 - [1 - \\beta_{\\mathrm{c}}/\\beta]_+^2)$. Here $a$ is the scattering length of the interaction potential, $[\\cdot]_+ = \\max\\{ 0, \\cdot \\}$ and $\\beta_{\\mathrm{c}}$ is the inverse Berezinskii--Kosterlitz--Thouless critical temperature for superfluidity. The result is valid in the dilute limit\r\n$a^2\\rho \\ll 1$ and if $\\beta \\rho \\gtrsim 1$."}],"ec_funded":1},{"language":[{"iso":"eng"}],"doi":"10.1016/j.cagd.2019.06.003","quality_controlled":"1","isi":1,"project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","name":"Alpha Shape Theory Extended","call_identifier":"H2020"},{"name":"Persistence and stability of geometric complexes","call_identifier":"FWF","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"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":["000485207800001"]},"oa":1,"month":"08","date_updated":"2023-09-07T13:15:29Z","date_created":"2019-07-07T21:59:20Z","volume":73,"author":[{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Katharina","last_name":"Ölsböck","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4672-8297","full_name":"Ölsböck, Katharina"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"7460"}]},"publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Elsevier","year":"2019","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2020-07-14T12:47:34Z","ec_funded":1,"date_published":"2019-08-01T00:00:00Z","page":"1-15","publication":"Computer Aided Geometric Design","citation":{"chicago":"Edelsbrunner, Herbert, and Katharina Ölsböck. “Holes and Dependences in an Ordered Complex.” Computer Aided Geometric Design. Elsevier, 2019. https://doi.org/10.1016/j.cagd.2019.06.003.","short":"H. Edelsbrunner, K. Ölsböck, Computer Aided Geometric Design 73 (2019) 1–15.","mla":"Edelsbrunner, Herbert, and Katharina Ölsböck. “Holes and Dependences in an Ordered Complex.” Computer Aided Geometric Design, vol. 73, Elsevier, 2019, pp. 1–15, doi:10.1016/j.cagd.2019.06.003.","apa":"Edelsbrunner, H., & Ölsböck, K. (2019). Holes and dependences in an ordered complex. Computer Aided Geometric Design. Elsevier. https://doi.org/10.1016/j.cagd.2019.06.003","ieee":"H. Edelsbrunner and K. Ölsböck, “Holes and dependences in an ordered complex,” Computer Aided Geometric Design, vol. 73. Elsevier, pp. 1–15, 2019.","ista":"Edelsbrunner H, Ölsböck K. 2019. Holes and dependences in an ordered complex. Computer Aided Geometric Design. 73, 1–15.","ama":"Edelsbrunner H, Ölsböck K. Holes and dependences in an ordered complex. Computer Aided Geometric Design. 2019;73:1-15. doi:10.1016/j.cagd.2019.06.003"},"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","file":[{"access_level":"open_access","file_name":"Elsevier_2019_Edelsbrunner.pdf","content_type":"application/pdf","file_size":2665013,"creator":"kschuh","relation":"main_file","file_id":"6624","checksum":"7c99be505dc7533257d42eb1830cef04","date_created":"2019-07-08T15:24:26Z","date_updated":"2020-07-14T12:47:34Z"}],"oa_version":"Published Version","title":"Holes and dependences in an ordered complex","status":"public","ddc":["000"],"intvolume":" 73","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6608","abstract":[{"text":"We use the canonical bases produced by the tri-partition algorithm in (Edelsbrunner and Ölsböck, 2018) to open and close holes in a polyhedral complex, K. In a concrete application, we consider the Delaunay mosaic of a finite set, we let K be an Alpha complex, and we use the persistence diagram of the distance function to guide the hole opening and closing operations. The dependences between the holes define a partial order on the cells in K that characterizes what can and what cannot be constructed using the operations. The relations in this partial order reveal structural information about the underlying filtration of complexes beyond what is expressed by the persistence diagram.","lang":"eng"}],"type":"journal_article"},{"_id":"6677","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Finding a Nash equilibrium is no easier than breaking Fiat-Shamir","oa_version":"Preprint","type":"conference","abstract":[{"lang":"eng","text":"The Fiat-Shamir heuristic transforms a public-coin interactive proof into a non-interactive argument, by replacing the verifier with a cryptographic hash function that is applied to the protocol’s transcript. Constructing hash functions for which this transformation is sound is a central and long-standing open question in cryptography.\r\n\r\nWe show that solving the END−OF−METERED−LINE problem is no easier than breaking the soundness of the Fiat-Shamir transformation when applied to the sumcheck protocol. In particular, if the transformed protocol is sound, then any hard problem in #P gives rise to a hard distribution in the class CLS, which is contained in PPAD. Our result opens up the possibility of sampling moderately-sized games for which it is hard to find a Nash equilibrium, by reducing the inversion of appropriately chosen one-way functions to #SAT.\r\n\r\nOur main technical contribution is a stateful incrementally verifiable procedure that, given a SAT instance over n variables, counts the number of satisfying assignments. This is accomplished via an exponential sequence of small steps, each computable in time poly(n). Incremental verifiability means that each intermediate state includes a sumcheck-based proof of its correctness, and the proof can be updated and verified in time poly(n)."}],"citation":{"ama":"Choudhuri AR, Hubáček P, Kamath Hosdurg C, Pietrzak KZ, Rosen A, Rothblum GN. Finding a Nash equilibrium is no easier than breaking Fiat-Shamir. In: Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing - STOC 2019. ACM Press; 2019:1103-1114. doi:10.1145/3313276.3316400","apa":"Choudhuri, A. R., Hubáček, P., Kamath Hosdurg, C., Pietrzak, K. Z., Rosen, A., & Rothblum, G. N. (2019). Finding a Nash equilibrium is no easier than breaking Fiat-Shamir. In Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing - STOC 2019 (pp. 1103–1114). Phoenix, AZ, United States: ACM Press. https://doi.org/10.1145/3313276.3316400","ieee":"A. R. Choudhuri, P. Hubáček, C. Kamath Hosdurg, K. Z. Pietrzak, A. Rosen, and G. N. Rothblum, “Finding a Nash equilibrium is no easier than breaking Fiat-Shamir,” in Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing - STOC 2019, Phoenix, AZ, United States, 2019, pp. 1103–1114.","ista":"Choudhuri AR, Hubáček P, Kamath Hosdurg C, Pietrzak KZ, Rosen A, Rothblum GN. 2019. Finding a Nash equilibrium is no easier than breaking Fiat-Shamir. Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing - STOC 2019. STOC: Symposium on Theory of Computing, 1103–1114.","short":"A.R. Choudhuri, P. Hubáček, C. Kamath Hosdurg, K.Z. Pietrzak, A. Rosen, G.N. Rothblum, in:, Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing - STOC 2019, ACM Press, 2019, pp. 1103–1114.","mla":"Choudhuri, Arka Rai, et al. “Finding a Nash Equilibrium Is No Easier than Breaking Fiat-Shamir.” Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing - STOC 2019, ACM Press, 2019, pp. 1103–14, doi:10.1145/3313276.3316400.","chicago":"Choudhuri, Arka Rai, Pavel Hubáček, Chethan Kamath Hosdurg, Krzysztof Z Pietrzak, Alon Rosen, and Guy N. Rothblum. “Finding a Nash Equilibrium Is No Easier than Breaking Fiat-Shamir.” In Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing - STOC 2019, 1103–14. ACM Press, 2019. https://doi.org/10.1145/3313276.3316400."},"publication":"Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing - STOC 2019","page":"1103-1114","date_published":"2019-06-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","year":"2019","publisher":"ACM Press","department":[{"_id":"KrPi"}],"publication_status":"published","related_material":{"record":[{"id":"7896","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Choudhuri, Arka Rai","first_name":"Arka Rai","last_name":"Choudhuri"},{"full_name":"Hubáček, Pavel","first_name":"Pavel","last_name":"Hubáček"},{"last_name":"Kamath Hosdurg","first_name":"Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","full_name":"Kamath Hosdurg, Chethan"},{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z"},{"first_name":"Alon","last_name":"Rosen","full_name":"Rosen, Alon"},{"first_name":"Guy N.","last_name":"Rothblum","full_name":"Rothblum, Guy N."}],"date_updated":"2023-09-07T13:15:55Z","date_created":"2019-07-24T09:20:53Z","ec_funded":1,"oa":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/549"}],"external_id":{"isi":["000523199100100"]},"project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"quality_controlled":"1","isi":1,"doi":"10.1145/3313276.3316400","conference":{"name":"STOC: Symposium on Theory of Computing","end_date":"2019-06-26","start_date":"2019-06-23","location":"Phoenix, AZ, United States"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781450367059"]},"month":"06"},{"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"UlWa"}],"year":"2019","date_updated":"2023-09-07T13:17:36Z","date_created":"2019-02-14T11:54:08Z","volume":61,"author":[{"last_name":"Lubiw","first_name":"Anna","full_name":"Lubiw, Anna"},{"last_name":"Masárová","first_name":"Zuzana","orcid":"0000-0002-6660-1322","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","full_name":"Masárová, Zuzana"},{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli"}],"related_material":{"record":[{"id":"683","relation":"earlier_version","status":"public"},{"id":"7944","relation":"dissertation_contains","status":"public"}]},"file_date_updated":"2020-07-14T12:47:14Z","isi":1,"quality_controlled":"1","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"external_id":{"isi":["000466130000009"],"arxiv":["1710.02741"]},"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":"10.1007/s00454-018-0035-8","month":"06","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"status":"public","ddc":["000"],"title":"A proof of the orbit conjecture for flipping edge-labelled triangulations","intvolume":" 61","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5986","file":[{"file_name":"2018_DiscreteGeometry_Lubiw.pdf","access_level":"open_access","creator":"dernst","file_size":556276,"content_type":"application/pdf","file_id":"5988","relation":"main_file","date_created":"2019-02-14T11:57:22Z","date_updated":"2020-07-14T12:47:14Z","checksum":"e1bff88f1d77001b53b78c485ce048d7"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Given a triangulation of a point set in the plane, a flip deletes an edge e whose removal leaves a convex quadrilateral, and replaces e by the opposite diagonal of the quadrilateral. It is well known that any triangulation of a point set can be reconfigured to any other triangulation by some sequence of flips. We explore this question in the setting where each edge of a triangulation has a label, and a flip transfers the label of the removed edge to the new edge. It is not true that every labelled triangulation of a point set can be reconfigured to every other labelled triangulation via a sequence of flips, but we characterize when this is possible. There is an obvious necessary condition: for each label l, if edge e has label l in the first triangulation and edge f has label l in the second triangulation, then there must be some sequence of flips that moves label l from e to f, ignoring all other labels. Bose, Lubiw, Pathak and Verdonschot formulated the Orbit Conjecture, which states that this necessary condition is also sufficient, i.e. that all labels can be simultaneously mapped to their destination if and only if each label individually can be mapped to its destination. We prove this conjecture. Furthermore, we give a polynomial-time algorithm (with 𝑂(𝑛8) being a crude bound on the run-time) to find a sequence of flips to reconfigure one labelled triangulation to another, if such a sequence exists, and we prove an upper bound of 𝑂(𝑛7) on the length of the flip sequence. Our proof uses the topological result that the sets of pairwise non-crossing edges on a planar point set form a simplicial complex that is homeomorphic to a high-dimensional ball (this follows from a result of Orden and Santos; we give a different proof based on a shelling argument). The dual cell complex of this simplicial ball, called the flip complex, has the usual flip graph as its 1-skeleton. We use properties of the 2-skeleton of the flip complex to prove the Orbit Conjecture.","lang":"eng"}],"issue":"4","article_type":"original","page":"880-898","publication":"Discrete & Computational Geometry","citation":{"ama":"Lubiw A, Masárová Z, Wagner U. A proof of the orbit conjecture for flipping edge-labelled triangulations. Discrete & Computational Geometry. 2019;61(4):880-898. doi:10.1007/s00454-018-0035-8","ista":"Lubiw A, Masárová Z, Wagner U. 2019. A proof of the orbit conjecture for flipping edge-labelled triangulations. Discrete & Computational Geometry. 61(4), 880–898.","apa":"Lubiw, A., Masárová, Z., & Wagner, U. (2019). A proof of the orbit conjecture for flipping edge-labelled triangulations. Discrete & Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-018-0035-8","ieee":"A. Lubiw, Z. Masárová, and U. Wagner, “A proof of the orbit conjecture for flipping edge-labelled triangulations,” Discrete & Computational Geometry, vol. 61, no. 4. Springer Nature, pp. 880–898, 2019.","mla":"Lubiw, Anna, et al. “A Proof of the Orbit Conjecture for Flipping Edge-Labelled Triangulations.” Discrete & Computational Geometry, vol. 61, no. 4, Springer Nature, 2019, pp. 880–98, doi:10.1007/s00454-018-0035-8.","short":"A. Lubiw, Z. Masárová, U. Wagner, Discrete & Computational Geometry 61 (2019) 880–898.","chicago":"Lubiw, Anna, Zuzana Masárová, and Uli Wagner. “A Proof of the Orbit Conjecture for Flipping Edge-Labelled Triangulations.” Discrete & Computational Geometry. Springer Nature, 2019. https://doi.org/10.1007/s00454-018-0035-8."},"date_published":"2019-06-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)"},{"publication_identifier":{"issn":["00268976"]},"month":"01","doi":"10.1080/00268976.2019.1567852","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000474641400008"]},"oa":1,"project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902","call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"isi":1,"quality_controlled":"1","ec_funded":1,"file_date_updated":"2020-07-14T12:47:13Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8958"}]},"author":[{"full_name":"Li, Xiang","id":"4B7E523C-F248-11E8-B48F-1D18A9856A87","last_name":"Li","first_name":"Xiang"},{"full_name":"Bighin, Giacomo","first_name":"Giacomo","last_name":"Bighin","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8823-9777"},{"first_name":"Enderalp","last_name":"Yakaboylu","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5973-0874","full_name":"Yakaboylu, Enderalp"},{"orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail"}],"date_updated":"2023-09-07T13:16:42Z","date_created":"2019-01-27T22:59:10Z","year":"2019","publisher":"Taylor and Francis","department":[{"_id":"MiLe"}],"publication_status":"published","article_processing_charge":"No","has_accepted_license":"1","day":"18","scopus_import":"1","date_published":"2019-01-18T00:00:00Z","citation":{"chicago":"Li, Xiang, Giacomo Bighin, Enderalp Yakaboylu, and Mikhail Lemeshko. “Variational Approaches to Quantum Impurities: From the Fröhlich Polaron to the Angulon.” Molecular Physics. Taylor and Francis, 2019. https://doi.org/10.1080/00268976.2019.1567852.","mla":"Li, Xiang, et al. “Variational Approaches to Quantum Impurities: From the Fröhlich Polaron to the Angulon.” Molecular Physics, Taylor and Francis, 2019, doi:10.1080/00268976.2019.1567852.","short":"X. Li, G. Bighin, E. Yakaboylu, M. Lemeshko, Molecular Physics (2019).","ista":"Li X, Bighin G, Yakaboylu E, Lemeshko M. 2019. Variational approaches to quantum impurities: from the Fröhlich polaron to the angulon. Molecular Physics.","ieee":"X. Li, G. Bighin, E. Yakaboylu, and M. Lemeshko, “Variational approaches to quantum impurities: from the Fröhlich polaron to the angulon,” Molecular Physics. Taylor and Francis, 2019.","apa":"Li, X., Bighin, G., Yakaboylu, E., & Lemeshko, M. (2019). Variational approaches to quantum impurities: from the Fröhlich polaron to the angulon. Molecular Physics. Taylor and Francis. https://doi.org/10.1080/00268976.2019.1567852","ama":"Li X, Bighin G, Yakaboylu E, Lemeshko M. Variational approaches to quantum impurities: from the Fröhlich polaron to the angulon. Molecular Physics. 2019. doi:10.1080/00268976.2019.1567852"},"publication":"Molecular Physics","abstract":[{"text":"Problems involving quantum impurities, in which one or a few particles are interacting with a macroscopic environment, represent a pervasive paradigm, spanning across atomic, molecular, and condensed-matter physics. In this paper we introduce new variational approaches to quantum impurities and apply them to the Fröhlich polaron–a quasiparticle formed out of an electron (or other point-like impurity) in a polar medium, and to the angulon–a quasiparticle formed out of a rotating molecule in a bosonic bath. We benchmark these approaches against established theories, evaluating their accuracy as a function of the impurity-bath coupling.","lang":"eng"}],"type":"journal_article","file":[{"file_id":"5896","relation":"main_file","checksum":"178964744b636a6f036372f4f090a657","date_updated":"2020-07-14T12:47:13Z","date_created":"2019-01-29T08:32:57Z","access_level":"open_access","file_name":"2019_MolecularPhysics_Li.pdf","creator":"dernst","file_size":1309966,"content_type":"application/pdf"}],"oa_version":"Published Version","_id":"5886","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Variational approaches to quantum impurities: from the Fröhlich polaron to the angulon","ddc":["530"],"status":"public"},{"volume":129,"date_updated":"2023-09-07T13:18:26Z","date_created":"2019-06-11T20:09:57Z","related_material":{"record":[{"id":"8032","status":"public","relation":"part_of_dissertation"}]},"author":[{"first_name":"Kristóf","last_name":"Huszár","id":"33C26278-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5445-5057","full_name":"Huszár, Kristóf"},{"last_name":"Spreer","first_name":"Jonathan","full_name":"Spreer, Jonathan"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"UlWa"}],"publication_status":"published","year":"2019","file_date_updated":"2020-07-14T12:47:33Z","language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.SoCG.2019.44","conference":{"name":"SoCG: Symposium on Computational Geometry","end_date":"2019-06-21","location":"Portland, Oregon, United States","start_date":"2019-06-18"},"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1812.05528"]},"oa":1,"publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-95977-104-7"]},"month":"06","oa_version":"Published Version","file":[{"checksum":"29d18c435368468aa85823dabb157e43","date_updated":"2020-07-14T12:47:33Z","date_created":"2019-06-12T06:45:33Z","relation":"main_file","file_id":"6557","content_type":"application/pdf","file_size":905885,"creator":"kschuh","access_level":"open_access","file_name":"2019_LIPIcs-Huszar.pdf"}],"intvolume":" 129","status":"public","ddc":["516"],"title":"3-manifold triangulations with small treewidth","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6556","abstract":[{"text":"Motivated by fixed-parameter tractable (FPT) problems in computational topology, we consider the treewidth tw(M) of a compact, connected 3-manifold M, defined to be the minimum treewidth of the face pairing graph of any triangulation T of M. In this setting the relationship between the topology of a 3-manifold and its treewidth is of particular interest. First, as a corollary of work of Jaco and Rubinstein, we prove that for any closed, orientable 3-manifold M the treewidth tw(M) is at most 4g(M)-2, where g(M) denotes Heegaard genus of M. In combination with our earlier work with Wagner, this yields that for non-Haken manifolds the Heegaard genus and the treewidth are within a constant factor. Second, we characterize all 3-manifolds of treewidth one: These are precisely the lens spaces and a single other Seifert fibered space. Furthermore, we show that all remaining orientable Seifert fibered spaces over the 2-sphere or a non-orientable surface have treewidth two. In particular, for every spherical 3-manifold we exhibit a triangulation of treewidth at most two. Our results further validate the parameter of treewidth (and other related parameters such as cutwidth or congestion) to be useful for topological computing, and also shed more light on the scope of existing FPT-algorithms in the field.","lang":"eng"}],"alternative_title":["LIPIcs"],"type":"conference","date_published":"2019-06-01T00:00:00Z","page":"44:1-44:20","citation":{"short":"K. Huszár, J. Spreer, in:, 35th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 44:1-44:20.","mla":"Huszár, Kristóf, and Jonathan Spreer. “3-Manifold Triangulations with Small Treewidth.” 35th International Symposium on Computational Geometry, vol. 129, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 44:1-44:20, doi:10.4230/LIPIcs.SoCG.2019.44.","chicago":"Huszár, Kristóf, and Jonathan Spreer. “3-Manifold Triangulations with Small Treewidth.” In 35th International Symposium on Computational Geometry, 129:44:1-44:20. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPIcs.SoCG.2019.44.","ama":"Huszár K, Spreer J. 3-manifold triangulations with small treewidth. In: 35th International Symposium on Computational Geometry. Vol 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:44:1-44:20. doi:10.4230/LIPIcs.SoCG.2019.44","ieee":"K. Huszár and J. Spreer, “3-manifold triangulations with small treewidth,” in 35th International Symposium on Computational Geometry, Portland, Oregon, United States, 2019, vol. 129, p. 44:1-44:20.","apa":"Huszár, K., & Spreer, J. (2019). 3-manifold triangulations with small treewidth. In 35th International Symposium on Computational Geometry (Vol. 129, p. 44:1-44:20). Portland, Oregon, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2019.44","ista":"Huszár K, Spreer J. 2019. 3-manifold triangulations with small treewidth. 35th International Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 129, 44:1-44:20."},"publication":"35th International Symposium on Computational Geometry","article_processing_charge":"No","has_accepted_license":"1","day":"01","keyword":["computational 3-manifold topology","fixed-parameter tractability","layered triangulations","structural graph theory","treewidth","cutwidth","Heegaard genus"],"scopus_import":"1"},{"abstract":[{"lang":"eng","text":"In graph theory, as well as in 3-manifold topology, there exist several width-type parameters to describe how \"simple\" or \"thin\" a given graph or 3-manifold is. These parameters, such as pathwidth or treewidth for graphs, or the concept of thin position for 3-manifolds, play an important role when studying algorithmic problems; in particular, there is a variety of problems in computational 3-manifold topology - some of them known to be computationally hard in general - that become solvable in polynomial time as soon as the dual graph of the input triangulation has bounded treewidth.\r\nIn view of these algorithmic results, it is natural to ask whether every 3-manifold admits a triangulation of bounded treewidth. We show that this is not the case, i.e., that there exists an infinite family of closed 3-manifolds not admitting triangulations of bounded pathwidth or treewidth (the latter implies the former, but we present two separate proofs).\r\nWe derive these results from work of Agol, of Scharlemann and Thompson, and of Scharlemann, Schultens and Saito by exhibiting explicit connections between the topology of a 3-manifold M on the one hand and width-type parameters of the dual graphs of triangulations of M on the other hand, answering a question that had been raised repeatedly by researchers in computational 3-manifold topology. In particular, we show that if a closed, orientable, irreducible, non-Haken 3-manifold M has a triangulation of treewidth (resp. pathwidth) k then the Heegaard genus of M is at most 18(k+1) (resp. 4(3k+1))."}],"issue":"2","type":"journal_article","file":[{"access_level":"open_access","file_name":"479-1917-1-PB.pdf","creator":"khuszar","content_type":"application/pdf","file_size":857590,"file_id":"7094","relation":"main_file","checksum":"c872d590d38d538404782bca20c4c3f5","date_updated":"2020-07-14T12:47:49Z","date_created":"2019-11-23T12:35:16Z"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7093","title":"On the treewidth of triangulated 3-manifolds","ddc":["514"],"status":"public","intvolume":" 10","day":"01","article_processing_charge":"No","has_accepted_license":"1","date_published":"2019-11-01T00:00:00Z","publication":"Journal of Computational Geometry","citation":{"apa":"Huszár, K., Spreer, J., & Wagner, U. (2019). On the treewidth of triangulated 3-manifolds. Journal of Computational Geometry. Computational Geometry Laborartoy. https://doi.org/10.20382/JOGC.V10I2A5","ieee":"K. Huszár, J. Spreer, and U. Wagner, “On the treewidth of triangulated 3-manifolds,” Journal of Computational Geometry, vol. 10, no. 2. Computational Geometry Laborartoy, pp. 70–98, 2019.","ista":"Huszár K, Spreer J, Wagner U. 2019. On the treewidth of triangulated 3-manifolds. Journal of Computational Geometry. 10(2), 70–98.","ama":"Huszár K, Spreer J, Wagner U. On the treewidth of triangulated 3-manifolds. Journal of Computational Geometry. 2019;10(2):70–98. doi:10.20382/JOGC.V10I2A5","chicago":"Huszár, Kristóf, Jonathan Spreer, and Uli Wagner. “On the Treewidth of Triangulated 3-Manifolds.” Journal of Computational Geometry. Computational Geometry Laborartoy, 2019. https://doi.org/10.20382/JOGC.V10I2A5.","short":"K. Huszár, J. Spreer, U. Wagner, Journal of Computational Geometry 10 (2019) 70–98.","mla":"Huszár, Kristóf, et al. “On the Treewidth of Triangulated 3-Manifolds.” Journal of Computational Geometry, vol. 10, no. 2, Computational Geometry Laborartoy, 2019, pp. 70–98, doi:10.20382/JOGC.V10I2A5."},"article_type":"original","page":"70–98","file_date_updated":"2020-07-14T12:47:49Z","author":[{"full_name":"Huszár, Kristóf","last_name":"Huszár","first_name":"Kristóf","orcid":"0000-0002-5445-5057","id":"33C26278-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Spreer, Jonathan","last_name":"Spreer","first_name":"Jonathan"},{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli"}],"related_material":{"record":[{"id":"285","status":"public","relation":"earlier_version"},{"id":"8032","status":"public","relation":"part_of_dissertation"}]},"date_created":"2019-11-23T12:14:09Z","date_updated":"2023-09-07T13:18:26Z","volume":10,"year":"2019","publication_status":"published","publisher":"Computational Geometry Laborartoy","department":[{"_id":"UlWa"}],"month":"11","publication_identifier":{"issn":["1920-180X"]},"doi":"10.20382/JOGC.V10I2A5","language":[{"iso":"eng"}],"external_id":{"arxiv":["1712.00434"]},"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"},{"abstract":[{"text":"During bacterial cell division, the tubulin-homolog FtsZ forms a ring-like structure at the center of the cell. This Z-ring not only organizes the division machinery, but treadmilling of FtsZ filaments was also found to play a key role in distributing proteins at the division site. What regulates the architecture, dynamics and stability of the Z-ring is currently unknown, but FtsZ-associated proteins are known to play an important role. Here, using an in vitro reconstitution approach, we studied how the well-conserved protein ZapA affects FtsZ treadmilling and filament organization into large-scale patterns. Using high-resolution fluorescence microscopy and quantitative image analysis, we found that ZapA cooperatively increases the spatial order of the filament network, but binds only transiently to FtsZ filaments and has no effect on filament length and treadmilling velocity. Together, our data provides a model for how FtsZ-associated proteins can increase the precision and stability of the bacterial cell division machinery in a switch-like manner.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2019_NatureComm_Caldas.pdf","creator":"dernst","content_type":"application/pdf","file_size":8488733,"file_id":"7208","relation":"main_file","checksum":"a1b44b427ba341383197790d0e8789fa","date_created":"2019-12-23T07:34:56Z","date_updated":"2020-07-14T12:47:53Z"}],"title":"Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA","status":"public","ddc":["570"],"intvolume":" 10","_id":"7197","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"17","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2019-12-17T00:00:00Z","article_type":"original","publication":"Nature Communications","citation":{"ieee":"P. R. Dos Santos Caldas, M. D. Lopez Pelegrin, D. J. G. Pearce, N. B. Budanur, J. Brugués, and M. Loose, “Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA,” Nature Communications, vol. 10. Springer Nature, 2019.","apa":"Dos Santos Caldas, P. R., Lopez Pelegrin, M. D., Pearce, D. J. G., Budanur, N. B., Brugués, J., & Loose, M. (2019). Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-13702-4","ista":"Dos Santos Caldas PR, Lopez Pelegrin MD, Pearce DJG, Budanur NB, Brugués J, Loose M. 2019. Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA. Nature Communications. 10, 5744.","ama":"Dos Santos Caldas PR, Lopez Pelegrin MD, Pearce DJG, Budanur NB, Brugués J, Loose M. Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA. Nature Communications. 2019;10. doi:10.1038/s41467-019-13702-4","chicago":"Dos Santos Caldas, Paulo R, Maria D Lopez Pelegrin, Daniel J. G. Pearce, Nazmi B Budanur, Jan Brugués, and Martin Loose. “Cooperative Ordering of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinker ZapA.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-13702-4.","short":"P.R. Dos Santos Caldas, M.D. Lopez Pelegrin, D.J.G. Pearce, N.B. Budanur, J. Brugués, M. Loose, Nature Communications 10 (2019).","mla":"Dos Santos Caldas, Paulo R., et al. “Cooperative Ordering of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinker ZapA.” Nature Communications, vol. 10, 5744, Springer Nature, 2019, doi:10.1038/s41467-019-13702-4."},"file_date_updated":"2020-07-14T12:47:53Z","ec_funded":1,"article_number":"5744","date_updated":"2023-09-07T13:18:51Z","date_created":"2019-12-20T12:22:57Z","volume":10,"author":[{"last_name":"Dos Santos Caldas","first_name":"Paulo R","orcid":"0000-0001-6730-4461","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","full_name":"Dos Santos Caldas, Paulo R"},{"full_name":"Lopez Pelegrin, Maria D","first_name":"Maria D","last_name":"Lopez Pelegrin","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pearce","first_name":"Daniel J. G.","full_name":"Pearce, Daniel J. G."},{"full_name":"Budanur, Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010","first_name":"Nazmi B","last_name":"Budanur"},{"first_name":"Jan","last_name":"Brugués","full_name":"Brugués, Jan"},{"full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","first_name":"Martin","last_name":"Loose"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8358"}]},"publication_status":"published","department":[{"_id":"MaLo"},{"_id":"BjHo"}],"publisher":"Springer Nature","year":"2019","month":"12","publication_identifier":{"issn":["2041-1723"]},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41467-019-13702-4","quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell","_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239"},{"_id":"260D98C8-B435-11E9-9278-68D0E5697425","name":"Reconstitution of Bacterial Cell Division Using Purified Components"}],"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":["000503009300001"]},"oa":1},{"author":[{"full_name":"Tkadlec, Josef","first_name":"Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684"},{"full_name":"Pavlogiannis, Andreas","first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Nowak, Martin A.","first_name":"Martin A.","last_name":"Nowak"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7196"}]},"date_created":"2019-12-23T13:36:50Z","date_updated":"2023-09-07T13:19:22Z","volume":2,"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer Nature","file_date_updated":"2020-07-14T12:47:53Z","ec_funded":1,"article_number":"138","doi":"10.1038/s42003-019-0373-y","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000465425700006"],"pmid":["31044163"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"month":"04","publication_identifier":{"issn":["2399-3642"]},"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"7211","checksum":"d1a69bfe73767e4246f0a38e4e1554dd","date_updated":"2020-07-14T12:47:53Z","date_created":"2019-12-23T13:39:30Z","access_level":"open_access","file_name":"2019_CommBio_Tkadlec.pdf","content_type":"application/pdf","file_size":1670274,"creator":"dernst"}],"_id":"7210","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["000"],"status":"public","title":"Population structure determines the tradeoff between fixation probability and fixation time","intvolume":" 2","abstract":[{"lang":"eng","text":"The rate of biological evolution depends on the fixation probability and on the fixation time of new mutants. Intensive research has focused on identifying population structures that augment the fixation probability of advantageous mutants. But these amplifiers of natural selection typically increase fixation time. Here we study population structures that achieve a tradeoff between fixation probability and time. First, we show that no amplifiers can have an asymptotically lower absorption time than the well-mixed population. Then we design population structures that substantially augment the fixation probability with just a minor increase in fixation time. Finally, we show that those structures enable higher effective rate of evolution than the well-mixed population provided that the rate of generating advantageous mutants is relatively low. Our work sheds light on how population structure affects the rate of evolution. Moreover, our structures could be useful for lab-based, medical, or industrial applications of evolutionary optimization."}],"type":"journal_article","date_published":"2019-04-23T00:00:00Z","publication":"Communications Biology","citation":{"short":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, Communications Biology 2 (2019).","mla":"Tkadlec, Josef, et al. “Population Structure Determines the Tradeoff between Fixation Probability and Fixation Time.” Communications Biology, vol. 2, 138, Springer Nature, 2019, doi:10.1038/s42003-019-0373-y.","chicago":"Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Population Structure Determines the Tradeoff between Fixation Probability and Fixation Time.” Communications Biology. Springer Nature, 2019. https://doi.org/10.1038/s42003-019-0373-y.","ama":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Population structure determines the tradeoff between fixation probability and fixation time. Communications Biology. 2019;2. doi:10.1038/s42003-019-0373-y","apa":"Tkadlec, J., Pavlogiannis, A., Chatterjee, K., & Nowak, M. A. (2019). Population structure determines the tradeoff between fixation probability and fixation time. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-019-0373-y","ieee":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Population structure determines the tradeoff between fixation probability and fixation time,” Communications Biology, vol. 2. Springer Nature, 2019.","ista":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2019. Population structure determines the tradeoff between fixation probability and fixation time. Communications Biology. 2, 138."},"article_type":"original","day":"23","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"keyword":["safety","risk","reliability and quality","software"],"has_accepted_license":"1","article_processing_charge":"No","day":"10","citation":{"ama":"Chatterjee K, Pavlogiannis A, Toman V. Value-centric dynamic partial order reduction. In: Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications. Vol 3. ACM; 2019. doi:10.1145/3360550","apa":"Chatterjee, K., Pavlogiannis, A., & Toman, V. (2019). Value-centric dynamic partial order reduction. In Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications (Vol. 3). Athens, Greece: ACM. https://doi.org/10.1145/3360550","ieee":"K. Chatterjee, A. Pavlogiannis, and V. Toman, “Value-centric dynamic partial order reduction,” in Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications, Athens, Greece, 2019, vol. 3.","ista":"Chatterjee K, Pavlogiannis A, Toman V. 2019. Value-centric dynamic partial order reduction. 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, 124.","short":"K. Chatterjee, A. Pavlogiannis, V. Toman, in:, Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications, ACM, 2019.","mla":"Chatterjee, Krishnendu, et al. “Value-Centric Dynamic Partial Order Reduction.” Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications, vol. 3, 124, ACM, 2019, doi:10.1145/3360550.","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, and Viktor Toman. “Value-Centric Dynamic Partial Order Reduction.” In Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications, Vol. 3. ACM, 2019. https://doi.org/10.1145/3360550."},"publication":"Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications","date_published":"2019-10-10T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"The verification of concurrent programs remains an open challenge, as thread interaction has to be accounted for, which leads to state-space explosion. Stateless model checking battles this problem by exploring traces rather than states of the program. As there are exponentially many traces, dynamic partial-order reduction (DPOR) techniques are used to partition the trace space into equivalence classes, and explore a few representatives from each class. The standard equivalence that underlies most DPOR techniques is the happens-before equivalence, however recent works have spawned a vivid interest towards coarser equivalences. The efficiency of such approaches is a product of two parameters: (i) the size of the partitioning induced by the equivalence, and (ii) the time spent by the exploration algorithm in each class of the partitioning. In this work, we present a new equivalence, called value-happens-before and show that it has two appealing features. First, value-happens-before is always at least as coarse as the happens-before equivalence, and can be even exponentially coarser. Second, the value-happens-before partitioning is efficiently explorable when the number of threads is bounded. We present an algorithm called value-centric DPOR (VCDPOR), which explores the underlying partitioning using polynomial time per class. Finally, we perform an experimental evaluation of VCDPOR on various benchmarks, and compare it against other state-of-the-art approaches. Our results show that value-happens-before typically induces a significant reduction in the size of the underlying partitioning, which leads to a considerable reduction in the running time for exploring the whole partitioning."}],"intvolume":" 3","status":"public","ddc":["000"],"title":"Value-centric dynamic partial order reduction","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10190","oa_version":"Published Version","file":[{"checksum":"2149979c46964c4d117af06ccb6c0834","success":1,"date_created":"2021-11-12T11:41:56Z","date_updated":"2021-11-12T11:41:56Z","relation":"main_file","file_id":"10278","file_size":570829,"content_type":"application/pdf","creator":"cchlebak","access_level":"open_access","file_name":"2019_ACM_Chatterjee.pdf"}],"publication_identifier":{"eissn":["2475-1421"]},"month":"10","project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1909.00989"]},"main_file_link":[{"url":"https://dl.acm.org/doi/10.1145/3360550","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1145/3360550","conference":{"name":"OOPSLA: Object-oriented Programming, Systems, Languages and Applications","end_date":"2019-10-25","location":"Athens, Greece","start_date":"2019-10-23"},"article_number":"124","file_date_updated":"2021-11-12T11:41:56Z","publisher":"ACM","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"publication_status":"published","acknowledgement":"The authors would also like to thank anonymous referees for their valuable comments and helpful suggestions. This work is supported by the Austrian Science Fund (FWF) NFN grants S11407-N23 (RiSE/SHiNE) and S11402-N23 (RiSE/SHiNE), by the Vienna Science and Technology Fund (WWTF) Project ICT15-003, and by the Austrian Science Fund (FWF) Schrodinger grant J-4220.\r\n","year":"2019","volume":3,"date_updated":"2023-09-07T13:30:27Z","date_created":"2021-10-27T14:57:06Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10199"}]},"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis"},{"first_name":"Viktor","last_name":"Toman","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9036-063X","full_name":"Toman, Viktor"}]},{"publication_identifier":{"isbn":["9781450361842"]},"month":"06","language":[{"iso":"eng"}],"doi":"10.1145/3323165.3323201","conference":{"name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","start_date":"2019-06-22","location":"Phoenix, AZ, United States","end_date":"2019-06-24"},"project":[{"grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/2003.09363","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2003.09363"],"isi":["000507618500018"]},"ec_funded":1,"date_updated":"2023-09-07T13:31:39Z","date_created":"2019-07-24T08:59:36Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10429"}]},"author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"},{"first_name":"Giorgi","last_name":"Nadiradze","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5634-0731","full_name":"Nadiradze, Giorgi"},{"first_name":"Nikita","last_name":"Koval","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","full_name":"Koval, Nikita"}],"publisher":"ACM Press","department":[{"_id":"DaAl"}],"publication_status":"published","year":"2019","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-06-01T00:00:00Z","page":"145-154","citation":{"chicago":"Alistarh, Dan-Adrian, Giorgi Nadiradze, and Nikita Koval. “Efficiency Guarantees for Parallel Incremental Algorithms under Relaxed Schedulers.” In 31st ACM Symposium on Parallelism in Algorithms and Architectures, 145–54. ACM Press, 2019. https://doi.org/10.1145/3323165.3323201.","short":"D.-A. Alistarh, G. Nadiradze, N. Koval, in:, 31st ACM Symposium on Parallelism in Algorithms and Architectures, ACM Press, 2019, pp. 145–154.","mla":"Alistarh, Dan-Adrian, et al. “Efficiency Guarantees for Parallel Incremental Algorithms under Relaxed Schedulers.” 31st ACM Symposium on Parallelism in Algorithms and Architectures, ACM Press, 2019, pp. 145–54, doi:10.1145/3323165.3323201.","apa":"Alistarh, D.-A., Nadiradze, G., & Koval, N. (2019). Efficiency guarantees for parallel incremental algorithms under relaxed schedulers. In 31st ACM Symposium on Parallelism in Algorithms and Architectures (pp. 145–154). Phoenix, AZ, United States: ACM Press. https://doi.org/10.1145/3323165.3323201","ieee":"D.-A. Alistarh, G. Nadiradze, and N. Koval, “Efficiency guarantees for parallel incremental algorithms under relaxed schedulers,” in 31st ACM Symposium on Parallelism in Algorithms and Architectures, Phoenix, AZ, United States, 2019, pp. 145–154.","ista":"Alistarh D-A, Nadiradze G, Koval N. 2019. Efficiency guarantees for parallel incremental algorithms under relaxed schedulers. 31st ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 145–154.","ama":"Alistarh D-A, Nadiradze G, Koval N. Efficiency guarantees for parallel incremental algorithms under relaxed schedulers. In: 31st ACM Symposium on Parallelism in Algorithms and Architectures. ACM Press; 2019:145-154. doi:10.1145/3323165.3323201"},"publication":"31st ACM Symposium on Parallelism in Algorithms and Architectures","abstract":[{"lang":"eng","text":"Several classic problems in graph processing and computational geometry are solved via incremental algorithms, which split computation into a series of small tasks acting on shared state, which gets updated progressively. While the sequential variant of such algorithms usually specifies a fixed (but sometimes random) order in which the tasks should be performed, a standard approach to parallelizing such algorithms is to relax this constraint to allow for out-of-order parallel execution. This is the case for parallel implementations of Dijkstra's single-source shortest-paths (SSSP) algorithm, and for parallel Delaunay mesh triangulation. While many software frameworks parallelize incremental computation in this way, it is still not well understood whether this relaxed ordering approach can still provide any complexity guarantees. In this paper, we address this problem, and analyze the efficiency guarantees provided by a range of incremental algorithms when parallelized via relaxed schedulers. We show that, for algorithms such as Delaunay mesh triangulation and sorting by insertion, schedulers with a maximum relaxation factor of k in terms of the maximum priority inversion allowed will introduce a maximum amount of wasted work of O(łog n poly(k)), where n is the number of tasks to be executed. For SSSP, we show that the additional work is O(poly(k), dmax / wmin), where dmax is the maximum distance between two nodes, and wmin is the minimum such distance. In practical settings where n >> k, this suggests that the overheads of relaxation will be outweighed by the improved scalability of the relaxed scheduler. On the negative side, we provide lower bounds showing that certain algorithms will inherently incur a non-trivial amount of wasted work due to scheduler relaxation, even for relatively benign relaxed schedulers."}],"type":"conference","oa_version":"Preprint","title":"Efficiency guarantees for parallel incremental algorithms under relaxed schedulers","status":"public","_id":"6673","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2019_JGP_Erdem.pdf","content_type":"application/pdf","file_size":2641297,"creator":"dernst","relation":"main_file","file_id":"7450","checksum":"5706b4ccd74ee3e50bf7ecb2a203df71","date_created":"2020-02-05T07:20:32Z","date_updated":"2020-07-14T12:47:57Z"}],"title":"A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2","ddc":["570"],"status":"public","intvolume":" 151","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7398","abstract":[{"lang":"eng","text":"Transporters of the solute carrier 6 (SLC6) family translocate their cognate substrate together with Na+ and Cl−. Detailed kinetic models exist for the transporters of GABA (GAT1/SLC6A1) and the monoamines dopamine (DAT/SLC6A3) and serotonin (SERT/SLC6A4). Here, we posited that the transport cycle of individual SLC6 transporters reflects the physiological requirements they operate under. We tested this hypothesis by analyzing the transport cycle of glycine transporter 1 (GlyT1/SLC6A9) and glycine transporter 2 (GlyT2/SLC6A5). GlyT2 is the only SLC6 family member known to translocate glycine, Na+, and Cl− in a 1:3:1 stoichiometry. We analyzed partial reactions in real time by electrophysiological recordings. Contrary to monoamine transporters, both GlyTs were found to have a high transport capacity driven by rapid return of the empty transporter after release of Cl− on the intracellular side. Rapid cycling of both GlyTs was further supported by highly cooperative binding of cosubstrate ions and substrate such that their forward transport mode was maintained even under conditions of elevated intracellular Na+ or Cl−. The most important differences in the transport cycle of GlyT1 and GlyT2 arose from the kinetics of charge movement and the resulting voltage-dependent rate-limiting reactions: the kinetics of GlyT1 were governed by transition of the substrate-bound transporter from outward- to inward-facing conformations, whereas the kinetics of GlyT2 were governed by Na+ binding (or a related conformational change). Kinetic modeling showed that the kinetics of GlyT1 are ideally suited for supplying the extracellular glycine levels required for NMDA receptor activation."}],"issue":"8","type":"journal_article","date_published":"2019-07-03T00:00:00Z","article_type":"original","page":"1035-1050","publication":"The Journal of General Physiology","citation":{"ama":"Erdem FA, Ilic M, Koppensteiner P, et al. A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2. The Journal of General Physiology. 2019;151(8):1035-1050. doi:10.1085/jgp.201912318","ieee":"F. A. Erdem et al., “A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2,” The Journal of General Physiology, vol. 151, no. 8. Rockefeller University Press, pp. 1035–1050, 2019.","apa":"Erdem, F. A., Ilic, M., Koppensteiner, P., Gołacki, J., Lubec, G., Freissmuth, M., & Sandtner, W. (2019). A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2. The Journal of General Physiology. Rockefeller University Press. https://doi.org/10.1085/jgp.201912318","ista":"Erdem FA, Ilic M, Koppensteiner P, Gołacki J, Lubec G, Freissmuth M, Sandtner W. 2019. A comparison of the transport kinetics of glycine transporter 1 and glycine transporter 2. The Journal of General Physiology. 151(8), 1035–1050.","short":"F.A. Erdem, M. Ilic, P. Koppensteiner, J. Gołacki, G. Lubec, M. Freissmuth, W. Sandtner, The Journal of General Physiology 151 (2019) 1035–1050.","mla":"Erdem, Fatma Asli, et al. “A Comparison of the Transport Kinetics of Glycine Transporter 1 and Glycine Transporter 2.” The Journal of General Physiology, vol. 151, no. 8, Rockefeller University Press, 2019, pp. 1035–50, doi:10.1085/jgp.201912318.","chicago":"Erdem, Fatma Asli, Marija Ilic, Peter Koppensteiner, Jakub Gołacki, Gert Lubec, Michael Freissmuth, and Walter Sandtner. “A Comparison of the Transport Kinetics of Glycine Transporter 1 and Glycine Transporter 2.” The Journal of General Physiology. Rockefeller University Press, 2019. https://doi.org/10.1085/jgp.201912318."},"day":"03","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_created":"2020-01-29T16:06:29Z","date_updated":"2023-09-07T14:52:23Z","volume":151,"author":[{"first_name":"Fatma Asli","last_name":"Erdem","full_name":"Erdem, Fatma Asli"},{"full_name":"Ilic, Marija","last_name":"Ilic","first_name":"Marija"},{"full_name":"Koppensteiner, Peter","orcid":"0000-0002-3509-1948","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner","first_name":"Peter"},{"first_name":"Jakub","last_name":"Gołacki","full_name":"Gołacki, Jakub"},{"last_name":"Lubec","first_name":"Gert","full_name":"Lubec, Gert"},{"first_name":"Michael","last_name":"Freissmuth","full_name":"Freissmuth, Michael"},{"full_name":"Sandtner, Walter","first_name":"Walter","last_name":"Sandtner"}],"publication_status":"published","publisher":"Rockefeller University Press","department":[{"_id":"RySh"}],"year":"2019","pmid":1,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file_date_updated":"2020-07-14T12:47:57Z","language":[{"iso":"eng"}],"doi":"10.1085/jgp.201912318","quality_controlled":"1","isi":1,"external_id":{"pmid":["31270129"],"isi":["000478792500008"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"month":"07","publication_identifier":{"eissn":["1540-7748"],"issn":["0022-1295"]}},{"date_published":"2019-09-19T00:00:00Z","article_type":"original","page":"1131-1146.e6","publication":"Molecular Cell","citation":{"mla":"Letts, James A., et al. “Structures of Respiratory Supercomplex I+III2 Reveal Functional and Conformational Crosstalk.” Molecular Cell, vol. 75, no. 6, Cell Press, 2019, p. 1131–1146.e6, doi:10.1016/j.molcel.2019.07.022.","short":"J.A. Letts, K. Fiedorczuk, G. Degliesposti, M. Skehel, L.A. Sazanov, Molecular Cell 75 (2019) 1131–1146.e6.","chicago":"Letts, James A, Karol Fiedorczuk, Gianluca Degliesposti, Mark Skehel, and Leonid A Sazanov. “Structures of Respiratory Supercomplex I+III2 Reveal Functional and Conformational Crosstalk.” Molecular Cell. Cell Press, 2019. https://doi.org/10.1016/j.molcel.2019.07.022.","ama":"Letts JA, Fiedorczuk K, Degliesposti G, Skehel M, Sazanov LA. Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk. Molecular Cell. 2019;75(6):1131-1146.e6. doi:10.1016/j.molcel.2019.07.022","ista":"Letts JA, Fiedorczuk K, Degliesposti G, Skehel M, Sazanov LA. 2019. Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk. Molecular Cell. 75(6), 1131–1146.e6.","ieee":"J. A. Letts, K. Fiedorczuk, G. Degliesposti, M. Skehel, and L. A. Sazanov, “Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk,” Molecular Cell, vol. 75, no. 6. Cell Press, p. 1131–1146.e6, 2019.","apa":"Letts, J. A., Fiedorczuk, K., Degliesposti, G., Skehel, M., & Sazanov, L. A. (2019). Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk. Molecular Cell. Cell Press. https://doi.org/10.1016/j.molcel.2019.07.022"},"day":"19","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:57Z","date_created":"2020-02-04T10:37:28Z","checksum":"5202f53a237d6650ece038fbf13bdcea","file_id":"7447","relation":"main_file","creator":"dernst","file_size":9654895,"content_type":"application/pdf","file_name":"2019_MolecularCell_Letts.pdf","access_level":"open_access"}],"ddc":["570"],"status":"public","title":"Structures of respiratory supercomplex I+III2 reveal functional and conformational crosstalk","intvolume":" 75","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7395","abstract":[{"text":"The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We demonstrate that CoQ trapping in the isolated SC I+III2 limits complex (C)I turnover, arguing against channeling. The SC structure, resolved at up to 3.8 Å in four distinct states, suggests that CoQ oxidation may be rate limiting because of unequal access of CoQ to the active sites of CIII2. CI shows a transition between “closed” and “open” conformations, accompanied by the striking rotation of a key transmembrane helix. Furthermore, the state of CI affects the conformational flexibility within CIII2, demonstrating crosstalk between the enzymes. CoQ was identified at only three of the four binding sites in CIII2, suggesting that interaction with CI disrupts CIII2 symmetry in a functionally relevant manner. Together, these observations indicate a more nuanced functional role for the SCs.","lang":"eng"}],"issue":"6","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1016/j.molcel.2019.07.022","quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes","_id":"2590DB08-B435-11E9-9278-68D0E5697425","grant_number":"701309"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31492636"],"isi":["000486614200006"]},"oa":1,"month":"09","publication_identifier":{"issn":["1097-2765"]},"date_updated":"2023-09-07T14:53:06Z","date_created":"2020-01-29T16:02:33Z","volume":75,"author":[{"last_name":"Letts","first_name":"James A","orcid":"0000-0002-9864-3586","id":"322DA418-F248-11E8-B48F-1D18A9856A87","full_name":"Letts, James A"},{"first_name":"Karol","last_name":"Fiedorczuk","id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0","full_name":"Fiedorczuk, Karol"},{"full_name":"Degliesposti, Gianluca","last_name":"Degliesposti","first_name":"Gianluca"},{"first_name":"Mark","last_name":"Skehel","full_name":"Skehel, Mark"},{"last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A"}],"publication_status":"published","publisher":"Cell Press","department":[{"_id":"LeSa"}],"year":"2019","pmid":1,"file_date_updated":"2020-07-14T12:47:57Z","ec_funded":1},{"type":"journal_article","abstract":[{"lang":"eng","text":"Biophysical modeling of neuronal networks helps to integrate and interpret rapidly growing and disparate experimental datasets at multiple scales. The NetPyNE tool (www.netpyne.org) provides both programmatic and graphical interfaces to develop data-driven multiscale network models in NEURON. NetPyNE clearly separates model parameters from implementation code. Users provide specifications at a high level via a standardized declarative language, for example connectivity rules, to create millions of cell-to-cell connections. NetPyNE then enables users to generate the NEURON network, run efficiently parallelized simulations, optimize and explore network parameters through automated batch runs, and use built-in functions for visualization and analysis – connectivity matrices, voltage traces, spike raster plots, local field potentials, and information theoretic measures. NetPyNE also facilitates model sharing by exporting and importing standardized formats (NeuroML and SONATA). NetPyNE is already being used to teach computational neuroscience students and by modelers to investigate brain regions and phenomena."}],"intvolume":" 8","status":"public","ddc":["570"],"title":"NetPyNE, a tool for data-driven multiscale modeling of brain circuits","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7405","file":[{"file_name":"2019_eLife_DuraBernal.pdf","access_level":"open_access","content_type":"application/pdf","file_size":6182359,"creator":"dernst","relation":"main_file","file_id":"7444","date_created":"2020-02-04T08:41:47Z","date_updated":"2020-07-14T12:47:57Z","checksum":"7014189c11c10a12feeeae37f054871d"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"31","article_type":"original","citation":{"ama":"Dura-Bernal S, Suter B, Gleeson P, et al. NetPyNE, a tool for data-driven multiscale modeling of brain circuits. eLife. 2019;8. doi:10.7554/elife.44494","apa":"Dura-Bernal, S., Suter, B., Gleeson, P., Cantarelli, M., Quintana, A., Rodriguez, F., … Lytton, W. W. (2019). NetPyNE, a tool for data-driven multiscale modeling of brain circuits. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.44494","ieee":"S. Dura-Bernal et al., “NetPyNE, a tool for data-driven multiscale modeling of brain circuits,” eLife, vol. 8. eLife Sciences Publications, 2019.","ista":"Dura-Bernal S, Suter B, Gleeson P, Cantarelli M, Quintana A, Rodriguez F, Kedziora DJ, Chadderdon GL, Kerr CC, Neymotin SA, McDougal RA, Hines M, Shepherd GM, Lytton WW. 2019. NetPyNE, a tool for data-driven multiscale modeling of brain circuits. eLife. 8, e44494.","short":"S. Dura-Bernal, B. Suter, P. Gleeson, M. Cantarelli, A. Quintana, F. Rodriguez, D.J. Kedziora, G.L. Chadderdon, C.C. Kerr, S.A. Neymotin, R.A. McDougal, M. Hines, G.M. Shepherd, W.W. Lytton, ELife 8 (2019).","mla":"Dura-Bernal, Salvador, et al. “NetPyNE, a Tool for Data-Driven Multiscale Modeling of Brain Circuits.” ELife, vol. 8, e44494, eLife Sciences Publications, 2019, doi:10.7554/elife.44494.","chicago":"Dura-Bernal, Salvador, Benjamin Suter, Padraig Gleeson, Matteo Cantarelli, Adrian Quintana, Facundo Rodriguez, David J Kedziora, et al. “NetPyNE, a Tool for Data-Driven Multiscale Modeling of Brain Circuits.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/elife.44494."},"publication":"eLife","date_published":"2019-05-31T00:00:00Z","article_number":"e44494","file_date_updated":"2020-07-14T12:47:57Z","department":[{"_id":"PeJo"}],"publisher":"eLife Sciences Publications","publication_status":"published","pmid":1,"year":"2019","volume":8,"date_updated":"2023-09-07T14:27:52Z","date_created":"2020-01-30T09:08:01Z","author":[{"full_name":"Dura-Bernal, Salvador","first_name":"Salvador","last_name":"Dura-Bernal"},{"orcid":"0000-0002-9885-6936","id":"4952F31E-F248-11E8-B48F-1D18A9856A87","last_name":"Suter","first_name":"Benjamin","full_name":"Suter, Benjamin"},{"last_name":"Gleeson","first_name":"Padraig","full_name":"Gleeson, Padraig"},{"last_name":"Cantarelli","first_name":"Matteo","full_name":"Cantarelli, Matteo"},{"full_name":"Quintana, Adrian","first_name":"Adrian","last_name":"Quintana"},{"first_name":"Facundo","last_name":"Rodriguez","full_name":"Rodriguez, Facundo"},{"last_name":"Kedziora","first_name":"David J","full_name":"Kedziora, David J"},{"last_name":"Chadderdon","first_name":"George L","full_name":"Chadderdon, George L"},{"full_name":"Kerr, Cliff C","last_name":"Kerr","first_name":"Cliff C"},{"first_name":"Samuel A","last_name":"Neymotin","full_name":"Neymotin, Samuel A"},{"full_name":"McDougal, Robert A","first_name":"Robert A","last_name":"McDougal"},{"full_name":"Hines, Michael","last_name":"Hines","first_name":"Michael"},{"last_name":"Shepherd","first_name":"Gordon MG","full_name":"Shepherd, Gordon MG"},{"full_name":"Lytton, William W","last_name":"Lytton","first_name":"William W"}],"publication_identifier":{"issn":["2050-084X"]},"month":"05","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000468968400001"],"pmid":["31025934"]},"language":[{"iso":"eng"}],"doi":"10.7554/elife.44494"},{"language":[{"iso":"eng"}],"doi":"10.1534/genetics.119.302045","quality_controlled":"1","isi":1,"project":[{"grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"}],"main_file_link":[{"url":"https://doi.org/10.1534/genetics.119.302045","open_access":"1"}],"external_id":{"pmid":["31113811"],"isi":["000474809300015"]},"oa":1,"month":"07","publication_identifier":{"issn":["0016-6731"],"eissn":["1943-2631"]},"date_created":"2020-01-29T16:15:44Z","date_updated":"2023-09-07T14:49:29Z","volume":212,"author":[{"last_name":"Veltsos","first_name":"Paris","full_name":"Veltsos, Paris"},{"full_name":"Ridout, Kate E.","last_name":"Ridout","first_name":"Kate E."},{"full_name":"Toups, Melissa A","first_name":"Melissa A","last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380"},{"full_name":"González-Martínez, Santiago C.","first_name":"Santiago C.","last_name":"González-Martínez"},{"full_name":"Muyle, Aline","first_name":"Aline","last_name":"Muyle"},{"first_name":"Olivier","last_name":"Emery","full_name":"Emery, Olivier"},{"last_name":"Rastas","first_name":"Pasi","full_name":"Rastas, Pasi"},{"full_name":"Hudzieczek, Vojtech","first_name":"Vojtech","last_name":"Hudzieczek"},{"full_name":"Hobza, Roman","last_name":"Hobza","first_name":"Roman"},{"last_name":"Vyskot","first_name":"Boris","full_name":"Vyskot, Boris"},{"last_name":"Marais","first_name":"Gabriel A. B.","full_name":"Marais, Gabriel A. B."},{"first_name":"Dmitry A.","last_name":"Filatov","full_name":"Filatov, Dmitry A."},{"first_name":"John R.","last_name":"Pannell","full_name":"Pannell, John R."}],"publication_status":"published","department":[{"_id":"BeVi"}],"publisher":"Genetics Society of America","year":"2019","pmid":1,"ec_funded":1,"date_published":"2019-07-01T00:00:00Z","article_type":"original","page":"815-835","publication":"Genetics","citation":{"ama":"Veltsos P, Ridout KE, Toups MA, et al. Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua. Genetics. 2019;212(3):815-835. doi:10.1534/genetics.119.302045","ista":"Veltsos P, Ridout KE, Toups MA, González-Martínez SC, Muyle A, Emery O, Rastas P, Hudzieczek V, Hobza R, Vyskot B, Marais GAB, Filatov DA, Pannell JR. 2019. Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua. Genetics. 212(3), 815–835.","ieee":"P. Veltsos et al., “Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua,” Genetics, vol. 212, no. 3. Genetics Society of America, pp. 815–835, 2019.","apa":"Veltsos, P., Ridout, K. E., Toups, M. A., González-Martínez, S. C., Muyle, A., Emery, O., … Pannell, J. R. (2019). Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.119.302045","mla":"Veltsos, Paris, et al. “Early Sex-Chromosome Evolution in the Diploid Dioecious Plant Mercurialis Annua.” Genetics, vol. 212, no. 3, Genetics Society of America, 2019, pp. 815–35, doi:10.1534/genetics.119.302045.","short":"P. Veltsos, K.E. Ridout, M.A. Toups, S.C. González-Martínez, A. Muyle, O. Emery, P. Rastas, V. Hudzieczek, R. Hobza, B. Vyskot, G.A.B. Marais, D.A. Filatov, J.R. Pannell, Genetics 212 (2019) 815–835.","chicago":"Veltsos, Paris, Kate E. Ridout, Melissa A Toups, Santiago C. González-Martínez, Aline Muyle, Olivier Emery, Pasi Rastas, et al. “Early Sex-Chromosome Evolution in the Diploid Dioecious Plant Mercurialis Annua.” Genetics. Genetics Society of America, 2019. https://doi.org/10.1534/genetics.119.302045."},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","status":"public","title":"Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua","intvolume":" 212","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7400","abstract":[{"text":"Suppressed recombination allows divergence between homologous sex chromosomes and the functionality of their genes. Here, we reveal patterns of the earliest stages of sex-chromosome evolution in the diploid dioecious herb Mercurialis annua on the basis of cytological analysis, de novo genome assembly and annotation, genetic mapping, exome resequencing of natural populations, and transcriptome analysis. The genome assembly contained 34,105 expressed genes, of which 10,076 were assigned to linkage groups. Genetic mapping and exome resequencing of individuals across the species range both identified the largest linkage group, LG1, as the sex chromosome. Although the sex chromosomes of M. annua are karyotypically homomorphic, we estimate that about one-third of the Y chromosome, containing 568 transcripts and spanning 22.3 cM in the corresponding female map, has ceased recombining. Nevertheless, we found limited evidence for Y-chromosome degeneration in terms of gene loss and pseudogenization, and most X- and Y-linked genes appear to have diverged in the period subsequent to speciation between M. annua and its sister species M. huetii, which shares the same sex-determining region. Taken together, our results suggest that the M. annua Y chromosome has at least two evolutionary strata: a small old stratum shared with M. huetii, and a more recent larger stratum that is probably unique to M. annua and that stopped recombining ∼1 MYA. Patterns of gene expression within the nonrecombining region are consistent with the idea that sexually antagonistic selection may have played a role in favoring suppressed recombination.","lang":"eng"}],"issue":"3","type":"journal_article"},{"language":[{"iso":"eng"}],"doi":"10.1242/dev.171397","quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://doi.org/10.1242/dev.171397","open_access":"1"}],"oa":1,"external_id":{"pmid":["30910826"],"isi":["000464583200006"]},"month":"04","publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"date_created":"2020-01-29T16:27:10Z","date_updated":"2023-09-07T14:47:00Z","volume":146,"author":[{"full_name":"Stürner, Tomke","first_name":"Tomke","last_name":"Stürner"},{"full_name":"Tatarnikova, Anastasia","first_name":"Anastasia","last_name":"Tatarnikova"},{"full_name":"Müller, Jan","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","first_name":"Jan","last_name":"Müller"},{"first_name":"Barbara","last_name":"Schaffran","full_name":"Schaffran, Barbara"},{"full_name":"Cuntz, Hermann","first_name":"Hermann","last_name":"Cuntz"},{"last_name":"Zhang","first_name":"Yun","full_name":"Zhang, Yun"},{"full_name":"Nemethova, Maria","first_name":"Maria","last_name":"Nemethova","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bogdan","first_name":"Sven","full_name":"Bogdan, Sven"},{"full_name":"Small, Vic","first_name":"Vic","last_name":"Small"},{"first_name":"Gaia","last_name":"Tavosanis","full_name":"Tavosanis, Gaia"}],"publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"The Company of Biologists","year":"2019","pmid":1,"article_number":"dev171397","date_published":"2019-04-04T00:00:00Z","article_type":"original","publication":"Development","citation":{"ama":"Stürner T, Tatarnikova A, Müller J, et al. Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo. Development. 2019;146(7). doi:10.1242/dev.171397","ista":"Stürner T, Tatarnikova A, Müller J, Schaffran B, Cuntz H, Zhang Y, Nemethova M, Bogdan S, Small V, Tavosanis G. 2019. Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo. Development. 146(7), dev171397.","apa":"Stürner, T., Tatarnikova, A., Müller, J., Schaffran, B., Cuntz, H., Zhang, Y., … Tavosanis, G. (2019). Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo. Development. The Company of Biologists. https://doi.org/10.1242/dev.171397","ieee":"T. Stürner et al., “Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo,” Development, vol. 146, no. 7. The Company of Biologists, 2019.","mla":"Stürner, Tomke, et al. “Transient Localization of the Arp2/3 Complex Initiates Neuronal Dendrite Branching in Vivo.” Development, vol. 146, no. 7, dev171397, The Company of Biologists, 2019, doi:10.1242/dev.171397.","short":"T. Stürner, A. Tatarnikova, J. Müller, B. Schaffran, H. Cuntz, Y. Zhang, M. Nemethova, S. Bogdan, V. Small, G. Tavosanis, Development 146 (2019).","chicago":"Stürner, Tomke, Anastasia Tatarnikova, Jan Müller, Barbara Schaffran, Hermann Cuntz, Yun Zhang, Maria Nemethova, Sven Bogdan, Vic Small, and Gaia Tavosanis. “Transient Localization of the Arp2/3 Complex Initiates Neuronal Dendrite Branching in Vivo.” Development. The Company of Biologists, 2019. https://doi.org/10.1242/dev.171397."},"day":"04","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","status":"public","title":"Transient localization of the Arp2/3 complex initiates neuronal dendrite branching in vivo","intvolume":" 146","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7404","abstract":[{"text":"The formation of neuronal dendrite branches is fundamental for the wiring and function of the nervous system. Indeed, dendrite branching enhances the coverage of the neuron's receptive field and modulates the initial processing of incoming stimuli. Complex dendrite patterns are achieved in vivo through a dynamic process of de novo branch formation, branch extension and retraction. The first step towards branch formation is the generation of a dynamic filopodium-like branchlet. The mechanisms underlying the initiation of dendrite branchlets are therefore crucial to the shaping of dendrites. Through in vivo time-lapse imaging of the subcellular localization of actin during the process of branching of Drosophila larva sensory neurons, combined with genetic analysis and electron tomography, we have identified the Actin-related protein (Arp) 2/3 complex as the major actin nucleator involved in the initiation of dendrite branchlet formation, under the control of the activator WAVE and of the small GTPase Rac1. Transient recruitment of an Arp2/3 component marks the site of branchlet initiation in vivo. These data position the activation of Arp2/3 as an early hub for the initiation of branchlet formation.","lang":"eng"}],"issue":"7","type":"journal_article"},{"month":"06","publication_identifier":{"isbn":["9781728136080"]},"conference":{"name":"LICS: Symposium on Logic in Computer Science","start_date":"2019-06-24","location":"Vancouver, BC, Canada","end_date":"2019-06-27"},"doi":"10.1109/lics.2019.8785706","language":[{"iso":"eng"}],"external_id":{"arxiv":["1802.03642"],"isi":["000805002800001"]},"main_file_link":[{"url":"https://arxiv.org/abs/1802.03642","open_access":"1"}],"oa":1,"isi":1,"quality_controlled":"1","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Laurent","last_name":"Doyen","full_name":"Doyen, Laurent"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"11402"}]},"date_created":"2020-01-29T16:18:33Z","date_updated":"2023-09-07T14:48:11Z","year":"2019","publication_status":"published","publisher":"IEEE","department":[{"_id":"KrCh"}],"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2019-06-01T00:00:00Z","publication":"34th Annual ACM/IEEE Symposium on Logic in Computer Science","citation":{"ista":"Chatterjee K, Doyen L. 2019. Graph planning with expected finite horizon. 34th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science, 1–13.","apa":"Chatterjee, K., & Doyen, L. (2019). Graph planning with expected finite horizon. In 34th Annual ACM/IEEE Symposium on Logic in Computer Science (pp. 1–13). Vancouver, BC, Canada: IEEE. https://doi.org/10.1109/lics.2019.8785706","ieee":"K. Chatterjee and L. Doyen, “Graph planning with expected finite horizon,” in 34th Annual ACM/IEEE Symposium on Logic in Computer Science, Vancouver, BC, Canada, 2019, pp. 1–13.","ama":"Chatterjee K, Doyen L. Graph planning with expected finite horizon. In: 34th Annual ACM/IEEE Symposium on Logic in Computer Science. IEEE; 2019:1-13. doi:10.1109/lics.2019.8785706","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected Finite Horizon.” In 34th Annual ACM/IEEE Symposium on Logic in Computer Science, 1–13. IEEE, 2019. https://doi.org/10.1109/lics.2019.8785706.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. “Graph Planning with Expected Finite Horizon.” 34th Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2019, pp. 1–13, doi:10.1109/lics.2019.8785706.","short":"K. Chatterjee, L. Doyen, in:, 34th Annual ACM/IEEE Symposium on Logic in Computer Science, IEEE, 2019, pp. 1–13."},"page":"1-13","abstract":[{"lang":"eng","text":"Graph planning gives rise to fundamental algorithmic questions such as shortest path, traveling salesman problem, etc. A classical problem in discrete planning is to consider a weighted graph and construct a path that maximizes the sum of weights for a given time horizon T. However, in many scenarios, the time horizon is not fixed, but the stopping time is chosen according to some distribution such that the expected stopping time is T. If the stopping time distribution is not known, then to ensure robustness, the distribution is chosen by an adversary, to represent the worst-case scenario. A stationary plan for every vertex always chooses the same outgoing edge. For fixed horizon or fixed stopping-time distribution, stationary plans are not sufficient for optimality. Quite surprisingly we show that when an adversary chooses the stopping-time distribution with expected stopping time T, then stationary plans are sufficient. While computing optimal stationary plans for fixed horizon is NP-complete, we show that computing optimal stationary plans under adversarial stopping-time distribution can be achieved in polynomial time. Consequently, our polynomial-time algorithm for adversarial stopping time also computes an optimal plan among all possible plans."}],"type":"conference","oa_version":"Preprint","_id":"7402","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Graph planning with expected finite horizon","status":"public"},{"article_type":"original","publication":"Quantum","citation":{"ama":"Vukics A, Dombi A, Fink JM, Domokos P. Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition. Quantum. 2019;3. doi:10.22331/q-2019-06-03-150","ieee":"A. Vukics, A. Dombi, J. M. Fink, and P. Domokos, “Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition,” Quantum, vol. 3. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2019.","apa":"Vukics, A., Dombi, A., Fink, J. M., & Domokos, P. (2019). Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition. Quantum. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften. https://doi.org/10.22331/q-2019-06-03-150","ista":"Vukics A, Dombi A, Fink JM, Domokos P. 2019. Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition. Quantum. 3, 150.","short":"A. Vukics, A. Dombi, J.M. Fink, P. Domokos, Quantum 3 (2019).","mla":"Vukics, A., et al. “Finite-Size Scaling of the Photon-Blockade Breakdown Dissipative Quantum Phase Transition.” Quantum, vol. 3, 150, Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2019, doi:10.22331/q-2019-06-03-150.","chicago":"Vukics, A., A. Dombi, Johannes M Fink, and P. Domokos. “Finite-Size Scaling of the Photon-Blockade Breakdown Dissipative Quantum Phase Transition.” Quantum. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2019. https://doi.org/10.22331/q-2019-06-03-150."},"date_published":"2019-06-03T00:00:00Z","day":"03","has_accepted_license":"1","article_processing_charge":"No","status":"public","ddc":["530"],"title":"Finite-size scaling of the photon-blockade breakdown dissipative quantum phase transition","intvolume":" 3","_id":"7451","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"checksum":"26b9ba8f0155d183f1ee55295934a17f","date_created":"2020-02-11T09:25:23Z","date_updated":"2020-07-14T12:47:58Z","file_id":"7483","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":5805248,"access_level":"open_access","file_name":"2019_Quantum_Vukics.pdf"}],"type":"journal_article","abstract":[{"text":"We prove that the observable telegraph signal accompanying the bistability in the photon-blockade-breakdown regime of the driven and lossy Jaynes–Cummings model is the finite-size precursor of what in the thermodynamic limit is a genuine first-order phase transition. We construct a finite-size scaling of the system parameters to a well-defined thermodynamic limit, in which the system remains the same microscopic system, but the telegraph signal becomes macroscopic both in its timescale and intensity. The existence of such a finite-size scaling completes and justifies the classification of the photon-blockade-breakdown effect as a first-order dissipative quantum phase transition.","lang":"eng"}],"isi":1,"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":["000469987500004"],"arxiv":["1809.09737"]},"language":[{"iso":"eng"}],"doi":"10.22331/q-2019-06-03-150","month":"06","publication_identifier":{"issn":["2521-327X"]},"publication_status":"published","department":[{"_id":"JoFi"}],"publisher":"Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften","year":"2019","date_updated":"2023-09-07T14:57:39Z","date_created":"2020-02-05T09:57:57Z","volume":3,"author":[{"full_name":"Vukics, A.","first_name":"A.","last_name":"Vukics"},{"full_name":"Dombi, A.","last_name":"Dombi","first_name":"A."},{"full_name":"Fink, Johannes M","last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Domokos, P.","first_name":"P.","last_name":"Domokos"}],"article_number":"150","file_date_updated":"2020-07-14T12:47:58Z"},{"year":"2019","publisher":"IEEE","department":[{"_id":"VlKo"}],"publication_status":"published","author":[{"id":"446560C6-F248-11E8-B48F-1D18A9856A87","last_name":"Swoboda","first_name":"Paul","full_name":"Swoboda, Paul"},{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"volume":"2019-June","date_created":"2020-02-09T23:00:52Z","date_updated":"2023-09-07T14:54:24Z","article_number":"11138-11147","ec_funded":1,"main_file_link":[{"url":"https://arxiv.org/abs/1806.05049","open_access":"1"}],"oa":1,"external_id":{"isi":["000542649304076"],"arxiv":["1806.05049"]},"project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"quality_controlled":"1","isi":1,"doi":"10.1109/CVPR.2019.01140","conference":{"name":"CVPR: Conference on Computer Vision and Pattern Recognition","end_date":"2019-06-20","start_date":"2019-06-15","location":"Long Beach, CA, United States"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781728132938"],"issn":["10636919"]},"month":"06","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7468","status":"public","title":"Map inference via block-coordinate Frank-Wolfe algorithm","oa_version":"Preprint","type":"conference","abstract":[{"text":"We present a new proximal bundle method for Maximum-A-Posteriori (MAP) inference in structured energy minimization problems. The method optimizes a Lagrangean relaxation of the original energy minimization problem using a multi plane block-coordinate Frank-Wolfe method that takes advantage of the specific structure of the Lagrangean decomposition. We show empirically that our method outperforms state-of-the-art Lagrangean decomposition based algorithms on some challenging Markov Random Field, multi-label discrete tomography and graph matching problems.","lang":"eng"}],"citation":{"ista":"Swoboda P, Kolmogorov V. 2019. Map inference via block-coordinate Frank-Wolfe algorithm. Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition vol. 2019–June, 11138–11147.","ieee":"P. Swoboda and V. 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In this work, we propose a new training procedure for multi-exit architectures based on the principle of knowledge distillation. The method encourage searly exits to mimic later, more accurate exits, by matching their output probabilities.\r\nExperiments on CIFAR100 and ImageNet show that distillation-based training significantly improves the accuracy of early exits while maintaining state-of-the-art accuracy for late ones. The method is particularly beneficial when training data is limited and it allows a straightforward extension to semi-supervised learning,i.e. making use of unlabeled data at training time. 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The convolutions are derivedas linear, shift-equivariant functions for various notions of shifts on set functions.The framework is fundamentally different from graph convolutions based on theLaplacian, as it provides not one but several basic shifts, one for each element inthe ground set. Prototypical experiments with several set function classificationtasks on synthetic datasets and on datasets derived from real-world hypergraphsdemonstrate the potential of our new powerset CNNs.","lang":"eng"}],"page":"927-938","citation":{"ieee":"C. Wendler, D.-A. Alistarh, and M. Püschel, “Powerset convolutional neural networks,” presented at the NIPS: Conference on Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32, pp. 927–938.","apa":"Wendler, C., Alistarh, D.-A., & Püschel, M. (2019). Powerset convolutional neural networks (Vol. 32, pp. 927–938). 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The first line of social immune defense is sanitary care, which is performed by colony members to protect their pathogen-exposed nestmates from developing an infection. If sanitary care fails and an infection becomes established, a second line of social immune defense is deployed to stop disease transmission within the colony and to protect the valuable queens, which together with the males are the reproductive individuals of the colony. Insect colonies are separated into these reproductive individuals and the sterile worker force, forming a superorganismal reproductive unit reminiscent of the differentiated germline and soma in a multicellular organism. Ultimately, the social immune response preserves the germline of the superorganism insect colony and increases overall fitness of the colony in case of disease. "}],"publication":"Encyclopedia of Animal Behavior","external_id":{"isi":["000248989500026"]},"citation":{"ama":"Cremer S, Kutzer M. Social immunity. In: Choe J, ed. Encyclopedia of Animal Behavior. 2nd ed. Elsevier; 2019:747-755. doi:10.1016/B978-0-12-809633-8.90721-0","ista":"Cremer S, Kutzer M. 2019.Social immunity. In: Encyclopedia of Animal Behavior. , 747–755.","ieee":"S. Cremer and M. Kutzer, “Social immunity,” in Encyclopedia of Animal Behavior, 2nd ed., J. Choe, Ed. Elsevier, 2019, pp. 747–755.","apa":"Cremer, S., & Kutzer, M. (2019). Social immunity. In J. Choe (Ed.), Encyclopedia of Animal Behavior (2nd ed., pp. 747–755). Elsevier. https://doi.org/10.1016/B978-0-12-809633-8.90721-0","mla":"Cremer, Sylvia, and Megan Kutzer. “Social Immunity.” Encyclopedia of Animal Behavior, edited by Jae Choe, 2nd ed., Elsevier, 2019, pp. 747–55, doi:10.1016/B978-0-12-809633-8.90721-0.","short":"S. Cremer, M. Kutzer, in:, J. Choe (Ed.), Encyclopedia of Animal Behavior, 2nd ed., Elsevier, 2019, pp. 747–755.","chicago":"Cremer, Sylvia, and Megan Kutzer. “Social Immunity.” In Encyclopedia of Animal Behavior, edited by Jae Choe, 2nd ed., 747–55. Elsevier, 2019. https://doi.org/10.1016/B978-0-12-809633-8.90721-0."},"isi":1,"quality_controlled":"1","page":"747-755","date_published":"2019-02-06T00:00:00Z","doi":"10.1016/B978-0-12-809633-8.90721-0","language":[{"iso":"eng"}],"scopus_import":"1","day":"06","month":"02","publication_identifier":{"eisbn":["9780128132524"],"isbn":["9780128132517"]},"article_processing_charge":"No"},{"scopus_import":"1","article_processing_charge":"No","publication_identifier":{"issn":["2518-6582"],"isbn":["9788412110104"]},"day":"10","month":"10","citation":{"ista":"Laccone F, Malomo L, Perez Rodriguez J, Pietroni N, Ponchio F, Bickel B, Cignoni P. 2019. FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels. IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE. IASS: International Association for Shell and Spatial Structures, 509–515.","ieee":"F. Laccone et al., “FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels,” in IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE, Barcelona, Spain, 2019, pp. 509–515.","apa":"Laccone, F., Malomo, L., Perez Rodriguez, J., Pietroni, N., Ponchio, F., Bickel, B., & Cignoni, P. (2019). FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels. In IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE (pp. 509–515). Barcelona, Spain: International Center for Numerical Methods in Engineering.","ama":"Laccone F, Malomo L, Perez Rodriguez J, et al. FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels. In: IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE. International Center for Numerical Methods in Engineering; 2019:509-515.","chicago":"Laccone, Francesco, Luigi Malomo, Jesus Perez Rodriguez, Nico Pietroni, Federico Ponchio, Bernd Bickel, and Paolo Cignoni. “FlexMaps Pavilion: A Twisted Arc Made of Mesostructured Flat Flexible Panels.” In IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE, 509–15. International Center for Numerical Methods in Engineering, 2019.","mla":"Laccone, Francesco, et al. “FlexMaps Pavilion: A Twisted Arc Made of Mesostructured Flat Flexible Panels.” IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE, International Center for Numerical Methods in Engineering, 2019, pp. 509–15.","short":"F. Laccone, L. Malomo, J. Perez Rodriguez, N. Pietroni, F. Ponchio, B. Bickel, P. Cignoni, in:, IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE, International Center for Numerical Methods in Engineering, 2019, pp. 509–515."},"external_id":{"isi":["000563497600059"]},"publication":"IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE","page":"509-515","quality_controlled":"1","isi":1,"date_published":"2019-10-10T00:00:00Z","conference":{"end_date":"2019-10-10","start_date":"2019-10-07","location":"Barcelona, Spain","name":"IASS: International Association for Shell and Spatial Structures"},"language":[{"iso":"eng"}],"type":"conference","abstract":[{"text":"Bending-active structures are able to efficiently produce complex curved shapes starting from flat panels. The desired deformation of the panels derives from the proper selection of their elastic properties. Optimized panels, called FlexMaps, are designed such that, once they are bent and assembled, the resulting static equilibrium configuration matches a desired input 3D shape. The FlexMaps elastic properties are controlled by locally varying spiraling geometric mesostructures, which are optimized in size and shape to match the global curvature (i.e., bending requests) of the target shape. The design pipeline starts from a quad mesh representing the input 3D shape, which defines the edge size and the total amount of spirals: every quad will embed one spiral. Then, an optimization algorithm tunes the geometry of the spirals by using a simplified pre-computed rod model. This rod model is derived from a non-linear regression algorithm which approximates the non-linear behavior of solid FEM spiral models subject to hundreds of load combinations. This innovative pipeline has been applied to the project of a lightweight plywood pavilion named FlexMaps Pavilion, which is a single-layer piecewise twisted arc that fits a bounding box of 3.90x3.96x3.25 meters.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9261","year":"2019","publisher":"International Center for Numerical Methods in Engineering","department":[{"_id":"BeBi"}],"publication_status":"published","title":"FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels","status":"public","author":[{"last_name":"Laccone","first_name":"Francesco","full_name":"Laccone, Francesco"},{"last_name":"Malomo","first_name":"Luigi","full_name":"Malomo, Luigi"},{"full_name":"Perez Rodriguez, Jesus","id":"2DC83906-F248-11E8-B48F-1D18A9856A87","last_name":"Perez Rodriguez","first_name":"Jesus"},{"last_name":"Pietroni","first_name":"Nico","full_name":"Pietroni, Nico"},{"first_name":"Federico","last_name":"Ponchio","full_name":"Ponchio, Federico"},{"full_name":"Bickel, Bernd","last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cignoni, Paolo","first_name":"Paolo","last_name":"Cignoni"}],"oa_version":"None","date_created":"2021-03-21T23:01:21Z","date_updated":"2023-09-08T11:21:54Z"},{"date_published":"2019-10-01T00:00:00Z","citation":{"chicago":"Kolesnikov, Alexander, Alina Kuznetsova, Christoph Lampert, and Vittorio Ferrari. “Detecting Visual Relationships Using Box Attention.” In Proceedings of the 2019 International Conference on Computer Vision Workshop. IEEE, 2019. https://doi.org/10.1109/ICCVW.2019.00217.","short":"A. Kolesnikov, A. Kuznetsova, C. Lampert, V. Ferrari, in:, Proceedings of the 2019 International Conference on Computer Vision Workshop, IEEE, 2019.","mla":"Kolesnikov, Alexander, et al. “Detecting Visual Relationships Using Box Attention.” Proceedings of the 2019 International Conference on Computer Vision Workshop, 1749–1753, IEEE, 2019, doi:10.1109/ICCVW.2019.00217.","ieee":"A. Kolesnikov, A. Kuznetsova, C. Lampert, and V. Ferrari, “Detecting visual relationships using box attention,” in Proceedings of the 2019 International Conference on Computer Vision Workshop, Seoul, South Korea, 2019.","apa":"Kolesnikov, A., Kuznetsova, A., Lampert, C., & Ferrari, V. (2019). Detecting visual relationships using box attention. In Proceedings of the 2019 International Conference on Computer Vision Workshop. Seoul, South Korea: IEEE. https://doi.org/10.1109/ICCVW.2019.00217","ista":"Kolesnikov A, Kuznetsova A, Lampert C, Ferrari V. 2019. Detecting visual relationships using box attention. Proceedings of the 2019 International Conference on Computer Vision Workshop. ICCVW: International Conference on Computer Vision Workshop, 1749–1753.","ama":"Kolesnikov A, Kuznetsova A, Lampert C, Ferrari V. Detecting visual relationships using box attention. In: Proceedings of the 2019 International Conference on Computer Vision Workshop. IEEE; 2019. doi:10.1109/ICCVW.2019.00217"},"publication":"Proceedings of the 2019 International Conference on Computer Vision Workshop","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Preprint","_id":"7640","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Detecting visual relationships using box attention","status":"public","abstract":[{"lang":"eng","text":"We propose a new model for detecting visual relationships, such as \"person riding motorcycle\" or \"bottle on table\". This task is an important step towards comprehensive structured mage understanding, going beyond detecting individual objects. Our main novelty is a Box Attention mechanism that allows to model pairwise interactions between objects using standard object detection pipelines. The resulting model is conceptually clean, expressive and relies on well-justified training and prediction procedures. Moreover, unlike previously proposed approaches, our model does not introduce any additional complex components or hyperparameters on top of those already required by the underlying detection model. We conduct an experimental evaluation on two datasets, V-COCO and Open Images, demonstrating strong quantitative and qualitative results."}],"type":"conference","doi":"10.1109/ICCVW.2019.00217","conference":{"name":"ICCVW: International Conference on Computer Vision Workshop","end_date":"2019-10-28","location":"Seoul, South Korea","start_date":"2019-10-27"},"language":[{"iso":"eng"}],"external_id":{"arxiv":["1807.02136"],"isi":["000554591601098"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1807.02136"}],"project":[{"name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"publication_identifier":{"isbn":["9781728150239"]},"month":"10","author":[{"id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","last_name":"Kolesnikov","first_name":"Alexander","full_name":"Kolesnikov, Alexander"},{"full_name":"Kuznetsova, Alina","last_name":"Kuznetsova","first_name":"Alina"},{"last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"},{"last_name":"Ferrari","first_name":"Vittorio","full_name":"Ferrari, Vittorio"}],"date_updated":"2023-09-08T11:18:37Z","date_created":"2020-04-05T22:00:51Z","year":"2019","department":[{"_id":"ChLa"}],"publisher":"IEEE","publication_status":"published","ec_funded":1,"article_number":"1749-1753"},{"scopus_import":"1","article_processing_charge":"No","publication_identifier":{"isbn":["9781728150239"]},"month":"10","day":"01","external_id":{"isi":["000554591600090"]},"citation":{"ieee":"A. Rannen-Triki, M. Berman, V. Kolmogorov, and M. B. Blaschko, “Function norms for neural networks,” in Proceedings of the 2019 International Conference on Computer Vision Workshop, Seoul, South Korea, 2019.","apa":"Rannen-Triki, A., Berman, M., Kolmogorov, V., & Blaschko, M. B. (2019). Function norms for neural networks. In Proceedings of the 2019 International Conference on Computer Vision Workshop. Seoul, South Korea: IEEE. https://doi.org/10.1109/ICCVW.2019.00097","ista":"Rannen-Triki A, Berman M, Kolmogorov V, Blaschko MB. 2019. Function norms for neural networks. Proceedings of the 2019 International Conference on Computer Vision Workshop. ICCVW: International Conference on Computer Vision Workshop, 748–752.","ama":"Rannen-Triki A, Berman M, Kolmogorov V, Blaschko MB. Function norms for neural networks. In: Proceedings of the 2019 International Conference on Computer Vision Workshop. IEEE; 2019. doi:10.1109/ICCVW.2019.00097","chicago":"Rannen-Triki, Amal, Maxim Berman, Vladimir Kolmogorov, and Matthew B. Blaschko. “Function Norms for Neural Networks.” In Proceedings of the 2019 International Conference on Computer Vision Workshop. IEEE, 2019. https://doi.org/10.1109/ICCVW.2019.00097.","short":"A. Rannen-Triki, M. Berman, V. Kolmogorov, M.B. Blaschko, in:, Proceedings of the 2019 International Conference on Computer Vision Workshop, IEEE, 2019.","mla":"Rannen-Triki, Amal, et al. “Function Norms for Neural Networks.” Proceedings of the 2019 International Conference on Computer Vision Workshop, 748–752, IEEE, 2019, doi:10.1109/ICCVW.2019.00097."},"publication":"Proceedings of the 2019 International Conference on Computer Vision Workshop","isi":1,"quality_controlled":"1","doi":"10.1109/ICCVW.2019.00097","date_published":"2019-10-01T00:00:00Z","conference":{"end_date":"2019-10-28","location":"Seoul, South Korea","start_date":"2019-10-27","name":"ICCVW: International Conference on Computer Vision Workshop"},"language":[{"iso":"eng"}],"type":"conference","article_number":"748-752","abstract":[{"text":"Deep neural networks (DNNs) have become increasingly important due to their excellent empirical performance on a wide range of problems. However, regularization is generally achieved by indirect means, largely due to the complex set of functions defined by a network and the difficulty in measuring function complexity. There exists no method in the literature for additive regularization based on a norm of the function, as is classically considered in statistical learning theory. In this work, we study the tractability of function norms for deep neural networks with ReLU activations. We provide, to the best of our knowledge, the first proof in the literature of the NP-hardness of computing function norms of DNNs of 3 or more layers. We also highlight a fundamental difference between shallow and deep networks. In the light on these results, we propose a new regularization strategy based on approximate function norms, and show its efficiency on a segmentation task with a DNN.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7639","year":"2019","publisher":"IEEE","department":[{"_id":"VlKo"}],"status":"public","publication_status":"published","title":"Function norms for neural networks","author":[{"first_name":"Amal","last_name":"Rannen-Triki","full_name":"Rannen-Triki, Amal"},{"full_name":"Berman, Maxim","first_name":"Maxim","last_name":"Berman"},{"full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matthew B.","last_name":"Blaschko","full_name":"Blaschko, Matthew B."}],"oa_version":"None","date_created":"2020-04-05T22:00:50Z","date_updated":"2023-09-08T11:19:12Z"},{"month":"07","publication_identifier":{"isbn":["9781119429142"]},"doi":"10.1002/9781119487845.ch4","language":[{"iso":"eng"}],"external_id":{"isi":["000261343000003"]},"isi":1,"quality_controlled":"1","author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"full_name":"Etheridge, Alison","first_name":"Alison","last_name":"Etheridge"}],"edition":"4","date_created":"2020-08-21T04:25:39Z","date_updated":"2023-09-08T11:24:15Z","year":"2019","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","editor":[{"full_name":"Balding, David","first_name":"David","last_name":"Balding"},{"last_name":"Moltke","first_name":"Ida","full_name":"Moltke, Ida"},{"full_name":"Marioni, John","first_name":"John","last_name":"Marioni"}],"day":"29","article_processing_charge":"No","date_published":"2019-07-29T00:00:00Z","publication":"Handbook of statistical genomics","citation":{"chicago":"Barton, Nicholas H, and Alison Etheridge. “Mathematical Models in Population Genetics.” In Handbook of Statistical Genomics, edited by David Balding, Ida Moltke, and John Marioni, 4th ed., 115–44. Wiley, 2019. https://doi.org/10.1002/9781119487845.ch4.","short":"N.H. Barton, A. Etheridge, in:, D. Balding, I. Moltke, J. Marioni (Eds.), Handbook of Statistical Genomics, 4th ed., Wiley, 2019, pp. 115–144.","mla":"Barton, Nicholas H., and Alison Etheridge. “Mathematical Models in Population Genetics.” Handbook of Statistical Genomics, edited by David Balding et al., 4th ed., Wiley, 2019, pp. 115–44, doi:10.1002/9781119487845.ch4.","apa":"Barton, N. H., & Etheridge, A. (2019). Mathematical models in population genetics. In D. Balding, I. Moltke, & J. Marioni (Eds.), Handbook of statistical genomics (4th ed., pp. 115–144). Wiley. https://doi.org/10.1002/9781119487845.ch4","ieee":"N. H. Barton and A. Etheridge, “Mathematical models in population genetics,” in Handbook of statistical genomics, 4th ed., D. Balding, I. Moltke, and J. Marioni, Eds. Wiley, 2019, pp. 115–144.","ista":"Barton NH, Etheridge A. 2019.Mathematical models in population genetics. In: Handbook of statistical genomics. , 115–144.","ama":"Barton NH, Etheridge A. Mathematical models in population genetics. In: Balding D, Moltke I, Marioni J, eds. Handbook of Statistical Genomics. 4th ed. Wiley; 2019:115-144. doi:10.1002/9781119487845.ch4"},"page":"115-144","abstract":[{"lang":"eng","text":"We review the history of population genetics, starting with its origins a century ago from the synthesis between Mendel and Darwin's ideas, through to the recent development of sophisticated schemes of inference from sequence data, based on the coalescent. We explain the close relation between the coalescent and a diffusion process, which we illustrate by their application to understand spatial structure. We summarise the powerful methods available for analysis of multiple loci, when linkage equilibrium can be assumed, and then discuss approaches to the more challenging case, where associations between alleles require that we follow genotype, rather than allele, frequencies. Though we can hardly cover the whole of population genetics, we give an overview of the current state of the subject, and future challenges to it."}],"type":"book_chapter","oa_version":"None","_id":"8281","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["576"],"title":"Mathematical models in population genetics","status":"public"},{"date_updated":"2023-09-08T11:20:02Z","date_created":"2020-07-30T10:45:34Z","oa_version":"Preprint","author":[{"id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","first_name":"Sergey","last_name":"Avvakumov","full_name":"Avvakumov, Sergey"},{"last_name":"Karasev","first_name":"R.","full_name":"Karasev, R."},{"full_name":"Skopenkov, A.","last_name":"Skopenkov","first_name":"A."}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8156"}]},"title":"Stronger counterexamples to the topological Tverberg conjecture","publication_status":"submitted","status":"public","department":[{"_id":"UlWa"}],"publisher":"arXiv","_id":"8184","year":"2019","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"We would like to thank F. Frick for helpful discussions","abstract":[{"text":"Denote by ∆N the N-dimensional simplex. A map f : ∆N → Rd is an almost r-embedding if fσ1∩. . .∩fσr = ∅ whenever σ1, . . . , σr are pairwise disjoint faces. A counterexample to the topological Tverberg conjecture asserts that if r is not a prime power and d ≥ 2r + 1, then there is an almost r-embedding ∆(d+1)(r−1) → Rd. This was improved by Blagojevi´c–Frick–Ziegler using a simple construction of higher-dimensional counterexamples by taking k-fold join power of lower-dimensional ones. We improve this further (for d large compared to r): If r is not a prime power and N := (d+ 1)r−r l\r\nd + 2 r + 1 m−2, then there is an almost r-embedding ∆N → Rd. For the r-fold van Kampen–Flores conjecture we also produce counterexamples which are stronger than previously known. Our proof is based on generalizations of the Mabillard–Wagner theorem on construction of almost r-embeddings from equivariant maps, and of the Ozaydin theorem on existence of equivariant maps. ","lang":"eng"}],"article_number":"1908.08731","type":"preprint","language":[{"iso":"eng"}],"date_published":"2019-08-23T00:00:00Z","isi":1,"project":[{"call_identifier":"FWF","name":"Algorithms for Embeddings and Homotopy Theory","_id":"26611F5C-B435-11E9-9278-68D0E5697425","grant_number":"P31312"}],"publication":"arXiv","external_id":{"arxiv":["1908.08731"],"isi":["000986519600004"]},"citation":{"chicago":"Avvakumov, Sergey, R. Karasev, and A. Skopenkov. “Stronger Counterexamples to the Topological Tverberg Conjecture.” ArXiv. arXiv, n.d.","short":"S. Avvakumov, R. Karasev, A. Skopenkov, ArXiv (n.d.).","mla":"Avvakumov, Sergey, et al. “Stronger Counterexamples to the Topological Tverberg Conjecture.” ArXiv, 1908.08731, arXiv.","ieee":"S. Avvakumov, R. Karasev, and A. Skopenkov, “Stronger counterexamples to the topological Tverberg conjecture,” arXiv. arXiv.","apa":"Avvakumov, S., Karasev, R., & Skopenkov, A. (n.d.). Stronger counterexamples to the topological Tverberg conjecture. arXiv. arXiv.","ista":"Avvakumov S, Karasev R, Skopenkov A. Stronger counterexamples to the topological Tverberg conjecture. arXiv, 1908.08731.","ama":"Avvakumov S, Karasev R, Skopenkov A. Stronger counterexamples to the topological Tverberg conjecture. arXiv."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1908.08731"}],"day":"23","month":"08","article_processing_charge":"No"},{"ec_funded":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrPi"}],"year":"2019","date_updated":"2023-09-08T11:33:20Z","date_created":"2019-05-13T08:13:46Z","volume":11443,"author":[{"full_name":"Fuchsbauer, Georg","last_name":"Fuchsbauer","first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Chethan","last_name":"Kamath Hosdurg","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","full_name":"Kamath Hosdurg, Chethan"},{"id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","last_name":"Klein","first_name":"Karen","full_name":"Klein, Karen"},{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z"}],"related_material":{"record":[{"id":"10035","relation":"dissertation_contains","status":"public"}]},"month":"04","publication_identifier":{"eissn":["16113349"],"isbn":["9783030172589"],"issn":["03029743"]},"quality_controlled":"1","project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2018/426"}],"language":[{"iso":"eng"}],"conference":{"name":"PKC: Public-Key Cryptograhy","start_date":"2019-04-14","location":"Beijing, China","end_date":"2019-04-17"},"doi":"10.1007/978-3-030-17259-6_11","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"A proxy re-encryption (PRE) scheme is a public-key encryption scheme that allows the holder of a key pk to derive a re-encryption key for any other key 𝑝𝑘′. This re-encryption key lets anyone transform ciphertexts under pk into ciphertexts under 𝑝𝑘′ without having to know the underlying message, while transformations from 𝑝𝑘′ to pk should not be possible (unidirectional). Security is defined in a multi-user setting against an adversary that gets the users’ public keys and can ask for re-encryption keys and can corrupt users by requesting their secret keys. Any ciphertext that the adversary cannot trivially decrypt given the obtained secret and re-encryption keys should be secure.\r\n\r\nAll existing security proofs for PRE only show selective security, where the adversary must first declare the users it wants to corrupt. This can be lifted to more meaningful adaptive security by guessing the set of corrupted users among the n users, which loses a factor exponential in Open image in new window , rendering the result meaningless already for moderate Open image in new window .\r\n\r\nJafargholi et al. (CRYPTO’17) proposed a framework that in some cases allows to give adaptive security proofs for schemes which were previously only known to be selectively secure, while avoiding the exponential loss that results from guessing the adaptive choices made by an adversary. We apply their framework to PREs that satisfy some natural additional properties. Concretely, we give a more fine-grained reduction for several unidirectional PREs, proving adaptive security at a much smaller loss. The loss depends on the graph of users whose edges represent the re-encryption keys queried by the adversary. For trees and chains the loss is quasi-polynomial in the size and for general graphs it is exponential in their depth and indegree (instead of their size as for previous reductions). Fortunately, trees and low-depth graphs cover many, if not most, interesting applications.\r\n\r\nOur results apply e.g. to the bilinear-map based PRE schemes by Ateniese et al. (NDSS’05 and CT-RSA’09), Gentry’s FHE-based scheme (STOC’09) and the LWE-based scheme by Chandran et al. (PKC’14).","lang":"eng"}],"title":"Adaptively secure proxy re-encryption","status":"public","intvolume":" 11443","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6430","oa_version":"Preprint","scopus_import":"1","day":"06","article_processing_charge":"No","page":"317-346","citation":{"ama":"Fuchsbauer G, Kamath Hosdurg C, Klein K, Pietrzak KZ. Adaptively secure proxy re-encryption. In: Vol 11443. Springer Nature; 2019:317-346. doi:10.1007/978-3-030-17259-6_11","apa":"Fuchsbauer, G., Kamath Hosdurg, C., Klein, K., & Pietrzak, K. Z. (2019). Adaptively secure proxy re-encryption (Vol. 11443, pp. 317–346). Presented at the PKC: Public-Key Cryptograhy, Beijing, China: Springer Nature. https://doi.org/10.1007/978-3-030-17259-6_11","ieee":"G. Fuchsbauer, C. Kamath Hosdurg, K. Klein, and K. Z. Pietrzak, “Adaptively secure proxy re-encryption,” presented at the PKC: Public-Key Cryptograhy, Beijing, China, 2019, vol. 11443, pp. 317–346.","ista":"Fuchsbauer G, Kamath Hosdurg C, Klein K, Pietrzak KZ. 2019. Adaptively secure proxy re-encryption. PKC: Public-Key Cryptograhy, LNCS, vol. 11443, 317–346.","short":"G. Fuchsbauer, C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, in:, Springer Nature, 2019, pp. 317–346.","mla":"Fuchsbauer, Georg, et al. Adaptively Secure Proxy Re-Encryption. Vol. 11443, Springer Nature, 2019, pp. 317–46, doi:10.1007/978-3-030-17259-6_11.","chicago":"Fuchsbauer, Georg, Chethan Kamath Hosdurg, Karen Klein, and Krzysztof Z Pietrzak. “Adaptively Secure Proxy Re-Encryption,” 11443:317–46. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-17259-6_11."},"date_published":"2019-04-06T00:00:00Z"},{"author":[{"full_name":"Mayzel, Jonathan","last_name":"Mayzel","first_name":"Jonathan"},{"first_name":"Victor","last_name":"Steinberg","full_name":"Steinberg, Victor"},{"orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","last_name":"Varshney","first_name":"Atul","full_name":"Varshney, Atul"}],"volume":10,"date_updated":"2023-09-08T11:39:02Z","date_created":"2019-03-05T13:18:30Z","year":"2019","publisher":"Springer Nature","department":[{"_id":"BjHo"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-14T12:47:18Z","article_number":"937","doi":"10.1038/s41467-019-08916-5","language":[{"iso":"eng"}],"external_id":{"isi":["000459704600001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["2041-1723"]},"month":"02","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":2646391,"creator":"dernst","file_name":"2019_NatureComm_Mayzel.pdf","access_level":"open_access","date_created":"2019-03-05T13:33:04Z","date_updated":"2020-07-14T12:47:18Z","checksum":"61192fc49e0d44907c2a4fe384e4b97f","relation":"main_file","file_id":"6070"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6069","intvolume":" 10","status":"public","title":"Stokes flow analogous to viscous electron current in graphene","ddc":["530","532"],"abstract":[{"lang":"eng","text":"Electron transport in two-dimensional conducting materials such as graphene, with dominant electron–electron interaction, exhibits unusual vortex flow that leads to a nonlocal current-field relation (negative resistance), distinct from the classical Ohm’s law. The transport behavior of these materials is best described by low Reynolds number hydrodynamics, where the constitutive pressure–speed relation is Stoke’s law. Here we report evidence of such vortices observed in a viscous flow of Newtonian fluid in a microfluidic device consisting of a rectangular cavity—analogous to the electronic system. We extend our experimental observations to elliptic cavities of different eccentricities, and validate them by numerically solving bi-harmonic equation obtained for the viscous flow with no-slip boundary conditions. We verify the existence of a predicted threshold at which vortices appear. Strikingly, we find that a two-dimensional theoretical model captures the essential features of three-dimensional Stokes flow in experiments."}],"type":"journal_article","date_published":"2019-02-26T00:00:00Z","citation":{"ama":"Mayzel J, Steinberg V, Varshney A. Stokes flow analogous to viscous electron current in graphene. Nature Communications. 2019;10. doi:10.1038/s41467-019-08916-5","ieee":"J. Mayzel, V. Steinberg, and A. Varshney, “Stokes flow analogous to viscous electron current in graphene,” Nature Communications, vol. 10. Springer Nature, 2019.","apa":"Mayzel, J., Steinberg, V., & Varshney, A. (2019). Stokes flow analogous to viscous electron current in graphene. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-08916-5","ista":"Mayzel J, Steinberg V, Varshney A. 2019. Stokes flow analogous to viscous electron current in graphene. Nature Communications. 10, 937.","short":"J. Mayzel, V. Steinberg, A. Varshney, Nature Communications 10 (2019).","mla":"Mayzel, Jonathan, et al. “Stokes Flow Analogous to Viscous Electron Current in Graphene.” Nature Communications, vol. 10, 937, Springer Nature, 2019, doi:10.1038/s41467-019-08916-5.","chicago":"Mayzel, Jonathan, Victor Steinberg, and Atul Varshney. “Stokes Flow Analogous to Viscous Electron Current in Graphene.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-08916-5."},"publication":"Nature Communications","article_processing_charge":"No","has_accepted_license":"1","day":"26","scopus_import":"1"},{"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000458175300001"],"arxiv":["1902.03763"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41467-019-08551-0","publication_identifier":{"issn":["2041-1723"]},"month":"02","department":[{"_id":"BjHo"}],"publisher":"Springer Nature","publication_status":"published","year":"2019","volume":10,"date_created":"2019-02-15T07:10:46Z","date_updated":"2023-09-08T11:39:54Z","author":[{"full_name":"Varshney, Atul","orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","last_name":"Varshney","first_name":"Atul"},{"first_name":"Victor","last_name":"Steinberg","full_name":"Steinberg, Victor"}],"article_number":"652","ec_funded":1,"file_date_updated":"2020-07-14T12:47:17Z","article_type":"original","citation":{"ista":"Varshney A, Steinberg V. 2019. Elastic alfven waves in elastic turbulence. Nature Communications. 10, 652.","ieee":"A. Varshney and V. Steinberg, “Elastic alfven waves in elastic turbulence,” Nature Communications, vol. 10. Springer Nature, 2019.","apa":"Varshney, A., & Steinberg, V. (2019). Elastic alfven waves in elastic turbulence. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-08551-0","ama":"Varshney A, Steinberg V. Elastic alfven waves in elastic turbulence. Nature Communications. 2019;10. doi:10.1038/s41467-019-08551-0","chicago":"Varshney, Atul, and Victor Steinberg. “Elastic Alfven Waves in Elastic Turbulence.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-08551-0.","mla":"Varshney, Atul, and Victor Steinberg. “Elastic Alfven Waves in Elastic Turbulence.” Nature Communications, vol. 10, 652, Springer Nature, 2019, doi:10.1038/s41467-019-08551-0.","short":"A. Varshney, V. Steinberg, Nature Communications 10 (2019)."},"publication":"Nature Communications","date_published":"2019-02-08T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"08","intvolume":" 10","ddc":["530"],"status":"public","title":"Elastic alfven waves in elastic turbulence","_id":"6014","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_name":"2019_NatureComm_Varshney.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1331490,"file_id":"6015","relation":"main_file","date_updated":"2020-07-14T12:47:17Z","date_created":"2019-02-15T07:15:00Z","checksum":"d3acf07eaad95ec040d8e8565fc9ac37"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Speed of sound waves in gases and liquids are governed by the compressibility of the medium. There exists another type of non-dispersive wave where the wave speed depends on stress instead of elasticity of the medium. A well-known example is the Alfven wave, which propagates through plasma permeated by a magnetic field with the speed determined by magnetic tension. An elastic analogue of Alfven waves has been predicted in a flow of dilute polymer solution where the elastic stress of the stretching polymers determines the elastic wave speed. Here we present quantitative evidence of elastic Alfven waves in elastic turbulence of a viscoelastic creeping flow between two obstacles in channel flow. The key finding in the experimental proof is a nonlinear dependence of the elastic wave speed cel on the Weissenberg number Wi, which deviates from predictions based on a model of linear polymer elasticity."}]},{"file":[{"date_created":"2019-05-14T11:51:51Z","date_updated":"2020-07-14T12:47:30Z","checksum":"a9ad2296726c9474ad5860c9c2f53622","relation":"main_file","file_id":"6452","content_type":"application/pdf","file_size":8365970,"creator":"dernst","file_name":"2019_iScience_Amberg.pdf","access_level":"open_access"}],"oa_version":"Published Version","intvolume":" 15","status":"public","title":"EGFR controls hair shaft differentiation in a p53-independent manner","ddc":["570"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6451","abstract":[{"text":"Epidermal growth factor receptor (EGFR) signaling controls skin development and homeostasis inmice and humans, and its deficiency causes severe skin inflammation, which might affect epidermalstem cell behavior. Here, we describe the inflammation-independent effects of EGFR deficiency dur-ing skin morphogenesis and in adult hair follicle stem cells. Expression and alternative splicing analysisof RNA sequencing data from interfollicular epidermis and outer root sheath indicate that EGFR con-trols genes involved in epidermal differentiation and also in centrosome function, DNA damage, cellcycle, and apoptosis. Genetic experiments employingp53deletion in EGFR-deficient epidermis revealthat EGFR signaling exhibitsp53-dependent functions in proliferative epidermal compartments, aswell asp53-independent functions in differentiated hair shaft keratinocytes. Loss of EGFR leads toabsence of LEF1 protein specifically in the innermost epithelial hair layers, resulting in disorganizationof medulla cells. Thus, our results uncover important spatial and temporal features of cell-autonomousEGFR functions in the epidermis.","lang":"eng"}],"type":"journal_article","date_published":"2019-05-31T00:00:00Z","page":"243-256","citation":{"ista":"Amberg N, Sotiropoulou PA, Heller G, Lichtenberger BM, Holcmann M, Camurdanoglu B, Baykuscheva-Gentscheva T, Blanpain C, Sibilia M. 2019. EGFR controls hair shaft differentiation in a p53-independent manner. iScience. 15, 243–256.","ieee":"N. Amberg et al., “EGFR controls hair shaft differentiation in a p53-independent manner,” iScience, vol. 15. Elsevier, pp. 243–256, 2019.","apa":"Amberg, N., Sotiropoulou, P. A., Heller, G., Lichtenberger, B. M., Holcmann, M., Camurdanoglu, B., … Sibilia, M. (2019). EGFR controls hair shaft differentiation in a p53-independent manner. IScience. Elsevier. https://doi.org/10.1016/j.isci.2019.04.018","ama":"Amberg N, Sotiropoulou PA, Heller G, et al. EGFR controls hair shaft differentiation in a p53-independent manner. iScience. 2019;15:243-256. doi:10.1016/j.isci.2019.04.018","chicago":"Amberg, Nicole, Panagiota A. Sotiropoulou, Gerwin Heller, Beate M. Lichtenberger, Martin Holcmann, Bahar Camurdanoglu, Temenuschka Baykuscheva-Gentscheva, Cedric Blanpain, and Maria Sibilia. “EGFR Controls Hair Shaft Differentiation in a P53-Independent Manner.” IScience. Elsevier, 2019. https://doi.org/10.1016/j.isci.2019.04.018.","mla":"Amberg, Nicole, et al. “EGFR Controls Hair Shaft Differentiation in a P53-Independent Manner.” IScience, vol. 15, Elsevier, 2019, pp. 243–56, doi:10.1016/j.isci.2019.04.018.","short":"N. Amberg, P.A. Sotiropoulou, G. Heller, B.M. Lichtenberger, M. Holcmann, B. Camurdanoglu, T. Baykuscheva-Gentscheva, C. Blanpain, M. Sibilia, IScience 15 (2019) 243–256."},"publication":"iScience","has_accepted_license":"1","article_processing_charge":"No","day":"31","volume":15,"date_updated":"2023-09-08T11:38:04Z","date_created":"2019-05-14T11:47:40Z","author":[{"full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg","first_name":"Nicole"},{"full_name":"Sotiropoulou, Panagiota A.","first_name":"Panagiota A.","last_name":"Sotiropoulou"},{"full_name":"Heller, Gerwin","last_name":"Heller","first_name":"Gerwin"},{"full_name":"Lichtenberger, Beate M.","first_name":"Beate M.","last_name":"Lichtenberger"},{"last_name":"Holcmann","first_name":"Martin","full_name":"Holcmann, Martin"},{"first_name":"Bahar","last_name":"Camurdanoglu","full_name":"Camurdanoglu, Bahar"},{"first_name":"Temenuschka","last_name":"Baykuscheva-Gentscheva","full_name":"Baykuscheva-Gentscheva, Temenuschka"},{"full_name":"Blanpain, Cedric","first_name":"Cedric","last_name":"Blanpain"},{"first_name":"Maria","last_name":"Sibilia","full_name":"Sibilia, Maria"}],"department":[{"_id":"SiHi"}],"publisher":"Elsevier","publication_status":"published","year":"2019","file_date_updated":"2020-07-14T12:47:30Z","language":[{"iso":"eng"}],"doi":"10.1016/j.isci.2019.04.018","isi":1,"quality_controlled":"1","external_id":{"isi":["000470104600022"]},"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"},"oa":1,"publication_identifier":{"issn":["2589-0042"]},"month":"05"},{"oa_version":"Preprint","_id":"10879","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 9","status":"public","title":"Perturbations of continuum random Schrödinger operators with applications to Anderson orthogonality and the spectral shift function","issue":"3","abstract":[{"lang":"eng","text":"We study effects of a bounded and compactly supported perturbation on multidimensional continuum random Schrödinger operators in the region of complete localisation. Our main emphasis is on Anderson orthogonality for random Schrödinger operators. Among others, we prove that Anderson orthogonality does occur for Fermi energies in the region of complete localisation with a non-zero probability. This partially confirms recent non-rigorous findings [V. Khemani et al., Nature Phys. 11 (2015), 560–565]. The spectral shift function plays an important role in our analysis of Anderson orthogonality. We identify it with the index of the corresponding pair of spectral projections and explore the consequences thereof. All our results rely on the main technical estimate of this paper which guarantees separate exponential decay of the disorder-averaged Schatten p-norm of χa(f(H)−f(Hτ))χb in a and b. Here, Hτ is a perturbation of the random Schrödinger operator H, χa is the multiplication operator corresponding to the indicator function of a unit cube centred about a∈Rd, and f is in a suitable class of functions of bounded variation with distributional derivative supported in the region of complete localisation for H."}],"type":"journal_article","date_published":"2019-03-01T00:00:00Z","citation":{"chicago":"Dietlein, Adrian M, Martin Gebert, and Peter Müller. “Perturbations of Continuum Random Schrödinger Operators with Applications to Anderson Orthogonality and the Spectral Shift Function.” Journal of Spectral Theory. European Mathematical Society Publishing House, 2019. https://doi.org/10.4171/jst/267.","short":"A.M. Dietlein, M. Gebert, P. Müller, Journal of Spectral Theory 9 (2019) 921–965.","mla":"Dietlein, Adrian M., et al. “Perturbations of Continuum Random Schrödinger Operators with Applications to Anderson Orthogonality and the Spectral Shift Function.” Journal of Spectral Theory, vol. 9, no. 3, European Mathematical Society Publishing House, 2019, pp. 921–65, doi:10.4171/jst/267.","apa":"Dietlein, A. M., Gebert, M., & Müller, P. (2019). Perturbations of continuum random Schrödinger operators with applications to Anderson orthogonality and the spectral shift function. Journal of Spectral Theory. European Mathematical Society Publishing House. https://doi.org/10.4171/jst/267","ieee":"A. M. Dietlein, M. Gebert, and P. Müller, “Perturbations of continuum random Schrödinger operators with applications to Anderson orthogonality and the spectral shift function,” Journal of Spectral Theory, vol. 9, no. 3. European Mathematical Society Publishing House, pp. 921–965, 2019.","ista":"Dietlein AM, Gebert M, Müller P. 2019. Perturbations of continuum random Schrödinger operators with applications to Anderson orthogonality and the spectral shift function. Journal of Spectral Theory. 9(3), 921–965.","ama":"Dietlein AM, Gebert M, Müller P. Perturbations of continuum random Schrödinger operators with applications to Anderson orthogonality and the spectral shift function. Journal of Spectral Theory. 2019;9(3):921-965. doi:10.4171/jst/267"},"publication":"Journal of Spectral Theory","page":"921-965","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1","keyword":["Random Schrödinger operators","spectral shift function","Anderson orthogonality"],"author":[{"full_name":"Dietlein, Adrian M","first_name":"Adrian M","last_name":"Dietlein","id":"317CB464-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gebert","first_name":"Martin","full_name":"Gebert, Martin"},{"full_name":"Müller, Peter","last_name":"Müller","first_name":"Peter"}],"volume":9,"date_created":"2022-03-18T12:36:42Z","date_updated":"2023-09-08T11:35:31Z","year":"2019","acknowledgement":"M.G. was supported by the DFG under grant GE 2871/1-1.","publisher":"European Mathematical Society Publishing House","department":[{"_id":"LaEr"}],"publication_status":"published","doi":"10.4171/jst/267","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1701.02956","open_access":"1"}],"external_id":{"isi":["000484709400006"],"arxiv":["1701.02956"]},"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["1664-039X"]},"month":"03"},{"department":[{"_id":"JaMa"}],"publisher":"American Institute of Mathematical Sciences","publication_status":"published","acknowledgement":"The second author has been partially supported by INdAM through the GNAMPA Research\r\nProject (2017) “Sistemi stocastici singolari: buona posizione e problemi di controllo”. The third\r\nauthor was partly funded by the Austrian Science Fund (FWF) project F 65.","year":"2019","volume":39,"date_created":"2022-03-18T12:33:34Z","date_updated":"2023-09-08T11:34:45Z","author":[{"first_name":"Franco","last_name":"Flandoli","full_name":"Flandoli, Franco"},{"full_name":"Priola, Enrico","first_name":"Enrico","last_name":"Priola"},{"id":"47491882-F248-11E8-B48F-1D18A9856A87","last_name":"Zanco","first_name":"Giovanni A","full_name":"Zanco, Giovanni A"}],"publication_identifier":{"issn":["1553-5231"]},"month":"06","project":[{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"}],"quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/1708.04156","open_access":"1"}],"external_id":{"arxiv":["1708.04156"],"isi":["000459954800003"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.3934/dcds.2019126","type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"Starting from a microscopic model for a system of neurons evolving in time which individually follow a stochastic integrate-and-fire type model, we study a mean-field limit of the system. Our model is described by a system of SDEs with discontinuous coefficients for the action potential of each neuron and takes into account the (random) spatial configuration of neurons allowing the interaction to depend on it. In the limit as the number of particles tends to infinity, we obtain a nonlinear Fokker-Planck type PDE in two variables, with derivatives only with respect to one variable and discontinuous coefficients. We also study strong well-posedness of the system of SDEs and prove the existence and uniqueness of a weak measure-valued solution to the PDE, obtained as the limit of the laws of the empirical measures for the system of particles."}],"intvolume":" 39","status":"public","title":"A mean-field model with discontinuous coefficients for neurons with spatial interaction","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10878","oa_version":"Preprint","keyword":["Applied Mathematics","Discrete Mathematics and Combinatorics","Analysis"],"scopus_import":"1","article_processing_charge":"No","day":"01","page":"3037-3067","article_type":"original","citation":{"short":"F. Flandoli, E. Priola, G.A. Zanco, Discrete and Continuous Dynamical Systems 39 (2019) 3037–3067.","mla":"Flandoli, Franco, et al. “A Mean-Field Model with Discontinuous Coefficients for Neurons with Spatial Interaction.” Discrete and Continuous Dynamical Systems, vol. 39, no. 6, American Institute of Mathematical Sciences, 2019, pp. 3037–67, doi:10.3934/dcds.2019126.","chicago":"Flandoli, Franco, Enrico Priola, and Giovanni A Zanco. “A Mean-Field Model with Discontinuous Coefficients for Neurons with Spatial Interaction.” Discrete and Continuous Dynamical Systems. American Institute of Mathematical Sciences, 2019. https://doi.org/10.3934/dcds.2019126.","ama":"Flandoli F, Priola E, Zanco GA. A mean-field model with discontinuous coefficients for neurons with spatial interaction. Discrete and Continuous Dynamical Systems. 2019;39(6):3037-3067. doi:10.3934/dcds.2019126","apa":"Flandoli, F., Priola, E., & Zanco, G. A. (2019). A mean-field model with discontinuous coefficients for neurons with spatial interaction. Discrete and Continuous Dynamical Systems. American Institute of Mathematical Sciences. https://doi.org/10.3934/dcds.2019126","ieee":"F. Flandoli, E. Priola, and G. A. Zanco, “A mean-field model with discontinuous coefficients for neurons with spatial interaction,” Discrete and Continuous Dynamical Systems, vol. 39, no. 6. American Institute of Mathematical Sciences, pp. 3037–3067, 2019.","ista":"Flandoli F, Priola E, Zanco GA. 2019. A mean-field model with discontinuous coefficients for neurons with spatial interaction. Discrete and Continuous Dynamical Systems. 39(6), 3037–3067."},"publication":"Discrete and Continuous Dynamical Systems","date_published":"2019-06-01T00:00:00Z"},{"date_created":"2019-10-08T12:57:14Z","date_updated":"2023-09-08T11:37:22Z","author":[{"last_name":"Foerster","first_name":"Klaus-Tycho","full_name":"Foerster, Klaus-Tycho"},{"first_name":"Janne","last_name":"Korhonen","id":"C5402D42-15BC-11E9-A202-CA2BE6697425","full_name":"Korhonen, Janne"},{"full_name":"Rybicki, Joel","orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","last_name":"Rybicki","first_name":"Joel"},{"first_name":"Stefan","last_name":"Schmid","full_name":"Schmid, Stefan"}],"department":[{"_id":"DaAl"}],"publisher":"ACM","publication_status":"published","year":"2019","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1145/3293611.3331581","conference":{"end_date":"2019-08-02","start_date":"2019-07-29","location":"Toronto, ON, Canada","name":"PODC: Symposium on Principles of Distributed Computing"},"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.03012"}],"external_id":{"isi":["000570442000037"],"arxiv":["1905.03012"]},"oa":1,"publication_identifier":{"isbn":["9781450362177"]},"month":"08","oa_version":"Preprint","title":"Does preprocessing help under congestion?","status":"public","_id":"6935","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"This paper investigates the power of preprocessing in the CONGEST model. Schmid and Suomela (ACM HotSDN 2013) introduced the SUPPORTED CONGEST model to study the application of distributed algorithms in Software-Defined Networks (SDNs). In this paper, we show that a large class of lower bounds in the CONGEST model still hold in the SUPPORTED model, highlighting the robustness of these bounds. This also raises the question how much does\r\npreprocessing help in the CONGEST model.","lang":"eng"}],"type":"conference","date_published":"2019-08-01T00:00:00Z","page":"259-261","citation":{"ista":"Foerster K-T, Korhonen J, Rybicki J, Schmid S. 2019. Does preprocessing help under congestion? Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 259–261.","ieee":"K.-T. Foerster, J. Korhonen, J. Rybicki, and S. Schmid, “Does preprocessing help under congestion?,” in Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing, Toronto, ON, Canada, 2019, pp. 259–261.","apa":"Foerster, K.-T., Korhonen, J., Rybicki, J., & Schmid, S. (2019). Does preprocessing help under congestion? In Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing (pp. 259–261). Toronto, ON, Canada: ACM. https://doi.org/10.1145/3293611.3331581","ama":"Foerster K-T, Korhonen J, Rybicki J, Schmid S. Does preprocessing help under congestion? In: Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing. ACM; 2019:259-261. doi:10.1145/3293611.3331581","chicago":"Foerster, Klaus-Tycho, Janne Korhonen, Joel Rybicki, and Stefan Schmid. “Does Preprocessing Help under Congestion?” In Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing, 259–61. ACM, 2019. https://doi.org/10.1145/3293611.3331581.","mla":"Foerster, Klaus-Tycho, et al. “Does Preprocessing Help under Congestion?” Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing, ACM, 2019, pp. 259–61, doi:10.1145/3293611.3331581.","short":"K.-T. Foerster, J. Korhonen, J. Rybicki, S. Schmid, in:, Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing, ACM, 2019, pp. 259–261."},"publication":"Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing","article_processing_charge":"No","day":"01","scopus_import":"1"},{"file_date_updated":"2020-07-14T12:44:47Z","ec_funded":1,"publist_id":"7785","date_created":"2018-12-11T11:44:50Z","date_updated":"2023-09-08T13:23:42Z","volume":65,"author":[{"full_name":"Nikolic, Nela","first_name":"Nela","last_name":"Nikolic","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9068-6090"}],"publication_status":"published","department":[{"_id":"CaGu"}],"publisher":"Springer","year":"2019","month":"02","language":[{"iso":"eng"}],"doi":"10.1007/s00294-018-0879-8","isi":1,"quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000456958800017"]},"abstract":[{"text":"Autoregulation is the direct modulation of gene expression by the product of the corresponding gene. Autoregulation of bacterial gene expression has been mostly studied at the transcriptional level, when a protein acts as the cognate transcriptional repressor. A recent study investigating dynamics of the bacterial toxin–antitoxin MazEF system has shown how autoregulation at both the transcriptional and post-transcriptional levels affects the heterogeneity of Escherichia coli populations. Toxin–antitoxin systems hold a crucial but still elusive part in bacterial response to stress. This perspective highlights how these modules can also serve as a great model system for investigating basic concepts in gene regulation. However, as the genomic background and environmental conditions substantially influence toxin activation, it is important to study (auto)regulation of toxin–antitoxin systems in well-defined setups as well as in conditions that resemble the environmental niche.","lang":"eng"}],"issue":"1","type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5930","checksum":"6779708b0b632a1a6ed28c56f5161142","date_updated":"2020-07-14T12:44:47Z","date_created":"2019-02-06T07:50:58Z","access_level":"open_access","file_name":"2019_CurrentGenetics_Nikolic.pdf","file_size":776399,"content_type":"application/pdf","creator":"dernst"}],"status":"public","title":"Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system","ddc":["570"],"intvolume":" 65","_id":"138","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_published":"2019-02-01T00:00:00Z","page":"133-138","publication":"Current Genetics","citation":{"chicago":"Nikolic, Nela. “Autoregulation of Bacterial Gene Expression: Lessons from the MazEF Toxin–Antitoxin System.” Current Genetics. Springer, 2019. https://doi.org/10.1007/s00294-018-0879-8.","short":"N. Nikolic, Current Genetics 65 (2019) 133–138.","mla":"Nikolic, Nela. “Autoregulation of Bacterial Gene Expression: Lessons from the MazEF Toxin–Antitoxin System.” Current Genetics, vol. 65, no. 1, Springer, 2019, pp. 133–38, doi:10.1007/s00294-018-0879-8.","ieee":"N. Nikolic, “Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system,” Current Genetics, vol. 65, no. 1. Springer, pp. 133–138, 2019.","apa":"Nikolic, N. (2019). Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. Current Genetics. Springer. https://doi.org/10.1007/s00294-018-0879-8","ista":"Nikolic N. 2019. Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. Current Genetics. 65(1), 133–138.","ama":"Nikolic N. Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. Current Genetics. 2019;65(1):133-138. doi:10.1007/s00294-018-0879-8"}},{"publist_id":"7770","year":"2019","publication_status":"published","publisher":"Elsevier","department":[{"_id":"JuFi"}],"author":[{"orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer","first_name":"Julian L","full_name":"Fischer, Julian L"},{"last_name":"Kneuss","first_name":"Olivier","full_name":"Kneuss, Olivier"}],"date_updated":"2023-09-08T13:25:35Z","date_created":"2018-12-11T11:44:54Z","volume":266,"month":"01","oa":1,"external_id":{"isi":["000449108500010"],"arxiv":["1408.1587"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1408.1587"}],"isi":1,"quality_controlled":"1","doi":"10.1016/j.jde.2018.07.045","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"We construct planar bi-Sobolev mappings whose local volume distortion is bounded from below by a given function f∈Lp with p>1. More precisely, for any 1<q<(p+1)/2 we construct W1,q-bi-Sobolev maps with identity boundary conditions; for f∈L∞, we provide bi-Lipschitz maps. The basic building block of our construction are bi-Lipschitz maps which stretch a given compact subset of the unit square by a given factor while preserving the boundary. The construction of these stretching maps relies on a slight strengthening of the celebrated covering result of Alberti, Csörnyei, and Preiss for measurable planar sets in the case of compact sets. We apply our result to a model functional in nonlinear elasticity, the integrand of which features fast blowup as the Jacobian determinant of the deformation becomes small. For such functionals, the derivation of the equilibrium equations for minimizers requires an additional regularization of test functions, which our maps provide.","lang":"eng"}],"issue":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"151","title":"Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity","status":"public","intvolume":" 266","oa_version":"Preprint","scopus_import":"1","day":"05","article_processing_charge":"No","publication":"Journal of Differential Equations","citation":{"mla":"Fischer, Julian L., and Olivier Kneuss. “Bi-Sobolev Solutions to the Prescribed Jacobian Inequality in the Plane with L p Data and Applications to Nonlinear Elasticity.” Journal of Differential Equations, vol. 266, no. 1, Elsevier, 2019, pp. 257–311, doi:10.1016/j.jde.2018.07.045.","short":"J.L. Fischer, O. Kneuss, Journal of Differential Equations 266 (2019) 257–311.","chicago":"Fischer, Julian L, and Olivier Kneuss. “Bi-Sobolev Solutions to the Prescribed Jacobian Inequality in the Plane with L p Data and Applications to Nonlinear Elasticity.” Journal of Differential Equations. Elsevier, 2019. https://doi.org/10.1016/j.jde.2018.07.045.","ama":"Fischer JL, Kneuss O. Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity. Journal of Differential Equations. 2019;266(1):257-311. doi:10.1016/j.jde.2018.07.045","ista":"Fischer JL, Kneuss O. 2019. Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity. Journal of Differential Equations. 266(1), 257–311.","ieee":"J. L. Fischer and O. Kneuss, “Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity,” Journal of Differential Equations, vol. 266, no. 1. Elsevier, pp. 257–311, 2019.","apa":"Fischer, J. L., & Kneuss, O. (2019). Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity. Journal of Differential Equations. Elsevier. https://doi.org/10.1016/j.jde.2018.07.045"},"page":"257 - 311","date_published":"2019-01-05T00:00:00Z"},{"author":[{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","first_name":"Nicole","last_name":"Amberg","full_name":"Amberg, Nicole"},{"orcid":"0000-0002-7903-3010","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","last_name":"Laukoter","first_name":"Susanne","full_name":"Laukoter, Susanne"},{"first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"}],"volume":149,"date_updated":"2023-09-11T13:40:26Z","date_created":"2018-12-11T11:44:14Z","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","year":"2019","publisher":"Wiley","department":[{"_id":"SiHi"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-14T12:45:45Z","doi":"10.1111/jnc.14601","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000462680200002"]},"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","grant_number":"RGP0053/2014","_id":"25D7962E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Molecular Mechanisms of Cerebral Cortex Development","_id":"25D61E48-B435-11E9-9278-68D0E5697425","grant_number":"618444"},{"_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"isi":1,"quality_controlled":"1","month":"04","oa_version":"Published Version","file":[{"file_name":"2019_Wiley_Amberg.pdf","access_level":"open_access","content_type":"application/pdf","file_size":889709,"creator":"kschuh","relation":"main_file","file_id":"7239","date_created":"2020-01-07T13:35:52Z","date_updated":"2020-07-14T12:45:45Z","checksum":"db027721a95d36f5de36aadcd0bdf7e6"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"27","intvolume":" 149","title":"Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex","status":"public","ddc":["570"],"issue":"1","abstract":[{"lang":"eng","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."}],"type":"journal_article","date_published":"2019-04-01T00:00:00Z","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","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.","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.","mla":"Amberg, Nicole, et al. “Epigenetic Cues Modulating the Generation of Cell Type Diversity in the Cerebral Cortex.” Journal of Neurochemistry, vol. 149, no. 1, Wiley, 2019, pp. 12–26, doi:10.1111/jnc.14601.","short":"N. Amberg, S. Laukoter, S. Hippenmeyer, Journal of Neurochemistry 149 (2019) 12–26.","chicago":"Amberg, Nicole, Susanne Laukoter, and Simon Hippenmeyer. “Epigenetic Cues Modulating the Generation of Cell Type Diversity in the Cerebral Cortex.” Journal of Neurochemistry. Wiley, 2019. https://doi.org/10.1111/jnc.14601."},"publication":"Journal of Neurochemistry","page":"12-26","article_type":"review","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1"},{"file":[{"date_updated":"2020-10-21T07:18:35Z","date_created":"2020-10-21T07:18:35Z","success":1,"checksum":"e38523787b3bc84006f2793de99ad70f","file_id":"8685","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":71590590,"file_name":"2018_NatureCellBio_Petridou_accepted.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","title":"Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling","status":"public","ddc":["570"],"intvolume":" 21","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5789","abstract":[{"lang":"eng","text":"Tissue morphogenesis is driven by mechanical forces that elicit changes in cell size, shape and motion. The extent by which forces deform tissues critically depends on the rheological properties of the recipient tissue. Yet, whether and how dynamic changes in tissue rheology affect tissue morphogenesis and how they are regulated within the developing organism remain unclear. Here, we show that blastoderm spreading at the onset of zebrafish morphogenesis relies on a rapid, pronounced and spatially patterned tissue fluidization. Blastoderm fluidization is temporally controlled by mitotic cell rounding-dependent cell–cell contact disassembly during the last rounds of cell cleavages. Moreover, fluidization is spatially restricted to the central blastoderm by local activation of non-canonical Wnt signalling within the blastoderm margin, increasing cell cohesion and thereby counteracting the effect of mitotic rounding on contact disassembly. Overall, our results identify a fluidity transition mediated by loss of cell cohesion as a critical regulator of embryo morphogenesis."}],"type":"journal_article","date_published":"2019-02-01T00:00:00Z","article_type":"original","page":"169–178","publication":"Nature Cell Biology","citation":{"mla":"Petridou, Nicoletta, et al. “Fluidization-Mediated Tissue Spreading by Mitotic Cell Rounding and Non-Canonical Wnt Signalling.” Nature Cell Biology, vol. 21, Nature Publishing Group, 2019, pp. 169–178, doi:10.1038/s41556-018-0247-4.","short":"N. Petridou, S. Grigolon, G. Salbreux, E.B. Hannezo, C.-P.J. Heisenberg, Nature Cell Biology 21 (2019) 169–178.","chicago":"Petridou, Nicoletta, Silvia Grigolon, Guillaume Salbreux, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Fluidization-Mediated Tissue Spreading by Mitotic Cell Rounding and Non-Canonical Wnt Signalling.” Nature Cell Biology. Nature Publishing Group, 2019. https://doi.org/10.1038/s41556-018-0247-4.","ama":"Petridou N, Grigolon S, Salbreux G, Hannezo EB, Heisenberg C-PJ. Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. Nature Cell Biology. 2019;21:169–178. doi:10.1038/s41556-018-0247-4","ista":"Petridou N, Grigolon S, Salbreux G, Hannezo EB, Heisenberg C-PJ. 2019. Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. Nature Cell Biology. 21, 169–178.","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"},"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_created":"2018-12-30T22:59:15Z","date_updated":"2023-09-11T14:03:28Z","volume":21,"author":[{"full_name":"Petridou, Nicoletta","first_name":"Nicoletta","last_name":"Petridou","id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8451-1195"},{"last_name":"Grigolon","first_name":"Silvia","full_name":"Grigolon, Silvia"},{"full_name":"Salbreux, Guillaume","first_name":"Guillaume","last_name":"Salbreux"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/when-a-fish-becomes-fluid/","relation":"press_release","description":"News on IST Homepage"}]},"publication_status":"published","department":[{"_id":"CaHe"},{"_id":"EdHa"}],"publisher":"Nature Publishing Group","year":"2019","pmid":1,"file_date_updated":"2020-10-21T07:18:35Z","ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41556-018-0247-4","isi":1,"quality_controlled":"1","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573"},{"_id":"253E54C8-B435-11E9-9278-68D0E5697425","grant_number":"ALTF710-2016","name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants (EMBO fellowship)"}],"external_id":{"pmid":["30559456"],"isi":["000457468300011"]},"oa":1,"month":"02","publication_identifier":{"issn":["14657392"]}},{"month":"02","publication_identifier":{"eissn":["1091-6490"]},"doi":"10.1073/pnas.1812015116","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1812015116"}],"external_id":{"pmid":[" 30728300"],"isi":["000459074400013"],"arxiv":["1806.10823"]},"isi":1,"quality_controlled":"1","author":[{"first_name":"Moritz","last_name":"Lang","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","full_name":"Lang, Moritz"},{"full_name":"Shkolnikov, Mikhail","last_name":"Shkolnikov","first_name":"Mikhail","orcid":"0000-0002-4310-178X","id":"35084A62-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Webpage","url":"https://ist.ac.at/en/news/famous-sandpile-model-shown-to-move-like-a-traveling-sand-dune/"}]},"date_created":"2018-12-11T11:45:08Z","date_updated":"2023-09-11T14:09:34Z","volume":116,"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","publisher":"National Academy of Sciences","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"TaHa"}],"day":"19","article_processing_charge":"No","scopus_import":"1","date_published":"2019-02-19T00:00:00Z","publication":"Proceedings of the National Academy of Sciences","citation":{"short":"M. Lang, M. Shkolnikov, Proceedings of the National Academy of Sciences 116 (2019) 2821–2830.","mla":"Lang, Moritz, and Mikhail Shkolnikov. “Harmonic Dynamics of the Abelian Sandpile.” Proceedings of the National Academy of Sciences, vol. 116, no. 8, National Academy of Sciences, 2019, pp. 2821–30, doi:10.1073/pnas.1812015116.","chicago":"Lang, Moritz, and Mikhail Shkolnikov. “Harmonic Dynamics of the Abelian Sandpile.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1812015116.","ama":"Lang M, Shkolnikov M. Harmonic dynamics of the Abelian sandpile. Proceedings of the National Academy of Sciences. 2019;116(8):2821-2830. doi:10.1073/pnas.1812015116","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."},"article_type":"original","page":"2821-2830","abstract":[{"lang":"eng","text":"The abelian sandpile serves as a model to study self-organized criticality, a phenomenon occurring in biological, physical and social processes. The identity of the abelian group is a fractal composed of self-similar patches, and its limit is subject of extensive collaborative research. Here, we analyze the evolution of the sandpile identity under harmonic fields of different orders. We show that this evolution corresponds to periodic cycles through the abelian group characterized by the smooth transformation and apparent conservation of the patches constituting the identity. The dynamics induced by second and third order harmonics resemble smooth stretchings, respectively translations, of the identity, while the ones induced by fourth order harmonics resemble magnifications and rotations. Starting with order three, the dynamics pass through extended regions of seemingly random configurations which spontaneously reassemble into accentuated patterns. We show that the space of harmonic functions projects to the extended analogue of the sandpile group, thus providing a set of universal coordinates identifying configurations between different domains. Since the original sandpile group is a subgroup of the extended one, this directly implies that it admits a natural renormalization. Furthermore, we show that the harmonic fields can be induced by simple Markov processes, and that the corresponding stochastic dynamics show remarkable robustness over hundreds of periods. Finally, we encode information into seemingly random configurations, and decode this information with an algorithm requiring minimal prior knowledge. Our results suggest that harmonic fields might split the sandpile group into sub-sets showing different critical coefficients, and that it might be possible to extend the fractal structure of the identity beyond the boundaries of its domain. "}],"issue":"8","type":"journal_article","oa_version":"Published Version","_id":"196","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Harmonic dynamics of the Abelian sandpile","intvolume":" 116"},{"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."}],"extern":"1","type":"conference","author":[{"orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco","full_name":"Locatello, Francesco"},{"last_name":"Tschannen","first_name":"Michael","full_name":"Tschannen, Michael"},{"full_name":"Bauer, Stefan","last_name":"Bauer","first_name":"Stefan"},{"last_name":"Rätsch","first_name":"Gunnar","full_name":"Rätsch, Gunnar"},{"last_name":"Schölkopf","first_name":"Bernhard","full_name":"Schölkopf, Bernhard"},{"first_name":"Olivier","last_name":"Bachem","full_name":"Bachem, Olivier"}],"oa_version":"Preprint","date_updated":"2023-09-12T07:01:34Z","date_created":"2023-08-22T14:06:37Z","_id":"14184","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"FrLo"}],"status":"public","publication_status":"published","title":"Disentangling factors of variation using few labels","article_processing_charge":"No","day":"20","month":"12","scopus_import":"1","date_published":"2019-12-20T00:00:00Z","conference":{"end_date":"2020-05-01","start_date":"2020-04-26","location":"Virtual","name":"ICLR: International Conference on Learning Representations"},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.01258"}],"external_id":{"arxiv":["1905.01258"]},"citation":{"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.","apa":"Locatello, F., Tschannen, M., Bauer, S., Rätsch, G., Schölkopf, B., & Bachem, O. (2019). Disentangling factors of variation using few labels. In 8th International Conference on Learning Representations. Virtual.","ieee":"F. Locatello, M. Tschannen, S. Bauer, G. Rätsch, B. Schölkopf, and O. Bachem, “Disentangling factors of variation using few labels,” in 8th International Conference on Learning Representations, Virtual, 2019.","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."},"oa":1,"publication":"8th International Conference on Learning Representations","quality_controlled":"1"},{"extern":"1","year":"2019","publication_status":"published","publisher":"ML Research Press","department":[{"_id":"FrLo"}],"author":[{"last_name":"Gresele","first_name":"Luigi","full_name":"Gresele, Luigi"},{"full_name":"Rubenstein, Paul K.","last_name":"Rubenstein","first_name":"Paul K."},{"full_name":"Mehrjou, Arash","first_name":"Arash","last_name":"Mehrjou"},{"full_name":"Locatello, Francesco","first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683"},{"full_name":"Schölkopf, Bernhard","last_name":"Schölkopf","first_name":"Bernhard"}],"date_updated":"2023-09-12T08:07:38Z","date_created":"2023-08-22T14:08:35Z","volume":115,"month":"05","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.06642"}],"external_id":{"arxiv":["1905.06642"]},"oa":1,"quality_controlled":"1","conference":{"name":"UAI: Uncertainty in Artificial Intelligence","end_date":"2019-07-25","location":"Tel Aviv, Israel","start_date":"2019-07-22"},"language":[{"iso":"eng"}],"type":"conference","alternative_title":["PMLR"],"abstract":[{"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.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14189","title":"The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA","status":"public","intvolume":" 115","oa_version":"Preprint","scopus_import":"1","day":"16","article_processing_charge":"No","publication":"Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence","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.","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.","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.","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.","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.","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."},"page":"217-227","date_published":"2019-05-16T00:00:00Z"},{"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"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14197","intvolume":" 32","title":"On the fairness of disentangled representations","status":"public","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"08","citation":{"ama":"Locatello F, Abbati G, Rainforth T, Bauer S, Schölkopf B, Bachem O. On the fairness of disentangled representations. In: Advances in Neural Information Processing Systems. Vol 32. ; 2019:14611–14624.","ista":"Locatello F, Abbati G, Rainforth T, Bauer S, Schölkopf B, Bachem O. 2019. On the fairness of disentangled representations. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32, 14611–14624.","ieee":"F. Locatello, G. Abbati, T. Rainforth, S. Bauer, B. Schölkopf, and O. Bachem, “On the fairness of disentangled representations,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32, pp. 14611–14624.","apa":"Locatello, F., Abbati, G., Rainforth, T., Bauer, S., Schölkopf, B., & Bachem, O. (2019). On the fairness of disentangled representations. In Advances in Neural Information Processing Systems (Vol. 32, pp. 14611–14624). Vancouver, Canada.","mla":"Locatello, Francesco, et al. “On the Fairness of Disentangled Representations.” Advances in Neural Information Processing Systems, vol. 32, 2019, pp. 14611–14624.","short":"F. Locatello, G. Abbati, T. Rainforth, S. Bauer, B. Schölkopf, O. Bachem, in:, Advances in Neural Information Processing Systems, 2019, pp. 14611–14624.","chicago":"Locatello, Francesco, Gabriele Abbati, Tom Rainforth, Stefan Bauer, Bernhard Schölkopf, and Olivier Bachem. “On the Fairness of Disentangled Representations.” In Advances in Neural Information Processing Systems, 32:14611–14624, 2019."},"publication":"Advances in Neural Information Processing Systems","page":"14611–14624","date_published":"2019-12-08T00:00:00Z","extern":"1","year":"2019","department":[{"_id":"FrLo"}],"publication_status":"published","author":[{"full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco"},{"full_name":"Abbati, Gabriele","first_name":"Gabriele","last_name":"Abbati"},{"full_name":"Rainforth, Tom","first_name":"Tom","last_name":"Rainforth"},{"first_name":"Stefan","last_name":"Bauer","full_name":"Bauer, Stefan"},{"first_name":"Bernhard","last_name":"Schölkopf","full_name":"Schölkopf, Bernhard"},{"full_name":"Bachem, Olivier","first_name":"Olivier","last_name":"Bachem"}],"volume":32,"date_updated":"2023-09-12T09:37:22Z","date_created":"2023-08-22T14:12:28Z","publication_identifier":{"isbn":["9781713807933"]},"month":"12","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.13662"}],"external_id":{"arxiv":["1905.13662"]},"quality_controlled":"1","conference":{"name":"NeurIPS: Neural Information Processing Systems","start_date":"2019-12-08","location":"Vancouver, Canada","end_date":"2019-12-14"},"language":[{"iso":"eng"}]},{"scopus_import":"1","day":"29","article_processing_charge":"No","page":"14291–14301","publication":"Advances in Neural Information Processing Systems","citation":{"mla":"Locatello, Francesco, et al. “Stochastic Frank-Wolfe for Composite Convex Minimization.” Advances in Neural Information Processing Systems, vol. 32, 2019, pp. 14291–14301.","short":"F. Locatello, A. Yurtsever, O. Fercoq, V. Cevher, in:, Advances in Neural Information Processing Systems, 2019, pp. 14291–14301.","chicago":"Locatello, Francesco, Alp Yurtsever, Olivier Fercoq, and Volkan Cevher. “Stochastic Frank-Wolfe for Composite Convex Minimization.” In Advances in Neural Information Processing Systems, 32:14291–14301, 2019.","ama":"Locatello F, Yurtsever A, Fercoq O, Cevher V. Stochastic Frank-Wolfe for composite convex minimization. In: Advances in Neural Information Processing Systems. Vol 32. ; 2019:14291–14301.","ista":"Locatello F, Yurtsever A, Fercoq O, Cevher V. 2019. Stochastic Frank-Wolfe for composite convex minimization. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32, 14291–14301.","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."},"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."}],"status":"public","title":"Stochastic Frank-Wolfe for composite convex minimization","intvolume":" 32","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14191","oa_version":"Preprint","month":"12","publication_identifier":{"isbn":["9781713807933"]},"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1901.10348"]},"main_file_link":[{"url":"https://arxiv.org/abs/1901.10348","open_access":"1"}],"language":[{"iso":"eng"}],"conference":{"name":"NeurIPS: Neural Information Processing Systems","end_date":"2019-12-14","location":"Vancouver, Canada","start_date":"2019-12-08"},"extern":"1","publication_status":"published","department":[{"_id":"FrLo"}],"year":"2019","date_updated":"2023-09-12T08:48:45Z","date_created":"2023-08-22T14:09:35Z","volume":32,"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"}]},{"publication":"Advances in Neural Information Processing Systems","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1905.12506"}],"oa":1,"external_id":{"arxiv":["1905.12506"]},"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."},"quality_controlled":"1","conference":{"end_date":"2019-12-14","start_date":"2019-12-08","location":"Vancouver, Canada","name":"NeurIPS: Neural Information Processing Systems"},"date_published":"2019-05-29T00:00:00Z","language":[{"iso":"eng"}],"day":"29","month":"05","publication_identifier":{"isbn":["9781713807933"]},"article_processing_charge":"No","_id":"14193","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Are disentangled representations helpful for abstract visual reasoning?","publication_status":"published","department":[{"_id":"FrLo"}],"intvolume":" 32","author":[{"last_name":"Steenkiste","first_name":"Sjoerd van","full_name":"Steenkiste, Sjoerd van"},{"orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco","full_name":"Locatello, Francesco"},{"full_name":"Schmidhuber, Jürgen","last_name":"Schmidhuber","first_name":"Jürgen"},{"first_name":"Olivier","last_name":"Bachem","full_name":"Bachem, Olivier"}],"date_created":"2023-08-22T14:09:53Z","date_updated":"2023-09-12T09:02:43Z","oa_version":"Preprint","volume":32,"type":"conference","abstract":[{"lang":"eng","text":"A disentangled representation encodes information about the salient factors\r\nof variation in the data independently. Although it is often argued that this\r\nrepresentational format is useful in learning to solve many real-world\r\ndown-stream tasks, there is little empirical evidence that supports this claim.\r\nIn this paper, we conduct a large-scale study that investigates whether\r\ndisentangled representations are more suitable for abstract reasoning tasks.\r\nUsing two new tasks similar to Raven's Progressive Matrices, we evaluate the\r\nusefulness of the representations learned by 360 state-of-the-art unsupervised\r\ndisentanglement models. Based on these representations, we train 3600 abstract\r\nreasoning models and observe that disentangled representations do in fact lead\r\nto better down-stream performance. In particular, they enable quicker learning\r\nusing fewer samples."}],"extern":"1"},{"article_processing_charge":"No","day":"09","scopus_import":"1","date_published":"2019-06-09T00:00:00Z","page":"4114-4124","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.","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.","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.","mla":"Locatello, Francesco, et al. “Challenging Common Assumptions in the Unsupervised Learning of Disentangled Representations.” Proceedings of the 36th International Conference on Machine Learning, vol. 97, ML Research Press, 2019, pp. 4114–24.","short":"F. Locatello, S. Bauer, M. Lucic, G. Rätsch, S. Gelly, B. Schölkopf, O. Bachem, in:, Proceedings of the 36th International Conference on Machine Learning, ML Research Press, 2019, pp. 4114–4124.","chicago":"Locatello, Francesco, Stefan Bauer, Mario Lucic, Gunnar Rätsch, Sylvain Gelly, Bernhard Schölkopf, and Olivier Bachem. “Challenging Common Assumptions in the Unsupervised Learning of Disentangled Representations.” In Proceedings of the 36th International Conference on Machine Learning, 97:4114–24. ML Research Press, 2019."},"publication":"Proceedings of the 36th International Conference on Machine Learning","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."}],"type":"conference","oa_version":"Preprint","intvolume":" 97","status":"public","title":"Challenging common assumptions in the unsupervised learning of disentangled representations","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14200","month":"06","language":[{"iso":"eng"}],"conference":{"end_date":"2019-06-15","location":"Long Beach, CA, United States","start_date":"2019-06-10","name":"International Conference on Machine Learning"},"quality_controlled":"1","external_id":{"arxiv":["1811.12359"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.12359"}],"oa":1,"extern":"1","volume":97,"date_created":"2023-08-22T14:13:08Z","date_updated":"2023-09-13T07:45:30Z","author":[{"orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco","full_name":"Locatello, Francesco"},{"full_name":"Bauer, Stefan","last_name":"Bauer","first_name":"Stefan"},{"first_name":"Mario","last_name":"Lucic","full_name":"Lucic, Mario"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"},{"full_name":"Gelly, Sylvain","first_name":"Sylvain","last_name":"Gelly"},{"full_name":"Schölkopf, Bernhard","last_name":"Schölkopf","first_name":"Bernhard"},{"full_name":"Bachem, Olivier","first_name":"Olivier","last_name":"Bachem"}],"department":[{"_id":"FrLo"}],"publisher":"ML Research Press","publication_status":"published","year":"2019"},{"oa_version":"Submitted Version","file":[{"date_updated":"2020-10-09T11:00:05Z","date_created":"2020-10-09T11:00:05Z","success":1,"checksum":"614c337d6424ccd3d48d1b1f9513510d","file_id":"8641","relation":"main_file","creator":"bkavcic","content_type":"application/pdf","file_size":5370762,"file_name":"lmt_sftmtr_V8.pdf","access_level":"open_access"}],"ddc":["530"],"status":"public","title":"Limiting shapes of confined lipid vesicles","intvolume":" 15","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5817","abstract":[{"lang":"eng","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."}],"issue":"4","type":"journal_article","date_published":"2019-01-10T00:00:00Z","article_type":"original","page":"602-614","publication":"Soft Matter","citation":{"chicago":"Kavcic, Bor, A. Sakashita, H. Noguchi, and P. Ziherl. “Limiting Shapes of Confined Lipid Vesicles.” Soft Matter. Royal Society of Chemistry, 2019. https://doi.org/10.1039/c8sm01956h.","short":"B. Kavcic, A. Sakashita, H. Noguchi, P. Ziherl, Soft Matter 15 (2019) 602–614.","mla":"Kavcic, Bor, et al. “Limiting Shapes of Confined Lipid Vesicles.” Soft Matter, vol. 15, no. 4, Royal Society of Chemistry, 2019, pp. 602–14, doi:10.1039/c8sm01956h.","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.","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"},"day":"10","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_created":"2019-01-11T07:37:47Z","date_updated":"2023-09-13T08:47:16Z","volume":15,"author":[{"full_name":"Kavcic, Bor","last_name":"Kavcic","first_name":"Bor","orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sakashita","first_name":"A.","full_name":"Sakashita, A."},{"full_name":"Noguchi, H.","first_name":"H.","last_name":"Noguchi"},{"full_name":"Ziherl, P.","first_name":"P.","last_name":"Ziherl"}],"publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"Royal Society of Chemistry","year":"2019","pmid":1,"license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","file_date_updated":"2020-10-09T11:00:05Z","language":[{"iso":"eng"}],"doi":"10.1039/c8sm01956h","quality_controlled":"1","isi":1,"external_id":{"isi":["000457329700003"],"pmid":["30629082"]},"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,"month":"01","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]}},{"article_type":"original","publication":"Calculus of Variations and Partial Differential Equations","citation":{"apa":"Erbar, M., Maas, J., & Wirth, M. (2019). On the geometry of geodesics in discrete optimal transport. Calculus of Variations and Partial Differential Equations. Springer. https://doi.org/10.1007/s00526-018-1456-1","ieee":"M. Erbar, J. Maas, and M. Wirth, “On the geometry of geodesics in discrete optimal transport,” Calculus of Variations and Partial Differential Equations, vol. 58, no. 1. Springer, 2019.","ista":"Erbar M, Maas J, Wirth M. 2019. On the geometry of geodesics in discrete optimal transport. Calculus of Variations and Partial Differential Equations. 58(1), 19.","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","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.","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."},"date_published":"2019-02-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","title":"On the geometry of geodesics in discrete optimal transport","ddc":["510"],"status":"public","intvolume":" 58","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"73","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5895","date_updated":"2020-07-14T12:47:55Z","date_created":"2019-01-28T15:37:11Z","checksum":"ba05ac2d69de4c58d2cd338b63512798","file_name":"2018_Calculus_Erbar.pdf","access_level":"open_access","file_size":645565,"content_type":"application/pdf","creator":"dernst"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We consider the space of probability measures on a discrete set X, endowed with a dynamical optimal transport metric. Given two probability measures supported in a subset Y⊆X, it is natural to ask whether they can be connected by a constant speed geodesic with support in Y at all times. Our main result answers this question affirmatively, under a suitable geometric condition on Y introduced in this paper. The proof relies on an extension result for subsolutions to discrete Hamilton-Jacobi equations, which is of independent interest."}],"issue":"1","quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"},{"name":"Taming Complexity in Partial Di erential Systems","call_identifier":"FWF","_id":"260482E2-B435-11E9-9278-68D0E5697425","grant_number":" F06504"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"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":["1805.06040"],"isi":["000452849400001"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00526-018-1456-1","month":"02","publication_identifier":{"issn":["09442669"]},"publication_status":"published","department":[{"_id":"JaMa"}],"publisher":"Springer","year":"2019","date_created":"2018-12-11T11:44:29Z","date_updated":"2023-09-13T09:12:35Z","volume":58,"author":[{"full_name":"Erbar, Matthias","last_name":"Erbar","first_name":"Matthias"},{"full_name":"Maas, Jan","first_name":"Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338"},{"full_name":"Wirth, Melchior","last_name":"Wirth","first_name":"Melchior"}],"article_number":"19","file_date_updated":"2020-07-14T12:47:55Z","ec_funded":1},{"extern":"1","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."}],"type":"conference","volume":32,"oa_version":"Preprint","date_updated":"2023-09-13T09:46:38Z","date_created":"2023-08-22T14:09:13Z","author":[{"last_name":"Gondal","first_name":"Muhammad Waleed","full_name":"Gondal, Muhammad Waleed"},{"first_name":"Manuel","last_name":"Wüthrich","full_name":"Wüthrich, Manuel"},{"full_name":"Miladinović, Đorđe","last_name":"Miladinović","first_name":"Đorđe"},{"full_name":"Locatello, Francesco","last_name":"Locatello","first_name":"Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"full_name":"Breidt, Martin","first_name":"Martin","last_name":"Breidt"},{"full_name":"Volchkov, Valentin","last_name":"Volchkov","first_name":"Valentin"},{"first_name":"Joel","last_name":"Akpo","full_name":"Akpo, Joel"},{"full_name":"Bachem, Olivier","first_name":"Olivier","last_name":"Bachem"},{"full_name":"Schölkopf, Bernhard","first_name":"Bernhard","last_name":"Schölkopf"},{"last_name":"Bauer","first_name":"Stefan","full_name":"Bauer, Stefan"}],"department":[{"_id":"FrLo"}],"intvolume":" 32","status":"public","title":"On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset","publication_status":"published","_id":"14190","year":"2019","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"isbn":["9781713807933"]},"article_processing_charge":"No","month":"06","day":"07","language":[{"iso":"eng"}],"date_published":"2019-06-07T00:00:00Z","conference":{"location":"Vancouver, Canada","start_date":"2019-12-08","end_date":"2019-12-14","name":"NeurIPS: Neural Information Processing Systems"},"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1906.03292"}],"external_id":{"arxiv":["1906.03292"]},"citation":{"chicago":"Gondal, Muhammad Waleed, Manuel Wüthrich, Đorđe Miladinović, Francesco Locatello, Martin Breidt, Valentin Volchkov, Joel Akpo, Olivier Bachem, Bernhard Schölkopf, and Stefan Bauer. “On the Transfer of Inductive Bias from Simulation to the Real World: A New Disentanglement Dataset.” In Advances in Neural Information Processing Systems, Vol. 32, 2019.","mla":"Gondal, Muhammad Waleed, et al. “On the Transfer of Inductive Bias from Simulation to the Real World: A New Disentanglement Dataset.” Advances in Neural Information Processing Systems, vol. 32, 2019.","short":"M.W. Gondal, M. Wüthrich, Đ. Miladinović, F. Locatello, M. Breidt, V. Volchkov, J. Akpo, O. Bachem, B. Schölkopf, S. Bauer, in:, Advances in Neural Information Processing Systems, 2019.","ista":"Gondal MW, Wüthrich M, Miladinović Đ, Locatello F, Breidt M, Volchkov V, Akpo J, Bachem O, Schölkopf B, Bauer S. 2019. On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32.","apa":"Gondal, M. W., Wüthrich, M., Miladinović, Đ., Locatello, F., Breidt, M., Volchkov, V., … Bauer, S. (2019). On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset. In Advances in Neural Information Processing Systems (Vol. 32). Vancouver, Canada.","ieee":"M. W. Gondal et al., “On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32.","ama":"Gondal MW, Wüthrich M, Miladinović Đ, et al. On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset. In: Advances in Neural Information Processing Systems. Vol 32. ; 2019."},"publication":"Advances in Neural Information Processing Systems"},{"day":"01","scopus_import":1,"date_published":"2019-10-01T00:00:00Z","publication":"ACM Transactions on Algorithms","citation":{"short":"H. Akitaya, R. Fulek, C. Tóth, ACM Transactions on Algorithms 15 (2019).","mla":"Akitaya, Hugo, et al. “Recognizing Weak Embeddings of Graphs.” ACM Transactions on Algorithms, vol. 15, no. 4, 50, ACM, 2019, doi:10.1145/3344549.","chicago":"Akitaya, Hugo, Radoslav Fulek, and Csaba Tóth. “Recognizing Weak Embeddings of Graphs.” ACM Transactions on Algorithms. ACM, 2019. https://doi.org/10.1145/3344549.","ama":"Akitaya H, Fulek R, Tóth C. Recognizing weak embeddings of graphs. ACM Transactions on Algorithms. 2019;15(4). doi:10.1145/3344549","apa":"Akitaya, H., Fulek, R., & Tóth, C. (2019). Recognizing weak embeddings of graphs. ACM Transactions on Algorithms. ACM. https://doi.org/10.1145/3344549","ieee":"H. Akitaya, R. Fulek, and C. Tóth, “Recognizing weak embeddings of graphs,” ACM Transactions on Algorithms, vol. 15, no. 4. ACM, 2019.","ista":"Akitaya H, Fulek R, Tóth C. 2019. Recognizing weak embeddings of graphs. ACM Transactions on Algorithms. 15(4), 50."},"article_type":"original","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","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6982","title":"Recognizing weak embeddings of graphs","status":"public","intvolume":" 15","month":"10","doi":"10.1145/3344549","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1709.09209"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.09209"}],"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs","grant_number":"M02281","_id":"261FA626-B435-11E9-9278-68D0E5697425"}],"article_number":"50","author":[{"last_name":"Akitaya","first_name":"Hugo","full_name":"Akitaya, Hugo"},{"orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","first_name":"Radoslav","full_name":"Fulek, Radoslav"},{"last_name":"Tóth","first_name":"Csaba","full_name":"Tóth, Csaba"}],"related_material":{"record":[{"id":"309","status":"public","relation":"earlier_version"}]},"date_updated":"2023-09-15T12:19:31Z","date_created":"2019-11-04T15:45:17Z","volume":15,"year":"2019","publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"ACM"},{"file_date_updated":"2020-07-14T12:47:43Z","year":"2019","department":[{"_id":"ToHe"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"631"},{"status":"public","relation":"part_of_dissertation","id":"647"},{"id":"140","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Giacobbe, Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8180-0904","first_name":"Mirco","last_name":"Giacobbe"}],"date_created":"2019-09-22T14:08:44Z","date_updated":"2023-09-19T09:30:43Z","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":[{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"}],"degree_awarded":"PhD","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Hybrid automata combine finite automata and dynamical systems, and model the interaction of digital with physical systems. Formal analysis that can guarantee the safety of all behaviors or rigorously witness failures, while unsolvable in general, has been tackled algorithmically using, e.g., abstraction, bounded model-checking, assisted theorem proving.\r\nNevertheless, very few methods have addressed the time-unbounded reachability analysis of hybrid automata and, for current sound and automatic tools, scalability remains critical. We develop methods for the polyhedral abstraction of hybrid automata, which construct coarse overapproximations and tightens them incrementally, in a CEGAR fashion. We use template polyhedra, i.e., polyhedra whose facets are normal to a given set of directions.\r\nWhile, previously, directions were given by the user, we introduce (1) the first method\r\nfor computing template directions from spurious counterexamples, so as to generalize and\r\neliminate them. The method applies naturally to convex hybrid automata, i.e., hybrid\r\nautomata with (possibly non-linear) convex constraints on derivatives only, while for linear\r\nODE requires further abstraction. Specifically, we introduce (2) the conic abstractions,\r\nwhich, partitioning the state space into appropriate (possibly non-uniform) cones, divide\r\ncurvy trajectories into relatively straight sections, suitable for polyhedral abstractions.\r\nFinally, we introduce (3) space-time interpolation, which, combining interval arithmetic\r\nand template refinement, computes appropriate (possibly non-uniform) time partitioning\r\nand template directions along spurious trajectories, so as to eliminate them.\r\nWe obtain sound and automatic methods for the reachability analysis over dense\r\nand unbounded time of convex hybrid automata and hybrid automata with linear ODE.\r\nWe build prototype tools and compare—favorably—our methods against the respective\r\nstate-of-the-art tools, on several benchmarks.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6894","status":"public","title":"Automatic time-unbounded reachability analysis of hybrid systems","ddc":["000"],"oa_version":"Published Version","file":[{"file_size":4100685,"content_type":"application/pdf","creator":"mgiacobbe","file_name":"giacobbe_thesis.pdf","access_level":"open_access","date_created":"2019-09-27T14:15:05Z","date_updated":"2020-07-14T12:47:43Z","checksum":"773beaf4a85dc2acc2c12b578fbe1965","relation":"main_file","file_id":"6916"},{"file_id":"6917","relation":"source_file","checksum":"97f1c3da71feefd27e6e625d32b4c75b","date_created":"2019-09-27T14:22:04Z","date_updated":"2020-07-14T12:47:43Z","access_level":"closed","file_name":"giacobbe_thesis_src.tar.gz","creator":"mgiacobbe","content_type":"application/gzip","file_size":7959732}],"article_processing_charge":"No","has_accepted_license":"1","day":"30","citation":{"ama":"Giacobbe M. Automatic time-unbounded reachability analysis of hybrid systems. 2019. doi:10.15479/AT:ISTA:6894","ista":"Giacobbe M. 2019. Automatic time-unbounded reachability analysis of hybrid systems. Institute of Science and Technology Austria.","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.","mla":"Giacobbe, Mirco. Automatic Time-Unbounded Reachability Analysis of Hybrid Systems. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6894.","short":"M. Giacobbe, Automatic Time-Unbounded Reachability Analysis of Hybrid Systems, Institute of Science and Technology Austria, 2019.","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."},"page":"132","date_published":"2019-09-30T00:00:00Z"},{"oa_version":"Published Version","date_updated":"2023-09-19T10:06:07Z","date_created":"2021-08-06T12:03:50Z","related_material":{"record":[{"id":"40","status":"public","relation":"used_in_publication"}]},"author":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"department":[{"_id":"NiBa"}],"publisher":"Dryad","title":"Data from: The consequences of an introgression event","status":"public","_id":"9805","year":"2019","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"lang":"eng","text":"The spread of adaptive alleles is fundamental to evolution, and in theory, this process is well‐understood. However, only rarely can we follow this process—whether it originates from the spread of a new mutation, or by introgression from another population. In this issue of Molecular Ecology, Hanemaaijer et al. (2018) report on a 25‐year long study of the mosquitoes Anopheles gambiae (Figure 1) and Anopheles coluzzi in Mali, based on genotypes at 15 single‐nucleotide polymorphism (SNP). The species are usually reproductively isolated from each other, but in 2002 and 2006, bursts of hybridization were observed, when F1 hybrids became abundant. Alleles backcrossed from A. gambiae into A. coluzzi, but after the first event, these declined over the following years. In contrast, after 2006, an insecticide resistance allele that had established in A. gambiae spread into A. coluzzi, and rose to high frequency there, over 6 years (~75 generations). Whole genome sequences of 74 individuals showed that A. gambiae SNP from across the genome had become common in the A. coluzzi population, but that most of these were clustered in 34 genes around the resistance locus. A new set of SNP from 25 of these genes were assayed over time; over the 4 years since near‐fixation of the resistance allele; some remained common, whereas others declined. What do these patterns tell us about this introgression event?"}],"type":"research_data_reference","date_published":"2019-01-09T00:00:00Z","doi":"10.5061/dryad.2kb6fh4","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.2kb6fh4"}],"citation":{"ista":"Barton NH. 2019. Data from: The consequences of an introgression event, Dryad, 10.5061/dryad.2kb6fh4.","ieee":"N. H. Barton, “Data from: The consequences of an introgression event.” Dryad, 2019.","apa":"Barton, N. H. (2019). Data from: The consequences of an introgression event. Dryad. https://doi.org/10.5061/dryad.2kb6fh4","ama":"Barton NH. Data from: The consequences of an introgression event. 2019. doi:10.5061/dryad.2kb6fh4","chicago":"Barton, Nicholas H. “Data from: The Consequences of an Introgression Event.” Dryad, 2019. https://doi.org/10.5061/dryad.2kb6fh4.","mla":"Barton, Nicholas H. Data from: The Consequences of an Introgression Event. Dryad, 2019, doi:10.5061/dryad.2kb6fh4.","short":"N.H. Barton, (2019)."},"article_processing_charge":"No","month":"01","day":"09"},{"_id":"8","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 39","status":"public","ddc":["570"],"title":"The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"8596","date_updated":"2020-10-02T09:33:28Z","date_created":"2020-10-02T09:33:28Z","checksum":"8f6925eb4cd1e8747d8ea25929c68de6","success":1,"file_name":"2019_JournNeuroscience_Trebuchet.pdf","access_level":"open_access","content_type":"application/pdf","file_size":9455414,"creator":"dernst"}],"type":"journal_article","issue":"2","abstract":[{"text":"Despite their different origins, Drosophila glia and hemocytes are related cell populations that provide an immune function. Drosophila hemocytes patrol the body cavity and act as macrophages outside the nervous system whereas glia originate from the neuroepithelium and provide the scavenger population of the nervous system. Drosophila glia are hence the functional orthologs of vertebrate microglia, even though the latter are cells of immune origin that subsequently move into the brain during development. Interestingly, the Drosophila immune cells within (glia) and outside the nervous system (hemocytes) require the same transcription factor Glide/Gcm for their development. This raises the issue of how do glia specifically differentiate in the nervous system and hemocytes in the procephalic mesoderm. The Repo homeodomain transcription factor and pan-glial direct target of Glide/Gcm is known to ensure glial terminal differentiation. Here we show that Repo also takes center stage in the process that discriminates between glia and hemocytes. First, Repo expression is repressed in the hemocyte anlagen by mesoderm-specific factors. Second, Repo ectopic activation in the procephalic mesoderm is sufficient to repress the expression of hemocyte-specific genes. Third, the lack of Repo triggers the expression of hemocyte markers in glia. Thus, a complex network of tissue-specific cues biases the potential of Glide/Gcm. These data allow us to revise the concept of fate determinants and help us understand the bases of cell specification. Both sexes were analyzed.SIGNIFICANCE STATEMENTDistinct cell types often require the same pioneer transcription factor, raising the issue of how does one factor trigger different fates. In Drosophila, glia and hemocytes provide a scavenger activity within and outside the nervous system, respectively. While they both require the Glide/Gcm transcription factor, glia originate from the ectoderm, hemocytes from the mesoderm. Here we show that tissue-specific factors inhibit the gliogenic potential of Glide/Gcm in the mesoderm by repressing the expression of the homeodomain protein Repo, a major glial-specific target of Glide/Gcm. Repo expression in turn inhibits the expression of hemocyte-specific genes in the nervous system. These cell-specific networks secure the establishment of the glial fate only in the nervous system and allow cell diversification.","lang":"eng"}],"citation":{"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.","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.","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.","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","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.","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"},"publication":"Journal of Neuroscience","page":"238-255","article_type":"original","date_published":"2019-01-09T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"09","pmid":1,"acknowledgement":"This work was supported by INSERM, CNRS, UDS, Ligue Régionale contre le Cancer, Hôpital de Strasbourg, Association pour la Recherche sur le Cancer (ARC) and Agence Nationale de la Recherche (ANR) grants. P.B.C. was funded by the ANR and by the ARSEP (Fondation pour l'Aide à la Recherche sur la Sclérose en Plaques), and G.T. by governmental and ARC fellowships. This work was also supported by grants from the Ataxia UK (2491) and the NC3R (NC/L000199/1) awarded to M.F. The Institut de Génétique et de Biologie Moléculaire et Cellulaire was also supported by a French state fund through the ANR labex. D.E.S. was funded by Marie Curie Grant CIG 334077/IRTIM. We thank B. Altenhein, K. Brückner, M. Crozatier, L. Waltzer, M. Logan, E. Kurant, R. Reuter, E. Kurucz, J.L Dimarcq, J. Hoffmann, C. Goodman, the DHSB, and the BDSC for reagents and flies. We also thank all of the laboratory members for comments on the manuscript; C. Diebold, C. Delaporte, M. Pezze, the fly, and imaging and antibody facilities for technical assistance; and D. Dembele for help with statistics. In addition, we thank Alison Brewer for help with Luciferase assays.","year":"2019","publisher":"Society for Neuroscience","department":[{"_id":"DaSi"}],"publication_status":"published","author":[{"full_name":"Trébuchet, Guillaume","first_name":"Guillaume","last_name":"Trébuchet"},{"first_name":"Pierre B","last_name":"Cattenoz","full_name":"Cattenoz, Pierre B"},{"first_name":"János","last_name":"Zsámboki","full_name":"Zsámboki, János"},{"full_name":"Mazaud, David","last_name":"Mazaud","first_name":"David"},{"full_name":"Siekhaus, Daria E","last_name":"Siekhaus","first_name":"Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fanto, Manolis","last_name":"Fanto","first_name":"Manolis"},{"last_name":"Giangrande","first_name":"Angela","full_name":"Giangrande, Angela"}],"volume":39,"date_created":"2018-12-11T11:44:07Z","date_updated":"2023-09-19T10:10:55Z","publist_id":"8048","ec_funded":1,"file_date_updated":"2020-10-02T09:33:28Z","oa":1,"external_id":{"isi":["000455189900006"],"pmid":["30504274"]},"project":[{"_id":"2536F660-B435-11E9-9278-68D0E5697425","grant_number":"334077","call_identifier":"FP7","name":"Investigating the role of transporters in invasive migration through junctions"}],"quality_controlled":"1","isi":1,"doi":"10.1523/JNEUROSCI.1059-18.2018","language":[{"iso":"eng"}],"month":"01"},{"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.","apa":"Ganev, I. V. (2019). The wonderful compactification for quantum groups. Journal of the London Mathematical Society. Wiley. https://doi.org/10.1112/jlms.12193","ieee":"I. V. Ganev, “The wonderful compactification for quantum groups,” Journal of the London Mathematical Society, vol. 99, no. 3. Wiley, pp. 778–806, 2019.","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","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","file":[{"creator":"kschuh","content_type":"application/pdf","file_size":431754,"access_level":"open_access","file_name":"2019_Wiley_Ganev.pdf","checksum":"1be56239b2cd740a0e9a084f773c22f6","date_updated":"2020-07-14T12:46:35Z","date_created":"2020-01-07T13:31:53Z","file_id":"7238","relation":"main_file"}],"oa_version":"Published Version","_id":"5","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["510"],"title":"The wonderful compactification for quantum groups","intvolume":" 99","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","doi":"10.1112/jlms.12193","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000470025900008"]},"oa":1,"isi":1,"quality_controlled":"1","month":"06","author":[{"last_name":"Ganev","first_name":"Iordan V","id":"447491B8-F248-11E8-B48F-1D18A9856A87","full_name":"Ganev, Iordan V"}],"date_created":"2018-12-11T11:44:06Z","date_updated":"2023-09-19T10:13:08Z","volume":99,"year":"2019","publication_status":"published","publisher":"Wiley","department":[{"_id":"TaHa"}],"file_date_updated":"2020-07-14T12:46:35Z","publist_id":"8052"},{"day":"12","article_processing_charge":"No","has_accepted_license":"1","page":"192","citation":{"mla":"Vasileva, Mina K. Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7172.","short":"M.K. Vasileva, Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2019.","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.","ama":"Vasileva MK. Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana. 2019. doi:10.15479/AT:ISTA:7172","ista":"Vasileva MK. 2019. Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria.","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."},"date_published":"2019-12-12T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","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."}],"title":"Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana","status":"public","ddc":["570"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7172","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:51Z","date_created":"2019-12-12T09:32:36Z","checksum":"ef981c1a3b1d9da0edcbedcff4970d37","relation":"source_file","file_id":"7175","file_size":20454014,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"mvasilev","file_name":"Thesis_Mina_final_upload_7.docx","access_level":"closed"},{"file_name":"Thesis_Mina_final_upload_7.pdf","access_level":"open_access","creator":"mvasilev","file_size":11565025,"content_type":"application/pdf","file_id":"7176","relation":"main_file","date_updated":"2020-07-14T12:47:51Z","date_created":"2019-12-12T09:33:10Z","checksum":"3882c4585e46c9cfb486e4225cad54ab"}],"month":"12","publication_identifier":{"eissn":["2663-337X"]},"oa":1,"supervisor":[{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:7172","file_date_updated":"2020-07-14T12:47:51Z","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JiFr"}],"year":"2019","date_updated":"2023-09-19T10:39:33Z","date_created":"2019-12-11T21:24:39Z","author":[{"last_name":"Vasileva","first_name":"Mina K","id":"3407EB18-F248-11E8-B48F-1D18A9856A87","full_name":"Vasileva, Mina K"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1346"},{"status":"public","relation":"part_of_dissertation","id":"6377"},{"status":"public","relation":"part_of_dissertation","id":"449"}]}},{"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":{"ama":"Cepeda Humerez SA. Estimating information flow in single cells. 2019. doi:10.15479/AT:ISTA:6473","apa":"Cepeda Humerez, S. A. (2019). Estimating information flow in single cells. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6473","ieee":"S. A. Cepeda Humerez, “Estimating information flow in single cells,” Institute of Science and Technology Austria, 2019.","ista":"Cepeda Humerez SA. 2019. Estimating information flow in single cells. Institute of Science and Technology Austria.","short":"S.A. Cepeda Humerez, Estimating Information Flow in Single Cells, Institute of Science and Technology Austria, 2019.","mla":"Cepeda Humerez, Sarah A. Estimating Information Flow in Single Cells. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6473.","chicago":"Cepeda Humerez, Sarah A. “Estimating Information Flow in Single Cells.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6473."},"page":"135","abstract":[{"lang":"eng","text":"Single cells are constantly interacting with their environment and each other, more importantly, the accurate perception of environmental cues is crucial for growth, survival, and reproduction. This communication between cells and their environment can be formalized in mathematical terms and be quantified as the information flow between them, as prescribed by information theory. \r\nThe recent availability of real–time dynamical patterns of signaling molecules in single cells has allowed us to identify encoding about the identity of the environment in the time–series. However, efficient estimation of the information transmitted by these signals has been a data–analysis challenge due to the high dimensionality of the trajectories and the limited number of samples. In the first part of this thesis, we develop and evaluate decoding–based estimation methods to lower bound the mutual information and derive model–based precise information estimates for biological reaction networks governed by the chemical master equation. This is followed by applying the decoding-based methods to study the intracellular representation of extracellular changes in budding yeast, by observing the transient dynamics of nuclear translocation of 10 transcription factors in response to 3 stress conditions. Additionally, we apply these estimators to previously published data on ERK and Ca2+ signaling and yeast stress response. We argue that this single cell decoding-based measure of information provides an unbiased, quantitative and interpretable measure for the fidelity of biological signaling processes. \r\nFinally, in the last section, we deal with gene regulation which is primarily controlled by transcription factors (TFs) that bind to the DNA to activate gene expression. The possibility that non-cognate TFs activate transcription diminishes the accuracy of regulation with potentially disastrous effects for the cell. This ’crosstalk’ acts as a previously unexplored source of noise in biochemical networks and puts a strong constraint on their performance. To mitigate erroneous initiation we propose an out of equilibrium scheme that implements kinetic proofreading. We show that such architectures are favored over their equilibrium counterparts for complex organisms despite introducing noise in gene expression. "}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"relation":"source_file","file_id":"6480","checksum":"75f9184c1346e10a5de5f9cc7338309a","date_updated":"2020-07-14T12:47:31Z","date_created":"2019-05-23T11:18:16Z","access_level":"closed","file_name":"Thesis_Cepeda.zip","content_type":"application/zip","file_size":23937464,"creator":"scepeda"},{"relation":"main_file","file_id":"6481","date_updated":"2020-07-14T12:47:31Z","date_created":"2019-05-23T11:18:13Z","checksum":"afdc0633ddbd71d5b13550d7fb4f4454","file_name":"CepedaThesis.pdf","access_level":"open_access","file_size":16646985,"content_type":"application/pdf","creator":"scepeda"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6473","ddc":["004"],"title":"Estimating information flow in single cells","status":"public","month":"05","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:6473","degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper"}],"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","first_name":"Sarah A","last_name":"Cepeda Humerez"}],"related_material":{"record":[{"id":"1576","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"6900"},{"id":"281","status":"public","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"2016"}]},"date_created":"2019-05-21T00:11:23Z","date_updated":"2023-09-19T15:13:26Z","year":"2019","publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"Institute of Science and Technology Austria"},{"status":"public","title":"Coevolution of transcription factors and their binding sites in sequence space","ddc":["576"],"_id":"6071","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"Thesis_final_PDFA_RoshanPrizak.pdf","content_type":"application/pdf","file_size":20995465,"creator":"rprizak","relation":"main_file","file_id":"6072","checksum":"e60a72de35d270b31f1a23d50f224ec0","date_created":"2019-03-06T16:05:07Z","date_updated":"2020-07-14T12:47:18Z"},{"title":"Latex files","file_id":"6073","relation":"source_file","checksum":"67c2630333d05ebafef5f018863a8465","date_updated":"2020-07-14T12:47:18Z","date_created":"2019-03-06T16:09:39Z","access_level":"closed","file_name":"thesis_v2_merge.zip","creator":"rprizak","file_size":85705272,"content_type":"application/zip"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","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"}],"page":"189","citation":{"mla":"Prizak, Roshan. Coevolution of Transcription Factors and Their Binding Sites in Sequence Space. Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:th6071.","short":"R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in Sequence Space, Institute of Science and Technology Austria, 2019.","chicago":"Prizak, Roshan. “Coevolution of Transcription Factors and Their Binding Sites in Sequence Space.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:th6071.","ama":"Prizak R. Coevolution of transcription factors and their binding sites in sequence space. 2019. doi:10.15479/at:ista:th6071","ista":"Prizak R. 2019. Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria.","ieee":"R. Prizak, “Coevolution of transcription factors and their binding sites in sequence space,” Institute of Science and Technology Austria, 2019.","apa":"Prizak, R. (2019). Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th6071"},"date_published":"2019-03-11T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"11","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"publication_status":"published","year":"2019","date_updated":"2023-09-22T10:00:48Z","date_created":"2019-03-06T16:16:10Z","related_material":{"record":[{"id":"1358","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"955"}]},"author":[{"full_name":"Prizak, Roshan","last_name":"Prizak","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:47:18Z","project":[{"name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27"}],"oa":1,"language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"doi":"10.15479/at:ista:th6071","publication_identifier":{"issn":["2663-337X"]},"month":"03"},{"publisher":"EMS Press","department":[{"_id":"TaHa"}],"publication_status":"published","year":"2019","volume":24,"date_created":"2020-02-02T23:01:06Z","date_updated":"2023-10-17T07:42:21Z","author":[{"id":"4D046628-F248-11E8-B48F-1D18A9856A87","first_name":"Tanya K","last_name":"Srivastava","full_name":"Srivastava, Tanya K"}],"file_date_updated":"2020-07-14T12:47:58Z","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1809.08970"],"isi":["000517806400019"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.25537/dm.2019v24.1135-1177","publication_identifier":{"issn":["1431-0635"],"eissn":["1431-0643"]},"month":"05","intvolume":" 24","ddc":["510"],"title":"On derived equivalences of k3 surfaces in positive characteristic","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7436","file":[{"relation":"main_file","file_id":"7438","checksum":"9a1a64bd49ab03fa4f738fb250fc4f90","date_updated":"2020-07-14T12:47:58Z","date_created":"2020-02-03T06:26:12Z","access_level":"open_access","file_name":"2019_DocumMath_Srivastava.pdf","content_type":"application/pdf","file_size":469730,"creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","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. "}],"page":"1135-1177","article_type":"original","citation":{"ama":"Srivastava TK. On derived equivalences of k3 surfaces in positive characteristic. Documenta Mathematica. 2019;24:1135-1177. doi:10.25537/dm.2019v24.1135-1177","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."},"publication":"Documenta Mathematica","date_published":"2019-05-20T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"20"},{"abstract":[{"lang":"eng","text":"We consider the totally asymmetric simple exclusion process (TASEP) with non-random initial condition having density ρ on ℤ− and λ on ℤ+, and a second class particle initially at the origin. For ρ<λ, there is a shock and the second class particle moves with speed 1−λ−ρ. For large time t, we show that the position of the second class particle fluctuates on a t1/3 scale and determine its limiting law. We also obtain the limiting distribution of the number of steps made by the second class particle until time t."}],"issue":"3","type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"72","title":"Limit law of a second class particle in TASEP with non-random initial condition","status":"public","intvolume":" 55","day":"25","article_processing_charge":"No","scopus_import":"1","date_published":"2019-09-25T00:00:00Z","publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","citation":{"short":"P. Ferrari, P. Ghosal, P. Nejjar, Annales de l’institut Henri Poincare (B) Probability and Statistics 55 (2019) 1203–1225.","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.","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.","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","apa":"Ferrari, P., Ghosal, P., & Nejjar, P. (2019). Limit law of a second class particle in TASEP with non-random initial condition. Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AIHP916","ieee":"P. Ferrari, P. Ghosal, and P. Nejjar, “Limit law of a second class particle in TASEP with non-random initial condition,” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 55, no. 3. Institute of Mathematical Statistics, pp. 1203–1225, 2019.","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."},"article_type":"original","page":"1203-1225","ec_funded":1,"author":[{"last_name":"Ferrari","first_name":"Patrick","full_name":"Ferrari, Patrick"},{"last_name":"Ghosal","first_name":"Promit","full_name":"Ghosal, Promit"},{"last_name":"Nejjar","first_name":"Peter","id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","full_name":"Nejjar, Peter"}],"date_updated":"2023-10-17T08:53:45Z","date_created":"2018-12-11T11:44:29Z","volume":55,"year":"2019","publication_status":"published","department":[{"_id":"LaEr"},{"_id":"JaMa"}],"publisher":"Institute of Mathematical Statistics","month":"09","publication_identifier":{"issn":["0246-0203"]},"doi":"10.1214/18-AIHP916","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1710.02323"}],"oa":1,"external_id":{"isi":["000487763200001"],"arxiv":["1710.02323"]},"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"},{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425"}]},{"scopus_import":"1","article_processing_charge":"No","publication_identifier":{"isbn":["9781943580576"]},"month":"05","day":"01","quality_controlled":"1","citation":{"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","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.","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","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.","short":"M. Khatoniar, N. Yama, A. Ghazaryan, S. Guddala, P. Ghaemi, V. Menon, in:, CLEO: Applications and Technology, Optica Publishing Group, 2019.","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."},"publication":"CLEO: Applications and Technology","language":[{"iso":"eng"}],"doi":"10.1364/cleo_at.2019.jtu2a.52","date_published":"2019-05-01T00:00:00Z","conference":{"end_date":"2019-05-10","start_date":"2019-05-05","location":"San Jose, CA, United States","name":"CLEO: Conference on Lasers and Electro-Optics"},"type":"conference","article_number":"paper JTu2A.52","abstract":[{"lang":"eng","text":"We demonstrate robust retention of valley coherence and its control via polariton pseudospin precession through the optical TE-TM splitting in bilayer WS2 microcavity exciton polaritons at room temperature."}],"publisher":"Optica Publishing Group","department":[{"_id":"MiLe"}],"title":"Room temperature control of valley coherence in bilayer WS2 exciton polaritons","publication_status":"published","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6646","year":"2019","oa_version":"None","date_updated":"2023-10-17T12:14:29Z","date_created":"2019-07-17T09:40:44Z","author":[{"first_name":"Mandeep","last_name":"Khatoniar","full_name":"Khatoniar, Mandeep"},{"full_name":"Yama, Nicholas","first_name":"Nicholas","last_name":"Yama"},{"full_name":"Ghazaryan, Areg","last_name":"Ghazaryan","first_name":"Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sriram","last_name":"Guddala","full_name":"Guddala, Sriram"},{"first_name":"Pouyan","last_name":"Ghaemi","full_name":"Ghaemi, Pouyan"},{"first_name":"Vinod","last_name":"Menon","full_name":"Menon, Vinod"}]},{"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."}],"article_number":"NM2A.5","type":"conference","date_created":"2020-01-05T23:00:48Z","date_updated":"2023-10-17T12:14:46Z","oa_version":"None","author":[{"full_name":"Rueda Sanchez, Alfredo R","first_name":"Alfredo R","last_name":"Rueda Sanchez","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860"},{"full_name":"Sedlmeir, Florian","first_name":"Florian","last_name":"Sedlmeir"},{"last_name":"Leuchs","first_name":"Gerd","full_name":"Leuchs, Gerd"},{"full_name":"Kumari, Madhuri","last_name":"Kumari","first_name":"Madhuri"},{"full_name":"Schwefel, Harald G.L.","first_name":"Harald G.L.","last_name":"Schwefel"}],"title":"Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity","publication_status":"published","status":"public","publisher":"Optica Publishing Group","department":[{"_id":"JoFi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7233","year":"2019","day":"15","month":"07","article_processing_charge":"No","publication_identifier":{"isbn":["9781557528209"]},"scopus_import":"1","language":[{"iso":"eng"}],"conference":{"name":"NLO: Nonlinear Optics","location":"Waikoloa Beach, Hawaii (HI), United States","start_date":"2019-07-15","end_date":"2019-07-19"},"doi":"10.1364/NLO.2019.NM2A.5","date_published":"2019-07-15T00:00:00Z","quality_controlled":"1","publication":"Nonlinear Optics, OSA Technical Digest","citation":{"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","ieee":"A. R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kumari, and H. G. L. Schwefel, “Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity,” in Nonlinear Optics, OSA Technical Digest, Waikoloa Beach, Hawaii (HI), United States, 2019.","apa":"Rueda Sanchez, A. R., Sedlmeir, F., Leuchs, G., Kumari, M., & Schwefel, H. G. L. (2019). Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity. In Nonlinear Optics, OSA Technical Digest. Waikoloa Beach, Hawaii (HI), United States: Optica Publishing Group. https://doi.org/10.1364/NLO.2019.NM2A.5","ista":"Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kumari M, Schwefel HGL. 2019. Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity. Nonlinear Optics, OSA Technical Digest. NLO: Nonlinear Optics, NM2A.5.","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."}},{"publisher":"Institut Henri Poincaré","department":[{"_id":"LaEr"}],"publication_status":"published","year":"2019","volume":55,"date_created":"2019-04-08T14:05:04Z","date_updated":"2023-10-17T12:20:20Z","related_material":{"record":[{"id":"149","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Alt, Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","last_name":"Alt","first_name":"Johannes"},{"first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"full_name":"Krüger, Torben H","last_name":"Krüger","first_name":"Torben H","orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nemish, Yuriy","orcid":"0000-0002-7327-856X","id":"4D902E6A-F248-11E8-B48F-1D18A9856A87","last_name":"Nemish","first_name":"Yuriy"}],"ec_funded":1,"project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"}],"isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.08343"}],"oa":1,"external_id":{"isi":["000467793600003"],"arxiv":["1706.08343"]},"language":[{"iso":"eng"}],"doi":"10.1214/18-AIHP894","publication_identifier":{"issn":["0246-0203"]},"month":"05","intvolume":" 55","title":"Location of the spectrum of Kronecker random matrices","status":"public","_id":"6240","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"For a general class of large non-Hermitian random block matrices X we prove that there are no eigenvalues away from a deterministic set with very high probability. This set is obtained from the Dyson equation of the Hermitization of X as the self-consistent approximation of the pseudospectrum. We demonstrate that the analysis of the matrix Dyson equation from (Probab. Theory Related Fields (2018)) offers a unified treatment of many structured matrix ensembles."}],"page":"661-696","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","apa":"Alt, J., Erdös, L., Krüger, T. H., & Nemish, Y. (2019). Location of the spectrum of Kronecker random matrices. Annales de l’institut Henri Poincare. Institut Henri Poincaré. https://doi.org/10.1214/18-AIHP894","ieee":"J. Alt, L. Erdös, T. H. Krüger, and Y. Nemish, “Location of the spectrum of Kronecker random matrices,” Annales de l’institut Henri Poincare, vol. 55, no. 2. Institut Henri Poincaré, pp. 661–696, 2019.","ista":"Alt J, Erdös L, Krüger TH, Nemish Y. 2019. Location of the spectrum of Kronecker random matrices. Annales de l’institut Henri Poincare. 55(2), 661–696.","short":"J. Alt, L. Erdös, T.H. Krüger, Y. Nemish, Annales de l’institut Henri Poincare 55 (2019) 661–696.","mla":"Alt, Johannes, et al. “Location of the Spectrum of Kronecker Random Matrices.” Annales de l’institut Henri Poincare, vol. 55, no. 2, Institut Henri Poincaré, 2019, pp. 661–96, doi:10.1214/18-AIHP894.","chicago":"Alt, Johannes, László Erdös, Torben H Krüger, and Yuriy Nemish. “Location of the Spectrum of Kronecker Random Matrices.” Annales de l’institut Henri Poincare. Institut Henri Poincaré, 2019. https://doi.org/10.1214/18-AIHP894."},"publication":"Annales de l'institut Henri Poincare","date_published":"2019-05-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01"},{"oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":2302307,"creator":"dernst","access_level":"open_access","file_name":"2019_PlosGenetics_Andergassen.pdf","checksum":"2f51fc91e4a4199827adc51d432ad864","date_updated":"2020-07-14T12:47:57Z","date_created":"2020-02-04T10:11:55Z","relation":"main_file","file_id":"7446"}],"intvolume":" 15","status":"public","title":"The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes","ddc":["570"],"_id":"7399","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"7","abstract":[{"text":"Long non-coding (lnc) RNAs are numerous and found throughout the mammalian genome, and many are thought to be involved in the regulation of gene expression. However, the majority remain relatively uncharacterised and of uncertain function making the use of model systems to uncover their mode of action valuable. Imprinted lncRNAs target and recruit epigenetic silencing factors to a cluster of imprinted genes on the same chromosome, making them one of the best characterized lncRNAs for silencing distant genes in cis. In this study we examined silencing of the distant imprinted gene Slc22a3 by the lncRNA Airn in the Igf2r imprinted cluster in mouse. Previously we proposed that imprinted lncRNAs may silence distant imprinted genes by disrupting promoter-enhancer interactions by being transcribed through the enhancer, which we called the enhancer interference hypothesis. Here we tested this hypothesis by first using allele-specific chromosome conformation capture (3C) to detect interactions between the Slc22a3 promoter and the locus of the Airn lncRNA that silences it on the paternal chromosome. In agreement with the model, we found interactions enriched on the maternal allele across the entire Airn gene consistent with multiple enhancer-promoter interactions. Therefore, to test the enhancer interference hypothesis we devised an approach to delete the entire Airn gene. However, the deletion showed that there are no essential enhancers for Slc22a2, Pde10a and Slc22a3 within the Airn gene, strongly indicating that the Airn RNA rather than its transcription is responsible for silencing distant imprinted genes. Furthermore, we found that silent imprinted genes were covered with large blocks of H3K27me3 on the repressed paternal allele. Therefore we propose an alternative hypothesis whereby the chromosome interactions may initially guide the lncRNA to target imprinted promoters and recruit repressive chromatin, and that these interactions are lost once silencing is established.","lang":"eng"}],"type":"journal_article","date_published":"2019-07-22T00:00:00Z","article_type":"original","citation":{"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","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.","apa":"Andergassen, D., Muckenhuber, M., Bammer, P. C., Kulinski, T. M., Theussl, H.-C., Shimizu, T., … Hudson, Q. J. (2019). The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008268","ieee":"D. Andergassen et al., “The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes,” PLoS Genetics, vol. 15, no. 7. Public Library of Science, 2019.","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.","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).","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."},"publication":"PLoS Genetics","article_processing_charge":"No","has_accepted_license":"1","day":"22","scopus_import":"1","volume":15,"date_updated":"2023-10-17T12:30:27Z","date_created":"2020-01-29T16:14:07Z","author":[{"last_name":"Andergassen","first_name":"Daniel","full_name":"Andergassen, Daniel"},{"first_name":"Markus","last_name":"Muckenhuber","full_name":"Muckenhuber, Markus"},{"full_name":"Bammer, Philipp C.","first_name":"Philipp C.","last_name":"Bammer"},{"full_name":"Kulinski, Tomasz M.","last_name":"Kulinski","first_name":"Tomasz M."},{"first_name":"Hans-Christian","last_name":"Theussl","full_name":"Theussl, Hans-Christian"},{"full_name":"Shimizu, Takahiko","last_name":"Shimizu","first_name":"Takahiko"},{"last_name":"Penninger","first_name":"Josef M.","full_name":"Penninger, Josef M."},{"full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","first_name":"Florian","last_name":"Pauler"},{"full_name":"Hudson, Quanah J.","first_name":"Quanah J.","last_name":"Hudson"}],"department":[{"_id":"SiHi"}],"publisher":"Public Library of Science","publication_status":"published","pmid":1,"year":"2019","file_date_updated":"2020-07-14T12:47:57Z","article_number":"e1008268","language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1008268","quality_controlled":"1","isi":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":["000478689100025"],"pmid":["31329595"]},"oa":1,"publication_identifier":{"issn":["1553-7404"]},"month":"07"},{"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,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["1553-7358"]},"month":"11","author":[{"full_name":"Wang, Jilin W. J. L.","last_name":"Wang","first_name":"Jilin W. J. L."},{"full_name":"Lombardi, Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425","orcid":"0000-0003-2623-5249","first_name":"Fabrizio","last_name":"Lombardi"},{"full_name":"Zhang, Xiyun","last_name":"Zhang","first_name":"Xiyun"},{"last_name":"Anaclet","first_name":"Christelle","full_name":"Anaclet, Christelle"},{"first_name":"Plamen Ch.","last_name":"Ivanov","full_name":"Ivanov, Plamen Ch."}],"volume":15,"date_created":"2019-11-25T08:20:47Z","date_updated":"2023-10-17T12:30:07Z","pmid":1,"year":"2019","publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-14T12:47:49Z","article_number":"e1007268","date_published":"2019-11-01T00:00:00Z","citation":{"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.","ieee":"J. W. J. L. Wang, F. Lombardi, X. Zhang, C. Anaclet, and P. C. Ivanov, “Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture,” PLoS Computational Biology, vol. 15, no. 11. Public Library of Science, 2019.","apa":"Wang, J. W. J. L., Lombardi, F., Zhang, X., Anaclet, C., & Ivanov, P. C. (2019). Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007268","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."},"publication":"PLoS Computational Biology","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","file":[{"file_size":3982516,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2019_PLOSComBio_Wang.pdf","checksum":"2a096a9c6dcc6eaa94077b2603bc6c12","date_created":"2019-11-25T08:24:01Z","date_updated":"2020-07-14T12:47:49Z","relation":"main_file","file_id":"7104"}],"oa_version":"Published Version","_id":"7103","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 15","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","issue":"11","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"}],"type":"journal_article"},{"conference":{"location":"Long Beach, CA, United States","start_date":"2019-06-10","end_date":"2019-06-15","name":"ICML: International Conference on Machine Learning"},"language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","month":"06","author":[{"full_name":"Bui Thi Mai, Phuong","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","last_name":"Bui Thi Mai","first_name":"Phuong"},{"first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"date_created":"2019-06-20T18:23:03Z","date_updated":"2023-10-17T12:31:38Z","volume":97,"year":"2019","publication_status":"published","department":[{"_id":"ChLa"}],"publisher":"ML Research Press","file_date_updated":"2020-07-14T12:47:33Z","date_published":"2019-06-13T00:00:00Z","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."},"page":"5142-5151","day":"13","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"paper.pdf","file_size":686432,"content_type":"application/pdf","creator":"bphuong","relation":"main_file","file_id":"6570","checksum":"a66d00e2694d749250f8507f301320ca","date_created":"2019-06-20T18:22:56Z","date_updated":"2020-07-14T12:47:33Z"}],"_id":"6569","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"title":"Towards understanding knowledge distillation","status":"public","intvolume":" 97","abstract":[{"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.","lang":"eng"}],"type":"conference"},{"title":"Robust learning from untrusted sources","status":"public","intvolume":" 97","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6590","oa_version":"Preprint","type":"conference","abstract":[{"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"}],"page":"3488-3498","publication":"Proceedings of the 36th International Conference on Machine Learning","citation":{"chicago":"Konstantinov, Nikola H, and Christoph Lampert. “Robust Learning from Untrusted Sources.” In Proceedings of the 36th International Conference on Machine Learning, 97:3488–98. ML Research Press, 2019.","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.","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.","ama":"Konstantinov NH, Lampert C. Robust learning from untrusted sources. In: Proceedings of the 36th International Conference on Machine Learning. Vol 97. ML Research Press; 2019:3488-3498."},"date_published":"2019-06-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","publication_status":"published","publisher":"ML Research Press","department":[{"_id":"ChLa"}],"year":"2019","date_created":"2019-06-27T14:18:23Z","date_updated":"2023-10-17T12:31:55Z","volume":97,"author":[{"full_name":"Konstantinov, Nikola H","first_name":"Nikola H","last_name":"Konstantinov","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"10799","relation":"dissertation_contains","status":"public"}]},"ec_funded":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"external_id":{"arxiv":["1901.10310"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1901.10310","open_access":"1"}],"language":[{"iso":"eng"}],"conference":{"location":"Long Beach, CA, USA","start_date":"2019-06-10","end_date":"2919-06-15","name":"ICML: International Conference on Machine Learning"},"month":"06"},{"day":"15","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2019-10-15T00:00:00Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"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","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.","ista":"Huang D, Sun Y, Ma Z, Ke M, Cui Y, Chen Z, Chen C, Ji C, Tran T, Yang L, Lam S, Han Y, Shu G, Friml J, Miao Y, Jiang L, Chen X. 2019. Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization. Proceedings of the National Academy of Sciences of the United States of America. 116(42), 21274–21284.","ama":"Huang D, Sun Y, Ma Z, et al. Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(42):21274-21284. doi:10.1073/pnas.1911892116","chicago":"Huang, D, Y Sun, Z Ma, M Ke, Y Cui, Z Chen, C Chen, et al. “Salicylic Acid-Mediated Plasmodesmal Closure via Remorin-Dependent Lipid Organization.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1911892116.","short":"D. Huang, Y. Sun, Z. Ma, M. Ke, Y. Cui, Z. Chen, C. Chen, C. Ji, T. Tran, L. Yang, S. Lam, Y. Han, G. Shu, J. Friml, Y. Miao, L. Jiang, X. Chen, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 21274–21284.","mla":"Huang, D., et al. “Salicylic Acid-Mediated Plasmodesmal Closure via Remorin-Dependent Lipid Organization.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 42, Proceedings of the National Academy of Sciences, 2019, pp. 21274–84, doi:10.1073/pnas.1911892116."},"article_type":"original","page":"21274-21284","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","type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"7012","checksum":"258c666bc6253eab81961f61169eefae","date_updated":"2020-07-14T12:47:46Z","date_created":"2019-11-13T08:22:28Z","access_level":"open_access","file_name":"2019_PNAS_Huang.pdf","content_type":"application/pdf","file_size":3287466,"creator":"dernst"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6999","status":"public","title":"Salicylic acid-mediated plasmodesmal closure via Remorin-dependent lipid organization","ddc":["580"],"intvolume":" 116","month":"10","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"doi":"10.1073/pnas.1911892116","language":[{"iso":"eng"}],"external_id":{"isi":["000490183000068"],"pmid":["31575745"]},"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"},"oa":1,"isi":1,"quality_controlled":"1","file_date_updated":"2020-07-14T12:47:46Z","author":[{"full_name":"Huang, D","first_name":"D","last_name":"Huang"},{"full_name":"Sun, Y","last_name":"Sun","first_name":"Y"},{"last_name":"Ma","first_name":"Z","full_name":"Ma, Z"},{"full_name":"Ke, M","first_name":"M","last_name":"Ke"},{"full_name":"Cui, Y","last_name":"Cui","first_name":"Y"},{"first_name":"Z","last_name":"Chen","full_name":"Chen, Z"},{"full_name":"Chen, C","last_name":"Chen","first_name":"C"},{"full_name":"Ji, C","last_name":"Ji","first_name":"C"},{"full_name":"Tran, TM","first_name":"TM","last_name":"Tran"},{"full_name":"Yang, L","first_name":"L","last_name":"Yang"},{"last_name":"Lam","first_name":"SM","full_name":"Lam, SM"},{"full_name":"Han, Y","first_name":"Y","last_name":"Han"},{"full_name":"Shu, G","first_name":"G","last_name":"Shu"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"full_name":"Miao, Y","last_name":"Miao","first_name":"Y"},{"first_name":"L","last_name":"Jiang","full_name":"Jiang, L"},{"last_name":"Chen","first_name":"X","full_name":"Chen, X"}],"related_material":{"link":[{"url":"https://doi.org/10.1073/pnas.2004738117","relation":"erratum"}]},"date_updated":"2023-10-17T12:32:37Z","date_created":"2019-11-12T11:42:05Z","volume":116,"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Proceedings of the National Academy of Sciences"}]