[{"day":"28","month":"11","publication_identifier":{"isbn":["9781538670248"]},"article_processing_charge":"No","scopus_import":"1","language":[{"iso":"eng"}],"conference":{"end_date":"2019-10-30","start_date":"2019-10-27","location":"Auckland, New Zealand","name":"ITSC: Intelligent Transportation Systems Conference"},"date_published":"2019-11-28T00:00:00Z","doi":"10.1109/ITSC.2019.8917514","isi":1,"quality_controlled":"1","publication":"2019 IEEE Intelligent Transportation Systems Conference","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"]},"abstract":[{"lang":"eng","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."}],"article_number":"8917514","type":"conference","date_created":"2019-12-29T23:00:47Z","date_updated":"2023-09-06T14:50:28Z","oa_version":"None","author":[{"full_name":"Osang, Georg F","first_name":"Georg F","last_name":"Osang","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8882-5116"},{"full_name":"Cook, James","first_name":"James","last_name":"Cook"},{"full_name":"Fabrikant, Alex","first_name":"Alex","last_name":"Fabrikant"},{"first_name":"Marco","last_name":"Gruteser","full_name":"Gruteser, Marco"}],"publication_status":"published","title":"LiveTraVeL: Real-time matching of transit vehicle trajectories to transit routes at scale","status":"public","department":[{"_id":"HeEd"}],"publisher":"IEEE","_id":"7216","year":"2019","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer Nature","year":"2019","date_created":"2020-01-05T23:00:47Z","date_updated":"2023-09-06T14:55:15Z","volume":11750,"author":[{"orcid":"0000-0002-3066-6941","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","last_name":"Kong","first_name":"Hui","full_name":"Kong, Hui"},{"full_name":"Bartocci, Ezio","first_name":"Ezio","last_name":"Bartocci"},{"first_name":"Yu","last_name":"Jiang","full_name":"Jiang, Yu"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"}],"month":"08","publication_identifier":{"isbn":["978-3-0302-9661-2"],"eissn":["1611-3349"],"issn":["0302-9743"]},"isi":1,"quality_controlled":"1","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.11514"}],"oa":1,"external_id":{"arxiv":["1907.11514"],"isi":["000611677700008"]},"language":[{"iso":"eng"}],"conference":{"name":"FORMATS: Formal Modeling and Analysis of Timed Systems","end_date":"2019-08-29","location":"Amsterdam, The Netherlands","start_date":"2019-08-27"},"doi":"10.1007/978-3-030-29662-9_8","alternative_title":["LNCS"],"type":"conference","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."}],"status":"public","title":"Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty","intvolume":" 11750","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7231","oa_version":"Preprint","scopus_import":"1","day":"13","article_processing_charge":"No","page":"123-141","publication":"17th International Conference on Formal Modeling and Analysis of Timed Systems","citation":{"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.","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","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.","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"},"date_published":"2019-08-13T00:00:00Z"},{"day":"24","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2019-12-24T00:00:00Z","publication":"eLife","citation":{"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.","short":"N.P. Amin-Wetzel, L. Neidhardt, Y. Yan, M.P. Mayer, D. Ron, ELife 8 (2019).","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.","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","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.","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"},"article_type":"original","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","oa_version":"Published Version","file":[{"date_updated":"2020-11-19T11:37:41Z","date_created":"2020-11-19T11:37:41Z","checksum":"29fcbcd8c1fc7f11a596ed7f14ea1c82","success":1,"relation":"main_file","file_id":"8777","content_type":"application/pdf","file_size":4817384,"creator":"dernst","file_name":"2019_eLife_AminWetzel.pdf","access_level":"open_access"}],"_id":"7340","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["570"],"title":"Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR","status":"public","intvolume":" 8","month":"12","publication_identifier":{"eissn":["2050084X"]},"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"},"external_id":{"pmid":["31873072"],"isi":["000512303700001"]},"oa":1,"isi":1,"quality_controlled":"1","file_date_updated":"2020-11-19T11:37:41Z","license":"https://creativecommons.org/licenses/by/4.0/","article_number":"e50793","author":[{"id":"E95D3014-9D8C-11E9-9C80-D2F8E5697425","last_name":"Amin-Wetzel","first_name":"Niko Paresh","full_name":"Amin-Wetzel, Niko Paresh"},{"full_name":"Neidhardt, Lisa","first_name":"Lisa","last_name":"Neidhardt"},{"first_name":"Yahui","last_name":"Yan","full_name":"Yan, Yahui"},{"last_name":"Mayer","first_name":"Matthias P.","full_name":"Mayer, Matthias P."},{"full_name":"Ron, David","first_name":"David","last_name":"Ron"}],"date_updated":"2023-09-06T14:58:02Z","date_created":"2020-01-19T23:00:39Z","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","department":[{"_id":"MaDe"}],"publisher":"eLife Sciences Publications"},{"type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"5","title":"eGFRD in all dimensions","status":"public","intvolume":" 150","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7422","oa_version":"Preprint","day":"07","article_processing_charge":"No","article_type":"original","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."},"date_published":"2019-02-07T00:00:00Z","article_number":"054108","publication_status":"published","publisher":"AIP Publishing","department":[{"_id":"GaTk"}],"year":"2019","date_created":"2020-01-30T10:34:36Z","date_updated":"2023-09-06T14:59:28Z","volume":150,"author":[{"full_name":"Sokolowski, Thomas R","orcid":"0000-0002-1287-3779","id":"3E999752-F248-11E8-B48F-1D18A9856A87","last_name":"Sokolowski","first_name":"Thomas R"},{"first_name":"Joris","last_name":"Paijmans","full_name":"Paijmans, Joris"},{"last_name":"Bossen","first_name":"Laurens","full_name":"Bossen, Laurens"},{"first_name":"Thomas","last_name":"Miedema","full_name":"Miedema, Thomas"},{"first_name":"Martijn","last_name":"Wehrens","full_name":"Wehrens, Martijn"},{"first_name":"Nils B.","last_name":"Becker","full_name":"Becker, Nils B."},{"first_name":"Kazunari","last_name":"Kaizu","full_name":"Kaizu, Kazunari"},{"first_name":"Koichi","last_name":"Takahashi","full_name":"Takahashi, Koichi"},{"full_name":"Dogterom, Marileen","last_name":"Dogterom","first_name":"Marileen"},{"full_name":"ten Wolde, Pieter Rein","last_name":"ten Wolde","first_name":"Pieter Rein"}],"month":"02","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"quality_controlled":"1","isi":1,"external_id":{"isi":["000458109300009"],"arxiv":["1708.09364"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1708.09364","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1063/1.5064867"},{"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1908.08129","open_access":"1"}],"external_id":{"isi":["000612918800018"],"arxiv":["1908.08129"]},"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","doi":"10.1007/978-3-030-35802-0_18","conference":{"name":"GD: Graph Drawing and Network Visualization","location":"Prague, Czech Republic","start_date":"2019-09-17","end_date":"2019-09-20"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-0303-5801-3"],"eissn":["1611-3349"],"issn":["0302-9743"]},"month":"11","year":"2019","department":[{"_id":"UlWa"}],"publisher":"Springer Nature","publication_status":"published","author":[{"full_name":"Arroyo Guevara, Alan M","last_name":"Arroyo Guevara","first_name":"Alan M","orcid":"0000-0003-2401-8670","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Derka, Martin","last_name":"Derka","first_name":"Martin"},{"full_name":"Parada, Irene","last_name":"Parada","first_name":"Irene"}],"volume":11904,"date_created":"2020-01-05T23:00:47Z","date_updated":"2023-09-06T14:56:00Z","ec_funded":1,"citation":{"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","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.","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","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.","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.","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."},"publication":"27th International Symposium on Graph Drawing and Network Visualization","page":"230-243","date_published":"2019-11-28T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"28","_id":"7230","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 11904","title":"Extending simple drawings","status":"public","oa_version":"Preprint","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","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."}]},{"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["978-3-0302-9661-2"]},"month":"08","doi":"10.1007/978-3-030-29662-9_4","conference":{"name":"FORMATS: Formal Modeling and Anaysis of Timed Systems","start_date":"2019-08-27","location":"Amsterdam, The Netherlands","end_date":"2019-08-29"},"language":[{"iso":"eng"}],"external_id":{"isi":["000611677700004"]},"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","author":[{"full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere","first_name":"Thomas"},{"last_name":"Maler","first_name":"Oded","full_name":"Maler, Oded"},{"full_name":"Nickovic, Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","last_name":"Nickovic","first_name":"Dejan"}],"volume":11750,"date_created":"2020-01-05T23:00:48Z","date_updated":"2023-09-06T14:57:17Z","year":"2019","department":[{"_id":"ToHe"}],"publisher":"Springer Nature","publication_status":"published","article_processing_charge":"No","day":"13","scopus_import":"1","date_published":"2019-08-13T00:00:00Z","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","page":"59-75","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"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"None","_id":"7232","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 11750","title":"Mixed-time signal temporal logic","status":"public"},{"intvolume":" 132","status":"public","title":"GGA2 and RAB13 promote activity-dependent β1-integrin recycling","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7420","oa_version":"Published Version","type":"journal_article","issue":"11","abstract":[{"lang":"eng","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."}],"article_type":"original","citation":{"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.","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","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.","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","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.","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)."},"publication":"Journal of Cell Science","date_published":"2019-06-07T00:00:00Z","article_processing_charge":"No","day":"07","publisher":"The Company of Biologists","department":[{"_id":"MiSi"}],"publication_status":"published","pmid":1,"year":"2019","volume":132,"date_created":"2020-01-30T10:31:42Z","date_updated":"2023-09-06T15:01:00Z","author":[{"last_name":"Sahgal","first_name":"Pranshu","full_name":"Sahgal, Pranshu"},{"full_name":"Alanko, Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7698-3061","first_name":"Jonna H","last_name":"Alanko"},{"full_name":"Icha, Jaroslav","last_name":"Icha","first_name":"Jaroslav"},{"full_name":"Paatero, Ilkka","first_name":"Ilkka","last_name":"Paatero"},{"full_name":"Hamidi, Hellyeh","first_name":"Hellyeh","last_name":"Hamidi"},{"first_name":"Antti","last_name":"Arjonen","full_name":"Arjonen, Antti"},{"first_name":"Mika","last_name":"Pietilä","full_name":"Pietilä, Mika"},{"full_name":"Rokka, Anne","last_name":"Rokka","first_name":"Anne"},{"full_name":"Ivaska, Johanna","first_name":"Johanna","last_name":"Ivaska"}],"article_number":"jcs233387","quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://doi.org/10.1242/jcs.233387","open_access":"1"}],"oa":1,"external_id":{"isi":["000473327900017"],"pmid":["31076515"]},"language":[{"iso":"eng"}],"doi":"10.1242/jcs.233387","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"month":"06"},{"article_type":"original","page":"441-479","publication":"Annales de l'Institut Henri Poincaré, Probabilités et Statistiques","citation":{"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","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","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.","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.","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."},"date_published":"2019-02-01T00:00:00Z","day":"01","article_processing_charge":"No","status":"public","title":"Finite rank perturbations in products of coupled random matrices: From one correlated to two Wishart ensembles","intvolume":" 55","_id":"7423","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","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","isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1704.05224","open_access":"1"}],"external_id":{"isi":["000456070200013"],"arxiv":["1704.05224"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1214/18-aihp888","month":"02","publication_identifier":{"issn":["0246-0203"]},"publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"Institute of Mathematical Statistics","year":"2019","date_created":"2020-01-30T10:36:50Z","date_updated":"2023-09-06T14:58:39Z","volume":55,"author":[{"full_name":"Akemann, Gernot","first_name":"Gernot","last_name":"Akemann"},{"last_name":"Checinski","first_name":"Tomasz","full_name":"Checinski, Tomasz"},{"full_name":"Liu, Dangzheng","last_name":"Liu","first_name":"Dangzheng","id":"2F947E34-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Strahov","first_name":"Eugene","full_name":"Strahov, Eugene"}]},{"language":[{"iso":"eng"}],"doi":"10.1111/mec.14990","isi":1,"quality_controlled":"1","external_id":{"isi":["000468200800004"],"pmid":["30576024"]},"publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"month":"04","volume":28,"date_updated":"2023-09-06T15:00:13Z","date_created":"2020-01-30T10:33:05Z","author":[{"full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","first_name":"Melissa A"},{"full_name":"Rodrigues, Nicolas","first_name":"Nicolas","last_name":"Rodrigues"},{"last_name":"Perrin","first_name":"Nicolas","full_name":"Perrin, Nicolas"},{"full_name":"Kirkpatrick, Mark","first_name":"Mark","last_name":"Kirkpatrick"}],"department":[{"_id":"BeVi"}],"publisher":"Wiley","publication_status":"published","pmid":1,"year":"2019","date_published":"2019-04-01T00:00:00Z","page":"1877-1889","article_type":"original","citation":{"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.","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.","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","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","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.","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.","short":"M.A. Toups, N. Rodrigues, N. Perrin, M. Kirkpatrick, Molecular Ecology 28 (2019) 1877–1889."},"publication":"Molecular Ecology","article_processing_charge":"No","day":"01","oa_version":"None","intvolume":" 28","title":"A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog","status":"public","_id":"7421","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"8","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."}],"type":"journal_article"},{"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783030176556","9783030176563"]},"month":"04","language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-17656-3_10","conference":{"name":"International Conference on the Theory and Applications of Cryptographic Techniques","end_date":"2019-05-23","start_date":"2019-05-19","location":"Darmstadt, Germany"},"project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000483516200010"]},"main_file_link":[{"url":"https://eprint.iacr.org/2019/252","open_access":"1"}],"oa":1,"ec_funded":1,"volume":11477,"date_created":"2020-01-30T09:26:14Z","date_updated":"2023-09-06T15:26:06Z","author":[{"last_name":"Abusalah","first_name":"Hamza M","id":"40297222-F248-11E8-B48F-1D18A9856A87","full_name":"Abusalah, Hamza M"},{"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"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z"},{"full_name":"Walter, Michael","orcid":"0000-0003-3186-2482","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","last_name":"Walter","first_name":"Michael"}],"publisher":"Springer International Publishing","department":[{"_id":"KrPi"}],"publication_status":"published","year":"2019","article_processing_charge":"No","day":"24","scopus_import":"1","date_published":"2019-04-24T00:00:00Z","page":"277-291","citation":{"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.","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.","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","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","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.","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."},"publication":"Advances in Cryptology – EUROCRYPT 2019","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","oa_version":"Submitted Version","intvolume":" 11477","status":"public","title":"Reversible proofs of sequential work","_id":"7411","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"ec_funded":1,"date_created":"2020-01-30T09:12:19Z","date_updated":"2023-09-06T15:27:29Z","volume":312,"author":[{"full_name":"Mckenzie, Catherine","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","last_name":"Mckenzie","first_name":"Catherine"},{"full_name":"Spanova, Miroslava","id":"44A924DC-F248-11E8-B48F-1D18A9856A87","last_name":"Spanova","first_name":"Miroslava"},{"full_name":"Johnson, Alexander J","first_name":"Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843"},{"full_name":"Kainrath, Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie","last_name":"Kainrath"},{"orcid":"0000-0002-9438-4783","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","last_name":"Zheden","first_name":"Vanessa","full_name":"Zheden, Vanessa"},{"last_name":"Sitte","first_name":"Harald H.","full_name":"Sitte, Harald H."},{"full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","first_name":"Harald L"}],"publication_status":"published","publisher":"Elsevier","department":[{"_id":"HaJa"},{"_id":"Bio"}],"year":"2019","pmid":1,"month":"01","publication_identifier":{"issn":["0165-0270"]},"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","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425"},{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","call_identifier":"FWF","name":"Molecular Drug Targets"}],"external_id":{"isi":["000456220900013"],"pmid":["30496761"]},"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","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","day":"15","article_processing_charge":"No","scopus_import":"1","date_published":"2019-01-15T00:00:00Z","article_type":"original","page":"114-121","publication":"Journal of Neuroscience Methods","citation":{"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.","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.","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.","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"}},{"month":"06","publication_identifier":{"isbn":["9781510886988"]},"quality_controlled":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1810.07766"}],"external_id":{"arxiv":["1810.07766"],"isi":["000684034307036"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"start_date":"2019-06-10","location":"Long Beach, CA, United States","end_date":"2019-06-15","name":"ICML: International Conference on Machine Learning"},"publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"IMLS","year":"2019","date_updated":"2023-09-06T15:21:48Z","date_created":"2020-02-02T23:01:06Z","volume":"2019-June","author":[{"first_name":"Chen","last_name":"Yu","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"},{"full_name":"Singla, Ankit","first_name":"Ankit","last_name":"Singla"},{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Zhang, Ce","first_name":"Ce","last_name":"Zhang"},{"full_name":"Liu, Ji","last_name":"Liu","first_name":"Ji"}],"scopus_import":"1","day":"01","article_processing_charge":"No","page":"12481-12512","publication":"36th International Conference on Machine Learning, ICML 2019","citation":{"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.","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.","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.","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."},"date_published":"2019-06-01T00:00:00Z","type":"conference","abstract":[{"lang":"eng","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."}],"status":"public","title":"Distributed learning over unreliable networks","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7437","oa_version":"Preprint"},{"ec_funded":1,"volume":48,"date_updated":"2023-09-06T15:25:29Z","date_created":"2020-01-30T09:27:32Z","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","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"VlKo"}],"publisher":"SIAM","publication_status":"published","year":"2019","publication_identifier":{"issn":["0097-5397"],"eissn":["1095-7111"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.1137/16m109332x","project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1809.01537","open_access":"1"}],"oa":1,"external_id":{"isi":["000493900200005"],"arxiv":["1809.01537"]},"issue":"5","abstract":[{"lang":"eng","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."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 48","status":"public","title":"A local lemma for focused stochastical algorithms","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7412","article_processing_charge":"No","day":"31","scopus_import":"1","date_published":"2019-10-31T00:00:00Z","page":"1583-1602","article_type":"original","citation":{"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","ista":"Achlioptas D, Iliopoulos F, Kolmogorov V. 2019. A local lemma for focused stochastical algorithms. SIAM Journal on Computing. 48(5), 1583–1602.","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.","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.","short":"D. Achlioptas, F. Iliopoulos, V. Kolmogorov, SIAM Journal on Computing 48 (2019) 1583–1602.","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."},"publication":"SIAM Journal on Computing"},{"month":"11","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"quality_controlled":"1","isi":1,"external_id":{"isi":["000498397300001"]},"language":[{"iso":"eng"}],"doi":"10.1145/3355089.3356565","article_number":"151","publication_status":"published","publisher":"ACM","department":[{"_id":"ChWo"}],"year":"2019","date_updated":"2023-09-06T15:22:23Z","date_created":"2020-01-30T10:19:43Z","volume":38,"author":[{"full_name":"Karlík, Ondřej","first_name":"Ondřej","last_name":"Karlík"},{"last_name":"Šik","first_name":"Martin","full_name":"Šik, Martin"},{"last_name":"Vévoda","first_name":"Petr","full_name":"Vévoda, Petr"},{"full_name":"Skrivan, Tomas","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","last_name":"Skrivan","first_name":"Tomas"},{"full_name":"Křivánek, Jaroslav","last_name":"Křivánek","first_name":"Jaroslav"}],"scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","publication":"ACM Transactions on Graphics","citation":{"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","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.","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.","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.","short":"O. Karlík, M. Šik, P. Vévoda, T. Skrivan, J. Křivánek, ACM Transactions on Graphics 38 (2019).","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."},"date_published":"2019-11-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","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."}],"issue":"6","title":"MIS compensation: Optimizing sampling techniques in multiple importance sampling","status":"public","intvolume":" 38","_id":"7418","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"None"},{"month":"06","publication_identifier":{"issn":["0001-5962"],"eissn":["1871-2509"]},"doi":"10.4310/acta.2019.v222.n2.a1","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1801.01389"}],"oa":1,"external_id":{"arxiv":["1801.01389"],"isi":["000495865300001"]},"quality_controlled":"1","isi":1,"author":[{"full_name":"Boccato, Chiara","first_name":"Chiara","last_name":"Boccato","id":"342E7E22-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Brennecke, Christian","first_name":"Christian","last_name":"Brennecke"},{"last_name":"Cenatiempo","first_name":"Serena","full_name":"Cenatiempo, Serena"},{"full_name":"Schlein, Benjamin","first_name":"Benjamin","last_name":"Schlein"}],"date_created":"2020-01-30T09:30:41Z","date_updated":"2023-09-06T15:24:31Z","volume":222,"year":"2019","publication_status":"published","publisher":"International Press of Boston","department":[{"_id":"RoSe"}],"day":"07","article_processing_charge":"No","scopus_import":"1","date_published":"2019-06-07T00:00:00Z","publication":"Acta Mathematica","citation":{"ista":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. 2019. Bogoliubov theory in the Gross–Pitaevskii limit. Acta Mathematica. 222(2), 219–335.","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.","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","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","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.","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."},"article_type":"original","page":"219-335","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."}],"issue":"2","type":"journal_article","oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7413","title":"Bogoliubov theory in the Gross–Pitaevskii limit","status":"public","intvolume":" 222"},{"doi":"10.1126/sciadv.aav9963","language":[{"iso":"eng"}],"external_id":{"isi":["000505069600008"],"pmid":["31840052"]},"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,"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"_id":"265B41B8-B435-11E9-9278-68D0E5697425","grant_number":"797747","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["2375-2548"]},"month":"12","author":[{"last_name":"Morales","first_name":"Hernán E.","full_name":"Morales, Hernán E."},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"full_name":"Larsson, Tomas","first_name":"Tomas","last_name":"Larsson"},{"first_name":"Marina","last_name":"Panova","full_name":"Panova, Marina"},{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"volume":5,"date_updated":"2023-09-06T15:35:56Z","date_created":"2020-01-29T15:58:27Z","pmid":1,"year":"2019","publisher":"AAAS","department":[{"_id":"NiBa"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-14T12:47:57Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","article_number":"eaav9963","date_published":"2019-12-04T00:00:00Z","citation":{"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.","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.","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.","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"},"publication":"Science Advances","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"04","scopus_import":"1","file":[{"file_size":1869449,"content_type":"application/pdf","creator":"dernst","file_name":"2019_ScienceAdvances_Morales.pdf","access_level":"open_access","date_created":"2020-02-03T13:33:25Z","date_updated":"2020-07-14T12:47:57Z","checksum":"af99a5dcdc66c6d6102051faf3be48d8","relation":"main_file","file_id":"7442"}],"oa_version":"Published Version","_id":"7393","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 5","title":"Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast","ddc":["570"],"status":"public","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."}],"type":"journal_article"},{"page":"699-719","article_type":"original","citation":{"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","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.","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","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.","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.","short":"J.M. Lopez Alonso, G.H. Choueiri, B. Hof, Journal of Fluid Mechanics 874 (2019) 699–719.","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."},"publication":"Journal of Fluid Mechanics","date_published":"2019-09-10T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"10","intvolume":" 874","status":"public","title":"Dynamics of viscoelastic pipe flow at low Reynolds numbers in the maximum drag reduction limit","_id":"7397","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","type":"journal_article","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"}],"isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1808.04080","open_access":"1"}],"oa":1,"external_id":{"isi":["000475349900001"],"arxiv":["1808.04080"]},"language":[{"iso":"eng"}],"doi":"10.1017/jfm.2019.486","publication_identifier":{"eissn":["1469-7645"],"issn":["0022-1120"]},"month":"09","publisher":"CUP","department":[{"_id":"BjHo"}],"publication_status":"published","year":"2019","volume":874,"date_updated":"2023-09-06T15:36:36Z","date_created":"2020-01-29T16:05:19Z","author":[{"full_name":"Lopez Alonso, Jose M","last_name":"Lopez Alonso","first_name":"Jose M","orcid":"0000-0002-0384-2022","id":"40770848-F248-11E8-B48F-1D18A9856A87"},{"id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","last_name":"Choueiri","first_name":"George H","full_name":"Choueiri, George H"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof","full_name":"Hof, Björn"}]},{"ec_funded":1,"file_date_updated":"2020-07-14T12:47:10Z","publisher":"Springer","department":[{"_id":"HeEd"}],"publication_status":"published","year":"2019","volume":62,"date_updated":"2023-09-07T12:07:12Z","date_created":"2018-12-16T22:59:20Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6287"}]},"author":[{"first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"orcid":"0000-0002-0659-3201","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","last_name":"Nikitenko","first_name":"Anton","full_name":"Nikitenko, Anton"}],"publication_identifier":{"issn":["01795376"],"eissn":["14320444"]},"month":"12","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","call_identifier":"H2020","name":"Alpha Shape Theory Extended"},{"name":"Persistence and stability of geometric complexes","call_identifier":"FWF","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000494042900008"],"arxiv":["1709.09380"]},"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/s00454-018-0049-2","type":"journal_article","issue":"4","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"}],"intvolume":" 62","title":"Poisson–Delaunay Mosaics of Order k","status":"public","ddc":["516"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"5678","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5932","date_created":"2019-02-06T10:10:46Z","date_updated":"2020-07-14T12:47:10Z","checksum":"f9d00e166efaccb5a76bbcbb4dcea3b4","file_name":"2018_DiscreteCompGeometry_Edelsbrunner.pdf","access_level":"open_access","file_size":599339,"content_type":"application/pdf","creator":"dernst"}],"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","page":"865–878","article_type":"original","citation":{"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.","short":"H. Edelsbrunner, A. Nikitenko, Discrete and Computational Geometry 62 (2019) 865–878.","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.","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","ista":"Edelsbrunner H, Nikitenko A. 2019. Poisson–Delaunay Mosaics of Order k. Discrete and Computational Geometry. 62(4), 865–878.","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.","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"},"publication":"Discrete and Computational Geometry","date_published":"2019-12-01T00:00:00Z"},{"year":"2019","department":[{"_id":"JoCs"}],"publisher":"Elsevier","publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"837"}],"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/reading-rats-minds/"}]},"author":[{"full_name":"Xu, Haibing","id":"310349D0-F248-11E8-B48F-1D18A9856A87","last_name":"Xu","first_name":"Haibing"},{"full_name":"Baracskay, Peter","id":"361CC00E-F248-11E8-B48F-1D18A9856A87","last_name":"Baracskay","first_name":"Peter"},{"id":"426376DC-F248-11E8-B48F-1D18A9856A87","first_name":"Joseph","last_name":"O'Neill","full_name":"O'Neill, Joseph"},{"orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L"}],"volume":101,"date_created":"2019-01-13T22:59:10Z","date_updated":"2023-09-07T12:06:37Z","ec_funded":1,"external_id":{"isi":["000454791500014"]},"main_file_link":[{"open_access":"1","url":"https://www.doi.org/10.1016/j.neuron.2018.11.015"}],"oa":1,"project":[{"grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","call_identifier":"FP7"}],"quality_controlled":"1","isi":1,"doi":"10.1016/j.neuron.2018.11.015","language":[{"iso":"eng"}],"publication_identifier":{"issn":["10974199"]},"month":"01","_id":"5828","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 101","title":"Assembly responses of hippocampal CA1 place cells predict learned behavior in goal-directed spatial tasks on the radial eight-arm maze","status":"public","oa_version":"Published Version","type":"journal_article","issue":"1","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."}],"citation":{"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.","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.","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","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","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.","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."},"publication":"Neuron","page":"119-132.e4","article_type":"original","date_published":"2019-01-02T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"02"},{"month":"04","publication_identifier":{"issn":["14240637"]},"external_id":{"isi":["000462444300008"],"arxiv":["1807.00739"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"},{"grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"doi":"10.1007/s00023-018-00757-0","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:12Z","ec_funded":1,"year":"2019","publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Springer","author":[{"full_name":"Moser, Thomas","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","last_name":"Moser","first_name":"Thomas"},{"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":"dissertation_contains","id":"52"}]},"date_created":"2019-01-20T22:59:17Z","date_updated":"2023-09-07T12:37:42Z","volume":20,"scopus_import":"1","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","publication":"Annales Henri Poincare","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."},"article_type":"original","page":"1325–1365","date_published":"2019-04-01T00:00:00Z","type":"journal_article","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."}],"issue":"4","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"5856","status":"public","title":"Energy contribution of a point-interacting impurity in a Fermi gas","ddc":["530"],"intvolume":" 20","oa_version":"Published Version","file":[{"file_id":"5894","relation":"main_file","checksum":"255e42f957a8e2b10aad2499c750a8d6","date_updated":"2020-07-14T12:47:12Z","date_created":"2019-01-28T15:27:17Z","access_level":"open_access","file_name":"2019_Annales_Moser.pdf","creator":"dernst","file_size":859846,"content_type":"application/pdf"}]}]