[{"file":[{"file_name":"2018_HSCC_Bakhirkin.pdf","content_type":"application/pdf","date_created":"2020-05-14T12:18:29Z","date_updated":"2020-07-14T12:45:17Z","checksum":"81eabc96430e84336ea88310ac0a1ad0","file_id":"7833","creator":"dernst","access_level":"open_access","file_size":5900421,"relation":"main_file"}],"month":"04","has_accepted_license":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"oa_version":"Submitted Version","project":[{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"}],"quality_controlled":"1","author":[{"first_name":"Alexey","last_name":"Bakhirkin","full_name":"Bakhirkin, Alexey"},{"id":"40960E6E-F248-11E8-B48F-1D18A9856A87","full_name":"Ferrere, Thomas","last_name":"Ferrere","first_name":"Thomas","orcid":"0000-0001-5199-3143"},{"last_name":"Maler","first_name":"Oded","full_name":"Maler, Oded"}],"conference":{"location":"Porto, Portugal","name":"HSCC: Hybrid Systems: Computation and Control","start_date":"2018-04-11","end_date":"2018-04-13"},"_id":"182","type":"conference","date_created":"2018-12-11T11:45:04Z","publication_identifier":{"isbn":["978-1-4503-5642-8 "]},"status":"public","ddc":["000"],"isi":1,"publication_status":"published","abstract":[{"lang":"eng","text":"We describe a new algorithm for the parametric identification problem for signal temporal logic (STL), stated as follows. Given a densetime real-valued signal w and a parameterized temporal logic formula φ, compute the subset of the parameter space that renders the formula satisfied by the signal. Unlike previous solutions, which were based on search in the parameter space or quantifier elimination, our procedure works recursively on φ and computes the evolution over time of the set of valid parameter assignments. This procedure is similar to that of monitoring or computing the robustness of φ relative to w. Our implementation and experiments demonstrate that this approach can work well in practice."}],"title":"Efficient parametric identification for STL","date_published":"2018-04-11T00:00:00Z","file_date_updated":"2020-07-14T12:45:17Z","publisher":"ACM","citation":{"apa":"Bakhirkin, A., Ferrere, T., &#38; Maler, O. (2018). Efficient parametric identification for STL. In <i>Proceedings of the 21st International Conference on Hybrid Systems</i> (pp. 177–186). Porto, Portugal: ACM. <a href=\"https://doi.org/10.1145/3178126.3178132\">https://doi.org/10.1145/3178126.3178132</a>","chicago":"Bakhirkin, Alexey, Thomas Ferrere, and Oded Maler. “Efficient Parametric Identification for STL.” In <i>Proceedings of the 21st International Conference on Hybrid Systems</i>, 177–86. ACM, 2018. <a href=\"https://doi.org/10.1145/3178126.3178132\">https://doi.org/10.1145/3178126.3178132</a>.","ista":"Bakhirkin A, Ferrere T, Maler O. 2018. Efficient parametric identification for STL. Proceedings of the 21st International Conference on Hybrid Systems. HSCC: Hybrid Systems: Computation and Control, HSCC Proceedings, , 177–186.","ama":"Bakhirkin A, Ferrere T, Maler O. Efficient parametric identification for STL. In: <i>Proceedings of the 21st International Conference on Hybrid Systems</i>. ACM; 2018:177-186. doi:<a href=\"https://doi.org/10.1145/3178126.3178132\">10.1145/3178126.3178132</a>","ieee":"A. Bakhirkin, T. Ferrere, and O. Maler, “Efficient parametric identification for STL,” in <i>Proceedings of the 21st International Conference on Hybrid Systems</i>, Porto, Portugal, 2018, pp. 177–186.","short":"A. Bakhirkin, T. Ferrere, O. Maler, in:, Proceedings of the 21st International Conference on Hybrid Systems, ACM, 2018, pp. 177–186.","mla":"Bakhirkin, Alexey, et al. “Efficient Parametric Identification for STL.” <i>Proceedings of the 21st International Conference on Hybrid Systems</i>, ACM, 2018, pp. 177–86, doi:<a href=\"https://doi.org/10.1145/3178126.3178132\">10.1145/3178126.3178132</a>."},"department":[{"_id":"ToHe"}],"date_updated":"2023-09-11T13:30:51Z","alternative_title":["HSCC Proceedings"],"external_id":{"isi":["000474781600020"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","publication":"Proceedings of the 21st International Conference on Hybrid Systems","publist_id":"7739","oa":1,"year":"2018","doi":"10.1145/3178126.3178132","page":"177 - 186","day":"11"},{"oa_version":"None","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","author":[{"full_name":"Bartocci, Ezio","last_name":"Bartocci","first_name":"Ezio"},{"full_name":"Ferrere, Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-3143","first_name":"Thomas","last_name":"Ferrere"},{"first_name":"Niveditha","last_name":"Manjunath","full_name":"Manjunath, Niveditha"},{"first_name":"Dejan","last_name":"Nickovic","full_name":"Nickovic, Dejan"}],"month":"04","article_processing_charge":"No","language":[{"iso":"eng"}],"_id":"183","type":"conference","date_created":"2018-12-11T11:45:04Z","status":"public","conference":{"name":"HSCC: Hybrid Systems: Computation and Control","location":"Porto, Portugal","end_date":"2018-04-13","start_date":"2018-04-11"},"citation":{"short":"E. Bartocci, T. Ferrere, N. Manjunath, D. Nickovic, in:, Association for Computing Machinery, Inc, 2018, pp. 197–206.","mla":"Bartocci, Ezio, et al. <i>Localizing Faults in Simulink/Stateflow Models with STL</i>. Association for Computing Machinery, Inc, 2018, pp. 197–206, doi:<a href=\"https://doi.org/10.1145/3178126.3178131\">10.1145/3178126.3178131</a>.","chicago":"Bartocci, Ezio, Thomas Ferrere, Niveditha Manjunath, and Dejan Nickovic. “Localizing Faults in Simulink/Stateflow Models with STL,” 197–206. Association for Computing Machinery, Inc, 2018. <a href=\"https://doi.org/10.1145/3178126.3178131\">https://doi.org/10.1145/3178126.3178131</a>.","ista":"Bartocci E, Ferrere T, Manjunath N, Nickovic D. 2018. Localizing faults in simulink/stateflow models with STL. HSCC: Hybrid Systems: Computation and Control, HSCC Proceedings, , 197–206.","ama":"Bartocci E, Ferrere T, Manjunath N, Nickovic D. Localizing faults in simulink/stateflow models with STL. In: Association for Computing Machinery, Inc; 2018:197-206. doi:<a href=\"https://doi.org/10.1145/3178126.3178131\">10.1145/3178126.3178131</a>","apa":"Bartocci, E., Ferrere, T., Manjunath, N., &#38; Nickovic, D. (2018). Localizing faults in simulink/stateflow models with STL (pp. 197–206). Presented at the HSCC: Hybrid Systems: Computation and Control, Porto, Portugal: Association for Computing Machinery, Inc. <a href=\"https://doi.org/10.1145/3178126.3178131\">https://doi.org/10.1145/3178126.3178131</a>","ieee":"E. Bartocci, T. Ferrere, N. Manjunath, and D. Nickovic, “Localizing faults in simulink/stateflow models with STL,” presented at the HSCC: Hybrid Systems: Computation and Control, Porto, Portugal, 2018, pp. 197–206."},"date_updated":"2023-09-13T08:48:46Z","department":[{"_id":"ToHe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000474781600022"]},"alternative_title":["HSCC Proceedings"],"isi":1,"abstract":[{"lang":"eng","text":"Fault-localization is considered to be a very tedious and time-consuming activity in the design of complex Cyber-Physical Systems (CPS). This laborious task essentially requires expert knowledge of the system in order to discover the cause of the fault. In this context, we propose a new procedure that AIDS designers in debugging Simulink/Stateflow hybrid system models, guided by Signal Temporal Logic (STL) specifications. The proposed method relies on three main ingredients: (1) a monitoring and a trace diagnostics procedure that checks whether a tested behavior satisfies or violates an STL specification, localizes time segments and interfaces variables contributing to the property violations; (2) a slicing procedure that maps these observable behavior segments to the internal states and transitions of the Simulink model; and (3) a spectrum-based fault-localization method that combines the previous analysis from multiple tests to identify the internal states and/or transitions that are the most likely to explain the fault. We demonstrate the applicability of our approach on two Simulink models from the automotive and the avionics domain."}],"publication_status":"published","title":"Localizing faults in simulink/stateflow models with STL","date_published":"2018-04-11T00:00:00Z","publisher":"Association for Computing Machinery, Inc","doi":"10.1145/3178126.3178131","day":"11","page":"197 - 206","year":"2018","acknowledgement":"This work was partially supported by the Austrian Science Fund (FWF) under grants S11402-N23 and S11405-N23 (RiSE/SHiNE), the CPS/IoT project (HRSM), the EU ICT COST Action IC1402 on Run-time Verification beyond Monitoring (ARVI), the AMASS project (ECSEL 692474), and the ENABLE-S3 project (ECSEL 692455). The CPS/IoT project receives support from the Austrian government through the Federal Ministry of Science, Research and Economy (BMWFW) in the funding program Hochschulraum-Strukturmittel (HRSM) 2016. The ECSEL Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and Austria, Denmark, Germany, Finland, Czech Republic, Italy, Spain, Portugal, Poland, Ireland, Belgium, France, Netherlands, United Kingdom, Slovakia, Norway.","scopus_import":"1","publist_id":"7738"},{"status":"public","type":"conference","_id":"184","date_created":"2018-12-11T11:45:04Z","conference":{"start_date":"2018-06-11","end_date":"2018-06-14","location":"Budapest, Hungary","name":"SoCG: Symposium on Computational Geometry"},"author":[{"first_name":"Xavier","last_name":"Goaoc","full_name":"Goaoc, Xavier"},{"last_name":"Paták","first_name":"Pavel","full_name":"Paták, Pavel"},{"id":"48B57058-F248-11E8-B48F-1D18A9856A87","full_name":"Patakova, Zuzana","first_name":"Zuzana","last_name":"Patakova","orcid":"0000-0002-3975-1683"},{"first_name":"Martin","last_name":"Tancer","orcid":"0000-0002-1191-6714","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","full_name":"Tancer, Martin"},{"full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","first_name":"Uli","last_name":"Wagner"}],"oa_version":"Published Version","quality_controlled":"1","volume":99,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","date_created":"2018-12-17T16:35:02Z","date_updated":"2020-07-14T12:45:18Z","file_name":"2018_LIPIcs_Goaoc.pdf","relation":"main_file","checksum":"d12bdd60f04a57307867704b5f930afd","file_id":"5725","creator":"dernst","access_level":"open_access","file_size":718414}],"month":"06","has_accepted_license":"1","year":"2018","doi":"10.4230/LIPIcs.SoCG.2018.41","page":"41:1 - 41:16","day":"11","acknowledgement":"Partially supported by the project EMBEDS II (CZ: 7AMB17FR029, FR: 38087RM) of Czech-French collaboration.","oa":1,"intvolume":"        99","publist_id":"7736","related_material":{"record":[{"id":"7108","relation":"later_version","status":"public"}]},"scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"citation":{"apa":"Goaoc, X., Paták, P., Patakova, Z., Tancer, M., &#38; Wagner, U. (2018). Shellability is NP-complete (Vol. 99, p. 41:1-41:16). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.41\">https://doi.org/10.4230/LIPIcs.SoCG.2018.41</a>","ista":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. 2018. Shellability is NP-complete. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 41:1-41:16.","chicago":"Goaoc, Xavier, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Shellability Is NP-Complete,” 99:41:1-41:16. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.41\">https://doi.org/10.4230/LIPIcs.SoCG.2018.41</a>.","ama":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:41:1-41:16. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.41\">10.4230/LIPIcs.SoCG.2018.41</a>","ieee":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “Shellability is NP-complete,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 41:1-41:16.","short":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 41:1-41:16.","mla":"Goaoc, Xavier, et al. <i>Shellability Is NP-Complete</i>. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 41:1-41:16, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.41\">10.4230/LIPIcs.SoCG.2018.41</a>."},"date_updated":"2023-09-06T11:10:57Z","department":[{"_id":"UlWa"}],"title":"Shellability is NP-complete","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_published":"2018-06-11T00:00:00Z","file_date_updated":"2020-07-14T12:45:18Z","ddc":["516","000"],"abstract":[{"lang":"eng","text":"We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial complex is shellable is NP-hard, hence NP-complete. This resolves a question raised, e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d ≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible pure d-dimensional complexes."}],"publication_status":"published"},{"citation":{"short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","mla":"Fulek, Radoslav, and Jan Kynčl. <i>Hanani-Tutte for Approximating Maps of Graphs</i>. Vol. 99, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.39\">10.4230/LIPIcs.SoCG.2018.39</a>.","apa":"Fulek, R., &#38; Kynčl, J. (2018). Hanani-Tutte for approximating maps of graphs (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.39\">https://doi.org/10.4230/LIPIcs.SoCG.2018.39</a>","ama":"Fulek R, Kynčl J. Hanani-Tutte for approximating maps of graphs. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.39\">10.4230/LIPIcs.SoCG.2018.39</a>","ista":"Fulek R, Kynčl J. 2018. Hanani-Tutte for approximating maps of graphs. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 39.","chicago":"Fulek, Radoslav, and Jan Kynčl. “Hanani-Tutte for Approximating Maps of Graphs,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.39\">https://doi.org/10.4230/LIPIcs.SoCG.2018.39</a>.","ieee":"R. Fulek and J. Kynčl, “Hanani-Tutte for approximating maps of graphs,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99."},"department":[{"_id":"UlWa"}],"date_updated":"2021-01-12T06:53:36Z","alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["510"],"publication_status":"published","abstract":[{"text":"We resolve in the affirmative conjectures of A. Skopenkov and Repovš (1998), and M. Skopenkov (2003) generalizing the classical Hanani-Tutte theorem to the setting of approximating maps of graphs on 2-dimensional surfaces by embeddings. Our proof of this result is constructive and almost immediately implies an efficient algorithm for testing whether a given piecewise linear map of a graph in a surface is approximable by an embedding. More precisely, an instance of this problem consists of (i) a graph G whose vertices are partitioned into clusters and whose inter-cluster edges are partitioned into bundles, and (ii) a region R of a 2-dimensional compact surface M given as the union of a set of pairwise disjoint discs corresponding to the clusters and a set of pairwise disjoint &quot;pipes&quot; corresponding to the bundles, connecting certain pairs of these discs. We are to decide whether G can be embedded inside M so that the vertices in every cluster are drawn in the corresponding disc, the edges in every bundle pass only through its corresponding pipe, and every edge crosses the boundary of each disc at most once.","lang":"eng"}],"title":"Hanani-Tutte for approximating maps of graphs","date_published":"2018-01-01T00:00:00Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file_date_updated":"2020-07-14T12:45:19Z","oa":1,"doi":"10.4230/LIPIcs.SoCG.2018.39","year":"2018","day":"01","scopus_import":1,"publist_id":"7735","intvolume":"        99","oa_version":"Published Version","quality_controlled":"1","project":[{"call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425","grant_number":"M02281","name":"Eliminating intersections in drawings of graphs"}],"author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","full_name":"Fulek, Radoslav","last_name":"Fulek","first_name":"Radoslav","orcid":"0000-0001-8485-1774"},{"first_name":"Jan","last_name":"Kynčl","full_name":"Kynčl, Jan"}],"file":[{"file_name":"2018_LIPIcs_Fulek.pdf","date_created":"2018-12-17T12:33:52Z","date_updated":"2020-07-14T12:45:19Z","content_type":"application/pdf","access_level":"open_access","file_size":718857,"file_id":"5701","checksum":"f1b94f1a75b37c414a1f61d59fb2cd4c","creator":"dernst","relation":"main_file"}],"article_number":"39","month":"01","has_accepted_license":"1","volume":99,"language":[{"iso":"eng"}],"_id":"185","type":"conference","date_created":"2018-12-11T11:45:04Z","status":"public","publication_identifier":{"isbn":["978-3-95977-066-8"]},"conference":{"location":"Budapest, Hungary","name":"SoCG: Symposium on Computational Geometry","start_date":"2018-06-11","end_date":"2018-06-14"}},{"page":"40.1 - 40.14","year":"2018","day":"11","doi":"10.4230/LIPIcs.SoCG.2018.40","oa":1,"publist_id":"7734","arxiv":1,"intvolume":"        99","scopus_import":"1","related_material":{"record":[{"status":"public","id":"11593","relation":"later_version"}]},"alternative_title":["LIPIcs"],"external_id":{"arxiv":["1803.05085"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14.","mla":"Fulek, Radoslav, and Jan Kynčl. <i>The ℤ2-Genus of Kuratowski Minors</i>. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.40\">10.4230/LIPIcs.SoCG.2018.40</a>.","ieee":"R. Fulek and J. Kynčl, “The ℤ2-Genus of Kuratowski minors,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 40.1-40.14.","apa":"Fulek, R., &#38; Kynčl, J. (2018). The ℤ2-Genus of Kuratowski minors (Vol. 99, p. 40.1-40.14). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.40\">https://doi.org/10.4230/LIPIcs.SoCG.2018.40</a>","ista":"Fulek R, Kynčl J. 2018. The ℤ2-Genus of Kuratowski minors. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 40.1-40.14.","chicago":"Fulek, Radoslav, and Jan Kynčl. “The ℤ2-Genus of Kuratowski Minors,” 99:40.1-40.14. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.40\">https://doi.org/10.4230/LIPIcs.SoCG.2018.40</a>.","ama":"Fulek R, Kynčl J. The ℤ2-Genus of Kuratowski minors. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:40.1-40.14. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.40\">10.4230/LIPIcs.SoCG.2018.40</a>"},"department":[{"_id":"UlWa"}],"date_updated":"2023-08-14T12:43:51Z","title":"The ℤ2-Genus of Kuratowski minors","date_published":"2018-06-11T00:00:00Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","abstract":[{"text":"A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The ℤ2-genus of a graph G is the minimum g such that G has an independently even drawing on the orientable surface of genus g. An unpublished result by Robertson and Seymour implies that for every t, every graph of sufficiently large genus contains as a minor a projective t × t grid or one of the following so-called t-Kuratowski graphs: K3, t, or t copies of K5 or K3,3 sharing at most 2 common vertices. We show that the ℤ2-genus of graphs in these families is unbounded in t; in fact, equal to their genus. Together, this implies that the genus of a graph is bounded from above by a function of its ℤ2-genus, solving a problem posed by Schaefer and Štefankovič, and giving an approximate version of the Hanani-Tutte theorem on orientable surfaces.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.05085"}],"status":"public","_id":"186","type":"conference","date_created":"2018-12-11T11:45:05Z","conference":{"end_date":"2018-06-14","start_date":"2018-06-11","name":"SoCG: Symposium on Computational Geometry","location":"Budapest, Hungary"},"author":[{"last_name":"Fulek","first_name":"Radoslav","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","full_name":"Fulek, Radoslav"},{"full_name":"Kynčl, Jan","last_name":"Kynčl","first_name":"Jan"}],"oa_version":"Submitted Version","quality_controlled":"1","project":[{"call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425","grant_number":"M02281","name":"Eliminating intersections in drawings of graphs"}],"volume":99,"article_processing_charge":"No","language":[{"iso":"eng"}],"month":"06"},{"acknowledgement":"This work is partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","year":"2018","day":"11","doi":"10.4230/LIPIcs.SoCG.2018.34","oa":1,"intvolume":"        99","publist_id":"7732","related_material":{"record":[{"id":"9317","relation":"later_version","status":"public"},{"relation":"dissertation_contains","id":"9056","status":"public"}]},"scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"alternative_title":["LIPIcs"],"date_updated":"2023-09-07T13:29:00Z","department":[{"_id":"HeEd"}],"citation":{"apa":"Edelsbrunner, H., &#38; Osang, G. F. (2018). The multi-cover persistence of Euclidean balls (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.34\">https://doi.org/10.4230/LIPIcs.SoCG.2018.34</a>","chicago":"Edelsbrunner, Herbert, and Georg F Osang. “The Multi-Cover Persistence of Euclidean Balls,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.34\">https://doi.org/10.4230/LIPIcs.SoCG.2018.34</a>.","ama":"Edelsbrunner H, Osang GF. The multi-cover persistence of Euclidean balls. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.34\">10.4230/LIPIcs.SoCG.2018.34</a>","ista":"Edelsbrunner H, Osang GF. 2018. The multi-cover persistence of Euclidean balls. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 34.","ieee":"H. Edelsbrunner and G. F. Osang, “The multi-cover persistence of Euclidean balls,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","mla":"Edelsbrunner, Herbert, and Georg F. Osang. <i>The Multi-Cover Persistence of Euclidean Balls</i>. Vol. 99, 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.34\">10.4230/LIPIcs.SoCG.2018.34</a>.","short":"H. Edelsbrunner, G.F. Osang, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018."},"date_published":"2018-06-11T00:00:00Z","file_date_updated":"2020-07-14T12:45:19Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","title":"The multi-cover persistence of Euclidean balls","abstract":[{"text":"Given a locally finite X ⊆ ℝd and a radius r ≥ 0, the k-fold cover of X and r consists of all points in ℝd that have k or more points of X within distance r. We consider two filtrations - one in scale obtained by fixing k and increasing r, and the other in depth obtained by fixing r and decreasing k - and we compute the persistence diagrams of both. While standard methods suffice for the filtration in scale, we need novel geometric and topological concepts for the filtration in depth. In particular, we introduce a rhomboid tiling in ℝd+1 whose horizontal integer slices are the order-k Delaunay mosaics of X, and construct a zigzag module from Delaunay mosaics that is isomorphic to the persistence module of the multi-covers. ","lang":"eng"}],"publication_status":"published","ddc":["516"],"status":"public","date_created":"2018-12-11T11:45:05Z","type":"conference","_id":"187","conference":{"name":"SoCG: Symposium on Computational Geometry","location":"Budapest, Hungary","end_date":"2018-06-14","start_date":"2018-06-11"},"author":[{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8882-5116","last_name":"Osang","first_name":"Georg F","full_name":"Osang, Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","project":[{"name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"volume":99,"has_accepted_license":"1","month":"06","article_number":"34","file":[{"file_size":528018,"access_level":"open_access","creator":"dernst","file_id":"5738","checksum":"d8c0533ad0018eb4ed1077475eb8fc18","relation":"main_file","file_name":"2018_LIPIcs_Edelsbrunner_Osang.pdf","date_updated":"2020-07-14T12:45:19Z","date_created":"2018-12-18T09:27:22Z","content_type":"application/pdf"}]},{"publication_status":"published","abstract":[{"lang":"eng","text":"Smallest enclosing spheres of finite point sets are central to methods in topological data analysis. Focusing on Bregman divergences to measure dissimilarity, we prove bounds on the location of the center of a smallest enclosing sphere. These bounds depend on the range of radii for which Bregman balls are convex."}],"ddc":["000"],"date_published":"2018-06-11T00:00:00Z","file_date_updated":"2020-07-14T12:45:20Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","title":"Smallest enclosing spheres and Chernoff points in Bregman geometry","department":[{"_id":"HeEd"}],"date_updated":"2021-01-12T06:53:48Z","citation":{"mla":"Edelsbrunner, Herbert, et al. <i>Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry</i>. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.35\">10.4230/LIPIcs.SoCG.2018.35</a>.","short":"H. Edelsbrunner, Z. Virk, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13.","ista":"Edelsbrunner H, Virk Z, Wagner H. 2018. Smallest enclosing spheres and Chernoff points in Bregman geometry. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 35:1-35:13.","chicago":"Edelsbrunner, Herbert, Ziga Virk, and Hubert Wagner. “Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry,” 99:35:1-35:13. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.35\">https://doi.org/10.4230/LIPIcs.SoCG.2018.35</a>.","ama":"Edelsbrunner H, Virk Z, Wagner H. Smallest enclosing spheres and Chernoff points in Bregman geometry. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:35:1-35:13. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.35\">10.4230/LIPIcs.SoCG.2018.35</a>","apa":"Edelsbrunner, H., Virk, Z., &#38; Wagner, H. (2018). Smallest enclosing spheres and Chernoff points in Bregman geometry (Vol. 99, p. 35:1-35:13). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.35\">https://doi.org/10.4230/LIPIcs.SoCG.2018.35</a>","ieee":"H. Edelsbrunner, Z. Virk, and H. Wagner, “Smallest enclosing spheres and Chernoff points in Bregman geometry,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 35:1-35:13."},"alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"publist_id":"7733","intvolume":"        99","oa":1,"acknowledgement":"This research is partially supported by the Office of Naval Research, through grant no. N62909-18-1-2038, and the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund","doi":"10.4230/LIPIcs.SoCG.2018.35","year":"2018","page":"35:1 - 35:13","day":"11","month":"06","has_accepted_license":"1","file":[{"relation":"main_file","access_level":"open_access","file_size":489080,"checksum":"7509403803b3ac1aee94bbc2ad293d21","file_id":"5724","creator":"dernst","date_created":"2018-12-17T16:31:31Z","date_updated":"2020-07-14T12:45:20Z","content_type":"application/pdf","file_name":"2018_LIPIcs_Edelsbrunner.pdf"}],"language":[{"iso":"eng"}],"volume":99,"project":[{"name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"quality_controlled":"1","oa_version":"Published Version","author":[{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ziga","last_name":"Virk","full_name":"Virk, Ziga"},{"full_name":"Wagner, Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Hubert"}],"conference":{"location":"Budapest, Hungary","name":"SoCG: Symposium on Computational Geometry","end_date":"2018-06-14","start_date":"2018-06-11"},"date_created":"2018-12-11T11:45:05Z","type":"conference","_id":"188","status":"public"},{"publication_identifier":{"issn":["0737-4038"]},"status":"public","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30169679"}],"_id":"19","type":"journal_article","article_type":"original","date_created":"2018-12-11T11:44:11Z","article_processing_charge":"No","volume":35,"language":[{"iso":"eng"}],"issue":"11","month":"08","author":[{"last_name":"Palmer","first_name":"Adam","full_name":"Palmer, Adam"},{"id":"3464AE84-F248-11E8-B48F-1D18A9856A87","full_name":"Chait, Remy P","first_name":"Remy P","last_name":"Chait","orcid":"0000-0003-0876-3187"},{"full_name":"Kishony, Roy","first_name":"Roy","last_name":"Kishony"}],"oa_version":"Submitted Version","quality_controlled":"1","publication":"Molecular Biology and Evolution","intvolume":"        35","publist_id":"8036","scopus_import":"1","page":"2669 - 2684","doi":"10.1093/molbev/msy163","year":"2018","day":"28","oa":1,"title":"Nonoptimal gene expression creates latent potential for antibiotic resistance","date_published":"2018-08-28T00:00:00Z","publisher":"Oxford University Press","pmid":1,"isi":1,"abstract":[{"text":"Bacteria regulate genes to survive antibiotic stress, but regulation can be far from perfect. When regulation is not optimal, mutations that change gene expression can contribute to antibiotic resistance. It is not systematically understood to what extent natural gene regulation is or is not optimal for distinct antibiotics, and how changes in expression of specific genes quantitatively affect antibiotic resistance. Here we discover a simple quantitative relation between fitness, gene expression, and antibiotic potency, which rationalizes our observation that a multitude of genes and even innate antibiotic defense mechanisms have expression that is critically nonoptimal under antibiotic treatment. First, we developed a pooled-strain drug-diffusion assay and screened Escherichia coli overexpression and knockout libraries, finding that resistance to a range of 31 antibiotics could result from changing expression of a large and functionally diverse set of genes, in a primarily but not exclusively drug-specific manner. Second, by synthetically controlling the expression of single-drug and multidrug resistance genes, we observed that their fitness-expression functions changed dramatically under antibiotic treatment in accordance with a log-sensitivity relation. Thus, because many genes are nonoptimally expressed under antibiotic treatment, many regulatory mutations can contribute to resistance by altering expression and by activating latent defenses.","lang":"eng"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["30169679"],"isi":["000452567200006"]},"citation":{"ama":"Palmer A, Chait RP, Kishony R. Nonoptimal gene expression creates latent potential for antibiotic resistance. <i>Molecular Biology and Evolution</i>. 2018;35(11):2669-2684. doi:<a href=\"https://doi.org/10.1093/molbev/msy163\">10.1093/molbev/msy163</a>","ista":"Palmer A, Chait RP, Kishony R. 2018. Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. 35(11), 2669–2684.","chicago":"Palmer, Adam, Remy P Chait, and Roy Kishony. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/molbev/msy163\">https://doi.org/10.1093/molbev/msy163</a>.","apa":"Palmer, A., Chait, R. P., &#38; Kishony, R. (2018). Nonoptimal gene expression creates latent potential for antibiotic resistance. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msy163\">https://doi.org/10.1093/molbev/msy163</a>","ieee":"A. Palmer, R. P. Chait, and R. Kishony, “Nonoptimal gene expression creates latent potential for antibiotic resistance,” <i>Molecular Biology and Evolution</i>, vol. 35, no. 11. Oxford University Press, pp. 2669–2684, 2018.","short":"A. Palmer, R.P. Chait, R. Kishony, Molecular Biology and Evolution 35 (2018) 2669–2684.","mla":"Palmer, Adam, et al. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” <i>Molecular Biology and Evolution</i>, vol. 35, no. 11, Oxford University Press, 2018, pp. 2669–84, doi:<a href=\"https://doi.org/10.1093/molbev/msy163\">10.1093/molbev/msy163</a>."},"date_updated":"2023-10-17T11:51:06Z","department":[{"_id":"CaGu"},{"_id":"GaTk"}]},{"title":"Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest","pmid":1,"date_published":"2018-07-11T00:00:00Z","publisher":"Wiley","isi":1,"publication_status":"published","abstract":[{"lang":"eng","text":"The German cockroach, Blattella germanica, is a worldwide pest that infests buildings, including homes, restaurants, and hospitals, often living in unsanitary conditions. As a disease vector and producer of allergens, this species has major health and economic impacts on humans. Factors contributing to the success of the German cockroach include its resistance to a broad range of insecticides, immunity to many pathogens, and its ability, as an extreme generalist omnivore, to survive on most food sources. The recently published genome shows that B. germanica has an exceptionally high number of protein coding genes. In this study, we investigate the functions of the 93 significantly expanded gene families with the aim to better understand the success of B. germanica as a major pest despite such inhospitable conditions. We find major expansions in gene families with functions related to the detoxification of insecticides and allelochemicals, defense against pathogens, digestion, sensory perception, and gene regulation. These expansions might have allowed B. germanica to develop multiple resistance mechanisms to insecticides and pathogens, and enabled a broad, flexible diet, thus explaining its success in unsanitary conditions and under recurrent chemical control. The findings and resources presented here provide insights for better understanding molecular mechanisms that will facilitate more effective cockroach control."}],"external_id":{"isi":["000443231000002"],"pmid":["29998472"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"M. Harrison, N. Arning, L. Kremer, G. Ylla, X. Belles, E. Bornberg Bauer, A.K. Huylmans, E. Jongepier, M. Puilachs, S. Richards, C. Schal, Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 330 (2018) 254–264.","mla":"Harrison, Mark, et al. “Expansions of Key Protein Families in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>, vol. 330, Wiley, 2018, pp. 254–64, doi:<a href=\"https://doi.org/10.1002/jez.b.22824\">10.1002/jez.b.22824</a>.","chicago":"Harrison, Mark, Nicolas Arning, Lucas Kremer, Guillem Ylla, Xavier Belles, Erich Bornberg Bauer, Ann K Huylmans, et al. “Expansions of Key Protein Families in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/jez.b.22824\">https://doi.org/10.1002/jez.b.22824</a>.","ista":"Harrison M, Arning N, Kremer L, Ylla G, Belles X, Bornberg Bauer E, Huylmans AK, Jongepier E, Puilachs M, Richards S, Schal C. 2018. Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 330, 254–264.","ama":"Harrison M, Arning N, Kremer L, et al. Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. 2018;330:254-264. doi:<a href=\"https://doi.org/10.1002/jez.b.22824\">10.1002/jez.b.22824</a>","apa":"Harrison, M., Arning, N., Kremer, L., Ylla, G., Belles, X., Bornberg Bauer, E., … Schal, C. (2018). Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. Wiley. <a href=\"https://doi.org/10.1002/jez.b.22824\">https://doi.org/10.1002/jez.b.22824</a>","ieee":"M. Harrison <i>et al.</i>, “Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest,” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>, vol. 330. Wiley, pp. 254–264, 2018."},"department":[{"_id":"BeVi"}],"date_updated":"2023-09-11T13:59:54Z","publication":"Journal of Experimental Zoology Part B: Molecular and Developmental Evolution","publist_id":"7730","intvolume":"       330","scopus_import":"1","year":"2018","doi":"10.1002/jez.b.22824","page":"254-264","day":"11","oa":1,"volume":330,"article_processing_charge":"No","language":[{"iso":"eng"}],"month":"07","author":[{"last_name":"Harrison","first_name":"Mark","full_name":"Harrison, Mark"},{"first_name":"Nicolas","last_name":"Arning","full_name":"Arning, Nicolas"},{"full_name":"Kremer, Lucas","last_name":"Kremer","first_name":"Lucas"},{"last_name":"Ylla","first_name":"Guillem","full_name":"Ylla, Guillem"},{"first_name":"Xavier","last_name":"Belles","full_name":"Belles, Xavier"},{"last_name":"Bornberg Bauer","first_name":"Erich","full_name":"Bornberg Bauer, Erich"},{"orcid":"0000-0001-8871-4961","first_name":"Ann K","last_name":"Huylmans","full_name":"Huylmans, Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jongepier, Evelien","last_name":"Jongepier","first_name":"Evelien"},{"last_name":"Puilachs","first_name":"Maria","full_name":"Puilachs, Maria"},{"first_name":"Stephen","last_name":"Richards","full_name":"Richards, Stephen"},{"full_name":"Schal, Coby","last_name":"Schal","first_name":"Coby"}],"oa_version":"Submitted Version","quality_controlled":"1","status":"public","main_file_link":[{"url":"https://onlinelibrary.wiley.com/doi/am-pdf/10.1002/jez.b.22824","open_access":"1"}],"article_type":"original","_id":"190","type":"journal_article","date_created":"2018-12-11T11:45:06Z"},{"citation":{"short":"P. Grones, M.F. Abas, J. Hajny, A. Jones, S. Waidmann, J. Kleine Vehn, J. Friml, Scientific Reports 8 (2018).","mla":"Grones, Peter, et al. “PID/WAG-Mediated Phosphorylation of the Arabidopsis PIN3 Auxin Transporter Mediates Polarity Switches during Gravitropism.” <i>Scientific Reports</i>, vol. 8, no. 1, 10279, Springer, 2018, doi:<a href=\"https://doi.org/10.1038/s41598-018-28188-1\">10.1038/s41598-018-28188-1</a>.","ieee":"P. Grones <i>et al.</i>, “PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism,” <i>Scientific Reports</i>, vol. 8, no. 1. Springer, 2018.","apa":"Grones, P., Abas, M. F., Hajny, J., Jones, A., Waidmann, S., Kleine Vehn, J., &#38; Friml, J. (2018). PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. <i>Scientific Reports</i>. Springer. <a href=\"https://doi.org/10.1038/s41598-018-28188-1\">https://doi.org/10.1038/s41598-018-28188-1</a>","chicago":"Grones, Peter, Melinda F Abas, Jakub Hajny, Angharad Jones, Sascha Waidmann, Jürgen Kleine Vehn, and Jiří Friml. “PID/WAG-Mediated Phosphorylation of the Arabidopsis PIN3 Auxin Transporter Mediates Polarity Switches during Gravitropism.” <i>Scientific Reports</i>. Springer, 2018. <a href=\"https://doi.org/10.1038/s41598-018-28188-1\">https://doi.org/10.1038/s41598-018-28188-1</a>.","ista":"Grones P, Abas MF, Hajny J, Jones A, Waidmann S, Kleine Vehn J, Friml J. 2018. PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. Scientific Reports. 8(1), 10279.","ama":"Grones P, Abas MF, Hajny J, et al. PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism. <i>Scientific Reports</i>. 2018;8(1). doi:<a href=\"https://doi.org/10.1038/s41598-018-28188-1\">10.1038/s41598-018-28188-1</a>"},"date_updated":"2025-05-07T11:12:31Z","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"isi":["000437673200053"]},"ddc":["581"],"isi":1,"abstract":[{"text":"Intercellular distribution of the plant hormone auxin largely depends on the polar subcellular distribution of the plasma membrane PIN-FORMED (PIN) auxin transporters. PIN polarity switches in response to different developmental and environmental signals have been shown to redirect auxin fluxes mediating certain developmental responses. PIN phosphorylation at different sites and by different kinases is crucial for PIN function. Here we investigate the role of PIN phosphorylation during gravitropic response. Loss- and gain-of-function mutants in PINOID and related kinases but not in D6PK kinase as well as mutations mimicking constitutive dephosphorylated or phosphorylated status of two clusters of predicted phosphorylation sites partially disrupted PIN3 phosphorylation and caused defects in gravitropic bending in roots and hypocotyls. In particular, they impacted PIN3 polarity rearrangements in response to gravity and during feed-back regulation by auxin itself. Thus PIN phosphorylation, besides regulating transport activity and apical-basal targeting, is also important for the rapid polarity switches in response to environmental and endogenous signals.","lang":"eng"}],"publication_status":"published","title":"PID/WAG-mediated phosphorylation of the Arabidopsis PIN3 auxin transporter mediates polarity switches during gravitropism","file_date_updated":"2020-07-14T12:45:20Z","date_published":"2018-07-06T00:00:00Z","publisher":"Springer","oa":1,"day":"06","year":"2018","doi":"10.1038/s41598-018-28188-1","related_material":{"record":[{"status":"public","id":"8822","relation":"dissertation_contains"}]},"scopus_import":"1","publication":"Scientific Reports","intvolume":"         8","publist_id":"7729","oa_version":"Published Version","project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"quality_controlled":"1","author":[{"first_name":"Peter","last_name":"Grones","id":"399876EC-F248-11E8-B48F-1D18A9856A87","full_name":"Grones, Peter"},{"full_name":"Abas, Melinda F","id":"3CFB3B1C-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda F","last_name":"Abas"},{"last_name":"Hajny","first_name":"Jakub","orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","full_name":"Hajny, Jakub"},{"first_name":"Angharad","last_name":"Jones","full_name":"Jones, Angharad"},{"first_name":"Sascha","last_name":"Waidmann","full_name":"Waidmann, Sascha"},{"first_name":"Jürgen","last_name":"Kleine Vehn","full_name":"Kleine Vehn, Jürgen"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí"}],"issue":"1","article_number":"10279","file":[{"file_name":"2018_ScientificReports_Grones.pdf","date_created":"2018-12-17T15:38:56Z","date_updated":"2020-07-14T12:45:20Z","content_type":"application/pdf","access_level":"open_access","file_size":2413876,"file_id":"5714","checksum":"266b03f4fb8198e83141617aaa99dcab","creator":"dernst","relation":"main_file"}],"month":"07","has_accepted_license":"1","article_processing_charge":"No","volume":8,"language":[{"iso":"eng"}],"_id":"191","type":"journal_article","date_created":"2018-12-11T11:45:06Z","status":"public","ec_funded":1},{"isi":1,"publication_status":"published","abstract":[{"text":"The phytohormone auxin is the information carrier in a plethora of developmental and physiological processes in plants(1). It has been firmly established that canonical, nuclear auxin signalling acts through regulation of gene transcription(2). Here, we combined microfluidics, live imaging, genetic engineering and computational modelling to reanalyse the classical case of root growth inhibition(3) by auxin. We show that Arabidopsis roots react to addition and removal of auxin by extremely rapid adaptation of growth rate. This process requires intracellular auxin perception but not transcriptional reprogramming. The formation of the canonical TIR1/AFB-Aux/IAA co-receptor complex is required for the growth regulation, hinting to a novel, non-transcriptional branch of this signalling pathway. Our results challenge the current understanding of root growth regulation by auxin and suggest another, presumably non-transcriptional, signalling output of the canonical auxin pathway.","lang":"eng"}],"title":"Rapid and reversible root growth inhibition by TIR1 auxin signalling","pmid":1,"date_published":"2018-06-25T00:00:00Z","publisher":"Springer Nature","citation":{"mla":"Fendrych, Matyas, et al. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” <i>Nature Plants</i>, vol. 4, no. 7, Springer Nature, 2018, pp. 453–59, doi:<a href=\"https://doi.org/10.1038/s41477-018-0190-1\">10.1038/s41477-018-0190-1</a>.","short":"M. Fendrych, M. Akhmanova, J. Merrin, M. Glanc, S. Hagihara, K. Takahashi, N. Uchida, K.U. Torii, J. Friml, Nature Plants 4 (2018) 453–459.","ista":"Fendrych M, Akhmanova M, Merrin J, Glanc M, Hagihara S, Takahashi K, Uchida N, Torii KU, Friml J. 2018. Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. 4(7), 453–459.","ama":"Fendrych M, Akhmanova M, Merrin J, et al. Rapid and reversible root growth inhibition by TIR1 auxin signalling. <i>Nature Plants</i>. 2018;4(7):453-459. doi:<a href=\"https://doi.org/10.1038/s41477-018-0190-1\">10.1038/s41477-018-0190-1</a>","chicago":"Fendrych, Matyas, Maria Akhmanova, Jack Merrin, Matous Glanc, Shinya Hagihara, Koji Takahashi, Naoyuki Uchida, Keiko U Torii, and Jiří Friml. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” <i>Nature Plants</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0190-1\">https://doi.org/10.1038/s41477-018-0190-1</a>.","apa":"Fendrych, M., Akhmanova, M., Merrin, J., Glanc, M., Hagihara, S., Takahashi, K., … Friml, J. (2018). Rapid and reversible root growth inhibition by TIR1 auxin signalling. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-018-0190-1\">https://doi.org/10.1038/s41477-018-0190-1</a>","ieee":"M. Fendrych <i>et al.</i>, “Rapid and reversible root growth inhibition by TIR1 auxin signalling,” <i>Nature Plants</i>, vol. 4, no. 7. Springer Nature, pp. 453–459, 2018."},"department":[{"_id":"JiFr"},{"_id":"DaSi"},{"_id":"NanoFab"}],"date_updated":"2023-09-15T12:11:03Z","external_id":{"isi":["000443221200017"],"pmid":["29942048"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-mechanism-for-the-plant-hormone-auxin-discovered/","description":"News on IST Homepage","relation":"press_release"}]},"publication":"Nature Plants","publist_id":"7728","intvolume":"         4","oa":1,"day":"25","doi":"10.1038/s41477-018-0190-1","page":"453 - 459","year":"2018","issue":"7","month":"06","volume":4,"article_processing_charge":"No","language":[{"iso":"eng"}],"oa_version":"Submitted Version","quality_controlled":"1","author":[{"orcid":"0000-0002-9767-8699","last_name":"Fendrych","first_name":"Matyas","full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"id":"3425EC26-F248-11E8-B48F-1D18A9856A87","full_name":"Akhmanova, Maria","last_name":"Akhmanova","first_name":"Maria","orcid":"0000-0003-1522-3162"},{"orcid":"0000-0001-5145-4609","last_name":"Merrin","first_name":"Jack","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Glanc","first_name":"Matous","full_name":"Glanc, Matous"},{"first_name":"Shinya","last_name":"Hagihara","full_name":"Hagihara, Shinya"},{"full_name":"Takahashi, Koji","last_name":"Takahashi","first_name":"Koji"},{"first_name":"Naoyuki","last_name":"Uchida","full_name":"Uchida, Naoyuki"},{"first_name":"Keiko U","last_name":"Torii","full_name":"Torii, Keiko U"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596"}],"article_type":"original","type":"journal_article","_id":"192","date_created":"2018-12-11T11:45:07Z","status":"public","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/29942048","open_access":"1"}]},{"citation":{"mla":"Alwen, Joel F., et al. “On the Memory Hardness of Data Independent Password Hashing Functions.” <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i>, ACM, 2018, pp. 51–65, doi:<a href=\"https://doi.org/10.1145/3196494.3196534\">10.1145/3196494.3196534</a>.","short":"J.F. Alwen, P. Gazi, C. Kamath Hosdurg, K. Klein, G.F. Osang, K.Z. Pietrzak, L. Reyzin, M. Rolinek, M. Rybar, in:, Proceedings of the 2018 on Asia Conference on Computer and Communication Security, ACM, 2018, pp. 51–65.","ieee":"J. F. Alwen <i>et al.</i>, “On the memory hardness of data independent password hashing functions,” in <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i>, Incheon, Republic of Korea, 2018, pp. 51–65.","apa":"Alwen, J. F., Gazi, P., Kamath Hosdurg, C., Klein, K., Osang, G. F., Pietrzak, K. Z., … Rybar, M. (2018). On the memory hardness of data independent password hashing functions. In <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i> (pp. 51–65). Incheon, Republic of Korea: ACM. <a href=\"https://doi.org/10.1145/3196494.3196534\">https://doi.org/10.1145/3196494.3196534</a>","ama":"Alwen JF, Gazi P, Kamath Hosdurg C, et al. On the memory hardness of data independent password hashing functions. In: <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i>. ACM; 2018:51-65. doi:<a href=\"https://doi.org/10.1145/3196494.3196534\">10.1145/3196494.3196534</a>","ista":"Alwen JF, Gazi P, Kamath Hosdurg C, Klein K, Osang GF, Pietrzak KZ, Reyzin L, Rolinek M, Rybar M. 2018. On the memory hardness of data independent password hashing functions. Proceedings of the 2018 on Asia Conference on Computer and Communication Security. ASIACCS: Asia Conference on Computer and Communications Security , 51–65.","chicago":"Alwen, Joel F, Peter Gazi, Chethan Kamath Hosdurg, Karen Klein, Georg F Osang, Krzysztof Z Pietrzak, Lenoid Reyzin, Michal Rolinek, and Michal Rybar. “On the Memory Hardness of Data Independent Password Hashing Functions.” In <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i>, 51–65. ACM, 2018. <a href=\"https://doi.org/10.1145/3196494.3196534\">https://doi.org/10.1145/3196494.3196534</a>."},"department":[{"_id":"KrPi"},{"_id":"HeEd"},{"_id":"VlKo"}],"date_updated":"2023-09-13T09:13:12Z","external_id":{"isi":["000516620100005"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"publication_status":"published","abstract":[{"text":"We show attacks on five data-independent memory-hard functions (iMHF) that were submitted to the password hashing competition (PHC). Informally, an MHF is a function which cannot be evaluated on dedicated hardware, like ASICs, at significantly lower hardware and/or energy cost than evaluating a single instance on a standard single-core architecture. Data-independent means the memory access pattern of the function is independent of the input; this makes iMHFs harder to construct than data-dependent ones, but the latter can be attacked by various side-channel attacks. Following [Alwen-Blocki'16], we capture the evaluation of an iMHF as a directed acyclic graph (DAG). The cumulative parallel pebbling complexity of this DAG is a measure for the hardware cost of evaluating the iMHF on an ASIC. Ideally, one would like the complexity of a DAG underlying an iMHF to be as close to quadratic in the number of nodes of the graph as possible. Instead, we show that (the DAGs underlying) the following iMHFs are far from this bound: Rig.v2, TwoCats and Gambit each having an exponent no more than 1.75. Moreover, we show that the complexity of the iMHF modes of the PHC finalists Pomelo and Lyra2 have exponents at most 1.83 and 1.67 respectively. To show this we investigate a combinatorial property of each underlying DAG (called its depth-robustness. By establishing upper bounds on this property we are then able to apply the general technique of [Alwen-Block'16] for analyzing the hardware costs of an iMHF.","lang":"eng"}],"title":"On the memory hardness of data independent password hashing functions","date_published":"2018-06-01T00:00:00Z","publisher":"ACM","oa":1,"day":"01","page":"51 - 65","doi":"10.1145/3196494.3196534","year":"2018","acknowledgement":"Leonid Reyzin was supported in part by IST Austria and by US NSF grants 1012910, 1012798, and 1422965; this research was performed while he was visiting IST Austria.","scopus_import":"1","publication":"Proceedings of the 2018 on Asia Conference on Computer and Communication Security","publist_id":"7723","oa_version":"Submitted Version","project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"},{"call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks"}],"quality_controlled":"1","author":[{"last_name":"Alwen","first_name":"Joel F","full_name":"Alwen, Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gazi, Peter","last_name":"Gazi","first_name":"Peter"},{"first_name":"Chethan","last_name":"Kamath Hosdurg","full_name":"Kamath Hosdurg, Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87"},{"id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","full_name":"Klein, Karen","last_name":"Klein","first_name":"Karen"},{"id":"464B40D6-F248-11E8-B48F-1D18A9856A87","full_name":"Osang, Georg F","first_name":"Georg F","last_name":"Osang","orcid":"0000-0002-8882-5116"},{"last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"},{"first_name":"Lenoid","last_name":"Reyzin","full_name":"Reyzin, Lenoid"},{"id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","full_name":"Rolinek, Michal","last_name":"Rolinek","first_name":"Michal"},{"id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","full_name":"Rybar, Michal","last_name":"Rybar","first_name":"Michal"}],"month":"06","article_processing_charge":"No","language":[{"iso":"eng"}],"_id":"193","type":"conference","date_created":"2018-12-11T11:45:07Z","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/783"}],"status":"public","conference":{"location":"Incheon, Republic of Korea","name":"ASIACCS: Asia Conference on Computer and Communications Security ","start_date":"2018-06-04","end_date":"2018-06-08"},"ec_funded":1},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"pmid":["29939785"],"isi":["000449359700035"]},"date_updated":"2023-09-13T09:37:32Z","department":[{"_id":"SyCr"}],"citation":{"ieee":"Z. Liutkeviciute <i>et al.</i>, “Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity,” <i>The FASEB Journal</i>, vol. 32, no. 12. FASEB, pp. 6808–6821, 2018.","ista":"Liutkeviciute Z, Gil Mansilla E, Eder T, Casillas Perez BE, Giulia Di Giglio M, Muratspahić E, Grebien F, Rattei T, Muttenthaler M, Cremer S, Gruber C. 2018. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. 32(12), 6808–6821.","chicago":"Liutkeviciute, Zita, Esther Gil Mansilla, Thomas Eder, Barbara E Casillas Perez, Maria Giulia Di Giglio, Edin Muratspahić, Florian Grebien, et al. “Oxytocin-like Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.” <i>The FASEB Journal</i>. FASEB, 2018. <a href=\"https://doi.org/10.1096/fj.201800443\">https://doi.org/10.1096/fj.201800443</a>.","ama":"Liutkeviciute Z, Gil Mansilla E, Eder T, et al. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. <i>The FASEB Journal</i>. 2018;32(12):6808-6821. doi:<a href=\"https://doi.org/10.1096/fj.201800443\">10.1096/fj.201800443</a>","apa":"Liutkeviciute, Z., Gil Mansilla, E., Eder, T., Casillas Perez, B. E., Giulia Di Giglio, M., Muratspahić, E., … Gruber, C. (2018). Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. <i>The FASEB Journal</i>. FASEB. <a href=\"https://doi.org/10.1096/fj.201800443\">https://doi.org/10.1096/fj.201800443</a>","mla":"Liutkeviciute, Zita, et al. “Oxytocin-like Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.” <i>The FASEB Journal</i>, vol. 32, no. 12, FASEB, 2018, pp. 6808–21, doi:<a href=\"https://doi.org/10.1096/fj.201800443\">10.1096/fj.201800443</a>.","short":"Z. Liutkeviciute, E. Gil Mansilla, T. Eder, B.E. Casillas Perez, M. Giulia Di Giglio, E. Muratspahić, F. Grebien, T. Rattei, M. Muttenthaler, S. Cremer, C. Gruber, The FASEB Journal 32 (2018) 6808–6821."},"date_published":"2018-11-29T00:00:00Z","publisher":"FASEB","pmid":1,"title":"Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity","abstract":[{"text":"Ants are emerging model systems to study cellular signaling because distinct castes possess different physiologic phenotypes within the same colony. Here we studied the functionality of inotocin signaling, an insect ortholog of mammalian oxytocin (OT), which was recently discovered in ants. In Lasius ants, we determined that specialization within the colony, seasonal factors, and physiologic conditions down-regulated the expression of the OT-like signaling system. Given this natural variation, we interrogated its function using RNAi knockdowns. Next-generation RNA sequencing of OT-like precursor knock-down ants highlighted its role in the regulation of genes involved in metabolism. Knock-down ants exhibited higher walking activity and increased self-grooming in the brood chamber. We propose that OT-like signaling in ants is important for regulating metabolic processes and locomotion.","lang":"eng"}],"publication_status":"published","isi":1,"doi":"10.1096/fj.201800443","day":"29","page":"6808-6821","year":"2018","oa":1,"intvolume":"        32","publist_id":"7721","publication":"The FASEB Journal","scopus_import":"1","author":[{"last_name":"Liutkeviciute","first_name":"Zita","full_name":"Liutkeviciute, Zita"},{"full_name":"Gil Mansilla, Esther","last_name":"Gil Mansilla","first_name":"Esther"},{"full_name":"Eder, Thomas","first_name":"Thomas","last_name":"Eder"},{"id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","full_name":"Casillas Perez, Barbara E","last_name":"Casillas Perez","first_name":"Barbara E"},{"first_name":"Maria","last_name":"Giulia Di Giglio","full_name":"Giulia Di Giglio, Maria"},{"full_name":"Muratspahić, Edin","last_name":"Muratspahić","first_name":"Edin"},{"full_name":"Grebien, Florian","first_name":"Florian","last_name":"Grebien"},{"last_name":"Rattei","first_name":"Thomas","full_name":"Rattei, Thomas"},{"last_name":"Muttenthaler","first_name":"Markus","full_name":"Muttenthaler, Markus"},{"full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer"},{"full_name":"Gruber, Christian","first_name":"Christian","last_name":"Gruber"}],"project":[{"name":"Individual function and social role of oxytocin-like neuropeptides in ants","_id":"25E3D34E-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"article_processing_charge":"No","volume":32,"month":"11","issue":"12","status":"public","main_file_link":[{"url":" https://doi.org/10.1096/fj.201800443","open_access":"1"}],"publication_identifier":{"issn":["08926638"]},"date_created":"2018-12-11T11:45:08Z","type":"journal_article","_id":"194","article_type":"original"},{"author":[{"id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","full_name":"Yakaboylu, Enderalp","first_name":"Enderalp","last_name":"Yakaboylu","orcid":"0000-0001-5973-0874"},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"quality_controlled":"1","oa_version":"Submitted Version","language":[{"iso":"eng"}],"volume":98,"article_processing_charge":"No","month":"07","article_number":"045402","issue":"4","status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.00308"}],"date_created":"2018-12-11T11:45:08Z","_id":"195","type":"journal_article","ec_funded":1,"external_id":{"isi":["000436939100007"],"arxiv":["1712.00308"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"MiLe"}],"date_updated":"2023-09-08T13:22:57Z","citation":{"ieee":"E. Yakaboylu and M. Lemeshko, “Anyonic statistics of quantum impurities in two dimensions,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 98, no. 4. American Physical Society, 2018.","ama":"Yakaboylu E, Lemeshko M. Anyonic statistics of quantum impurities in two dimensions. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2018;98(4). doi:<a href=\"https://doi.org/10.1103/PhysRevB.98.045402\">10.1103/PhysRevB.98.045402</a>","ista":"Yakaboylu E, Lemeshko M. 2018. Anyonic statistics of quantum impurities in two dimensions. Physical Review B - Condensed Matter and Materials Physics. 98(4), 045402.","chicago":"Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anyonic Statistics of Quantum Impurities in Two Dimensions.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevB.98.045402\">https://doi.org/10.1103/PhysRevB.98.045402</a>.","apa":"Yakaboylu, E., &#38; Lemeshko, M. (2018). Anyonic statistics of quantum impurities in two dimensions. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.98.045402\">https://doi.org/10.1103/PhysRevB.98.045402</a>","mla":"Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anyonic Statistics of Quantum Impurities in Two Dimensions.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 98, no. 4, 045402, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevB.98.045402\">10.1103/PhysRevB.98.045402</a>.","short":"E. Yakaboylu, M. Lemeshko, Physical Review B - Condensed Matter and Materials Physics 98 (2018)."},"date_published":"2018-07-15T00:00:00Z","publisher":"American Physical Society","title":"Anyonic statistics of quantum impurities in two dimensions","publication_status":"published","abstract":[{"text":"We demonstrate that identical impurities immersed in a two-dimensional many-particle bath can be viewed as flux-tube-charged-particle composites described by fractional statistics. In particular, we find that the bath manifests itself as an external magnetic flux tube with respect to the impurities, and hence the time-reversal symmetry is broken for the effective Hamiltonian describing the impurities. The emerging flux tube acts as a statistical gauge field after a certain critical coupling. This critical coupling corresponds to the intersection point between the quasiparticle state and the phonon wing, where the angular momentum is transferred from the impurity to the bath. This amounts to a novel configuration with emerging anyons. The proposed setup paves the way to realizing anyons using electrons interacting with superfluid helium or lattice phonons, as well as using atomic impurities in ultracold gases.","lang":"eng"}],"isi":1,"day":"15","doi":"10.1103/PhysRevB.98.045402","year":"2018","oa":1,"arxiv":1,"intvolume":"        98","publication":"Physical Review B - Condensed Matter and Materials Physics","scopus_import":"1"},{"publisher":"Institute of Science and Technology Austria","file_date_updated":"2020-07-14T12:45:22Z","date_published":"2018-05-25T00:00:00Z","title":"Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images","abstract":[{"lang":"eng","text":"Modern computer vision systems heavily rely on statistical machine learning models, which typically require large amounts of labeled data to be learned reliably. Moreover, very recently computer vision research widely adopted techniques for representation learning, which further increase the demand for labeled data. However, for many important practical problems there is relatively small amount of labeled data available, so it is problematic to leverage full potential of the representation learning methods. One way to overcome this obstacle is to invest substantial resources into producing large labelled datasets. Unfortunately, this can be prohibitively expensive in practice. In this thesis we focus on the alternative way of tackling the aforementioned issue. We concentrate on methods, which make use of weakly-labeled or even unlabeled data. Specifically, the first half of the thesis is dedicated to the semantic image segmentation task. We develop a technique, which achieves competitive segmentation performance and only requires annotations in a form of global image-level labels instead of dense segmentation masks. Subsequently, we present a new methodology, which further improves segmentation performance by leveraging tiny additional feedback from a human annotator. By using our methods practitioners can greatly reduce the amount of data annotation effort, which is required to learn modern image segmentation models. In the second half of the thesis we focus on methods for learning from unlabeled visual data. We study a family of autoregressive models for modeling structure of natural images and discuss potential applications of these models. Moreover, we conduct in-depth study of one of these applications, where we develop the state-of-the-art model for the probabilistic image colorization task."}],"publication_status":"published","ddc":["004"],"degree_awarded":"PhD","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["ISTA Thesis"],"date_updated":"2023-09-07T12:51:46Z","department":[{"_id":"ChLa"}],"citation":{"short":"A. Kolesnikov, Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images, Institute of Science and Technology Austria, 2018.","mla":"Kolesnikov, Alexander. <i>Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1021\">10.15479/AT:ISTA:th_1021</a>.","apa":"Kolesnikov, A. (2018). <i>Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1021\">https://doi.org/10.15479/AT:ISTA:th_1021</a>","chicago":"Kolesnikov, Alexander. “Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1021\">https://doi.org/10.15479/AT:ISTA:th_1021</a>.","ista":"Kolesnikov A. 2018. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria.","ama":"Kolesnikov A. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1021\">10.15479/AT:ISTA:th_1021</a>","ieee":"A. Kolesnikov, “Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images,” Institute of Science and Technology Austria, 2018."},"publist_id":"7718","supervisor":[{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887"}],"acknowledgement":"I also gratefully acknowledge the support of NVIDIA Corporation with the donation of the GPUs used for this research.","year":"2018","page":"113","doi":"10.15479/AT:ISTA:th_1021","day":"25","oa":1,"language":[{"iso":"eng"}],"article_processing_charge":"No","has_accepted_license":"1","month":"05","file":[{"date_updated":"2020-07-14T12:45:22Z","date_created":"2018-12-12T10:14:57Z","content_type":"application/pdf","file_name":"IST-2018-1021-v1+1_thesis-unsigned-pdfa.pdf","relation":"main_file","file_size":12918758,"access_level":"open_access","creator":"system","file_id":"5113","checksum":"bc678e02468d8ebc39dc7267dfb0a1c4"},{"date_updated":"2020-07-14T12:45:22Z","date_created":"2019-04-05T09:34:49Z","content_type":"application/zip","file_name":"2018_Thesis_Kolesnikov_source.zip","relation":"source_file","file_size":55973760,"access_level":"closed","creator":"dernst","checksum":"bc66973b086da5a043f1162dcfb1fde4","file_id":"6225"}],"author":[{"id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","full_name":"Kolesnikov, Alexander","last_name":"Kolesnikov","first_name":"Alexander"}],"project":[{"name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"oa_version":"Published Version","ec_funded":1,"pubrep_id":"1021","status":"public","publication_identifier":{"issn":["2663-337X"]},"date_created":"2018-12-11T11:45:09Z","_id":"197","type":"dissertation"},{"article_number":"20180073","file":[{"checksum":"444e1a9d98eb0e780671be82b13025f3","file_id":"5955","creator":"dernst","access_level":"open_access","file_size":219837,"relation":"main_file","file_name":"2018_RS_IbsenJensen.pdf","content_type":"application/pdf","date_created":"2019-02-12T07:54:37Z","date_updated":"2020-07-14T12:45:22Z"}],"issue":"140","has_accepted_license":"1","month":"03","volume":15,"article_processing_charge":"No","language":[{"iso":"eng"}],"oa_version":"Submitted Version","project":[{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"quality_controlled":"1","author":[{"full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen","first_name":"Rasmus"},{"id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef","last_name":"Tkadlec","first_name":"Josef","orcid":"0000-0002-1097-9684"},{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"ec_funded":1,"article_type":"original","_id":"198","type":"journal_article","date_created":"2018-12-11T11:45:09Z","publication_identifier":{"eissn":["1742-5662"]},"status":"public","isi":1,"ddc":["000"],"publication_status":"published","abstract":[{"lang":"eng","text":"We consider a class of students learning a language from a teacher. The situation can be interpreted as a group of child learners receiving input from the linguistic environment. The teacher provides sample sentences. The students try to learn the grammar from the teacher. In addition to just listening to the teacher, the students can also communicate with each other. The students hold hypotheses about the grammar and change them if they receive counter evidence. The process stops when all students have converged to the correct grammar. We study how the time to convergence depends on the structure of the classroom by introducing and evaluating various complexity measures. We find that structured communication between students, although potentially introducing confusion, can greatly reduce some of the complexity measures. Our theory can also be interpreted as applying to the scientific process, where nature is the teacher and the scientists are the students."}],"title":"Language acquisition with communication between learners","pmid":1,"file_date_updated":"2020-07-14T12:45:22Z","date_published":"2018-03-01T00:00:00Z","publisher":"The Royal Society","citation":{"chicago":"Ibsen-Jensen, Rasmus, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Language Acquisition with Communication between Learners.” <i>Journal of the Royal Society Interface</i>. The Royal Society, 2018. <a href=\"https://doi.org/10.1098/rsif.2018.0073\">https://doi.org/10.1098/rsif.2018.0073</a>.","ama":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. Language acquisition with communication between learners. <i>Journal of the Royal Society Interface</i>. 2018;15(140). doi:<a href=\"https://doi.org/10.1098/rsif.2018.0073\">10.1098/rsif.2018.0073</a>","ista":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. 2018. Language acquisition with communication between learners. Journal of the Royal Society Interface. 15(140), 20180073.","apa":"Ibsen-Jensen, R., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2018). Language acquisition with communication between learners. <i>Journal of the Royal Society Interface</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsif.2018.0073\">https://doi.org/10.1098/rsif.2018.0073</a>","ieee":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, and M. Nowak, “Language acquisition with communication between learners,” <i>Journal of the Royal Society Interface</i>, vol. 15, no. 140. The Royal Society, 2018.","mla":"Ibsen-Jensen, Rasmus, et al. “Language Acquisition with Communication between Learners.” <i>Journal of the Royal Society Interface</i>, vol. 15, no. 140, 20180073, The Royal Society, 2018, doi:<a href=\"https://doi.org/10.1098/rsif.2018.0073\">10.1098/rsif.2018.0073</a>.","short":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, M. Nowak, Journal of the Royal Society Interface 15 (2018)."},"department":[{"_id":"KrCh"}],"date_updated":"2023-10-18T06:36:00Z","external_id":{"isi":["000428576200023"],"pmid":["29593089"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","related_material":{"link":[{"url":"https://dx.doi.org/10.6084/m9.figshare.c.4028971","relation":"supplementary_material"}],"record":[{"status":"public","id":"9814","relation":"research_data"}]},"publication":"Journal of the Royal Society Interface","publist_id":"7715","intvolume":"        15","oa":1,"year":"2018","doi":"10.1098/rsif.2018.0073","day":"01"},{"type":"journal_article","_id":"199","date_created":"2018-12-11T11:45:09Z","status":"public","oa_version":"Published Version","quality_controlled":"1","author":[{"first_name":"Wen","last_name":"Ma","full_name":"Ma, Wen"},{"last_name":"Veltsos","first_name":"Paris","full_name":"Veltsos, Paris"},{"orcid":"0000-0002-9752-7380","last_name":"Toups","first_name":"Melissa A","full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rodrigues","first_name":"Nicolas","full_name":"Rodrigues, Nicolas"},{"first_name":"Roberto","last_name":"Sermier","full_name":"Sermier, Roberto"},{"first_name":"Daniel","last_name":"Jeffries","full_name":"Jeffries, Daniel"},{"full_name":"Perrin, Nicolas","last_name":"Perrin","first_name":"Nicolas"}],"issue":"6","file":[{"relation":"main_file","file_size":3985796,"access_level":"open_access","creator":"dernst","file_id":"5905","checksum":"423069beb1cd3cdd25bf3f464b38f1d7","date_updated":"2020-07-14T12:45:22Z","date_created":"2019-02-01T07:52:28Z","content_type":"application/pdf","file_name":"2018_Genes_Ma.pdf"}],"article_number":"294","has_accepted_license":"1","month":"06","article_processing_charge":"No","volume":9,"language":[{"iso":"eng"}],"oa":1,"doi":"10.3390/genes9060294","year":"2018","day":"12","scopus_import":"1","publication":"Genes","intvolume":"         9","publist_id":"7714","citation":{"mla":"Ma, Wen, et al. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” <i>Genes</i>, vol. 9, no. 6, 294, MDPI AG, 2018, doi:<a href=\"https://doi.org/10.3390/genes9060294\">10.3390/genes9060294</a>.","short":"W. Ma, P. Veltsos, M.A. Toups, N. Rodrigues, R. Sermier, D. Jeffries, N. Perrin, Genes 9 (2018).","ieee":"W. Ma <i>et al.</i>, “Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes,” <i>Genes</i>, vol. 9, no. 6. MDPI AG, 2018.","ista":"Ma W, Veltsos P, Toups MA, Rodrigues N, Sermier R, Jeffries D, Perrin N. 2018. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 9(6), 294.","ama":"Ma W, Veltsos P, Toups MA, et al. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. <i>Genes</i>. 2018;9(6). doi:<a href=\"https://doi.org/10.3390/genes9060294\">10.3390/genes9060294</a>","chicago":"Ma, Wen, Paris Veltsos, Melissa A Toups, Nicolas Rodrigues, Roberto Sermier, Daniel Jeffries, and Nicolas Perrin. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” <i>Genes</i>. MDPI AG, 2018. <a href=\"https://doi.org/10.3390/genes9060294\">https://doi.org/10.3390/genes9060294</a>.","apa":"Ma, W., Veltsos, P., Toups, M. A., Rodrigues, N., Sermier, R., Jeffries, D., &#38; Perrin, N. (2018). Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. <i>Genes</i>. MDPI AG. <a href=\"https://doi.org/10.3390/genes9060294\">https://doi.org/10.3390/genes9060294</a>"},"date_updated":"2023-09-19T10:15:31Z","department":[{"_id":"BeVi"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000436494200026"]},"isi":1,"ddc":["570"],"abstract":[{"lang":"eng","text":"Sex-biased genes are central to the study of sexual selection, sexual antagonism, and sex chromosome evolution. We describe a comprehensive de novo assembled transcriptome in the common frog Rana temporaria based on five developmental stages and three adult tissues from both sexes, obtained from a population with karyotypically homomorphic but genetically differentiated sex chromosomes. This allows the study of sex-biased gene expression throughout development, and its effect on the rate of gene evolution while accounting for pleiotropic expression, which is known to negatively correlate with the evolutionary rate. Overall, sex-biased genes had little overlap among developmental stages and adult tissues. Late developmental stages and gonad tissues had the highest numbers of stage-or tissue-specific genes. We find that pleiotropic gene expression is a better predictor than sex bias for the evolutionary rate of genes, though it often interacts with sex bias. Although genetically differentiated, the sex chromosomes were not enriched in sex-biased genes, possibly due to a very recent arrest of XY recombination. These results extend our understanding of the developmental dynamics, tissue specificity, and genomic localization of sex-biased genes."}],"publication_status":"published","title":"Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes","publisher":"MDPI AG","date_published":"2018-06-12T00:00:00Z","file_date_updated":"2020-07-14T12:45:22Z"},{"oa":1,"day":"27","page":"12241-12246","doi":"10.1073/pnas.1810565115","year":"2018","scopus_import":"1","related_material":{"link":[{"url":"https://ist.ac.at/en/news/no-cooperation-without-open-communication/","description":"News on IST Homepage","relation":"press_release"}],"record":[{"id":"10293","relation":"dissertation_contains","status":"public"}]},"publication":"PNAS","intvolume":"       115","citation":{"ieee":"C. Hilbe, L. Schmid, J. Tkadlec, K. Chatterjee, and M. Nowak, “Indirect reciprocity with private, noisy, and incomplete information,” <i>PNAS</i>, vol. 115, no. 48. National Academy of Sciences, pp. 12241–12246, 2018.","chicago":"Hilbe, Christian, Laura Schmid, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Indirect Reciprocity with Private, Noisy, and Incomplete Information.” <i>PNAS</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1810565115\">https://doi.org/10.1073/pnas.1810565115</a>.","ama":"Hilbe C, Schmid L, Tkadlec J, Chatterjee K, Nowak M. Indirect reciprocity with private, noisy, and incomplete information. <i>PNAS</i>. 2018;115(48):12241-12246. doi:<a href=\"https://doi.org/10.1073/pnas.1810565115\">10.1073/pnas.1810565115</a>","ista":"Hilbe C, Schmid L, Tkadlec J, Chatterjee K, Nowak M. 2018. Indirect reciprocity with private, noisy, and incomplete information. PNAS. 115(48), 12241–12246.","apa":"Hilbe, C., Schmid, L., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2018). Indirect reciprocity with private, noisy, and incomplete information. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1810565115\">https://doi.org/10.1073/pnas.1810565115</a>","short":"C. Hilbe, L. Schmid, J. Tkadlec, K. Chatterjee, M. Nowak, PNAS 115 (2018) 12241–12246.","mla":"Hilbe, Christian, et al. “Indirect Reciprocity with Private, Noisy, and Incomplete Information.” <i>PNAS</i>, vol. 115, no. 48, National Academy of Sciences, 2018, pp. 12241–46, doi:<a href=\"https://doi.org/10.1073/pnas.1810565115\">10.1073/pnas.1810565115</a>."},"department":[{"_id":"KrCh"}],"date_updated":"2025-07-14T09:10:09Z","external_id":{"pmid":["30429320"],"isi":["000451351000063"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"publication_status":"published","abstract":[{"lang":"eng","text":"Indirect reciprocity explores how humans act when their reputation is at stake, and which social norms they use to assess the actions of others. A crucial question in indirect reciprocity is which social norms can maintain stable cooperation in a society. Past research has highlighted eight such norms, called “leading-eight” strategies. This past research, however, is based on the assumption that all relevant information about other population members is publicly available and that everyone agrees on who is good or bad. Instead, here we explore the reputation dynamics when information is private and noisy. We show that under these conditions, most leading-eight strategies fail to evolve. Those leading-eight strategies that do evolve are unable to sustain full cooperation.Indirect reciprocity is a mechanism for cooperation based on shared moral systems and individual reputations. It assumes that members of a community routinely observe and assess each other and that they use this information to decide who is good or bad, and who deserves cooperation. When information is transmitted publicly, such that all community members agree on each other’s reputation, previous research has highlighted eight crucial moral systems. These “leading-eight” strategies can maintain cooperation and resist invasion by defectors. However, in real populations individuals often hold their own private views of others. Once two individuals disagree about their opinion of some third party, they may also see its subsequent actions in a different light. Their opinions may further diverge over time. Herein, we explore indirect reciprocity when information transmission is private and noisy. We find that in the presence of perception errors, most leading-eight strategies cease to be stable. Even if a leading-eight strategy evolves, cooperation rates may drop considerably when errors are common. Our research highlights the role of reliable information and synchronized reputations to maintain stable moral systems."}],"title":"Indirect reciprocity with private, noisy, and incomplete information","pmid":1,"publisher":"National Academy of Sciences","date_published":"2018-11-27T00:00:00Z","type":"journal_article","_id":"2","date_created":"2018-12-11T11:44:05Z","status":"public","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30429320","open_access":"1"}],"ec_funded":1,"oa_version":"Submitted Version","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","author":[{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian","first_name":"Christian","last_name":"Hilbe","orcid":"0000-0001-5116-955X"},{"id":"38B437DE-F248-11E8-B48F-1D18A9856A87","full_name":"Schmid, Laura","first_name":"Laura","last_name":"Schmid","orcid":"0000-0002-6978-7329"},{"orcid":"0000-0002-1097-9684","last_name":"Tkadlec","first_name":"Josef","full_name":"Tkadlec, Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"issue":"48","month":"11","volume":115,"article_processing_charge":"No","language":[{"iso":"eng"}]},{"file":[{"relation":"main_file","file_size":4629784,"access_level":"open_access","creator":"dernst","checksum":"a56516e734dab589dc7f3e1915973b4d","file_id":"5712","date_updated":"2020-07-14T12:45:23Z","date_created":"2018-12-17T14:52:57Z","content_type":"application/pdf","file_name":"2018_BMCGenomics_Higareda.pdf"}],"issue":"1","month":"11","has_accepted_license":"1","volume":19,"article_processing_charge":"No","language":[{"iso":"eng"}],"oa_version":"Published Version","quality_controlled":"1","author":[{"full_name":"Higareda Almaraz, Juan","last_name":"Higareda Almaraz","first_name":"Juan"},{"last_name":"Karbiener","first_name":"Michael","full_name":"Karbiener, Michael"},{"last_name":"Giroud","first_name":"Maude","full_name":"Giroud, Maude"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian","first_name":"Florian","last_name":"Pauler","orcid":"0000-0002-7462-0048"},{"last_name":"Gerhalter","first_name":"Teresa","full_name":"Gerhalter, Teresa"},{"first_name":"Stephan","last_name":"Herzig","full_name":"Herzig, Stephan"},{"first_name":"Marcel","last_name":"Scheideler","full_name":"Scheideler, Marcel"}],"article_type":"original","_id":"20","type":"journal_article","date_created":"2018-12-11T11:44:12Z","status":"public","publication_identifier":{"issn":["1471-2164"]},"ddc":["570"],"isi":1,"publication_status":"published","abstract":[{"text":"Background: Norepinephrine (NE) signaling has a key role in white adipose tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under certain conditions, conversion of white into brite (brown-in-white) adipocytes. However, acute effects of NE stimulation have not been described at the transcriptional network level. Results: We used RNA-seq to uncover a broad transcriptional response. The inference of protein-protein and protein-DNA interaction networks allowed us to identify a set of immediate-early genes (IEGs) with high betweenness, validating our approach and suggesting a hierarchical control of transcriptional regulation. In addition, we identified a transcriptional regulatory network with IEGs as master regulators, including HSF1 and NFIL3 as novel NE-induced IEG candidates. Moreover, a functional enrichment analysis and gene clustering into functional modules suggest a crosstalk between metabolic, signaling, and immune responses. Conclusions: Altogether, our network biology approach explores for the first time the immediate-early systems level response of human adipocytes to acute sympathetic activation, thereby providing a first network basis of early cell fate programs and crosstalks between metabolic and transcriptional networks required for proper WAT function.","lang":"eng"}],"title":"Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","file_date_updated":"2020-07-14T12:45:23Z","date_published":"2018-11-03T00:00:00Z","publisher":"BioMed Central","citation":{"mla":"Higareda Almaraz, Juan, et al. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” <i>BMC Genomics</i>, vol. 19, no. 1, BioMed Central, 2018, doi:<a href=\"https://doi.org/10.1186/s12864-018-5173-0\">10.1186/s12864-018-5173-0</a>.","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, BMC Genomics 19 (2018).","ieee":"J. Higareda Almaraz <i>et al.</i>, “Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes,” <i>BMC Genomics</i>, vol. 19, no. 1. BioMed Central, 2018.","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., &#38; Scheideler, M. (2018). Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. <i>BMC Genomics</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s12864-018-5173-0\">https://doi.org/10.1186/s12864-018-5173-0</a>","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 19(1).","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. <i>BMC Genomics</i>. 2018;19(1). doi:<a href=\"https://doi.org/10.1186/s12864-018-5173-0\">10.1186/s12864-018-5173-0</a>","chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” <i>BMC Genomics</i>. BioMed Central, 2018. <a href=\"https://doi.org/10.1186/s12864-018-5173-0\">https://doi.org/10.1186/s12864-018-5173-0</a>."},"department":[{"_id":"SiHi"}],"date_updated":"2023-09-13T09:10:47Z","external_id":{"isi":["000450976700002"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","related_material":{"record":[{"status":"public","id":"9807","relation":"research_data"},{"status":"public","id":"9808","relation":"research_data"}]},"publication":"BMC Genomics","publist_id":"8035","intvolume":"        19","oa":1,"doi":"10.1186/s12864-018-5173-0","year":"2018","day":"03","acknowledgement":"This work was funded by the German Centre for Diabetes Research (DZD) and the Austrian Science Fund (FWF, P25729-B19)."},{"year":"2018","day":"21","page":"146","doi":"10.15479/AT:ISTA:th_963","oa":1,"publist_id":"7713","supervisor":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"related_material":{"record":[{"id":"563","relation":"part_of_dissertation","status":"public"},{"id":"1074","relation":"part_of_dissertation","status":"public"}]},"degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"department":[{"_id":"NiBa"}],"date_updated":"2025-05-28T11:57:06Z","citation":{"mla":"Ringbauer, Harald. <i>Inferring Recent Demography from Spatial Genetic Structure</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">10.15479/AT:ISTA:th_963</a>.","short":"H. Ringbauer, Inferring Recent Demography from Spatial Genetic Structure, Institute of Science and Technology Austria, 2018.","apa":"Ringbauer, H. (2018). <i>Inferring recent demography from spatial genetic structure</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">https://doi.org/10.15479/AT:ISTA:th_963</a>","ama":"Ringbauer H. Inferring recent demography from spatial genetic structure. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">10.15479/AT:ISTA:th_963</a>","chicago":"Ringbauer, Harald. “Inferring Recent Demography from Spatial Genetic Structure.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_963\">https://doi.org/10.15479/AT:ISTA:th_963</a>.","ista":"Ringbauer H. 2018. Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria.","ieee":"H. Ringbauer, “Inferring recent demography from spatial genetic structure,” Institute of Science and Technology Austria, 2018."},"file_date_updated":"2020-07-14T12:45:23Z","publisher":"Institute of Science and Technology Austria","date_published":"2018-02-21T00:00:00Z","title":"Inferring recent demography from spatial genetic structure","publication_status":"published","abstract":[{"text":"This thesis is concerned with the inference of current population structure based on geo-referenced genetic data. The underlying idea is that population structure affects its spatial genetic structure. Therefore, genotype information can be utilized to estimate important demographic parameters such as migration rates. These indirect estimates of population structure have become very attractive, as genotype data is now widely available. However, there also has been much concern about these approaches. Importantly, genetic structure can be influenced by many complex patterns, which often cannot be disentangled. Moreover, many methods merely fit heuristic patterns of genetic structure, and do not build upon population genetics theory. Here, I describe two novel inference methods that address these shortcomings. In Chapter 2, I introduce an inference scheme based on a new type of signal, identity by descent (IBD) blocks. Recently, it has become feasible to detect such long blocks of genome shared between pairs of samples. These blocks are direct traces of recent coalescence events. As such, they contain ample signal for inferring recent demography. I examine sharing of IBD blocks in two-dimensional populations with local migration. Using a diffusion approximation, I derive formulas for an isolation by distance pattern of long IBD blocks and show that sharing of long IBD blocks approaches rapid exponential decay for growing sample distance. I describe an inference scheme based on these results. It can robustly estimate the dispersal rate and population density, which is demonstrated on simulated data. I also show an application to estimate mean migration and the rate of recent population growth within Eastern Europe. Chapter 3 is about a novel method to estimate barriers to gene flow in a two dimensional population. This inference scheme utilizes geographically localized allele frequency fluctuations - a classical isolation by distance signal. The strength of these local fluctuations increases on average next to a barrier, and there is less correlation across it. I again use a framework of diffusion of ancestral lineages to model this effect, and provide an efficient numerical implementation to fit the results to geo-referenced biallelic SNP data. This inference scheme is able to robustly estimate strong barriers to gene flow, as tests on simulated data confirm.","lang":"eng"}],"ddc":["576"],"status":"public","publication_identifier":{"issn":["2663-337X"]},"date_created":"2018-12-11T11:45:10Z","type":"dissertation","_id":"200","pubrep_id":"963","author":[{"last_name":"Ringbauer","first_name":"Harald","orcid":"0000-0002-4884-9682","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","full_name":"Ringbauer, Harald"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"article_processing_charge":"No","has_accepted_license":"1","month":"02","file":[{"date_created":"2018-12-12T10:14:55Z","date_updated":"2020-07-14T12:45:23Z","content_type":"application/pdf","file_name":"IST-2018-963-v1+1_thesis.pdf","relation":"main_file","access_level":"open_access","file_size":5792935,"checksum":"8cc534d2b528ae017acf80874cce48c9","file_id":"5111","creator":"system"},{"relation":"source_file","creator":"dernst","file_id":"6224","checksum":"6af18d7e5a7e2728ceda2f41ee24f628","file_size":113365,"access_level":"closed","content_type":"application/zip","date_updated":"2020-07-14T12:45:23Z","date_created":"2019-04-05T09:30:12Z","file_name":"2018_thesis_ringbauer_source.zip"}]}]