[{"citation":{"ama":"Chatterjee K, Henzinger TA, Otop J. Nested weighted limit-average automata of bounded width. In: Vol 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPIcs.MFCS.2016.24","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2016). Nested weighted limit-average automata of bounded width (Vol. 58). Presented at the MFCS: Mathematical Foundations of Computer Science (SG), Krakow; Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2016.24","ista":"Chatterjee K, Henzinger TA, Otop J. 2016. Nested weighted limit-average automata of bounded width. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 58, 24.","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted limit-average automata of bounded width,” presented at the MFCS: Mathematical Foundations of Computer Science (SG), Krakow; Poland, 2016, vol. 58.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted Limit-Average Automata of Bounded Width,” Vol. 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPIcs.MFCS.2016.24.","mla":"Chatterjee, Krishnendu, et al. Nested Weighted Limit-Average Automata of Bounded Width. Vol. 58, 24, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPIcs.MFCS.2016.24.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016."},"ddc":["004"],"file_date_updated":"2018-12-12T10:17:31Z","article_number":"24","month":"08","file":[{"access_level":"open_access","date_updated":"2018-12-12T10:17:31Z","date_created":"2018-12-12T10:17:31Z","file_size":564560,"file_id":"5286","relation":"main_file","file_name":"IST-2017-795-v1+1_LIPIcs-MFCS-2016-24.pdf","creator":"system","content_type":"application/pdf"}],"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"first_name":"Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan"}],"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23\r\n(RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna\r\nScience and Technology Fund (WWTF) through project ICT15-003 and by the National Science Centre\r\n(NCN), Poland under grant 2014/15/D/ST6/04543.","_id":"1090","language":[{"iso":"eng"}],"pubrep_id":"795","date_updated":"2021-01-12T06:48:12Z","day":"01","title":"Nested weighted limit-average automata of bounded width","doi":"10.4230/LIPIcs.MFCS.2016.24","oa":1,"year":"2016","ec_funded":1,"has_accepted_license":"1","conference":{"name":"MFCS: Mathematical Foundations of Computer Science (SG)","location":"Krakow; Poland","end_date":"2016-08-26","start_date":"2016-08-22"},"date_created":"2018-12-11T11:50:05Z","alternative_title":["LIPIcs"],"scopus_import":1,"oa_version":"Published Version","intvolume":" 58","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2016-08-01T00:00:00Z","status":"public","publist_id":"6286","abstract":[{"text":" While weighted automata provide a natural framework to express quantitative properties, many basic properties like average response time cannot be expressed with weighted automata. Nested weighted automata extend weighted automata and consist of a master automaton and a set of slave automata that are invoked by the master automaton. Nested weighted automata are strictly more expressive than weighted automata (e.g., average response time can be expressed with nested weighted automata), but the basic decision questions have higher complexity (e.g., for deterministic automata, the emptiness question for nested weighted automata is PSPACE-hard, whereas the corresponding complexity for weighted automata is PTIME). We consider a natural subclass of nested weighted automata where at any point at most a bounded number k of slave automata can be active. We focus on automata whose master value function is the limit average. We show that these nested weighted automata with bounded width are strictly more expressive than weighted automata (e.g., average response time with no overlapping requests can be expressed with bound k=1, but not with non-nested weighted automata). We show that the complexity of the basic decision problems (i.e., emptiness and universality) for the subclass with k constant matches the complexity for weighted automata. Moreover, when k is part of the input given in unary we establish PSPACE-completeness.","lang":"eng"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"}],"quality_controlled":"1","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"volume":58,"type":"conference"},{"author":[{"full_name":"Daca, Przemyslaw","last_name":"Daca","first_name":"Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9041-0905","full_name":"Petrov, Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrov","first_name":"Tatjana"}],"file":[{"content_type":"application/pdf","file_name":"IST-2017-794-v1+1_LIPIcs-CONCUR-2016-20.pdf","relation":"main_file","creator":"system","file_size":501827,"file_id":"4895","access_level":"open_access","date_created":"2018-12-12T10:11:39Z","date_updated":"2018-12-12T10:11:39Z"}],"month":"08","article_number":"20","file_date_updated":"2018-12-12T10:11:39Z","ddc":["004"],"citation":{"short":"P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","mla":"Daca, Przemyslaw, et al. Linear Distances between Markov Chains. Vol. 59, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPIcs.CONCUR.2016.20.","ieee":"P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Linear distances between Markov chains,” presented at the CONCUR: Concurrency Theory, Quebec City; Canada, 2016, vol. 59.","chicago":"Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov. “Linear Distances between Markov Chains,” Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPIcs.CONCUR.2016.20.","apa":"Daca, P., Henzinger, T. A., Kretinsky, J., & Petrov, T. (2016). Linear distances between Markov chains (Vol. 59). Presented at the CONCUR: Concurrency Theory, Quebec City; Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2016.20","ista":"Daca P, Henzinger TA, Kretinsky J, Petrov T. 2016. Linear distances between Markov chains. CONCUR: Concurrency Theory, LIPIcs, vol. 59, 20.","ama":"Daca P, Henzinger TA, Kretinsky J, Petrov T. Linear distances between Markov chains. In: Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPIcs.CONCUR.2016.20"},"_id":"1093","pubrep_id":"794","language":[{"iso":"eng"}],"acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989\r\n(QUAREM), the Austrian Science Fund (FWF) under grants project S11402-N23 (RiSE and SHiNE)\r\nand Z211-N23 (Wittgenstein Award), by the Czech Science Foundation Grant No. P202/12/G061, and\r\nby the SNSF Advanced Postdoc. Mobility Fellowship – grant number P300P2_161067.","doi":"10.4230/LIPIcs.CONCUR.2016.20","title":"Linear distances between Markov chains","date_updated":"2023-09-07T11:58:33Z","day":"01","ec_funded":1,"year":"2016","conference":{"location":"Quebec City; Canada","name":"CONCUR: Concurrency Theory","start_date":"2016-08-23","end_date":"2016-08-26"},"has_accepted_license":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"1155","status":"public"}]},"oa":1,"oa_version":"Published Version","date_created":"2018-12-11T11:50:06Z","scopus_import":1,"alternative_title":["LIPIcs"],"publist_id":"6283","status":"public","date_published":"2016-08-01T00:00:00Z","abstract":[{"lang":"eng","text":"We introduce a general class of distances (metrics) between Markov chains, which are based on linear behaviour. This class encompasses distances given topologically (such as the total variation distance or trace distance) as well as by temporal logics or automata. We investigate which of the distances can be approximated by observing the systems, i.e. by black-box testing or simulation, and we provide both negative and positive results. "}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":" 59","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"}],"department":[{"_id":"ToHe"},{"_id":"KrCh"},{"_id":"CaGu"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","type":"conference","volume":59},{"status":"public","date_published":"2016-08-12T00:00:00Z","publist_id":"6281","publication":"High-Resolution Imaging of Cellular Proteins","abstract":[{"text":"Immunogold labeling of freeze-fracture replicas has recently been used for high-resolution visualization of protein localization in electron microscopy. This method has higher labeling efficiency than conventional immunogold methods for membrane molecules allowing precise quantitative measurements. However, one of the limitations of freeze-fracture replica immunolabeling is difficulty in keeping structural orientation and identifying labeled profiles in complex tissues like brain. The difficulty is partly due to fragmentation of freeze-fracture replica preparations during labeling procedures and limited morphological clues on the replica surface. To overcome these issues, we introduce here a grid-glued replica method combined with SEM observation. This method allows histological staining before dissolving the tissue and easy handling of replicas during immunogold labeling, and keeps the whole replica surface intact without fragmentation. The procedure described here is also useful for matched double-replica analysis allowing further identification of labeled profiles in corresponding P-face and E-face.","lang":"eng"}],"intvolume":" 1474","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"None","date_created":"2018-12-11T11:50:06Z","alternative_title":["Methods in Molecular Biology"],"volume":1474,"type":"book_chapter","project":[{"call_identifier":"FP7","name":"Localization of ion channels and receptors by two and three-dimensional immunoelectron microscopic approaches","_id":"25CD3DD2-B435-11E9-9278-68D0E5697425","grant_number":"604102"}],"quality_controlled":"1","department":[{"_id":"RySh"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"publisher":"Springer","publication_status":"published","page":"203 - 216","acknowledgement":"We thank Prof. Elek Molnár for providing us a pan-AMPAR anti-body used in Fig.2 and Dr. Ludek Lovicar for technical assistance in scanning electron microscope imaging. This work was supported by the European Union (HBP—Project Ref. 604102). ","language":[{"iso":"eng"}],"_id":"1094","month":"08","author":[{"id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Harada","first_name":"Harumi","orcid":"0000-0001-7429-7896","full_name":"Harada, Harumi"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"citation":{"short":"H. Harada, R. Shigemoto, in:, High-Resolution Imaging of Cellular Proteins, Springer, 2016, pp. 203–216.","mla":"Harada, Harumi, and Ryuichi Shigemoto. “Immunogold Protein Localization on Grid-Glued Freeze-Fracture Replicas.” High-Resolution Imaging of Cellular Proteins, vol. 1474, Springer, 2016, pp. 203–16, doi:10.1007/978-1-4939-6352-2_12.","ieee":"H. Harada and R. Shigemoto, “Immunogold protein localization on grid-glued freeze-fracture replicas,” in High-Resolution Imaging of Cellular Proteins, vol. 1474, Springer, 2016, pp. 203–216.","chicago":"Harada, Harumi, and Ryuichi Shigemoto. “Immunogold Protein Localization on Grid-Glued Freeze-Fracture Replicas.” In High-Resolution Imaging of Cellular Proteins, 1474:203–16. Springer, 2016. https://doi.org/10.1007/978-1-4939-6352-2_12.","apa":"Harada, H., & Shigemoto, R. (2016). Immunogold protein localization on grid-glued freeze-fracture replicas. In High-Resolution Imaging of Cellular Proteins (Vol. 1474, pp. 203–216). Springer. https://doi.org/10.1007/978-1-4939-6352-2_12","ista":"Harada H, Shigemoto R. 2016.Immunogold protein localization on grid-glued freeze-fracture replicas. In: High-Resolution Imaging of Cellular Proteins. Methods in Molecular Biology, vol. 1474, 203–216.","ama":"Harada H, Shigemoto R. Immunogold protein localization on grid-glued freeze-fracture replicas. In: High-Resolution Imaging of Cellular Proteins. Vol 1474. Springer; 2016:203-216. doi:10.1007/978-1-4939-6352-2_12"},"ec_funded":1,"year":"2016","article_processing_charge":"No","title":"Immunogold protein localization on grid-glued freeze-fracture replicas","doi":"10.1007/978-1-4939-6352-2_12","date_updated":"2023-09-05T14:09:01Z","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"]},"day":"12"},{"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","quality_controlled":"1","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"ToHe"}],"type":"conference","volume":59,"date_created":"2018-12-11T11:50:07Z","scopus_import":1,"alternative_title":["LIPIcs"],"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":" 59","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication":"Leibniz International Proceedings in Informatics","publist_id":"6280","status":"public","date_published":"2016-08-01T00:00:00Z","abstract":[{"text":" The semantics of concurrent data structures is usually given by a sequential specification and a consistency condition. Linearizability is the most popular consistency condition due to its simplicity and general applicability. Nevertheless, for applications that do not require all guarantees offered by linearizability, recent research has focused on improving performance and scalability of concurrent data structures by relaxing their semantics. In this paper, we present local linearizability, a relaxed consistency condition that is applicable to container-type concurrent data structures like pools, queues, and stacks. While linearizability requires that the effect of each operation is observed by all threads at the same time, local linearizability only requires that for each thread T, the effects of its local insertion operations and the effects of those removal operations that remove values inserted by T are observed by all threads at the same time. We investigate theoretical and practical properties of local linearizability and its relationship to many existing consistency conditions. We present a generic implementation method for locally linearizable data structures that uses existing linearizable data structures as building blocks. Our implementations show performance and scalability improvements over the original building blocks and outperform the fastest existing container-type implementations. ","lang":"eng"}],"date_updated":"2021-01-12T06:48:14Z","day":"01","doi":"10.4230/LIPIcs.CONCUR.2016.6","title":"Local linearizability for concurrent container-type data structures","oa":1,"ec_funded":1,"year":"2016","conference":{"name":"CONCUR: Concurrency Theory","location":"Quebec City; Canada","end_date":"2016-08-26","start_date":"2016-08-23"},"has_accepted_license":"1","ddc":["004"],"citation":{"ista":"Haas A, Henzinger TA, Holzer A, Kirsch C, Lippautz M, Payer H, Sezgin A, Sokolova A, Veith H. 2016. Local linearizability for concurrent container-type data structures. Leibniz International Proceedings in Informatics. CONCUR: Concurrency Theory, LIPIcs, vol. 59, 6.","apa":"Haas, A., Henzinger, T. A., Holzer, A., Kirsch, C., Lippautz, M., Payer, H., … Veith, H. (2016). Local linearizability for concurrent container-type data structures. In Leibniz International Proceedings in Informatics (Vol. 59). Quebec City; Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2016.6","ama":"Haas A, Henzinger TA, Holzer A, et al. Local linearizability for concurrent container-type data structures. In: Leibniz International Proceedings in Informatics. Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPIcs.CONCUR.2016.6","mla":"Haas, Andreas, et al. “Local Linearizability for Concurrent Container-Type Data Structures.” Leibniz International Proceedings in Informatics, vol. 59, 6, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPIcs.CONCUR.2016.6.","short":"A. Haas, T.A. Henzinger, A. Holzer, C. Kirsch, M. Lippautz, H. Payer, A. Sezgin, A. Sokolova, H. Veith, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","chicago":"Haas, Andreas, Thomas A Henzinger, Andreas Holzer, Christoph Kirsch, Michael Lippautz, Hannes Payer, Ali Sezgin, Ana Sokolova, and Helmut Veith. “Local Linearizability for Concurrent Container-Type Data Structures.” In Leibniz International Proceedings in Informatics, Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPIcs.CONCUR.2016.6.","ieee":"A. Haas et al., “Local linearizability for concurrent container-type data structures,” in Leibniz International Proceedings in Informatics, Quebec City; Canada, 2016, vol. 59."},"file":[{"file_size":589747,"file_id":"4795","access_level":"open_access","date_updated":"2018-12-12T10:10:10Z","date_created":"2018-12-12T10:10:10Z","content_type":"application/pdf","file_name":"IST-2017-793-v1+1_LIPIcs-CONCUR-2016-6.pdf","relation":"main_file","creator":"system"}],"author":[{"full_name":"Haas, Andreas","last_name":"Haas","first_name":"Andreas"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andreas","last_name":"Holzer","full_name":"Holzer, Andreas"},{"last_name":"Kirsch","first_name":"Christoph","full_name":"Kirsch, Christoph"},{"full_name":"Lippautz, Michael","last_name":"Lippautz","first_name":"Michael"},{"full_name":"Payer, Hannes","last_name":"Payer","first_name":"Hannes"},{"full_name":"Sezgin, Ali","last_name":"Sezgin","first_name":"Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ana","last_name":"Sokolova","full_name":"Sokolova, Ana"},{"full_name":"Veith, Helmut","last_name":"Veith","first_name":"Helmut"}],"month":"08","article_number":"6","file_date_updated":"2018-12-12T10:10:10Z","language":[{"iso":"eng"}],"_id":"1095","pubrep_id":"793","acknowledgement":"This work has been supported by the National Research Network RiSE on Rigorous Systems Engineering\r\n(Austrian Science Fund (FWF): S11402-N23, S11403-N23, S11404-N23, S11411-N23), a Google\r\nPhD Fellowship, an Erwin Schrödinger Fellowship (Austrian Science Fund (FWF): J3696-N26), EPSRC\r\ngrants EP/H005633/1 and EP/K008528/1, the Vienna Science and Technology Fund (WWTF) trough\r\ngrant PROSEED, the European Research Council (ERC) under grant 267989 (QUAREM) and by the\r\nAustrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award)."},{"year":"2016","related_material":{"record":[{"relation":"part_of_dissertation","id":"7186","status":"public"}]},"type":"journal_article","volume":37,"quality_controlled":"1","doi":"10.1016/j.devcel.2016.05.024","department":[{"_id":"CaHe"}],"title":"Actin rings of power","date_updated":"2023-09-07T12:56:41Z","publisher":"Cell Press","day":"20","publication_status":"published","publist_id":"6279","issue":"6","publication":"Developmental Cell","status":"public","date_published":"2016-06-20T00:00:00Z","page":"493 - 506","_id":"1096","language":[{"iso":"eng"}],"intvolume":" 37","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"id":"3436488C-F248-11E8-B48F-1D18A9856A87","last_name":"Schwayer","first_name":"Cornelia","full_name":"Schwayer, Cornelia","orcid":"0000-0001-5130-2226"},{"first_name":"Mateusz K","last_name":"Sikora","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","full_name":"Sikora, Mateusz K"},{"full_name":"Slovakova, Jana","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","first_name":"Jana","last_name":"Slovakova"},{"id":"4039350E-F248-11E8-B48F-1D18A9856A87","last_name":"Kardos","first_name":"Roland","full_name":"Kardos, Roland"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"oa_version":"None","month":"06","citation":{"apa":"Schwayer, C., Sikora, M. K., Slovakova, J., Kardos, R., & Heisenberg, C.-P. J. (2016). Actin rings of power. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2016.05.024","ista":"Schwayer C, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. 2016. Actin rings of power. Developmental Cell. 37(6), 493–506.","ama":"Schwayer C, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. Actin rings of power. Developmental Cell. 2016;37(6):493-506. doi:10.1016/j.devcel.2016.05.024","short":"C. Schwayer, M.K. Sikora, J. Slovakova, R. Kardos, C.-P.J. Heisenberg, Developmental Cell 37 (2016) 493–506.","mla":"Schwayer, Cornelia, et al. “Actin Rings of Power.” Developmental Cell, vol. 37, no. 6, Cell Press, 2016, pp. 493–506, doi:10.1016/j.devcel.2016.05.024.","ieee":"C. Schwayer, M. K. Sikora, J. Slovakova, R. Kardos, and C.-P. J. Heisenberg, “Actin rings of power,” Developmental Cell, vol. 37, no. 6. Cell Press, pp. 493–506, 2016.","chicago":"Schwayer, Cornelia, Mateusz K Sikora, Jana Slovakova, Roland Kardos, and Carl-Philipp J Heisenberg. “Actin Rings of Power.” Developmental Cell. Cell Press, 2016. https://doi.org/10.1016/j.devcel.2016.05.024."},"date_created":"2018-12-11T11:50:07Z","scopus_import":1},{"volume":35,"type":"conference","publisher":"ACM","publication_status":"published","project":[{"call_identifier":"H2020","_id":"25082902-B435-11E9-9278-68D0E5697425","name":"Soft-bodied intelligence for Manipulation","grant_number":"645599"}],"quality_controlled":"1","department":[{"_id":"BeBi"}],"intvolume":" 35","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2016-11-01T00:00:00Z","publist_id":"6278","abstract":[{"lang":"eng","text":"We present an interactive system for computational design, optimization, and fabrication of multicopters. Our computational approach allows non-experts to design, explore, and evaluate a wide range of different multicopters. We provide users with an intuitive interface for assembling a multicopter from a collection of components (e.g., propellers, motors, and carbon fiber rods). Our algorithm interactively optimizes shape and controller parameters of the current design to ensure its proper operation. In addition, we allow incorporating a variety of other metrics (such as payload, battery usage, size, and cost) into the design process and exploring tradeoffs between them. We show the efficacy of our method and system by designing, optimizing, fabricating, and operating multicopters with complex geometries and propeller configurations. We also demonstrate the ability of our optimization algorithm to improve the multicopter performance under different metrics."}],"date_created":"2018-12-11T11:50:07Z","alternative_title":["ACM Transactions on Graphics"],"scopus_import":1,"oa_version":"Submitted Version","oa":1,"year":"2016","ec_funded":1,"has_accepted_license":"1","conference":{"end_date":"2016-12-08","start_date":"2016-12-05","name":"SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia","location":"Macao, China"},"date_updated":"2021-01-12T06:48:15Z","day":"01","title":"Computational multicopter design","doi":"10.1145/2980179.2982427","acknowledgement":"We thank Nobuyuki Umetani for his insightful suggestions in our discussions. We thank Alan Schultz and his colleagues at NRL for building the hexacopter and for the valuable discussions. We thank Randall Davis, Boris Katz, and Howard Shrobe at MIT for their advice. We are grateful to Nick Bandiera for preprocessing mechanical parts and providing 3D printing technical support; Charles Blouin from RCBenchmark for dynamometer hardware support; Brian Saavedra for the composition UI; Yingzhe Yuan for data acquisition and video recording in the experiments; Michael Foshey and David Kim for their comments on the draft of the paper. \r\n\r\n\r\nThis work was partially supported by Air Force Research Laboratory’s sponsorship of Julia: A Fresh Approach to Technical Computing and Data Processing (Sponsor Award ID FA8750-15-2- 0272, MIT Award ID 024831-00003), and NSF Expedition project (Sponsor Award ID CCF-1138967, MIT Award ID 020610-00002). The views expressed herein are not endorsed by the sponsors. This project has also received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No 645599. ","_id":"1097","language":[{"iso":"eng"}],"pubrep_id":"759","issue":"6","citation":{"mla":"Du, Tao, et al. Computational Multicopter Design. Vol. 35, no. 6, 227, ACM, 2016, doi:10.1145/2980179.2982427.","short":"T. Du, A. Schulz, B. Zhu, B. Bickel, W. Matusik, in:, ACM, 2016.","ieee":"T. Du, A. Schulz, B. Zhu, B. Bickel, and W. Matusik, “Computational multicopter design,” presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China, 2016, vol. 35, no. 6.","chicago":"Du, Tao, Adriana Schulz, Bo Zhu, Bernd Bickel, and Wojciech Matusik. “Computational Multicopter Design,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2980179.2982427.","apa":"Du, T., Schulz, A., Zhu, B., Bickel, B., & Matusik, W. (2016). Computational multicopter design (Vol. 35). Presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China: ACM. https://doi.org/10.1145/2980179.2982427","ista":"Du T, Schulz A, Zhu B, Bickel B, Matusik W. 2016. Computational multicopter design. SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, ACM Transactions on Graphics, vol. 35, 227.","ama":"Du T, Schulz A, Zhu B, Bickel B, Matusik W. Computational multicopter design. In: Vol 35. ACM; 2016. doi:10.1145/2980179.2982427"},"ddc":["006"],"month":"11","file_date_updated":"2018-12-12T10:17:42Z","article_number":"227","author":[{"full_name":"Du, Tao","last_name":"Du","first_name":"Tao"},{"first_name":"Adriana","last_name":"Schulz","full_name":"Schulz, Adriana"},{"full_name":"Zhu, Bo","first_name":"Bo","last_name":"Zhu"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"},{"first_name":"Wojciech","last_name":"Matusik","full_name":"Matusik, Wojciech"}],"file":[{"content_type":"application/pdf","creator":"system","relation":"main_file","file_name":"IST-2017-759-v1+1_copter.pdf","file_id":"5298","file_size":33114420,"date_updated":"2018-12-12T10:17:42Z","date_created":"2018-12-12T10:17:42Z","access_level":"open_access"}]},{"acknowledgement":"This work was in parts funded by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 308036.\r\n\r\n","pubrep_id":"775","_id":"1098","language":[{"iso":"eng"}],"page":"3619-3627","citation":{"ama":"Pentina A, Urner R. Lifelong learning with weighted majority votes. In: Vol 29. Neural Information Processing Systems; 2016:3619-3627.","ista":"Pentina A, Urner R. 2016. Lifelong learning with weighted majority votes. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 3619–3627.","apa":"Pentina, A., & Urner, R. (2016). Lifelong learning with weighted majority votes (Vol. 29, pp. 3619–3627). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain: Neural Information Processing Systems.","chicago":"Pentina, Anastasia, and Ruth Urner. “Lifelong Learning with Weighted Majority Votes,” 29:3619–27. Neural Information Processing Systems, 2016.","ieee":"A. Pentina and R. Urner, “Lifelong learning with weighted majority votes,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain, 2016, vol. 29, pp. 3619–3627.","mla":"Pentina, Anastasia, and Ruth Urner. Lifelong Learning with Weighted Majority Votes. Vol. 29, Neural Information Processing Systems, 2016, pp. 3619–27.","short":"A. Pentina, R. Urner, in:, Neural Information Processing Systems, 2016, pp. 3619–3627."},"ddc":["006"],"month":"12","file_date_updated":"2018-12-12T10:12:43Z","file":[{"content_type":"application/pdf","creator":"system","file_name":"IST-2017-775-v1+1_main.pdf","relation":"main_file","file_id":"4961","file_size":237111,"date_updated":"2018-12-12T10:12:42Z","date_created":"2018-12-12T10:12:42Z","access_level":"open_access"},{"content_type":"application/pdf","creator":"system","file_name":"IST-2017-775-v1+2_supplementary.pdf","relation":"main_file","file_id":"4962","file_size":185818,"date_updated":"2018-12-12T10:12:43Z","date_created":"2018-12-12T10:12:43Z","access_level":"open_access"}],"author":[{"id":"42E87FC6-F248-11E8-B48F-1D18A9856A87","first_name":"Anastasia","last_name":"Pentina","full_name":"Pentina, Anastasia"},{"full_name":"Urner, Ruth","last_name":"Urner","first_name":"Ruth"}],"oa":1,"ec_funded":1,"year":"2016","has_accepted_license":"1","conference":{"start_date":"2016-12-05","end_date":"2016-12-10","location":"Barcelona, Spain","name":"NIPS: Neural Information Processing Systems"},"date_updated":"2021-01-12T06:48:15Z","day":"01","title":"Lifelong learning with weighted majority votes","intvolume":" 29","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2016-12-01T00:00:00Z","publist_id":"6277","abstract":[{"text":"Better understanding of the potential benefits of information transfer and representation learning is an important step towards the goal of building intelligent systems that are able to persist in the world and learn over time. In this work, we consider a setting where the learner encounters a stream of tasks but is able to retain only limited information from each encountered task, such as a learned predictor. In contrast to most previous works analyzing this scenario, we do not make any distributional assumptions on the task generating process. Instead, we formulate a complexity measure that captures the diversity of the observed tasks. We provide a lifelong learning algorithm with error guarantees for every observed task (rather than on average). We show sample complexity reductions in comparison to solving every task in isolation in terms of our task complexity measure. Further, our algorithmic framework can naturally be viewed as learning a representation from encountered tasks with a neural network.","lang":"eng"}],"date_created":"2018-12-11T11:50:08Z","alternative_title":["Advances in Neural Information Processing Systems"],"scopus_import":1,"oa_version":"Published Version","volume":29,"type":"conference","publisher":"Neural Information Processing Systems","publication_status":"published","project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","call_identifier":"FP7"}],"quality_controlled":"1","department":[{"_id":"ChLa"}]},{"_id":"1099","pubrep_id":"760","language":[{"iso":"eng"}],"acknowledgement":"The armadillo, bunny and dragon models are courtesy of the Stanford 3D Scanning Repository. The bimba, fertility and elephant models are courtesy of the AIM@SHAPE Shape Repository. \r\nThis project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement\r\nNo. 645599.","issue":"6","ddc":["000","005"],"citation":{"ama":"Malomo L, Pietroni N, Bickel B, Cignoni P. FlexMolds: Automatic design of flexible shells for molding. In: Vol 35. ACM; 2016. doi:10.1145/2980179.2982397","apa":"Malomo, L., Pietroni, N., Bickel, B., & Cignoni, P. (2016). FlexMolds: Automatic design of flexible shells for molding (Vol. 35). Presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China: ACM. https://doi.org/10.1145/2980179.2982397","ista":"Malomo L, Pietroni N, Bickel B, Cignoni P. 2016. FlexMolds: Automatic design of flexible shells for molding. SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, ACM Transactions on Graphics, vol. 35, 223.","ieee":"L. Malomo, N. Pietroni, B. Bickel, and P. Cignoni, “FlexMolds: Automatic design of flexible shells for molding,” presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China, 2016, vol. 35, no. 6.","chicago":"Malomo, Luigi, Nico Pietroni, Bernd Bickel, and Paolo Cignoni. “FlexMolds: Automatic Design of Flexible Shells for Molding,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2980179.2982397.","short":"L. Malomo, N. Pietroni, B. Bickel, P. Cignoni, in:, ACM, 2016.","mla":"Malomo, Luigi, et al. FlexMolds: Automatic Design of Flexible Shells for Molding. Vol. 35, no. 6, 223, ACM, 2016, doi:10.1145/2980179.2982397."},"author":[{"full_name":"Malomo, Luigi","last_name":"Malomo","first_name":"Luigi"},{"last_name":"Pietroni","first_name":"Nico","full_name":"Pietroni, Nico"},{"first_name":"Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"},{"full_name":"Cignoni, Paolo","last_name":"Cignoni","first_name":"Paolo"}],"file":[{"file_id":"4918","file_size":11122029,"date_created":"2018-12-12T10:12:01Z","date_updated":"2018-12-12T10:12:01Z","access_level":"open_access","content_type":"application/pdf","creator":"system","file_name":"IST-2017-760-v1+1_flexmolds.pdf","relation":"main_file"}],"article_number":"223","month":"11","file_date_updated":"2018-12-12T10:12:01Z","oa":1,"conference":{"location":"Macao, China","name":"SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia","start_date":"2016-12-05","end_date":"2016-12-08"},"has_accepted_license":"1","ec_funded":1,"year":"2016","day":"01","date_updated":"2021-01-12T06:48:16Z","doi":"10.1145/2980179.2982397","title":"FlexMolds: Automatic design of flexible shells for molding","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 35","abstract":[{"lang":"eng","text":"We present FlexMolds, a novel computational approach to automatically design flexible, reusable molds that, once 3D printed, allow us to physically fabricate, by means of liquid casting, multiple copies of complex shapes with rich surface details and complex topology. The approach to design such flexible molds is based on a greedy bottom-up search of possible cuts over an object, evaluating for each possible cut the feasibility of the resulting mold. We use a dynamic simulation approach to evaluate candidate molds, providing a heuristic to generate forces that are able to open, detach, and remove a complex mold from the object it surrounds. We have tested the approach with a number of objects with nontrivial shapes and topologies."}],"publist_id":"6276","date_published":"2016-11-01T00:00:00Z","status":"public","scopus_import":1,"alternative_title":["ACM Transactions on Graphics"],"date_created":"2018-12-11T11:50:08Z","oa_version":"Submitted Version","type":"conference","volume":35,"publication_status":"published","publisher":"ACM","department":[{"_id":"BeBi"}],"quality_controlled":"1","project":[{"call_identifier":"H2020","grant_number":"645599","_id":"25082902-B435-11E9-9278-68D0E5697425","name":"Soft-bodied intelligence for Manipulation"}]},{"title":"Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation","doi":"10.1016/j.celrep.2016.06.036","date_updated":"2024-03-25T23:30:13Z","day":"19","ec_funded":1,"year":"2016","related_material":{"record":[{"status":"public","id":"961","relation":"dissertation_contains"},{"id":"50","relation":"dissertation_contains","status":"public"}]},"has_accepted_license":"1","oa":1,"file_date_updated":"2018-12-12T10:11:04Z","month":"07","file":[{"file_id":"4857","file_size":3921947,"date_updated":"2018-12-12T10:11:04Z","date_created":"2018-12-12T10:11:04Z","access_level":"open_access","content_type":"application/pdf","creator":"system","relation":"main_file","file_name":"IST-2017-754-v1+1_1-s2.0-S2211124716307768-main.pdf"}],"author":[{"full_name":"Sako, Keisuke","orcid":"0000-0002-6453-8075","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","last_name":"Sako","first_name":"Keisuke"},{"full_name":"Pradhan, Saurabh","first_name":"Saurabh","last_name":"Pradhan"},{"id":"419EECCC-F248-11E8-B48F-1D18A9856A87","last_name":"Barone","first_name":"Vanessa","orcid":"0000-0003-2676-3367","full_name":"Barone, Vanessa"},{"first_name":"Álvaro","last_name":"Inglés Prieto","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5409-8571","full_name":"Inglés Prieto, Álvaro"},{"last_name":"Mueller","first_name":"Patrick","full_name":"Mueller, Patrick"},{"full_name":"Ruprecht, Verena","orcid":"0000-0003-4088-8633","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","last_name":"Ruprecht","first_name":"Verena"},{"full_name":"Capek, Daniel","orcid":"0000-0001-5199-9940","id":"31C42484-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","last_name":"Capek"},{"full_name":"Galande, Sanjeev","first_name":"Sanjeev","last_name":"Galande"},{"last_name":"Janovjak","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"citation":{"ama":"Sako K, Pradhan S, Barone V, et al. Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. Cell Reports. 2016;16(3):866-877. doi:10.1016/j.celrep.2016.06.036","apa":"Sako, K., Pradhan, S., Barone, V., Inglés Prieto, Á., Mueller, P., Ruprecht, V., … Heisenberg, C.-P. J. (2016). Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2016.06.036","ista":"Sako K, Pradhan S, Barone V, Inglés Prieto Á, Mueller P, Ruprecht V, Capek D, Galande S, Janovjak HL, Heisenberg C-PJ. 2016. Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. Cell Reports. 16(3), 866–877.","ieee":"K. Sako et al., “Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation,” Cell Reports, vol. 16, no. 3. Cell Press, pp. 866–877, 2016.","chicago":"Sako, Keisuke, Saurabh Pradhan, Vanessa Barone, Álvaro Inglés Prieto, Patrick Mueller, Verena Ruprecht, Daniel Capek, Sanjeev Galande, Harald L Janovjak, and Carl-Philipp J Heisenberg. “Optogenetic Control of Nodal Signaling Reveals a Temporal Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation.” Cell Reports. Cell Press, 2016. https://doi.org/10.1016/j.celrep.2016.06.036.","mla":"Sako, Keisuke, et al. “Optogenetic Control of Nodal Signaling Reveals a Temporal Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation.” Cell Reports, vol. 16, no. 3, Cell Press, 2016, pp. 866–77, doi:10.1016/j.celrep.2016.06.036.","short":"K. Sako, S. Pradhan, V. Barone, Á. Inglés Prieto, P. Mueller, V. Ruprecht, D. Capek, S. Galande, H.L. Janovjak, C.-P.J. Heisenberg, Cell Reports 16 (2016) 866–877."},"ddc":["570","576"],"issue":"3","page":"866 - 877","acknowledgement":"We are grateful to members of the C.-P.H. and H.J. labs for discussions, R. Hauschild and the different Scientific Service Units at IST Austria for technical help, M. Dravecka for performing initial experiments, A. Schier for reading an earlier version of the manuscript, K.W. Rogers for technical help, and C. Hill, A. Bruce, and L. Solnica-Krezel for sending plasmids. This work was supported by grants from the Austrian Science Foundation (FWF): (T560-B17) and (I 812-B12) to V.R. and C.-P.H., and from the European Union (EU FP7): (6275) to H.J. A.I.-P. is supported by a Ramon Areces fellowship.","language":[{"iso":"eng"}],"_id":"1100","pubrep_id":"754","project":[{"name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation","_id":"2529486C-B435-11E9-9278-68D0E5697425","grant_number":"T 560-B17","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation","_id":"2527D5CC-B435-11E9-9278-68D0E5697425","grant_number":"I 812-B12"},{"grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology","_id":"25548C20-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"quality_controlled":"1","department":[{"_id":"CaHe"},{"_id":"HaJa"}],"acknowledged_ssus":[{"_id":"SSU"}],"publisher":"Cell Press","publication_status":"published","volume":16,"type":"journal_article","oa_version":"Published Version","date_created":"2018-12-11T11:50:08Z","scopus_import":1,"status":"public","date_published":"2016-07-19T00:00:00Z","publist_id":"6275","publication":"Cell Reports","abstract":[{"text":"During metazoan development, the temporal pattern of morphogen signaling is critical for organizing cell fates in space and time. Yet, tools for temporally controlling morphogen signaling within the embryo are still scarce. Here, we developed a photoactivatable Nodal receptor to determine how the temporal pattern of Nodal signaling affects cell fate specification during zebrafish gastrulation. By using this receptor to manipulate the duration of Nodal signaling in vivo by light, we show that extended Nodal signaling within the organizer promotes prechordal plate specification and suppresses endoderm differentiation. Endoderm differentiation is suppressed by extended Nodal signaling inducing expression of the transcriptional repressor goosecoid (gsc) in prechordal plate progenitors, which in turn restrains Nodal signaling from upregulating the endoderm differentiation gene sox17 within these cells. Thus, optogenetic manipulation of Nodal signaling identifies a critical role of Nodal signaling duration for organizer cell fate specification during gastrulation.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":" 16","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"year":"2016","type":"journal_article","volume":1,"article_processing_charge":"No","doi":"10.1021/acssensors.6b00576","department":[{"_id":"HaJa"}],"title":"Rangefinder: A semisynthetic FRET sensor design algorithm","quality_controlled":"1","day":"10","publication_status":"published","date_updated":"2023-03-30T11:32:33Z","publisher":"American Chemical Society","page":"1286 - 1290","abstract":[{"text":"Optical sensors based on the phenomenon of Förster resonance energy transfer (FRET) are powerful tools that have advanced the study of small molecules in biological systems. However, sensor construction is not trivial and often requires multiple rounds of engineering or an ability to screen large numbers of variants. A method that would allow the accurate rational design of FRET sensors would expedite the production of biologically useful sensors. Here, we present Rangefinder, a computational algorithm that allows rapid in silico screening of dye attachment sites in a ligand-binding protein for the conjugation of a dye molecule to act as a Förster acceptor for a fused fluorescent protein. We present three ratiometric fluorescent sensors designed with Rangefinder, including a maltose sensor with a dynamic range of >300% and the first sensors for the most abundant sialic acid in human cells, N-acetylneuraminic acid. Provided a ligand-binding protein exists, it is our expectation that this model will facilitate the design of an optical sensor for any small molecule of interest.","lang":"eng"}],"publist_id":"6274","publication":"ACS SENSORS","issue":"11","status":"public","date_published":"2016-11-10T00:00:00Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"_id":"1101","intvolume":" 1","acknowledgement":"J.A.M., J.H.W., and W.H.Z. were supported by Australian\r\nPostgraduate Awards (APA), AS Sargeson Supplementary\r\nscholarships, and RSC supplementary scholarships. C.J.J.\r\nacknowledges support from a Human Frontiers in Science\r\nYoung Investigator Award and a Discovery Project and Future\r\nFellowship from the Australian Research Council. M.L.O. is\r\nsupported by an Australian Research Council Discovery Project\r\n(DP130102153) and the Merit Allocation Scheme of the\r\nNational Computational Infrastructure.","oa_version":"None","author":[{"last_name":"Mitchell","first_name":"Joshua","full_name":"Mitchell, Joshua"},{"full_name":"Whitfield, Jason","first_name":"Jason","last_name":"Whitfield"},{"first_name":"William","last_name":"Zhang","full_name":"Zhang, William"},{"full_name":"Henneberger, Christian","first_name":"Christian","last_name":"Henneberger"},{"orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","last_name":"Janovjak"},{"full_name":"O'Mara, Megan","last_name":"O'Mara","first_name":"Megan"},{"first_name":"Colin","last_name":"Jackson","full_name":"Jackson, Colin"}],"month":"11","scopus_import":"1","date_created":"2018-12-11T11:50:09Z","citation":{"ama":"Mitchell J, Whitfield J, Zhang W, et al. Rangefinder: A semisynthetic FRET sensor design algorithm. ACS SENSORS. 2016;1(11):1286-1290. doi:10.1021/acssensors.6b00576","apa":"Mitchell, J., Whitfield, J., Zhang, W., Henneberger, C., Janovjak, H. L., O’Mara, M., & Jackson, C. (2016). Rangefinder: A semisynthetic FRET sensor design algorithm. ACS SENSORS. American Chemical Society. https://doi.org/10.1021/acssensors.6b00576","ista":"Mitchell J, Whitfield J, Zhang W, Henneberger C, Janovjak HL, O’Mara M, Jackson C. 2016. Rangefinder: A semisynthetic FRET sensor design algorithm. ACS SENSORS. 1(11), 1286–1290.","ieee":"J. Mitchell et al., “Rangefinder: A semisynthetic FRET sensor design algorithm,” ACS SENSORS, vol. 1, no. 11. American Chemical Society, pp. 1286–1290, 2016.","chicago":"Mitchell, Joshua, Jason Whitfield, William Zhang, Christian Henneberger, Harald L Janovjak, Megan O’Mara, and Colin Jackson. “Rangefinder: A Semisynthetic FRET Sensor Design Algorithm.” ACS SENSORS. American Chemical Society, 2016. https://doi.org/10.1021/acssensors.6b00576.","mla":"Mitchell, Joshua, et al. “Rangefinder: A Semisynthetic FRET Sensor Design Algorithm.” ACS SENSORS, vol. 1, no. 11, American Chemical Society, 2016, pp. 1286–90, doi:10.1021/acssensors.6b00576.","short":"J. Mitchell, J. Whitfield, W. Zhang, C. Henneberger, H.L. Janovjak, M. O’Mara, C. Jackson, ACS SENSORS 1 (2016) 1286–1290."}},{"citation":{"apa":"Kolesnikov, A., & Lampert, C. (2016). Improving weakly-supervised object localization by micro-annotation. In Proceedings of the British Machine Vision Conference 2016 (Vol. 2016–September, p. 92.1-92.12). York, United Kingdom: BMVA Press. https://doi.org/10.5244/C.30.92","ista":"Kolesnikov A, Lampert C. 2016. Improving weakly-supervised object localization by micro-annotation. Proceedings of the British Machine Vision Conference 2016. BMVC: British Machine Vision Conference vol. 2016–September, 92.1-92.12.","ama":"Kolesnikov A, Lampert C. Improving weakly-supervised object localization by micro-annotation. In: Proceedings of the British Machine Vision Conference 2016. Vol 2016-September. BMVA Press; 2016:92.1-92.12. doi:10.5244/C.30.92","mla":"Kolesnikov, Alexander, and Christoph Lampert. “Improving Weakly-Supervised Object Localization by Micro-Annotation.” Proceedings of the British Machine Vision Conference 2016, vol. 2016–September, BMVA Press, 2016, p. 92.1-92.12, doi:10.5244/C.30.92.","short":"A. Kolesnikov, C. Lampert, in:, Proceedings of the British Machine Vision Conference 2016, BMVA Press, 2016, p. 92.1-92.12.","ieee":"A. Kolesnikov and C. Lampert, “Improving weakly-supervised object localization by micro-annotation,” in Proceedings of the British Machine Vision Conference 2016, York, United Kingdom, 2016, vol. 2016–September, p. 92.1-92.12.","chicago":"Kolesnikov, Alexander, and Christoph Lampert. “Improving Weakly-Supervised Object Localization by Micro-Annotation.” In Proceedings of the British Machine Vision Conference 2016, 2016–September:92.1-92.12. BMVA Press, 2016. https://doi.org/10.5244/C.30.92."},"month":"09","author":[{"first_name":"Alexander","last_name":"Kolesnikov","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","full_name":"Kolesnikov, Alexander"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert"}],"acknowledgement":"This work was funded in parts by the European Research Council\r\nunder the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC grant\r\nagreement no 308036. We gratefully acknowledge the support of NVIDIA Corporation with\r\nthe donation of the GPUs used for this research.","language":[{"iso":"eng"}],"_id":"1102","page":"92.1-92.12","date_updated":"2021-01-12T06:48:18Z","day":"01","title":"Improving weakly-supervised object localization by micro-annotation","doi":"10.5244/C.30.92","oa":1,"ec_funded":1,"year":"2016","conference":{"location":"York, United Kingdom","name":"BMVC: British Machine Vision Conference","start_date":"2016-09-19","end_date":"2016-09-22"},"date_created":"2018-12-11T11:50:09Z","scopus_import":1,"oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2016-09-01T00:00:00Z","status":"public","publist_id":"6273","publication":"Proceedings of the British Machine Vision Conference 2016","abstract":[{"lang":"eng","text":"Weakly-supervised object localization methods tend to fail for object classes that consistently co-occur with the same background elements, e.g. trains on tracks. We propose a method to overcome these failures by adding a very small amount of model-specific additional annotation. The main idea is to cluster a deep network\\'s mid-level representations and assign object or distractor labels to each cluster. Experiments show substantially improved localization results on the challenging ILSVC2014 dataset for bounding box detection and the PASCAL VOC2012 dataset for semantic segmentation."}],"publisher":"BMVA Press","publication_status":"published","project":[{"call_identifier":"FP7","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding"}],"quality_controlled":"1","department":[{"_id":"ChLa"}],"volume":"2016-September","type":"conference","main_file_link":[{"url":"http://www.bmva.org/bmvc/2016/papers/paper092/paper092.pdf","open_access":"1"}]},{"date_created":"2018-12-11T11:50:09Z","citation":{"ama":"Gurung A, Deka A, Bartocci E, Bogomolov S, Grosu R, Ray R. Parallel reachability analysis for hybrid systems. In: IEEE; 2016. doi:10.1109/MEMCOD.2016.7797741","apa":"Gurung, A., Deka, A., Bartocci, E., Bogomolov, S., Grosu, R., & Ray, R. (2016). Parallel reachability analysis for hybrid systems. Presented at the MEMOCODE: International Conference on Formal Methods and Models for System Design, Kanpur, India : IEEE. https://doi.org/10.1109/MEMCOD.2016.7797741","ista":"Gurung A, Deka A, Bartocci E, Bogomolov S, Grosu R, Ray R. 2016. Parallel reachability analysis for hybrid systems. MEMOCODE: International Conference on Formal Methods and Models for System Design, 7797741.","ieee":"A. Gurung, A. Deka, E. Bartocci, S. Bogomolov, R. Grosu, and R. Ray, “Parallel reachability analysis for hybrid systems,” presented at the MEMOCODE: International Conference on Formal Methods and Models for System Design, Kanpur, India , 2016.","chicago":"Gurung, Amit, Arup Deka, Ezio Bartocci, Sergiy Bogomolov, Radu Grosu, and Rajarshi Ray. “Parallel Reachability Analysis for Hybrid Systems.” IEEE, 2016. https://doi.org/10.1109/MEMCOD.2016.7797741.","short":"A. Gurung, A. Deka, E. Bartocci, S. Bogomolov, R. Grosu, R. Ray, in:, IEEE, 2016.","mla":"Gurung, Amit, et al. Parallel Reachability Analysis for Hybrid Systems. 7797741, IEEE, 2016, doi:10.1109/MEMCOD.2016.7797741."},"scopus_import":1,"article_number":"7797741","month":"12","author":[{"first_name":"Amit","last_name":"Gurung","full_name":"Gurung, Amit"},{"first_name":"Arup","last_name":"Deka","full_name":"Deka, Arup"},{"first_name":"Ezio","last_name":"Bartocci","full_name":"Bartocci, Ezio"},{"full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov","first_name":"Sergiy"},{"last_name":"Grosu","first_name":"Radu","full_name":"Grosu, Radu"},{"full_name":"Ray, Rajarshi","last_name":"Ray","first_name":"Rajarshi"}],"oa_version":"Preprint","acknowledgement":"This work was supported in part by DST-SERB, GoI under Project No. YSS/2014/000623 and by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award).","language":[{"iso":"eng"}],"_id":"1103","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2016-12-27T00:00:00Z","publist_id":"6272","abstract":[{"lang":"eng","text":"We propose two parallel state-space-exploration algorithms for hybrid automaton (HA), with the goal of enhancing performance on multi-core shared-memory systems. The first uses the parallel, breadth-first-search algorithm (PBFS) of the SPIN model checker, when traversing the discrete modes of the HA, and enhances it with a parallel exploration of the continuous states within each mode. We show that this simple-minded extension of PBFS does not provide the desired load balancing in many HA benchmarks. The second algorithm is a task-parallel BFS algorithm (TP-BFS), which uses a cheap precomputation of the cost associated with the post operations (both continuous and discrete) in order to improve load balancing. We illustrate the TP-BFS and the cost precomputation of the post operators on a support-function-based algorithm for state-space exploration. The performance comparison of the two algorithms shows that, in general, TP-BFS provides a better utilization/load-balancing of the CPU. Both algorithms are implemented in the model checker XSpeed. Our experiments show a maximum speed-up of more than 2000 χ on a navigation benchmark, with respect to SpaceEx LGG scenario. In order to make the comparison fair, we employed an equal number of post operations in both tools. To the best of our knowledge, this paper represents the first attempt to provide parallel, reachability-analysis algorithms for HA."}],"publisher":"IEEE","date_updated":"2021-01-12T06:48:18Z","publication_status":"published","day":"27","project":[{"call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"quality_controlled":"1","department":[{"_id":"ToHe"}],"title":"Parallel reachability analysis for hybrid systems","doi":"10.1109/MEMCOD.2016.7797741","oa":1,"type":"conference","ec_funded":1,"year":"2016","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.05473"}],"conference":{"end_date":"2016-11-20","start_date":"2016-11-18","name":"MEMOCODE: International Conference on Formal Methods and Models for System Design","location":"Kanpur, India "}},{"publication_status":"published","publisher":"Neural Information Processing Systems","department":[{"_id":"GaTk"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7"}],"quality_controlled":"1","volume":29,"type":"conference","main_file_link":[{"url":"http://papers.nips.cc/paper/6153-estimating-nonlinear-neural-response-functions-using-gp-priors-and-kronecker-methods"}],"alternative_title":["Advances in Neural Information Processing Systems"],"scopus_import":1,"date_created":"2018-12-11T11:50:10Z","oa_version":"None","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 29","abstract":[{"lang":"eng","text":"Jointly characterizing neural responses in terms of several external variables promises novel insights into circuit function, but remains computationally prohibitive in practice. Here we use gaussian process (GP) priors and exploit recent advances in fast GP inference and learning based on Kronecker methods, to efficiently estimate multidimensional nonlinear tuning functions. Our estimator require considerably less data than traditional methods and further provides principled uncertainty estimates. We apply these tools to hippocampal recordings during open field exploration and use them to characterize the joint dependence of CA1 responses on the position of the animal and several other variables, including the animal\\'s speed, direction of motion, and network oscillations.Our results provide an unprecedentedly detailed quantification of the tuning of hippocampal neurons. The model\\'s generality suggests that our approach can be used to estimate neural response properties in other brain regions."}],"date_published":"2016-12-01T00:00:00Z","status":"public","publist_id":"6265","day":"01","date_updated":"2021-01-12T06:48:19Z","title":"Estimating nonlinear neural response functions using GP priors and Kronecker methods","conference":{"name":"NIPS: Neural Information Processing Systems","location":"Barcelona; Spain","end_date":"2016-12-10","start_date":"2016-12-05"},"year":"2016","ec_funded":1,"citation":{"ama":"Savin C, Tkačik G. Estimating nonlinear neural response functions using GP priors and Kronecker methods. In: Vol 29. Neural Information Processing Systems; 2016:3610-3618.","apa":"Savin, C., & Tkačik, G. (2016). Estimating nonlinear neural response functions using GP priors and Kronecker methods (Vol. 29, pp. 3610–3618). Presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain: Neural Information Processing Systems.","ista":"Savin C, Tkačik G. 2016. Estimating nonlinear neural response functions using GP priors and Kronecker methods. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 3610–3618.","ieee":"C. Savin and G. Tkačik, “Estimating nonlinear neural response functions using GP priors and Kronecker methods,” presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain, 2016, vol. 29, pp. 3610–3618.","chicago":"Savin, Cristina, and Gašper Tkačik. “Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods,” 29:3610–18. Neural Information Processing Systems, 2016.","short":"C. Savin, G. Tkačik, in:, Neural Information Processing Systems, 2016, pp. 3610–3618.","mla":"Savin, Cristina, and Gašper Tkačik. Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods. Vol. 29, Neural Information Processing Systems, 2016, pp. 3610–18."},"month":"12","author":[{"id":"3933349E-F248-11E8-B48F-1D18A9856A87","last_name":"Savin","first_name":"Cristina","full_name":"Savin, Cristina"},{"orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik"}],"acknowledgement":"We thank Jozsef Csicsvari for kindly sharing the CA1 data.\r\nThis work was supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme(FP7/2007-2013) under REA grant agreement no. 291734.","language":[{"iso":"eng"}],"_id":"1105","page":"3610-3618"},{"external_id":{"pmid":["27697922"]},"doi":"10.1083/jcb.201603053","title":"Nuclear envelope rupture is induced by actin-based nucleus confinement","date_updated":"2022-07-18T08:33:47Z","day":"03","publication_identifier":{"issn":["0021-9525","1540-8140"]},"year":"2016","oa":1,"article_processing_charge":"No","author":[{"first_name":"Emily M.","last_name":"Hatch","full_name":"Hatch, Emily M."},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","last_name":"HETZER","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W"}],"month":"10","keyword":["Cell Biology"],"citation":{"ista":"Hatch EM, Hetzer M. 2016. Nuclear envelope rupture is induced by actin-based nucleus confinement. Journal of Cell Biology. 215(1), 27–36.","apa":"Hatch, E. M., & Hetzer, M. (2016). Nuclear envelope rupture is induced by actin-based nucleus confinement. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201603053","ama":"Hatch EM, Hetzer M. Nuclear envelope rupture is induced by actin-based nucleus confinement. Journal of Cell Biology. 2016;215(1):27-36. doi:10.1083/jcb.201603053","short":"E.M. Hatch, M. Hetzer, Journal of Cell Biology 215 (2016) 27–36.","mla":"Hatch, Emily M., and Martin Hetzer. “Nuclear Envelope Rupture Is Induced by Actin-Based Nucleus Confinement.” Journal of Cell Biology, vol. 215, no. 1, Rockefeller University Press, 2016, pp. 27–36, doi:10.1083/jcb.201603053.","chicago":"Hatch, Emily M., and Martin Hetzer. “Nuclear Envelope Rupture Is Induced by Actin-Based Nucleus Confinement.” Journal of Cell Biology. Rockefeller University Press, 2016. https://doi.org/10.1083/jcb.201603053.","ieee":"E. M. Hatch and M. Hetzer, “Nuclear envelope rupture is induced by actin-based nucleus confinement,” Journal of Cell Biology, vol. 215, no. 1. Rockefeller University Press, pp. 27–36, 2016."},"article_type":"original","issue":"1","page":"27-36","language":[{"iso":"eng"}],"_id":"11069","quality_controlled":"1","pmid":1,"publisher":"Rockefeller University Press","publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1083/jcb.201603053","open_access":"1"}],"type":"journal_article","volume":215,"oa_version":"Published Version","date_created":"2022-04-07T07:47:42Z","extern":"1","scopus_import":"1","publication":"Journal of Cell Biology","status":"public","date_published":"2016-10-03T00:00:00Z","abstract":[{"text":"Repeated rounds of nuclear envelope (NE) rupture and repair have been observed in laminopathy and cancer cells and result in intermittent loss of nucleus compartmentalization. Currently, the causes of NE rupture are unclear. Here, we show that NE rupture in cancer cells relies on the assembly of contractile actin bundles that interact with the nucleus via the linker of nucleoskeleton and cytoskeleton (LINC) complex. We found that the loss of actin bundles or the LINC complex did not rescue nuclear lamina defects, a previously identified determinant of nuclear membrane stability, but did decrease the number and size of chromatin hernias. Finally, NE rupture inhibition could be rescued in cells treated with actin-depolymerizing drugs by mechanically constraining nucleus height. These data suggest a model of NE rupture where weak membrane areas, caused by defects in lamina organization, rupture because of an increase in intranuclear pressure from actin-based nucleus confinement.","lang":"eng"}],"intvolume":" 215","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd"},{"year":"2016","oa":1,"article_processing_charge":"No","doi":"10.1101/gad.287417.116","title":"Nucleoporin-mediated regulation of cell identity genes","external_id":{"pmid":["27807035"]},"day":"02","publication_identifier":{"eissn":["1549-5477"],"issn":["0890-9369"]},"date_updated":"2022-07-18T08:33:49Z","page":"2253-2258","issue":"20","language":[{"iso":"eng"}],"_id":"11070","author":[{"full_name":"Ibarra, Arkaitz","last_name":"Ibarra","first_name":"Arkaitz"},{"last_name":"Benner","first_name":"Chris","full_name":"Benner, Chris"},{"first_name":"Swati","last_name":"Tyagi","full_name":"Tyagi, Swati"},{"full_name":"Cool, Jonah","last_name":"Cool","first_name":"Jonah"},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","first_name":"Martin W","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X"}],"month":"11","article_type":"original","keyword":["Developmental Biology","Genetics"],"citation":{"mla":"Ibarra, Arkaitz, et al. “Nucleoporin-Mediated Regulation of Cell Identity Genes.” Genes & Development, vol. 30, no. 20, Cold Spring Harbor Laboratory, 2016, pp. 2253–58, doi:10.1101/gad.287417.116.","short":"A. Ibarra, C. Benner, S. Tyagi, J. Cool, M. Hetzer, Genes & Development 30 (2016) 2253–2258.","chicago":"Ibarra, Arkaitz, Chris Benner, Swati Tyagi, Jonah Cool, and Martin Hetzer. “Nucleoporin-Mediated Regulation of Cell Identity Genes.” Genes & Development. Cold Spring Harbor Laboratory, 2016. https://doi.org/10.1101/gad.287417.116.","ieee":"A. Ibarra, C. Benner, S. Tyagi, J. Cool, and M. Hetzer, “Nucleoporin-mediated regulation of cell identity genes,” Genes & Development, vol. 30, no. 20. Cold Spring Harbor Laboratory, pp. 2253–2258, 2016.","ista":"Ibarra A, Benner C, Tyagi S, Cool J, Hetzer M. 2016. Nucleoporin-mediated regulation of cell identity genes. Genes & Development. 30(20), 2253–2258.","apa":"Ibarra, A., Benner, C., Tyagi, S., Cool, J., & Hetzer, M. (2016). Nucleoporin-mediated regulation of cell identity genes. Genes & Development. Cold Spring Harbor Laboratory. https://doi.org/10.1101/gad.287417.116","ama":"Ibarra A, Benner C, Tyagi S, Cool J, Hetzer M. Nucleoporin-mediated regulation of cell identity genes. Genes & Development. 2016;30(20):2253-2258. doi:10.1101/gad.287417.116"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/gad.287417.116"}],"type":"journal_article","volume":30,"quality_controlled":"1","pmid":1,"publication_status":"published","publisher":"Cold Spring Harbor Laboratory","abstract":[{"text":"The organization of the genome in the three-dimensional space of the nucleus is coupled with cell type-specific gene expression. However, how nuclear architecture influences transcription that governs cell identity remains unknown. Here, we show that nuclear pore complex (NPC) components Nup93 and Nup153 bind superenhancers (SE), regulatory structures that drive the expression of key genes that specify cell identity. We found that nucleoporin-associated SEs localize preferentially to the nuclear periphery, and absence of Nup153 and Nup93 results in dramatic transcriptional changes of SE-associated genes. Our results reveal a crucial role of NPC components in the regulation of cell type-specifying genes and highlight nuclear architecture as a regulatory layer of genome functions in cell fate.","lang":"eng"}],"publication":"Genes & Development","date_published":"2016-11-02T00:00:00Z","status":"public","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","intvolume":" 30","oa_version":"Published Version","scopus_import":"1","extern":"1","date_created":"2022-04-07T07:48:08Z"},{"pmid":1,"quality_controlled":"1","publication_status":"published","publisher":"Cold Spring Harbor Laboratory","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/gad.280941.116"}],"volume":30,"type":"journal_article","oa_version":"Published Version","extern":"1","scopus_import":"1","date_created":"2022-04-07T07:48:20Z","abstract":[{"text":"Nuclear pore complexes (NPCs) emerged as nuclear transport channels in eukaryotic cells ∼1.5 billion years ago. While the primary role of NPCs is to regulate nucleo–cytoplasmic transport, recent research suggests that certain NPC proteins have additionally acquired the role of affecting gene expression at the nuclear periphery and in the nucleoplasm in metazoans. Here we identify a widely expressed variant of the transmembrane nucleoporin (Nup) Pom121 (named sPom121, for “soluble Pom121”) that arose by genomic rearrangement before the divergence of hominoids. sPom121 lacks the nuclear membrane-anchoring domain and thus does not localize to the NPC. Instead, sPom121 colocalizes and interacts with nucleoplasmic Nup98, a previously identified transcriptional regulator, at gene promoters to control transcription of its target genes in human cells. Interestingly, sPom121 transcripts appear independently in several mammalian species, suggesting convergent innovation of Nup-mediated transcription regulation during mammalian evolution. Our findings implicate alternate transcription initiation as a mechanism to increase the functional diversity of NPC components.","lang":"eng"}],"status":"public","date_published":"2016-05-19T00:00:00Z","publication":"Genes & Development","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","intvolume":" 30","title":"Evolution of a transcriptional regulator from a transmembrane nucleoporin","doi":"10.1101/gad.280941.116","external_id":{"pmid":["27198230"]},"publication_identifier":{"issn":["0890-9369"],"eissn":["1549-5477"]},"day":"19","date_updated":"2022-07-18T08:33:50Z","year":"2016","article_processing_charge":"No","oa":1,"month":"05","author":[{"first_name":"Tobias M.","last_name":"Franks","full_name":"Franks, Tobias M."},{"full_name":"Benner, Chris","last_name":"Benner","first_name":"Chris"},{"full_name":"Narvaiza, Iñigo","last_name":"Narvaiza","first_name":"Iñigo"},{"last_name":"Marchetto","first_name":"Maria C.N.","full_name":"Marchetto, Maria C.N."},{"last_name":"Young","first_name":"Janet M.","full_name":"Young, Janet M."},{"last_name":"Malik","first_name":"Harmit S.","full_name":"Malik, Harmit S."},{"first_name":"Fred H.","last_name":"Gage","full_name":"Gage, Fred H."},{"orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","last_name":"HETZER","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"}],"article_type":"original","keyword":["Developmental Biology","Genetics"],"citation":{"ieee":"T. M. Franks et al., “Evolution of a transcriptional regulator from a transmembrane nucleoporin,” Genes & Development, vol. 30, no. 10. Cold Spring Harbor Laboratory, pp. 1155–1171, 2016.","chicago":"Franks, Tobias M., Chris Benner, Iñigo Narvaiza, Maria C.N. Marchetto, Janet M. Young, Harmit S. Malik, Fred H. Gage, and Martin Hetzer. “Evolution of a Transcriptional Regulator from a Transmembrane Nucleoporin.” Genes & Development. Cold Spring Harbor Laboratory, 2016. https://doi.org/10.1101/gad.280941.116.","short":"T.M. Franks, C. Benner, I. Narvaiza, M.C.N. Marchetto, J.M. Young, H.S. Malik, F.H. Gage, M. Hetzer, Genes & Development 30 (2016) 1155–1171.","mla":"Franks, Tobias M., et al. “Evolution of a Transcriptional Regulator from a Transmembrane Nucleoporin.” Genes & Development, vol. 30, no. 10, Cold Spring Harbor Laboratory, 2016, pp. 1155–71, doi:10.1101/gad.280941.116.","ama":"Franks TM, Benner C, Narvaiza I, et al. Evolution of a transcriptional regulator from a transmembrane nucleoporin. Genes & Development. 2016;30(10):1155-1171. doi:10.1101/gad.280941.116","apa":"Franks, T. M., Benner, C., Narvaiza, I., Marchetto, M. C. N., Young, J. M., Malik, H. S., … Hetzer, M. (2016). Evolution of a transcriptional regulator from a transmembrane nucleoporin. Genes & Development. Cold Spring Harbor Laboratory. https://doi.org/10.1101/gad.280941.116","ista":"Franks TM, Benner C, Narvaiza I, Marchetto MCN, Young JM, Malik HS, Gage FH, Hetzer M. 2016. Evolution of a transcriptional regulator from a transmembrane nucleoporin. Genes & Development. 30(10), 1155–1171."},"page":"1155-1171","issue":"10","_id":"11071","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"_id":"11072","article_type":"original","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry"],"citation":{"ieee":"R. A. H. van de Ven et al., “p120-catenin prevents multinucleation through control of MKLP1-dependent RhoA activity during cytokinesis,” Nature Communications, vol. 7. Springer Nature, 2016.","chicago":"Ven, Robert A.H. van de, Jolien S. de Groot, Danielle Park, Robert van Domselaar, Danielle de Jong, Karoly Szuhai, Elsken van der Wall, et al. “P120-Catenin Prevents Multinucleation through Control of MKLP1-Dependent RhoA Activity during Cytokinesis.” Nature Communications. Springer Nature, 2016. https://doi.org/10.1038/ncomms13874.","short":"R.A.H. van de Ven, J.S. de Groot, D. Park, R. van Domselaar, D. de Jong, K. Szuhai, E. van der Wall, O.M. Rueda, H.R. Ali, C. Caldas, P.J. van Diest, M. Hetzer, E. Sahai, P.W.B. Derksen, Nature Communications 7 (2016).","mla":"van de Ven, Robert A. H., et al. “P120-Catenin Prevents Multinucleation through Control of MKLP1-Dependent RhoA Activity during Cytokinesis.” Nature Communications, vol. 7, 13874, Springer Nature, 2016, doi:10.1038/ncomms13874.","ama":"van de Ven RAH, de Groot JS, Park D, et al. p120-catenin prevents multinucleation through control of MKLP1-dependent RhoA activity during cytokinesis. Nature Communications. 2016;7. doi:10.1038/ncomms13874","apa":"van de Ven, R. A. H., de Groot, J. S., Park, D., van Domselaar, R., de Jong, D., Szuhai, K., … Derksen, P. W. B. (2016). p120-catenin prevents multinucleation through control of MKLP1-dependent RhoA activity during cytokinesis. Nature Communications. Springer Nature. https://doi.org/10.1038/ncomms13874","ista":"van de Ven RAH, de Groot JS, Park D, van Domselaar R, de Jong D, Szuhai K, van der Wall E, Rueda OM, Ali HR, Caldas C, van Diest PJ, Hetzer M, Sahai E, Derksen PWB. 2016. p120-catenin prevents multinucleation through control of MKLP1-dependent RhoA activity during cytokinesis. Nature Communications. 7, 13874."},"article_number":"13874","month":"12","author":[{"last_name":"van de Ven","first_name":"Robert A.H.","full_name":"van de Ven, Robert A.H."},{"full_name":"de Groot, Jolien S.","last_name":"de Groot","first_name":"Jolien S."},{"full_name":"Park, Danielle","first_name":"Danielle","last_name":"Park"},{"last_name":"van Domselaar","first_name":"Robert","full_name":"van Domselaar, Robert"},{"full_name":"de Jong, Danielle","first_name":"Danielle","last_name":"de Jong"},{"first_name":"Karoly","last_name":"Szuhai","full_name":"Szuhai, Karoly"},{"last_name":"van der Wall","first_name":"Elsken","full_name":"van der Wall, Elsken"},{"full_name":"Rueda, Oscar M.","last_name":"Rueda","first_name":"Oscar M."},{"full_name":"Ali, H. Raza","first_name":"H. Raza","last_name":"Ali"},{"full_name":"Caldas, Carlos","first_name":"Carlos","last_name":"Caldas"},{"first_name":"Paul J.","last_name":"van Diest","full_name":"van Diest, Paul J."},{"orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","last_name":"HETZER","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"},{"first_name":"Erik","last_name":"Sahai","full_name":"Sahai, Erik"},{"full_name":"Derksen, Patrick W.B.","first_name":"Patrick W.B.","last_name":"Derksen"}],"article_processing_charge":"No","oa":1,"related_material":{"link":[{"url":"https://doi.org/10.1038/ncomms16030","relation":"erratum"}]},"year":"2016","publication_identifier":{"issn":["2041-1723"]},"day":"22","date_updated":"2022-07-18T08:34:32Z","title":"p120-catenin prevents multinucleation through control of MKLP1-dependent RhoA activity during cytokinesis","doi":"10.1038/ncomms13874","external_id":{"pmid":["28004812"]},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","intvolume":" 7","abstract":[{"lang":"eng","text":"Spatiotemporal activation of RhoA and actomyosin contraction underpins cellular adhesion and division. Loss of cell–cell adhesion and chromosomal instability are cardinal events that drive tumour progression. Here, we show that p120-catenin (p120) not only controls cell–cell adhesion, but also acts as a critical regulator of cytokinesis. We find that p120 regulates actomyosin contractility through concomitant binding to RhoA and the centralspindlin component MKLP1, independent of cadherin association. In anaphase, p120 is enriched at the cleavage furrow where it binds MKLP1 to spatially control RhoA GTPase cycling. Binding of p120 to MKLP1 during cytokinesis depends on the N-terminal coiled-coil domain of p120 isoform 1A. Importantly, clinical data show that loss of p120 expression is a common event in breast cancer that strongly correlates with multinucleation and adverse patient survival. In summary, our study identifies p120 loss as a driver event of chromosomal instability in cancer.\r\n"}],"status":"public","date_published":"2016-12-22T00:00:00Z","publication":"Nature Communications","scopus_import":"1","extern":"1","date_created":"2022-04-07T07:48:34Z","oa_version":"Published Version","volume":7,"type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/ncomms13874"}],"publication_status":"published","publisher":"Springer Nature","pmid":1,"quality_controlled":"1"},{"citation":{"chicago":"Rueda, Alfredo, Florian Sedlmeir, Michele Collodo, Ulrich Vogl, Birgit Stiller, Georg Schunk, Dimitry Strekalov, et al. “Efficient Single Sideband Microwave to Optical Conversion Using a LiNbO₃ WGM-Resonator.” IEEE, 2016. https://doi.org/10.1364/CLEO_SI.2016.SF2G.3.","ieee":"A. Rueda et al., “Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator,” presented at the CLEO: Conference on Lasers and Electro Optics, San Jose, CA, USA, 2016.","mla":"Rueda, Alfredo, et al. Efficient Single Sideband Microwave to Optical Conversion Using a LiNbO₃ WGM-Resonator. 7788479, IEEE, 2016, doi:10.1364/CLEO_SI.2016.SF2G.3.","short":"A. Rueda, F. Sedlmeir, M. Collodo, U. Vogl, B. Stiller, G. Schunk, D. Strekalov, C. Marquardt, J.M. Fink, O. Painter, G. Leuchs, H. Schwefel, in:, IEEE, 2016.","ama":"Rueda A, Sedlmeir F, Collodo M, et al. Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator. In: IEEE; 2016. doi:10.1364/CLEO_SI.2016.SF2G.3","ista":"Rueda A, Sedlmeir F, Collodo M, Vogl U, Stiller B, Schunk G, Strekalov D, Marquardt C, Fink JM, Painter O, Leuchs G, Schwefel H. 2016. Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator. CLEO: Conference on Lasers and Electro Optics, 7788479.","apa":"Rueda, A., Sedlmeir, F., Collodo, M., Vogl, U., Stiller, B., Schunk, G., … Schwefel, H. (2016). Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator. Presented at the CLEO: Conference on Lasers and Electro Optics, San Jose, CA, USA: IEEE. https://doi.org/10.1364/CLEO_SI.2016.SF2G.3"},"date_created":"2018-12-11T11:50:14Z","scopus_import":"1","month":"12","article_number":"7788479","oa_version":"Preprint","author":[{"last_name":"Rueda","first_name":"Alfredo","full_name":"Rueda, Alfredo"},{"first_name":"Florian","last_name":"Sedlmeir","full_name":"Sedlmeir, Florian"},{"last_name":"Collodo","first_name":"Michele","full_name":"Collodo, Michele"},{"full_name":"Vogl, Ulrich","first_name":"Ulrich","last_name":"Vogl"},{"full_name":"Stiller, Birgit","first_name":"Birgit","last_name":"Stiller"},{"full_name":"Schunk, Georg","first_name":"Georg","last_name":"Schunk"},{"first_name":"Dimitry","last_name":"Strekalov","full_name":"Strekalov, Dimitry"},{"full_name":"Marquardt, Christoph","first_name":"Christoph","last_name":"Marquardt"},{"first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"},{"full_name":"Painter, Oskar","first_name":"Oskar","last_name":"Painter"},{"first_name":"Gerd","last_name":"Leuchs","full_name":"Leuchs, Gerd"},{"first_name":"Harald","last_name":"Schwefel","full_name":"Schwefel, Harald"}],"language":[{"iso":"eng"}],"_id":"1115","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2016-12-16T00:00:00Z","publist_id":"6251","abstract":[{"lang":"eng","text":"We present a coherent microwave to telecom signal converter based on the electro-optical effect using a crystalline WGM-resonator coupled to a 3D microwave cavity, achieving high photon conversion efficiency of 0.1% with MHz bandwidth."}],"publisher":"IEEE","date_updated":"2022-09-06T07:23:25Z","publication_status":"published","day":"16","quality_controlled":"1","department":[{"_id":"JoFi"}],"title":"Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator","doi":"10.1364/CLEO_SI.2016.SF2G.3","oa":1,"article_processing_charge":"No","type":"conference","main_file_link":[{"url":"https://arxiv.org/abs/1601.07261","open_access":"1"}],"year":"2016","related_material":{"link":[{"relation":"other","url":"http://ieeexplore.ieee.org/document/7788479/"}]},"conference":{"end_date":"2016-06-10","start_date":"2016-06-05","name":"CLEO: Conference on Lasers and Electro Optics","location":"San Jose, CA, USA"}},{"type":"dissertation","publisher":"Institute of Science and Technology Austria","publication_status":"published","project":[{"call_identifier":"H2020","grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"supervisor":[{"orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","last_name":"Bollback","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"JoBo"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6239","status":"public","date_published":"2016-12-01T00:00:00Z","abstract":[{"text":"Horizontal gene transfer (HGT), the lateral acquisition of genes across existing species\r\nboundaries, is a major evolutionary force shaping microbial genomes that facilitates\r\nadaptation to new environments as well as resistance to antimicrobial drugs. As such,\r\nunderstanding the mechanisms and constraints that determine the outcomes of HGT\r\nevents is crucial to understand the dynamics of HGT and to design better strategies to\r\novercome the challenges that originate from it.\r\nFollowing the insertion and expression of a newly transferred gene, the success of an\r\nHGT event will depend on the fitness effect it has on the recipient (host) cell. Therefore,\r\npredicting the impact of HGT on the genetic composition of a population critically\r\ndepends on the distribution of fitness effects (DFE) of horizontally transferred genes.\r\nHowever, to date, we have little knowledge of the DFE of newly transferred genes, and\r\nhence little is known about the shape and scale of this distribution.\r\nIt is particularly important to better understand the selective barriers that determine\r\nthe fitness effects of newly transferred genes. In spite of substantial bioinformatics\r\nefforts to identify horizontally transferred genes and selective barriers, a systematic\r\nexperimental approach to elucidate the roles of different selective barriers in defining\r\nthe fate of a transfer event has largely been absent. Similarly, although the fact that\r\nenvironment might alter the fitness effect of a horizontally transferred gene may seem\r\nobvious, little attention has been given to it in a systematic experimental manner.\r\nIn this study, we developed a systematic experimental approach that consists of\r\ntransferring 44 arbitrarily selected Salmonella typhimurium orthologous genes into an\r\nEscherichia coli host, and estimating the fitness effects of these transferred genes at a\r\nconstant expression level by performing competition assays against the wild type.\r\nIn chapter 2, we performed one-to-one competition assays between a mutant strain\r\ncarrying a transferred gene and the wild type strain. By using flow cytometry we\r\nestimated selection coefficients for the transferred genes with a precision level of 10-3,and obtained the DFE of horizontally transferred genes. We then investigated if these\r\nfitness effects could be predicted by any of the intrinsic properties of the genes, namely,\r\nfunctional category, degree of complexity (protein-protein interactions), GC content,\r\ncodon usage and length. Our analyses revealed that the functional category and length\r\nof the genes act as potential selective barriers. Finally, using the same procedure with\r\nthe endogenous E. coli orthologs of these 44 genes, we demonstrated that gene dosage is\r\nthe most prominent selective barrier to HGT.\r\nIn chapter 3, using the same set of genes we investigated the role of environment on the\r\nsuccess of HGT events. Under six different environments with different levels of stress\r\nwe performed more complex competition assays, where we mixed all 44 mutant strains\r\ncarrying transferred genes with the wild type strain. To estimate the fitness effects of\r\ngenes relative to wild type we used next generation sequencing. We found that the DFEs\r\nof horizontally transferred genes are highly dependent on the environment, with\r\nabundant gene–by-environment interactions. Furthermore, we demonstrated a\r\nrelationship between average fitness effect of a gene across all environments and its\r\nenvironmental variance, and thus its predictability. Finally, in spite of the fitness effects\r\nof genes being highly environment-dependent, we still observed a common shape of\r\nDFEs across all tested environments.","lang":"eng"}],"date_created":"2018-12-11T11:50:16Z","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","article_processing_charge":"No","oa":1,"year":"2016","ec_funded":1,"has_accepted_license":"1","date_updated":"2023-09-07T11:42:26Z","day":"01","publication_identifier":{"issn":["2663-337X"]},"title":"Selective barriers to horizontal gene transfer","language":[{"iso":"eng"}],"_id":"1121","acknowledgement":"This study was supported by European Research Council ERC CoG 2014 – EVOLHGT,\r\nunder the grant number 648440.\r\n\r\nIt is a pleasure to thank the many people who made this thesis possible.\r\nI would like to first thank my advisor, Jonathan Paul Bollback for providing guidance in\r\nall aspects of my life, encouragement, sound advice, and good teaching over the last six\r\nyears.\r\nI would also like to thank the members of my dissertation committee – Călin C. Guet\r\nand John F. Baines – not only for their time and guidance, but for their intellectual\r\ncontributions to my development as a scientist.\r\nI would like to thank Flavia Gama and Rodrigo Redondo who have taught me all the\r\nskills in the laboratory with their graciousness and friendship. Also special thanks to\r\nBollback group for their support and for providing a stimulating and fun environment:\r\nIsabella Tomanek, Fabienne Jesse, Claudia Igler, and Pavel Payne.\r\nJerneja Beslagic is not only an amazing assistant, she also has a smile brighter and\r\nwarmer than the sunshine, bringing happiness to every moment. Always keep your light\r\nNeja, I will miss our invaluable chatters a lot.","degree_awarded":"PhD","page":"75","ddc":["570"],"citation":{"mla":"Acar, Hande. Selective Barriers to Horizontal Gene Transfer. Institute of Science and Technology Austria, 2016.","short":"H. Acar, Selective Barriers to Horizontal Gene Transfer, Institute of Science and Technology Austria, 2016.","chicago":"Acar, Hande. “Selective Barriers to Horizontal Gene Transfer.” Institute of Science and Technology Austria, 2016.","ieee":"H. Acar, “Selective barriers to horizontal gene transfer,” Institute of Science and Technology Austria, 2016.","ista":"Acar H. 2016. Selective barriers to horizontal gene transfer. Institute of Science and Technology Austria.","apa":"Acar, H. (2016). Selective barriers to horizontal gene transfer. Institute of Science and Technology Austria.","ama":"Acar H. Selective barriers to horizontal gene transfer. 2016."},"file":[{"checksum":"94bbbc754c36115bf37f8fc11fad43c4","creator":"dernst","relation":"main_file","file_name":"PhDThesis_HandeAcar_1230.pdf","content_type":"application/pdf","date_updated":"2019-08-13T11:17:50Z","date_created":"2019-08-13T11:17:50Z","access_level":"closed","file_id":"6814","file_size":3682711},{"success":1,"file_id":"9184","file_size":3682711,"date_updated":"2021-02-22T11:51:13Z","date_created":"2021-02-22T11:51:13Z","access_level":"open_access","content_type":"application/pdf","creator":"dernst","checksum":"94bbbc754c36115bf37f8fc11fad43c4","relation":"main_file","file_name":"2016_Thesis_HandeAcar.pdf"}],"author":[{"orcid":"0000-0003-1986-9753","full_name":"Acar, Hande","last_name":"Acar","first_name":"Hande","id":"2DDF136A-F248-11E8-B48F-1D18A9856A87"}],"month":"12","file_date_updated":"2021-02-22T11:51:13Z"},{"related_material":{"record":[{"relation":"other","id":"5558","status":"public"}]},"has_accepted_license":"1","year":"2016","article_processing_charge":"No","oa":1,"title":"Tracking, correcting and absorbing water surface waves","doi":"10.15479/AT:ISTA:th_640","publication_identifier":{"issn":["2663-337X"]},"day":"15","date_updated":"2024-02-21T13:50:48Z","page":"114","degree_awarded":"PhD","acknowledgement":"First and foremost I would like to thank Chris. I have been incredibly lucky to have\r\nyou as my advisor. Your integrity and aspiration to do the right thing in all walks of\r\nlife is something I admire and aspire to. I also really appreciate the fact that when\r\nworking with you it felt like we were equals. I think we had a very synergetic work\r\nrelationship: I learned immensely from you, but I dare say that you learned a few\r\nthings from me as well. ;)\r\nNext, I would like to thank my amazing committee. Hao, it was a fantastic\r\nexperience working with you. You showed me how to persevere and keep morale\r\nhigh when things were looking the most bleak before the deadline. You are an\r\nincredible motivator and super fun to be around! Vladimir, thanks for the shared\r\nlunches and the poker games. Sorry for not bringing them back when I got busy.\r\nAlso, sorry for embarrassing you by asking about your guitar playing that one\r\ntime. You really are quite awesome! Nils, one of the friendliest and most humble\r\npeople you will meet and a top notch researcher to boot! Thank you for joining\r\nmy committee late!\r\nI would also like to acknowledge the Visual Computing group at IST Austria\r\nfrom whom I have learned so much. The excellent discussions we had in reading\r\ngroups and research meetings really helped me become a better researcher!\r\nNext, I would like to thank all the amazing people that I met during my PhD\r\nstudies, both at IST Austria, in Vienna and elsewhere. ","_id":"1122","language":[{"iso":"eng"}],"file_date_updated":"2018-12-12T10:13:02Z","month":"07","file":[{"date_created":"2018-12-12T10:13:02Z","date_updated":"2018-12-12T10:13:02Z","access_level":"open_access","file_id":"4982","file_size":13869345,"creator":"system","relation":"main_file","file_name":"IST-2016-640-v1+1_2016_Bojsen-Hansen_TCaAWSW.pdf","content_type":"application/pdf"}],"author":[{"id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","last_name":"Bojsen-Hansen","first_name":"Morten","full_name":"Bojsen-Hansen, Morten","orcid":"0000-0002-4417-3224"}],"citation":{"apa":"Bojsen-Hansen, M. (2016). Tracking, correcting and absorbing water surface waves. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_640","ista":"Bojsen-Hansen M. 2016. Tracking, correcting and absorbing water surface waves. Institute of Science and Technology Austria.","ama":"Bojsen-Hansen M. Tracking, correcting and absorbing water surface waves. 2016. doi:10.15479/AT:ISTA:th_640","short":"M. Bojsen-Hansen, Tracking, Correcting and Absorbing Water Surface Waves, Institute of Science and Technology Austria, 2016.","mla":"Bojsen-Hansen, Morten. Tracking, Correcting and Absorbing Water Surface Waves. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:th_640.","ieee":"M. Bojsen-Hansen, “Tracking, correcting and absorbing water surface waves,” Institute of Science and Technology Austria, 2016.","chicago":"Bojsen-Hansen, Morten. “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:th_640."},"ddc":["004","005","006","532","621"],"type":"dissertation","department":[{"_id":"ChWo"}],"supervisor":[{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"}],"publication_status":"published","publisher":"Institute of Science and Technology Austria","abstract":[{"text":"Computer graphics is an extremely exciting field for two reasons. On the one hand,\r\nthere is a healthy injection of pragmatism coming from the visual effects industry\r\nthat want robust algorithms that work so they can produce results at an increasingly\r\nfrantic pace. On the other hand, they must always try to push the envelope and\r\nachieve the impossible to wow their audiences in the next blockbuster, which means\r\nthat the industry has not succumb to conservatism, and there is plenty of room to\r\ntry out new and crazy ideas if there is a chance that it will pan into something\r\nuseful.\r\nWater simulation has been in visual effects for decades, however it still remains\r\nextremely challenging because of its high computational cost and difficult artdirectability.\r\nThe work in this thesis tries to address some of these difficulties.\r\nSpecifically, we make the following three novel contributions to the state-of-the-art\r\nin water simulation for visual effects.\r\nFirst, we develop the first algorithm that can convert any sequence of closed\r\nsurfaces in time into a moving triangle mesh. State-of-the-art methods at the time\r\ncould only handle surfaces with fixed connectivity, but we are the first to be able to\r\nhandle surfaces that merge and split apart. This is important for water simulation\r\npractitioners, because it allows them to convert splashy water surfaces extracted\r\nfrom particles or simulated using grid-based level sets into triangle meshes that can\r\nbe either textured and enhanced with extra surface dynamics as a post-process.\r\nWe also apply our algorithm to other phenomena that merge and split apart, such\r\nas morphs and noisy reconstructions of human performances.\r\nSecond, we formulate a surface-based energy that measures the deviation of a\r\nwater surface froma physically valid state. Such discrepancies arise when there is a\r\nmismatch in the degrees of freedom between the water surface and the underlying\r\nphysics solver. This commonly happens when practitioners use a moving triangle\r\nmesh with a grid-based physics solver, or when high-resolution grid-based surfaces\r\nare combined with low-resolution physics. Following the direction of steepest\r\ndescent on our surface-based energy, we can either smooth these artifacts or turn\r\nthem into high-resolution waves by interpreting the energy as a physical potential.\r\nThird, we extend state-of-the-art techniques in non-reflecting boundaries to handle spatially and time-varying background flows. This allows a novel new\r\nworkflow where practitioners can re-simulate part of an existing simulation, such\r\nas removing a solid obstacle, adding a new splash or locally changing the resolution.\r\nSuch changes can easily lead to new waves in the re-simulated region that would\r\nreflect off of the new simulation boundary, effectively ruining the illusion of a\r\nseamless simulation boundary between the existing and new simulations. Our\r\nnon-reflecting boundaries makes sure that such waves are absorbed.","lang":"eng"}],"date_published":"2016-07-15T00:00:00Z","status":"public","publist_id":"6238","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"date_created":"2018-12-11T11:50:16Z"}]