[{"title":"KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons","status":"public","type":"journal_article","publisher":"Oxford University Press","citation":{"apa":"Booker, S., Althof, D., Gross, A., Loreth, D., Müller, J., Unger, A., … Kulik, Á. (2016). KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons. Cerebral Cortex. Oxford University Press. https://doi.org/10.1093/cercor/bhw090","mla":"Booker, Sam, et al. “KCTD12 Auxiliary Proteins Modulate Kinetics of GABAB Receptor-Mediated Inhibition in Cholecystokinin-Containing Interneurons.” Cerebral Cortex, vol. 27, no. 3, Oxford University Press, 2016, pp. 2318–34, doi:10.1093/cercor/bhw090.","short":"S. Booker, D. Althof, A. Gross, D. Loreth, J. Müller, A. Unger, B. Fakler, A. Varro, M. Watanabe, M. Gassmann, B. Bettler, R. Shigemoto, I. Vida, Á. Kulik, Cerebral Cortex 27 (2016) 2318–2334.","chicago":"Booker, Sam, Daniel Althof, Anna Gross, Desiree Loreth, Johanna Müller, Andreas Unger, Bernd Fakler, et al. “KCTD12 Auxiliary Proteins Modulate Kinetics of GABAB Receptor-Mediated Inhibition in Cholecystokinin-Containing Interneurons.” Cerebral Cortex. Oxford University Press, 2016. https://doi.org/10.1093/cercor/bhw090.","ama":"Booker S, Althof D, Gross A, et al. KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons. Cerebral Cortex. 2016;27(3):2318-2334. doi:10.1093/cercor/bhw090","ieee":"S. Booker et al., “KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons,” Cerebral Cortex, vol. 27, no. 3. Oxford University Press, pp. 2318–2334, 2016.","ista":"Booker S, Althof D, Gross A, Loreth D, Müller J, Unger A, Fakler B, Varro A, Watanabe M, Gassmann M, Bettler B, Shigemoto R, Vida I, Kulik Á. 2016. KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons. Cerebral Cortex. 27(3), 2318–2334."},"acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft (DFG SFB 780 A2, A.K.; SFB TR3 I.V. and EXC 257, I.V.; FOR 2143, A.K. and I.V.), Spemann Graduate School (D.A.), BIOSS-2 (A6, A.K.), the Swiss National Science Foundation (3100A0-117816, B.B.), The McNaught Bequest (S.A.B. and I.V.), and Tenovus Scotland (I.V.).\r\n\r\n\r\nWe thank Cheryl Hutton and Chinmaya Sadangi for their contributions to neuronal reconstruction as well as Natalie Wernet, Sigrun Nestel, Anikó Schneider, Ina Wolter, and Ulrich Noeller for their excellent technical support. VGAT-Venus transgenic rats were generated by Drs Y. Yanagawa, M. Hirabayashi, and Y. Kawaguchi in National Institute for Physiological Sciences, Okazaki, Japan, using pCS2-Venus provided by Dr A. Miyawaki. The monoclonal mouse CCK antibody was generously provided by Dr G.V. Ohning, CURE Center, UCLA, CA. ","quality_controlled":"1","department":[{"_id":"RySh"}],"doi":"10.1093/cercor/bhw090","date_created":"2018-12-11T11:50:03Z","page":"2318 - 2334","_id":"1083","intvolume":" 27","author":[{"last_name":"Booker","first_name":"Sam","full_name":"Booker, Sam"},{"last_name":"Althof","first_name":"Daniel","full_name":"Althof, Daniel"},{"full_name":"Gross, Anna","last_name":"Gross","first_name":"Anna"},{"full_name":"Loreth, Desiree","last_name":"Loreth","first_name":"Desiree"},{"full_name":"Müller, Johanna","first_name":"Johanna","last_name":"Müller"},{"last_name":"Unger","first_name":"Andreas","full_name":"Unger, Andreas"},{"first_name":"Bernd","last_name":"Fakler","full_name":"Fakler, Bernd"},{"full_name":"Varro, Andrea","last_name":"Varro","first_name":"Andrea"},{"full_name":"Watanabe, Masahiko","last_name":"Watanabe","first_name":"Masahiko"},{"first_name":"Martin","last_name":"Gassmann","full_name":"Gassmann, Martin"},{"last_name":"Bettler","first_name":"Bernhard","full_name":"Bettler, Bernhard"},{"orcid":"0000-0001-8761-9444","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"},{"last_name":"Vida","first_name":"Imre","full_name":"Vida, Imre"},{"first_name":"Ákos","last_name":"Kulik","full_name":"Kulik, Ákos"}],"volume":27,"abstract":[{"text":" Cholecystokinin-expressing interneurons (CCK-INs) mediate behavior state-dependent inhibition in cortical circuits and themselves receive strong GABAergic input. However, it remains unclear to what extent GABABreceptors (GABABRs) contribute to their inhibitory control. Using immunoelectron microscopy, we found that CCK-INs in the rat hippocampus possessed high levels of dendritic GABABRs and KCTD12 auxiliary proteins, whereas postsynaptic effector Kir3 channels were present at lower levels. Consistently, whole-cell recordings revealed slow GABABR-mediated inhibitory postsynaptic currents (IPSCs) in most CCK-INs. In spite of the higher surface density of GABABRs in CCK-INs than in CA1 principal cells, the amplitudes of IPSCs were comparable, suggesting that the expression of Kir3 channels is the limiting factor for the GABABR currents in these INs. Morphological analysis showed that CCK-INs were diverse, comprising perisomatic-targeting basket cells (BCs), as well as dendrite-targeting (DT) interneurons, including a previously undescribed DT type. GABABR-mediated IPSCs in CCK-INs were large in BCs, but small in DT subtypes. In response to prolonged activation, GABABR-mediated currents displayed strong desensitization, which was absent in KCTD12-deficient mice. This study highlights that GABABRs differentially control CCK-IN subtypes, and the kinetics and desensitization of GABABR-mediated currents are modulated by KCTD12 proteins. ","lang":"eng"}],"date_published":"2016-04-12T00:00:00Z","issue":"3","publication_status":"published","date_updated":"2021-01-12T06:48:09Z","month":"04","oa_version":"None","publication":"Cerebral Cortex","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"12","publist_id":"6297","language":[{"iso":"eng"}],"year":"2016"},{"scopus_import":1,"file":[{"file_name":"IST-2017-795-v1+1_LIPIcs-MFCS-2016-24.pdf","file_size":564560,"access_level":"open_access","date_updated":"2018-12-12T10:17:31Z","content_type":"application/pdf","date_created":"2018-12-12T10:17:31Z","creator":"system","relation":"main_file","file_id":"5286"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"}],"date_created":"2018-12-11T11:50:05Z","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan","first_name":"Jan","last_name":"Otop"}],"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"}],"volume":58,"date_published":"2016-08-01T00:00:00Z","file_date_updated":"2018-12-12T10:17:31Z","ec_funded":1,"day":"01","year":"2016","language":[{"iso":"eng"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Nested weighted limit-average automata of bounded width","type":"conference","status":"public","pubrep_id":"795","citation":{"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","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.","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.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","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","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.","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."},"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.","quality_controlled":"1","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"doi":"10.4230/LIPIcs.MFCS.2016.24","_id":"1090","intvolume":" 58","article_number":"24","has_accepted_license":"1","alternative_title":["LIPIcs"],"publication_status":"published","oa":1,"conference":{"start_date":"2016-08-22","end_date":"2016-08-26","name":"MFCS: Mathematical Foundations of Computer Science (SG)","location":"Krakow; Poland"},"ddc":["004"],"date_updated":"2021-01-12T06:48:12Z","oa_version":"Published Version","month":"08","publist_id":"6286","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"file":[{"date_updated":"2018-12-12T10:11:39Z","content_type":"application/pdf","file_name":"IST-2017-794-v1+1_LIPIcs-CONCUR-2016-20.pdf","access_level":"open_access","file_size":501827,"file_id":"4895","creator":"system","date_created":"2018-12-12T10:11:39Z","relation":"main_file"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","scopus_import":1,"date_created":"2018-12-11T11:50:06Z","project":[{"grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"},{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF"}],"file_date_updated":"2018-12-12T10:11:39Z","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. "}],"volume":59,"date_published":"2016-08-01T00:00:00Z","author":[{"last_name":"Daca","first_name":"Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","full_name":"Daca, Przemyslaw"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"},{"orcid":"0000-0002-8122-2881","first_name":"Jan","last_name":"Kretinsky","full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9041-0905","first_name":"Tatjana","last_name":"Petrov","full_name":"Petrov, Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87"}],"day":"01","year":"2016","language":[{"iso":"eng"}],"ec_funded":1,"citation":{"short":"P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","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.","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","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.","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.","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."},"status":"public","type":"conference","pubrep_id":"794","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Linear distances between Markov chains","_id":"1093","intvolume":" 59","doi":"10.4230/LIPIcs.CONCUR.2016.20","department":[{"_id":"ToHe"},{"_id":"KrCh"},{"_id":"CaGu"}],"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.","quality_controlled":"1","alternative_title":["LIPIcs"],"has_accepted_license":"1","article_number":"20","related_material":{"record":[{"relation":"dissertation_contains","id":"1155","status":"public"}]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6283","month":"08","oa_version":"Published Version","date_updated":"2023-09-07T11:58:33Z","ddc":["004"],"oa":1,"publication_status":"published","conference":{"name":"CONCUR: Concurrency Theory","start_date":"2016-08-23","end_date":"2016-08-26","location":"Quebec City; Canada"}},{"date_updated":"2023-09-05T14:09:01Z","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"]},"publication_status":"published","publist_id":"6281","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"08","oa_version":"None","alternative_title":["Methods in Molecular Biology"],"department":[{"_id":"RySh"}],"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). ","quality_controlled":"1","page":"203 - 216","_id":"1094","intvolume":" 1474","doi":"10.1007/978-1-4939-6352-2_12","type":"book_chapter","status":"public","title":"Immunogold protein localization on grid-glued freeze-fracture replicas","acknowledged_ssus":[{"_id":"EM-Fac"}],"citation":{"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.","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","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.","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.","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."},"article_processing_charge":"No","ec_funded":1,"day":"12","year":"2016","language":[{"iso":"eng"}],"publication":"High-Resolution Imaging of Cellular Proteins","volume":1474,"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"}],"date_published":"2016-08-12T00:00:00Z","author":[{"id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","full_name":"Harada, Harumi","orcid":"0000-0001-7429-7896","first_name":"Harumi","last_name":"Harada"},{"orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"project":[{"name":"Localization of ion channels and receptors by two and three-dimensional immunoelectron microscopic approaches","_id":"25CD3DD2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"604102"}],"date_created":"2018-12-11T11:50:06Z","publisher":"Springer"},{"department":[{"_id":"ToHe"}],"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).","quality_controlled":"1","_id":"1095","intvolume":" 59","doi":"10.4230/LIPIcs.CONCUR.2016.6","status":"public","type":"conference","pubrep_id":"793","title":"Local linearizability for concurrent container-type data structures","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"citation":{"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.","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","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.","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","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.","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."},"date_updated":"2021-01-12T06:48:14Z","ddc":["004"],"oa":1,"publication_status":"published","conference":{"location":"Quebec City; Canada","start_date":"2016-08-23","name":"CONCUR: Concurrency Theory","end_date":"2016-08-26"},"publist_id":"6280","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"08","oa_version":"Published Version","article_number":"6","alternative_title":["LIPIcs"],"has_accepted_license":"1","project":[{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"},{"call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"}],"date_created":"2018-12-11T11:50:07Z","scopus_import":1,"file":[{"file_id":"4795","relation":"main_file","creator":"system","date_created":"2018-12-12T10:10:10Z","content_type":"application/pdf","date_updated":"2018-12-12T10:10:10Z","file_size":589747,"access_level":"open_access","file_name":"IST-2017-793-v1+1_LIPIcs-CONCUR-2016-6.pdf"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","ec_funded":1,"day":"01","language":[{"iso":"eng"}],"year":"2016","publication":"Leibniz International Proceedings in Informatics","volume":59,"abstract":[{"lang":"eng","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. "}],"date_published":"2016-08-01T00:00:00Z","author":[{"first_name":"Andreas","last_name":"Haas","full_name":"Haas, Andreas"},{"first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"last_name":"Holzer","first_name":"Andreas","full_name":"Holzer, Andreas"},{"first_name":"Christoph","last_name":"Kirsch","full_name":"Kirsch, Christoph"},{"last_name":"Lippautz","first_name":"Michael","full_name":"Lippautz, Michael"},{"full_name":"Payer, Hannes","first_name":"Hannes","last_name":"Payer"},{"full_name":"Sezgin, Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","last_name":"Sezgin","first_name":"Ali"},{"last_name":"Sokolova","first_name":"Ana","full_name":"Sokolova, Ana"},{"full_name":"Veith, Helmut","last_name":"Veith","first_name":"Helmut"}],"file_date_updated":"2018-12-12T10:10:10Z"},{"scopus_import":1,"title":"Actin rings of power","status":"public","type":"journal_article","publisher":"Cell Press","citation":{"ista":"Schwayer C, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. 2016. Actin rings of power. Developmental Cell. 37(6), 493–506.","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.","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","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.","short":"C. Schwayer, M.K. Sikora, J. Slovakova, R. Kardos, C.-P.J. Heisenberg, Developmental Cell 37 (2016) 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","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."},"quality_controlled":"1","department":[{"_id":"CaHe"}],"date_created":"2018-12-11T11:50:07Z","doi":"10.1016/j.devcel.2016.05.024","_id":"1096","page":"493 - 506","intvolume":" 37","author":[{"full_name":"Schwayer, Cornelia","id":"3436488C-F248-11E8-B48F-1D18A9856A87","first_name":"Cornelia","last_name":"Schwayer","orcid":"0000-0001-5130-2226"},{"first_name":"Mateusz K","last_name":"Sikora","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","full_name":"Sikora, Mateusz K"},{"last_name":"Slovakova","first_name":"Jana","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","full_name":"Slovakova, Jana"},{"id":"4039350E-F248-11E8-B48F-1D18A9856A87","full_name":"Kardos, Roland","first_name":"Roland","last_name":"Kardos"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"volume":37,"date_published":"2016-06-20T00:00:00Z","issue":"6","publication_status":"published","date_updated":"2023-09-07T12:56:41Z","oa_version":"None","publication":"Developmental Cell","month":"06","day":"20","publist_id":"6279","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7186"}]},"year":"2016","language":[{"iso":"eng"}]},{"doi":"10.1145/2980179.2982427","_id":"1097","intvolume":" 35","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. ","quality_controlled":"1","department":[{"_id":"BeBi"}],"citation":{"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.","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.","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","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.","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.","ama":"Du T, Schulz A, Zhu B, Bickel B, Matusik W. Computational multicopter design. In: Vol 35. ACM; 2016. doi:10.1145/2980179.2982427"},"title":"Computational multicopter design","type":"conference","status":"public","pubrep_id":"759","oa_version":"Submitted Version","month":"11","publist_id":"6278","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"publication_status":"published","conference":{"start_date":"2016-12-05","name":"SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia","end_date":"2016-12-08","location":"Macao, China"},"ddc":["006"],"date_updated":"2021-01-12T06:48:15Z","has_accepted_license":"1","alternative_title":["ACM Transactions on Graphics"],"article_number":"227","date_created":"2018-12-11T11:50:07Z","project":[{"_id":"25082902-B435-11E9-9278-68D0E5697425","name":"Soft-bodied intelligence for Manipulation","call_identifier":"H2020","grant_number":"645599"}],"file":[{"date_updated":"2018-12-12T10:17:42Z","content_type":"application/pdf","file_name":"IST-2017-759-v1+1_copter.pdf","access_level":"open_access","file_size":33114420,"file_id":"5298","date_created":"2018-12-12T10:17:42Z","creator":"system","relation":"main_file"}],"publisher":"ACM","scopus_import":1,"day":"01","language":[{"iso":"eng"}],"year":"2016","ec_funded":1,"file_date_updated":"2018-12-12T10:17:42Z","issue":"6","author":[{"full_name":"Du, Tao","first_name":"Tao","last_name":"Du"},{"last_name":"Schulz","first_name":"Adriana","full_name":"Schulz, Adriana"},{"last_name":"Zhu","first_name":"Bo","full_name":"Zhu, Bo"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385"},{"last_name":"Matusik","first_name":"Wojciech","full_name":"Matusik, Wojciech"}],"volume":35,"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_published":"2016-11-01T00:00:00Z"},{"file_date_updated":"2018-12-12T10:12:43Z","volume":29,"abstract":[{"lang":"eng","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."}],"date_published":"2016-12-01T00:00:00Z","author":[{"id":"42E87FC6-F248-11E8-B48F-1D18A9856A87","full_name":"Pentina, Anastasia","first_name":"Anastasia","last_name":"Pentina"},{"full_name":"Urner, Ruth","last_name":"Urner","first_name":"Ruth"}],"day":"01","language":[{"iso":"eng"}],"year":"2016","ec_funded":1,"file":[{"file_name":"IST-2017-775-v1+1_main.pdf","access_level":"open_access","file_size":237111,"date_updated":"2018-12-12T10:12:42Z","content_type":"application/pdf","creator":"system","date_created":"2018-12-12T10:12:42Z","relation":"main_file","file_id":"4961"},{"file_id":"4962","relation":"main_file","date_created":"2018-12-12T10:12:43Z","creator":"system","content_type":"application/pdf","date_updated":"2018-12-12T10:12:43Z","file_size":185818,"access_level":"open_access","file_name":"IST-2017-775-v1+2_supplementary.pdf"}],"publisher":"Neural Information Processing Systems","scopus_import":1,"date_created":"2018-12-11T11:50:08Z","project":[{"call_identifier":"FP7","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"alternative_title":["Advances in Neural Information Processing Systems"],"has_accepted_license":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6277","month":"12","oa_version":"Published Version","ddc":["006"],"date_updated":"2021-01-12T06:48:15Z","publication_status":"published","oa":1,"conference":{"location":"Barcelona, Spain","end_date":"2016-12-10","start_date":"2016-12-05","name":"NIPS: Neural Information Processing Systems"},"citation":{"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.","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.","chicago":"Pentina, Anastasia, and Ruth Urner. “Lifelong Learning with Weighted Majority Votes,” 29:3619–27. Neural Information Processing Systems, 2016.","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.","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."},"status":"public","type":"conference","pubrep_id":"775","title":"Lifelong learning with weighted majority votes","page":"3619-3627","_id":"1098","intvolume":" 29","department":[{"_id":"ChLa"}],"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","quality_controlled":"1"},{"language":[{"iso":"eng"}],"year":"2016","day":"01","ec_funded":1,"issue":"6","file_date_updated":"2018-12-12T10:12:01Z","date_published":"2016-11-01T00:00:00Z","abstract":[{"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.","lang":"eng"}],"volume":35,"author":[{"full_name":"Malomo, Luigi","first_name":"Luigi","last_name":"Malomo"},{"last_name":"Pietroni","first_name":"Nico","full_name":"Pietroni, Nico"},{"full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385"},{"last_name":"Cignoni","first_name":"Paolo","full_name":"Cignoni, Paolo"}],"project":[{"grant_number":"645599","call_identifier":"H2020","name":"Soft-bodied intelligence for Manipulation","_id":"25082902-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:50:08Z","publisher":"ACM","file":[{"relation":"main_file","date_created":"2018-12-12T10:12:01Z","creator":"system","file_id":"4918","file_size":11122029,"access_level":"open_access","file_name":"IST-2017-760-v1+1_flexmolds.pdf","content_type":"application/pdf","date_updated":"2018-12-12T10:12:01Z"}],"scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6276","oa_version":"Submitted Version","month":"11","ddc":["000","005"],"date_updated":"2021-01-12T06:48:16Z","conference":{"end_date":"2016-12-08","name":"SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia","start_date":"2016-12-05","location":"Macao, China"},"oa":1,"publication_status":"published","alternative_title":["ACM Transactions on Graphics"],"has_accepted_license":"1","article_number":"223","intvolume":" 35","_id":"1099","doi":"10.1145/2980179.2982397","department":[{"_id":"BeBi"}],"quality_controlled":"1","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.","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","short":"L. Malomo, N. Pietroni, B. Bickel, P. Cignoni, in:, ACM, 2016.","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.","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","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.","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."},"pubrep_id":"760","type":"conference","status":"public","title":"FlexMolds: Automatic design of flexible shells for molding"},{"has_accepted_license":"1","oa_version":"Published Version","month":"07","related_material":{"record":[{"status":"public","id":"961","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"50","status":"public"}]},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"6275","publication_status":"published","oa":1,"ddc":["570","576"],"date_updated":"2024-03-25T23:30:13Z","citation":{"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.","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.","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","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.","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.","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"},"acknowledged_ssus":[{"_id":"SSU"}],"title":"Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","type":"journal_article","pubrep_id":"754","doi":"10.1016/j.celrep.2016.06.036","page":"866 - 877","_id":"1100","intvolume":" 16","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.","quality_controlled":"1","department":[{"_id":"CaHe"},{"_id":"HaJa"}],"file_date_updated":"2018-12-12T10:11:04Z","issue":"3","author":[{"orcid":"0000-0002-6453-8075","last_name":"Sako","first_name":"Keisuke","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","full_name":"Sako, Keisuke"},{"full_name":"Pradhan, Saurabh","last_name":"Pradhan","first_name":"Saurabh"},{"orcid":"0000-0003-2676-3367","first_name":"Vanessa","last_name":"Barone","full_name":"Barone, Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Inglés Prieto, Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","first_name":"Álvaro","last_name":"Inglés Prieto","orcid":"0000-0002-5409-8571"},{"full_name":"Mueller, Patrick","first_name":"Patrick","last_name":"Mueller"},{"orcid":"0000-0003-4088-8633","last_name":"Ruprecht","first_name":"Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","full_name":"Ruprecht, Verena"},{"orcid":"0000-0001-5199-9940","last_name":"Capek","first_name":"Daniel","full_name":"Capek, Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Galande, Sanjeev","first_name":"Sanjeev","last_name":"Galande"},{"last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"volume":16,"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"}],"date_published":"2016-07-19T00:00:00Z","publication":"Cell Reports","day":"19","year":"2016","language":[{"iso":"eng"}],"ec_funded":1,"file":[{"file_id":"4857","date_created":"2018-12-12T10:11:04Z","creator":"system","relation":"main_file","date_updated":"2018-12-12T10:11:04Z","content_type":"application/pdf","file_name":"IST-2017-754-v1+1_1-s2.0-S2211124716307768-main.pdf","access_level":"open_access","file_size":3921947}],"publisher":"Cell Press","scopus_import":1,"project":[{"name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation","_id":"2529486C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"T 560-B17"},{"call_identifier":"FWF","grant_number":"I 812-B12","name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation","_id":"2527D5CC-B435-11E9-9278-68D0E5697425"},{"grant_number":"303564","call_identifier":"FP7","name":"Microbial Ion Channels for Synthetic Neurobiology","_id":"25548C20-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:50:08Z"},{"type":"journal_article","status":"public","scopus_import":"1","title":"Rangefinder: A semisynthetic FRET sensor design algorithm","publisher":"American Chemical Society","article_processing_charge":"No","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","short":"J. Mitchell, J. Whitfield, W. Zhang, C. Henneberger, H.L. Janovjak, M. O’Mara, C. Jackson, ACS SENSORS 1 (2016) 1286–1290.","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.","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","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.","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."},"department":[{"_id":"HaJa"}],"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.","quality_controlled":"1","page":"1286 - 1290","_id":"1101","intvolume":" 1","date_created":"2018-12-11T11:50:09Z","doi":"10.1021/acssensors.6b00576","volume":1,"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"}],"date_published":"2016-11-10T00:00:00Z","author":[{"full_name":"Mitchell, Joshua","first_name":"Joshua","last_name":"Mitchell"},{"last_name":"Whitfield","first_name":"Jason","full_name":"Whitfield, Jason"},{"first_name":"William","last_name":"Zhang","full_name":"Zhang, William"},{"first_name":"Christian","last_name":"Henneberger","full_name":"Henneberger, Christian"},{"last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Megan","last_name":"O'Mara","full_name":"O'Mara, Megan"},{"full_name":"Jackson, Colin","last_name":"Jackson","first_name":"Colin"}],"issue":"11","date_updated":"2023-03-30T11:32:33Z","publication_status":"published","day":"10","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6274","year":"2016","language":[{"iso":"eng"}],"publication":"ACS SENSORS","month":"11","oa_version":"None"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6273","oa_version":"Published Version","month":"09","date_updated":"2021-01-12T06:48:18Z","conference":{"location":"York, United Kingdom","name":"BMVC: British Machine Vision Conference","start_date":"2016-09-19","end_date":"2016-09-22"},"publication_status":"published","oa":1,"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","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.","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","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.","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.","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."},"type":"conference","status":"public","title":"Improving weakly-supervised object localization by micro-annotation","page":"92.1-92.12","_id":"1102","doi":"10.5244/C.30.92","department":[{"_id":"ChLa"}],"quality_controlled":"1","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.","date_published":"2016-09-01T00:00:00Z","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."}],"volume":"2016-September","author":[{"id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","full_name":"Kolesnikov, Alexander","last_name":"Kolesnikov","first_name":"Alexander"},{"last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"year":"2016","day":"01","publication":"Proceedings of the British Machine Vision Conference 2016","ec_funded":1,"main_file_link":[{"url":"http://www.bmva.org/bmvc/2016/papers/paper092/paper092.pdf","open_access":"1"}],"publisher":"BMVA Press","scopus_import":1,"project":[{"call_identifier":"FP7","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding"}],"date_created":"2018-12-11T11:50:09Z"},{"article_number":"7797741","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."}],"date_published":"2016-12-27T00:00:00Z","author":[{"full_name":"Gurung, Amit","first_name":"Amit","last_name":"Gurung"},{"full_name":"Deka, Arup","last_name":"Deka","first_name":"Arup"},{"full_name":"Bartocci, Ezio","last_name":"Bartocci","first_name":"Ezio"},{"orcid":"0000-0002-0686-0365","first_name":"Sergiy","last_name":"Bogomolov","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","full_name":"Bogomolov, Sergiy"},{"full_name":"Grosu, Radu","last_name":"Grosu","first_name":"Radu"},{"first_name":"Rajarshi","last_name":"Ray","full_name":"Ray, Rajarshi"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6272","day":"27","year":"2016","language":[{"iso":"eng"}],"month":"12","oa_version":"Preprint","date_updated":"2021-01-12T06:48:18Z","ec_funded":1,"oa":1,"publication_status":"published","conference":{"location":"Kanpur, India ","name":"MEMOCODE: International Conference on Formal Methods and Models for System Design","end_date":"2016-11-20","start_date":"2016-11-18"},"publisher":"IEEE","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","short":"A. Gurung, A. Deka, E. Bartocci, S. Bogomolov, R. Grosu, R. Ray, in:, IEEE, 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.","mla":"Gurung, Amit, et al. Parallel Reachability Analysis for Hybrid Systems. 7797741, 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","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.","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."},"main_file_link":[{"url":"https://arxiv.org/abs/1606.05473","open_access":"1"}],"type":"conference","status":"public","title":"Parallel reachability analysis for hybrid systems","scopus_import":1,"_id":"1103","project":[{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7"},{"call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"},{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:50:09Z","doi":"10.1109/MEMCOD.2016.7797741","department":[{"_id":"ToHe"}],"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).","quality_controlled":"1"},{"date_updated":"2021-01-12T06:48:19Z","conference":{"location":"Barcelona; Spain","name":"NIPS: Neural Information Processing Systems","start_date":"2016-12-05","end_date":"2016-12-10"},"publication_status":"published","publist_id":"6265","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"12","oa_version":"None","alternative_title":["Advances in Neural Information Processing Systems"],"department":[{"_id":"GaTk"}],"quality_controlled":"1","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.","intvolume":" 29","_id":"1105","page":"3610-3618","type":"conference","status":"public","title":"Estimating nonlinear neural response functions using GP priors and Kronecker methods","citation":{"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.","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.","short":"C. Savin, G. Tkačik, in:, Neural Information Processing Systems, 2016, 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.","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.","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.","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."},"ec_funded":1,"language":[{"iso":"eng"}],"year":"2016","day":"01","date_published":"2016-12-01T00:00:00Z","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."}],"volume":29,"author":[{"last_name":"Savin","first_name":"Cristina","full_name":"Savin, Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper"}],"date_created":"2018-12-11T11:50:10Z","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"scopus_import":1,"main_file_link":[{"url":"http://papers.nips.cc/paper/6153-estimating-nonlinear-neural-response-functions-using-gp-priors-and-kronecker-methods"}],"publisher":"Neural Information Processing Systems"},{"publication_status":"published","oa":1,"conference":{"end_date":"2016-06-10","start_date":"2016-06-05","name":"CLEO: Conference on Lasers and Electro Optics","location":"San Jose, CA, USA"},"date_updated":"2022-09-06T07:23:25Z","month":"12","oa_version":"Preprint","related_material":{"link":[{"url":"http://ieeexplore.ieee.org/document/7788479/","relation":"other"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6251","day":"16","language":[{"iso":"eng"}],"year":"2016","author":[{"last_name":"Rueda","first_name":"Alfredo","full_name":"Rueda, Alfredo"},{"full_name":"Sedlmeir, Florian","last_name":"Sedlmeir","first_name":"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"},{"first_name":"Georg","last_name":"Schunk","full_name":"Schunk, Georg"},{"last_name":"Strekalov","first_name":"Dimitry","full_name":"Strekalov, Dimitry"},{"first_name":"Christoph","last_name":"Marquardt","full_name":"Marquardt, Christoph"},{"full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X"},{"full_name":"Painter, Oskar","first_name":"Oskar","last_name":"Painter"},{"last_name":"Leuchs","first_name":"Gerd","full_name":"Leuchs, Gerd"},{"full_name":"Schwefel, Harald","first_name":"Harald","last_name":"Schwefel"}],"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."}],"article_number":"7788479","date_published":"2016-12-16T00:00:00Z","quality_controlled":"1","department":[{"_id":"JoFi"}],"doi":"10.1364/CLEO_SI.2016.SF2G.3","date_created":"2018-12-11T11:50:14Z","_id":"1115","title":"Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator","scopus_import":"1","type":"conference","status":"public","publisher":"IEEE","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.","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","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.","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","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.","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."},"article_processing_charge":"No","main_file_link":[{"url":"https://arxiv.org/abs/1601.07261","open_access":"1"}]},{"project":[{"grant_number":"648440","call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425","name":"Selective Barriers to Horizontal Gene Transfer"}],"date_created":"2018-12-11T11:50:16Z","supervisor":[{"first_name":"Jonathan P","last_name":"Bollback","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P"}],"publisher":"Institute of Science and Technology Austria","file":[{"file_id":"6814","checksum":"94bbbc754c36115bf37f8fc11fad43c4","relation":"main_file","creator":"dernst","date_created":"2019-08-13T11:17:50Z","content_type":"application/pdf","date_updated":"2019-08-13T11:17:50Z","access_level":"closed","file_size":3682711,"file_name":"PhDThesis_HandeAcar_1230.pdf"},{"content_type":"application/pdf","date_updated":"2021-02-22T11:51:13Z","access_level":"open_access","file_size":3682711,"file_name":"2016_Thesis_HandeAcar.pdf","file_id":"9184","relation":"main_file","checksum":"94bbbc754c36115bf37f8fc11fad43c4","creator":"dernst","date_created":"2021-02-22T11:51:13Z","success":1}],"ec_funded":1,"language":[{"iso":"eng"}],"year":"2016","day":"01","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"}],"author":[{"first_name":"Hande","last_name":"Acar","orcid":"0000-0003-1986-9753","full_name":"Acar, Hande","id":"2DDF136A-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2021-02-22T11:51:13Z","department":[{"_id":"JoBo"}],"degree_awarded":"PhD","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.","page":"75","_id":"1121","type":"dissertation","status":"public","title":"Selective barriers to horizontal gene transfer","article_processing_charge":"No","citation":{"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.","mla":"Acar, Hande. Selective Barriers to Horizontal Gene Transfer. Institute of Science and Technology Austria, 2016.","ama":"Acar H. Selective barriers to horizontal gene transfer. 2016.","chicago":"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."},"publication_identifier":{"issn":["2663-337X"]},"ddc":["570"],"date_updated":"2023-09-07T11:42:26Z","oa":1,"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6239","month":"12","oa_version":"Published Version","alternative_title":["ISTA Thesis"],"has_accepted_license":"1"},{"related_material":{"record":[{"status":"public","id":"5558","relation":"other"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6238","oa_version":"Published Version","month":"07","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2024-02-21T13:50:48Z","ddc":["004","005","006","532","621"],"publication_status":"published","oa":1,"alternative_title":["ISTA Thesis"],"has_accepted_license":"1","_id":"1122","page":"114","doi":"10.15479/AT:ISTA:th_640","department":[{"_id":"ChWo"}],"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. ","degree_awarded":"PhD","citation":{"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.","short":"M. Bojsen-Hansen, Tracking, Correcting and Absorbing Water Surface Waves, Institute of Science and Technology Austria, 2016.","ama":"Bojsen-Hansen M. Tracking, correcting and absorbing water surface waves. 2016. doi:10.15479/AT:ISTA:th_640","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","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.","ista":"Bojsen-Hansen M. 2016. Tracking, correcting and absorbing water surface waves. Institute of Science and Technology Austria.","ieee":"M. Bojsen-Hansen, “Tracking, correcting and absorbing water surface waves,” Institute of Science and Technology Austria, 2016."},"article_processing_charge":"No","type":"dissertation","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Tracking, correcting and absorbing water surface waves","language":[{"iso":"eng"}],"year":"2016","day":"15","file_date_updated":"2018-12-12T10:13:02Z","date_published":"2016-07-15T00:00:00Z","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"}],"author":[{"orcid":"0000-0002-4417-3224","first_name":"Morten","last_name":"Bojsen-Hansen","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","full_name":"Bojsen-Hansen, Morten"}],"date_created":"2018-12-11T11:50:16Z","publisher":"Institute of Science and Technology Austria","file":[{"file_id":"4982","date_created":"2018-12-12T10:13:02Z","creator":"system","relation":"main_file","date_updated":"2018-12-12T10:13:02Z","content_type":"application/pdf","file_name":"IST-2016-640-v1+1_2016_Bojsen-Hansen_TCaAWSW.pdf","file_size":13869345,"access_level":"open_access"}],"supervisor":[{"last_name":"Wojtan","first_name":"Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J"}]},{"article_processing_charge":"No","citation":{"ama":"Mabillard I. Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture. 2016.","short":"I. Mabillard, Eliminating Higher-Multiplicity Intersections: An r-Fold Whitney Trick for the Topological Tverberg Conjecture, Institute of Science and Technology Austria, 2016.","chicago":"Mabillard, Isaac. “Eliminating Higher-Multiplicity Intersections: An r-Fold Whitney Trick for the Topological Tverberg Conjecture.” Institute of Science and Technology Austria, 2016.","mla":"Mabillard, Isaac. Eliminating Higher-Multiplicity Intersections: An r-Fold Whitney Trick for the Topological Tverberg Conjecture. Institute of Science and Technology Austria, 2016.","apa":"Mabillard, I. (2016). Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture. Institute of Science and Technology Austria.","ieee":"I. Mabillard, “Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture,” Institute of Science and Technology Austria, 2016.","ista":"Mabillard I. 2016. Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture. Institute of Science and Technology Austria."},"title":"Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture","type":"dissertation","status":"public","page":"55","_id":"1123","degree_awarded":"PhD","acknowledgement":"Foremost, I would like to thank Uli Wagner for introducing me to the exciting interface between\r\ntopology and combinatorics, and for our subsequent years of fruitful collaboration.\r\nIn our creative endeavors to eliminate intersection points, we had the chance to be joined later\r\nby Sergey Avvakumov and Arkadiy Skopenkov, which led us to new surprises in dimension 12.\r\nMy stay at EPFL and IST Austria was made very agreeable thanks to all these wonderful\r\npeople: Cyril Becker, Marek Filakovsky, Peter Franek, Radoslav Fulek, Peter Gazi, Kristof Huszar,\r\nMarek Krcal, Zuzana Masarova, Arnaud de Mesmay, Filip Moric, Michal Rybar, Martin Tancer,\r\nand Stephan Zhechev.\r\nFinally, I would like to thank my thesis committee Herbert Edelsbrunner and Roman Karasev\r\nfor their careful reading of the present manuscript and for the many improvements they suggested.","department":[{"_id":"UlWa"}],"has_accepted_license":"1","alternative_title":["ISTA Thesis"],"month":"08","oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"2159","relation":"part_of_dissertation"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6237","oa":1,"publication_status":"published","date_updated":"2023-09-07T11:56:28Z","ddc":["500"],"publication_identifier":{"issn":["2663-337X"]},"publisher":"Institute of Science and Technology Austria","file":[{"file_name":"Thesis_final version_Mabillard_w_signature_page.pdf","file_size":2227916,"access_level":"closed","date_updated":"2019-08-13T08:45:27Z","content_type":"application/pdf","creator":"dernst","date_created":"2019-08-13T08:45:27Z","checksum":"2d140cc924cd1b764544906fc22684ef","relation":"main_file","file_id":"6809"},{"file_name":"2016_Mabillard_Thesis.pdf","file_size":2227916,"access_level":"open_access","date_updated":"2021-02-22T11:36:34Z","content_type":"application/pdf","creator":"dernst","date_created":"2021-02-22T11:36:34Z","relation":"main_file","checksum":"2d140cc924cd1b764544906fc22684ef","file_id":"9178","success":1}],"supervisor":[{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","first_name":"Uli","last_name":"Wagner"}],"date_created":"2018-12-11T11:50:16Z","file_date_updated":"2021-02-22T11:36:34Z","author":[{"id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","full_name":"Mabillard, Isaac","last_name":"Mabillard","first_name":"Isaac"}],"abstract":[{"lang":"eng","text":"Motivated by topological Tverberg-type problems in topological combinatorics and by classical\r\nresults about embeddings (maps without double points), we study the question whether a finite\r\nsimplicial complex K can be mapped into Rd without triple, quadruple, or, more generally, r-fold points (image points with at least r distinct preimages), for a given multiplicity r ≤ 2. In particular, we are interested in maps f : K → Rd that have no global r -fold intersection points, i.e., no r -fold points with preimages in r pairwise disjoint simplices of K , and we seek necessary and sufficient conditions for the existence of such maps.\r\n\r\nWe present higher-multiplicity analogues of several classical results for embeddings, in particular of the completeness of the Van Kampen obstruction for embeddability of k -dimensional\r\ncomplexes into R2k , k ≥ 3. Speciffically, we show that under suitable restrictions on the dimensions(viz., if dimK = (r ≥ 1)k and d = rk \\ for some k ≥ 3), a well-known deleted product criterion (DPC ) is not only necessary but also sufficient for the existence of maps without global r -fold points. Our main technical tool is a higher-multiplicity version of the classical Whitney trick , by which pairs of isolated r -fold points of opposite sign can be eliminated by local modiffications of the map, assuming codimension d – dimK ≥ 3.\r\n\r\nAn important guiding idea for our work was that suffciency of the DPC, together with an old\r\nresult of Özaydin's on the existence of equivariant maps, might yield an approach to disproving the remaining open cases of the the long-standing topological Tverberg conjecture , i.e., to construct maps from the N -simplex σN to Rd without r-Tverberg points when r not a prime power and\r\nN = (d + 1)(r – 1). Unfortunately, our proof of the sufficiency of the DPC requires codimension d – dimK ≥ 3, which is not satisfied for K = σN .\r\n\r\nIn 2015, Frick [16] found a very elegant way to overcome this \\codimension 3 obstacle" and\r\nto construct the first counterexamples to the topological Tverberg conjecture for all parameters(d; r ) with d ≥ 3r + 1 and r not a prime power, by a reduction1 to a suitable lower-dimensional skeleton, for which the codimension 3 restriction is satisfied and maps without r -Tverberg points exist by Özaydin's result and sufficiency of the DPC.\r\n\r\nIn this thesis, we present a different construction (which does not use the constraint method) that yields counterexamples for d ≥ 3r , r not a prime power. "}],"date_published":"2016-08-01T00:00:00Z","day":"01","year":"2016","language":[{"iso":"eng"}]},{"type":"dissertation","status":"public","title":"Optical functionalization of human class A orphan G-protein coupled receptors","supervisor":[{"first_name":"Harald L","last_name":"Janovjak","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","file":[{"file_name":"MORRI_PhD_thesis_FINALPLUSSIGNATURES (2).pdf","access_level":"closed","file_size":4785167,"date_updated":"2019-08-13T10:50:00Z","content_type":"application/pdf","date_created":"2019-08-13T10:50:00Z","creator":"dernst","relation":"main_file","checksum":"b439803ac0827cdddd56562a54e3b53b","file_id":"6812"},{"creator":"dernst","date_created":"2021-02-22T11:42:06Z","checksum":"dd4136247fe472e7d47880ec68ac8de0","relation":"main_file","file_id":"9180","file_name":"2016_MORRI_Thesis.pdf","file_size":4495669,"access_level":"open_access","date_updated":"2021-02-22T11:42:06Z","content_type":"application/pdf","success":1}],"citation":{"mla":"Morri, Maurizio. Optical Functionalization of Human Class A Orphan G-Protein Coupled Receptors. Institute of Science and Technology Austria, 2016.","apa":"Morri, M. (2016). Optical functionalization of human class A orphan G-protein coupled receptors. Institute of Science and Technology Austria.","short":"M. Morri, Optical Functionalization of Human Class A Orphan G-Protein Coupled Receptors, Institute of Science and Technology Austria, 2016.","ama":"Morri M. Optical functionalization of human class A orphan G-protein coupled receptors. 2016.","chicago":"Morri, Maurizio. “Optical Functionalization of Human Class A Orphan G-Protein Coupled Receptors.” Institute of Science and Technology Austria, 2016.","ista":"Morri M. 2016. Optical functionalization of human class A orphan G-protein coupled receptors. Institute of Science and Technology Austria.","ieee":"M. Morri, “Optical functionalization of human class A orphan G-protein coupled receptors,” Institute of Science and Technology Austria, 2016."},"article_processing_charge":"No","department":[{"_id":"HaJa"}],"degree_awarded":"PhD","_id":"1124","page":"129","date_created":"2018-12-11T11:50:17Z","date_published":"2016-03-01T00:00:00Z","author":[{"full_name":"Morri, Maurizio","id":"4863116E-F248-11E8-B48F-1D18A9856A87","first_name":"Maurizio","last_name":"Morri"}],"alternative_title":["ISTA Thesis"],"has_accepted_license":"1","file_date_updated":"2021-02-22T11:42:06Z","date_updated":"2023-09-07T11:43:03Z","ddc":["570"],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","oa":1,"day":"01","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6236","year":"2016","language":[{"iso":"eng"}],"month":"03","oa_version":"Published Version"},{"has_accepted_license":"1","alternative_title":["ISTA Thesis"],"publication_status":"published","oa":1,"date_updated":"2025-05-28T11:57:05Z","ddc":["576"],"publication_identifier":{"issn":["2663-337X"]},"month":"07","oa_version":"Published Version","publist_id":"6235","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"id":"2023","relation":"part_of_dissertation","status":"public"}]},"title":"Evolutionary proccesses in variable emvironments","type":"dissertation","status":"public","citation":{"ama":"Novak S. Evolutionary proccesses in variable emvironments. 2016.","chicago":"Novak, Sebastian. “Evolutionary Proccesses in Variable Emvironments.” Institute of Science and Technology Austria, 2016.","short":"S. Novak, Evolutionary Proccesses in Variable Emvironments, Institute of Science and Technology Austria, 2016.","mla":"Novak, Sebastian. Evolutionary Proccesses in Variable Emvironments. Institute of Science and Technology Austria, 2016.","apa":"Novak, S. (2016). Evolutionary proccesses in variable emvironments. Institute of Science and Technology Austria.","ista":"Novak S. 2016. Evolutionary proccesses in variable emvironments. Institute of Science and Technology Austria.","ieee":"S. Novak, “Evolutionary proccesses in variable emvironments,” Institute of Science and Technology Austria, 2016."},"article_processing_charge":"No","degree_awarded":"PhD","department":[{"_id":"NiBa"}],"_id":"1125","page":"124","author":[{"first_name":"Sebastian","last_name":"Novak","orcid":"0000-0002-2519-824X","full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","text":"Natural environments are never constant but subject to spatial and temporal change on\r\nall scales, increasingly so due to human activity. Hence, it is crucial to understand the\r\nimpact of environmental variation on evolutionary processes. In this thesis, I present\r\nthree topics that share the common theme of environmental variation, yet illustrate its\r\neffect from different perspectives.\r\nFirst, I show how a temporally fluctuating environment gives rise to second-order\r\nselection on a modifier for stress-induced mutagenesis. Without fluctuations, when\r\npopulations are adapted to their environment, mutation rates are minimized. I argue\r\nthat a stress-induced mutator mechanism may only be maintained if the population is\r\nrepeatedly subjected to diverse environmental challenges, and I outline implications of\r\nthe presented results to antibiotic treatment strategies.\r\nSecond, I discuss my work on the evolution of dispersal. Besides reproducing\r\nknown results about the effect of heterogeneous habitats on dispersal, it identifies\r\nspatial changes in dispersal type frequencies as a source for selection for increased\r\npropensities to disperse. This concept contains effects of relatedness that are known\r\nto promote dispersal, and I explain how it identifies other forces selecting for dispersal\r\nand puts them on a common scale.\r\nThird, I analyse genetic variances of phenotypic traits under multivariate stabilizing\r\nselection. For the case of constant environments, I generalize known formulae of\r\nequilibrium variances to multiple traits and discuss how the genetic variance of a focal\r\ntrait is influenced by selection on background traits. I conclude by presenting ideas and\r\npreliminary work aiming at including environmental fluctuations in the form of moving\r\ntrait optima into the model."}],"date_published":"2016-07-01T00:00:00Z","file_date_updated":"2021-02-22T13:42:47Z","day":"01","language":[{"iso":"eng"}],"year":"2016","supervisor":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"file":[{"file_id":"6811","relation":"main_file","checksum":"81dcc838dfcf7aa0b1a27ecf4fe2da4e","date_created":"2019-08-13T09:01:00Z","creator":"dernst","content_type":"application/pdf","date_updated":"2019-08-13T09:01:00Z","file_size":3564901,"access_level":"closed","file_name":"Novak_thesis.pdf"},{"date_updated":"2021-02-22T13:42:47Z","content_type":"application/pdf","file_name":"2016_Novak_Thesis.pdf","access_level":"open_access","file_size":2814384,"file_id":"9186","creator":"dernst","date_created":"2021-02-22T13:42:47Z","checksum":"30808d2f7ca920e09f63a95cdc49bffd","relation":"main_file","success":1}],"publisher":"Institute of Science and Technology Austria","date_created":"2018-12-11T11:50:17Z"}]