[{"publication":"Frontiers in Cellular Neuroscience","department":[{"_id":"SiHi"},{"_id":"MaLo"}],"date_published":"2017-06-28T00:00:00Z","publist_id":"6445","intvolume":" 11","day":"28","ddc":["570"],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"status":"public","date_updated":"2026-08-14T22:31:06Z","external_id":{"isi":["000404486700001"]},"file_date_updated":"2020-07-14T12:48:16Z","year":"2017","abstract":[{"lang":"eng","text":"The human cerebral cortex is the seat of our cognitive abilities and composed of an extraordinary number of neurons, organized in six distinct layers. The establishment of specific morphological and physiological features in individual neurons needs to be regulated with high precision. Impairments in the sequential developmental programs instructing corticogenesis lead to alterations in the cortical cytoarchitecture which is thought to represent the major underlying cause for several neurological disorders including neurodevelopmental and psychiatric diseases. In this review we discuss the role of cell polarity at sequential stages during cortex development. We first provide an overview of morphological cell polarity features in cortical neural stem cells and newly-born postmitotic neurons. We then synthesize a conceptual molecular and biochemical framework how cell polarity is established at the cellular level through a break in symmetry in nascent cortical projection neurons. Lastly we provide a perspective how the molecular mechanisms applying to single cells could be probed and integrated in an in vivo and tissue-wide context."}],"author":[{"last_name":"Hansen","id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H","full_name":"Hansen, Andi H"},{"orcid":"0000-0001-6335-9748","id":"459064DC-F248-11E8-B48F-1D18A9856A87","last_name":"Düllberg","full_name":"Düllberg, Christian F","first_name":"Christian F"},{"id":"34CAE85C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1919-7416","last_name":"Mieck","first_name":"Christine","full_name":"Mieck, Christine"},{"last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","first_name":"Martin","full_name":"Loose, Martin"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Frontiers Research Foundation","_id":"960","article_number":"176","file":[{"date_created":"2018-12-12T10:09:40Z","creator":"system","checksum":"dc1f5a475b918d09a0f9f587400b1626","file_id":"4764","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:48:16Z","file_size":2153858,"relation":"main_file","file_name":"IST-2017-830-v1+1_2017_Hansen_CellPolarity.pdf"}],"pubrep_id":"830","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1662-5102"]},"date_created":"2018-12-11T11:49:25Z","doi":"10.3389/fncel.2017.00176","type":"journal_article","scopus_import":"1","volume":11,"publication_status":"published","citation":{"ama":"Hansen AH, Düllberg CF, Mieck C, Loose M, Hippenmeyer S. Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. Frontiers in Cellular Neuroscience. 2017;11. doi:10.3389/fncel.2017.00176","short":"A.H. Hansen, C.F. Düllberg, C. Mieck, M. Loose, S. Hippenmeyer, Frontiers in Cellular Neuroscience 11 (2017).","ista":"Hansen AH, Düllberg CF, Mieck C, Loose M, Hippenmeyer S. 2017. Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. Frontiers in Cellular Neuroscience. 11, 176.","ieee":"A. H. Hansen, C. F. Düllberg, C. Mieck, M. Loose, and S. Hippenmeyer, “Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks,” Frontiers in Cellular Neuroscience, vol. 11. Frontiers Research Foundation, 2017.","apa":"Hansen, A. H., Düllberg, C. F., Mieck, C., Loose, M., & Hippenmeyer, S. (2017). Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks. Frontiers in Cellular Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncel.2017.00176","mla":"Hansen, Andi H., et al. “Cell Polarity in Cerebral Cortex Development - Cellular Architecture Shaped by Biochemical Networks.” Frontiers in Cellular Neuroscience, vol. 11, 176, Frontiers Research Foundation, 2017, doi:10.3389/fncel.2017.00176.","chicago":"Hansen, Andi H, Christian F Düllberg, Christine Mieck, Martin Loose, and Simon Hippenmeyer. “Cell Polarity in Cerebral Cortex Development - Cellular Architecture Shaped by Biochemical Networks.” Frontiers in Cellular Neuroscience. Frontiers Research Foundation, 2017. https://doi.org/10.3389/fncel.2017.00176."},"isi":1,"project":[{"_id":"25D61E48-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Cerebral Cortex Development","grant_number":"618444","call_identifier":"FP7"},{"grant_number":"RGP0053/2014","_id":"25D7962E-B435-11E9-9278-68D0E5697425","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level"},{"grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"},{"name":"The biochemical basis of PAR polarization","_id":"25985A36-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"T00817-B21"}],"quality_controlled":"1","article_processing_charge":"Yes","oa":1,"oa_version":"Published Version","has_accepted_license":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"9962","status":"public"}]},"language":[{"iso":"eng"}],"ec_funded":1,"month":"06","title":"Cell polarity in cerebral cortex development - cellular architecture shaped by biochemical networks"},{"publication":"PLoS Computational Biology","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"day":"18","intvolume":" 13","publist_id":"7004","date_published":"2017-07-18T00:00:00Z","external_id":{"isi":["000406619800014"]},"date_updated":"2026-08-14T22:31:14Z","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"ddc":["576"],"year":"2017","file_date_updated":"2020-07-14T12:47:46Z","publisher":"Public Library of Science","author":[{"full_name":"Lukacisinova, Marta","first_name":"Marta","orcid":"0000-0002-2519-8004","id":"4342E402-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisinova"},{"orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak","full_name":"Novak, Sebastian","first_name":"Sebastian"},{"full_name":"Paixao, Tiago","first_name":"Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao"}],"abstract":[{"lang":"eng","text":"Mutator strains are expected to evolve when the availability and effect of beneficial mutations are high enough to counteract the disadvantage from deleterious mutations that will inevitably accumulate. As the population becomes more adapted to its environment, both availability and effect of beneficial mutations necessarily decrease and mutation rates are predicted to decrease. It has been shown that certain molecular mechanisms can lead to increased mutation rates when the organism finds itself in a stressful environment. While this may be a correlated response to other functions, it could also be an adaptive mechanism, raising mutation rates only when it is most advantageous. Here, we use a mathematical model to investigate the plausibility of the adaptive hypothesis. We show that such a mechanism can be mantained if the population is subjected to diverse stresses. By simulating various antibiotic treatment schemes, we find that combination treatments can reduce the effectiveness of second-order selection on stress-induced mutagenesis. We discuss the implications of our results to strategies of antibiotic therapy."}],"article_number":"e1005609","_id":"696","corr_author":"1","pubrep_id":"894","file":[{"file_id":"5117","checksum":"9143c290fa6458ed2563bff4b295554a","creator":"system","date_created":"2018-12-12T10:15:01Z","file_size":3775716,"date_updated":"2020-07-14T12:47:46Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf"}],"publication_identifier":{"issn":["1553-734X"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1371/journal.pcbi.1005609","date_created":"2018-12-11T11:47:58Z","volume":13,"scopus_import":"1","article_type":"original","type":"journal_article","publication_status":"published","quality_controlled":"1","article_processing_charge":"No","project":[{"call_identifier":"FP7","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"isi":1,"citation":{"ama":"Lukacisinova M, Novak S, Paixao T. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 2017;13(7). doi:10.1371/journal.pcbi.1005609","short":"M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017).","apa":"Lukacisinova, M., Novak, S., & Paixao, T. (2017). Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes,” PLoS Computational Biology, vol. 13, no. 7. Public Library of Science, 2017.","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 13(7), e1005609.","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” PLoS Computational Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.","mla":"Lukacisinova, Marta, et al. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” PLoS Computational Biology, vol. 13, no. 7, e1005609, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609."},"related_material":{"record":[{"status":"public","id":"9849","relation":"research_data"},{"relation":"research_data","status":"public","id":"9850"},{"relation":"research_data","status":"public","id":"9851"},{"id":"9852","status":"public","relation":"research_data"},{"relation":"dissertation_contains","id":"6263","status":"public"}]},"has_accepted_license":"1","issue":"7","oa_version":"Published Version","oa":1,"ec_funded":1,"month":"07","title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","language":[{"iso":"eng"}]},{"author":[{"last_name":"Ukai","first_name":"Hikari","full_name":"Ukai, Hikari"},{"last_name":"Kawahara","full_name":"Kawahara, Aiko","first_name":"Aiko"},{"last_name":"Hirayama","full_name":"Hirayama, Keiko","first_name":"Keiko"},{"first_name":"Matthew J","full_name":"Case, Matthew J","id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87","last_name":"Case"},{"full_name":"Aino, Shotaro","first_name":"Shotaro","last_name":"Aino"},{"full_name":"Miyabe, Masahiro","first_name":"Masahiro","last_name":"Miyabe"},{"first_name":"Ken","full_name":"Wakita, Ken","last_name":"Wakita"},{"last_name":"Oogi","first_name":"Ryohei","full_name":"Oogi, Ryohei"},{"first_name":"Michiyo","full_name":"Kasayuki, Michiyo","last_name":"Kasayuki"},{"full_name":"Kawashima, Shihomi","first_name":"Shihomi","last_name":"Kawashima"},{"last_name":"Sugimoto","full_name":"Sugimoto, Shunichi","first_name":"Shunichi"},{"last_name":"Chikamatsu","first_name":"Kanako","full_name":"Chikamatsu, Kanako"},{"last_name":"Nitta","full_name":"Nitta, Noritaka","first_name":"Noritaka"},{"first_name":"Tsuneyuki","full_name":"Koga, Tsuneyuki","last_name":"Koga"},{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto"},{"last_name":"Takai","full_name":"Takai, Toshiyuki","first_name":"Toshiyuki"},{"first_name":"Isao","full_name":"Ito, Isao","last_name":"Ito"}],"abstract":[{"text":"Left-right asymmetry is a fundamental feature of higher-order brain structure; however, the molecular basis of brain asymmetry remains unclear. We recently identified structural and functional asymmetries in mouse hippocampal circuitry that result from the asymmetrical distribution of two distinct populations of pyramidal cell synapses that differ in the density of the NMDA receptor subunit GluRε2 (also known as NR2B, GRIN2B or GluN2B). By examining the synaptic distribution of ε2 subunits, we previously found that β2-microglobulin-deficient mice, which lack cell surface expression of the vast majority of major histocompatibility complex class I (MHCI) proteins, do not exhibit circuit asymmetry. In the present study, we conducted electrophysiological and anatomical analyses on the hippocampal circuitry of mice with a knockout of the paired immunoglobulin-like receptor B (PirB), an MHCI receptor. As in β2-microglobulin-deficient mice, the PirB-deficient hippocampus lacked circuit asymmetries. This finding that MHCI loss-of-function mice and PirB knockout mice have identical phenotypes suggests that MHCI signals that produce hippocampal asymmetries are transduced through PirB. Our results provide evidence for a critical role of the MHCI/PirB signaling system in the generation of asymmetries in hippocampal circuitry.","lang":"eng"}],"publisher":"Public Library of Science","file_date_updated":"2020-07-14T12:47:40Z","year":"2017","pubrep_id":"897","file":[{"relation":"main_file","file_name":"IST-2017-897-v1+1_journal.pone.0179377.pdf","checksum":"24dd19c46fb1c761b0bcbbcd1025a3a8","date_created":"2018-12-12T10:12:16Z","creator":"system","file_id":"4934","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:47:40Z","file_size":5798454}],"_id":"682","article_number":"e0179377","department":[{"_id":"RySh"}],"publication":"PLoS One","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"status":"public","ddc":["571"],"date_updated":"2026-08-14T22:31:15Z","external_id":{"isi":["000402923200125"]},"publist_id":"7034","date_published":"2017-06-01T00:00:00Z","day":"01","intvolume":" 12","citation":{"chicago":"Ukai, Hikari, Aiko Kawahara, Keiko Hirayama, Matthew J Case, Shotaro Aino, Masahiro Miyabe, Ken Wakita, et al. “PirB Regulates Asymmetries in Hippocampal Circuitry.” PLoS One. Public Library of Science, 2017. https://doi.org/10.1371/journal.pone.0179377.","mla":"Ukai, Hikari, et al. “PirB Regulates Asymmetries in Hippocampal Circuitry.” PLoS One, vol. 12, no. 6, e0179377, Public Library of Science, 2017, doi:10.1371/journal.pone.0179377.","apa":"Ukai, H., Kawahara, A., Hirayama, K., Case, M. J., Aino, S., Miyabe, M., … Ito, I. (2017). PirB regulates asymmetries in hippocampal circuitry. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0179377","ieee":"H. Ukai et al., “PirB regulates asymmetries in hippocampal circuitry,” PLoS One, vol. 12, no. 6. Public Library of Science, 2017.","ista":"Ukai H, Kawahara A, Hirayama K, Case MJ, Aino S, Miyabe M, Wakita K, Oogi R, Kasayuki M, Kawashima S, Sugimoto S, Chikamatsu K, Nitta N, Koga T, Shigemoto R, Takai T, Ito I. 2017. PirB regulates asymmetries in hippocampal circuitry. PLoS One. 12(6), e0179377.","short":"H. Ukai, A. Kawahara, K. Hirayama, M.J. Case, S. Aino, M. Miyabe, K. Wakita, R. Oogi, M. Kasayuki, S. Kawashima, S. Sugimoto, K. Chikamatsu, N. Nitta, T. Koga, R. Shigemoto, T. Takai, I. Ito, PLoS One 12 (2017).","ama":"Ukai H, Kawahara A, Hirayama K, et al. PirB regulates asymmetries in hippocampal circuitry. PLoS One. 2017;12(6). doi:10.1371/journal.pone.0179377"},"isi":1,"quality_controlled":"1","article_processing_charge":"No","publication_status":"published","language":[{"iso":"eng"}],"month":"06","title":"PirB regulates asymmetries in hippocampal circuitry","issue":"6","oa_version":"Published Version","oa":1,"related_material":{"record":[{"status":"public","id":"51","relation":"dissertation_contains"}]},"has_accepted_license":"1","publication_identifier":{"issn":["1932-6203"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","volume":12,"scopus_import":"1","article_type":"original","date_created":"2018-12-11T11:47:54Z","doi":"10.1371/journal.pone.0179377"},{"date_published":"2017-08-01T00:00:00Z","publist_id":"6364","intvolume":" 46","day":"01","ddc":["570"],"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"status":"public","external_id":{"isi":["000408077400015"]},"date_updated":"2026-08-14T22:31:14Z","department":[{"_id":"ToBo"}],"publication":"Current Opinion in Biotechnology","_id":"1027","file":[{"relation":"main_file","success":1,"file_name":"2017_CurrentOpinion_Lukaciinova.pdf","file_id":"5846","date_created":"2019-01-18T09:57:57Z","creator":"dernst","date_updated":"2019-01-18T09:57:57Z","file_size":858338,"content_type":"application/pdf","access_level":"open_access"}],"pubrep_id":"801","corr_author":"1","file_date_updated":"2019-01-18T09:57:57Z","page":"90 - 97","year":"2017","abstract":[{"lang":"eng","text":"The rising prevalence of antibiotic resistant bacteria is an increasingly serious public health challenge. To address this problem, recent work ranging from clinical studies to theoretical modeling has provided valuable insights into the mechanisms of resistance, its emergence and spread, and ways to counteract it. A deeper understanding of the underlying dynamics of resistance evolution will require a combination of experimental and theoretical expertise from different disciplines and new technology for studying evolution in the laboratory. Here, we review recent advances in the quantitative understanding of the mechanisms and evolution of antibiotic resistance. We focus on key theoretical concepts and new technology that enables well-controlled experiments. We further highlight key challenges that can be met in the near future to ultimately develop effective strategies for combating resistance."}],"author":[{"id":"4342E402-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-8004","last_name":"Lukacisinova","first_name":"Marta","full_name":"Lukacisinova, Marta"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias"}],"publisher":"Elsevier","date_created":"2018-12-11T11:49:45Z","doi":"10.1016/j.copbio.2017.02.013","type":"journal_article","article_type":"original","scopus_import":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","volume":46,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"oa_version":"Published Version","has_accepted_license":"1","related_material":{"record":[{"id":"6263","status":"public","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"ec_funded":1,"month":"08","title":"Toward a quantitative understanding of antibiotic resistance evolution","publication_status":"published","isi":1,"citation":{"ama":"Lukacisinova M, Bollenbach MT. Toward a quantitative understanding of antibiotic resistance evolution. Current Opinion in Biotechnology. 2017;46:90-97. doi:10.1016/j.copbio.2017.02.013","short":"M. Lukacisinova, M.T. Bollenbach, Current Opinion in Biotechnology 46 (2017) 90–97.","ista":"Lukacisinova M, Bollenbach MT. 2017. Toward a quantitative understanding of antibiotic resistance evolution. Current Opinion in Biotechnology. 46, 90–97.","ieee":"M. Lukacisinova and M. T. Bollenbach, “Toward a quantitative understanding of antibiotic resistance evolution,” Current Opinion in Biotechnology, vol. 46. Elsevier, pp. 90–97, 2017.","apa":"Lukacisinova, M., & Bollenbach, M. T. (2017). Toward a quantitative understanding of antibiotic resistance evolution. Current Opinion in Biotechnology. Elsevier. https://doi.org/10.1016/j.copbio.2017.02.013","mla":"Lukacisinova, Marta, and Mark Tobias Bollenbach. “Toward a Quantitative Understanding of Antibiotic Resistance Evolution.” Current Opinion in Biotechnology, vol. 46, Elsevier, 2017, pp. 90–97, doi:10.1016/j.copbio.2017.02.013.","chicago":"Lukacisinova, Marta, and Mark Tobias Bollenbach. “Toward a Quantitative Understanding of Antibiotic Resistance Evolution.” Current Opinion in Biotechnology. Elsevier, 2017. https://doi.org/10.1016/j.copbio.2017.02.013."},"project":[{"grant_number":"P27201-B22","call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions"},{"name":"Optimality principles in responses to antibiotics","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"303507"},{"name":"Revealing the fundamental limits of cell growth","_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013"}],"article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1"},{"quality_controlled":"1","article_processing_charge":"No","citation":{"chicago":"Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin Biology.” Auxins and Cytokinins in Plant Biology. Springer, 2017. https://doi.org/10.1007/978-1-4939-6831-2_1.","mla":"Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin Biology.” Auxins and Cytokinins in Plant Biology, vol. 1569, Springer, 2017, pp. 1–29, doi:10.1007/978-1-4939-6831-2_1.","ista":"Hurny A, Benková E. 2017. Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. 1569, 1–29.","ieee":"A. Hurny and E. Benková, “Methodological advances in auxin and cytokinin biology,” Auxins and Cytokinins in Plant Biology, vol. 1569. Springer, pp. 1–29, 2017.","apa":"Hurny, A., & Benková, E. (2017). Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. Springer. https://doi.org/10.1007/978-1-4939-6831-2_1","short":"A. Hurny, E. Benková, Auxins and Cytokinins in Plant Biology 1569 (2017) 1–29.","ama":"Hurny A, Benková E. Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. 2017;1569:1-29. doi:10.1007/978-1-4939-6831-2_1"},"project":[{"name":"Hormone cross-talk drives nutrient dependent plant development","_id":"2542D156-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I 1774-B16"}],"publication_status":"published","title":"Methodological advances in auxin and cytokinin biology","month":"03","language":[{"iso":"eng"}],"alternative_title":["Methods in Molecular Biology"],"has_accepted_license":"1","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"539"}]},"oa":1,"oa_version":"Submitted Version","publication_identifier":{"issn":["1064-3745"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","volume":1569,"type":"journal_article","doi":"10.1007/978-1-4939-6831-2_1","date_created":"2018-12-11T11:49:45Z","publisher":"Springer","abstract":[{"text":"The history of auxin and cytokinin biology including the initial discoveries by father–son duo Charles Darwin and Francis Darwin (1880), and Gottlieb Haberlandt (1919) is a beautiful demonstration of unceasing continuity of research. Novel findings are integrated into existing hypotheses and models and deepen our understanding of biological principles. At the same time new questions are triggered and hand to hand with this new methodologies are developed to address these new challenges.","lang":"eng"}],"author":[{"first_name":"Andrej","full_name":"Hurny, Andrej","last_name":"Hurny","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3638-1426"},{"last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","full_name":"Benková, Eva"}],"year":"2017","page":"1 - 29","file_date_updated":"2019-10-15T07:47:05Z","corr_author":"1","file":[{"file_id":"5068","creator":"system","date_created":"2018-12-12T10:14:18Z","date_updated":"2019-10-15T07:47:05Z","file_size":840646,"access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"IST-2018-1019-v1+1_Hurny_MethodsMolBiol_2017.pdf"}],"pubrep_id":"1019","_id":"1024","department":[{"_id":"EvBe"}],"publication":"Auxins and Cytokinins in Plant Biology","date_updated":"2026-08-14T22:31:16Z","ddc":["575"],"status":"public","intvolume":" 1569","day":"17","date_published":"2017-03-17T00:00:00Z","publist_id":"6369"},{"publist_id":"6362","date_published":"2017-03-20T00:00:00Z","day":"20","intvolume":" 56","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"status":"public","ddc":["540"],"external_id":{"isi":["000398154000038"]},"date_updated":"2026-08-14T22:31:17Z","das_tickbox":"1","publication":"Angewandte Chemie International Edition","department":[{"_id":"CaGu"},{"_id":"HaJa"}],"_id":"1028","acknowledgement":"This work was supported by a grant from the European Unions Seventh Framework Programme (CIG-303564). E.R. was supported by the graduate program MolecularDrugTargets (Austrian Science Fund (FWF), W1232) and a FemTech fellowship (Austrian Research Promotion Agency, 3580812)","file":[{"file_name":"2017_communications_Kainrath.pdf","success":1,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_size":2614942,"date_updated":"2019-01-18T09:39:55Z","date_created":"2019-01-18T09:39:55Z","creator":"dernst","file_id":"5845"}],"corr_author":"1","file_date_updated":"2019-01-18T09:39:55Z","year":"2017","page":"4608-4611","author":[{"full_name":"Kainrath, Stephanie","first_name":"Stephanie","last_name":"Kainrath","orcid":"0000-0002-6709-2195","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Stadler","full_name":"Stadler, Manuela","first_name":"Manuela"},{"id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7218-7738","last_name":"Gschaider-Reichhart","first_name":"Eva","full_name":"Gschaider-Reichhart, Eva"},{"full_name":"Distel, Martin","first_name":"Martin","last_name":"Distel"},{"full_name":"Janovjak, Harald L","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak"}],"abstract":[{"lang":"eng","text":"Optogenetics and photopharmacology provide spatiotemporally precise control over protein interactions and protein function in cells and animals. Optogenetic methods that are sensitive to green light and can be used to break protein complexes are not broadly available but would enable multichromatic experiments with previously inaccessible biological targets. Herein, we repurposed cobalamin (vitamin B12) binding domains of bacterial CarH transcription factors for green-light-induced receptor dissociation. In cultured cells, we observed oligomerization-induced cell signaling for the fibroblast growth factor receptor 1 fused to cobalamin-binding domains in the dark that was rapidly eliminated upon illumination. In zebrafish embryos expressing fusion receptors, green light endowed control over aberrant fibroblast growth factor signaling during development. Green-light-induced domain dissociation and light-inactivated receptors will critically expand the optogenetic toolbox for control of biological processes."}],"publisher":"Wiley","date_created":"2018-12-11T11:49:46Z","doi":"10.1002/anie.201611998","type":"journal_article","volume":56,"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1433-7851"]},"issue":"16","oa_version":"Published Version","oa":1,"related_material":{"record":[{"id":"418","status":"public","relation":"dissertation_contains"},{"relation":"part_of_dissertation","status":"public","id":"7680"}]},"has_accepted_license":"1","language":[{"iso":"eng"}],"month":"03","title":"Green-light-induced inactivation of receptor signaling using cobalamin-binding domains","ec_funded":1,"publication_status":"published","project":[{"call_identifier":"FP7","grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology","_id":"25548C20-B435-11E9-9278-68D0E5697425"},{"grant_number":"W1232-B24","call_identifier":"FWF","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets"}],"isi":1,"citation":{"chicago":"Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Green-Light-Induced Inactivation of Receptor Signaling Using Cobalamin-Binding Domains.” Angewandte Chemie International Edition. Wiley, 2017. https://doi.org/10.1002/anie.201611998.","mla":"Kainrath, Stephanie, et al. “Green-Light-Induced Inactivation of Receptor Signaling Using Cobalamin-Binding Domains.” Angewandte Chemie International Edition, vol. 56, no. 16, Wiley, 2017, pp. 4608–11, doi:10.1002/anie.201611998.","apa":"Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., & Janovjak, H. L. (2017). Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201611998","ieee":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak, “Green-light-induced inactivation of receptor signaling using cobalamin-binding domains,” Angewandte Chemie International Edition, vol. 56, no. 16. Wiley, pp. 4608–4611, 2017.","ista":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie International Edition. 56(16), 4608–4611.","short":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak, Angewandte Chemie International Edition 56 (2017) 4608–4611.","ama":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie International Edition. 2017;56(16):4608-4611. doi:10.1002/anie.201611998"},"article_processing_charge":"No","quality_controlled":"1"},{"_id":"1082","page":"1965-1973","year":"2016","main_file_link":[{"url":"https://arxiv.org/abs/1605.07332","open_access":"1"}],"publisher":"Neural Information Processing Systems Foundation","author":[{"last_name":"Chalk","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7782-4436","first_name":"Matthew J","full_name":"Chalk, Matthew J"},{"full_name":"Marre, Olivier","first_name":"Olivier","last_name":"Marre"},{"full_name":"Tkacik, Gasper","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik"}],"abstract":[{"lang":"eng","text":"In many applications, it is desirable to extract only the relevant aspects of data. A principled way to do this is the information bottleneck (IB) method, where one seeks a code that maximises information about a relevance variable, Y, while constraining the information encoded about the original data, X. Unfortunately however, the IB method is computationally demanding when data are high-dimensional and/or non-gaussian. Here we propose an approximate variational scheme for maximising a lower bound on the IB objective, analogous to variational EM. Using this method, we derive an IB algorithm to recover features that are both relevant and sparse. Finally, we demonstrate how kernelised versions of the algorithm can be used to address a broad range of problems with non-linear relation between X and Y."}],"day":"01","intvolume":" 29","publist_id":"6298","date_published":"2016-12-01T00:00:00Z","date_updated":"2025-06-03T11:33:51Z","external_id":{"arxiv":["1605.07332"]},"status":"public","conference":{"start_date":"2016-12-05","name":"NIPS: Neural Information Processing Systems","end_date":"2016-12-10","location":"Barcelona, Spain"},"department":[{"_id":"GaTk"}],"related_material":{"link":[{"relation":"other","url":"https://papers.nips.cc/paper/6101-relevant-sparse-codes-with-variational-information-bottleneck"}]},"alternative_title":["Advances in Neural Information Processing Systems"],"oa_version":"Preprint","oa":1,"month":"12","title":"Relevant sparse codes with variational information bottleneck","language":[{"iso":"eng"}],"publication_status":"published","quality_controlled":"1","article_processing_charge":"No","citation":{"ama":"Chalk MJ, Marre O, Tkačik G. Relevant sparse codes with variational information bottleneck. In: Vol 29. Neural Information Processing Systems Foundation; 2016:1965-1973.","short":"M.J. Chalk, O. Marre, G. Tkačik, in:, Neural Information Processing Systems Foundation, 2016, pp. 1965–1973.","ieee":"M. J. Chalk, O. Marre, and G. Tkačik, “Relevant sparse codes with variational information bottleneck,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain, 2016, vol. 29, pp. 1965–1973.","apa":"Chalk, M. J., Marre, O., & Tkačik, G. (2016). Relevant sparse codes with variational information bottleneck (Vol. 29, pp. 1965–1973). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain: Neural Information Processing Systems Foundation.","ista":"Chalk MJ, Marre O, Tkačik G. 2016. Relevant sparse codes with variational information bottleneck. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 1965–1973.","mla":"Chalk, Matthew J., et al. Relevant Sparse Codes with Variational Information Bottleneck. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp. 1965–73.","chicago":"Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Relevant Sparse Codes with Variational Information Bottleneck,” 29:1965–73. Neural Information Processing Systems Foundation, 2016."},"date_created":"2018-12-11T11:50:03Z","volume":29,"arxiv":1,"scopus_import":"1","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"department":[{"_id":"RySh"}],"publication":"Cerebral Cortex","date_published":"2016-04-12T00:00:00Z","publist_id":"6297","day":"12","intvolume":" 27","status":"public","date_updated":"2025-09-22T14:19:11Z","external_id":{"isi":["000397636600048"]},"year":"2016","page":"2318 - 2334","abstract":[{"lang":"eng","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. "}],"author":[{"last_name":"Booker","first_name":"Sam","full_name":"Booker, Sam"},{"full_name":"Althof, Daniel","first_name":"Daniel","last_name":"Althof"},{"last_name":"Gross","first_name":"Anna","full_name":"Gross, Anna"},{"last_name":"Loreth","first_name":"Desiree","full_name":"Loreth, Desiree"},{"full_name":"Müller, Johanna","first_name":"Johanna","last_name":"Müller"},{"first_name":"Andreas","full_name":"Unger, Andreas","last_name":"Unger"},{"last_name":"Fakler","full_name":"Fakler, Bernd","first_name":"Bernd"},{"full_name":"Varro, Andrea","first_name":"Andrea","last_name":"Varro"},{"last_name":"Watanabe","full_name":"Watanabe, Masahiko","first_name":"Masahiko"},{"last_name":"Gassmann","full_name":"Gassmann, Martin","first_name":"Martin"},{"first_name":"Bernhard","full_name":"Bettler, Bernhard","last_name":"Bettler"},{"first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","last_name":"Shigemoto"},{"full_name":"Vida, Imre","first_name":"Imre","last_name":"Vida"},{"full_name":"Kulik, Ákos","first_name":"Ákos","last_name":"Kulik"}],"publisher":"Oxford University Press","_id":"1083","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. ","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:50:03Z","doi":"10.1093/cercor/bhw090","type":"journal_article","scopus_import":"1","volume":27,"publication_status":"published","isi":1,"citation":{"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.","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.","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","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.","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.","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"},"article_processing_charge":"No","quality_controlled":"1","oa_version":"None","issue":"3","language":[{"iso":"eng"}],"title":"KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons","month":"04"},{"project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"}],"citation":{"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","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted Limit-Average Automata of Bounded Width,” Vol. 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPIcs.MFCS.2016.24.","mla":"Chatterjee, Krishnendu, et al. Nested Weighted Limit-Average Automata of Bounded Width. Vol. 58, 24, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPIcs.MFCS.2016.24.","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, Krakow; Poland, 2016, vol. 58.","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, Krakow; Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2016.24","ista":"Chatterjee K, Henzinger TA, Otop J. 2016. Nested weighted limit-average automata of bounded width. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 58, 24."},"article_processing_charge":"No","quality_controlled":"1","publication_status":"published","language":[{"iso":"eng"}],"title":"Nested weighted limit-average automata of bounded width","ec_funded":1,"month":"08","oa_version":"Published Version","oa":1,"alternative_title":["LIPIcs"],"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","volume":58,"scopus_import":"1","date_created":"2018-12-11T11:50:05Z","doi":"10.4230/LIPIcs.MFCS.2016.24","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","last_name":"Otop","full_name":"Otop, Jan","first_name":"Jan"}],"abstract":[{"lang":"eng","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."}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file_date_updated":"2018-12-12T10:17:31Z","year":"2016","pubrep_id":"795","file":[{"file_id":"5286","date_created":"2018-12-12T10:17:31Z","creator":"system","file_size":564560,"date_updated":"2018-12-12T10:17:31Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"IST-2017-795-v1+1_LIPIcs-MFCS-2016-24.pdf"}],"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23\r\n(RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna\r\nScience and Technology Fund (WWTF) through project ICT15-003 and by the National Science Centre\r\n(NCN), Poland under grant 2014/15/D/ST6/04543.","_id":"1090","article_number":"24","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"conference":{"name":"MFCS: Mathematical Foundations of Computer Science","start_date":"2016-08-22","end_date":"2016-08-26","location":"Krakow; Poland"},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"status":"public","ddc":["004"],"date_updated":"2025-07-10T11:50:02Z","publist_id":"6286","date_published":"2016-08-01T00:00:00Z","day":"01","intvolume":" 58"},{"department":[{"_id":"ToHe"},{"_id":"KrCh"},{"_id":"CaGu"}],"conference":{"start_date":"2016-08-23","name":"CONCUR: Concurrency Theory","location":"Quebec City; Canada","end_date":"2016-08-26"},"status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"ddc":["004"],"date_updated":"2026-04-15T10:02:12Z","publist_id":"6283","date_published":"2016-08-01T00:00:00Z","day":"01","intvolume":" 59","author":[{"last_name":"Daca","id":"49351290-F248-11E8-B48F-1D18A9856A87","full_name":"Daca, Przemyslaw","first_name":"Przemyslaw"},{"first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","last_name":"Kretinsky","first_name":"Jan","full_name":"Kretinsky, Jan"},{"orcid":"0000-0002-9041-0905","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrov","full_name":"Petrov, Tatjana","first_name":"Tatjana"}],"abstract":[{"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. ","lang":"eng"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file_date_updated":"2018-12-12T10:11:39Z","year":"2016","pubrep_id":"794","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.","file":[{"relation":"main_file","file_name":"IST-2017-794-v1+1_LIPIcs-CONCUR-2016-20.pdf","date_created":"2018-12-12T10:11:39Z","creator":"system","file_id":"4895","access_level":"open_access","content_type":"application/pdf","file_size":501827,"date_updated":"2018-12-12T10:11:39Z"}],"_id":"1093","article_number":"20","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"conference","volume":59,"scopus_import":1,"date_created":"2018-12-11T11:50:06Z","doi":"10.4230/LIPIcs.CONCUR.2016.20","project":[{"grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","call_identifier":"FWF"}],"citation":{"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","short":"P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","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.","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.","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.","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."},"quality_controlled":"1","publication_status":"published","language":[{"iso":"eng"}],"month":"08","ec_funded":1,"title":"Linear distances between Markov chains","oa_version":"Published Version","oa":1,"related_material":{"record":[{"status":"public","id":"1155","relation":"dissertation_contains"}]},"alternative_title":["LIPIcs"],"has_accepted_license":"1"},{"oa_version":"None","alternative_title":["Methods in Molecular Biology"],"language":[{"iso":"eng"}],"month":"08","ec_funded":1,"title":"Immunogold protein localization on grid-glued freeze-fracture replicas","publication_status":"published","citation":{"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.","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","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.","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.","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."},"project":[{"call_identifier":"FP7","grant_number":"604102","name":"Localization of ion channels and receptors by two and three-dimensional immunoelectron microscopic approaches","_id":"25CD3DD2-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","article_processing_charge":"No","date_created":"2018-12-11T11:50:06Z","doi":"10.1007/978-1-4939-6352-2_12","type":"book_chapter","volume":1474,"publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledged_ssus":[{"_id":"EM-Fac"}],"_id":"1094","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). ","page":"203 - 216","year":"2016","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"}],"author":[{"last_name":"Harada","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7429-7896","first_name":"Harumi","full_name":"Harada, Harumi"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi"}],"publisher":"Springer","date_published":"2016-08-12T00:00:00Z","publist_id":"6281","intvolume":" 1474","day":"12","status":"public","date_updated":"2025-04-15T07:12:21Z","department":[{"_id":"RySh"}],"publication":"High-Resolution Imaging of Cellular Proteins"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"conference","volume":59,"scopus_import":1,"date_created":"2018-12-11T11:50:07Z","doi":"10.4230/LIPIcs.CONCUR.2016.6","project":[{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","call_identifier":"FWF"}],"citation":{"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.","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.","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.","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","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.","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.","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"},"quality_controlled":"1","publication_status":"published","language":[{"iso":"eng"}],"title":"Local linearizability for concurrent container-type data structures","month":"08","ec_funded":1,"oa_version":"Published Version","oa":1,"alternative_title":["LIPIcs"],"has_accepted_license":"1","publication":"Leibniz International Proceedings in Informatics","department":[{"_id":"ToHe"}],"conference":{"end_date":"2016-08-26","location":"Quebec City; Canada","start_date":"2016-08-23","name":"CONCUR: Concurrency Theory"},"status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"ddc":["004"],"date_updated":"2025-04-15T06:25:58Z","publist_id":"6280","date_published":"2016-08-01T00:00:00Z","intvolume":" 59","day":"01","author":[{"full_name":"Haas, Andreas","first_name":"Andreas","last_name":"Haas"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A"},{"last_name":"Holzer","first_name":"Andreas","full_name":"Holzer, Andreas"},{"full_name":"Kirsch, Christoph","first_name":"Christoph","last_name":"Kirsch"},{"full_name":"Lippautz, Michael","first_name":"Michael","last_name":"Lippautz"},{"last_name":"Payer","full_name":"Payer, Hannes","first_name":"Hannes"},{"last_name":"Sezgin","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","full_name":"Sezgin, Ali","first_name":"Ali"},{"last_name":"Sokolova","full_name":"Sokolova, Ana","first_name":"Ana"},{"last_name":"Veith","full_name":"Veith, Helmut","first_name":"Helmut"}],"abstract":[{"text":" The semantics of concurrent data structures is usually given by a sequential specification and a consistency condition. Linearizability is the most popular consistency condition due to its simplicity and general applicability. Nevertheless, for applications that do not require all guarantees offered by linearizability, recent research has focused on improving performance and scalability of concurrent data structures by relaxing their semantics. In this paper, we present local linearizability, a relaxed consistency condition that is applicable to container-type concurrent data structures like pools, queues, and stacks. While linearizability requires that the effect of each operation is observed by all threads at the same time, local linearizability only requires that for each thread T, the effects of its local insertion operations and the effects of those removal operations that remove values inserted by T are observed by all threads at the same time. We investigate theoretical and practical properties of local linearizability and its relationship to many existing consistency conditions. We present a generic implementation method for locally linearizable data structures that uses existing linearizable data structures as building blocks. Our implementations show performance and scalability improvements over the original building blocks and outperform the fastest existing container-type implementations. ","lang":"eng"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file_date_updated":"2018-12-12T10:10:10Z","year":"2016","pubrep_id":"793","file":[{"file_name":"IST-2017-793-v1+1_LIPIcs-CONCUR-2016-6.pdf","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2018-12-12T10:10:10Z","file_size":589747,"date_created":"2018-12-12T10:10:10Z","creator":"system","file_id":"4795"}],"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).","_id":"1095","article_number":"6"},{"quality_controlled":"1","article_processing_charge":"No","citation":{"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","ista":"Schwayer C, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. 2016. Actin rings of power. Developmental Cell. 37(6), 493–506.","mla":"Schwayer, Cornelia, et al. “Actin Rings of Power.” Developmental Cell, vol. 37, no. 6, Cell Press, 2016, pp. 493–506, doi:10.1016/j.devcel.2016.05.024.","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.","ama":"Schwayer C, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. Actin rings of power. Developmental Cell. 2016;37(6):493-506. doi:10.1016/j.devcel.2016.05.024","short":"C. Schwayer, M.K. Sikora, J. Slovakova, R. Kardos, C.-P.J. Heisenberg, Developmental Cell 37 (2016) 493–506."},"isi":1,"publication_status":"published","title":"Actin rings of power","month":"06","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"7186","status":"public"}]},"oa_version":"None","issue":"6","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":37,"scopus_import":"1","type":"journal_article","doi":"10.1016/j.devcel.2016.05.024","date_created":"2018-12-11T11:50:07Z","publisher":"Cell Press","author":[{"last_name":"Schwayer","orcid":"0000-0001-5130-2226","id":"3436488C-F248-11E8-B48F-1D18A9856A87","full_name":"Schwayer, Cornelia","first_name":"Cornelia"},{"full_name":"Sikora, Mateusz K","first_name":"Mateusz K","last_name":"Sikora","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jana","full_name":"Slovakova, Jana","last_name":"Slovakova","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roland","full_name":"Kardos, Roland","id":"4039350E-F248-11E8-B48F-1D18A9856A87","last_name":"Kardos"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J"}],"page":"493 - 506","year":"2016","_id":"1096","publication":"Developmental Cell","department":[{"_id":"CaHe"}],"date_updated":"2026-04-08T13:55:28Z","external_id":{"isi":["000378204200005"]},"status":"public","intvolume":" 37","day":"20","publist_id":"6279","date_published":"2016-06-20T00:00:00Z"},{"date_updated":"2025-09-22T14:17:29Z","external_id":{"isi":["000388446200069"]},"ddc":["006"],"status":"public","intvolume":" 35","day":"01","date_published":"2016-11-01T00:00:00Z","publist_id":"6278","department":[{"_id":"BeBi"}],"conference":{"end_date":"2016-12-08","location":"Macao, China","name":"SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia","start_date":"2016-12-05"},"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. ","file":[{"file_size":33114420,"date_updated":"2018-12-12T10:17:42Z","content_type":"application/pdf","access_level":"open_access","file_id":"5298","creator":"system","date_created":"2018-12-12T10:17:42Z","file_name":"IST-2017-759-v1+1_copter.pdf","relation":"main_file"}],"pubrep_id":"759","article_number":"227","_id":"1097","publisher":"ACM","abstract":[{"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.","lang":"eng"}],"author":[{"last_name":"Du","full_name":"Du, Tao","first_name":"Tao"},{"last_name":"Schulz","first_name":"Adriana","full_name":"Schulz, Adriana"},{"last_name":"Zhu","first_name":"Bo","full_name":"Zhu, Bo"},{"full_name":"Bickel, Bernd","first_name":"Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Matusik","full_name":"Matusik, Wojciech","first_name":"Wojciech"}],"year":"2016","file_date_updated":"2018-12-12T10:17:42Z","scopus_import":"1","volume":35,"type":"conference","doi":"10.1145/2980179.2982427","date_created":"2018-12-11T11:50:07Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Computational multicopter design","month":"11","ec_funded":1,"language":[{"iso":"eng"}],"has_accepted_license":"1","alternative_title":["ACM Transactions on Graphics"],"oa":1,"issue":"6","oa_version":"Submitted Version","quality_controlled":"1","article_processing_charge":"No","isi":1,"citation":{"short":"T. Du, A. Schulz, B. Zhu, B. Bickel, W. Matusik, in:, ACM, 2016.","ama":"Du T, Schulz A, Zhu B, Bickel B, Matusik W. Computational multicopter design. In: Vol 35. ACM; 2016. doi:10.1145/2980179.2982427","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.","mla":"Du, Tao, et al. Computational Multicopter Design. Vol. 35, no. 6, 227, ACM, 2016, doi:10.1145/2980179.2982427.","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","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."},"project":[{"_id":"25082902-B435-11E9-9278-68D0E5697425","name":"Soft-bodied intelligence for Manipulation","grant_number":"645599","call_identifier":"H2020"}],"publication_status":"published"},{"quality_controlled":"1","article_processing_charge":"No","project":[{"grant_number":"308036","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding"}],"citation":{"short":"A. Pentina, R. Urner, in:, Neural Information Processing Systems Foundation, 2016, pp. 3619–3627.","ama":"Pentina A, Urner R. Lifelong learning with weighted majority votes. In: Vol 29. Neural Information Processing Systems Foundation; 2016:3619-3627.","mla":"Pentina, Anastasia, and Ruth Urner. Lifelong Learning with Weighted Majority Votes. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp. 3619–27.","chicago":"Pentina, Anastasia, and Ruth Urner. “Lifelong Learning with Weighted Majority Votes,” 29:3619–27. Neural Information Processing Systems Foundation, 2016.","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 Foundation.","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.","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."},"publication_status":"published","month":"12","ec_funded":1,"title":"Lifelong learning with weighted majority votes","language":[{"iso":"eng"}],"has_accepted_license":"1","alternative_title":["Advances in Neural Information Processing Systems"],"oa_version":"Published Version","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":29,"scopus_import":"1","type":"conference","date_created":"2018-12-11T11:50:08Z","publisher":"Neural Information Processing Systems Foundation","author":[{"id":"42E87FC6-F248-11E8-B48F-1D18A9856A87","last_name":"Pentina","full_name":"Pentina, Anastasia","first_name":"Anastasia"},{"first_name":"Ruth","full_name":"Urner, Ruth","last_name":"Urner"}],"abstract":[{"text":"Better understanding of the potential benefits of information transfer and representation learning is an important step towards the goal of building intelligent systems that are able to persist in the world and learn over time. In this work, we consider a setting where the learner encounters a stream of tasks but is able to retain only limited information from each encountered task, such as a learned predictor. In contrast to most previous works analyzing this scenario, we do not make any distributional assumptions on the task generating process. Instead, we formulate a complexity measure that captures the diversity of the observed tasks. We provide a lifelong learning algorithm with error guarantees for every observed task (rather than on average). We show sample complexity reductions in comparison to solving every task in isolation in terms of our task complexity measure. Further, our algorithmic framework can naturally be viewed as learning a representation from encountered tasks with a neural network.","lang":"eng"}],"page":"3619-3627","year":"2016","file_date_updated":"2018-12-12T10:12:43Z","pubrep_id":"775","file":[{"file_size":237111,"date_updated":"2018-12-12T10:12:42Z","content_type":"application/pdf","access_level":"open_access","file_id":"4961","date_created":"2018-12-12T10:12:42Z","creator":"system","file_name":"IST-2017-775-v1+1_main.pdf","relation":"main_file"},{"access_level":"open_access","content_type":"application/pdf","date_updated":"2018-12-12T10:12:43Z","file_size":185818,"date_created":"2018-12-12T10:12:43Z","creator":"system","file_id":"4962","file_name":"IST-2017-775-v1+2_supplementary.pdf","relation":"main_file"}],"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","_id":"1098","department":[{"_id":"ChLa"}],"conference":{"start_date":"2016-12-05","name":"NIPS: Neural Information Processing Systems","location":"Barcelona, Spain","end_date":"2016-12-10"},"date_updated":"2025-06-03T11:35:58Z","status":"public","ddc":["006"],"intvolume":" 29","day":"01","publist_id":"6277","date_published":"2016-12-01T00:00:00Z"},{"quality_controlled":"1","article_processing_charge":"No","project":[{"call_identifier":"H2020","grant_number":"645599","name":"Soft-bodied intelligence for Manipulation","_id":"25082902-B435-11E9-9278-68D0E5697425"}],"isi":1,"citation":{"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.","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.","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.","apa":"Malomo, L., Pietroni, N., Bickel, B., & Cignoni, P. (2016). FlexMolds: Automatic design of flexible shells for molding (Vol. 35). Presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China: ACM. https://doi.org/10.1145/2980179.2982397","ista":"Malomo L, Pietroni N, Bickel B, Cignoni P. 2016. FlexMolds: Automatic design of flexible shells for molding. SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, ACM Transactions on Graphics, vol. 35, 223.","short":"L. Malomo, N. Pietroni, B. Bickel, P. Cignoni, in:, ACM, 2016.","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"},"publication_status":"published","ec_funded":1,"title":"FlexMolds: Automatic design of flexible shells for molding","month":"11","language":[{"iso":"eng"}],"has_accepted_license":"1","alternative_title":["ACM Transactions on Graphics"],"oa_version":"Submitted Version","issue":"6","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":35,"scopus_import":"1","type":"conference","doi":"10.1145/2980179.2982397","date_created":"2018-12-11T11:50:08Z","publisher":"ACM","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","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel"},{"first_name":"Paolo","full_name":"Cignoni, Paolo","last_name":"Cignoni"}],"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"}],"year":"2016","file_date_updated":"2018-12-12T10:12:01Z","pubrep_id":"760","file":[{"file_id":"4918","creator":"system","date_created":"2018-12-12T10:12:01Z","date_updated":"2018-12-12T10:12:01Z","file_size":11122029,"access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"IST-2017-760-v1+1_flexmolds.pdf"}],"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.","article_number":"223","_id":"1099","department":[{"_id":"BeBi"}],"conference":{"end_date":"2016-12-08","location":"Macao, China","name":"SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia","start_date":"2016-12-05"},"external_id":{"isi":["000388446200065"]},"date_updated":"2025-09-22T14:16:02Z","status":"public","ddc":["000","005"],"intvolume":" 35","day":"01","publist_id":"6276","date_published":"2016-11-01T00:00:00Z"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":1,"scopus_import":"1","type":"journal_article","doi":"10.1021/acssensors.6b00576","date_created":"2018-12-11T11:50:09Z","quality_controlled":"1","article_processing_charge":"No","isi":1,"citation":{"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.","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.","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.","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","short":"J. Mitchell, J. Whitfield, W. Zhang, C. Henneberger, H.L. Janovjak, M. O’Mara, C. Jackson, ACS SENSORS 1 (2016) 1286–1290.","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"},"publication_status":"published","month":"11","title":"Rangefinder: A semisynthetic FRET sensor design algorithm","language":[{"iso":"eng"}],"issue":"11","oa_version":"None","department":[{"_id":"HaJa"}],"publication":"ACS SENSORS","date_updated":"2025-09-22T14:14:58Z","external_id":{"isi":["000388914800003"]},"status":"public","intvolume":" 1","day":"10","publist_id":"6274","date_published":"2016-11-10T00:00:00Z","publisher":"American Chemical Society","author":[{"first_name":"Joshua","full_name":"Mitchell, Joshua","last_name":"Mitchell"},{"last_name":"Whitfield","full_name":"Whitfield, Jason","first_name":"Jason"},{"last_name":"Zhang","full_name":"Zhang, William","first_name":"William"},{"last_name":"Henneberger","first_name":"Christian","full_name":"Henneberger, Christian"},{"full_name":"Janovjak, Harald L","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak"},{"full_name":"O'Mara, Megan","first_name":"Megan","last_name":"O'Mara"},{"full_name":"Jackson, Colin","first_name":"Colin","last_name":"Jackson"}],"abstract":[{"lang":"eng","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."}],"year":"2016","page":"1286 - 1290","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.","_id":"1101"},{"doi":"10.5244/C.30.92","date_created":"2018-12-11T11:50:09Z","scopus_import":"1","volume":"2016-September","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"oa_version":"Published Version","month":"09","ec_funded":1,"title":"Improving weakly-supervised object localization by micro-annotation","language":[{"iso":"eng"}],"publication_status":"published","quality_controlled":"1","article_processing_charge":"No","citation":{"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","short":"A. Kolesnikov, C. Lampert, in:, Proceedings of the British Machine Vision Conference 2016, BMVA Press, 2016, p. 92.1-92.12.","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","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.","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.","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."},"project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","call_identifier":"FP7"}],"day":"01","date_published":"2016-09-01T00:00:00Z","publist_id":"6273","date_updated":"2026-06-18T10:46:30Z","ddc":["000"],"status":"public","conference":{"name":"BMVC: British Machine Vision Conference","start_date":"2016-09-19","end_date":"2016-09-22","location":"York, United Kingdom"},"publication":"Proceedings of the British Machine Vision Conference 2016","department":[{"_id":"ChLa"}],"_id":"1102","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.","page":"92.1-92.12","year":"2016","main_file_link":[{"open_access":"1","url":"http://www.bmva.org/bmvc/2016/papers/paper092/paper092.pdf"}],"publisher":"BMVA Press","abstract":[{"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.","lang":"eng"}],"author":[{"first_name":"Alexander","full_name":"Kolesnikov, Alexander","last_name":"Kolesnikov","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}]},{"title":"Parallel reachability analysis for hybrid systems","ec_funded":1,"month":"12","language":[{"iso":"eng"}],"oa_version":"Preprint","oa":1,"quality_controlled":"1","article_processing_charge":"No","project":[{"call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF"}],"citation":{"short":"A. Gurung, A. Deka, E. Bartocci, S. Bogomolov, R. Grosu, R. Ray, in:, IEEE, 2016.","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","mla":"Gurung, Amit, et al. Parallel Reachability Analysis for Hybrid Systems. 7797741, IEEE, 2016, doi:10.1109/MEMCOD.2016.7797741.","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.","ieee":"A. Gurung, A. Deka, E. Bartocci, S. Bogomolov, R. Grosu, and R. Ray, “Parallel reachability analysis for hybrid systems,” presented at the MEMOCODE: Conference on Formal Methods and Models for System Design, Kanpur, India , 2016.","apa":"Gurung, A., Deka, A., Bartocci, E., Bogomolov, S., Grosu, R., & Ray, R. (2016). Parallel reachability analysis for hybrid systems. Presented at the MEMOCODE: Conference on Formal Methods and Models for System Design, Kanpur, India : IEEE. https://doi.org/10.1109/MEMCOD.2016.7797741","ista":"Gurung A, Deka A, Bartocci E, Bogomolov S, Grosu R, Ray R. 2016. Parallel reachability analysis for hybrid systems. MEMOCODE: Conference on Formal Methods and Models for System Design, 7797741."},"publication_status":"published","arxiv":1,"scopus_import":"1","type":"conference","doi":"10.1109/MEMCOD.2016.7797741","date_created":"2018-12-11T11:50:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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).","article_number":"7797741","_id":"1103","publisher":"IEEE","author":[{"last_name":"Gurung","first_name":"Amit","full_name":"Gurung, Amit"},{"last_name":"Deka","full_name":"Deka, Arup","first_name":"Arup"},{"last_name":"Bartocci","first_name":"Ezio","full_name":"Bartocci, Ezio"},{"first_name":"Sergiy","full_name":"Bogomolov, Sergiy","last_name":"Bogomolov","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0686-0365"},{"first_name":"Radu","full_name":"Grosu, Radu","last_name":"Grosu"},{"last_name":"Ray","first_name":"Rajarshi","full_name":"Ray, Rajarshi"}],"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."}],"year":"2016","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.05473"}],"date_updated":"2025-06-04T11:52:29Z","external_id":{"arxiv":["1606.05473"]},"status":"public","day":"27","publist_id":"6272","date_published":"2016-12-27T00:00:00Z","department":[{"_id":"ToHe"}],"conference":{"location":"Kanpur, India ","end_date":"2016-11-20","name":"MEMOCODE: Conference on Formal Methods and Models for System Design","start_date":"2016-11-18"}},{"article_processing_charge":"No","quality_controlled":"1","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734"}],"citation":{"ama":"Savin C, Tkačik G. Estimating nonlinear neural response functions using GP priors and Kronecker methods. In: Vol 29. Neural Information Processing Systems Foundation; 2016:3610-3618.","short":"C. Savin, G. Tkačik, in:, Neural Information Processing Systems Foundation, 2016, 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.","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.","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 Foundation.","mla":"Savin, Cristina, and Gašper Tkačik. Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp. 3610–18.","chicago":"Savin, Cristina, and Gašper Tkačik. “Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods,” 29:3610–18. Neural Information Processing Systems Foundation, 2016."},"publication_status":"published","month":"12","ec_funded":1,"title":"Estimating nonlinear neural response functions using GP priors and Kronecker methods","language":[{"iso":"eng"}],"alternative_title":["Advances in Neural Information Processing Systems"],"oa_version":"None","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":29,"scopus_import":"1","type":"conference","date_created":"2018-12-11T11:50:10Z","publisher":"Neural Information Processing Systems Foundation","author":[{"full_name":"Savin, Cristina","first_name":"Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","last_name":"Savin"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper","full_name":"Tkacik, Gasper"}],"abstract":[{"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.","lang":"eng"}],"year":"2016","page":"3610-3618","main_file_link":[{"url":"http://papers.nips.cc/paper/6153-estimating-nonlinear-neural-response-functions-using-gp-priors-and-kronecker-methods","open_access":"1"}],"corr_author":"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.","_id":"1105","department":[{"_id":"GaTk"}],"conference":{"location":"Barcelona; Spain","end_date":"2016-12-10","start_date":"2016-12-05","name":"NIPS: Neural Information Processing Systems"},"date_updated":"2025-06-03T11:36:49Z","status":"public","intvolume":" 29","day":"01","publist_id":"6265","date_published":"2016-12-01T00:00:00Z"}]