[{"publication_status":"published","publist_id":"7551","publication_identifier":{"eissn":["2405-4712"]},"oa_version":"Published Version","date_created":"2018-12-11T11:45:46Z","title":"The science of living matter for tomorrow","oa":1,"doi":"10.1016/j.cels.2018.04.003","department":[{"_id":"AnKi"}],"month":"04","article_type":"letter_note","volume":6,"author":[{"first_name":"Guntram","full_name":"Bauer, Guntram","last_name":"Bauer"},{"first_name":"Nikta","full_name":"Fakhri, Nikta","last_name":"Fakhri"},{"full_name":"Kicheva, Anna","last_name":"Kicheva","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998"},{"last_name":"Kondev","full_name":"Kondev, Jané","first_name":"Jané"},{"first_name":"Karsten","full_name":"Kruse, Karsten","last_name":"Kruse"},{"first_name":"Hiroyuki","last_name":"Noji","full_name":"Noji, Hiroyuki"},{"last_name":"Riveline","full_name":"Riveline, Daniel","first_name":"Daniel"},{"full_name":"Saunders, Timothy","last_name":"Saunders","first_name":"Timothy"},{"first_name":"Mukund","last_name":"Thatta","full_name":"Thatta, Mukund"},{"last_name":"Wieschaus","full_name":"Wieschaus, Eric","first_name":"Eric"}],"publisher":"Cell Press","article_processing_charge":"No","pmid":1,"quality_controlled":"1","type":"journal_article","external_id":{"isi":["000432192100003"],"pmid":["29698645"]},"_id":"314","abstract":[{"lang":"eng","text":"The interface of physics and biology pro-vides a fruitful environment for generatingnew concepts and exciting ways forwardto understanding living matter. Examplesof successful studies include the estab-lishment and readout of morphogen gra-dients during development, signal pro-cessing in protein and genetic networks,the role of fluctuations in determining thefates of cells and tissues, and collectiveeffects in proteins and in tissues. It is nothard to envision that significant further ad-vances will translate to societal benefitsby initiating the development of new de-vices and strategies for curing disease.However, research at the interface posesvarious challenges, in particular for youngscientists, and current institutions arerarely designed to facilitate such scientificprograms. In this Letter, we propose aninternational initiative that addressesthese challenges through the establish-ment of a worldwide network of platformsfor cross-disciplinary training and incuba-tors for starting new collaborations."}],"language":[{"iso":"eng"}],"day":"25","citation":{"short":"G. Bauer, N. Fakhri, A. Kicheva, J. Kondev, K. Kruse, H. Noji, D. Riveline, T. Saunders, M. Thatta, E. Wieschaus, Cell Systems 6 (2018) 400–402.","ieee":"G. Bauer <i>et al.</i>, “The science of living matter for tomorrow,” <i>Cell Systems</i>, vol. 6, no. 4. Cell Press, pp. 400–402, 2018.","mla":"Bauer, Guntram, et al. “The Science of Living Matter for Tomorrow.” <i>Cell Systems</i>, vol. 6, no. 4, Cell Press, 2018, pp. 400–02, doi:<a href=\"https://doi.org/10.1016/j.cels.2018.04.003\">10.1016/j.cels.2018.04.003</a>.","apa":"Bauer, G., Fakhri, N., Kicheva, A., Kondev, J., Kruse, K., Noji, H., … Wieschaus, E. (2018). The science of living matter for tomorrow. <i>Cell Systems</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cels.2018.04.003\">https://doi.org/10.1016/j.cels.2018.04.003</a>","ista":"Bauer G, Fakhri N, Kicheva A, Kondev J, Kruse K, Noji H, Riveline D, Saunders T, Thatta M, Wieschaus E. 2018. The science of living matter for tomorrow. Cell Systems. 6(4), 400–402.","ama":"Bauer G, Fakhri N, Kicheva A, et al. The science of living matter for tomorrow. <i>Cell Systems</i>. 2018;6(4):400-402. doi:<a href=\"https://doi.org/10.1016/j.cels.2018.04.003\">10.1016/j.cels.2018.04.003</a>","chicago":"Bauer, Guntram, Nikta Fakhri, Anna Kicheva, Jané Kondev, Karsten Kruse, Hiroyuki Noji, Daniel Riveline, Timothy Saunders, Mukund Thatta, and Eric Wieschaus. “The Science of Living Matter for Tomorrow.” <i>Cell Systems</i>. Cell Press, 2018. <a href=\"https://doi.org/10.1016/j.cels.2018.04.003\">https://doi.org/10.1016/j.cels.2018.04.003</a>."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2018","intvolume":"         6","main_file_link":[{"url":"https://doi.org/10.1016/j.cels.2018.04.003","open_access":"1"}],"date_published":"2018-04-25T00:00:00Z","isi":1,"publication":"Cell Systems","date_updated":"2023-09-19T10:11:25Z","status":"public","page":"400 - 402","scopus_import":"1","issue":"4"},{"publist_id":"7550","publication_status":"published","file":[{"access_level":"open_access","date_created":"2019-01-22T08:30:03Z","file_size":6968201,"content_type":"application/pdf","file_name":"2017_PLOS_Polechova.pdf","checksum":"908c52751bba30c55ed36789e5e4c84d","creator":"dernst","relation":"main_file","date_updated":"2020-07-14T12:46:01Z","file_id":"5870"}],"publication_identifier":{"issn":["1544-9173"]},"title":"Is the sky the limit? On the expansion threshold of a species’ range","date_created":"2018-12-11T11:45:46Z","oa_version":"Published Version","doi":"10.1371/journal.pbio.2005372","oa":1,"volume":16,"author":[{"last_name":"Polechova","full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","first_name":"Jitka"}],"department":[{"_id":"NiBa"}],"month":"06","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","publisher":"Public Library of Science","related_material":{"record":[{"id":"9839","status":"public","relation":"research_data"}]},"abstract":[{"lang":"eng","text":"More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range."}],"_id":"315","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","has_accepted_license":"1","day":"15","citation":{"ista":"Polechova J. 2018. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 16(6), e2005372.","ama":"Polechova J. Is the sky the limit? On the expansion threshold of a species’ range. <i>PLoS Biology</i>. 2018;16(6). doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005372\">10.1371/journal.pbio.2005372</a>","chicago":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” <i>PLoS Biology</i>. Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pbio.2005372\">https://doi.org/10.1371/journal.pbio.2005372</a>.","ieee":"J. Polechova, “Is the sky the limit? On the expansion threshold of a species’ range,” <i>PLoS Biology</i>, vol. 16, no. 6. Public Library of Science, 2018.","short":"J. Polechova, PLoS Biology 16 (2018).","mla":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” <i>PLoS Biology</i>, vol. 16, no. 6, e2005372, Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005372\">10.1371/journal.pbio.2005372</a>.","apa":"Polechova, J. (2018). Is the sky the limit? On the expansion threshold of a species’ range. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2005372\">https://doi.org/10.1371/journal.pbio.2005372</a>"},"intvolume":"        16","article_number":"e2005372","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"date_published":"2018-06-15T00:00:00Z","file_date_updated":"2020-07-14T12:46:01Z","date_updated":"2025-07-10T11:52:27Z","publication":"PLoS Biology","status":"public","issue":"6","scopus_import":"1"},{"page":"861-883","status":"public","ec_funded":1,"issue":"3","scopus_import":"1","publication":"Genetics","date_updated":"2025-04-15T06:50:00Z","isi":1,"intvolume":"       209","year":"2018","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-07-01T00:00:00Z","main_file_link":[{"url":"https://www.biorxiv.org/node/80098.abstract","open_access":"1"}],"_id":"316","abstract":[{"text":"Self-incompatibility (SI) is a genetically based recognition system that functions to prevent self-fertilization and mating among related plants. An enduring puzzle in SI is how the high diversity observed in nature arises and is maintained. Based on the underlying recognition mechanism, SI can be classified into two main groups: self- and non-self recognition. Most work has focused on diversification within self-recognition systems despite expected differences between the two groups in the evolutionary pathways and outcomes of diversification. Here, we use a deterministic population genetic model and stochastic simulations to investigate how novel S-haplotypes evolve in a gametophytic non-self recognition (SRNase/S Locus F-box (SLF)) SI system. For this model the pathways for diversification involve either the maintenance or breakdown of SI and can vary in the order of mutations of the female (SRNase) and male (SLF) components. We show analytically that diversification can occur with high inbreeding depression and self-pollination, but this varies with evolutionary pathway and level of completeness (which determines the number of potential mating partners in the population), and in general is more likely for lower haplotype number. The conditions for diversification are broader in stochastic simulations of finite population size. However, the number of haplotypes observed under high inbreeding and moderate to high self-pollination is less than that commonly observed in nature. Diversification was observed through pathways that maintain SI as well as through self-compatible intermediates. Yet the lifespan of diversified haplotypes was sensitive to their level of completeness. By examining diversification in a non-self recognition SI system, this model extends our understanding of the evolution and maintenance of haplotype diversity observed in a self recognition system common in flowering plants.","lang":"eng"}],"language":[{"iso":"eng"}],"external_id":{"isi":["000437171700017"]},"type":"journal_article","quality_controlled":"1","citation":{"apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., &#38; Pickup, M. (2018). Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.118.300748\">https://doi.org/10.1534/genetics.118.300748</a>","mla":"Bodova, Katarina, et al. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” <i>Genetics</i>, vol. 209, no. 3, Genetics Society of America, 2018, pp. 861–83, doi:<a href=\"https://doi.org/10.1534/genetics.118.300748\">10.1534/genetics.118.300748</a>.","ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system,” <i>Genetics</i>, vol. 209, no. 3. Genetics Society of America, pp. 861–883, 2018.","short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, Genetics 209 (2018) 861–883.","chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.118.300748\">https://doi.org/10.1534/genetics.118.300748</a>.","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. <i>Genetics</i>. 2018;209(3):861-883. doi:<a href=\"https://doi.org/10.1534/genetics.118.300748\">10.1534/genetics.118.300748</a>","ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 209(3), 861–883."},"day":"01","article_processing_charge":"No","publisher":"Genetics Society of America","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/recognizing-others-but-not-yourself-new-insights-into-the-evolution-of-plant-mating/"}],"record":[{"relation":"research_data","id":"9813","status":"public"}]},"oa":1,"doi":"10.1534/genetics.118.300748","volume":209,"author":[{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina","orcid":"0000-0002-7214-0171","full_name":"Bodova, Katarina","last_name":"Bodova"},{"last_name":"Priklopil","full_name":"Priklopil, Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","first_name":"Tadeas"},{"orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","full_name":"Field, David","last_name":"Field"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H"},{"last_name":"Pickup","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda"}],"article_type":"original","project":[{"name":"Mating system and the evolutionary dynamics of hybrid zones","call_identifier":"FP7","_id":"25B36484-B435-11E9-9278-68D0E5697425","grant_number":"329960"},{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"month":"07","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"title":"Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system","date_created":"2018-12-11T11:45:47Z","oa_version":"Preprint","publication_status":"published"},{"publist_id":"7548","publication_status":"published","file":[{"relation":"main_file","creator":"system","date_updated":"2020-07-14T12:46:02Z","file_id":"5256","file_name":"IST-2018-1016-v1+1_2018_Brauns_Palladium_gates.pdf","checksum":"20af238ca4ba6491b77270be8d826bf5","date_created":"2018-12-12T10:17:04Z","file_size":1850530,"content_type":"application/pdf","access_level":"open_access"}],"oa_version":"Published Version","date_created":"2018-12-11T11:45:47Z","title":"Palladium gates for reproducible quantum dots in silicon","pubrep_id":"1016","oa":1,"doi":"10.1038/s41598-018-24004-y","month":"04","department":[{"_id":"GeKa"}],"volume":8,"author":[{"first_name":"Matthias","id":"33F94E3C-F248-11E8-B48F-1D18A9856A87","last_name":"Brauns","full_name":"Brauns, Matthias"},{"full_name":"Amitonov, Sergey","last_name":"Amitonov","first_name":"Sergey"},{"full_name":"Spruijtenburg, Paul","last_name":"Spruijtenburg","first_name":"Paul"},{"first_name":"Floris","last_name":"Zwanenburg","full_name":"Zwanenburg, Floris"}],"publisher":"Nature Publishing Group","corr_author":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","type":"journal_article","quality_controlled":"1","_id":"317","language":[{"iso":"eng"}],"abstract":[{"text":"We replace the established aluminium gates for the formation of quantum dots in silicon with gates made from palladium. We study the morphology of both aluminium and palladium gates with transmission electron microscopy. The native aluminium oxide is found to be formed all around the aluminium gates, which could lead to the formation of unintentional dots. Therefore, we report on a novel fabrication route that replaces aluminium and its native oxide by palladium with atomic-layer-deposition-grown aluminium oxide. Using this approach, we show the formation of low-disorder gate-defined quantum dots, which are reproducibly fabricated. Furthermore, palladium enables us to further shrink the gate design, allowing us to perform electron transport measurements in the few-electron regime in devices comprising only two gate layers, a major technological advancement. It remains to be seen, whether the introduction of palladium gates can improve the excellent results on electron and nuclear spin qubits defined with an aluminium gate stack.","lang":"eng"}],"external_id":{"isi":["000429404300013"]},"has_accepted_license":"1","citation":{"chicago":"Brauns, Matthias, Sergey Amitonov, Paul Spruijtenburg, and Floris Zwanenburg. “Palladium Gates for Reproducible Quantum Dots in Silicon.” <i>Scientific Reports</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41598-018-24004-y\">https://doi.org/10.1038/s41598-018-24004-y</a>.","ista":"Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. 2018. Palladium gates for reproducible quantum dots in silicon. Scientific Reports. 8(1), 5690.","ama":"Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. Palladium gates for reproducible quantum dots in silicon. <i>Scientific Reports</i>. 2018;8(1). doi:<a href=\"https://doi.org/10.1038/s41598-018-24004-y\">10.1038/s41598-018-24004-y</a>","apa":"Brauns, M., Amitonov, S., Spruijtenburg, P., &#38; Zwanenburg, F. (2018). Palladium gates for reproducible quantum dots in silicon. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41598-018-24004-y\">https://doi.org/10.1038/s41598-018-24004-y</a>","ieee":"M. Brauns, S. Amitonov, P. Spruijtenburg, and F. Zwanenburg, “Palladium gates for reproducible quantum dots in silicon,” <i>Scientific Reports</i>, vol. 8, no. 1. Nature Publishing Group, 2018.","short":"M. Brauns, S. Amitonov, P. Spruijtenburg, F. Zwanenburg, Scientific Reports 8 (2018).","mla":"Brauns, Matthias, et al. “Palladium Gates for Reproducible Quantum Dots in Silicon.” <i>Scientific Reports</i>, vol. 8, no. 1, 5690, Nature Publishing Group, 2018, doi:<a href=\"https://doi.org/10.1038/s41598-018-24004-y\">10.1038/s41598-018-24004-y</a>."},"day":"09","year":"2018","ddc":["539"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"         8","article_number":"5690","date_published":"2018-04-09T00:00:00Z","file_date_updated":"2020-07-14T12:46:02Z","isi":1,"publication":"Scientific Reports","date_updated":"2024-10-09T20:58:34Z","status":"public","scopus_import":"1","issue":"1"},{"quality_controlled":"1","type":"journal_article","external_id":{"isi":["000426150700002"],"pmid":["29486189"]},"_id":"318","abstract":[{"text":"The insect’s fat body combines metabolic and immunological functions. In this issue of Developmental Cell, Franz et al. (2018) show that in Drosophila, cells of the fat body are not static, but can actively “swim” toward sites of epithelial injury, where they physically clog the wound and locally secrete antimicrobial peptides.","lang":"eng"}],"language":[{"iso":"eng"}],"day":"26","citation":{"ista":"Casano AM, Sixt MK. 2018. A fat lot of good for wound healing. Developmental Cell. 44(4), 405–406.","ama":"Casano AM, Sixt MK. A fat lot of good for wound healing. <i>Developmental Cell</i>. 2018;44(4):405-406. doi:<a href=\"https://doi.org/10.1016/j.devcel.2018.02.009\">10.1016/j.devcel.2018.02.009</a>","chicago":"Casano, Alessandra M, and Michael K Sixt. “A Fat Lot of Good for Wound Healing.” <i>Developmental Cell</i>. Cell Press, 2018. <a href=\"https://doi.org/10.1016/j.devcel.2018.02.009\">https://doi.org/10.1016/j.devcel.2018.02.009</a>.","ieee":"A. M. Casano and M. K. Sixt, “A fat lot of good for wound healing,” <i>Developmental Cell</i>, vol. 44, no. 4. Cell Press, pp. 405–406, 2018.","short":"A.M. Casano, M.K. Sixt, Developmental Cell 44 (2018) 405–406.","mla":"Casano, Alessandra M., and Michael K. Sixt. “A Fat Lot of Good for Wound Healing.” <i>Developmental Cell</i>, vol. 44, no. 4, Cell Press, 2018, pp. 405–06, doi:<a href=\"https://doi.org/10.1016/j.devcel.2018.02.009\">10.1016/j.devcel.2018.02.009</a>.","apa":"Casano, A. M., &#38; Sixt, M. K. (2018). A fat lot of good for wound healing. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2018.02.009\">https://doi.org/10.1016/j.devcel.2018.02.009</a>"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2018","intvolume":"        44","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29486189"}],"date_published":"2018-02-26T00:00:00Z","isi":1,"date_updated":"2024-10-09T20:58:17Z","publication":"Developmental Cell","status":"public","page":"405 - 406","scopus_import":"1","issue":"4","publication_status":"published","publist_id":"7547","oa_version":"Published Version","title":"A fat lot of good for wound healing","date_created":"2018-12-11T11:45:47Z","oa":1,"doi":"10.1016/j.devcel.2018.02.009","acknowledgement":"Short Survey","department":[{"_id":"MiSi"}],"month":"02","volume":44,"author":[{"id":"3DBA3F4E-F248-11E8-B48F-1D18A9856A87","first_name":"Alessandra M","orcid":"0000-0002-6009-6804","last_name":"Casano","full_name":"Casano, Alessandra M"},{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"}],"publisher":"Cell Press","article_processing_charge":"No","corr_author":"1","pmid":1},{"citation":{"chicago":"Chen, Ting, Bartosz Kula, Balint Nagy, Ruxandra Barzan, Andrea Gall, Ingrid Ehrlich, and Maria Kukley. “In Vivo Regulation of Oligodendrocyte Processor Cell Proliferation and Differentiation by the AMPA-Receptor Subunit GluA2.” <i>Cell Reports</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.celrep.2018.09.066\">https://doi.org/10.1016/j.celrep.2018.09.066</a>.","ama":"Chen T, Kula B, Nagy B, et al. In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2. <i>Cell Reports</i>. 2018;25(4):852-861.e7. doi:<a href=\"https://doi.org/10.1016/j.celrep.2018.09.066\">10.1016/j.celrep.2018.09.066</a>","ista":"Chen T, Kula B, Nagy B, Barzan R, Gall A, Ehrlich I, Kukley M. 2018. In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2. Cell Reports. 25(4), 852–861.e7.","apa":"Chen, T., Kula, B., Nagy, B., Barzan, R., Gall, A., Ehrlich, I., &#38; Kukley, M. (2018). In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2018.09.066\">https://doi.org/10.1016/j.celrep.2018.09.066</a>","mla":"Chen, Ting, et al. “In Vivo Regulation of Oligodendrocyte Processor Cell Proliferation and Differentiation by the AMPA-Receptor Subunit GluA2.” <i>Cell Reports</i>, vol. 25, no. 4, Elsevier, 2018, p. 852–861.e7, doi:<a href=\"https://doi.org/10.1016/j.celrep.2018.09.066\">10.1016/j.celrep.2018.09.066</a>.","ieee":"T. Chen <i>et al.</i>, “In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2,” <i>Cell Reports</i>, vol. 25, no. 4. Elsevier, p. 852–861.e7, 2018.","short":"T. Chen, B. Kula, B. Nagy, R. Barzan, A. Gall, I. Ehrlich, M. Kukley, Cell Reports 25 (2018) 852–861.e7."},"day":"23","has_accepted_license":"1","quality_controlled":"1","type":"journal_article","external_id":{"isi":["000448219500005"]},"_id":"32","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The functional role of AMPA receptor (AMPAR)-mediated synaptic signaling between neurons and oligodendrocyte precursor cells (OPCs) remains enigmatic. We modified the properties of AMPARs at axon-OPC synapses in the mouse corpus callosum in vivo during the peak of myelination by targeting the GluA2 subunit. Expression of the unedited (Ca2+ permeable) or the pore-dead GluA2 subunit of AMPARs triggered proliferation of OPCs and reduced their differentiation into oligodendrocytes. Expression of the cytoplasmic C-terminal (GluA2(813-862)) of the GluA2 subunit (C-tail), a modification designed to affect the interaction between GluA2 and AMPAR-binding proteins and to perturb trafficking of GluA2-containing AMPARs, decreased the differentiation of OPCs without affecting their proliferation. These findings suggest that ionotropic and non-ionotropic properties of AMPARs in OPCs, as well as specific aspects of AMPAR-mediated signaling at axon-OPC synapses in the mouse corpus callosum, are important for balancing the response of OPCs to proliferation and differentiation cues. In the brain, oligodendrocyte precursor cells (OPCs) receive glutamatergic AMPA-receptor-mediated synaptic input from neurons. Chen et al. show that modifying AMPA-receptor properties at axon-OPC synapses alters proliferation and differentiation of OPCs. This expands the traditional view of synaptic transmission by suggesting neurons also use synapses to modulate behavior of glia."}],"date_published":"2018-10-23T00:00:00Z","ddc":["570"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2018","intvolume":"        25","isi":1,"date_updated":"2023-09-11T14:13:32Z","publication":"Cell Reports","file_date_updated":"2020-07-14T12:46:03Z","scopus_import":"1","issue":"4","page":"852 - 861.e7","status":"public","file":[{"content_type":"application/pdf","date_created":"2018-12-17T12:42:57Z","file_size":4461997,"access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"5703","date_updated":"2020-07-14T12:46:03Z","checksum":"d9f74277fd57176e04732707d575cf08","file_name":"2018_CellReports_Chen.pdf"}],"publication_status":"published","publist_id":"8023","oa_version":"Published Version","title":"In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2","date_created":"2018-12-11T11:44:16Z","department":[{"_id":"SaSi"}],"month":"10","author":[{"first_name":"Ting","full_name":"Chen, Ting","last_name":"Chen"},{"last_name":"Kula","full_name":"Kula, Bartosz","first_name":"Bartosz"},{"last_name":"Nagy","full_name":"Nagy, Balint","first_name":"Balint","id":"30F830CE-02D1-11E9-9BAA-DAF4881429F2","orcid":"0000-0002-4002-4686"},{"full_name":"Barzan, Ruxandra","last_name":"Barzan","first_name":"Ruxandra"},{"last_name":"Gall","full_name":"Gall, Andrea","first_name":"Andrea"},{"last_name":"Ehrlich","full_name":"Ehrlich, Ingrid","first_name":"Ingrid"},{"full_name":"Kukley, Maria","last_name":"Kukley","first_name":"Maria"}],"volume":25,"doi":"10.1016/j.celrep.2018.09.066","oa":1,"acknowledgement":"This work was supported by Deutsche Forschungsgemeinschaft (DFG) grant KU2569/1-1 (to M.K.); DFG project EXC307Centre for Integrative Neuroscience (CIN), including grant Pool Project 2011-12 (jointly to M.K. and I.E.); and the Charitable Hertie Foundation (to I.E.). CIN is an Excellence Cluster funded by the DFG within the framework of the Excellence Initiative for 2008–2018. M.K. is supported by the Tistou & Charlotte Kerstan Foundation.","publisher":"Elsevier","article_processing_charge":"No","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"}},{"date_created":"2018-12-11T11:45:48Z","title":"Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons","oa_version":"Published Version","publist_id":"7545","publication_status":"published","file":[{"access_level":"open_access","file_size":3180444,"date_created":"2018-12-17T10:37:50Z","content_type":"application/pdf","file_name":"2018_Neuron_Hu.pdf","checksum":"76070f3729f9c603e1080d0151aa2b11","date_updated":"2020-07-14T12:46:03Z","creator":"dernst","file_id":"5690","relation":"main_file"}],"corr_author":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"Yes (in subscription journal)","publisher":"Elsevier","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/a-certain-type-of-neurons-is-more-energy-efficient-than-previously-assumed/"}]},"doi":"10.1016/j.neuron.2018.02.024","oa":1,"author":[{"first_name":"Hua","id":"4AC0145C-F248-11E8-B48F-1D18A9856A87","last_name":"Hu","full_name":"Hu, Hua"},{"first_name":"Fabian","full_name":"Roth, Fabian","last_name":"Roth"},{"full_name":"Vandael, David H","last_name":"Vandael","first_name":"David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7577-1676"},{"last_name":"Jonas","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","orcid":"0000-0001-5001-4804"}],"volume":98,"project":[{"name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","grant_number":"268548","call_identifier":"FP7","_id":"25C0F108-B435-11E9-9278-68D0E5697425"},{"grant_number":"692692","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"name":"Mechanisms of transmitter release at GABAergic synapses","call_identifier":"FWF","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","grant_number":"P24909-B24"},{"name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"department":[{"_id":"PeJo"}],"month":"04","intvolume":"        98","year":"2018","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["570"],"date_published":"2018-04-04T00:00:00Z","_id":"320","language":[{"iso":"eng"}],"abstract":[{"text":"Fast-spiking, parvalbumin-expressing GABAergic interneurons (PV+-BCs) express a complex machinery of rapid signaling mechanisms, including specialized voltage-gated ion channels to generate brief action potentials (APs). However, short APs are associated with overlapping Na+ and K+ fluxes and are therefore energetically expensive. How the potentially vicious combination of high AP frequency and inefficient spike generation can be reconciled with limited energy supply is presently unclear. To address this question, we performed direct recordings from the PV+-BC axon, the subcellular structure where active conductances for AP initiation and propagation are located. Surprisingly, the energy required for the AP was, on average, only ∼1.6 times the theoretical minimum. High energy efficiency emerged from the combination of fast inactivation of Na+ channels and delayed activation of Kv3-type K+ channels, which minimized ion flux overlap during APs. Thus, the complementary tuning of axonal Na+ and K+ channel gating optimizes both fast signaling properties and metabolic efficiency. Hu et al. demonstrate that action potentials in parvalbumin-expressing GABAergic interneuron axons are energetically efficient, which is highly unexpected given their brief duration. High energy efficiency emerges from the combination of fast inactivation of voltage-gated Na+ channels and delayed activation of Kv3 channels in the axon. ","lang":"eng"}],"external_id":{"isi":["000429192100016"]},"type":"journal_article","quality_controlled":"1","has_accepted_license":"1","citation":{"apa":"Hu, H., Roth, F., Vandael, D. H., &#38; Jonas, P. M. (2018). Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2018.02.024\">https://doi.org/10.1016/j.neuron.2018.02.024</a>","mla":"Hu, Hua, et al. “Complementary Tuning of Na+ and K+ Channel Gating Underlies Fast and Energy-Efficient Action Potentials in GABAergic Interneuron Axons.” <i>Neuron</i>, vol. 98, no. 1, Elsevier, 2018, pp. 156–65, doi:<a href=\"https://doi.org/10.1016/j.neuron.2018.02.024\">10.1016/j.neuron.2018.02.024</a>.","ieee":"H. Hu, F. Roth, D. H. Vandael, and P. M. Jonas, “Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons,” <i>Neuron</i>, vol. 98, no. 1. Elsevier, pp. 156–165, 2018.","short":"H. Hu, F. Roth, D.H. Vandael, P.M. Jonas, Neuron 98 (2018) 156–165.","chicago":"Hu, Hua, Fabian Roth, David H Vandael, and Peter M Jonas. “Complementary Tuning of Na+ and K+ Channel Gating Underlies Fast and Energy-Efficient Action Potentials in GABAergic Interneuron Axons.” <i>Neuron</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.neuron.2018.02.024\">https://doi.org/10.1016/j.neuron.2018.02.024</a>.","ama":"Hu H, Roth F, Vandael DH, Jonas PM. Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons. <i>Neuron</i>. 2018;98(1):156-165. doi:<a href=\"https://doi.org/10.1016/j.neuron.2018.02.024\">10.1016/j.neuron.2018.02.024</a>","ista":"Hu H, Roth F, Vandael DH, Jonas PM. 2018. Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons. Neuron. 98(1), 156–165."},"day":"04","page":"156 - 165","status":"public","issue":"1","ec_funded":1,"scopus_import":"1","file_date_updated":"2020-07-14T12:46:03Z","date_updated":"2025-04-15T08:29:04Z","publication":"Neuron","isi":1},{"external_id":{"isi":["000428901200001"]},"_id":"321","abstract":[{"lang":"eng","text":"The twelve papers in this special section focus on learning systems with shared information for computer vision and multimedia communication analysis. In the real world, a realistic setting for computer vision or multimedia recognition problems is that we have some classes containing lots of training data and many classes containing a small amount of training data. Therefore, how to use frequent classes to help learning rare classes for which it is harder to collect the training data is an open question. Learning with shared information is an emerging topic in machine learning, computer vision and multimedia analysis. There are different levels of components that can be shared during concept modeling and machine learning stages, such as sharing generic object parts, sharing attributes, sharing transformations, sharing regularization parameters and sharing training examples, etc. Regarding the specific methods, multi-task learning, transfer learning and deep learning can be seen as using different strategies to share information. These learning with shared information methods are very effective in solving real-world large-scale problems."}],"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","citation":{"chicago":"Darrell, Trevor, Christoph Lampert, Nico Sebe, Ying Wu, and Yan Yan. “Guest Editors’ Introduction to the Special Section on Learning with Shared Information for Computer Vision and Multimedia Analysis.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE, 2018. <a href=\"https://doi.org/10.1109/TPAMI.2018.2804998\">https://doi.org/10.1109/TPAMI.2018.2804998</a>.","ista":"Darrell T, Lampert C, Sebe N, Wu Y, Yan Y. 2018. Guest editors’ introduction to the special section on learning with Shared information for computer vision and multimedia analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. 40(5), 1029–1031.","ama":"Darrell T, Lampert C, Sebe N, Wu Y, Yan Y. Guest editors’ introduction to the special section on learning with Shared information for computer vision and multimedia analysis. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. 2018;40(5):1029-1031. doi:<a href=\"https://doi.org/10.1109/TPAMI.2018.2804998\">10.1109/TPAMI.2018.2804998</a>","apa":"Darrell, T., Lampert, C., Sebe, N., Wu, Y., &#38; Yan, Y. (2018). Guest editors’ introduction to the special section on learning with Shared information for computer vision and multimedia analysis. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE. <a href=\"https://doi.org/10.1109/TPAMI.2018.2804998\">https://doi.org/10.1109/TPAMI.2018.2804998</a>","ieee":"T. Darrell, C. Lampert, N. Sebe, Y. Wu, and Y. Yan, “Guest editors’ introduction to the special section on learning with Shared information for computer vision and multimedia analysis,” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 40, no. 5. IEEE, pp. 1029–1031, 2018.","short":"T. Darrell, C. Lampert, N. Sebe, Y. Wu, Y. Yan, IEEE Transactions on Pattern Analysis and Machine Intelligence 40 (2018) 1029–1031.","mla":"Darrell, Trevor, et al. “Guest Editors’ Introduction to the Special Section on Learning with Shared Information for Computer Vision and Multimedia Analysis.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 40, no. 5, IEEE, 2018, pp. 1029–31, doi:<a href=\"https://doi.org/10.1109/TPAMI.2018.2804998\">10.1109/TPAMI.2018.2804998</a>."},"day":"01","has_accepted_license":"1","intvolume":"        40","ddc":["000"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2018","date_published":"2018-05-01T00:00:00Z","file_date_updated":"2020-07-14T12:46:03Z","date_updated":"2024-10-09T20:58:26Z","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","isi":1,"status":"public","page":"1029 - 1031","issue":"5","scopus_import":"1","publication_status":"published","publist_id":"7544","file":[{"file_id":"7835","creator":"dernst","date_updated":"2020-07-14T12:46:03Z","relation":"main_file","checksum":"b19c75da06faf3291a3ca47dfa50ef63","file_name":"2018_IEEE_Darrell.pdf","content_type":"application/pdf","date_created":"2020-05-14T12:50:48Z","file_size":141724,"access_level":"open_access"}],"title":"Guest editors' introduction to the special section on learning with Shared information for computer vision and multimedia analysis","date_created":"2018-12-11T11:45:48Z","oa_version":"Published Version","doi":"10.1109/TPAMI.2018.2804998","oa":1,"author":[{"last_name":"Darrell","full_name":"Darrell, Trevor","first_name":"Trevor"},{"full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","orcid":"0000-0001-8622-7887"},{"full_name":"Sebe, Nico","last_name":"Sebe","first_name":"Nico"},{"full_name":"Wu, Ying","last_name":"Wu","first_name":"Ying"},{"last_name":"Yan","full_name":"Yan, Yan","first_name":"Yan"}],"volume":40,"month":"05","department":[{"_id":"ChLa"}],"article_type":"original","article_processing_charge":"No","corr_author":"1","publisher":"IEEE"},{"scopus_import":"1","ec_funded":1,"status":"public","page":"92 - 128","isi":1,"date_updated":"2025-04-14T09:12:46Z","publication":"Journal of Algebra","main_file_link":[{"url":"https://arxiv.org/abs/1412.7211","open_access":"1"}],"date_published":"2018-07-15T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2018","intvolume":"       506","citation":{"mla":"Ganev, Iordan V. “Quantizations of Multiplicative Hypertoric Varieties at a Root of Unity.” <i>Journal of Algebra</i>, vol. 506, World Scientific Publishing, 2018, pp. 92–128, doi:<a href=\"https://doi.org/10.1016/j.jalgebra.2018.03.015\">10.1016/j.jalgebra.2018.03.015</a>.","short":"I.V. Ganev, Journal of Algebra 506 (2018) 92–128.","ieee":"I. V. Ganev, “Quantizations of multiplicative hypertoric varieties at a root of unity,” <i>Journal of Algebra</i>, vol. 506. World Scientific Publishing, pp. 92–128, 2018.","apa":"Ganev, I. V. (2018). Quantizations of multiplicative hypertoric varieties at a root of unity. <i>Journal of Algebra</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1016/j.jalgebra.2018.03.015\">https://doi.org/10.1016/j.jalgebra.2018.03.015</a>","ama":"Ganev IV. Quantizations of multiplicative hypertoric varieties at a root of unity. <i>Journal of Algebra</i>. 2018;506:92-128. doi:<a href=\"https://doi.org/10.1016/j.jalgebra.2018.03.015\">10.1016/j.jalgebra.2018.03.015</a>","ista":"Ganev IV. 2018. Quantizations of multiplicative hypertoric varieties at a root of unity. Journal of Algebra. 506, 92–128.","chicago":"Ganev, Iordan V. “Quantizations of Multiplicative Hypertoric Varieties at a Root of Unity.” <i>Journal of Algebra</i>. World Scientific Publishing, 2018. <a href=\"https://doi.org/10.1016/j.jalgebra.2018.03.015\">https://doi.org/10.1016/j.jalgebra.2018.03.015</a>."},"day":"15","quality_controlled":"1","type":"journal_article","external_id":{"isi":["000433270600005"],"arxiv":["1412.7211"]},"abstract":[{"lang":"eng","text":"We construct quantizations of multiplicative hypertoric varieties using an algebra of q-difference operators on affine space, where q is a root of unity in C. The quantization defines a matrix bundle (i.e. Azumaya algebra) over the multiplicative hypertoric variety and admits an explicit finite étale splitting. The global sections of this Azumaya algebra is a hypertoric quantum group, and we prove a localization theorem. We introduce a general framework of Frobenius quantum moment maps and their Hamiltonian reductions; our results shed light on an instance of this framework."}],"_id":"322","language":[{"iso":"eng"}],"publisher":"World Scientific Publishing","article_processing_charge":"No","corr_author":"1","month":"07","department":[{"_id":"TaHa"}],"project":[{"grant_number":"320593","call_identifier":"FP7","_id":"25E549F4-B435-11E9-9278-68D0E5697425","name":"Arithmetic and physics of Higgs moduli spaces"}],"author":[{"first_name":"Iordan V","id":"447491B8-F248-11E8-B48F-1D18A9856A87","full_name":"Ganev, Iordan V","last_name":"Ganev"}],"volume":506,"doi":"10.1016/j.jalgebra.2018.03.015","oa":1,"acknowledgement":"National Science Foundation: Graduate Research Fellowship and grant No.0932078000; ERC Advanced Grant “Arithmetic and Physics of Higgs moduli spaces” No. 320593 \r\nThe author is grateful to David Jordan for suggesting this project and providing guidance throughout, particularly for the formulation of Frobenius quantum moment maps and key ideas in the proofs of Theorems 3.12 and 4.8. Special thanks to David Ben-Zvi (the author's PhD advisor) for numerous discussions and constant encouragement, and for suggesting the term ‘hypertoric quantum group.’ Many results appearing in the current paper were proven independently by Nicholas Cooney; the author is grateful to Nicholas for sharing his insight on various topics, including Proposition 3.8. The author also thanks Nicholas Proudfoot for relating the definition of multiplicative hypertoric varieties, as well as the content of Remark 2.14. The author also benefited immensely from the close reading and detailed comments of an anonymous referee, and from conversations with Justin Hilburn, Kobi Kremnitzer, Michael McBreen, Tom Nevins, Travis Schedler, and Ben Webster. \r\n\r\n\r\n\r\n","oa_version":"Preprint","date_created":"2018-12-11T11:45:49Z","title":"Quantizations of multiplicative hypertoric varieties at a root of unity","arxiv":1,"publication_status":"published","publist_id":"7543"},{"status":"public","scopus_import":"1","issue":"POPL","date_updated":"2024-10-21T06:02:40Z","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"         2","article_number":"34","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.04037"}],"date_published":"2018-01-01T00:00:00Z","type":"conference","quality_controlled":"1","_id":"325","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Probabilistic programs extend classical imperative programs with real-valued random variables and random branching. The most basic liveness property for such programs is the termination property. The qualitative (aka almost-sure) termination problem asks whether a given program program terminates with probability 1. While ranking functions provide a sound and complete method for non-probabilistic programs, the extension of them to probabilistic programs is achieved via ranking supermartingales (RSMs). Although deep theoretical results have been established about RSMs, their application to probabilistic programs with nondeterminism has been limited only to programs of restricted control-flow structure. For non-probabilistic programs, lexicographic ranking functions provide a compositional and practical approach for termination analysis of real-world programs. In this work we introduce lexicographic RSMs and show that they present a sound method for almost-sure termination of probabilistic programs with nondeterminism. We show that lexicographic RSMs provide a tool for compositional reasoning about almost-sure termination, and for probabilistic programs with linear arithmetic they can be synthesized efficiently (in polynomial time). We also show that with additional restrictions even asymptotic bounds on expected termination time can be obtained through lexicographic RSMs. Finally, we present experimental results on benchmarks adapted from previous work to demonstrate the effectiveness of our approach."}],"external_id":{"arxiv":["1709.04037"]},"citation":{"ama":"Agrawal S, Chatterjee K, Novotný P. Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs. In: Vol 2. ACM; 2018. doi:<a href=\"https://doi.org/10.1145/3158122\">10.1145/3158122</a>","ista":"Agrawal S, Chatterjee K, Novotný P. 2018. Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs. POPL: Principles of Programming Languages vol. 2, 34.","chicago":"Agrawal, Sheshansh, Krishnendu Chatterjee, and Petr Novotný. “Lexicographic Ranking Supermartingales: An Efficient Approach to Termination of Probabilistic Programs,” Vol. 2. ACM, 2018. <a href=\"https://doi.org/10.1145/3158122\">https://doi.org/10.1145/3158122</a>.","mla":"Agrawal, Sheshansh, et al. <i>Lexicographic Ranking Supermartingales: An Efficient Approach to Termination of Probabilistic Programs</i>. Vol. 2, no. POPL, 34, ACM, 2018, doi:<a href=\"https://doi.org/10.1145/3158122\">10.1145/3158122</a>.","short":"S. Agrawal, K. Chatterjee, P. Novotný, in:, ACM, 2018.","ieee":"S. Agrawal, K. Chatterjee, and P. Novotný, “Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs,” presented at the POPL: Principles of Programming Languages, Los Angeles, CA, USA, 2018, vol. 2, no. POPL.","apa":"Agrawal, S., Chatterjee, K., &#38; Novotný, P. (2018). Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs (Vol. 2). Presented at the POPL: Principles of Programming Languages, Los Angeles, CA, USA: ACM. <a href=\"https://doi.org/10.1145/3158122\">https://doi.org/10.1145/3158122</a>"},"day":"01","publisher":"ACM","doi":"10.1145/3158122","oa":1,"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"month":"01","department":[{"_id":"KrCh"}],"volume":2,"author":[{"full_name":"Agrawal, Sheshansh","last_name":"Agrawal","first_name":"Sheshansh"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","last_name":"Novotny","full_name":"Novotny, Petr"}],"arxiv":1,"oa_version":"Preprint","title":"Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs","date_created":"2018-12-11T11:45:50Z","publist_id":"7540","conference":{"name":"POPL: Principles of Programming Languages","start_date":"2018-01-07","end_date":"2018-01-13","location":"Los Angeles, CA, USA"},"publication_status":"published"},{"date_updated":"2023-09-19T09:58:40Z","publication":"European Journal of Neuroscience","acknowledged_ssus":[{"_id":"EM-Fac"}],"isi":1,"file_date_updated":"2020-07-14T12:46:06Z","issue":"9","scopus_import":"1","page":"1033 - 1042","status":"public","has_accepted_license":"1","day":"07","citation":{"chicago":"Sawada, Kazuaki, Ryosuke Kawakami, Ryuichi Shigemoto, and Tomomi Nemoto. “Super Resolution Structural Analysis of Dendritic Spines Using Three-Dimensional Structured Illumination Microscopy in Cleared Mouse Brain Slices.” <i>European Journal of Neuroscience</i>. Wiley, 2018. <a href=\"https://doi.org/10.1111/ejn.13901\">https://doi.org/10.1111/ejn.13901</a>.","ama":"Sawada K, Kawakami R, Shigemoto R, Nemoto T. Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. <i>European Journal of Neuroscience</i>. 2018;47(9):1033-1042. doi:<a href=\"https://doi.org/10.1111/ejn.13901\">10.1111/ejn.13901</a>","ista":"Sawada K, Kawakami R, Shigemoto R, Nemoto T. 2018. Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. European Journal of Neuroscience. 47(9), 1033–1042.","apa":"Sawada, K., Kawakami, R., Shigemoto, R., &#38; Nemoto, T. (2018). Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. <i>European Journal of Neuroscience</i>. Wiley. <a href=\"https://doi.org/10.1111/ejn.13901\">https://doi.org/10.1111/ejn.13901</a>","mla":"Sawada, Kazuaki, et al. “Super Resolution Structural Analysis of Dendritic Spines Using Three-Dimensional Structured Illumination Microscopy in Cleared Mouse Brain Slices.” <i>European Journal of Neuroscience</i>, vol. 47, no. 9, Wiley, 2018, pp. 1033–42, doi:<a href=\"https://doi.org/10.1111/ejn.13901\">10.1111/ejn.13901</a>.","short":"K. Sawada, R. Kawakami, R. Shigemoto, T. Nemoto, European Journal of Neuroscience 47 (2018) 1033–1042.","ieee":"K. Sawada, R. Kawakami, R. Shigemoto, and T. Nemoto, “Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices,” <i>European Journal of Neuroscience</i>, vol. 47, no. 9. Wiley, pp. 1033–1042, 2018."},"abstract":[{"text":"Three-dimensional (3D) super-resolution microscopy technique structured illumination microscopy (SIM) imaging of dendritic spines along the dendrite has not been previously performed in fixed tissues, mainly due to deterioration of the stripe pattern of the excitation laser induced by light scattering and optical aberrations. To address this issue and solve these optical problems, we applied a novel clearing reagent, LUCID, to fixed brains. In SIM imaging, the penetration depth and the spatial resolution were improved in LUCID-treated slices, and 160-nm spatial resolution was obtained in a large portion of the imaging volume on a single apical dendrite. Furthermore, in a morphological analysis of spine heads of layer V pyramidal neurons (L5PNs) in the medial prefrontal cortex (mPFC) of chronic dexamethasone (Dex)-treated mice, SIM imaging revealed an altered distribution of spine forms that could not be detected by high-NA confocal imaging. Thus, super-resolution SIM imaging represents a promising high-throughput method for revealing spine morphologies in single dendrites.","lang":"eng"}],"_id":"326","language":[{"iso":"eng"}],"external_id":{"isi":["000431496400001"]},"type":"journal_article","quality_controlled":"1","date_published":"2018-03-07T00:00:00Z","intvolume":"        47","year":"2018","ddc":["570"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Sawada","full_name":"Sawada, Kazuaki","first_name":"Kazuaki"},{"first_name":"Ryosuke","last_name":"Kawakami","full_name":"Kawakami, Ryosuke"},{"orcid":"0000-0001-8761-9444","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi"},{"first_name":"Tomomi","full_name":"Nemoto, Tomomi","last_name":"Nemoto"}],"volume":47,"month":"03","department":[{"_id":"RySh"}],"doi":"10.1111/ejn.13901","oa":1,"tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"article_processing_charge":"No","publisher":"Wiley","file":[{"access_level":"open_access","date_created":"2018-12-17T16:16:50Z","file_size":4850261,"content_type":"application/pdf","file_name":"2018_EJN_Sawada.pdf","checksum":"98e901d8229e44aa8f3b51d248dedd09","date_updated":"2020-07-14T12:46:06Z","creator":"dernst","file_id":"5721","relation":"main_file"}],"publist_id":"7539","publication_status":"published","date_created":"2018-12-11T11:45:50Z","title":"Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices","oa_version":"Published Version"},{"oa_version":"Preprint","title":"Slow dynamics in translation-invariant quantum lattice models","date_created":"2018-12-11T11:45:50Z","arxiv":1,"publication_status":"published","publist_id":"7538","publisher":"American Physical Society","article_processing_charge":"No","month":"03","department":[{"_id":"MaSe"}],"author":[{"last_name":"Michailidis","full_name":"Michailidis, Alexios","orcid":"0000-0002-8443-1064","first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Žnidarič","full_name":"Žnidarič, Marko","first_name":"Marko"},{"first_name":"Mariya","last_name":"Medvedyeva","full_name":"Medvedyeva, Mariya"},{"last_name":"Abanin","full_name":"Abanin, Dmitry","first_name":"Dmitry"},{"first_name":"Tomaž","full_name":"Prosen, Tomaž","last_name":"Prosen"},{"first_name":"Zlatko","last_name":"Papić","full_name":"Papić, Zlatko"}],"volume":97,"doi":"10.1103/PhysRevB.97.104307","oa":1,"acknowledgement":"We thank F. Huveneers for useful discussions. Z.P. and A.M. acknowledge support by EPSRC Grant No. EP/P009409/1 and and the Royal Society Research Grant No. RG160635. Statement of compliance with EPSRC policy framework on research data: This publication is theoretical work that does not require supporting research data. D.A. acknowledges support by the Swiss National Science Foundation. M.Z., M.M. and T.P. acknowledge Grants J1-7279 (M.Z.) and N1-0025 (M.M. and T.P.) of Slovenian Research Agency, and Advanced Grant of European Research Council, Grant No. 694544 - OMNES (T.P.).","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.05026"}],"date_published":"2018-03-19T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","article_number":"104307","intvolume":"        97","day":"19","citation":{"mla":"Michailidis, Alexios, et al. “Slow Dynamics in Translation-Invariant Quantum Lattice Models.” <i>Physical Review B</i>, vol. 97, no. 10, 104307, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevB.97.104307\">10.1103/PhysRevB.97.104307</a>.","ieee":"A. Michailidis, M. Žnidarič, M. Medvedyeva, D. Abanin, T. Prosen, and Z. Papić, “Slow dynamics in translation-invariant quantum lattice models,” <i>Physical Review B</i>, vol. 97, no. 10. American Physical Society, 2018.","short":"A. Michailidis, M. Žnidarič, M. Medvedyeva, D. Abanin, T. Prosen, Z. Papić, Physical Review B 97 (2018).","apa":"Michailidis, A., Žnidarič, M., Medvedyeva, M., Abanin, D., Prosen, T., &#38; Papić, Z. (2018). Slow dynamics in translation-invariant quantum lattice models. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.97.104307\">https://doi.org/10.1103/PhysRevB.97.104307</a>","ama":"Michailidis A, Žnidarič M, Medvedyeva M, Abanin D, Prosen T, Papić Z. Slow dynamics in translation-invariant quantum lattice models. <i>Physical Review B</i>. 2018;97(10). doi:<a href=\"https://doi.org/10.1103/PhysRevB.97.104307\">10.1103/PhysRevB.97.104307</a>","ista":"Michailidis A, Žnidarič M, Medvedyeva M, Abanin D, Prosen T, Papić Z. 2018. Slow dynamics in translation-invariant quantum lattice models. Physical Review B. 97(10), 104307.","chicago":"Michailidis, Alexios, Marko Žnidarič, Mariya Medvedyeva, Dmitry Abanin, Tomaž Prosen, and Zlatko Papić. “Slow Dynamics in Translation-Invariant Quantum Lattice Models.” <i>Physical Review B</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevB.97.104307\">https://doi.org/10.1103/PhysRevB.97.104307</a>."},"quality_controlled":"1","type":"journal_article","external_id":{"isi":["000427798800005"],"arxiv":["1706.05026"]},"_id":"327","language":[{"iso":"eng"}],"abstract":[{"text":"Many-body quantum systems typically display fast dynamics and ballistic spreading of information. Here we address the open problem of how slow the dynamics can be after a generic breaking of integrability by local interactions. We develop a method based on degenerate perturbation theory that reveals slow dynamical regimes and delocalization processes in general translation invariant models, along with accurate estimates of their delocalization time scales. Our results shed light on the fundamental questions of the robustness of quantum integrable systems and the possibility of many-body localization without disorder. As an example, we construct a large class of one-dimensional lattice models where, despite the absence of asymptotic localization, the transient dynamics is exceptionally slow, i.e., the dynamics is indistinguishable from that of many-body localized systems for the system sizes and time scales accessible in experiments and numerical simulations.","lang":"eng"}],"scopus_import":"1","issue":"10","status":"public","isi":1,"publication":"Physical Review B","date_updated":"2025-06-04T07:50:22Z"},{"year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"124501","intvolume":"       120","main_file_link":[{"url":"https://arxiv.org/abs/1703.06271","open_access":"1"}],"date_published":"2018-03-19T00:00:00Z","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"_id":"328","abstract":[{"lang":"eng","text":"The drag of turbulent flows can be drastically decreased by adding small amounts of high molecular weight polymers. While drag reduction initially increases with polymer concentration, it eventually saturates to what is known as the maximum drag reduction (MDR) asymptote; this asymptote is generally attributed to the dynamics being reduced to a marginal yet persistent state of subdued turbulent motion. Contrary to this accepted view, we show that, for an appropriate choice of parameters, polymers can reduce the drag beyond the suggested asymptotic limit, eliminating turbulence and giving way to laminar flow. At higher polymer concentrations, however, the laminar state becomes unstable, resulting in a fluctuating flow with the characteristic drag of the MDR asymptote. Our findings indicate that the asymptotic state is hence dynamically disconnected from ordinary turbulence. © 2018 American Physical Society."}],"external_id":{"arxiv":["1703.06271"],"isi":["000427804000005"]},"citation":{"apa":"Choueiri, G. H., Lopez Alonso, J. M., &#38; Hof, B. (2018). Exceeding the asymptotic limit of polymer drag reduction. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.120.124501\">https://doi.org/10.1103/PhysRevLett.120.124501</a>","short":"G.H. Choueiri, J.M. Lopez Alonso, B. Hof, Physical Review Letters 120 (2018).","ieee":"G. H. Choueiri, J. M. Lopez Alonso, and B. Hof, “Exceeding the asymptotic limit of polymer drag reduction,” <i>Physical Review Letters</i>, vol. 120, no. 12. American Physical Society, 2018.","mla":"Choueiri, George H., et al. “Exceeding the Asymptotic Limit of Polymer Drag Reduction.” <i>Physical Review Letters</i>, vol. 120, no. 12, 124501, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.120.124501\">10.1103/PhysRevLett.120.124501</a>.","chicago":"Choueiri, George H, Jose M Lopez Alonso, and Björn Hof. “Exceeding the Asymptotic Limit of Polymer Drag Reduction.” <i>Physical Review Letters</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevLett.120.124501\">https://doi.org/10.1103/PhysRevLett.120.124501</a>.","ista":"Choueiri GH, Lopez Alonso JM, Hof B. 2018. Exceeding the asymptotic limit of polymer drag reduction. Physical Review Letters. 120(12), 124501.","ama":"Choueiri GH, Lopez Alonso JM, Hof B. Exceeding the asymptotic limit of polymer drag reduction. <i>Physical Review Letters</i>. 2018;120(12). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.120.124501\">10.1103/PhysRevLett.120.124501</a>"},"day":"19","status":"public","scopus_import":"1","ec_funded":1,"issue":"12","acknowledged_ssus":[{"_id":"SSU"}],"isi":1,"date_updated":"2025-06-04T07:52:00Z","publication":"Physical Review Letters","arxiv":1,"oa_version":"Preprint","date_created":"2018-12-11T11:45:51Z","title":"Exceeding the asymptotic limit of polymer drag reduction","publist_id":"7537","publication_status":"published","publisher":"American Physical Society","corr_author":"1","article_processing_charge":"No","acknowledgement":"The authors thank Philipp Maier and the IST Austria workshop for their dedicated technical support.","oa":1,"doi":"10.1103/PhysRevLett.120.124501","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Decoding the complexity of turbulence at its origin","grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"department":[{"_id":"BjHo"}],"month":"03","author":[{"first_name":"George H","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","full_name":"Choueiri, George H","last_name":"Choueiri"},{"orcid":"0000-0002-0384-2022","first_name":"Jose M","id":"40770848-F248-11E8-B48F-1D18A9856A87","full_name":"Lopez Alonso, Jose M","last_name":"Lopez Alonso"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","last_name":"Hof","full_name":"Hof, Björn"}],"volume":120},{"status":"public","issue":"10","scopus_import":"1","file_date_updated":"2020-07-14T12:46:06Z","publication":"PeerJ","date_updated":"2023-10-17T12:24:43Z","isi":1,"intvolume":"      2018","article_number":"e5325","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"year":"2018","date_published":"2018-10-01T00:00:00Z","external_id":{"pmid":["30294507"],"isi":["000447204400001"]},"language":[{"iso":"eng"}],"_id":"33","abstract":[{"text":"Secondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia in the southern peninsulas. With the advent of multi-locus markers, secondary contact can be investigated using various molecular signatures including gradients of allele frequency, admixture clines, and local increase of genetic differentiation. We use coalescent simulations to investigate if molecular data provide enough information to distinguish between secondary contact following range expansion and an alternative evolutionary scenario consisting of a barrier to gene flow in an isolation-by-distance model. We find that an excess of linkage disequilibrium and of genetic diversity at the suture zone is a unique signature of secondary contact. We also find that the directionality index ψ, which was proposed to study range expansion, is informative to distinguish between the two hypotheses. However, although evidence for secondary contact is usually conveyed by statistics related to admixture coefficients, we find that they can be confounded by isolation-by-distance. We recommend to account for the spatial repartition of individuals when investigating secondary contact in order to better reflect the complex spatio-temporal evolution of populations and species.","lang":"eng"}],"quality_controlled":"1","type":"journal_article","day":"01","citation":{"apa":"Bertl, J., Ringbauer, H., &#38; Blum, M. (2018). Can secondary contact following range expansion be distinguished from barriers to gene flow? <i>PeerJ</i>. PeerJ. <a href=\"https://doi.org/10.7717/peerj.5325\">https://doi.org/10.7717/peerj.5325</a>","short":"J. Bertl, H. Ringbauer, M. Blum, PeerJ 2018 (2018).","ieee":"J. Bertl, H. Ringbauer, and M. Blum, “Can secondary contact following range expansion be distinguished from barriers to gene flow?,” <i>PeerJ</i>, vol. 2018, no. 10. PeerJ, 2018.","mla":"Bertl, Johanna, et al. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” <i>PeerJ</i>, vol. 2018, no. 10, e5325, PeerJ, 2018, doi:<a href=\"https://doi.org/10.7717/peerj.5325\">10.7717/peerj.5325</a>.","chicago":"Bertl, Johanna, Harald Ringbauer, and Michaël Blum. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” <i>PeerJ</i>. PeerJ, 2018. <a href=\"https://doi.org/10.7717/peerj.5325\">https://doi.org/10.7717/peerj.5325</a>.","ista":"Bertl J, Ringbauer H, Blum M. 2018. Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. 2018(10), e5325.","ama":"Bertl J, Ringbauer H, Blum M. Can secondary contact following range expansion be distinguished from barriers to gene flow? <i>PeerJ</i>. 2018;2018(10). doi:<a href=\"https://doi.org/10.7717/peerj.5325\">10.7717/peerj.5325</a>"},"has_accepted_license":"1","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publisher":"PeerJ","pmid":1,"oa":1,"doi":"10.7717/peerj.5325","acknowledgement":"Johanna Bertl was supported by the Vienna Graduate School of Population Genetics (Austrian Science Fund (FWF): W1225-B20) and worked on this project while employed at the Department of Statistics and Operations Research, University of Vienna, Austria. This article was developed in the framework of the Grenoble Alpes Data Institute, which is supported by the French National Research Agency under the “Investissments d’avenir” program (ANR-15-IDEX-02).","author":[{"full_name":"Bertl, Johanna","last_name":"Bertl","first_name":"Johanna"},{"last_name":"Ringbauer","full_name":"Ringbauer, Harald","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","first_name":"Harald","orcid":"0000-0002-4884-9682"},{"first_name":"Michaël","last_name":"Blum","full_name":"Blum, Michaël"}],"volume":2018,"department":[{"_id":"NiBa"}],"month":"10","title":"Can secondary contact following range expansion be distinguished from barriers to gene flow?","date_created":"2018-12-11T11:44:16Z","oa_version":"Published Version","publication_status":"published","publist_id":"8022","file":[{"file_name":"2018_PeerJ_Bertl.pdf","checksum":"3334886c4b39678db4c4b74299ca14ba","file_id":"5692","date_updated":"2020-07-14T12:46:06Z","relation":"main_file","creator":"dernst","access_level":"open_access","file_size":1328344,"date_created":"2018-12-17T10:46:06Z","content_type":"application/pdf"}]},{"citation":{"ama":"Clarke EM, Henzinger TA, Veith H, Bloem R. <i>Handbook of Model Checking</i>. 1st ed. Cham: Springer Nature; 2018. doi:<a href=\"https://doi.org/10.1007/978-3-319-10575-8\">10.1007/978-3-319-10575-8</a>","ista":"Clarke EM, Henzinger TA, Veith H, Bloem R. 2018. Handbook of Model Checking 1st ed., Cham: Springer Nature, XLVIII, 1212p.","chicago":"Clarke, Edmund M., Thomas A Henzinger, Helmut Veith, and Roderick Bloem. <i>Handbook of Model Checking</i>. 1st ed. Cham: Springer Nature, 2018. <a href=\"https://doi.org/10.1007/978-3-319-10575-8\">https://doi.org/10.1007/978-3-319-10575-8</a>.","mla":"Clarke, Edmund M., et al. <i>Handbook of Model Checking</i>. 1st ed., Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1007/978-3-319-10575-8\">10.1007/978-3-319-10575-8</a>.","short":"E.M. Clarke, T.A. Henzinger, H. Veith, R. Bloem, Handbook of Model Checking, 1st ed., Springer Nature, Cham, 2018.","ieee":"E. M. Clarke, T. A. Henzinger, H. Veith, and R. Bloem, <i>Handbook of Model Checking</i>, 1st ed. Cham: Springer Nature, 2018.","apa":"Clarke, E. M., Henzinger, T. A., Veith, H., &#38; Bloem, R. (2018). <i>Handbook of Model Checking</i> (1st ed.). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-10575-8\">https://doi.org/10.1007/978-3-319-10575-8</a>"},"day":"08","edition":"1","_id":"3300","abstract":[{"lang":"eng","text":"This book first explores the origins of this idea, grounded in theoretical work on temporal logic and automata. The editors and authors are among the world's leading researchers in this domain, and they contributed 32 chapters representing a thorough view of the development and application of the technique. Topics covered include binary decision diagrams, symbolic model checking, satisfiability modulo theories, partial-order reduction, abstraction, interpolation, concurrency, security protocols, games, probabilistic model checking, and process algebra, and chapters on the transfer of theory to industrial practice, property specification languages for hardware, and verification of real-time systems and hybrid systems.\r\n\r\nThe book will be valuable for researchers and graduate students engaged with the development of formal methods and verification tools."}],"language":[{"iso":"eng"}],"quality_controlled":"1","publication_status":"published","publist_id":"3340","type":"book","title":"Handbook of Model Checking","date_created":"2018-12-11T12:02:32Z","date_published":"2018-06-08T00:00:00Z","oa_version":"None","place":"Cham","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"isbn":["978-3-319-10574-1"],"eisbn":["978-3-319-10575-8"]},"year":"2018","author":[{"first_name":"Edmund M.","last_name":"Clarke","full_name":"Clarke, Edmund M."},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"full_name":"Veith, Helmut","last_name":"Veith","first_name":"Helmut"},{"last_name":"Bloem","full_name":"Bloem, Roderick","first_name":"Roderick"}],"date_updated":"2021-12-21T10:49:36Z","month":"06","department":[{"_id":"ToHe"}],"doi":"10.1007/978-3-319-10575-8","scopus_import":"1","article_processing_charge":"No","page":"XLVIII, 1212","status":"public","publisher":"Springer Nature"},{"conference":{"location":"Delft, Netherlands","end_date":"2018-06-29","start_date":"2018-06-24","name":"ICAPS: International Conference on Automated Planning and Scheduling"},"publication_status":"published","publist_id":"8021","oa_version":"Preprint","date_created":"2018-12-11T11:44:16Z","title":"Sensor synthesis for POMDPs with reachability objectives","arxiv":1,"month":"06","department":[{"_id":"KrCh"}],"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"volume":2018,"author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Chemlík","full_name":"Chemlík, Martin","first_name":"Martin"},{"last_name":"Topcu","full_name":"Topcu, Ufuk","first_name":"Ufuk"}],"oa":1,"doi":"10.1609/icaps.v28i1.13875","publisher":"AAAI Press","article_processing_charge":"No","citation":{"apa":"Chatterjee, K., Chemlík, M., &#38; Topcu, U. (2018). Sensor synthesis for POMDPs with reachability objectives. In <i>28th International Conference on Automated Planning and Scheduling</i> (Vol. 2018, pp. 47–55). Delft, Netherlands: AAAI Press. <a href=\"https://doi.org/10.1609/icaps.v28i1.13875\">https://doi.org/10.1609/icaps.v28i1.13875</a>","short":"K. Chatterjee, M. Chemlík, U. Topcu, in:, 28th International Conference on Automated Planning and Scheduling, AAAI Press, 2018, pp. 47–55.","ieee":"K. Chatterjee, M. Chemlík, and U. Topcu, “Sensor synthesis for POMDPs with reachability objectives,” in <i>28th International Conference on Automated Planning and Scheduling</i>, Delft, Netherlands, 2018, vol. 2018, pp. 47–55.","mla":"Chatterjee, Krishnendu, et al. “Sensor Synthesis for POMDPs with Reachability Objectives.” <i>28th International Conference on Automated Planning and Scheduling</i>, vol. 2018, AAAI Press, 2018, pp. 47–55, doi:<a href=\"https://doi.org/10.1609/icaps.v28i1.13875\">10.1609/icaps.v28i1.13875</a>.","chicago":"Chatterjee, Krishnendu, Martin Chemlík, and Ufuk Topcu. “Sensor Synthesis for POMDPs with Reachability Objectives.” In <i>28th International Conference on Automated Planning and Scheduling</i>, 2018:47–55. AAAI Press, 2018. <a href=\"https://doi.org/10.1609/icaps.v28i1.13875\">https://doi.org/10.1609/icaps.v28i1.13875</a>.","ista":"Chatterjee K, Chemlík M, Topcu U. 2018. Sensor synthesis for POMDPs with reachability objectives. 28th International Conference on Automated Planning and Scheduling. ICAPS: International Conference on Automated Planning and Scheduling vol. 2018, 47–55.","ama":"Chatterjee K, Chemlík M, Topcu U. Sensor synthesis for POMDPs with reachability objectives. In: <i>28th International Conference on Automated Planning and Scheduling</i>. Vol 2018. AAAI Press; 2018:47-55. doi:<a href=\"https://doi.org/10.1609/icaps.v28i1.13875\">10.1609/icaps.v28i1.13875</a>"},"day":"01","quality_controlled":"1","type":"conference","external_id":{"arxiv":["1710.00675"],"isi":["000492986200006"]},"_id":"34","abstract":[{"lang":"eng","text":"Partially observable Markov decision processes (POMDPs) are widely used in probabilistic planning problems in which an agent interacts with an environment using noisy and imprecise sensors. We study a setting in which the sensors are only partially defined and the goal is to synthesize “weakest” additional sensors, such that in the resulting POMDP, there is a small-memory policy for the agent that almost-surely (with probability 1) satisfies a reachability objective. We show that the problem is NP-complete, and present a symbolic algorithm by encoding the problem into SAT instances. We illustrate trade-offs between the amount of memory of the policy and the number of additional sensors on a simple example. We have implemented our approach and consider three classical POMDP examples from the literature, and show that in all the examples the number of sensors can be significantly decreased (as compared to the existing solutions in the literature) without increasing the complexity of the policies."}],"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1710.00675"}],"date_published":"2018-06-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","intvolume":"      2018","isi":1,"publication":"28th International Conference on Automated Planning and Scheduling","date_updated":"2025-04-15T07:23:29Z","scopus_import":"1","ec_funded":1,"page":"47 - 55","status":"public"},{"volume":37,"author":[{"full_name":"Jeschke, Stefan","last_name":"Jeschke","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan"},{"id":"486A5A46-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas","last_name":"Skrivan","full_name":"Skrivan, Tomas"},{"first_name":"Matthias","full_name":"Mueller Fischer, Matthias","last_name":"Mueller Fischer"},{"full_name":"Chentanez, Nuttapong","last_name":"Chentanez","first_name":"Nuttapong"},{"first_name":"Miles","full_name":"Macklin, Miles","last_name":"Macklin"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","full_name":"Wojtan, Christopher J"}],"project":[{"name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"}],"department":[{"_id":"ChWo"}],"month":"07","doi":"10.1145/3197517.3201336","oa":1,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-water-simulation-captures-small-details-even-in-large-scenes/","description":"News on IST Homepage","relation":"press_release"}]},"tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"article_processing_charge":"No","publisher":"ACM","file":[{"file_size":22185016,"date_created":"2018-12-18T09:59:23Z","content_type":"application/pdf","access_level":"open_access","creator":"dernst","date_updated":"2020-07-14T12:44:45Z","file_id":"5744","relation":"main_file","file_name":"2018_ACM_Jeschke.pdf","checksum":"db75ebabe2ec432bf41389e614d6ef62"}],"publist_id":"7789","publication_status":"published","alternative_title":["SIGGRAPH"],"date_created":"2018-12-11T11:44:48Z","title":"Water surface wavelets","oa_version":"Published Version","date_updated":"2024-10-22T09:58:20Z","publication":"ACM Transactions on Graphics","acknowledged_ssus":[{"_id":"ScienComp"}],"isi":1,"file_date_updated":"2020-07-14T12:44:45Z","ec_funded":1,"issue":"4","scopus_import":"1","status":"public","has_accepted_license":"1","day":"30","citation":{"chicago":"Jeschke, Stefan, Tomas Skrivan, Matthias Mueller Fischer, Nuttapong Chentanez, Miles Macklin, and Chris Wojtan. “Water Surface Wavelets.” <i>ACM Transactions on Graphics</i>. ACM, 2018. <a href=\"https://doi.org/10.1145/3197517.3201336\">https://doi.org/10.1145/3197517.3201336</a>.","ama":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. Water surface wavelets. <i>ACM Transactions on Graphics</i>. 2018;37(4). doi:<a href=\"https://doi.org/10.1145/3197517.3201336\">10.1145/3197517.3201336</a>","ista":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. 2018. Water surface wavelets. ACM Transactions on Graphics. 37(4), 94.","apa":"Jeschke, S., Skrivan, T., Mueller Fischer, M., Chentanez, N., Macklin, M., &#38; Wojtan, C. (2018). Water surface wavelets. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/3197517.3201336\">https://doi.org/10.1145/3197517.3201336</a>","mla":"Jeschke, Stefan, et al. “Water Surface Wavelets.” <i>ACM Transactions on Graphics</i>, vol. 37, no. 4, 94, ACM, 2018, doi:<a href=\"https://doi.org/10.1145/3197517.3201336\">10.1145/3197517.3201336</a>.","short":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, C. Wojtan, ACM Transactions on Graphics 37 (2018).","ieee":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, and C. Wojtan, “Water surface wavelets,” <i>ACM Transactions on Graphics</i>, vol. 37, no. 4. ACM, 2018."},"abstract":[{"text":"The current state of the art in real-time two-dimensional water wave simulation requires developers to choose between efficient Fourier-based methods, which lack interactions with moving obstacles, and finite-difference or finite element methods, which handle environmental interactions but are significantly more expensive. This paper attempts to bridge this long-standing gap between complexity and performance, by proposing a new wave simulation method that can faithfully simulate wave interactions with moving obstacles in real time while simultaneously preserving minute details and accommodating very large simulation domains.\r\n\r\nPrevious methods for simulating 2D water waves directly compute the change in height of the water surface, a strategy which imposes limitations based on the CFL condition (fast moving waves require small time steps) and Nyquist's limit (small wave details require closely-spaced simulation variables). This paper proposes a novel wavelet transformation that discretizes the liquid motion in terms of amplitude-like functions that vary over space, frequency, and direction, effectively generalizing Fourier-based methods to handle local interactions. Because these new variables change much more slowly over space than the original water height function, our change of variables drastically reduces the limitations of the CFL condition and Nyquist limit, allowing us to simulate highly detailed water waves at very large visual resolutions. Our discretization is amenable to fast summation and easy to parallelize. We also present basic extensions like pre-computed wave paths and two-way solid fluid coupling. Finally, we argue that our discretization provides a convenient set of variables for artistic manipulation, which we illustrate with a novel wave-painting interface.","lang":"eng"}],"_id":"134","language":[{"iso":"eng"}],"external_id":{"isi":["000448185000055"]},"type":"journal_article","quality_controlled":"1","date_published":"2018-07-30T00:00:00Z","intvolume":"        37","article_number":"94","year":"2018","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","ddc":["000"]},{"publisher":"Wiley","article_processing_charge":"No","oa":1,"doi":"10.1111/cgf.13351","article_type":"original","project":[{"name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"department":[{"_id":"ChWo"}],"month":"05","volume":37,"author":[{"full_name":"Sato, Takahiro","last_name":"Sato","first_name":"Takahiro"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","full_name":"Wojtan, Christopher J"},{"first_name":"Nils","full_name":"Thuerey, Nils","last_name":"Thuerey"},{"full_name":"Igarashi, Takeo","last_name":"Igarashi","first_name":"Takeo"},{"first_name":"Ryoichi","full_name":"Ando, Ryoichi","last_name":"Ando"}],"publication_identifier":{"issn":["0167-7055"]},"oa_version":"Submitted Version","date_created":"2018-12-11T11:44:49Z","title":"Extended narrow band FLIP for liquid simulations","alternative_title":["Eurographics"],"publication_status":"published","file":[{"file_name":"exnbflip.pdf","checksum":"8edb90da8a72395eb5d970580e0925b6","creator":"wojtan","date_updated":"2020-10-08T08:38:23Z","file_id":"8627","relation":"main_file","access_level":"open_access","date_created":"2020-10-08T08:38:23Z","file_size":54309947,"success":1,"content_type":"application/pdf"}],"status":"public","page":"169 - 177","scopus_import":"1","issue":"2","ec_funded":1,"file_date_updated":"2020-10-08T08:38:23Z","isi":1,"publication":"Computer Graphics Forum","date_updated":"2024-10-22T09:58:20Z","year":"2018","ddc":["006"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"        37","date_published":"2018-05-22T00:00:00Z","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"_id":"135","abstract":[{"lang":"eng","text":"The Fluid Implicit Particle method (FLIP) reduces numerical dissipation by combining particles with grids. To improve performance, the subsequent narrow band FLIP method (NB‐FLIP) uses a FLIP‐based fluid simulation only near the liquid surface and a traditional grid‐based fluid simulation away from the surface. This spatially‐limited FLIP simulation significantly reduces the number of particles and alleviates a computational bottleneck. In this paper, we extend the NB‐FLIP idea even further, by allowing a simulation to transition between a FLIP‐like fluid simulation and a grid‐based simulation in arbitrary locations, not just near the surface. This approach leads to even more savings in memory and computation, because we can concentrate the particles only in areas where they are needed. More importantly, this new method allows us to seamlessly transition to smooth implicit surface geometry wherever the particle‐based simulation is unnecessary. Consequently, our method leads to a practical algorithm for avoiding the noisy surface artifacts associated with particle‐based liquid simulations, while simultaneously maintaining the benefits of a FLIP simulation in regions of dynamic motion."}],"external_id":{"isi":["000434085600016"]},"has_accepted_license":"1","citation":{"mla":"Sato, Takahiro, et al. “Extended Narrow Band FLIP for Liquid Simulations.” <i>Computer Graphics Forum</i>, vol. 37, no. 2, Wiley, 2018, pp. 169–77, doi:<a href=\"https://doi.org/10.1111/cgf.13351\">10.1111/cgf.13351</a>.","short":"T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, Computer Graphics Forum 37 (2018) 169–177.","ieee":"T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, and R. Ando, “Extended narrow band FLIP for liquid simulations,” <i>Computer Graphics Forum</i>, vol. 37, no. 2. Wiley, pp. 169–177, 2018.","apa":"Sato, T., Wojtan, C., Thuerey, N., Igarashi, T., &#38; Ando, R. (2018). Extended narrow band FLIP for liquid simulations. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.13351\">https://doi.org/10.1111/cgf.13351</a>","ama":"Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. Extended narrow band FLIP for liquid simulations. <i>Computer Graphics Forum</i>. 2018;37(2):169-177. doi:<a href=\"https://doi.org/10.1111/cgf.13351\">10.1111/cgf.13351</a>","ista":"Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. 2018. Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. 37(2), 169–177.","chicago":"Sato, Takahiro, Chris Wojtan, Nils Thuerey, Takeo Igarashi, and Ryoichi Ando. “Extended Narrow Band FLIP for Liquid Simulations.” <i>Computer Graphics Forum</i>. Wiley, 2018. <a href=\"https://doi.org/10.1111/cgf.13351\">https://doi.org/10.1111/cgf.13351</a>."},"day":"22"},{"issue":"2","scopus_import":"1","status":"public","publication":"Physical Review E","date_updated":"2023-10-10T13:29:10Z","isi":1,"date_published":"2018-08-13T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1808.02088","open_access":"1"}],"intvolume":"        98","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"13","citation":{"apa":"Suri, B., Tithof, J., Grigoriev, R., &#38; Schatz, M. (2018). Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.98.023105\">https://doi.org/10.1103/PhysRevE.98.023105</a>","mla":"Suri, Balachandra, et al. “Unstable Equilibria and Invariant Manifolds in Quasi-Two-Dimensional Kolmogorov-like Flow.” <i>Physical Review E</i>, vol. 98, no. 2, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevE.98.023105\">10.1103/PhysRevE.98.023105</a>.","ieee":"B. Suri, J. Tithof, R. Grigoriev, and M. Schatz, “Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow,” <i>Physical Review E</i>, vol. 98, no. 2. American Physical Society, 2018.","short":"B. Suri, J. Tithof, R. Grigoriev, M. Schatz, Physical Review E 98 (2018).","chicago":"Suri, Balachandra, Jeffrey Tithof, Roman Grigoriev, and Michael Schatz. “Unstable Equilibria and Invariant Manifolds in Quasi-Two-Dimensional Kolmogorov-like Flow.” <i>Physical Review E</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevE.98.023105\">https://doi.org/10.1103/PhysRevE.98.023105</a>.","ama":"Suri B, Tithof J, Grigoriev R, Schatz M. Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. <i>Physical Review E</i>. 2018;98(2). doi:<a href=\"https://doi.org/10.1103/PhysRevE.98.023105\">10.1103/PhysRevE.98.023105</a>","ista":"Suri B, Tithof J, Grigoriev R, Schatz M. 2018. Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical Review E. 98(2)."},"language":[{"iso":"eng"}],"_id":"136","abstract":[{"lang":"eng","text":"Recent studies suggest that unstable, nonchaotic solutions of the Navier-Stokes equation may provide deep insights into fluid turbulence. In this article, we present a combined experimental and numerical study exploring the dynamical role of unstable equilibrium solutions and their invariant manifolds in a weakly turbulent, electromagnetically driven, shallow fluid layer. Identifying instants when turbulent evolution slows down, we compute 31 unstable equilibria of a realistic two-dimensional model of the flow. We establish the dynamical relevance of these unstable equilibria by showing that they are closely visited by the turbulent flow. We also establish the dynamical relevance of unstable manifolds by verifying that they are shadowed by turbulent trajectories departing from the neighborhoods of unstable equilibria over large distances in state space."}],"external_id":{"arxiv":["1808.02088"],"isi":["000441466800010"]},"type":"journal_article","quality_controlled":"1","article_processing_charge":"No","publisher":"American Physical Society","volume":98,"author":[{"id":"47A5E706-F248-11E8-B48F-1D18A9856A87","first_name":"Balachandra","last_name":"Suri","full_name":"Suri, Balachandra"},{"first_name":"Jeffrey","full_name":"Tithof, Jeffrey","last_name":"Tithof"},{"full_name":"Grigoriev, Roman","last_name":"Grigoriev","first_name":"Roman"},{"last_name":"Schatz","full_name":"Schatz, Michael","first_name":"Michael"}],"month":"08","department":[{"_id":"BjHo"}],"doi":"10.1103/PhysRevE.98.023105","oa":1,"title":"Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow","date_created":"2018-12-11T11:44:49Z","oa_version":"Submitted Version","arxiv":1,"publication_status":"published"},{"publication":"Nature Chemical Biology","date_updated":"2025-04-15T06:43:11Z","isi":1,"issue":"9","scopus_import":"1","status":"public","page":"861 - 869","day":"30","citation":{"short":"W. Zhang, M. Herde, J. Mitchell, J. Whitfield, A. Wulff, V. Vongsouthi, I. Sanchez-Romero, P. Gulakova, D. Minge, B. Breithausen, S. Schoch, H.L. Janovjak, C. Jackson, C. Henneberger, Nature Chemical Biology 14 (2018) 861–869.","ieee":"W. Zhang <i>et al.</i>, “Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS,” <i>Nature Chemical Biology</i>, vol. 14, no. 9. Nature Publishing Group, pp. 861–869, 2018.","mla":"Zhang, William, et al. “Monitoring Hippocampal Glycine with the Computationally Designed Optical Sensor GlyFS.” <i>Nature Chemical Biology</i>, vol. 14, no. 9, Nature Publishing Group, 2018, pp. 861–69, doi:<a href=\"https://doi.org/10.1038/s41589-018-0108-2\">10.1038/s41589-018-0108-2</a>.","apa":"Zhang, W., Herde, M., Mitchell, J., Whitfield, J., Wulff, A., Vongsouthi, V., … Henneberger, C. (2018). Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. <i>Nature Chemical Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41589-018-0108-2\">https://doi.org/10.1038/s41589-018-0108-2</a>","ista":"Zhang W, Herde M, Mitchell J, Whitfield J, Wulff A, Vongsouthi V, Sanchez-Romero I, Gulakova P, Minge D, Breithausen B, Schoch S, Janovjak HL, Jackson C, Henneberger C. 2018. Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. 14(9), 861–869.","ama":"Zhang W, Herde M, Mitchell J, et al. Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. <i>Nature Chemical Biology</i>. 2018;14(9):861-869. doi:<a href=\"https://doi.org/10.1038/s41589-018-0108-2\">10.1038/s41589-018-0108-2</a>","chicago":"Zhang, William, Michel Herde, Joshua Mitchell, Jason Whitfield, Andreas Wulff, Vanessa Vongsouthi, Inmaculada Sanchez-Romero, et al. “Monitoring Hippocampal Glycine with the Computationally Designed Optical Sensor GlyFS.” <i>Nature Chemical Biology</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41589-018-0108-2\">https://doi.org/10.1038/s41589-018-0108-2</a>."},"external_id":{"pmid":["30061718 "],"isi":["000442174500013"]},"_id":"137","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Fluorescent sensors are an essential part of the experimental toolbox of the life sciences, where they are used ubiquitously to visualize intra- and extracellular signaling. In the brain, optical neurotransmitter sensors can shed light on temporal and spatial aspects of signal transmission by directly observing, for instance, neurotransmitter release and spread. Here we report the development and application of the first optical sensor for the amino acid glycine, which is both an inhibitory neurotransmitter and a co-agonist of the N-methyl-d-aspartate receptors (NMDARs) involved in synaptic plasticity. Computational design of a glycine-specific binding protein allowed us to produce the optical glycine FRET sensor (GlyFS), which can be used with single and two-photon excitation fluorescence microscopy. We took advantage of this newly developed sensor to test predictions about the uneven spatial distribution of glycine in extracellular space and to demonstrate that extracellular glycine levels are controlled by plasticity-inducing stimuli."}],"quality_controlled":"1","type":"journal_article","date_published":"2018-07-30T00:00:00Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30061718","open_access":"1"}],"intvolume":"        14","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2018","volume":14,"author":[{"first_name":"William","last_name":"Zhang","full_name":"Zhang, William"},{"full_name":"Herde, Michel","last_name":"Herde","first_name":"Michel"},{"full_name":"Mitchell, Joshua","last_name":"Mitchell","first_name":"Joshua"},{"full_name":"Whitfield, Jason","last_name":"Whitfield","first_name":"Jason"},{"full_name":"Wulff, Andreas","last_name":"Wulff","first_name":"Andreas"},{"full_name":"Vongsouthi, Vanessa","last_name":"Vongsouthi","first_name":"Vanessa"},{"last_name":"Sanchez Romero","full_name":"Sanchez Romero, Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","first_name":"Inmaculada"},{"full_name":"Gulakova, Polina","last_name":"Gulakova","first_name":"Polina"},{"first_name":"Daniel","last_name":"Minge","full_name":"Minge, Daniel"},{"first_name":"Björn","full_name":"Breithausen, Björn","last_name":"Breithausen"},{"last_name":"Schoch","full_name":"Schoch, Susanne","first_name":"Susanne"},{"last_name":"Janovjak","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jackson, Colin","last_name":"Jackson","first_name":"Colin"},{"full_name":"Henneberger, Christian","last_name":"Henneberger","first_name":"Christian"}],"month":"07","department":[{"_id":"HaJa"}],"article_type":"original","project":[{"name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors","_id":"255BFFFA-B435-11E9-9278-68D0E5697425","grant_number":"RGY0084/2012"}],"oa":1,"doi":"10.1038/s41589-018-0108-2","pmid":1,"article_processing_charge":"No","publisher":"Nature Publishing Group","publication_status":"published","publist_id":"7786","title":"Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS","date_created":"2018-12-11T11:44:49Z","oa_version":"Submitted Version"}]