[{"date_updated":"2025-03-31T16:01:18Z","type":"journal_article","abstract":[{"text":"We discuss thermodynamic properties of harmonically trapped\r\nimperfect quantum gases. The spatial inhomogeneity of these systems imposes\r\na redefinition of the mean-field interparticle potential energy as compared\r\nto the homogeneous case. In our approach, it takes the form a\r\n2N2 ωd, where\r\nN is the number of particles, ω—the harmonic trap frequency, d—system’s\r\ndimensionality, and a is a parameter characterizing the interparticle interaction.\r\nWe provide arguments that this model corresponds to the limiting case of\r\na long-ranged interparticle potential of vanishingly small amplitude. This\r\nconclusion is drawn from a computation similar to the well-known Kac scaling\r\nprocedure, which is presented here in a form adapted to the case of an isotropic\r\nharmonic trap. We show that within the model, the imperfect gas of trapped\r\nrepulsive bosons undergoes the Bose–Einstein condensation provided d > 1.\r\nThe main result of our analysis is that in d = 1 the gas of attractive imperfect\r\nfermions with a = −aF < 0 is thermodynamically equivalent to the gas of\r\nrepulsive bosons with a = aB > 0 provided the parameters aF and aB fulfill\r\nthe relation aB + aF = \u001f. This result supplements similar recent conclusion\r\nabout thermodynamic equivalence of two-dimensional (2D) uniform imperfect\r\nrepulsive Bose and attractive Fermi gases.","lang":"eng"}],"publication_identifier":{"eissn":["1742-5468"]},"date_created":"2019-09-01T22:00:59Z","publication":"Journal of Statistical Mechanics: Theory and Experiment","oa":1,"title":"Thermodynamics of inhomogeneous imperfect quantum gases in harmonic traps","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1810.02209"}],"status":"public","citation":{"ista":"Mysliwy K, Napiórkowski M. 2019. Thermodynamics of inhomogeneous imperfect quantum gases in harmonic traps. Journal of Statistical Mechanics: Theory and Experiment. 2019(6), 063101.","mla":"Mysliwy, Krzysztof, and Marek Napiórkowski. “Thermodynamics of Inhomogeneous Imperfect Quantum Gases in Harmonic Traps.” <i>Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2019, no. 6, 063101, IOP Publishing, 2019, doi:<a href=\"https://doi.org/10.1088/1742-5468/ab190d\">10.1088/1742-5468/ab190d</a>.","chicago":"Mysliwy, Krzysztof, and Marek Napiórkowski. “Thermodynamics of Inhomogeneous Imperfect Quantum Gases in Harmonic Traps.” <i>Journal of Statistical Mechanics: Theory and Experiment</i>. IOP Publishing, 2019. <a href=\"https://doi.org/10.1088/1742-5468/ab190d\">https://doi.org/10.1088/1742-5468/ab190d</a>.","short":"K. Mysliwy, M. Napiórkowski, Journal of Statistical Mechanics: Theory and Experiment 2019 (2019).","ama":"Mysliwy K, Napiórkowski M. Thermodynamics of inhomogeneous imperfect quantum gases in harmonic traps. <i>Journal of Statistical Mechanics: Theory and Experiment</i>. 2019;2019(6). doi:<a href=\"https://doi.org/10.1088/1742-5468/ab190d\">10.1088/1742-5468/ab190d</a>","apa":"Mysliwy, K., &#38; Napiórkowski, M. (2019). Thermodynamics of inhomogeneous imperfect quantum gases in harmonic traps. <i>Journal of Statistical Mechanics: Theory and Experiment</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1742-5468/ab190d\">https://doi.org/10.1088/1742-5468/ab190d</a>","ieee":"K. Mysliwy and M. Napiórkowski, “Thermodynamics of inhomogeneous imperfect quantum gases in harmonic traps,” <i>Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2019, no. 6. IOP Publishing, 2019."},"arxiv":1,"language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"Preprint","month":"06","doi":"10.1088/1742-5468/ab190d","day":"13","ec_funded":1,"publication_status":"published","department":[{"_id":"RoSe"}],"volume":2019,"intvolume":"      2019","isi":1,"author":[{"id":"316457FC-F248-11E8-B48F-1D18A9856A87","full_name":"Mysliwy, Krzysztof","last_name":"Mysliwy","first_name":"Krzysztof"},{"first_name":"Marek","last_name":"Napiórkowski","full_name":"Napiórkowski, Marek"}],"_id":"6840","external_id":{"isi":["000471650100001"],"arxiv":["1810.02209"]},"issue":"6","article_number":"063101","year":"2019","publisher":"IOP Publishing","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","date_published":"2019-06-13T00:00:00Z"},{"department":[{"_id":"LaEr"}],"publication_status":"published","doi":"10.1016/j.jmaa.2019.123435","day":"15","ec_funded":1,"month":"12","language":[{"iso":"eng"}],"oa_version":"Preprint","quality_controlled":"1","arxiv":1,"citation":{"short":"G.P. Gehér, T. Titkos, D. Virosztek, Journal of Mathematical Analysis and Applications 480 (2019).","mla":"Gehér, György Pál, et al. “On Isometric Embeddings of Wasserstein Spaces – the Discrete Case.” <i>Journal of Mathematical Analysis and Applications</i>, vol. 480, no. 2, 123435, Elsevier, 2019, doi:<a href=\"https://doi.org/10.1016/j.jmaa.2019.123435\">10.1016/j.jmaa.2019.123435</a>.","chicago":"Gehér, György Pál, Tamás Titkos, and Daniel Virosztek. “On Isometric Embeddings of Wasserstein Spaces – the Discrete Case.” <i>Journal of Mathematical Analysis and Applications</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.jmaa.2019.123435\">https://doi.org/10.1016/j.jmaa.2019.123435</a>.","ista":"Gehér GP, Titkos T, Virosztek D. 2019. On isometric embeddings of Wasserstein spaces – the discrete case. Journal of Mathematical Analysis and Applications. 480(2), 123435.","ieee":"G. P. Gehér, T. Titkos, and D. Virosztek, “On isometric embeddings of Wasserstein spaces – the discrete case,” <i>Journal of Mathematical Analysis and Applications</i>, vol. 480, no. 2. Elsevier, 2019.","ama":"Gehér GP, Titkos T, Virosztek D. On isometric embeddings of Wasserstein spaces – the discrete case. <i>Journal of Mathematical Analysis and Applications</i>. 2019;480(2). doi:<a href=\"https://doi.org/10.1016/j.jmaa.2019.123435\">10.1016/j.jmaa.2019.123435</a>","apa":"Gehér, G. P., Titkos, T., &#38; Virosztek, D. (2019). On isometric embeddings of Wasserstein spaces – the discrete case. <i>Journal of Mathematical Analysis and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmaa.2019.123435\">https://doi.org/10.1016/j.jmaa.2019.123435</a>"},"main_file_link":[{"url":"https://arxiv.org/abs/1809.01101","open_access":"1"}],"status":"public","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"On isometric embeddings of Wasserstein spaces – the discrete case","article_type":"original","oa":1,"publication":"Journal of Mathematical Analysis and Applications","date_created":"2019-09-01T22:01:01Z","publication_identifier":{"issn":["0022-247X"],"eissn":["1096-0813"]},"abstract":[{"text":"The aim of this short paper is to offer a complete characterization of all (not necessarily surjective) isometric embeddings of the Wasserstein space Wp(X), where S is a countable discrete metric space and 0<p<∞ is any parameter value. Roughly speaking, we will prove that any isometric embedding can be described by a special kind of X×(0,1]-indexed family of nonnegative finite measures. Our result implies that a typical non-surjective isometric embedding of Wp(X) splits mass and does not preserve the shape of measures. In order to stress that the lack of surjectivity is what makes things challenging, we will prove alternatively that Wp(X) is isometrically rigid for all 0<p<∞.","lang":"eng"}],"type":"journal_article","date_updated":"2025-07-10T11:53:55Z","date_published":"2019-12-15T00:00:00Z","article_processing_charge":"No","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"publisher":"Elsevier","year":"2019","article_number":"123435","_id":"6843","external_id":{"arxiv":["1809.01101"],"isi":["000486563900031"]},"issue":"2","author":[{"full_name":"Gehér, György Pál","last_name":"Gehér","first_name":"György Pál"},{"first_name":"Tamás","last_name":"Titkos","full_name":"Titkos, Tamás"},{"id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","full_name":"Virosztek, Daniel","last_name":"Virosztek","first_name":"Daniel","orcid":"0000-0003-1109-5511"}],"isi":1,"intvolume":"       480","volume":480},{"ddc":["570"],"project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"publisher":"Wiley","year":"2019","date_published":"2019-09-01T00:00:00Z","page":"686-696","article_processing_charge":"No","intvolume":"       235","volume":235,"_id":"6844","issue":"3","external_id":{"isi":["000482426800017"]},"author":[{"first_name":"Noemi","full_name":"Picco, Noemi","last_name":"Picco"},{"orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rodarte","full_name":"Rodarte, Julio","id":"3C70A038-F248-11E8-B48F-1D18A9856A87","first_name":"Julio"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen","last_name":"Streicher","first_name":"Carmen"},{"first_name":"Zoltán","full_name":"Molnár, Zoltán","last_name":"Molnár"},{"last_name":"Maini","full_name":"Maini, Philip K.","first_name":"Philip K."},{"first_name":"Thomas E.","full_name":"Woolley, Thomas E.","last_name":"Woolley"}],"isi":1,"tmp":{"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","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"file":[{"creator":"dernst","file_size":1192994,"date_updated":"2020-07-14T12:47:42Z","file_name":"2019_JournalAnatomy_Picco.pdf","file_id":"6845","date_created":"2019-09-02T12:05:18Z","checksum":"160f960844b204057f20896e0e1f8ee7","relation":"main_file","content_type":"application/pdf","access_level":"open_access"}],"citation":{"chicago":"Picco, Noemi, Simon Hippenmeyer, Julio Rodarte, Carmen Streicher, Zoltán Molnár, Philip K. Maini, and Thomas E. Woolley. “A Mathematical Insight into Cell Labelling Experiments for Clonal Analysis.” <i>Journal of Anatomy</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/joa.13001\">https://doi.org/10.1111/joa.13001</a>.","short":"N. Picco, S. Hippenmeyer, J. Rodarte, C. Streicher, Z. Molnár, P.K. Maini, T.E. Woolley, Journal of Anatomy 235 (2019) 686–696.","mla":"Picco, Noemi, et al. “A Mathematical Insight into Cell Labelling Experiments for Clonal Analysis.” <i>Journal of Anatomy</i>, vol. 235, no. 3, Wiley, 2019, pp. 686–96, doi:<a href=\"https://doi.org/10.1111/joa.13001\">10.1111/joa.13001</a>.","ista":"Picco N, Hippenmeyer S, Rodarte J, Streicher C, Molnár Z, Maini PK, Woolley TE. 2019. A mathematical insight into cell labelling experiments for clonal analysis. Journal of Anatomy. 235(3), 686–696.","ieee":"N. Picco <i>et al.</i>, “A mathematical insight into cell labelling experiments for clonal analysis,” <i>Journal of Anatomy</i>, vol. 235, no. 3. Wiley, pp. 686–696, 2019.","apa":"Picco, N., Hippenmeyer, S., Rodarte, J., Streicher, C., Molnár, Z., Maini, P. K., &#38; Woolley, T. E. (2019). A mathematical insight into cell labelling experiments for clonal analysis. <i>Journal of Anatomy</i>. Wiley. <a href=\"https://doi.org/10.1111/joa.13001\">https://doi.org/10.1111/joa.13001</a>","ama":"Picco N, Hippenmeyer S, Rodarte J, et al. A mathematical insight into cell labelling experiments for clonal analysis. <i>Journal of Anatomy</i>. 2019;235(3):686-696. doi:<a href=\"https://doi.org/10.1111/joa.13001\">10.1111/joa.13001</a>"},"status":"public","scopus_import":"1","department":[{"_id":"SiHi"}],"publication_status":"published","doi":"10.1111/joa.13001","day":"01","ec_funded":1,"month":"09","language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"Published Version","publication":"Journal of Anatomy","date_created":"2019-09-02T11:57:28Z","publication_identifier":{"eissn":["1469-7580"],"issn":["0021-8782"]},"abstract":[{"lang":"eng","text":"Studying the progression of the proliferative and differentiative patterns of neural stem cells at the individual cell level is crucial to the understanding of cortex development and how the disruption of such patterns can lead to malformations and neurodevelopmental diseases. However, our understanding of the precise lineage progression programme at single-cell resolution is still incomplete due to the technical variations in lineage- tracing approaches. One of the key challenges involves developing a robust theoretical framework in which we can integrate experimental observations and introduce correction factors to obtain a reliable and representative description of the temporal modulation of proliferation and differentiation. In order to obtain more conclusive insights, we carry out virtual clonal analysis using mathematical modelling and compare our results against experimental data. Using a dataset obtained with Mosaic Analysis with Double Markers, we illustrate how the theoretical description can be exploited to interpret and reconcile the disparity between virtual and experimental results."}],"type":"journal_article","date_updated":"2025-04-14T07:43:05Z","file_date_updated":"2020-07-14T12:47:42Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"A mathematical insight into cell labelling experiments for clonal analysis","article_type":"original","oa":1,"has_accepted_license":"1"},{"pmid":1,"date_published":"2019-07-05T00:00:00Z","page":"461-493","article_processing_charge":"No","ddc":["576"],"publisher":"Annual Reviews","year":"2019","_id":"6855","external_id":{"pmid":["31283361"],"isi":["000485148400020"]},"author":[{"first_name":"Guy","last_name":"Sella","full_name":"Sella, Guy"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"isi":1,"intvolume":"        20","volume":20,"department":[{"_id":"NiBa"}],"publication_status":"published","doi":"10.1146/annurev-genom-083115-022316","day":"05","corr_author":"1","month":"07","language":[{"iso":"eng"}],"oa_version":"Published Version","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"ieee":"G. Sella and N. H. Barton, “Thinking about the evolution of complex traits in the era of genome-wide association studies,” <i>Annual Review of Genomics and Human Genetics</i>, vol. 20. Annual Reviews, pp. 461–493, 2019.","apa":"Sella, G., &#38; Barton, N. H. (2019). Thinking about the evolution of complex traits in the era of genome-wide association studies. <i>Annual Review of Genomics and Human Genetics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-genom-083115-022316\">https://doi.org/10.1146/annurev-genom-083115-022316</a>","ama":"Sella G, Barton NH. Thinking about the evolution of complex traits in the era of genome-wide association studies. <i>Annual Review of Genomics and Human Genetics</i>. 2019;20:461-493. doi:<a href=\"https://doi.org/10.1146/annurev-genom-083115-022316\">10.1146/annurev-genom-083115-022316</a>","mla":"Sella, Guy, and Nicholas H. Barton. “Thinking about the Evolution of Complex Traits in the Era of Genome-Wide Association Studies.” <i>Annual Review of Genomics and Human Genetics</i>, vol. 20, Annual Reviews, 2019, pp. 461–93, doi:<a href=\"https://doi.org/10.1146/annurev-genom-083115-022316\">10.1146/annurev-genom-083115-022316</a>.","chicago":"Sella, Guy, and Nicholas H Barton. “Thinking about the Evolution of Complex Traits in the Era of Genome-Wide Association Studies.” <i>Annual Review of Genomics and Human Genetics</i>. Annual Reviews, 2019. <a href=\"https://doi.org/10.1146/annurev-genom-083115-022316\">https://doi.org/10.1146/annurev-genom-083115-022316</a>.","short":"G. Sella, N.H. Barton, Annual Review of Genomics and Human Genetics 20 (2019) 461–493.","ista":"Sella G, Barton NH. 2019. Thinking about the evolution of complex traits in the era of genome-wide association studies. Annual Review of Genomics and Human Genetics. 20, 461–493."},"file":[{"access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"23d3978cf4739a89ce2c3e779f9305ca","date_created":"2019-09-09T07:22:12Z","file_id":"6862","file_name":"2019_AnnualReview_Sella.pdf","date_updated":"2020-07-14T12:47:42Z","file_size":411491,"creator":"dernst"}],"status":"public","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Thinking about the evolution of complex traits in the era of genome-wide association studies","oa":1,"has_accepted_license":"1","publication":"Annual Review of Genomics and Human Genetics","date_created":"2019-09-07T14:28:29Z","publication_identifier":{"eissn":["1545-293X"],"issn":["1527-8204"]},"abstract":[{"lang":"eng","text":"Many traits of interest are highly heritable and genetically complex, meaning that much of the variation they exhibit arises from differences at numerous loci in the genome. Complex traits and their evolution have been studied for more than a century, but only in the last decade have genome-wide association studies (GWASs) in humans begun to reveal their genetic basis. Here, we bring these threads of research together to ask how findings from GWASs can further our understanding of the processes that give rise to heritable variation in complex traits and of the genetic basis of complex trait evolution in response to changing selection pressures (i.e., of polygenic adaptation). Conversely, we ask how evolutionary thinking helps us to interpret findings from GWASs and informs related efforts of practical importance."}],"type":"journal_article","date_updated":"2024-10-09T20:58:59Z","file_date_updated":"2020-07-14T12:47:42Z"},{"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow","has_accepted_license":"1","oa":1,"abstract":[{"text":"Plant mating systems play a key role in structuring genetic variation both within and between species. In hybrid zones, the outcomes and dynamics of hybridization are usually interpreted as the balance between gene flow and selection against hybrids. Yet, mating systems can introduce selective forces that alter these expectations; with diverse outcomes for the level and direction of gene flow depending on variation in outcrossing and whether the mating systems of the species pair are the same or divergent. We present a survey of hybridization in 133 species pairs from 41 plant families and examine how patterns of hybridization vary with mating system. We examine if hybrid zone mode, level of gene flow, asymmetries in gene flow and the frequency of reproductive isolating barriers vary in relation to mating system/s of the species pair. We combine these results with a simulation model and examples from the literature to address two general themes: (i) the two‐way interaction between introgression and the evolution of reproductive systems, and (ii) how mating system can facilitate or restrict interspecific gene flow. We conclude that examining mating system with hybridization provides unique opportunities to understand divergence and the processes underlying reproductive isolation.","lang":"eng"}],"publication":"New Phytologist","date_created":"2019-09-07T14:35:40Z","publication_identifier":{"issn":["0028-646X"],"eissn":["1469-8137"]},"file_date_updated":"2020-07-14T12:47:42Z","type":"journal_article","date_updated":"2025-04-15T07:17:08Z","month":"11","department":[{"_id":"NiBa"}],"publication_status":"published","ec_funded":1,"doi":"10.1111/nph.16180","day":"01","oa_version":"Published Version","language":[{"iso":"eng"}],"quality_controlled":"1","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"short":"M. Pickup, N.H. Barton, Y. Brandvain, C. Fraisse, S. Yakimowski, T. Dixit, C. Lexer, E. Cereghetti, D. Field, New Phytologist 224 (2019) 1035–1047.","mla":"Pickup, Melinda, et al. “Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries to Gene Flow.” <i>New Phytologist</i>, vol. 224, no. 3, Wiley, 2019, pp. 1035–47, doi:<a href=\"https://doi.org/10.1111/nph.16180\">10.1111/nph.16180</a>.","chicago":"Pickup, Melinda, Nicholas H Barton, Yaniv Brandvain, Christelle Fraisse, Sarah Yakimowski, Tanmay Dixit, Christian Lexer, Eva Cereghetti, and David Field. “Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries to Gene Flow.” <i>New Phytologist</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/nph.16180\">https://doi.org/10.1111/nph.16180</a>.","ista":"Pickup M, Barton NH, Brandvain Y, Fraisse C, Yakimowski S, Dixit T, Lexer C, Cereghetti E, Field D. 2019. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. 224(3), 1035–1047.","ieee":"M. Pickup <i>et al.</i>, “Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow,” <i>New Phytologist</i>, vol. 224, no. 3. Wiley, pp. 1035–1047, 2019.","ama":"Pickup M, Barton NH, Brandvain Y, et al. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. <i>New Phytologist</i>. 2019;224(3):1035-1047. doi:<a href=\"https://doi.org/10.1111/nph.16180\">10.1111/nph.16180</a>","apa":"Pickup, M., Barton, N. H., Brandvain, Y., Fraisse, C., Yakimowski, S., Dixit, T., … Field, D. (2019). Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.16180\">https://doi.org/10.1111/nph.16180</a>"},"file":[{"date_updated":"2020-07-14T12:47:42Z","file_size":1511958,"creator":"dernst","date_created":"2019-11-13T08:15:05Z","file_id":"7011","file_name":"2019_NewPhytologist_Pickup.pdf","content_type":"application/pdf","relation":"main_file","checksum":"21e4c95599bbcaf7c483b89954658672","access_level":"open_access"}],"scopus_import":"1","_id":"6856","external_id":{"pmid":["31505037"]},"issue":"3","author":[{"last_name":"Pickup","full_name":"Pickup, Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","first_name":"Melinda"},{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"},{"last_name":"Brandvain","full_name":"Brandvain, Yaniv","first_name":"Yaniv"},{"orcid":"0000-0001-8441-5075","first_name":"Christelle","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse"},{"first_name":"Sarah","last_name":"Yakimowski","full_name":"Yakimowski, Sarah"},{"last_name":"Dixit","full_name":"Dixit, Tanmay","first_name":"Tanmay"},{"full_name":"Lexer, Christian","last_name":"Lexer","first_name":"Christian"},{"first_name":"Eva","full_name":"Cereghetti, Eva","id":"71AA91B4-05ED-11EA-8BEB-F5833E63BD63","last_name":"Cereghetti"},{"last_name":"Field","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David"}],"intvolume":"       224","volume":224,"date_published":"2019-11-01T00:00:00Z","pmid":1,"article_processing_charge":"No","page":"1035-1047","project":[{"_id":"25B36484-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Mating system and the evolutionary dynamics of hybrid zones","grant_number":"329960"},{"grant_number":"M02463","call_identifier":"FWF","name":"Sex chromosomes and species barriers","_id":"2662AADE-B435-11E9-9278-68D0E5697425"}],"publisher":"Wiley","ddc":["570"],"year":"2019"},{"intvolume":"        41","volume":41,"external_id":{"isi":["000489502000001"]},"_id":"6857","issue":"11","author":[{"last_name":"Giese","full_name":"Giese, B","first_name":"B"},{"full_name":"Friess, J L","last_name":"Friess","first_name":"J L"},{"first_name":"M F ","full_name":"Schetelig, M F ","last_name":"Schetelig"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"},{"full_name":"Messer, Philip","last_name":"Messer","first_name":"Philip"},{"full_name":"Debarre, Florence","last_name":"Debarre","first_name":"Florence"},{"last_name":"Meimberg","full_name":"Meimberg, H","first_name":"H"},{"last_name":"Windbichler","full_name":"Windbichler, N","first_name":"N"},{"first_name":"C","full_name":"Boete, C","last_name":"Boete"}],"isi":1,"publisher":"Wiley","ddc":["570"],"article_number":"1900151","year":"2019","date_published":"2019-11-01T00:00:00Z","article_processing_charge":"No","abstract":[{"text":"Gene Drives are regarded as future tools with a high potential for population control. Due to their inherent ability to overcome the rules of Mendelian inheritance, gene drives (GD) may spread genes rapidly through populations of sexually reproducing organisms. A release of organisms carrying a GD would constitute a paradigm shift in the handling of genetically modified organisms because gene drive organisms (GDO) are designed to drive their transgenes into wild populations and thereby increase the number of GDOs. The rapid development in this field and its focus on wild populations demand a prospective risk assessment with a focus on exposure related aspects. Presently, it is unclear how adequate risk management could be guaranteed to limit the spread of GDs in time and space, in order to avoid potential adverse effects in socio‐ecological systems.\r\n\r\nThe recent workshop on the “Evaluation of Spatial and Temporal Control of Gene Drives” hosted by the Institute of Safety/Security and Risk Sciences (ISR) in Vienna aimed at gaining some insight into the potential population dynamic behavior of GDs and appropriate measures of control. Scientists from France, Germany, England, and the USA discussed both topics in this meeting on April 4–5, 2019. This article summarizes results of the workshop.","lang":"eng"}],"publication_identifier":{"eissn":["1521-1878"]},"publication":"BioEssays","date_created":"2019-09-07T14:40:03Z","file_date_updated":"2020-07-14T12:47:42Z","date_updated":"2023-08-30T06:56:26Z","type":"journal_article","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna","oa":1,"has_accepted_license":"1","status":"public","citation":{"ieee":"B. Giese <i>et al.</i>, “Gene Drives: Dynamics and regulatory matters – A report from the workshop ‘Evaluation of spatial and temporal control of Gene Drives’, 4 – 5 April 2019, Vienna,” <i>BioEssays</i>, vol. 41, no. 11. Wiley, 2019.","apa":"Giese, B., Friess, J. L., Schetelig, M. F., Barton, N. H., Messer, P., Debarre, F., … Boete, C. (2019). Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. <i>BioEssays</i>. Wiley. <a href=\"https://doi.org/10.1002/bies.201900151\">https://doi.org/10.1002/bies.201900151</a>","ama":"Giese B, Friess JL, Schetelig MF, et al. Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. <i>BioEssays</i>. 2019;41(11). doi:<a href=\"https://doi.org/10.1002/bies.201900151\">10.1002/bies.201900151</a>","short":"B. Giese, J.L. Friess, M.F. Schetelig, N.H. Barton, P. Messer, F. Debarre, H. Meimberg, N. Windbichler, C. Boete, BioEssays 41 (2019).","chicago":"Giese, B, J L Friess, M F  Schetelig, Nicholas H Barton, Philip Messer, Florence Debarre, H Meimberg, N Windbichler, and C Boete. “Gene Drives: Dynamics and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” <i>BioEssays</i>. Wiley, 2019. <a href=\"https://doi.org/10.1002/bies.201900151\">https://doi.org/10.1002/bies.201900151</a>.","mla":"Giese, B., et al. “Gene Drives: Dynamics and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” <i>BioEssays</i>, vol. 41, no. 11, 1900151, Wiley, 2019, doi:<a href=\"https://doi.org/10.1002/bies.201900151\">10.1002/bies.201900151</a>.","ista":"Giese B, Friess JL, Schetelig MF, Barton NH, Messer P, Debarre F, Meimberg H, Windbichler N, Boete C. 2019. Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 41(11), 1900151."},"file":[{"date_updated":"2020-07-14T12:47:42Z","creator":"dernst","file_size":193248,"file_id":"6939","date_created":"2019-10-11T06:59:26Z","file_name":"2019_BioEssays_Giese.pdf","content_type":"application/pdf","checksum":"8cc7551bff70b2658f8d5630f228ee12","relation":"main_file","access_level":"open_access"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"scopus_import":"1","month":"11","doi":"10.1002/bies.201900151","day":"01","publication_status":"published","department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"quality_controlled":"1","oa_version":"Published Version"},{"intvolume":"         6","volume":6,"issue":"2","_id":"6858","external_id":{"isi":["000467957400025"]},"isi":1,"author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"}],"publisher":"Oxford University Press","ddc":["570"],"year":"2019","date_published":"2019-03-01T00:00:00Z","article_processing_charge":"No","page":"291-292","publication_identifier":{"issn":["2095-5138"],"eissn":["2053-714X"]},"publication":"National Science Review","date_created":"2019-09-07T14:43:02Z","file_date_updated":"2020-10-02T09:16:44Z","date_updated":"2023-08-29T07:51:09Z","type":"journal_article","article_type":"review","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Is speciation driven by cycles of mixing and isolation?","has_accepted_license":"1","oa":1,"status":"public","citation":{"ieee":"N. H. Barton, “Is speciation driven by cycles of mixing and isolation?,” <i>National Science Review</i>, vol. 6, no. 2. Oxford University Press, pp. 291–292, 2019.","ama":"Barton NH. Is speciation driven by cycles of mixing and isolation? <i>National Science Review</i>. 2019;6(2):291-292. doi:<a href=\"https://doi.org/10.1093/nsr/nwy113\">10.1093/nsr/nwy113</a>","apa":"Barton, N. H. (2019). Is speciation driven by cycles of mixing and isolation? <i>National Science Review</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/nsr/nwy113\">https://doi.org/10.1093/nsr/nwy113</a>","chicago":"Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?” <i>National Science Review</i>. Oxford University Press, 2019. <a href=\"https://doi.org/10.1093/nsr/nwy113\">https://doi.org/10.1093/nsr/nwy113</a>.","short":"N.H. Barton, National Science Review 6 (2019) 291–292.","mla":"Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?” <i>National Science Review</i>, vol. 6, no. 2, Oxford University Press, 2019, pp. 291–92, doi:<a href=\"https://doi.org/10.1093/nsr/nwy113\">10.1093/nsr/nwy113</a>.","ista":"Barton NH. 2019. Is speciation driven by cycles of mixing and isolation? National Science Review. 6(2), 291–292."},"file":[{"file_name":"2019_NSR_Barton.pdf","date_created":"2020-10-02T09:16:44Z","file_id":"8595","file_size":106463,"creator":"dernst","date_updated":"2020-10-02T09:16:44Z","success":1,"access_level":"open_access","relation":"main_file","checksum":"571d60fa21a568607d1fd04e119da88c","content_type":"application/pdf"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"scopus_import":"1","month":"03","day":"01","doi":"10.1093/nsr/nwy113","department":[{"_id":"NiBa"}],"publication_status":"published","oa_version":"Published Version","quality_controlled":"1","language":[{"iso":"eng"}]},{"pmid":1,"date_published":"2019-08-23T00:00:00Z","article_processing_charge":"No","publisher":"AAAS","year":"2019","article_number":"eaaw9144","issue":"6455","_id":"6859","external_id":{"pmid":["31439765"],"isi":["000482464000043"]},"isi":1,"author":[{"last_name":"Zhou","full_name":"Zhou, Long","id":"3E751364-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1864-8951","first_name":"Long"},{"orcid":"0000-0002-0977-7989","first_name":"Leonid A","full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov"}],"intvolume":"       365","volume":365,"related_material":{"link":[{"description":"News on IST Website","url":"https://ist.ac.at/en/news/structure-of-protein-nano-turbine-revealed/","relation":"press_release"}]},"month":"08","publication_status":"published","department":[{"_id":"LeSa"}],"day":"23","doi":"10.1126/science.aaw9144","acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"None","language":[{"iso":"eng"}],"quality_controlled":"1","status":"public","citation":{"ista":"Zhou L, Sazanov LA. 2019. Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase. Science. 365(6455), eaaw9144.","chicago":"Zhou, Long, and Leonid A Sazanov. “Structure and Conformational Plasticity of the Intact Thermus Thermophilus V/A-Type ATPase.” <i>Science</i>. AAAS, 2019. <a href=\"https://doi.org/10.1126/science.aaw9144\">https://doi.org/10.1126/science.aaw9144</a>.","mla":"Zhou, Long, and Leonid A. Sazanov. “Structure and Conformational Plasticity of the Intact Thermus Thermophilus V/A-Type ATPase.” <i>Science</i>, vol. 365, no. 6455, eaaw9144, AAAS, 2019, doi:<a href=\"https://doi.org/10.1126/science.aaw9144\">10.1126/science.aaw9144</a>.","short":"L. Zhou, L.A. Sazanov, Science 365 (2019).","ama":"Zhou L, Sazanov LA. Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase. <i>Science</i>. 2019;365(6455). doi:<a href=\"https://doi.org/10.1126/science.aaw9144\">10.1126/science.aaw9144</a>","apa":"Zhou, L., &#38; Sazanov, L. A. (2019). Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.aaw9144\">https://doi.org/10.1126/science.aaw9144</a>","ieee":"L. Zhou and L. A. Sazanov, “Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase,” <i>Science</i>, vol. 365, no. 6455. AAAS, 2019."},"scopus_import":"1","title":"Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"V (vacuolar)/A (archaeal)-type adenosine triphosphatases (ATPases), found in archaeaand eubacteria, couple ATP hydrolysis or synthesis to proton translocation across theplasma membrane using the rotary-catalysis mechanism. They belong to the V-typeATPase family, which differs from the mitochondrial/chloroplast F-type ATP synthasesin overall architecture. We solved cryo–electron microscopy structures of the intactThermus thermophilusV/A-ATPase, reconstituted into lipid nanodiscs, in three rotationalstates and two substates. These structures indicate substantial flexibility betweenV1and Voin a working enzyme, which results from mechanical competition between centralshaft rotation and resistance from the peripheral stalks. We also describedetails of adenosine diphosphate inhibition release, V1-Votorque transmission, andproton translocation, which are relevant for the entire V-type ATPase family."}],"publication":"Science","date_created":"2019-09-07T19:04:45Z","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"type":"journal_article","date_updated":"2023-08-29T07:52:02Z"},{"volume":9,"intvolume":"         9","author":[{"first_name":"M.","full_name":"Fenu, M.","last_name":"Fenu"},{"first_name":"T.","last_name":"Bettermann","full_name":"Bettermann, T."},{"last_name":"Vogl","full_name":"Vogl, C.","first_name":"C."},{"orcid":"0000-0002-8821-8236","first_name":"Nasser","full_name":"Darwish-Miranda, Nasser","id":"39CD9926-F248-11E8-B48F-1D18A9856A87","last_name":"Darwish-Miranda"},{"first_name":"J.","last_name":"Schramel","full_name":"Schramel, J."},{"full_name":"Jenner, F.","last_name":"Jenner","first_name":"F."},{"last_name":"Ribitsch","full_name":"Ribitsch, I.","first_name":"I."}],"isi":1,"issue":"1","_id":"6867","external_id":{"pmid":["31477739"],"isi":["000483697800007"]},"year":"2019","article_number":"12625","publisher":"Springer Nature","ddc":["570"],"article_processing_charge":"No","date_published":"2019-09-02T00:00:00Z","pmid":1,"file_date_updated":"2020-07-14T12:47:42Z","type":"journal_article","date_updated":"2026-04-03T09:39:11Z","abstract":[{"lang":"eng","text":"A novel magnetic scratch method achieves repeatability, reproducibility and geometric control greater than pipette scratch assays and closely approximating the precision of cell exclusion assays while inducing the cell injury inherently necessary for wound healing assays. The magnetic scratch is affordable, easily implemented and standardisable and thus may contribute toward better comparability of data generated in different studies and laboratories."}],"publication":"Scientific Reports","date_created":"2019-09-15T22:00:42Z","publication_identifier":{"eissn":["2045-2322"]},"has_accepted_license":"1","oa":1,"title":"A novel magnet-based scratch method for standardisation of wound-healing assays","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","scopus_import":"1","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"ista":"Fenu M, Bettermann T, Vogl C, Darwish-Miranda N, Schramel J, Jenner F, Ribitsch I. 2019. A novel magnet-based scratch method for standardisation of wound-healing assays. Scientific Reports. 9(1), 12625.","mla":"Fenu, M., et al. “A Novel Magnet-Based Scratch Method for Standardisation of Wound-Healing Assays.” <i>Scientific Reports</i>, vol. 9, no. 1, 12625, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41598-019-48930-7\">10.1038/s41598-019-48930-7</a>.","short":"M. Fenu, T. Bettermann, C. Vogl, N. Darwish-Miranda, J. Schramel, F. Jenner, I. Ribitsch, Scientific Reports 9 (2019).","chicago":"Fenu, M., T. Bettermann, C. Vogl, Nasser Darwish-Miranda, J. Schramel, F. Jenner, and I. Ribitsch. “A Novel Magnet-Based Scratch Method for Standardisation of Wound-Healing Assays.” <i>Scientific Reports</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41598-019-48930-7\">https://doi.org/10.1038/s41598-019-48930-7</a>.","ama":"Fenu M, Bettermann T, Vogl C, et al. A novel magnet-based scratch method for standardisation of wound-healing assays. <i>Scientific Reports</i>. 2019;9(1). doi:<a href=\"https://doi.org/10.1038/s41598-019-48930-7\">10.1038/s41598-019-48930-7</a>","apa":"Fenu, M., Bettermann, T., Vogl, C., Darwish-Miranda, N., Schramel, J., Jenner, F., &#38; Ribitsch, I. (2019). A novel magnet-based scratch method for standardisation of wound-healing assays. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-019-48930-7\">https://doi.org/10.1038/s41598-019-48930-7</a>","ieee":"M. Fenu <i>et al.</i>, “A novel magnet-based scratch method for standardisation of wound-healing assays,” <i>Scientific Reports</i>, vol. 9, no. 1. Springer Nature, 2019."},"file":[{"checksum":"9cfd986d4108e288cc72276ef047ab0c","relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"dernst","file_size":3523795,"date_updated":"2020-07-14T12:47:42Z","file_name":"2019_ScientificReports_Fenu.pdf","date_created":"2019-09-16T12:42:40Z","file_id":"6879"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"quality_controlled":"1","month":"09","publication_status":"published","department":[{"_id":"Bio"}],"doi":"10.1038/s41598-019-48930-7","day":"02"},{"article_processing_charge":"No","date_published":"2019-09-09T00:00:00Z","article_number":"e42766","year":"2019","publisher":"eLife Sciences Publications","ddc":["570"],"author":[{"first_name":"Niklas","last_name":"Byczkowicz","full_name":"Byczkowicz, Niklas"},{"last_name":"Eshra","full_name":"Eshra, Abdelmoneim","first_name":"Abdelmoneim"},{"first_name":"Jacqueline-Claire","last_name":"Montanaro-Punzengruber","id":"3786AB44-F248-11E8-B48F-1D18A9856A87","full_name":"Montanaro-Punzengruber, Jacqueline-Claire"},{"first_name":"Andrea","last_name":"Trevisiol","full_name":"Trevisiol, Andrea"},{"first_name":"Johannes","last_name":"Hirrlinger","full_name":"Hirrlinger, Johannes"},{"first_name":"Maarten Hp","full_name":"Kole, Maarten Hp","last_name":"Kole"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444"},{"last_name":"Hallermann","full_name":"Hallermann, Stefan","first_name":"Stefan"}],"isi":1,"external_id":{"isi":["000485663900001"]},"_id":"6868","volume":8,"intvolume":"         8","oa_version":"Published Version","quality_controlled":"1","language":[{"iso":"eng"}],"month":"09","doi":"10.7554/eLife.42766","day":"09","department":[{"_id":"RySh"}],"publication_status":"published","scopus_import":"1","status":"public","file":[{"access_level":"open_access","relation":"main_file","checksum":"c350b7861ef0fb537cae8a3232aec016","content_type":"application/pdf","file_name":"2019_eLife_Byczkowicz.pdf","date_created":"2019-09-16T13:14:33Z","file_id":"6880","file_size":4008137,"creator":"dernst","date_updated":"2020-07-14T12:47:42Z"}],"citation":{"ieee":"N. Byczkowicz <i>et al.</i>, “HCN channel-mediated neuromodulation can control action potential velocity and fidelity in central axons,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019.","ama":"Byczkowicz N, Eshra A, Montanaro-Punzengruber J-C, et al. HCN channel-mediated neuromodulation can control action potential velocity and fidelity in central axons. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/eLife.42766\">10.7554/eLife.42766</a>","apa":"Byczkowicz, N., Eshra, A., Montanaro-Punzengruber, J.-C., Trevisiol, A., Hirrlinger, J., Kole, M. H., … Hallermann, S. (2019). HCN channel-mediated neuromodulation can control action potential velocity and fidelity in central axons. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.42766\">https://doi.org/10.7554/eLife.42766</a>","mla":"Byczkowicz, Niklas, et al. “HCN Channel-Mediated Neuromodulation Can Control Action Potential Velocity and Fidelity in Central Axons.” <i>ELife</i>, vol. 8, e42766, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/eLife.42766\">10.7554/eLife.42766</a>.","short":"N. Byczkowicz, A. Eshra, J.-C. Montanaro-Punzengruber, A. Trevisiol, J. Hirrlinger, M.H. Kole, R. Shigemoto, S. Hallermann, ELife 8 (2019).","chicago":"Byczkowicz, Niklas, Abdelmoneim Eshra, Jacqueline-Claire Montanaro-Punzengruber, Andrea Trevisiol, Johannes Hirrlinger, Maarten Hp Kole, Ryuichi Shigemoto, and Stefan Hallermann. “HCN Channel-Mediated Neuromodulation Can Control Action Potential Velocity and Fidelity in Central Axons.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/eLife.42766\">https://doi.org/10.7554/eLife.42766</a>.","ista":"Byczkowicz N, Eshra A, Montanaro-Punzengruber J-C, Trevisiol A, Hirrlinger J, Kole MH, Shigemoto R, Hallermann S. 2019. HCN channel-mediated neuromodulation can control action potential velocity and fidelity in central axons. eLife. 8, e42766."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"has_accepted_license":"1","oa":1,"article_type":"original","title":"HCN channel-mediated neuromodulation can control action potential velocity and fidelity in central axons","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file_date_updated":"2020-07-14T12:47:42Z","date_updated":"2026-04-03T09:40:28Z","type":"journal_article","abstract":[{"lang":"eng","text":"Hyperpolarization-activated cyclic-nucleotide-gated (HCN) channels control electrical rhythmicity and excitability in the heart and brain, but the function of HCN channels at the subcellular level in axons remains poorly understood. Here, we show that the action potential conduction velocity in both myelinated and unmyelinated central axons can be bidirectionally modulated by a HCN channel blocker, cyclic adenosine monophosphate (cAMP), and neuromodulators. Recordings from mouse cerebellar mossy fiber boutons show that HCN channels ensure reliable high-frequency firing and are strongly modulated by cAMP (EC50 40 mM; estimated endogenous cAMP concentration 13 mM). In addition, immunogold-electron microscopy revealed HCN2 as the dominating subunit in cerebellar mossy fibers. Computational modeling indicated that HCN2 channels control conduction velocity primarily by altering the resting membrane potential\r\nand are associated with significant metabolic costs. These results suggest that the cAMP-HCN pathway provides neuromodulators with an opportunity to finely tune energy consumption and temporal delays across axons in the brain."}],"publication_identifier":{"eissn":["2050-084X"]},"date_created":"2019-09-15T22:00:43Z","publication":"eLife"},{"related_material":{"record":[{"status":"public","relation":"later_version","id":"9239"}]},"corr_author":"1","month":"08","publication_status":"published","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"ec_funded":1,"day":"01","doi":"10.4230/LIPICS.MFCS.2019.11","arxiv":1,"oa_version":"Published Version","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"access_level":"open_access","checksum":"6346e116a4f4ed1414174d96d2c4fbd7","relation":"main_file","content_type":"application/pdf","file_name":"2019_LIPIcs_Avni.pdf","file_id":"6913","date_created":"2019-09-27T11:45:15Z","creator":"kschuh","file_size":554457,"date_updated":"2020-07-14T12:47:42Z"}],"citation":{"ista":"Avni G, Henzinger TA, Zikelic D. 2019. Bidding mechanisms in graph games. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 138, 11.","short":"G. Avni, T.A. Henzinger, D. Zikelic, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","chicago":"Avni, Guy, Thomas A Henzinger, and Dorde Zikelic. “Bidding Mechanisms in Graph Games,” Vol. 138. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. <a href=\"https://doi.org/10.4230/LIPICS.MFCS.2019.11\">https://doi.org/10.4230/LIPICS.MFCS.2019.11</a>.","mla":"Avni, Guy, et al. <i>Bidding Mechanisms in Graph Games</i>. Vol. 138, 11, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:<a href=\"https://doi.org/10.4230/LIPICS.MFCS.2019.11\">10.4230/LIPICS.MFCS.2019.11</a>.","ama":"Avni G, Henzinger TA, Zikelic D. Bidding mechanisms in graph games. In: Vol 138. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:<a href=\"https://doi.org/10.4230/LIPICS.MFCS.2019.11\">10.4230/LIPICS.MFCS.2019.11</a>","apa":"Avni, G., Henzinger, T. A., &#38; Zikelic, D. (2019). Bidding mechanisms in graph games (Vol. 138). Presented at the MFCS: Mathematical Foundations of Computer Science, Aachen, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.MFCS.2019.11\">https://doi.org/10.4230/LIPICS.MFCS.2019.11</a>","ieee":"G. Avni, T. A. Henzinger, and D. Zikelic, “Bidding mechanisms in graph games,” presented at the MFCS: Mathematical Foundations of Computer Science, Aachen, Germany, 2019, vol. 138."},"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Bidding mechanisms in graph games","conference":{"name":"MFCS: Mathematical Foundations of Computer Science","start_date":"2019-08-26","location":"Aachen, Germany","end_date":"2019-08-30"},"oa":1,"has_accepted_license":"1","abstract":[{"text":"In two-player games on graphs, the players move a token through a graph to produce a finite or infinite path, which determines the qualitative winner or quantitative payoff of the game. We study bidding games in which the players bid for the right to move the token. Several bidding rules were studied previously. In Richman bidding, in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Poorman bidding is similar except that the winner of the bidding pays the \"bank\" rather than the other player. Taxman bidding spans the spectrum between Richman and poorman bidding. They are parameterized by a constant tau in [0,1]: portion tau of the winning bid is paid to the other player, and portion 1-tau to the bank. While finite-duration (reachability) taxman games have been studied before, we present, for the first time, results on infinite-duration taxman games. It was previously shown that both Richman and poorman infinite-duration games with qualitative objectives reduce to reachability games, and we show a similar result here. Our most interesting results concern quantitative taxman games, namely mean-payoff games, where poorman and Richman bidding differ significantly. A central quantity in these games is the ratio between the two players' initial budgets. While in poorman mean-payoff games, the optimal payoff of a player depends on the initial ratio, in Richman bidding, the payoff depends only on the structure of the game. In both games the optimal payoffs can be found using (different) probabilistic connections with random-turn games in which in each turn, instead of bidding, a coin is tossed to determine which player moves. While the value with Richman bidding equals the value of a random-turn game with an un-biased coin, with poorman bidding, the bias in the coin is the initial ratio of the budgets. We give a complete classification of mean-payoff taxman games that is based on a probabilistic connection: the value of a taxman bidding game with parameter tau and initial ratio r, equals the value of a random-turn game that uses a coin with bias F(tau, r) = (r+tau * (1-r))/(1+tau). Thus, we show that Richman bidding is the exception; namely, for every tau <1, the value of the game depends on the initial ratio. Our proof technique simplifies and unifies the previous proof techniques for both Richman and poorman bidding. ","lang":"eng"}],"date_created":"2019-09-18T08:04:26Z","file_date_updated":"2020-07-14T12:47:42Z","type":"conference","date_updated":"2025-07-10T11:53:57Z","date_published":"2019-08-01T00:00:00Z","article_processing_charge":"No","project":[{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"Formal Methods meets Algorithmic Game Theory","call_identifier":"FWF","grant_number":"M02369","_id":"264B3912-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S11402-N23","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","ddc":["004"],"year":"2019","article_number":"11","alternative_title":["LIPIcs"],"external_id":{"arxiv":["1905.03835"]},"_id":"6884","author":[{"orcid":"0000-0001-5588-8287","first_name":"Guy","last_name":"Avni","full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A"},{"full_name":"Zikelic, Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","orcid":"0000-0002-4681-1699","first_name":"Dorde"}],"intvolume":"       138","volume":138},{"status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"access_level":"open_access","relation":"main_file","checksum":"4985e26e1572d1575d64d38acabd71d6","content_type":"application/pdf","file_name":"2019_LIPIcs_Chatterjee.pdf","date_created":"2019-09-27T12:09:35Z","file_id":"6914","file_size":538120,"creator":"kschuh","date_updated":"2020-07-14T12:47:43Z"}],"citation":{"mla":"Chatterjee, Krishnendu, et al. <i>Long-Run Average Behavior of Vector Addition Systems with States</i>. Vol. 140, 27, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:<a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.27\">10.4230/LIPICS.CONCUR.2019.27</a>.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Long-Run Average Behavior of Vector Addition Systems with States,” Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. <a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.27\">https://doi.org/10.4230/LIPICS.CONCUR.2019.27</a>.","ista":"Chatterjee K, Henzinger TA, Otop J. 2019. Long-run average behavior of vector addition systems with states. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 140, 27.","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Long-run average behavior of vector addition systems with states,” presented at the CONCUR: Conference on Concurrency Theory, Amsterdam, Netherlands, 2019, vol. 140.","ama":"Chatterjee K, Henzinger TA, Otop J. Long-run average behavior of vector addition systems with states. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:<a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.27\">10.4230/LIPICS.CONCUR.2019.27</a>","apa":"Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2019). Long-run average behavior of vector addition systems with states (Vol. 140). Presented at the CONCUR: Conference on Concurrency Theory, Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.27\">https://doi.org/10.4230/LIPICS.CONCUR.2019.27</a>"},"scopus_import":"1","month":"08","corr_author":"1","publication_status":"published","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"day":"01","doi":"10.4230/LIPICS.CONCUR.2019.27","oa_version":"Published Version","language":[{"iso":"eng"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":"A vector addition system with states (VASS) consists of a finite set of states and counters. A configuration is a state and a value for each counter; a transition changes the state and each counter is incremented, decremented, or left unchanged. While qualitative properties such as state and configuration reachability have been studied for VASS, we consider the long-run average cost of infinite computations of VASS. The cost of a configuration is for each state, a linear combination of the counter values. In the special case of uniform cost functions, the linear combination is the same for all states. The (regular) long-run emptiness problem is, given a VASS, a cost function, and a threshold value, if there is a (lasso-shaped) computation such that the long-run average value of the cost function does not exceed the threshold. For uniform cost functions, we show that the regular long-run emptiness problem is (a) decidable in polynomial time for integer-valued VASS, and (b) decidable but nonelementarily hard for natural-valued VASS (i.e., nonnegative counters). For general cost functions, we show that the problem is (c) NP-complete for integer-valued VASS, and (d) undecidable for natural-valued VASS. Our most interesting result is for (c) integer-valued VASS with general cost functions, where we establish a connection between the regular long-run emptiness problem and quadratic Diophantine inequalities. The general (nonregular) long-run emptiness problem is equally hard as the regular problem in all cases except (c), where it remains open. "}],"date_created":"2019-09-18T08:06:14Z","file_date_updated":"2020-07-14T12:47:43Z","type":"conference","date_updated":"2025-07-10T11:53:58Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Long-run average behavior of vector addition systems with states","conference":{"start_date":"2019-08-27","name":"CONCUR: Conference on Concurrency Theory","end_date":"2019-08-30","location":"Amsterdam, Netherlands"},"oa":1,"has_accepted_license":"1","project":[{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11402-N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","ddc":["000"],"year":"2019","article_number":"27","date_published":"2019-08-01T00:00:00Z","article_processing_charge":"No","intvolume":"       140","volume":140,"alternative_title":["LIPIcs"],"_id":"6885","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"},{"full_name":"Otop, Jan","last_name":"Otop","first_name":"Jan"}]},{"alternative_title":["LIPIcs"],"_id":"6886","external_id":{"arxiv":["1905.03588"]},"author":[{"first_name":"Milad","last_name":"Aghajohari","full_name":"Aghajohari, Milad"},{"id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Avni, Guy","last_name":"Avni","first_name":"Guy","orcid":"0000-0001-5588-8287"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A"}],"intvolume":"       140","volume":140,"date_published":"2019-08-01T00:00:00Z","article_processing_charge":"No","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"},{"_id":"264B3912-B435-11E9-9278-68D0E5697425","grant_number":"M02369","call_identifier":"FWF","name":"Formal Methods meets Algorithmic Game Theory"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","ddc":["000"],"year":"2019","article_number":"20","title":"Determinacy in discrete-bidding infinite-duration games","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"name":"CONCUR: Conference on Concurrency Theory","start_date":"2019-08-27","location":"Amsterdam, Netherlands","end_date":"2019-08-30"},"has_accepted_license":"1","oa":1,"abstract":[{"lang":"eng","text":"In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the winner of the game. Such games are central in formal methods since they model the interaction between a non-terminating system and its environment. In bidding games the players bid for the right to move the token: in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Bidding games are known to have a clean and elegant mathematical structure that relies on the ability of the players to submit arbitrarily small bids. Many applications, however, require a fixed granularity for the bids, which can represent, for example, the monetary value expressed in cents. We study, for the first time, the combination of discrete-bidding and infinite-duration games. Our most important result proves that these games form a large determined subclass of concurrent games, where determinacy is the strong property that there always exists exactly one player who can guarantee winning the game. In particular, we show that, in contrast to non-discrete bidding games, the mechanism with which tied bids are resolved plays an important role in discrete-bidding games. We study several natural tie-breaking mechanisms and show that, while some do not admit determinacy, most natural mechanisms imply determinacy for every pair of initial budgets. "}],"date_created":"2019-09-18T08:06:58Z","file_date_updated":"2020-07-14T12:47:43Z","license":"https://creativecommons.org/licenses/by/3.0/","type":"conference","date_updated":"2025-07-10T11:53:58Z","month":"08","corr_author":"1","publication_status":"published","department":[{"_id":"ToHe"}],"day":"01","doi":"10.4230/LIPICS.CONCUR.2019.20","arxiv":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","quality_controlled":"1","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"file":[{"file_size":741425,"creator":"kschuh","date_updated":"2020-07-14T12:47:43Z","file_name":"2019_LIPIcs_Aghajohari.pdf","date_created":"2019-09-27T12:21:38Z","file_id":"6915","relation":"main_file","checksum":"4df6d3575c506edb17215adada03cc8e","content_type":"application/pdf","access_level":"open_access"}],"citation":{"ieee":"M. Aghajohari, G. Avni, and T. A. Henzinger, “Determinacy in discrete-bidding infinite-duration games,” presented at the CONCUR: Conference on Concurrency Theory, Amsterdam, Netherlands, 2019, vol. 140.","apa":"Aghajohari, M., Avni, G., &#38; Henzinger, T. A. (2019). Determinacy in discrete-bidding infinite-duration games (Vol. 140). Presented at the CONCUR: Conference on Concurrency Theory, Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.20\">https://doi.org/10.4230/LIPICS.CONCUR.2019.20</a>","ama":"Aghajohari M, Avni G, Henzinger TA. Determinacy in discrete-bidding infinite-duration games. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:<a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.20\">10.4230/LIPICS.CONCUR.2019.20</a>","chicago":"Aghajohari, Milad, Guy Avni, and Thomas A Henzinger. “Determinacy in Discrete-Bidding Infinite-Duration Games,” Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. <a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.20\">https://doi.org/10.4230/LIPICS.CONCUR.2019.20</a>.","mla":"Aghajohari, Milad, et al. <i>Determinacy in Discrete-Bidding Infinite-Duration Games</i>. Vol. 140, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:<a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.20\">10.4230/LIPICS.CONCUR.2019.20</a>.","short":"M. Aghajohari, G. Avni, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","ista":"Aghajohari M, Avni G, Henzinger TA. 2019. Determinacy in discrete-bidding infinite-duration games. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 140, 20."},"scopus_import":"1"},{"date_published":"2019-08-01T00:00:00Z","article_processing_charge":"No","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","project":[{"grant_number":"S11407","call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"}],"ddc":["000"],"article_number":"7","year":"2019","_id":"6887","alternative_title":["LIPIcs"],"author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"first_name":"Wolfgang","last_name":"Dvorák","full_name":"Dvorák, Wolfgang"},{"orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Svozil, Alexander","last_name":"Svozil","first_name":"Alexander"}],"intvolume":"       140","volume":140,"month":"08","corr_author":"1","doi":"10.4230/LIPICS.CONCUR.2019.7","day":"01","ec_funded":1,"department":[{"_id":"KrCh"}],"publication_status":"published","oa_version":"Published Version","language":[{"iso":"eng"}],"quality_controlled":"1","status":"public","file":[{"access_level":"open_access","relation":"main_file","checksum":"e1f0e4061212454574f34a1368d018ec","content_type":"application/pdf","file_name":"2019_LIPIcs_Chatterjee.pdf","date_created":"2019-10-01T08:20:30Z","file_id":"6922","file_size":730112,"creator":"kschuh","date_updated":"2020-07-14T12:47:43Z"}],"citation":{"mla":"Chatterjee, Krishnendu, et al. “Near-Linear Time Algorithms for Streett Objectives in Graphs and MDPs.” <i>Leibniz International Proceedings in Informatics</i>, vol. 140, 7, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:<a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.7\">10.4230/LIPICS.CONCUR.2019.7</a>.","short":"K. Chatterjee, W. Dvorák, M. Henzinger, A. Svozil, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika Henzinger, and Alexander Svozil. “Near-Linear Time Algorithms for Streett Objectives in Graphs and MDPs.” In <i>Leibniz International Proceedings in Informatics</i>, Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. <a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.7\">https://doi.org/10.4230/LIPICS.CONCUR.2019.7</a>.","ista":"Chatterjee K, Dvorák W, Henzinger M, Svozil A. 2019. Near-linear time algorithms for Streett objectives in graphs and MDPs. Leibniz International Proceedings in Informatics. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 140, 7.","ieee":"K. Chatterjee, W. Dvorák, M. Henzinger, and A. Svozil, “Near-linear time algorithms for Streett objectives in graphs and MDPs,” in <i>Leibniz International Proceedings in Informatics</i>, Amsterdam, Netherlands, 2019, vol. 140.","ama":"Chatterjee K, Dvorák W, Henzinger M, Svozil A. Near-linear time algorithms for Streett objectives in graphs and MDPs. In: <i>Leibniz International Proceedings in Informatics</i>. Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:<a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.7\">10.4230/LIPICS.CONCUR.2019.7</a>","apa":"Chatterjee, K., Dvorák, W., Henzinger, M., &#38; Svozil, A. (2019). Near-linear time algorithms for Streett objectives in graphs and MDPs. In <i>Leibniz International Proceedings in Informatics</i> (Vol. 140). Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.7\">https://doi.org/10.4230/LIPICS.CONCUR.2019.7</a>"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"scopus_import":"1","title":"Near-linear time algorithms for Streett objectives in graphs and MDPs","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"name":"CONCUR: Conference on Concurrency Theory","start_date":"2019-08-27","location":"Amsterdam, Netherlands","end_date":"2019-08-30"},"oa":1,"has_accepted_license":"1","abstract":[{"lang":"eng","text":"The fundamental model-checking problem, given as input a model and a specification, asks for the algorithmic verification of whether the model satisfies the specification. Two classical models for reactive systems are graphs and Markov decision processes (MDPs). A basic specification formalism in the verification of reactive systems is the strong fairness (aka Streett) objective, where given different types of requests and corresponding grants, the requirement is that for each type, if the request event happens infinitely often, then the corresponding grant event must also happen infinitely often. All omega-regular objectives can be expressed as Streett objectives and hence they are canonical in verification. Consider graphs/MDPs with n vertices, m edges, and a Streett objectives with k pairs, and let b denote the size of the description of the Streett objective for the sets of requests and grants. The current best-known algorithm for the problem requires time O(min(n^2, m sqrt{m log n}) + b log n). In this work we present randomized near-linear time algorithms, with expected running time O~(m + b), where the O~ notation hides poly-log factors. Our randomized algorithms are near-linear in the size of the input, and hence optimal up to poly-log factors. "}],"publication":"Leibniz International Proceedings in Informatics","date_created":"2019-09-18T08:07:58Z","file_date_updated":"2020-07-14T12:47:43Z","date_updated":"2025-07-10T11:53:59Z","type":"conference"},{"volume":"2019-May","_id":"6888","external_id":{"isi":["000494942300011"]},"alternative_title":["ICRA"],"isi":1,"author":[{"last_name":"Lechner","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias","first_name":"Mathias"},{"full_name":"Hasani, Ramin","last_name":"Hasani","first_name":"Ramin"},{"first_name":"Manuel","last_name":"Zimmer","full_name":"Zimmer, Manuel"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000−0002−2985−7724"},{"first_name":"Radu","full_name":"Grosu, Radu","last_name":"Grosu"}],"publisher":"IEEE","project":[{"grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"ddc":["000"],"article_number":"8793840","year":"2019","date_published":"2019-05-01T00:00:00Z","article_processing_charge":"No","abstract":[{"text":"In this paper, we design novel liquid time-constant recurrent neural networks for robotic control, inspired by the brain of the nematode, C. elegans. In the worm's nervous system, neurons communicate through nonlinear time-varying synaptic links established amongst them by their particular wiring structure. This property enables neurons to express liquid time-constants dynamics and therefore allows the network to originate complex behaviors with a small number of neurons. We identify neuron-pair communication motifs as design operators and use them to configure compact neuronal network structures to govern sequential robotic tasks. The networks are systematically designed to map the environmental observations to motor actions, by their hierarchical topology from sensory neurons, through recurrently-wired interneurons, to motor neurons. The networks are then parametrized in a supervised-learning scheme by a search-based algorithm. We demonstrate that obtained networks realize interpretable dynamics. We evaluate their performance in controlling mobile and arm robots, and compare their attributes to other artificial neural network-based control agents. Finally, we experimentally show their superior resilience to environmental noise, compared to the existing machine learning-based methods.","lang":"eng"}],"publication_identifier":{"isbn":["9781538660270"]},"publication":"Proceedings - IEEE International Conference on Robotics and Automation","date_created":"2019-09-18T08:09:51Z","file_date_updated":"2020-10-08T17:30:38Z","date_updated":"2025-09-10T10:42:55Z","type":"conference","title":"Designing worm-inspired neural networks for interpretable robotic control","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","conference":{"location":"Montreal, QC, Canada","end_date":"2019-05-24","name":"ICRA: International Conference on Robotics and Automation","start_date":"2019-05-20"},"has_accepted_license":"1","oa":1,"status":"public","file":[{"checksum":"f5545a6b60c3ffd01feb3613f81d03b6","relation":"main_file","content_type":"application/pdf","access_level":"open_access","success":1,"creator":"dernst","file_size":3265107,"date_updated":"2020-10-08T17:30:38Z","file_name":"2019_ICRA_Lechner.pdf","file_id":"8636","date_created":"2020-10-08T17:30:38Z"}],"citation":{"ieee":"M. Lechner, R. Hasani, M. Zimmer, T. A. Henzinger, and R. Grosu, “Designing worm-inspired neural networks for interpretable robotic control,” in <i>Proceedings - IEEE International Conference on Robotics and Automation</i>, Montreal, QC, Canada, 2019, vol. 2019–May.","apa":"Lechner, M., Hasani, R., Zimmer, M., Henzinger, T. A., &#38; Grosu, R. (2019). Designing worm-inspired neural networks for interpretable robotic control. In <i>Proceedings - IEEE International Conference on Robotics and Automation</i> (Vol. 2019–May). Montreal, QC, Canada: IEEE. <a href=\"https://doi.org/10.1109/icra.2019.8793840\">https://doi.org/10.1109/icra.2019.8793840</a>","ama":"Lechner M, Hasani R, Zimmer M, Henzinger TA, Grosu R. Designing worm-inspired neural networks for interpretable robotic control. In: <i>Proceedings - IEEE International Conference on Robotics and Automation</i>. Vol 2019-May. IEEE; 2019. doi:<a href=\"https://doi.org/10.1109/icra.2019.8793840\">10.1109/icra.2019.8793840</a>","mla":"Lechner, Mathias, et al. “Designing Worm-Inspired Neural Networks for Interpretable Robotic Control.” <i>Proceedings - IEEE International Conference on Robotics and Automation</i>, vol. 2019–May, 8793840, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/icra.2019.8793840\">10.1109/icra.2019.8793840</a>.","short":"M. Lechner, R. Hasani, M. Zimmer, T.A. Henzinger, R. Grosu, in:, Proceedings - IEEE International Conference on Robotics and Automation, IEEE, 2019.","chicago":"Lechner, Mathias, Ramin Hasani, Manuel Zimmer, Thomas A Henzinger, and Radu Grosu. “Designing Worm-Inspired Neural Networks for Interpretable Robotic Control.” In <i>Proceedings - IEEE International Conference on Robotics and Automation</i>, Vol. 2019–May. IEEE, 2019. <a href=\"https://doi.org/10.1109/icra.2019.8793840\">https://doi.org/10.1109/icra.2019.8793840</a>.","ista":"Lechner M, Hasani R, Zimmer M, Henzinger TA, Grosu R. 2019. Designing worm-inspired neural networks for interpretable robotic control. Proceedings - IEEE International Conference on Robotics and Automation. ICRA: International Conference on Robotics and Automation, ICRA, vol. 2019–May, 8793840."},"scopus_import":"1","month":"05","doi":"10.1109/icra.2019.8793840","day":"01","publication_status":"published","department":[{"_id":"ToHe"}],"quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Submitted Version"},{"project":[{"grant_number":"S11407","call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","ddc":["000"],"year":"2019","article_number":"6","date_published":"2019-08-01T00:00:00Z","article_processing_charge":"No","intvolume":"       140","volume":140,"alternative_title":["LIPIcs"],"_id":"6889","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"last_name":"Piterman","full_name":"Piterman, Nir","first_name":"Nir"}],"status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"ama":"Chatterjee K, Piterman N. Combinations of Qualitative Winning for Stochastic Parity Games. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:<a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.6\">10.4230/LIPICS.CONCUR.2019.6</a>","apa":"Chatterjee, K., &#38; Piterman, N. (2019). Combinations of Qualitative Winning for Stochastic Parity Games (Vol. 140). Presented at the CONCUR: Conference on Concurrency Theory, Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.6\">https://doi.org/10.4230/LIPICS.CONCUR.2019.6</a>","ieee":"K. Chatterjee and N. Piterman, “Combinations of Qualitative Winning for Stochastic Parity Games,” presented at the CONCUR: Conference on Concurrency Theory, Amsterdam, Netherlands, 2019, vol. 140.","ista":"Chatterjee K, Piterman N. 2019. Combinations of Qualitative Winning for Stochastic Parity Games. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 140, 6.","mla":"Chatterjee, Krishnendu, and Nir Piterman. <i>Combinations of Qualitative Winning for Stochastic Parity Games</i>. Vol. 140, 6, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:<a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.6\">10.4230/LIPICS.CONCUR.2019.6</a>.","chicago":"Chatterjee, Krishnendu, and Nir Piterman. “Combinations of Qualitative Winning for Stochastic Parity Games,” Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. <a href=\"https://doi.org/10.4230/LIPICS.CONCUR.2019.6\">https://doi.org/10.4230/LIPICS.CONCUR.2019.6</a>.","short":"K. Chatterjee, N. Piterman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019."},"file":[{"access_level":"open_access","checksum":"7b2ecfd4d9d02360308c0ca986fc10a7","relation":"main_file","content_type":"application/pdf","file_name":"2019_LIPIcs_Chatterjee.pdf","date_created":"2019-10-01T08:49:45Z","file_id":"6923","creator":"kschuh","file_size":509163,"date_updated":"2020-07-14T12:47:43Z"}],"scopus_import":"1","month":"08","department":[{"_id":"KrCh"}],"publication_status":"published","doi":"10.4230/LIPICS.CONCUR.2019.6","day":"01","quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We study Markov decision processes and turn-based stochastic games with parity conditions. There are three qualitative winning criteria, namely, sure winning, which requires all paths to satisfy the condition, almost-sure winning, which requires the condition to be satisfied with probability 1, and limit-sure winning, which requires the condition to be satisfied with probability arbitrarily close to 1. We study the combination of two of these criteria for parity conditions, e.g., there are two parity conditions one of which must be won surely, and the other almost-surely. The problem has been studied recently by Berthon et al. for MDPs with combination of sure and almost-sure winning, under infinite-memory strategies, and the problem has been established to be in NP cap co-NP. Even in MDPs there is a difference between finite-memory and infinite-memory strategies. Our main results for combination of sure and almost-sure winning are as follows: (a) we show that for MDPs with finite-memory strategies the problem is in NP cap co-NP; (b) we show that for turn-based stochastic games the problem is co-NP-complete, both for finite-memory and infinite-memory strategies; and (c) we present algorithmic results for the finite-memory case, both for MDPs and turn-based stochastic games, by reduction to non-stochastic parity games. In addition we show that all the above complexity results also carry over to combination of sure and limit-sure winning, and results for all other combinations can be derived from existing results in the literature. Thus we present a complete picture for the study of combinations of two qualitative winning criteria for parity conditions in MDPs and turn-based stochastic games. "}],"date_created":"2019-09-18T08:11:43Z","file_date_updated":"2020-07-14T12:47:43Z","type":"conference","date_updated":"2025-07-10T11:53:59Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Combinations of Qualitative Winning for Stochastic Parity Games","conference":{"end_date":"2019-08-30","location":"Amsterdam, Netherlands","start_date":"2019-08-27","name":"CONCUR: Conference on Concurrency Theory"},"oa":1,"has_accepted_license":"1"},{"publisher":"Elsevier","year":"2019","pmid":1,"date_published":"2019-08-27T00:00:00Z","editor":[{"full_name":"Rey, Félix A.","last_name":"Rey","first_name":"Félix A."}],"page":"117-159","article_processing_charge":"No","intvolume":"       105","volume":105,"external_id":{"pmid":["    31522703"],"isi":["000501594500006"]},"_id":"6890","author":[{"first_name":"Martin","orcid":"0000-0003-1756-6564","last_name":"Obr","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Obr, Martin"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","last_name":"Schur","first_name":"Florian KM","orcid":"0000-0003-4790-8078"}],"isi":1,"citation":{"mla":"Obr, Martin, and Florian KM Schur. “Structural Analysis of Pleomorphic and Asymmetric Viruses Using Cryo-Electron Tomography and Subtomogram Averaging.” <i>Complementary Strategies to Study Virus Structure and Function</i>, edited by Félix A. Rey, vol. 105, Elsevier, 2019, pp. 117–59, doi:<a href=\"https://doi.org/10.1016/bs.aivir.2019.07.008\">10.1016/bs.aivir.2019.07.008</a>.","chicago":"Obr, Martin, and Florian KM Schur. “Structural Analysis of Pleomorphic and Asymmetric Viruses Using Cryo-Electron Tomography and Subtomogram Averaging.” In <i>Complementary Strategies to Study Virus Structure and Function</i>, edited by Félix A. Rey, 105:117–59. Advances in Virus Research. Elsevier, 2019. <a href=\"https://doi.org/10.1016/bs.aivir.2019.07.008\">https://doi.org/10.1016/bs.aivir.2019.07.008</a>.","short":"M. Obr, F.K. Schur, in:, F.A. Rey (Ed.), Complementary Strategies to Study Virus Structure and Function, Elsevier, 2019, pp. 117–159.","ista":"Obr M, Schur FK. 2019.Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. In: Complementary Strategies to Study Virus Structure and Function. vol. 105, 117–159.","ieee":"M. Obr and F. K. Schur, “Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging,” in <i>Complementary Strategies to Study Virus Structure and Function</i>, vol. 105, F. A. Rey, Ed. Elsevier, 2019, pp. 117–159.","ama":"Obr M, Schur FK. Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. In: Rey FA, ed. <i>Complementary Strategies to Study Virus Structure and Function</i>. Vol 105. Advances in Virus Research. Elsevier; 2019:117-159. doi:<a href=\"https://doi.org/10.1016/bs.aivir.2019.07.008\">10.1016/bs.aivir.2019.07.008</a>","apa":"Obr, M., &#38; Schur, F. K. (2019). Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. In F. A. Rey (Ed.), <i>Complementary Strategies to Study Virus Structure and Function</i> (Vol. 105, pp. 117–159). Elsevier. <a href=\"https://doi.org/10.1016/bs.aivir.2019.07.008\">https://doi.org/10.1016/bs.aivir.2019.07.008</a>"},"status":"public","scopus_import":"1","day":"27","doi":"10.1016/bs.aivir.2019.07.008","department":[{"_id":"FlSc"}],"publication_status":"published","month":"08","oa_version":"None","quality_controlled":"1","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9780128184561"],"issn":["0065-3527"]},"date_created":"2019-09-18T08:15:37Z","publication":"Complementary Strategies to Study Virus Structure and Function","abstract":[{"text":"Describing the protein interactions that form pleomorphic and asymmetric viruses represents a considerable challenge to most structural biology techniques, including X-ray crystallography and single particle cryo-electron microscopy. Obtaining a detailed understanding of these interactions is nevertheless important, considering the number of relevant human pathogens that do not follow strict icosahedral or helical symmetry. Cryo-electron tomography and subtomogram averaging methods provide structural insights into complex biological environments and are well suited to go beyond structures of perfectly symmetric viruses. This chapter discusses recent developments showing that cryo-ET and subtomogram averaging can provide high-resolution insights into hitherto unknown structural features of pleomorphic and asymmetric virus particles. It also describes how these methods have significantly added to our understanding of retrovirus capsid assemblies in immature and mature viruses. Additional examples of irregular viruses and their associated proteins, whose structures have been studied via cryo-ET and subtomogram averaging, further support the versatility of these methods.","lang":"eng"}],"series_title":"Advances in Virus Research","date_updated":"2023-08-30T06:56:00Z","type":"book_chapter","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging"},{"year":"2019","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","ddc":["000"],"article_processing_charge":"No","page":"132","date_published":"2019-09-30T00:00:00Z","author":[{"first_name":"Mirco","orcid":"0000-0001-8180-0904","last_name":"Giacobbe","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","full_name":"Giacobbe, Mirco"}],"alternative_title":["ISTA Thesis"],"_id":"6894","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"citation":{"ieee":"M. Giacobbe, “Automatic time-unbounded reachability analysis of hybrid systems,” Institute of Science and Technology Austria, 2019.","apa":"Giacobbe, M. (2019). <i>Automatic time-unbounded reachability analysis of hybrid systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6894\">https://doi.org/10.15479/AT:ISTA:6894</a>","ama":"Giacobbe M. Automatic time-unbounded reachability analysis of hybrid systems. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6894\">10.15479/AT:ISTA:6894</a>","short":"M. Giacobbe, Automatic Time-Unbounded Reachability Analysis of Hybrid Systems, Institute of Science and Technology Austria, 2019.","mla":"Giacobbe, Mirco. <i>Automatic Time-Unbounded Reachability Analysis of Hybrid Systems</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6894\">10.15479/AT:ISTA:6894</a>.","chicago":"Giacobbe, Mirco. “Automatic Time-Unbounded Reachability Analysis of Hybrid Systems.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6894\">https://doi.org/10.15479/AT:ISTA:6894</a>.","ista":"Giacobbe M. 2019. Automatic time-unbounded reachability analysis of hybrid systems. Institute of Science and Technology Austria."},"file":[{"file_size":4100685,"creator":"mgiacobbe","date_updated":"2020-07-14T12:47:43Z","file_name":"giacobbe_thesis.pdf","date_created":"2019-09-27T14:15:05Z","file_id":"6916","relation":"main_file","checksum":"773beaf4a85dc2acc2c12b578fbe1965","content_type":"application/pdf","access_level":"open_access"},{"access_level":"closed","relation":"source_file","checksum":"97f1c3da71feefd27e6e625d32b4c75b","content_type":"application/gzip","file_name":"giacobbe_thesis_src.tar.gz","file_id":"6917","date_created":"2019-09-27T14:22:04Z","file_size":7959732,"creator":"mgiacobbe","date_updated":"2020-07-14T12:47:43Z"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"647","relation":"part_of_dissertation","status":"public"},{"id":"631","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"140","status":"public"}]},"corr_author":"1","month":"09","publication_status":"published","department":[{"_id":"ToHe"}],"day":"30","doi":"10.15479/AT:ISTA:6894","file_date_updated":"2020-07-14T12:47:43Z","type":"dissertation","date_updated":"2026-04-16T09:55:03Z","abstract":[{"text":"Hybrid automata combine finite automata and dynamical systems, and model the interaction of digital with physical systems. Formal analysis that can guarantee the safety of all behaviors or rigorously witness failures, while unsolvable in general, has been tackled algorithmically using, e.g., abstraction, bounded model-checking, assisted theorem proving.\r\nNevertheless, very few methods have addressed the time-unbounded reachability analysis of hybrid automata and, for current sound and automatic tools, scalability remains critical. We develop methods for the polyhedral abstraction of hybrid automata, which construct coarse overapproximations and tightens them incrementally, in a CEGAR fashion. We use template polyhedra, i.e., polyhedra whose facets are normal to a given set of directions.\r\nWhile, previously, directions were given by the user, we introduce (1) the first method\r\nfor computing template directions from spurious counterexamples, so as to generalize and\r\neliminate them. The method applies naturally to convex hybrid automata, i.e., hybrid\r\nautomata with (possibly non-linear) convex constraints on derivatives only, while for linear\r\nODE requires further abstraction. Specifically, we introduce (2) the conic abstractions,\r\nwhich, partitioning the state space into appropriate (possibly non-uniform) cones, divide\r\ncurvy trajectories into relatively straight sections, suitable for polyhedral abstractions.\r\nFinally, we introduce (3) space-time interpolation, which, combining interval arithmetic\r\nand template refinement, computes appropriate (possibly non-uniform) time partitioning\r\nand template directions along spurious trajectories, so as to eliminate them.\r\nWe obtain sound and automatic methods for the reachability analysis over dense\r\nand unbounded time of convex hybrid automata and hybrid automata with linear ODE.\r\nWe build prototype tools and compare—favorably—our methods against the respective\r\nstate-of-the-art tools, on several benchmarks.","lang":"eng"}],"supervisor":[{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A"}],"date_created":"2019-09-22T14:08:44Z","publication_identifier":{"eissn":["2663-337X"]},"has_accepted_license":"1","oa":1,"OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","title":"Automatic time-unbounded reachability analysis of hybrid systems"},{"pmid":1,"date_published":"2019-12-01T00:00:00Z","article_processing_charge":"No","publisher":"Elsevier","article_number":"146458","year":"2019","external_id":{"isi":["000491646600033"],"pmid":["31521639"]},"_id":"6896","author":[{"first_name":"Bárbara","last_name":"Oliveira","full_name":"Oliveira, Bárbara","id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Aysan Çerağ","last_name":"Yahya","full_name":"Yahya, Aysan Çerağ","id":"365A65F8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia"}],"isi":1,"intvolume":"      1724","volume":1724,"month":"12","doi":"10.1016/j.brainres.2019.146458","day":"01","publication_status":"published","department":[{"_id":"GaNo"}],"quality_controlled":"1","oa_version":"None","language":[{"iso":"eng"}],"status":"public","citation":{"mla":"Oliveira, Bárbara, et al. “Modeling Cell-Cell Interactions in the Brain Using Cerebral Organoids.” <i>Brain Research</i>, vol. 1724, 146458, Elsevier, 2019, doi:<a href=\"https://doi.org/10.1016/j.brainres.2019.146458\">10.1016/j.brainres.2019.146458</a>.","short":"B. Oliveira, A.Ç. Yahya, G. Novarino, Brain Research 1724 (2019).","chicago":"Oliveira, Bárbara, Aysan Çerağ Yahya, and Gaia Novarino. “Modeling Cell-Cell Interactions in the Brain Using Cerebral Organoids.” <i>Brain Research</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.brainres.2019.146458\">https://doi.org/10.1016/j.brainres.2019.146458</a>.","ista":"Oliveira B, Yahya AÇ, Novarino G. 2019. Modeling cell-cell interactions in the brain using cerebral organoids. Brain Research. 1724, 146458.","ieee":"B. Oliveira, A. Ç. Yahya, and G. Novarino, “Modeling cell-cell interactions in the brain using cerebral organoids,” <i>Brain Research</i>, vol. 1724. Elsevier, 2019.","ama":"Oliveira B, Yahya AÇ, Novarino G. Modeling cell-cell interactions in the brain using cerebral organoids. <i>Brain Research</i>. 2019;1724. doi:<a href=\"https://doi.org/10.1016/j.brainres.2019.146458\">10.1016/j.brainres.2019.146458</a>","apa":"Oliveira, B., Yahya, A. Ç., &#38; Novarino, G. (2019). Modeling cell-cell interactions in the brain using cerebral organoids. <i>Brain Research</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.brainres.2019.146458\">https://doi.org/10.1016/j.brainres.2019.146458</a>"},"scopus_import":"1","article_type":"original","title":"Modeling cell-cell interactions in the brain using cerebral organoids","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Until recently, a great amount of brain studies have been conducted in human post mortem tissues, cell lines and model organisms. These researches provided useful insights regarding cell-cell interactions occurring in the brain. However, such approaches suffer from technical limitations and inaccurate modeling of the tissue 3D cytoarchitecture. Importantly, they might lack a human genetic background essential for disease modeling. With the development of protocols to generate human cerebral organoids, we are now closer to reproducing the early stages of human brain development in vitro. As a result, more relevant cell-cell interaction studies can be conducted.\r\n\r\nIn this review, we discuss the advantages of 3D cultures over 2D in modulating brain cell-cell interactions during physiological and pathological development, as well as the progress made in developing organoids in which neurons, macroglia, microglia and vascularization are present. Finally, we debate the limitations of those models and possible future directions."}],"publication_identifier":{"eissn":["1872-6240"],"issn":["0006-8993"]},"date_created":"2019-09-22T22:00:35Z","publication":"Brain Research","date_updated":"2025-07-10T11:54:01Z","type":"journal_article"},{"citation":{"ista":"Zhu Q, Gallemi M, Pospíšil J, Žádníková P, Strnad M, Benková E. 2019. Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis. Development. 146(17), dev175919.","short":"Q. Zhu, M. Gallemi, J. Pospíšil, P. Žádníková, M. Strnad, E. Benková, Development 146 (2019).","mla":"Zhu, Qiang, et al. “Root Gravity Response Module Guides Differential Growth Determining Both Root Bending and Apical Hook Formation in Arabidopsis.” <i>Development</i>, vol. 146, no. 17, dev175919, The Company of Biologists, 2019, doi:<a href=\"https://doi.org/10.1242/dev.175919\">10.1242/dev.175919</a>.","chicago":"Zhu, Qiang, Marçal Gallemi, Jiří Pospíšil, Petra Žádníková, Miroslav Strnad, and Eva Benková. “Root Gravity Response Module Guides Differential Growth Determining Both Root Bending and Apical Hook Formation in Arabidopsis.” <i>Development</i>. The Company of Biologists, 2019. <a href=\"https://doi.org/10.1242/dev.175919\">https://doi.org/10.1242/dev.175919</a>.","ama":"Zhu Q, Gallemi M, Pospíšil J, Žádníková P, Strnad M, Benková E. Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis. <i>Development</i>. 2019;146(17). doi:<a href=\"https://doi.org/10.1242/dev.175919\">10.1242/dev.175919</a>","apa":"Zhu, Q., Gallemi, M., Pospíšil, J., Žádníková, P., Strnad, M., &#38; Benková, E. (2019). Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.175919\">https://doi.org/10.1242/dev.175919</a>","ieee":"Q. Zhu, M. Gallemi, J. Pospíšil, P. Žádníková, M. Strnad, and E. Benková, “Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis,” <i>Development</i>, vol. 146, no. 17. The Company of Biologists, 2019."},"status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1242/dev.175919"}],"scopus_import":"1","acknowledgement":"We thank Jiri Friml and Phillip Brewer for inspiring discussion and for help in preparing the manuscript. This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Bioimaging Facility\r\n(BIF), the Life Science Facility (LSF).\r\nThis work was supported by grants from the European Research Council (Starting Independent Research Grant ERC-2007-Stg- 207362-HCPO to E.B.). J.P. and M.S. received funds from European Regional Development Fund-Project ‘Centre for Experimental Plant Biology’ (No. CZ.02.1.01/0.0/0.0/16_019/0000738).","department":[{"_id":"EvBe"}],"publication_status":"published","doi":"10.1242/dev.175919","ec_funded":1,"day":"12","month":"09","oa_version":"Published Version","quality_controlled":"1","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"date_created":"2019-09-22T22:00:36Z","publication":"Development","publication_identifier":{"eissn":["1477-9129"]},"abstract":[{"lang":"eng","text":"The apical hook is a transiently formed structure that plays a protective role when the germinating seedling penetrates through the soil towards the surface. Crucial for proper bending is the local auxin maxima, which defines the concave (inner) side of the hook curvature. As no sign of asymmetric auxin distribution has been reported in embryonic hypocotyls prior to hook formation, the question of how auxin asymmetry is established in the early phases of seedling germination remains largely unanswered. Here, we analyzed the auxin distribution and expression of PIN auxin efflux carriers from early phases of germination, and show that bending of the root in response to gravity is the crucial initial cue that governs the hypocotyl bending required for apical hook formation. Importantly, polar auxin transport machinery is established gradually after germination starts as a result of tight root-hypocotyl interaction and a proper balance between abscisic acid and gibberellins."}],"type":"journal_article","date_updated":"2026-06-18T19:13:37Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Root gravity response module guides differential growth determining both root bending and apical hook formation in Arabidopsis","article_type":"original","oa":1,"ddc":["580"],"project":[{"call_identifier":"FP7","name":"Hormonal cross-talk in plant organogenesis","grant_number":"207362","_id":"253FCA6A-B435-11E9-9278-68D0E5697425"}],"publisher":"The Company of Biologists","year":"2019","article_number":"dev175919","date_published":"2019-09-12T00:00:00Z","pmid":1,"article_processing_charge":"No","intvolume":"       146","volume":146,"_id":"6897","issue":"17","external_id":{"pmid":["31391194"],"isi":["000486297400011"]},"isi":1,"author":[{"id":"40A4B9E6-F248-11E8-B48F-1D18A9856A87","full_name":"Zhu, Qiang","last_name":"Zhu","first_name":"Qiang"},{"last_name":"Gallemi","id":"460C6802-F248-11E8-B48F-1D18A9856A87","full_name":"Gallemi, Marçal","first_name":"Marçal","orcid":"0000-0003-4675-6893"},{"last_name":"Pospíšil","full_name":"Pospíšil, Jiří","first_name":"Jiří"},{"first_name":"Petra","full_name":"Žádníková, Petra","last_name":"Žádníková"},{"first_name":"Miroslav","last_name":"Strnad","full_name":"Strnad, Miroslav"},{"first_name":"Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"}]}]