[{"oa_version":"Published Version","file":[{"file_id":"8611","creator":"dernst","relation":"main_file","file_name":"2020_LIPIcsCONCUR_Avni.pdf","success":1,"file_size":868510,"checksum":"8f33b098e73724e0ac817f764d8e1a2d","date_created":"2020-10-05T14:13:19Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-10-05T14:13:19Z"}],"ddc":["000"],"type":"conference","publication_status":"published","alternative_title":["LIPIcs"],"_id":"8599","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"ToHe"}],"publication_identifier":{"issn":["18688969"],"isbn":["9783959771603"]},"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"}],"month":"08","year":"2020","abstract":[{"text":"A graph game is a two-player zero-sum game in which the players move a token throughout a graph to produce an infinite path, which determines the winner or payoff of the game. In bidding games, both players have budgets, and in each turn, we hold an \"auction\" (bidding) to determine which player moves the token. In this survey, we consider several bidding mechanisms and study their effect on the properties of the game. Specifically, bidding games, and in particular bidding games of infinite duration, have an intriguing equivalence with random-turn games in which in each turn, the player who moves is chosen randomly. We show how minor changes in the bidding mechanism lead to unexpected differences in the equivalence with random-turn games.","lang":"eng"}],"scopus_import":"1","date_updated":"2021-01-12T08:20:13Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"status":"public","author":[{"orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"license":"https://creativecommons.org/licenses/by/3.0/","citation":{"mla":"Avni, Guy, and Thomas A. Henzinger. “A Survey of Bidding Games on Graphs.” 31st International Conference on Concurrency Theory, vol. 171, 2, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.CONCUR.2020.2.","chicago":"Avni, Guy, and Thomas A Henzinger. “A Survey of Bidding Games on Graphs.” In 31st International Conference on Concurrency Theory, Vol. 171. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.CONCUR.2020.2.","apa":"Avni, G., & Henzinger, T. A. (2020). A survey of bidding games on graphs. In 31st International Conference on Concurrency Theory (Vol. 171). Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2020.2","short":"G. Avni, T.A. Henzinger, in:, 31st International Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","ista":"Avni G, Henzinger TA. 2020. A survey of bidding games on graphs. 31st International Conference on Concurrency Theory. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 171, 2.","ieee":"G. Avni and T. A. Henzinger, “A survey of bidding games on graphs,” in 31st International Conference on Concurrency Theory, Virtual, 2020, vol. 171.","ama":"Avni G, Henzinger TA. A survey of bidding games on graphs. In: 31st International Conference on Concurrency Theory. Vol 171. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.CONCUR.2020.2"},"date_created":"2020-10-04T22:01:36Z","quality_controlled":"1","conference":{"location":"Virtual","end_date":"2020-09-04","start_date":"2020-09-01","name":"CONCUR: Conference on Concurrency Theory"},"oa":1,"article_number":"2","title":"A survey of bidding games on graphs","intvolume":" 171","has_accepted_license":"1","date_published":"2020-08-06T00:00:00Z","acknowledgement":"We would like to thank all our collaborators Milad Aghajohari, Ventsislav Chonev, Rasmus Ibsen-Jensen, Ismäel Jecker, Petr Novotný, Josef Tkadlec, and Ðorđe Žikelić; we hope the collaboration was as fun and meaningful for you as it was for us.","day":"06","publication":"31st International Conference on Concurrency Theory","volume":171,"tmp":{"short":"CC BY (3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png"},"article_processing_charge":"No","doi":"10.4230/LIPIcs.CONCUR.2020.2","file_date_updated":"2020-10-05T14:13:19Z"},{"publication":"31st International Conference on Concurrency Theory","day":"06","volume":171,"intvolume":" 171","has_accepted_license":"1","date_published":"2020-08-06T00:00:00Z","doi":"10.4230/LIPIcs.CONCUR.2020.23","file_date_updated":"2020-10-05T14:04:25Z","tmp":{"short":"CC BY (3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png"},"article_processing_charge":"No","oa":1,"article_number":"23","citation":{"short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, 31st International Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","ista":"Chatterjee K, Henzinger TA, Otop J. 2020. Multi-dimensional long-run average problems for vector addition systems with states. 31st International Conference on Concurrency Theory. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 171, 23.","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Multi-dimensional long-run average problems for vector addition systems with states,” in 31st International Conference on Concurrency Theory, Virtual, 2020, vol. 171.","ama":"Chatterjee K, Henzinger TA, Otop J. Multi-dimensional long-run average problems for vector addition systems with states. In: 31st International Conference on Concurrency Theory. Vol 171. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.CONCUR.2020.23","mla":"Chatterjee, Krishnendu, et al. “Multi-Dimensional Long-Run Average Problems for Vector Addition Systems with States.” 31st International Conference on Concurrency Theory, vol. 171, 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.CONCUR.2020.23.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Multi-Dimensional Long-Run Average Problems for Vector Addition Systems with States.” In 31st International Conference on Concurrency Theory, Vol. 171. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.CONCUR.2020.23.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2020). Multi-dimensional long-run average problems for vector addition systems with states. In 31st International Conference on Concurrency Theory (Vol. 171). Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2020.23"},"date_created":"2020-10-04T22:01:36Z","arxiv":1,"quality_controlled":"1","conference":{"start_date":"2020-09-01","name":"CONCUR: Conference on Concurrency Theory","end_date":"2020-09-04","location":"Virtual"},"title":"Multi-dimensional long-run average problems for vector addition systems with states","date_updated":"2021-01-12T08:20:15Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"abstract":[{"text":"A vector addition system with states (VASS) consists of a finite set of states and counters. A transition changes the current state to the next state, and every counter is either incremented, or decremented, or left unchanged. A state and value for each counter is a configuration; and a computation is an infinite sequence of configurations with transitions between successive configurations. A probabilistic VASS consists of a VASS along with a probability distribution over the transitions for each state. Qualitative properties such as state and configuration reachability have been widely studied for VASS. In this work we consider multi-dimensional long-run average objectives for VASS and probabilistic VASS. For a counter, the cost of a configuration is the value of the counter; and the long-run average value of a computation for the counter is the long-run average of the costs of the configurations in the computation. The multi-dimensional long-run average problem given a VASS and a threshold value for each counter, asks whether there is a computation such that for each counter the long-run average value for the counter does not exceed the respective threshold. For probabilistic VASS, instead of the existence of a computation, we consider whether the expected long-run average value for each counter does not exceed the respective threshold. Our main results are as follows: we show that the multi-dimensional long-run average problem (a) is NP-complete for integer-valued VASS; (b) is undecidable for natural-valued VASS (i.e., nonnegative counters); and (c) can be solved in polynomial time for probabilistic integer-valued VASS, and probabilistic natural-valued VASS when all computations are non-terminating.","lang":"eng"}],"scopus_import":"1","status":"public","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan","last_name":"Otop"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","type":"conference","file":[{"date_created":"2020-10-05T14:04:25Z","checksum":"5039752f644c4b72b9361d21a5e31baf","success":1,"file_size":601231,"date_updated":"2020-10-05T14:04:25Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"8610","creator":"dernst","file_name":"2020_LIPIcsCONCUR_Chatterjee.pdf"}],"ddc":["000"],"oa_version":"Published Version","alternative_title":["LIPIcs"],"publication_status":"published","external_id":{"arxiv":["2007.08917"]},"_id":"8600","publication_identifier":{"issn":["18688969"],"isbn":["9783959771603"]},"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"},{"grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"year":"2020","month":"08","department":[{"_id":"KrCh"},{"_id":"ToHe"}]},{"author":[{"last_name":"Liu","full_name":"Liu, D","first_name":"D"},{"first_name":"R","full_name":"Kumar, R","last_name":"Kumar"},{"first_name":"Claus","last_name":"LAN","full_name":"LAN, Claus"},{"orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J"},{"first_name":"W","last_name":"Siao","full_name":"Siao, W"},{"full_name":"Vanhoutte, I","last_name":"Vanhoutte","first_name":"I"},{"first_name":"P","full_name":"Wang, P","last_name":"Wang"},{"first_name":"KW","full_name":"Bender, KW","last_name":"Bender"},{"full_name":"Yperman, K","last_name":"Yperman","first_name":"K"},{"first_name":"S","last_name":"Martins","full_name":"Martins, S"},{"first_name":"X","last_name":"Zhao","full_name":"Zhao, X"},{"last_name":"Vert","full_name":"Vert, G","first_name":"G"},{"first_name":"D","full_name":"Van Damme, D","last_name":"Van Damme"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří"},{"first_name":"E","last_name":"Russinova","full_name":"Russinova, E"}],"status":"public","date_updated":"2023-09-05T12:21:32Z","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) and its core endocytic machinery are evolutionarily conserved across all eukaryotes. In mammals, the heterotetrameric adaptor protein complex-2 (AP-2) sorts plasma membrane (PM) cargoes into vesicles through the recognition of motifs based on tyrosine or di-leucine in their cytoplasmic tails. However, in plants, very little is known on how PM proteins are sorted for CME and whether similar motifs are required. In Arabidopsis thaliana, the brassinosteroid (BR) receptor, BR INSENSITIVE1 (BRI1), undergoes endocytosis that depends on clathrin and AP-2. Here we demonstrate that BRI1 binds directly to the medium AP-2 subunit, AP2M. The cytoplasmic domain of BRI1 contains five putative canonical surface-exposed tyrosine-based endocytic motifs. The tyrosine-to-phenylalanine substitution in Y898KAI reduced BRI1 internalization without affecting its kinase activity. Consistently, plants carrying the BRI1Y898F mutation were hypersensitive to BRs. Our study demonstrates that AP-2-dependent internalization of PM proteins via the recognition of functional tyrosine motifs also operates in plants."}],"main_file_link":[{"open_access":"1","url":"https://europepmc.org/article/MED/32958564"}],"scopus_import":"1","isi":1,"publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298x"]},"month":"11","year":"2020","project":[{"name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"},{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"JiFr"}],"article_type":"original","publisher":"American Society of Plant Biologists","type":"journal_article","oa_version":"Published Version","issue":"11","_id":"8607","external_id":{"pmid":["32958564"],"isi":["000600226800021"]},"publication_status":"published","doi":"10.1105/tpc.20.00384","article_processing_charge":"No","ec_funded":1,"volume":32,"day":"01","publication":"Plant Cell","pmid":1,"intvolume":" 32","date_published":"2020-11-01T00:00:00Z","page":"3598-3612","title":"Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based Motif","oa":1,"date_created":"2020-10-05T12:45:16Z","citation":{"apa":"Liu, D., Kumar, R., LAN, C., Johnson, A. J., Siao, W., Vanhoutte, I., … Russinova, E. (2020). Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based Motif. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.20.00384","chicago":"Liu, D, R Kumar, Claus LAN, Alexander J Johnson, W Siao, I Vanhoutte, P Wang, et al. “Endocytosis of BRASSINOSTEROID INSENSITIVE1 Is Partly Driven by a Canonical Tyrosine-Based Motif.” Plant Cell. American Society of Plant Biologists, 2020. https://doi.org/10.1105/tpc.20.00384.","mla":"Liu, D., et al. “Endocytosis of BRASSINOSTEROID INSENSITIVE1 Is Partly Driven by a Canonical Tyrosine-Based Motif.” Plant Cell, vol. 32, no. 11, American Society of Plant Biologists, 2020, pp. 3598–612, doi:10.1105/tpc.20.00384.","ama":"Liu D, Kumar R, LAN C, et al. Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based Motif. Plant Cell. 2020;32(11):3598-3612. doi:10.1105/tpc.20.00384","ista":"Liu D, Kumar R, LAN C, Johnson AJ, Siao W, Vanhoutte I, Wang P, Bender K, Yperman K, Martins S, Zhao X, Vert G, Van Damme D, Friml J, Russinova E. 2020. Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based Motif. Plant Cell. 32(11), 3598–3612.","ieee":"D. Liu et al., “Endocytosis of BRASSINOSTEROID INSENSITIVE1 is partly driven by a canonical tyrosine-based Motif,” Plant Cell, vol. 32, no. 11. American Society of Plant Biologists, pp. 3598–3612, 2020.","short":"D. Liu, R. Kumar, C. LAN, A.J. Johnson, W. Siao, I. Vanhoutte, P. Wang, K. Bender, K. Yperman, S. Martins, X. Zhao, G. Vert, D. Van Damme, J. Friml, E. Russinova, Plant Cell 32 (2020) 3598–3612."},"quality_controlled":"1"},{"doi":"10.1101/2020.09.15.262782","ec_funded":1,"author":[{"first_name":"Xiaofei","last_name":"Gao","full_name":"Gao, Xiaofei"},{"first_name":"Jun-Liszt","full_name":"Li, Jun-Liszt","last_name":"Li"},{"last_name":"Chen","full_name":"Chen, Xingjun","first_name":"Xingjun"},{"last_name":"Ci","full_name":"Ci, Bo","first_name":"Bo"},{"first_name":"Fei","full_name":"Chen, Fei","last_name":"Chen"},{"first_name":"Nannan","last_name":"Lu","full_name":"Lu, Nannan"},{"last_name":"Shen","full_name":"Shen, Bo","first_name":"Bo"},{"last_name":"Zheng","full_name":"Zheng, Lijun","first_name":"Lijun"},{"first_name":"Jie-Min","last_name":"Jia","full_name":"Jia, Jie-Min"},{"full_name":"Yi, Yating","last_name":"Yi","first_name":"Yating"},{"last_name":"Zhang","full_name":"Zhang, Shiwen","first_name":"Shiwen"},{"last_name":"Shi","full_name":"Shi, Ying-Chao","first_name":"Ying-Chao"},{"last_name":"Shi","full_name":"Shi, Kaibin","first_name":"Kaibin"},{"last_name":"Propson","full_name":"Propson, Nicholas E","first_name":"Nicholas E"},{"last_name":"Huang","full_name":"Huang, Yubin","first_name":"Yubin"},{"last_name":"Poinsatte","full_name":"Poinsatte, Katherine","first_name":"Katherine"},{"first_name":"Zhaohuan","full_name":"Zhang, Zhaohuan","last_name":"Zhang"},{"last_name":"Yue","full_name":"Yue, Yuanlei","first_name":"Yuanlei"},{"last_name":"Bosco","full_name":"Bosco, Dale B","first_name":"Dale B"},{"first_name":"Ying-mei","last_name":"Lu","full_name":"Lu, Ying-mei"},{"first_name":"Shi-bing","full_name":"Yang, Shi-bing","last_name":"Yang"},{"first_name":"Ralf H.","last_name":"Adams","full_name":"Adams, Ralf H."},{"last_name":"Lindner","full_name":"Lindner, Volkhard","first_name":"Volkhard"},{"full_name":"Huang, Fen","last_name":"Huang","first_name":"Fen"},{"first_name":"Long-Jun","full_name":"Wu, Long-Jun","last_name":"Wu"},{"last_name":"Zheng","full_name":"Zheng, Hui","first_name":"Hui"},{"first_name":"Feng","last_name":"Han","full_name":"Han, Feng"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Stowe, Ann M.","last_name":"Stowe","first_name":"Ann M."},{"last_name":"Peng","full_name":"Peng, Bo","first_name":"Bo"},{"full_name":"Margeta, Marta","last_name":"Margeta","first_name":"Marta"},{"first_name":"Xiaoqun","last_name":"Wang","full_name":"Wang, Xiaoqun"},{"first_name":"Qiang","last_name":"Liu","full_name":"Liu, Qiang"},{"full_name":"Körbelin, Jakob","last_name":"Körbelin","first_name":"Jakob"},{"full_name":"Trepel, Martin","last_name":"Trepel","first_name":"Martin"},{"first_name":"Hui","full_name":"Lu, Hui","last_name":"Lu"},{"last_name":"Zhou","full_name":"Zhou, Bo O.","first_name":"Bo O."},{"full_name":"Zhao, Hu","last_name":"Zhao","first_name":"Hu"},{"last_name":"Su","full_name":"Su, Wenzhi","first_name":"Wenzhi"},{"full_name":"Bachoo, Robert M.","last_name":"Bachoo","first_name":"Robert M."},{"full_name":"Ge, Woo-ping","last_name":"Ge","first_name":"Woo-ping"}],"article_processing_charge":"No","status":"public","date_updated":"2021-01-12T08:20:19Z","publication":"bioRxiv","acknowledgement":"The project was initiated in the Jan lab at UCSF. We thank Lily Jan and Yuh-Nung Jan’s generous support. We thank Liqun Luo’s lab for providing MADM-7 mice and Rolf A Brekken for VEGF-antibodies. Drs. Yuanquan Song (UPenn), Zhaozhu Hu (JHU), Ji Hu (ShanghaiTech), Yang Xiang (U. Mass), Hao Wang (Zhejiang U.) and Ruikang Wang (U. Washington) for critical input, colleagues at Children’s Research Institute, Departments of Neuroscience, Neurology and Neurotherapeutics, Pediatrics from UT Southwestern, and colleagues from the Jan lab for discussion. Dr. Bridget Samuels, Sean Morrison (UT Southwestern), and Nannan Lu (Zhejiang U.) for critical reading. We acknowledge the assistance of the CIBR Imaging core. We also thank UT Southwestern Live Cell Imaging Facility, a Shared Resource of the Harold C. Simmons Cancer Center, supported in part by an NCI Cancer Center Support Grant, P30 CA142543K. This work is supported by CIBR funds and the American Heart Association AWRP Summer 2016 Innovative Research Grant (17IRG33410377) to W-P.G.; National Natural Science Foundation of China (No.81370031) to Z.Z.;National Key Research and Development Program of China (2016YFE0125400)to F.H.;National Natural Science Foundations of China (No. 81473202) to Y.L.; National Natural Science Foundation of China (No.31600839) and Shenzhen Science and Technology Research Program (JCYJ20170818163320865) to B.P.; National Natural Science Foundation of China (No. 31800864) and Westlake University start-up funds to J-M. J. NIH R01NS088627 to W.L.J.; NIH: R01 AG020670 and RF1AG054111 to H.Z.; R01 NS088555 to A.M.S., and European Research Council No.725780 to S.H.;W-P.G. was a recipient of Bugher-American Heart Association Dan Adams Thinking Outside the Box Award.","day":"15","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The brain vasculature supplies neurons with glucose and oxygen, but little is known about how vascular plasticity contributes to brain function. Using longitudinal in vivo imaging, we reported that a substantial proportion of blood vessels in the adult brain sporadically occluded and regressed. Their regression proceeded through sequential stages of blood-flow occlusion, endothelial cell collapse, relocation or loss of pericytes, and retraction of glial endfeet. Regressing vessels were found to be widespread in mouse, monkey and human brains. Both brief occlusions of the middle cerebral artery and lipopolysaccharide-mediated inflammation induced an increase of vessel regression. Blockage of leukocyte adhesion to endothelial cells alleviated LPS-induced vessel regression. We further revealed that blood vessel regression caused a reduction of neuronal activity due to a dysfunction in mitochondrial metabolism and glutamate production. Our results elucidate the mechanism of vessel regression and its role in neuronal function in the adult brain.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.09.15.262782"}],"date_published":"2020-09-15T00:00:00Z","month":"09","year":"2020","project":[{"grant_number":"725780","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"title":"Reduction of neuronal activity mediated by blood-vessel regression in the brain","department":[{"_id":"SiHi"}],"publisher":"Cold Spring Harbor Laboratory","oa":1,"citation":{"mla":"Gao, Xiaofei, et al. “Reduction of Neuronal Activity Mediated by Blood-Vessel Regression in the Brain.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2020.09.15.262782.","chicago":"Gao, Xiaofei, Jun-Liszt Li, Xingjun Chen, Bo Ci, Fei Chen, Nannan Lu, Bo Shen, et al. “Reduction of Neuronal Activity Mediated by Blood-Vessel Regression in the Brain.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2020.09.15.262782.","apa":"Gao, X., Li, J.-L., Chen, X., Ci, B., Chen, F., Lu, N., … Ge, W. (n.d.). Reduction of neuronal activity mediated by blood-vessel regression in the brain. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.09.15.262782","ieee":"X. Gao et al., “Reduction of neuronal activity mediated by blood-vessel regression in the brain,” bioRxiv. Cold Spring Harbor Laboratory.","short":"X. Gao, J.-L. Li, X. Chen, B. Ci, F. Chen, N. Lu, B. Shen, L. Zheng, J.-M. Jia, Y. Yi, S. Zhang, Y.-C. Shi, K. Shi, N.E. Propson, Y. Huang, K. Poinsatte, Z. Zhang, Y. Yue, D.B. Bosco, Y. Lu, S. Yang, R.H. Adams, V. Lindner, F. Huang, L.-J. Wu, H. Zheng, F. Han, S. Hippenmeyer, A.M. Stowe, B. Peng, M. Margeta, X. Wang, Q. Liu, J. Körbelin, M. Trepel, H. Lu, B.O. Zhou, H. Zhao, W. Su, R.M. Bachoo, W. Ge, BioRxiv (n.d.).","ista":"Gao X, Li J-L, Chen X, Ci B, Chen F, Lu N, Shen B, Zheng L, Jia J-M, Yi Y, Zhang S, Shi Y-C, Shi K, Propson NE, Huang Y, Poinsatte K, Zhang Z, Yue Y, Bosco DB, Lu Y, Yang S, Adams RH, Lindner V, Huang F, Wu L-J, Zheng H, Han F, Hippenmeyer S, Stowe AM, Peng B, Margeta M, Wang X, Liu Q, Körbelin J, Trepel M, Lu H, Zhou BO, Zhao H, Su W, Bachoo RM, Ge W. Reduction of neuronal activity mediated by blood-vessel regression in the brain. bioRxiv, 10.1101/2020.09.15.262782.","ama":"Gao X, Li J-L, Chen X, et al. Reduction of neuronal activity mediated by blood-vessel regression in the brain. bioRxiv. doi:10.1101/2020.09.15.262782"},"date_created":"2020-10-06T08:58:59Z","type":"preprint","oa_version":"Preprint","_id":"8616","publication_status":"submitted"},{"publication_identifier":{"issn":["2663-337X"]},"project":[{"grant_number":"W1232-B24","name":"Molecular Drug Targets","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"_id":"05A0D778-7A3F-11EA-A408-12923DDC885E","name":"Neural stem cells in autism and epilepsy","grant_number":"F07807"}],"year":"2020","month":"10","department":[{"_id":"GaNo"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"orcid":"0000-0002-7673-7178","last_name":"Novarino","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"}],"ddc":["610"],"type":"dissertation","file":[{"creator":"jmorande","file_id":"8621","relation":"main_file","file_name":"Jasmin_Morandell_Thesis-2020_final.pdf","checksum":"7ee83e42de3e5ce2fedb44dff472f75f","file_size":16155786,"date_created":"2020-10-07T14:41:49Z","content_type":"application/pdf","embargo":"2021-10-15","access_level":"open_access","date_updated":"2021-10-16T22:30:04Z"},{"relation":"source_file","creator":"jmorande","file_id":"8622","file_name":"Jasmin_Morandell_Thesis-2020_final.zip","date_created":"2020-10-07T14:45:07Z","embargo_to":"open_access","file_size":24344152,"checksum":"5e0464af453734210ce7aab7b4a92e3a","date_updated":"2021-10-16T22:30:04Z","content_type":"application/x-zip-compressed","access_level":"closed"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"publication_status":"published","_id":"8620","status":"public","author":[{"full_name":"Morandell, Jasmin","last_name":"Morandell","first_name":"Jasmin","id":"4739D480-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-09-10T12:04:25Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"7800","relation":"part_of_dissertation","status":"public"},{"id":"8131","relation":"part_of_dissertation","status":"public"}]},"abstract":[{"lang":"eng","text":"The development of the human brain occurs through a tightly regulated series of dynamic and adaptive processes during prenatal and postnatal life. A disruption of this strictly orchestrated series of events can lead to a number of neurodevelopmental conditions, including Autism Spectrum Disorders (ASDs). ASDs are a very common, etiologically and phenotypically heterogeneous group of disorders sharing the core symptoms of social interaction and communication deficits and restrictive and repetitive interests and behaviors. They are estimated to affect one in 59 individuals in the U.S. and, over the last three decades, mutations in more than a hundred genetic loci have been convincingly linked to ASD pathogenesis. Yet, for the vast majority of these ASD-risk genes their role during brain development and precise molecular function still remain elusive.\r\nDe novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin 3 (CUL3) lead to ASD. In the study described here, we used Cul3 mouse models to evaluate the consequences of Cul3 mutations in vivo. Our results show that Cul3 heterozygous knockout mice exhibit deficits in motor coordination as well as ASD-relevant social and cognitive impairments. Cul3+/-, Cul3+/fl Emx1-Cre and Cul3fl/fl Emx1-Cre mutant brains display cortical lamination abnormalities due to defective migration of post-mitotic excitatory neurons, as well as reduced numbers of excitatory and inhibitory neurons. In line with the observed abnormal cortical organization, Cul3 heterozygous deletion is associated with decreased spontaneous excitatory and inhibitory activity in the cortex. At the molecular level we show that Cul3 regulates cytoskeletal and adhesion protein abundance in the mouse embryonic cortex. Abnormal regulation of cytoskeletal proteins in Cul3 mutant neural cells results in atypical organization of the actin mesh at the cell leading edge. Of note, heterozygous deletion of Cul3 in adult mice does not induce the majority of the behavioral defects observed in constitutive Cul3 haploinsufficient animals, pointing to a critical time-window for Cul3 deficiency.\r\nIn conclusion, our data indicate that Cul3 plays a critical role in the regulation of cytoskeletal proteins and neuronal migration. ASD-associated defects and behavioral abnormalities are primarily due to dosage sensitive Cul3 functions at early brain developmental stages."}],"page":"138","title":"Illuminating the role of Cul3 in autism spectrum disorder pathogenesis","oa":1,"citation":{"ista":"Morandell J. 2020. Illuminating the role of Cul3 in autism spectrum disorder pathogenesis. Institute of Science and Technology Austria.","ieee":"J. Morandell, “Illuminating the role of Cul3 in autism spectrum disorder pathogenesis,” Institute of Science and Technology Austria, 2020.","short":"J. Morandell, Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis, Institute of Science and Technology Austria, 2020.","ama":"Morandell J. Illuminating the role of Cul3 in autism spectrum disorder pathogenesis. 2020. doi:10.15479/AT:ISTA:8620","mla":"Morandell, Jasmin. Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8620.","chicago":"Morandell, Jasmin. “Illuminating the Role of Cul3 in Autism Spectrum Disorder Pathogenesis.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8620.","apa":"Morandell, J. (2020). Illuminating the role of Cul3 in autism spectrum disorder pathogenesis. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8620"},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"date_created":"2020-10-07T14:53:13Z","doi":"10.15479/AT:ISTA:8620","file_date_updated":"2021-10-16T22:30:04Z","article_processing_charge":"No","day":"12","acknowledgement":"I would like to especially thank Armel Nicolas from the Proteomics and Christoph Sommer from the Bioimaging Facilities for the data analysis, and to thank the team of the Preclinical Facility, especially Sabina Deixler, Angela Schlerka, Anita Lepold, Mihalea Mihai and Michael Schun for taking care of the mouse line maintenance and their great support.","has_accepted_license":"1","degree_awarded":"PhD","date_published":"2020-10-12T00:00:00Z"},{"page":"3-18","title":"Monitorability under assumptions","oa":1,"date_created":"2020-10-07T15:05:37Z","citation":{"short":"T.A. Henzinger, N.E. Sarac, in:, Runtime Verification, Springer Nature, 2020, pp. 3–18.","ieee":"T. A. Henzinger and N. E. Sarac, “Monitorability under assumptions,” in Runtime Verification, Los Angeles, CA, United States, 2020, vol. 12399, pp. 3–18.","ista":"Henzinger TA, Sarac NE. 2020. Monitorability under assumptions. Runtime Verification. RV: Runtime Verification, LNCS, vol. 12399, 3–18.","ama":"Henzinger TA, Sarac NE. Monitorability under assumptions. In: Runtime Verification. Vol 12399. Springer Nature; 2020:3-18. doi:10.1007/978-3-030-60508-7_1","chicago":"Henzinger, Thomas A, and Naci E Sarac. “Monitorability under Assumptions.” In Runtime Verification, 12399:3–18. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-60508-7_1.","apa":"Henzinger, T. A., & Sarac, N. E. (2020). Monitorability under assumptions. In Runtime Verification (Vol. 12399, pp. 3–18). Los Angeles, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-030-60508-7_1","mla":"Henzinger, Thomas A., and Naci E. Sarac. “Monitorability under Assumptions.” Runtime Verification, vol. 12399, Springer Nature, 2020, pp. 3–18, doi:10.1007/978-3-030-60508-7_1."},"quality_controlled":"1","conference":{"start_date":"2020-10-06","name":"RV: Runtime Verification","location":"Los Angeles, CA, United States","end_date":"2020-10-09"},"doi":"10.1007/978-3-030-60508-7_1","file_date_updated":"2020-10-15T14:28:06Z","article_processing_charge":"No","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","publication":"Runtime Verification","day":"02","volume":12399,"has_accepted_license":"1","intvolume":" 12399","date_published":"2020-10-02T00:00:00Z","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783030605070","9783030605087"],"issn":["0302-9743"]},"isi":1,"project":[{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"month":"10","year":"2020","department":[{"_id":"ToHe"}],"publisher":"Springer Nature","file":[{"content_type":"application/pdf","access_level":"open_access","date_updated":"2020-10-15T14:28:06Z","checksum":"00661f9b7034f52e18bf24fa552b8194","file_size":478148,"success":1,"date_created":"2020-10-15T14:28:06Z","file_name":"monitorability.pdf","creator":"esarac","file_id":"8665","relation":"main_file"}],"oa_version":"Submitted Version","ddc":["000"],"type":"conference","external_id":{"isi":["000728160600001"]},"publication_status":"published","alternative_title":["LNCS"],"_id":"8623","status":"public","author":[{"orcid":"0000-0002-2985-7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E","last_name":"Sarac","full_name":"Sarac, Naci E"}],"date_updated":"2023-09-05T15:08:26Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We introduce the monitoring of trace properties under assumptions. An assumption limits the space of possible traces that the monitor may encounter. An assumption may result from knowledge about the system that is being monitored, about the environment, or about another, connected monitor. We define monitorability under assumptions and study its theoretical properties. In particular, we show that for every assumption A, the boolean combinations of properties that are safe or co-safe relative to A are monitorable under A. We give several examples and constructions on how an assumption can make a non-monitorable property monitorable, and how an assumption can make a monitorable property monitorable with fewer resources, such as integer registers."}],"scopus_import":"1"},{"oa":1,"article_number":"064501","citation":{"mla":"Suri, Balachandra, et al. “Capturing Turbulent Dynamics and Statistics in Experiments with Unstable Periodic Orbits.” Physical Review Letters, vol. 125, no. 6, 064501, American Physical Society, 2020, doi:10.1103/physrevlett.125.064501.","apa":"Suri, B., Kageorge, L., Grigoriev, R. O., & Schatz, M. F. (2020). Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.125.064501","chicago":"Suri, Balachandra, Logan Kageorge, Roman O. Grigoriev, and Michael F. Schatz. “Capturing Turbulent Dynamics and Statistics in Experiments with Unstable Periodic Orbits.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/physrevlett.125.064501.","ama":"Suri B, Kageorge L, Grigoriev RO, Schatz MF. Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits. Physical Review Letters. 2020;125(6). doi:10.1103/physrevlett.125.064501","ieee":"B. Suri, L. Kageorge, R. O. Grigoriev, and M. F. Schatz, “Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits,” Physical Review Letters, vol. 125, no. 6. American Physical Society, 2020.","ista":"Suri B, Kageorge L, Grigoriev RO, Schatz MF. 2020. Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits. Physical Review Letters. 125(6), 064501.","short":"B. Suri, L. Kageorge, R.O. Grigoriev, M.F. Schatz, Physical Review Letters 125 (2020)."},"date_created":"2020-10-08T17:27:32Z","quality_controlled":"1","arxiv":1,"title":"Capturing turbulent dynamics and statistics in experiments with unstable periodic orbits","acknowledgement":"M. F. S. and R. O. G. acknowledge funding from the National Science Foundation (CMMI-1234436, DMS1125302, CMMI-1725587) and Defense Advanced Research Projects Agency (HR0011-16-2-0033). B. S.has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme FP7/2007–2013/ under REA Grant Agreement No. 291734.","day":"05","publication":"Physical Review Letters","volume":125,"intvolume":" 125","date_published":"2020-08-05T00:00:00Z","doi":"10.1103/physrevlett.125.064501","ec_funded":1,"article_processing_charge":"No","publisher":"American Physical Society","oa_version":"Preprint","type":"journal_article","publication_status":"published","external_id":{"isi":["000555785600005"],"arxiv":["2008.02367"]},"_id":"8634","issue":"6","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"isi":1,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"month":"08","year":"2020","department":[{"_id":"BjHo"}],"article_type":"original","date_updated":"2023-09-05T12:08:29Z","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","main_file_link":[{"url":"https://arxiv.org/abs/2008.02367","open_access":"1"}],"keyword":["General Physics and Astronomy"],"abstract":[{"text":"In laboratory studies and numerical simulations, we observe clear signatures of unstable time-periodic solutions in a moderately turbulent quasi-two-dimensional flow. We validate the dynamical relevance of such solutions by demonstrating that turbulent flows in both experiment and numerics transiently display time-periodic dynamics when they shadow unstable periodic orbits (UPOs). We show that UPOs we computed are also statistically significant, with turbulent flows spending a sizable fraction of the total time near these solutions. As a result, the average rates of energy input and dissipation for the turbulent flow and frequently visited UPOs differ only by a few percent.","lang":"eng"}],"status":"public","author":[{"full_name":"Suri, Balachandra","last_name":"Suri","id":"47A5E706-F248-11E8-B48F-1D18A9856A87","first_name":"Balachandra"},{"first_name":"Logan","full_name":"Kageorge, Logan","last_name":"Kageorge"},{"first_name":"Roman O.","last_name":"Grigoriev","full_name":"Grigoriev, Roman O."},{"first_name":"Michael F.","last_name":"Schatz","full_name":"Schatz, Michael F."}]},{"author":[{"last_name":"Deichler","full_name":"Deichler, Alfonso","first_name":"Alfonso"},{"first_name":"Denisse","last_name":"Carrasco","full_name":"Carrasco, Denisse"},{"first_name":"Luciana","last_name":"Lopez-Jury","full_name":"Lopez-Jury, Luciana"},{"last_name":"Vega Zuniga","full_name":"Vega Zuniga, Tomas A","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas A"},{"full_name":"Marquez, Natalia","last_name":"Marquez","first_name":"Natalia"},{"first_name":"Jorge","last_name":"Mpodozis","full_name":"Mpodozis, Jorge"},{"last_name":"Marin","full_name":"Marin, Gonzalo","first_name":"Gonzalo"}],"status":"public","abstract":[{"lang":"eng","text":"The parabigeminal nucleus (PBG) is the mammalian homologue to the isthmic complex of other vertebrates. Optogenetic stimulation of the PBG induces freezing and escape in mice, a result thought to be caused by a PBG projection to the central nucleus of the amygdala. However, the isthmic complex, including the PBG, has been classically considered satellite nuclei of the Superior Colliculus (SC), which upon stimulation of its medial part also triggers fear and avoidance reactions. As the PBG-SC connectivity is not well characterized, we investigated whether the topology of the PBG projection to the SC could be related to the behavioral consequences of PBG stimulation. To that end, we performed immunohistochemistry, in situ hybridization and neural tracer injections in the SC and PBG in a diurnal rodent, the Octodon degus. We found that all PBG neurons expressed both glutamatergic and cholinergic markers and were distributed in clearly defined anterior (aPBG) and posterior (pPBG) subdivisions. The pPBG is connected reciprocally and topographically to the ipsilateral SC, whereas the aPBG receives afferent axons from the ipsilateral SC and projected exclusively to the contralateral SC. This contralateral projection forms a dense field of terminals that is restricted to the medial SC, in correspondence with the SC representation of the aerial binocular field which, we also found, in O. degus prompted escape reactions upon looming stimulation. Therefore, this specialized topography allows binocular interactions in the SC region controlling responses to aerial predators, suggesting a link between the mechanisms by which the SC and PBG produce defensive behaviors."}],"scopus_import":"1","date_updated":"2023-08-22T09:58:21Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"department":[{"_id":"MaJö"}],"article_type":"original","isi":1,"publication_identifier":{"eissn":["20452322"]},"month":"10","year":"2020","oa_version":"Published Version","file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-10-12T12:39:10Z","success":1,"checksum":"f6dd99954f1c0ffb4da5a1d2d739bf31","file_size":3906744,"date_created":"2020-10-12T12:39:10Z","file_name":"2020_ScientificReport_Deichler.pdf","file_id":"8651","creator":"dernst","relation":"main_file"}],"ddc":["570"],"type":"journal_article","_id":"8643","publication_status":"published","external_id":{"isi":["000577142600032"]},"publisher":"Springer Nature","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/s41598-020-72848-0","file_date_updated":"2020-10-12T12:39:10Z","has_accepted_license":"1","intvolume":" 10","date_published":"2020-10-01T00:00:00Z","volume":10,"day":"01","publication":"Scientific Reports","acknowledgement":"We thank Elisa Sentis and Solano Henriquez for their expert technical assistance. Dr. David Sterratt for his helpful advice in using the Retistruct package. Dr. Joao Botelho for his valuable assistance in scanning the retinas. To Mrs. Diane Greenstein for kindly reading and correcting our manuscript. Macarena Ruiz for her helpful comments during figures elaboration. Dr. Alexia Nunez-Parra for kindly providing us with the transgenic mouse line. Dr. Harald Luksch for granting us access to the confocal microscope at his lab. This study was supported by: FONDECYT 1151432 (to G.M.), FONDECYT 1170027 (to J.M.) and Doctoral fellowship CONICYT 21161599 (to A.D.).","title":"A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents","date_created":"2020-10-11T22:01:14Z","citation":{"mla":"Deichler, Alfonso, et al. “A Specialized Reciprocal Connectivity Suggests a Link between the Mechanisms by Which the Superior Colliculus and Parabigeminal Nucleus Produce Defensive Behaviors in Rodents.” Scientific Reports, vol. 10, 16220, Springer Nature, 2020, doi:10.1038/s41598-020-72848-0.","apa":"Deichler, A., Carrasco, D., Lopez-Jury, L., Vega Zuniga, T. A., Marquez, N., Mpodozis, J., & Marin, G. (2020). A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-72848-0","chicago":"Deichler, Alfonso, Denisse Carrasco, Luciana Lopez-Jury, Tomas A Vega Zuniga, Natalia Marquez, Jorge Mpodozis, and Gonzalo Marin. “A Specialized Reciprocal Connectivity Suggests a Link between the Mechanisms by Which the Superior Colliculus and Parabigeminal Nucleus Produce Defensive Behaviors in Rodents.” Scientific Reports. Springer Nature, 2020. https://doi.org/10.1038/s41598-020-72848-0.","ama":"Deichler A, Carrasco D, Lopez-Jury L, et al. A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. 2020;10. doi:10.1038/s41598-020-72848-0","short":"A. Deichler, D. Carrasco, L. Lopez-Jury, T.A. Vega Zuniga, N. Marquez, J. Mpodozis, G. Marin, Scientific Reports 10 (2020).","ieee":"A. Deichler et al., “A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents,” Scientific Reports, vol. 10. Springer Nature, 2020.","ista":"Deichler A, Carrasco D, Lopez-Jury L, Vega Zuniga TA, Marquez N, Mpodozis J, Marin G. 2020. A specialized reciprocal connectivity suggests a link between the mechanisms by which the superior colliculus and parabigeminal nucleus produce defensive behaviors in rodents. Scientific Reports. 10, 16220."},"quality_controlled":"1","article_number":"16220","oa":1},{"title":"Detecting composite orders in layered models via machine learning","quality_controlled":"1","citation":{"short":"W. Rzadkowski, N. Defenu, S. Chiacchiera, A. Trombettoni, G. Bighin, New Journal of Physics 22 (2020).","ieee":"W. Rzadkowski, N. Defenu, S. Chiacchiera, A. Trombettoni, and G. Bighin, “Detecting composite orders in layered models via machine learning,” New Journal of Physics, vol. 22, no. 9. IOP Publishing, 2020.","ista":"Rzadkowski W, Defenu N, Chiacchiera S, Trombettoni A, Bighin G. 2020. Detecting composite orders in layered models via machine learning. New Journal of Physics. 22(9), 093026.","ama":"Rzadkowski W, Defenu N, Chiacchiera S, Trombettoni A, Bighin G. Detecting composite orders in layered models via machine learning. New Journal of Physics. 2020;22(9). doi:10.1088/1367-2630/abae44","chicago":"Rzadkowski, Wojciech, N Defenu, S Chiacchiera, A Trombettoni, and Giacomo Bighin. “Detecting Composite Orders in Layered Models via Machine Learning.” New Journal of Physics. IOP Publishing, 2020. https://doi.org/10.1088/1367-2630/abae44.","apa":"Rzadkowski, W., Defenu, N., Chiacchiera, S., Trombettoni, A., & Bighin, G. (2020). Detecting composite orders in layered models via machine learning. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/abae44","mla":"Rzadkowski, Wojciech, et al. “Detecting Composite Orders in Layered Models via Machine Learning.” New Journal of Physics, vol. 22, no. 9, 093026, IOP Publishing, 2020, doi:10.1088/1367-2630/abae44."},"date_created":"2020-10-11T22:01:14Z","article_number":"093026","oa":1,"ec_funded":1,"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2020-10-12T12:18:47Z","doi":"10.1088/1367-2630/abae44","date_published":"2020-09-01T00:00:00Z","intvolume":" 22","has_accepted_license":"1","volume":22,"acknowledgement":"We thank Gesualdo Delfino, Michele Fabrizio, Piero Ferrarese, Robert Konik, Christoph Lampert and Mikhail Lemeshko for stimulating discussions at various stages of this work. WR has received funding from the EU Horizon 2020 program under the Marie Skłodowska-Curie Grant Agreement No. 665385 and is a recipient of a DOC Fellowship of the Austrian Academy of Sciences. GB acknowledges support from the Austrian Science Fund (FWF), under project No. M2641-N27. ND acknowledges support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) via Collaborative Research Center SFB 1225 (ISOQUANT)--project-id 273811115--and under Germany's Excellence Strategy 'EXC-2181/1-390900948' (the Heidelberg STRUCTURES Excellence Cluster).","publication":"New Journal of Physics","day":"01","article_type":"original","department":[{"_id":"MiLe"}],"month":"09","year":"2020","project":[{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"Analytic and machine learning approaches to composite quantum impurities","_id":"05A235A0-7A3F-11EA-A408-12923DDC885E","grant_number":"25681"},{"call_identifier":"FWF","name":"A path-integral approach to composite impurities","_id":"26986C82-B435-11E9-9278-68D0E5697425","grant_number":"M02641"}],"isi":1,"publication_identifier":{"issn":["13672630"]},"issue":"9","_id":"8644","publication_status":"published","external_id":{"isi":["000573298000001"]},"type":"journal_article","oa_version":"Published Version","ddc":["530"],"file":[{"file_id":"8650","creator":"dernst","relation":"main_file","file_name":"2020_NewJournalPhysics_Rzdkowski.pdf","checksum":"c9238fff422e7a957c3a0d559f756b3a","success":1,"file_size":2725143,"date_created":"2020-10-12T12:18:47Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-10-12T12:18:47Z"}],"publisher":"IOP Publishing","author":[{"orcid":"0000-0002-1106-4419","last_name":"Rzadkowski","full_name":"Rzadkowski, Wojciech","id":"48C55298-F248-11E8-B48F-1D18A9856A87","first_name":"Wojciech"},{"first_name":"N","last_name":"Defenu","full_name":"Defenu, N"},{"full_name":"Chiacchiera, S","last_name":"Chiacchiera","first_name":"S"},{"full_name":"Trombettoni, A","last_name":"Trombettoni","first_name":"A"},{"first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8823-9777","last_name":"Bighin","full_name":"Bighin, Giacomo"}],"status":"public","scopus_import":"1","abstract":[{"text":"Determining the phase diagram of systems consisting of smaller subsystems 'connected' via a tunable coupling is a challenging task relevant for a variety of physical settings. A general question is whether new phases, not present in the uncoupled limit, may arise. We use machine learning and a suitable quasidistance between different points of the phase diagram to study layered spin models, in which the spin variables constituting each of the uncoupled systems (to which we refer as layers) are coupled to each other via an interlayer coupling. In such systems, in general, composite order parameters involving spins of different layers may emerge as a consequence of the interlayer coupling. We focus on the layered Ising and Ashkin–Teller models as a paradigmatic case study, determining their phase diagram via the application of a machine learning algorithm to the Monte Carlo data. Remarkably our technique is able to correctly characterize all the system phases also in the case of hidden order parameters, i.e. order parameters whose expression in terms of the microscopic configurations would require additional preprocessing of the data fed to the algorithm. We correctly retrieve the three known phases of the Ashkin–Teller model with ferromagnetic couplings, including the phase described by a composite order parameter. For the bilayer and trilayer Ising models the phases we find are only the ferromagnetic and the paramagnetic ones. Within the approach we introduce, owing to the construction of convolutional neural networks, naturally suitable for layered image-like data with arbitrary number of layers, no preprocessing of the Monte Carlo data is needed, also with regard to its spatial structure. The physical meaning of our results is discussed and compared with analytical data, where available. Yet, the method can be used without any a priori knowledge of the phases one seeks to find and can be applied to other models and structures.","lang":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10759"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2024-08-07T07:16:53Z"},{"publication":"Bioinformatics","day":"15","acknowledgement":"This work was supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013, ERC grant agreement 335980_EinME) and Startup package to the Ivankov laboratory at Skolkovo Institute of Science and Technology. The work was started at the School of Molecular and Theoretical Biology 2017 supported by the Zimin Foundation. N.S.B. was supported by the Woman Scientists Support Grant in Centre for Genomic Regulation (CRG). ","volume":36,"pmid":1,"has_accepted_license":"1","intvolume":" 36","date_published":"2020-03-15T00:00:00Z","doi":"10.1093/bioinformatics/btz841","file_date_updated":"2020-10-12T12:02:09Z","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"article_processing_charge":"No","ec_funded":1,"oa":1,"date_created":"2020-10-11T22:01:14Z","citation":{"short":"L.A. Esteban, L.R. Lonishin, D.M. Bobrovskiy, G. Leleytner, N.S. Bogatyreva, F. Kondrashov, D.N. Ivankov, Bioinformatics 36 (2020) 1960–1962.","ieee":"L. A. Esteban et al., “HypercubeME: Two hundred million combinatorially complete datasets from a single experiment,” Bioinformatics, vol. 36, no. 6. Oxford Academic, pp. 1960–1962, 2020.","ista":"Esteban LA, Lonishin LR, Bobrovskiy DM, Leleytner G, Bogatyreva NS, Kondrashov F, Ivankov DN. 2020. HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. 36(6), 1960–1962.","ama":"Esteban LA, Lonishin LR, Bobrovskiy DM, et al. HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. 2020;36(6):1960-1962. doi:10.1093/bioinformatics/btz841","chicago":"Esteban, Laura A, Lyubov R Lonishin, Daniil M Bobrovskiy, Gregory Leleytner, Natalya S Bogatyreva, Fyodor Kondrashov, and Dmitry N Ivankov. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” Bioinformatics. Oxford Academic, 2020. https://doi.org/10.1093/bioinformatics/btz841.","apa":"Esteban, L. A., Lonishin, L. R., Bobrovskiy, D. M., Leleytner, G., Bogatyreva, N. S., Kondrashov, F., & Ivankov, D. N. (2020). HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. Oxford Academic. https://doi.org/10.1093/bioinformatics/btz841","mla":"Esteban, Laura A., et al. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” Bioinformatics, vol. 36, no. 6, Oxford Academic, 2020, pp. 1960–62, doi:10.1093/bioinformatics/btz841."},"quality_controlled":"1","page":"1960-1962","title":"HypercubeME: Two hundred million combinatorially complete datasets from a single experiment","date_updated":"2023-08-22T09:57:29Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Epistasis, the context-dependence of the contribution of an amino acid substitution to fitness, is common in evolution. To detect epistasis, fitness must be measured for at least four genotypes: the reference genotype, two different single mutants and a double mutant with both of the single mutations. For higher-order epistasis of the order n, fitness has to be measured for all 2n genotypes of an n-dimensional hypercube in genotype space forming a ‘combinatorially complete dataset’. So far, only a handful of such datasets have been produced by manual curation. Concurrently, random mutagenesis experiments have produced measurements of fitness and other phenotypes in a high-throughput manner, potentially containing a number of combinatorially complete datasets. We present an effective recursive algorithm for finding all hypercube structures in random mutagenesis experimental data. To test the algorithm, we applied it to the data from a recent HIS3 protein dataset and found all 199 847 053 unique combinatorially complete genotype combinations of dimensionality ranging from 2 to 12. The algorithm may be useful for researchers looking for higher-order epistasis in their high-throughput experimental data."}],"scopus_import":"1","license":"https://creativecommons.org/licenses/by-nc/4.0/","status":"public","author":[{"first_name":"Laura A","full_name":"Esteban, Laura A","last_name":"Esteban"},{"last_name":"Lonishin","full_name":"Lonishin, Lyubov R","first_name":"Lyubov R"},{"first_name":"Daniil M","last_name":"Bobrovskiy","full_name":"Bobrovskiy, Daniil M"},{"first_name":"Gregory","last_name":"Leleytner","full_name":"Leleytner, Gregory"},{"first_name":"Natalya S","last_name":"Bogatyreva","full_name":"Bogatyreva, Natalya S"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor"},{"first_name":"Dmitry N ","full_name":"Ivankov, Dmitry N ","last_name":"Ivankov"}],"publisher":"Oxford Academic","type":"journal_article","oa_version":"Published Version","ddc":["000","570"],"file":[{"file_id":"8649","creator":"dernst","relation":"main_file","file_name":"2020_Bioinformatics_Esteban.pdf","checksum":"21d6f71839deb3b83e4a356193f72767","success":1,"file_size":308341,"date_created":"2020-10-12T12:02:09Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-10-12T12:02:09Z"}],"publication_status":"published","external_id":{"isi":["000538696800054"],"pmid":["31742320"]},"_id":"8645","issue":"6","publication_identifier":{"issn":["1367-4803"],"eissn":["1460-2059"]},"isi":1,"project":[{"grant_number":"335980","_id":"26120F5C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Systematic investigation of epistasis in molecular evolution"}],"month":"03","year":"2020","department":[{"_id":"FyKo"}],"article_type":"original"},{"date_published":"2020-10-09T00:00:00Z","has_accepted_license":"1","intvolume":" 3","publication":"Communications Physics","acknowledgement":"This work has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.V. and A.G.). M.L. acknowledges support by the Austrian Science Fund (FWF), under project No. P29902-N27, and by the European Research Council (ERC) Starting\r\nGrant No. 801770 (ANGULON).","day":"09","volume":3,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes","ec_funded":1,"file_date_updated":"2020-10-14T15:16:28Z","doi":"10.1038/s42005-020-00445-8","quality_controlled":"1","citation":{"ama":"Ghazaryan A, Lemeshko M, Volosniev A. Filtering spins by scattering from a lattice of point magnets. Communications Physics. 2020;3. doi:10.1038/s42005-020-00445-8","ieee":"A. Ghazaryan, M. Lemeshko, and A. Volosniev, “Filtering spins by scattering from a lattice of point magnets,” Communications Physics, vol. 3. Springer Nature, 2020.","short":"A. Ghazaryan, M. Lemeshko, A. Volosniev, Communications Physics 3 (2020).","ista":"Ghazaryan A, Lemeshko M, Volosniev A. 2020. Filtering spins by scattering from a lattice of point magnets. Communications Physics. 3, 178.","mla":"Ghazaryan, Areg, et al. “Filtering Spins by Scattering from a Lattice of Point Magnets.” Communications Physics, vol. 3, 178, Springer Nature, 2020, doi:10.1038/s42005-020-00445-8.","apa":"Ghazaryan, A., Lemeshko, M., & Volosniev, A. (2020). Filtering spins by scattering from a lattice of point magnets. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-020-00445-8","chicago":"Ghazaryan, Areg, Mikhail Lemeshko, and Artem Volosniev. “Filtering Spins by Scattering from a Lattice of Point Magnets.” Communications Physics. Springer Nature, 2020. https://doi.org/10.1038/s42005-020-00445-8."},"date_created":"2020-10-13T09:48:59Z","oa":1,"article_number":"178","title":"Filtering spins by scattering from a lattice of point magnets","scopus_import":"1","abstract":[{"lang":"eng","text":"Nature creates electrons with two values of the spin projection quantum number. In certain applications, it is important to filter electrons with one spin projection from the rest. Such filtering is not trivial, since spin-dependent interactions are often weak, and cannot lead to any substantial effect. Here we propose an efficient spin filter based upon scattering from a two-dimensional crystal, which is made of aligned point magnets. The polarization of the outgoing electron flux is controlled by the crystal, and reaches maximum at specific values of the parameters. In our scheme, polarization increase is accompanied by higher reflectivity of the crystal. High transmission is feasible in scattering from a quantum cavity made of two crystals. Our findings can be used for studies of low-energy spin-dependent scattering from two-dimensional ordered structures made of magnetic atoms or aligned chiral molecules."}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-22T09:58:46Z","status":"public","author":[{"first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg","last_name":"Ghazaryan","orcid":"0000-0001-9666-3543"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"},{"last_name":"Volosniev","full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","external_id":{"isi":["000581681000001"]},"_id":"8652","oa_version":"Published Version","type":"journal_article","ddc":["530"],"file":[{"file_name":"2020_CommPhysics_Ghazaryan.pdf","creator":"dernst","file_id":"8662","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-10-14T15:16:28Z","success":1,"file_size":1462934,"checksum":"60cd35b99f0780acffc7b6060e49ec8b","date_created":"2020-10-14T15:16:28Z"}],"publisher":"Springer Nature","article_type":"original","department":[{"_id":"MiLe"}],"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902"},{"grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"month":"10","year":"2020","publication_identifier":{"issn":["2399-3650"]},"isi":1},{"page":"117","title":"The evolution of gene expression by copy number and point mutations","oa":1,"citation":{"short":"I. Tomanek, The Evolution of Gene Expression by Copy Number and Point Mutations, Institute of Science and Technology Austria, 2020.","ista":"Tomanek I. 2020. The evolution of gene expression by copy number and point mutations. Institute of Science and Technology Austria.","ieee":"I. Tomanek, “The evolution of gene expression by copy number and point mutations,” Institute of Science and Technology Austria, 2020.","ama":"Tomanek I. The evolution of gene expression by copy number and point mutations. 2020. doi:10.15479/AT:ISTA:8653","mla":"Tomanek, Isabella. The Evolution of Gene Expression by Copy Number and Point Mutations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8653.","chicago":"Tomanek, Isabella. “The Evolution of Gene Expression by Copy Number and Point Mutations.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8653.","apa":"Tomanek, I. (2020). The evolution of gene expression by copy number and point mutations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8653"},"date_created":"2020-10-13T13:02:33Z","doi":"10.15479/AT:ISTA:8653","file_date_updated":"2021-10-20T22:30:03Z","article_processing_charge":"No","day":"13","degree_awarded":"PhD","has_accepted_license":"1","date_published":"2020-10-13T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"month":"10","year":"2020","department":[{"_id":"CaGu"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052"}],"file":[{"relation":"source_file","creator":"itomanek","file_id":"8666","file_name":"Thesis_ITomanek_final_201016.docx","date_created":"2020-10-16T12:14:21Z","embargo_to":"open_access","checksum":"c01d9f59794b4b70528f37637c17ad02","file_size":25131884,"date_updated":"2021-10-20T22:30:03Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed"},{"relation":"main_file","file_id":"8667","creator":"itomanek","file_name":"Thesis_ITomanek_final_201016.pdf","date_created":"2020-10-16T12:14:21Z","file_size":15405675,"checksum":"f8edbc3b0f81a780e13ca1e561d42d8b","date_updated":"2021-10-20T22:30:03Z","embargo":"2021-10-19","access_level":"open_access","content_type":"application/pdf"}],"oa_version":"Published Version","type":"dissertation","ddc":["576"],"alternative_title":["ISTA Thesis"],"publication_status":"published","_id":"8653","status":"public","author":[{"full_name":"Tomanek, Isabella","last_name":"Tomanek","orcid":"0000-0001-6197-363X","id":"3981F020-F248-11E8-B48F-1D18A9856A87","first_name":"Isabella"}],"date_updated":"2023-09-07T13:22:42Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"7652","relation":"research_data","status":"public"}]},"keyword":["duplication","amplification","promoter","CNV","AMGET","experimental evolution","Escherichia coli"],"abstract":[{"lang":"eng","text":"Mutations are the raw material of evolution and come in many different flavors. Point mutations change a single letter in the DNA sequence, while copy number mutations like duplications or deletions add or remove many letters of the DNA sequence simultaneously. Each type of mutation exhibits specific properties like its rate of formation and reversal. \r\nGene expression is a fundamental phenotype that can be altered by both, point and copy number mutations. The following thesis is concerned with the dynamics of gene expression evolution and how it is affected by the properties exhibited by point and copy number mutations. Specifically, we are considering i) copy number mutations during adaptation to fluctuating environments and ii) the interaction of copy number and point mutations during adaptation to constant environments. "}]},{"_id":"8657","publication_status":"published","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","file":[{"file_size":52636162,"checksum":"d708ecd62b6fcc3bc1feb483b8dbe9eb","date_created":"2020-10-15T06:41:20Z","content_type":"application/pdf","access_level":"open_access","embargo":"2021-10-06","date_updated":"2021-10-07T22:30:03Z","creator":"bkavcic","file_id":"8663","relation":"main_file","file_name":"kavcicB_thesis202009.pdf"},{"content_type":"application/zip","access_level":"closed","date_updated":"2021-10-07T22:30:03Z","checksum":"bb35f2352a04db19164da609f00501f3","file_size":321681247,"date_created":"2020-10-15T06:41:53Z","embargo_to":"open_access","file_name":"2020b.zip","creator":"bkavcic","file_id":"8664","relation":"source_file"}],"type":"dissertation","ddc":["571","530","570"],"supervisor":[{"orcid":"0000-0002-6699-1455","last_name":"Tkačik","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"}],"year":"2020","month":"10","publication_identifier":{"isbn":["978-3-99078-011-4"],"issn":["2663-337X"]},"abstract":[{"lang":"eng","text":"Synthesis of proteins – translation – is a fundamental process of life. Quantitative studies anchor translation into the context of bacterial physiology and reveal several mathematical relationships, called “growth laws,” which capture physiological feedbacks between protein synthesis and cell growth. Growth laws describe the dependency of the ribosome abundance as a function of growth rate, which can change depending on the growth conditions. Perturbations of translation reveal that bacteria employ a compensatory strategy in which the reduced translation capability results in increased expression of the translation machinery.\r\nPerturbations of translation are achieved in various ways; clinically interesting is the application of translation-targeting antibiotics – translation inhibitors. The antibiotic effects on bacterial physiology are often poorly understood. Bacterial responses to two or more simultaneously applied antibiotics are even more puzzling. The combined antibiotic effect determines the type of drug interaction, which ranges from synergy (the effect is stronger than expected) to antagonism (the effect is weaker) and suppression (one of the drugs loses its potency).\r\nIn the first part of this work, we systematically measure the pairwise interaction network for translation inhibitors that interfere with different steps in translation. We find that the interactions are surprisingly diverse and tend to be more antagonistic. To explore the underlying mechanisms, we begin with a minimal biophysical model of combined antibiotic action. We base this model on the kinetics of antibiotic uptake and binding together with the physiological response described by the growth laws. The biophysical model explains some drug interactions, but not all; it specifically fails to predict suppression.\r\nIn the second part of this work, we hypothesize that elusive suppressive drug interactions result from the interplay between ribosomes halted in different stages of translation. To elucidate this putative mechanism of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using in- ducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks partially causes these interactions.\r\nWe extend this approach by varying two translation bottlenecks simultaneously. This approach reveals the suppression of translocation inhibition by inhibited translation. We rationalize this effect by modeling dense traffic of ribosomes that move on transcripts in a translation factor-mediated manner. This model predicts a dissolution of traffic jams caused by inhibited translocation when the density of ribosome traffic is reduced by lowered initiation. We base this model on the growth laws and quantitative relationships between different translation and growth parameters.\r\nIn the final part of this work, we describe a set of tools aimed at quantification of physiological and translation parameters. We further develop a simple model that directly connects the abundance of a translation factor with the growth rate, which allows us to extract physiological parameters describing initiation. We demonstrate the development of tools for measuring translation rate.\r\nThis thesis showcases how a combination of high-throughput growth rate mea- surements, genetics, and modeling can reveal mechanisms of drug interactions. Furthermore, by a gradual transition from combinations of antibiotics to precise genetic interventions, we demonstrated the equivalency between genetic and chemi- cal perturbations of translation. These findings tile the path for quantitative studies of antibiotic combinations and illustrate future approaches towards the quantitative description of translation."}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7673"},{"status":"public","relation":"part_of_dissertation","id":"8250"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"date_updated":"2023-09-07T13:20:48Z","author":[{"full_name":"Kavcic, Bor","last_name":"Kavcic","orcid":"0000-0001-6041-254X","first_name":"Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87"}],"status":"public","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"}],"date_created":"2020-10-13T16:46:14Z","citation":{"mla":"Kavcic, Bor. Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8657.","apa":"Kavcic, B. (2020). Perturbations of protein synthesis: from antibiotics to genetics and physiology. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8657","chicago":"Kavcic, Bor. “Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8657.","ama":"Kavcic B. Perturbations of protein synthesis: from antibiotics to genetics and physiology. 2020. doi:10.15479/AT:ISTA:8657","ieee":"B. Kavcic, “Perturbations of protein synthesis: from antibiotics to genetics and physiology,” Institute of Science and Technology Austria, 2020.","short":"B. Kavcic, Perturbations of Protein Synthesis: From Antibiotics to Genetics and Physiology, Institute of Science and Technology Austria, 2020.","ista":"Kavcic B. 2020. Perturbations of protein synthesis: from antibiotics to genetics and physiology. Institute of Science and Technology Austria."},"oa":1,"title":"Perturbations of protein synthesis: from antibiotics to genetics and physiology","page":"271","date_published":"2020-10-14T00:00:00Z","has_accepted_license":"1","degree_awarded":"PhD","acknowledgement":"I thank Life Science Facilities for their continuous support with providing top-notch laboratory materials, keeping the devices humming, and coordinating the repairs and building of custom-designed laboratory equipment with the MIBA Machine shop.","day":"14","article_processing_charge":"No","file_date_updated":"2021-10-07T22:30:03Z","doi":"10.15479/AT:ISTA:8657"},{"publisher":"Springer Nature","file":[{"file_name":"2020_NatureComm_Sznurkowska.pdf","file_id":"8677","creator":"dernst","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-10-19T11:27:46Z","file_size":5540540,"checksum":"0ecc0eab72d2d50694852579611a6624","success":1,"date_created":"2020-10-19T11:27:46Z"}],"type":"journal_article","oa_version":"Published Version","ddc":["570"],"external_id":{"pmid":["33028844"],"isi":["000577244600003"]},"publication_status":"published","_id":"8669","publication_identifier":{"eissn":["20411723"]},"isi":1,"month":"10","year":"2020","department":[{"_id":"EdHa"}],"article_type":"original","date_updated":"2023-08-22T10:18:17Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"abstract":[{"text":"Pancreatic islets play an essential role in regulating blood glucose level. Although the molecular pathways underlying islet cell differentiation are beginning to be resolved, the cellular basis of islet morphogenesis and fate allocation remain unclear. By combining unbiased and targeted lineage tracing, we address the events leading to islet formation in the mouse. From the statistical analysis of clones induced at multiple embryonic timepoints, here we show that, during the secondary transition, islet formation involves the aggregation of multiple equipotent endocrine progenitors that transition from a phase of stochastic amplification by cell division into a phase of sublineage restriction and limited islet fission. Together, these results explain quantitatively the heterogeneous size distribution and degree of polyclonality of maturing islets, as well as dispersion of progenitors within and between islets. Further, our results show that, during the secondary transition, α- and β-cells are generated in a contemporary manner. Together, these findings provide insight into the cellular basis of islet development.","lang":"eng"}],"scopus_import":"1","status":"public","author":[{"first_name":"Magdalena K.","full_name":"Sznurkowska, Magdalena K.","last_name":"Sznurkowska"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","full_name":"Hannezo, Edouard B"},{"first_name":"Roberta","last_name":"Azzarelli","full_name":"Azzarelli, Roberta"},{"first_name":"Lemonia","full_name":"Chatzeli, Lemonia","last_name":"Chatzeli"},{"first_name":"Tatsuro","full_name":"Ikeda, Tatsuro","last_name":"Ikeda"},{"last_name":"Yoshida","full_name":"Yoshida, Shosei","first_name":"Shosei"},{"first_name":"Anna","last_name":"Philpott","full_name":"Philpott, Anna"},{"first_name":"Benjamin D","full_name":"Simons, Benjamin D","last_name":"Simons"}],"oa":1,"article_number":"5037","date_created":"2020-10-18T22:01:35Z","citation":{"ama":"Sznurkowska MK, Hannezo EB, Azzarelli R, et al. Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. 2020;11. doi:10.1038/s41467-020-18837-3","ista":"Sznurkowska MK, Hannezo EB, Azzarelli R, Chatzeli L, Ikeda T, Yoshida S, Philpott A, Simons BD. 2020. Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. 11, 5037.","short":"M.K. Sznurkowska, E.B. Hannezo, R. Azzarelli, L. Chatzeli, T. Ikeda, S. Yoshida, A. Philpott, B.D. Simons, Nature Communications 11 (2020).","ieee":"M. K. Sznurkowska et al., “Tracing the cellular basis of islet specification in mouse pancreas,” Nature Communications, vol. 11. Springer Nature, 2020.","mla":"Sznurkowska, Magdalena K., et al. “Tracing the Cellular Basis of Islet Specification in Mouse Pancreas.” Nature Communications, vol. 11, 5037, Springer Nature, 2020, doi:10.1038/s41467-020-18837-3.","apa":"Sznurkowska, M. K., Hannezo, E. B., Azzarelli, R., Chatzeli, L., Ikeda, T., Yoshida, S., … Simons, B. D. (2020). Tracing the cellular basis of islet specification in mouse pancreas. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-18837-3","chicago":"Sznurkowska, Magdalena K., Edouard B Hannezo, Roberta Azzarelli, Lemonia Chatzeli, Tatsuro Ikeda, Shosei Yoshida, Anna Philpott, and Benjamin D Simons. “Tracing the Cellular Basis of Islet Specification in Mouse Pancreas.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-18837-3."},"quality_controlled":"1","title":"Tracing the cellular basis of islet specification in mouse pancreas","publication":"Nature Communications","day":"07","volume":11,"pmid":1,"intvolume":" 11","has_accepted_license":"1","date_published":"2020-10-07T00:00:00Z","doi":"10.1038/s41467-020-18837-3","file_date_updated":"2020-10-19T11:27:46Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No"},{"article_type":"original","department":[{"_id":"JaMa"}],"month":"10","year":"2020","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"}],"isi":1,"publication_identifier":{"issn":["00222488"]},"_id":"8670","issue":"10","external_id":{"isi":["000578529200001"],"arxiv":["2007.06644"]},"publication_status":"published","oa_version":"Preprint","type":"journal_article","publisher":"AIP Publishing","author":[{"id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425","first_name":"Haonan","last_name":"Zhang","full_name":"Zhang, Haonan"}],"status":"public","scopus_import":"1","abstract":[{"lang":"eng","text":"The α–z Rényi relative entropies are a two-parameter family of Rényi relative entropies that are quantum generalizations of the classical α-Rényi relative entropies. In the work [Adv. Math. 365, 107053 (2020)], we decided the full range of (α, z) for which the data processing inequality (DPI) is valid. In this paper, we give algebraic conditions for the equality in DPI. For the full range of parameters (α, z), we give necessary conditions and sufficient conditions. For most parameters, we give equivalent conditions. This generalizes and strengthens the results of Leditzky et al. [Lett. Math. Phys. 107, 61–80 (2017)]."}],"main_file_link":[{"url":"https://arxiv.org/abs/2007.06644","open_access":"1"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-22T10:32:29Z","title":"Equality conditions of data processing inequality for α-z Rényi relative entropies","quality_controlled":"1","arxiv":1,"citation":{"ama":"Zhang H. Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. 2020;61(10). doi:10.1063/5.0022787","ista":"Zhang H. 2020. Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. 61(10), 102201.","ieee":"H. Zhang, “Equality conditions of data processing inequality for α-z Rényi relative entropies,” Journal of Mathematical Physics, vol. 61, no. 10. AIP Publishing, 2020.","short":"H. Zhang, Journal of Mathematical Physics 61 (2020).","apa":"Zhang, H. (2020). Equality conditions of data processing inequality for α-z Rényi relative entropies. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0022787","chicago":"Zhang, Haonan. “Equality Conditions of Data Processing Inequality for α-z Rényi Relative Entropies.” Journal of Mathematical Physics. AIP Publishing, 2020. https://doi.org/10.1063/5.0022787.","mla":"Zhang, Haonan. “Equality Conditions of Data Processing Inequality for α-z Rényi Relative Entropies.” Journal of Mathematical Physics, vol. 61, no. 10, 102201, AIP Publishing, 2020, doi:10.1063/5.0022787."},"date_created":"2020-10-18T22:01:36Z","article_number":"102201","oa":1,"ec_funded":1,"article_processing_charge":"No","doi":"10.1063/5.0022787","date_published":"2020-10-01T00:00:00Z","intvolume":" 61","volume":61,"acknowledgement":"This research was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411. The author would like to thank Anna Vershynina and Sarah Chehade for their helpful comments.","publication":"Journal of Mathematical Physics","day":"01"},{"article_processing_charge":"No","doi":"10.29252/ijmsi.15.2.117","file_date_updated":"2020-10-19T11:14:20Z","intvolume":" 15","has_accepted_license":"1","date_published":"2020-10-01T00:00:00Z","volume":15,"day":"01","acknowledgement":"We are very grateful to the anonymous reviewer for detailed comments and suggestions that significantly improved the presentation of this paper. The research was partially supported by a DOC fellowship of the Austrian Academy of Sciences.","publication":"Iranian Journal of Mathematical Sciences and Informatics","title":"A note on belief structures and s-approximation spaces","page":"117-128","citation":{"ista":"Shakiba A, Goharshady AK, Hooshmandasl MR, Alambardar Meybodi M. 2020. A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. 15(2), 117–128.","ieee":"A. Shakiba, A. K. Goharshady, M. R. Hooshmandasl, and M. Alambardar Meybodi, “A note on belief structures and s-approximation spaces,” Iranian Journal of Mathematical Sciences and Informatics, vol. 15, no. 2. Iranian Academic Center for Education, Culture and Research, pp. 117–128, 2020.","short":"A. Shakiba, A.K. Goharshady, M.R. Hooshmandasl, M. Alambardar Meybodi, Iranian Journal of Mathematical Sciences and Informatics 15 (2020) 117–128.","ama":"Shakiba A, Goharshady AK, Hooshmandasl MR, Alambardar Meybodi M. A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. 2020;15(2):117-128. doi:10.29252/ijmsi.15.2.117","chicago":"Shakiba, A., Amir Kafshdar Goharshady, M.R. Hooshmandasl, and M. Alambardar Meybodi. “A Note on Belief Structures and S-Approximation Spaces.” Iranian Journal of Mathematical Sciences and Informatics. Iranian Academic Center for Education, Culture and Research, 2020. https://doi.org/10.29252/ijmsi.15.2.117.","apa":"Shakiba, A., Goharshady, A. K., Hooshmandasl, M. R., & Alambardar Meybodi, M. (2020). A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. Iranian Academic Center for Education, Culture and Research. https://doi.org/10.29252/ijmsi.15.2.117","mla":"Shakiba, A., et al. “A Note on Belief Structures and S-Approximation Spaces.” Iranian Journal of Mathematical Sciences and Informatics, vol. 15, no. 2, Iranian Academic Center for Education, Culture and Research, 2020, pp. 117–28, doi:10.29252/ijmsi.15.2.117."},"date_created":"2020-10-18T22:01:36Z","arxiv":1,"quality_controlled":"1","oa":1,"author":[{"first_name":"A.","last_name":"Shakiba","full_name":"Shakiba, A."},{"first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584"},{"full_name":"Hooshmandasl, M.R.","last_name":"Hooshmandasl","first_name":"M.R."},{"first_name":"M.","last_name":"Alambardar Meybodi","full_name":"Alambardar Meybodi, M."}],"status":"public","abstract":[{"lang":"eng","text":"We study relations between evidence theory and S-approximation spaces. Both theories have their roots in the analysis of Dempsterchr('39')s multivalued mappings and lower and upper probabilities, and have close relations to rough sets. We show that an S-approximation space, satisfying a monotonicity condition, can induce a natural belief structure which is a fundamental block in evidence theory. We also demonstrate that one can induce a natural belief structure on one set, given a belief structure on another set, if the two sets are related by a partial monotone S-approximation space. "}],"scopus_import":"1","date_updated":"2023-10-16T09:25:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"article_type":"original","publication_identifier":{"issn":["1735-4463"],"eissn":["2008-9473"]},"year":"2020","month":"10","project":[{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"}],"ddc":["000"],"type":"journal_article","file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-10-19T11:14:20Z","checksum":"f299661a6d51cda6d255a76be696f48d","file_size":261688,"success":1,"date_created":"2020-10-19T11:14:20Z","file_name":"2020_ijmsi_Shakiba_accepted.pdf","file_id":"8676","creator":"dernst","relation":"main_file"}],"oa_version":"Submitted Version","issue":"2","_id":"8671","publication_status":"published","external_id":{"arxiv":["1805.10672"]},"publisher":"Iranian Academic Center for Education, Culture and Research"},{"publisher":"Elsevier","external_id":{"isi":["000582501100012"],"pmid":["32979313"]},"publication_status":"published","_id":"8672","issue":"2","oa_version":"Published Version","ddc":["570"],"type":"journal_article","file":[{"file_id":"9086","creator":"dernst","relation":"main_file","file_name":"2020_DevelopmCell_Chaigne.pdf","file_size":6929686,"checksum":"88e1a031a61689165d19a19c2f16d795","success":1,"date_created":"2021-02-04T10:20:02Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2021-02-04T10:20:02Z"}],"month":"10","year":"2020","publication_identifier":{"issn":["15345807"],"eissn":["18781551"]},"isi":1,"article_type":"original","department":[{"_id":"EdHa"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-22T10:16:58Z","scopus_import":"1","abstract":[{"lang":"eng","text":"Cell fate transitions are key to development and homeostasis. It is thus essential to understand the cellular mechanisms controlling fate transitions. Cell division has been implicated in fate decisions in many stem cell types, including neuronal and epithelial progenitors. In other stem cells, such as embryonic stem (ES) cells, the role of division remains unclear. Here, we show that exit from naive pluripotency in mouse ES cells generally occurs after a division. We further show that exit timing is strongly correlated between sister cells, which remain connected by cytoplasmic bridges long after division, and that bridge abscission progressively accelerates as cells exit naive pluripotency. Finally, interfering with abscission impairs naive pluripotency exit, and artificially inducing abscission accelerates it. Altogether, our data indicate that a switch in the division machinery leading to faster abscission regulates pluripotency exit. Our study identifies abscission as a key cellular process coupling cell division to fate transitions."}],"status":"public","author":[{"first_name":"Agathe","full_name":"Chaigne, Agathe","last_name":"Chaigne"},{"first_name":"Céline","last_name":"Labouesse","full_name":"Labouesse, Céline"},{"full_name":"White, Ian J.","last_name":"White","first_name":"Ian J."},{"last_name":"Agnew","full_name":"Agnew, Meghan","first_name":"Meghan"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kevin J.","last_name":"Chalut","full_name":"Chalut, Kevin J."},{"full_name":"Paluch, Ewa K.","last_name":"Paluch","first_name":"Ewa K."}],"oa":1,"quality_controlled":"1","date_created":"2020-10-18T22:01:37Z","citation":{"apa":"Chaigne, A., Labouesse, C., White, I. J., Agnew, M., Hannezo, E. B., Chalut, K. J., & Paluch, E. K. (2020). Abscission couples cell division to embryonic stem cell fate. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2020.09.001","chicago":"Chaigne, Agathe, Céline Labouesse, Ian J. White, Meghan Agnew, Edouard B Hannezo, Kevin J. Chalut, and Ewa K. Paluch. “Abscission Couples Cell Division to Embryonic Stem Cell Fate.” Developmental Cell. Elsevier, 2020. https://doi.org/10.1016/j.devcel.2020.09.001.","mla":"Chaigne, Agathe, et al. “Abscission Couples Cell Division to Embryonic Stem Cell Fate.” Developmental Cell, vol. 55, no. 2, Elsevier, 2020, pp. 195–208, doi:10.1016/j.devcel.2020.09.001.","ama":"Chaigne A, Labouesse C, White IJ, et al. Abscission couples cell division to embryonic stem cell fate. Developmental Cell. 2020;55(2):195-208. doi:10.1016/j.devcel.2020.09.001","ieee":"A. Chaigne et al., “Abscission couples cell division to embryonic stem cell fate,” Developmental Cell, vol. 55, no. 2. Elsevier, pp. 195–208, 2020.","ista":"Chaigne A, Labouesse C, White IJ, Agnew M, Hannezo EB, Chalut KJ, Paluch EK. 2020. Abscission couples cell division to embryonic stem cell fate. Developmental Cell. 55(2), 195–208.","short":"A. Chaigne, C. Labouesse, I.J. White, M. Agnew, E.B. Hannezo, K.J. Chalut, E.K. Paluch, Developmental Cell 55 (2020) 195–208."},"page":"195-208","title":"Abscission couples cell division to embryonic stem cell fate","pmid":1,"day":"26","acknowledgement":"This work was supported by the Medical Research Council UK (MRC Program award MC_UU_12018/5 ), the European Research Council (starting grant 311637 -MorphoCorDiv and consolidator grant 820188 -NanoMechShape to E.K.P.), and the Leverhulme Trust (Leverhulme Prize in Biological Sciences to E.K.P.). K.J.C. acknowledges support from the Royal Society (Royal Society Research Fellowship). A.C. acknowledges support from EMBO ( ALTF 2015-563 ), the Wellcome Trust ( 201334/Z/16/Z ), and the Fondation Bettencourt-Schueller (Prix Jeune Chercheur, 2015).","publication":"Developmental Cell","volume":55,"date_published":"2020-10-26T00:00:00Z","intvolume":" 55","has_accepted_license":"1","file_date_updated":"2021-02-04T10:20:02Z","doi":"10.1016/j.devcel.2020.09.001","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No"},{"doi":"10.1016/j.neuron.2020.08.030","file_date_updated":"2020-12-10T14:42:09Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","day":"09","publication":"Neuron","acknowledgement":"We thank J. Angibaud for organotypic cultures and R. Chereau and J. Tonnesen for help with the STED microscope; also D. Gonzales and the Neurocentre Magendie INSERM U1215 Genotyping Platform, for breeding management and genotyping. This work was supported by the Wellcome Trust Principal Fellowships 101896 and 212251, ERC Advanced Grant 323113, ERC Proof-of-Concept Grant 767372, EC FP7 ITN 606950, and EU CSA 811011 (D.A.R.); NRW-Rückkehrerpogramm, UCL Excellence Fellowship, German Research Foundation (DFG) SPP1757 and SFB1089 (C.H.); Human Frontiers Science Program (C.H., C.J.J., and H.J.); EMBO Long-Term Fellowship (L.B.); Marie Curie FP7 PIRG08-GA-2010-276995 (A.P.), ASTROMODULATION (S.R.); Equipe FRM DEQ 201 303 26519, Conseil Régional d’Aquitaine R12056GG, INSERM (S.H.R.O.); ANR SUPERTri, ANR Castro (ANR-17-CE16-0002), R-13-BSV4-0007-01, Université de Bordeaux, labex BRAIN (S.H.R.O. and U.V.N.); CNRS (A.P., S.H.R.O., and U.V.N.); HFSP, ANR CEXC, and France-BioImaging ANR-10-INSB-04 (U.V.N.); and FP7 MemStick Project No. 201600 (M.G.S.).","volume":108,"pmid":1,"has_accepted_license":"1","intvolume":" 108","date_published":"2020-12-09T00:00:00Z","page":"P919-936.E11","title":"LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia","oa":1,"citation":{"mla":"Henneberger, Christian, et al. “LTP Induction Boosts Glutamate Spillover by Driving Withdrawal of Perisynaptic Astroglia.” Neuron, vol. 108, no. 5, Elsevier, 2020, p. P919–936.E11, doi:10.1016/j.neuron.2020.08.030.","apa":"Henneberger, C., Bard, L., Panatier, A., Reynolds, J. P., Kopach, O., Medvedev, N. I., … Rusakov, D. A. (2020). LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2020.08.030","chicago":"Henneberger, Christian, Lucie Bard, Aude Panatier, James P. Reynolds, Olga Kopach, Nikolay I. Medvedev, Daniel Minge, et al. “LTP Induction Boosts Glutamate Spillover by Driving Withdrawal of Perisynaptic Astroglia.” Neuron. Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.08.030.","ama":"Henneberger C, Bard L, Panatier A, et al. LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia. Neuron. 2020;108(5):P919-936.E11. doi:10.1016/j.neuron.2020.08.030","ista":"Henneberger C, Bard L, Panatier A, Reynolds JP, Kopach O, Medvedev NI, Minge D, Herde MK, Anders S, Kraev I, Heller JP, Rama S, Zheng K, Jensen TP, Sanchez-Romero I, Jackson CJ, Janovjak HL, Ottersen OP, Nagelhus EA, Oliet SHR, Stewart MG, Nägerl UVa, Rusakov DA. 2020. LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia. Neuron. 108(5), P919–936.E11.","ieee":"C. Henneberger et al., “LTP induction boosts glutamate spillover by driving withdrawal of perisynaptic astroglia,” Neuron, vol. 108, no. 5. Elsevier, p. P919–936.E11, 2020.","short":"C. Henneberger, L. Bard, A. Panatier, J.P. Reynolds, O. Kopach, N.I. Medvedev, D. Minge, M.K. Herde, S. Anders, I. Kraev, J.P. Heller, S. Rama, K. Zheng, T.P. Jensen, I. Sanchez-Romero, C.J. Jackson, H.L. Janovjak, O.P. Ottersen, E.A. Nagelhus, S.H.R. Oliet, M.G. Stewart, U.Va. Nägerl, D.A. Rusakov, Neuron 108 (2020) P919–936.E11."},"date_created":"2020-10-18T22:01:38Z","quality_controlled":"1","status":"public","author":[{"last_name":"Henneberger","full_name":"Henneberger, Christian","first_name":"Christian"},{"last_name":"Bard","full_name":"Bard, Lucie","first_name":"Lucie"},{"last_name":"Panatier","full_name":"Panatier, Aude","first_name":"Aude"},{"first_name":"James P.","last_name":"Reynolds","full_name":"Reynolds, James P."},{"last_name":"Kopach","full_name":"Kopach, Olga","first_name":"Olga"},{"first_name":"Nikolay I.","full_name":"Medvedev, Nikolay I.","last_name":"Medvedev"},{"first_name":"Daniel","last_name":"Minge","full_name":"Minge, Daniel"},{"last_name":"Herde","full_name":"Herde, Michel K.","first_name":"Michel K."},{"first_name":"Stefanie","last_name":"Anders","full_name":"Anders, Stefanie"},{"first_name":"Igor","full_name":"Kraev, Igor","last_name":"Kraev"},{"first_name":"Janosch P.","last_name":"Heller","full_name":"Heller, Janosch P."},{"first_name":"Sylvain","full_name":"Rama, Sylvain","last_name":"Rama"},{"last_name":"Zheng","full_name":"Zheng, Kaiyu","first_name":"Kaiyu"},{"full_name":"Jensen, Thomas P.","last_name":"Jensen","first_name":"Thomas P."},{"last_name":"Sanchez-Romero","full_name":"Sanchez-Romero, Inmaculada","first_name":"Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Colin J.","full_name":"Jackson, Colin J.","last_name":"Jackson"},{"last_name":"Janovjak","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L"},{"full_name":"Ottersen, Ole Petter","last_name":"Ottersen","first_name":"Ole Petter"},{"first_name":"Erlend Arnulf","last_name":"Nagelhus","full_name":"Nagelhus, Erlend Arnulf"},{"last_name":"Oliet","full_name":"Oliet, Stephane H.R.","first_name":"Stephane H.R."},{"first_name":"Michael G.","last_name":"Stewart","full_name":"Stewart, Michael G."},{"last_name":"Nägerl","full_name":"Nägerl, U. VAlentin","first_name":"U. VAlentin"},{"first_name":"Dmitri A. ","full_name":"Rusakov, Dmitri A. ","last_name":"Rusakov"}],"date_updated":"2023-08-22T09:59:29Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Extrasynaptic actions of glutamate are limited by high-affinity transporters expressed by perisynaptic astroglial processes (PAPs): this helps maintain point-to-point transmission in excitatory circuits. Memory formation in the brain is associated with synaptic remodeling, but how this affects PAPs and therefore extrasynaptic glutamate actions is poorly understood. Here, we used advanced imaging methods, in situ and in vivo, to find that a classical synaptic memory mechanism, long-term potentiation (LTP), triggers withdrawal of PAPs from potentiated synapses. Optical glutamate sensors combined with patch-clamp and 3D molecular localization reveal that LTP induction thus prompts spatial retreat of astroglial glutamate transporters, boosting glutamate spillover and NMDA-receptor-mediated inter-synaptic cross-talk. The LTP-triggered PAP withdrawal involves NKCC1 transporters and the actin-controlling protein cofilin but does not depend on major Ca2+-dependent cascades in astrocytes. We have therefore uncovered a mechanism by which a memory trace at one synapse could alter signal handling by multiple neighboring connections."}],"scopus_import":"1","publication_identifier":{"issn":["08966273"],"eissn":["10974199"]},"isi":1,"year":"2020","month":"12","department":[{"_id":"HaJa"}],"article_type":"original","publisher":"Elsevier","file":[{"file_size":7518960,"success":1,"checksum":"054562bb50165ef9a1f46631c1c5e36b","date_created":"2020-12-10T14:42:09Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-12-10T14:42:09Z","creator":"dernst","file_id":"8939","relation":"main_file","file_name":"2020_Neuron_Henneberger.pdf"}],"type":"journal_article","ddc":["570"],"oa_version":"Published Version","external_id":{"isi":["000603428000010"],"pmid":["32976770"]},"publication_status":"published","_id":"8674","issue":"5"},{"_id":"8679","external_id":{"isi":["000583337200011"]},"publication_status":"published","type":"journal_article","oa_version":"None","publisher":"Springer Nature","article_type":"original","department":[{"_id":"ToHe"}],"month":"10","year":"2020","project":[{"grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"isi":1,"publication_identifier":{"eissn":["2522-5839"]},"scopus_import":"1","abstract":[{"text":"A central goal of artificial intelligence in high-stakes decision-making applications is to design a single algorithm that simultaneously expresses generalizability by learning coherent representations of their world and interpretable explanations of its dynamics. Here, we combine brain-inspired neural computation principles and scalable deep learning architectures to design compact neural controllers for task-specific compartments of a full-stack autonomous vehicle control system. We discover that a single algorithm with 19 control neurons, connecting 32 encapsulated input features to outputs by 253 synapses, learns to map high-dimensional inputs into steering commands. This system shows superior generalizability, interpretability and robustness compared with orders-of-magnitude larger black-box learning systems. The obtained neural agents enable high-fidelity autonomy for task-specific parts of a complex autonomous system.","lang":"eng"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-deep-learning-models/","relation":"press_release","description":"News on IST Homepage"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-22T10:36:06Z","author":[{"first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias","last_name":"Lechner"},{"last_name":"Hasani","full_name":"Hasani, Ramin","first_name":"Ramin"},{"last_name":"Amini","full_name":"Amini, Alexander","first_name":"Alexander"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"},{"last_name":"Rus","full_name":"Rus, Daniela","first_name":"Daniela"},{"first_name":"Radu","full_name":"Grosu, Radu","last_name":"Grosu"}],"status":"public","quality_controlled":"1","date_created":"2020-10-19T13:46:06Z","citation":{"ista":"Lechner M, Hasani R, Amini A, Henzinger TA, Rus D, Grosu R. 2020. Neural circuit policies enabling auditable autonomy. Nature Machine Intelligence. 2, 642–652.","ieee":"M. Lechner, R. Hasani, A. Amini, T. A. Henzinger, D. Rus, and R. Grosu, “Neural circuit policies enabling auditable autonomy,” Nature Machine Intelligence, vol. 2. Springer Nature, pp. 642–652, 2020.","short":"M. Lechner, R. Hasani, A. Amini, T.A. Henzinger, D. Rus, R. Grosu, Nature Machine Intelligence 2 (2020) 642–652.","ama":"Lechner M, Hasani R, Amini A, Henzinger TA, Rus D, Grosu R. Neural circuit policies enabling auditable autonomy. Nature Machine Intelligence. 2020;2:642-652. doi:10.1038/s42256-020-00237-3","chicago":"Lechner, Mathias, Ramin Hasani, Alexander Amini, Thomas A Henzinger, Daniela Rus, and Radu Grosu. “Neural Circuit Policies Enabling Auditable Autonomy.” Nature Machine Intelligence. Springer Nature, 2020. https://doi.org/10.1038/s42256-020-00237-3.","apa":"Lechner, M., Hasani, R., Amini, A., Henzinger, T. A., Rus, D., & Grosu, R. (2020). Neural circuit policies enabling auditable autonomy. Nature Machine Intelligence. Springer Nature. https://doi.org/10.1038/s42256-020-00237-3","mla":"Lechner, Mathias, et al. “Neural Circuit Policies Enabling Auditable Autonomy.” Nature Machine Intelligence, vol. 2, Springer Nature, 2020, pp. 642–52, doi:10.1038/s42256-020-00237-3."},"title":"Neural circuit policies enabling auditable autonomy","page":"642-652","date_published":"2020-10-01T00:00:00Z","intvolume":" 2","volume":2,"day":"01","publication":"Nature Machine Intelligence","article_processing_charge":"No","doi":"10.1038/s42256-020-00237-3"},{"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/803635v1"}],"keyword":["Multidisciplinary"],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/sticking-together/"}]},"abstract":[{"text":"Animal development entails the organization of specific cell types in space and time, and spatial patterns must form in a robust manner. In the zebrafish spinal cord, neural progenitors form stereotypic patterns despite noisy morphogen signaling and large-scale cellular rearrangements during morphogenesis and growth. By directly measuring adhesion forces and preferences for three types of endogenous neural progenitors, we provide evidence for the differential adhesion model in which differences in intercellular adhesion mediate cell sorting. Cell type–specific combinatorial expression of different classes of cadherins (N-cadherin, cadherin 11, and protocadherin 19) results in homotypic preference ex vivo and patterning robustness in vivo. Furthermore, the differential adhesion code is regulated by the sonic hedgehog morphogen gradient. We propose that robust patterning during tissue morphogenesis results from interplay between adhesion-based self-organization and morphogen-directed patterning.","lang":"eng"}],"scopus_import":"1","date_updated":"2023-08-22T10:36:35Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"status":"public","author":[{"first_name":"Tony Y.-C.","last_name":"Tsai","full_name":"Tsai, Tony Y.-C."},{"full_name":"Sikora, Mateusz K","last_name":"Sikora","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","first_name":"Mateusz K"},{"full_name":"Xia, Peng","last_name":"Xia","orcid":"0000-0002-5419-7756","first_name":"Peng","id":"4AB6C7D0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Colak-Champollion, Tugba","last_name":"Colak-Champollion","first_name":"Tugba"},{"first_name":"Holger","last_name":"Knaut","full_name":"Knaut, Holger"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"last_name":"Megason","full_name":"Megason, Sean G.","first_name":"Sean G."}],"oa_version":"Preprint","type":"journal_article","publication_status":"published","external_id":{"isi":["000579169000053"]},"_id":"8680","issue":"6512","publisher":"American Association for the Advancement of Science","department":[{"_id":"CaHe"}],"article_type":"original","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"isi":1,"project":[{"grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"}],"year":"2020","month":"10","intvolume":" 370","date_published":"2020-10-02T00:00:00Z","day":"02","acknowledgement":"We thank the members of the Megason and Heisenberg labs for critical discussions of and technical assistance during the work and B. Appel, S. Holley, J. Jontes, and D. Gilmour for transgenic fish. This work is supported by the Damon Runyon Cancer Foundation, a NICHD K99 fellowship (1K99HD092623), a Travelling Fellowship of the Company of Biologists, a Collaborative Research grant from the Burroughs Wellcome Foundation (T.Y.-C.T.), NIH grant 01GM107733 (T.Y.-C.T. and S.G.M.), NIH grant R01NS102322 (T.C.-C. and H.K.), and an ERC advanced grant\r\n(MECSPEC) (C.-P.H.).","publication":"Science","volume":370,"article_processing_charge":"No","ec_funded":1,"doi":"10.1126/science.aba6637","citation":{"short":"T.Y.-C. Tsai, M.K. Sikora, P. Xia, T. Colak-Champollion, H. Knaut, C.-P.J. Heisenberg, S.G. Megason, Science 370 (2020) 113–116.","ieee":"T. Y.-C. Tsai et al., “An adhesion code ensures robust pattern formation during tissue morphogenesis,” Science, vol. 370, no. 6512. American Association for the Advancement of Science, pp. 113–116, 2020.","ista":"Tsai TY-C, Sikora MK, Xia P, Colak-Champollion T, Knaut H, Heisenberg C-PJ, Megason SG. 2020. An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. 370(6512), 113–116.","ama":"Tsai TY-C, Sikora MK, Xia P, et al. An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. 2020;370(6512):113-116. doi:10.1126/science.aba6637","chicago":"Tsai, Tony Y.-C., Mateusz K Sikora, Peng Xia, Tugba Colak-Champollion, Holger Knaut, Carl-Philipp J Heisenberg, and Sean G. Megason. “An Adhesion Code Ensures Robust Pattern Formation during Tissue Morphogenesis.” Science. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.aba6637.","apa":"Tsai, T. Y.-C., Sikora, M. K., Xia, P., Colak-Champollion, T., Knaut, H., Heisenberg, C.-P. J., & Megason, S. G. (2020). An adhesion code ensures robust pattern formation during tissue morphogenesis. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aba6637","mla":"Tsai, Tony Y. C., et al. “An Adhesion Code Ensures Robust Pattern Formation during Tissue Morphogenesis.” Science, vol. 370, no. 6512, American Association for the Advancement of Science, 2020, pp. 113–16, doi:10.1126/science.aba6637."},"date_created":"2020-10-19T14:09:38Z","quality_controlled":"1","oa":1,"title":"An adhesion code ensures robust pattern formation during tissue morphogenesis","page":"113-116"}]