[{"date_published":"2018-03-19T00:00:00Z","doi":"10.1038/s41562-018-0320-9","date_created":"2018-12-11T11:46:22Z","page":"469–477","day":"19","publication":"Nature Human Behaviour","has_accepted_license":"1","isi":1,"year":"2018","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"title":"Partners and rivals in direct reciprocity","publist_id":"7404","author":[{"first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","last_name":"Hilbe"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"external_id":{"isi":["000446612000016"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"C. Hilbe, K. Chatterjee, M. Nowak, Nature Human Behaviour 2 (2018) 469–477.","ieee":"C. Hilbe, K. Chatterjee, and M. Nowak, “Partners and rivals in direct reciprocity,” Nature Human Behaviour, vol. 2. Nature Publishing Group, pp. 469–477, 2018.","ama":"Hilbe C, Chatterjee K, Nowak M. Partners and rivals in direct reciprocity. Nature Human Behaviour. 2018;2:469–477. doi:10.1038/s41562-018-0320-9","apa":"Hilbe, C., Chatterjee, K., & Nowak, M. (2018). Partners and rivals in direct reciprocity. Nature Human Behaviour. Nature Publishing Group. https://doi.org/10.1038/s41562-018-0320-9","mla":"Hilbe, Christian, et al. “Partners and Rivals in Direct Reciprocity.” Nature Human Behaviour, vol. 2, Nature Publishing Group, 2018, pp. 469–477, doi:10.1038/s41562-018-0320-9.","ista":"Hilbe C, Chatterjee K, Nowak M. 2018. Partners and rivals in direct reciprocity. Nature Human Behaviour. 2, 469–477.","chicago":"Hilbe, Christian, Krishnendu Chatterjee, and Martin Nowak. “Partners and Rivals in Direct Reciprocity.” Nature Human Behaviour. Nature Publishing Group, 2018. https://doi.org/10.1038/s41562-018-0320-9."},"project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"volume":2,"related_material":{"link":[{"relation":"erratum","url":"http://doi.org/10.1038/s41562-018-0342-3"}]},"ec_funded":1,"file":[{"date_updated":"2020-07-14T12:46:25Z","file_size":598033,"creator":"dernst","date_created":"2019-11-19T08:19:51Z","file_name":"2018_NatureHumanBeh_Hilbe.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"571b8cc0ba14e8d5d8b18e439a9835eb","file_id":"7052"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"03","intvolume":" 2","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"Reciprocity is a major factor in human social life and accounts for a large part of cooperation in our communities. Direct reciprocity arises when repeated interactions occur between the same individuals. The framework of iterated games formalizes this phenomenon. Despite being introduced more than five decades ago, the concept keeps offering beautiful surprises. Recent theoretical research driven by new mathematical tools has proposed a remarkable dichotomy among the crucial strategies: successful individuals either act as partners or as rivals. Rivals strive for unilateral advantages by applying selfish or extortionate strategies. Partners aim to share the payoff for mutual cooperation, but are ready to fight back when being exploited. Which of these behaviours evolves depends on the environment. Whereas small population sizes and a limited number of rounds favour rivalry, partner strategies are selected when populations are large and relationships stable. Only partners allow for evolution of cooperation, while the rivals’ attempt to put themselves first leads to defection. Hilbe et al. synthesize recent theoretical work on zero-determinant and ‘rival’ versus ‘partner’ strategies in social dilemmas. They describe the environments under which these contrasting selfish or cooperative strategies emerge in evolution.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:25Z","department":[{"_id":"KrCh"}],"ddc":["000"],"date_updated":"2023-09-13T09:38:54Z","status":"public","article_type":"review","type":"journal_article","_id":"419"},{"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:48:03Z","ddc":["000"],"date_updated":"2023-09-13T09:35:46Z","status":"public","type":"conference","conference":{"start_date":"2018-09-04","location":"Bejing, China","end_date":"2018-09-06","name":"FORMATS: Formal Modeling and Analysis of Timed Systems"},"_id":"78","volume":11022,"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"7831","checksum":"436b7574934324cfa7d1d3986fddc65b","date_updated":"2020-07-14T12:48:03Z","file_size":374851,"creator":"dernst","date_created":"2020-05-14T11:34:34Z","file_name":"2018_LNCS_Bakhirkin.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-030-00150-6"]},"publication_status":"published","month":"08","intvolume":" 11022","alternative_title":["LNCS"],"scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"We provide a procedure for detecting the sub-segments of an incrementally observed Boolean signal ω that match a given temporal pattern ϕ. As a pattern specification language, we use timed regular expressions, a formalism well-suited for expressing properties of concurrent asynchronous behaviors embedded in metric time. We construct a timed automaton accepting the timed language denoted by ϕ and modify it slightly for the purpose of matching. We then apply zone-based reachability computation to this automaton while it reads ω, and retrieve all the matching segments from the results. Since the procedure is automaton based, it can be applied to patterns specified by other formalisms such as timed temporal logics reducible to timed automata or directly encoded as timed automata. The procedure has been implemented and its performance on synthetic examples is demonstrated.","lang":"eng"}],"title":"Online timed pattern matching using automata","publist_id":"7976","author":[{"last_name":"Bakhirkin","full_name":"Bakhirkin, Alexey","first_name":"Alexey"},{"orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","last_name":"Ferrere","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"first_name":"Dejan","last_name":"Nickovic","full_name":"Nickovic, Dejan"},{"full_name":"Maler, Oded","last_name":"Maler","first_name":"Oded"},{"last_name":"Asarin","full_name":"Asarin, Eugene","first_name":"Eugene"}],"external_id":{"isi":["000884993200013"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. Online timed pattern matching using automata. In: Vol 11022. Springer; 2018:215-232. doi:10.1007/978-3-030-00151-3_13","apa":"Bakhirkin, A., Ferrere, T., Nickovic, D., Maler, O., & Asarin, E. (2018). Online timed pattern matching using automata (Vol. 11022, pp. 215–232). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Bejing, China: Springer. https://doi.org/10.1007/978-3-030-00151-3_13","short":"A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, E. Asarin, in:, Springer, 2018, pp. 215–232.","ieee":"A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, and E. Asarin, “Online timed pattern matching using automata,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Bejing, China, 2018, vol. 11022, pp. 215–232.","mla":"Bakhirkin, Alexey, et al. Online Timed Pattern Matching Using Automata. Vol. 11022, Springer, 2018, pp. 215–32, doi:10.1007/978-3-030-00151-3_13.","ista":"Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. 2018. Online timed pattern matching using automata. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11022, 215–232.","chicago":"Bakhirkin, Alexey, Thomas Ferrere, Dejan Nickovic, Oded Maler, and Eugene Asarin. “Online Timed Pattern Matching Using Automata,” 11022:215–32. Springer, 2018. https://doi.org/10.1007/978-3-030-00151-3_13."},"project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"}],"date_published":"2018-08-26T00:00:00Z","doi":"10.1007/978-3-030-00151-3_13","date_created":"2018-12-11T11:44:31Z","page":"215 - 232","day":"26","has_accepted_license":"1","isi":1,"year":"2018","quality_controlled":"1","publisher":"Springer","oa":1},{"month":"04","intvolume":" 8","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We replace the established aluminium gates for the formation of quantum dots in silicon with gates made from palladium. We study the morphology of both aluminium and palladium gates with transmission electron microscopy. The native aluminium oxide is found to be formed all around the aluminium gates, which could lead to the formation of unintentional dots. Therefore, we report on a novel fabrication route that replaces aluminium and its native oxide by palladium with atomic-layer-deposition-grown aluminium oxide. Using this approach, we show the formation of low-disorder gate-defined quantum dots, which are reproducibly fabricated. Furthermore, palladium enables us to further shrink the gate design, allowing us to perform electron transport measurements in the few-electron regime in devices comprising only two gate layers, a major technological advancement. It remains to be seen, whether the introduction of palladium gates can improve the excellent results on electron and nuclear spin qubits defined with an aluminium gate stack."}],"issue":"1","volume":8,"file":[{"creator":"system","date_updated":"2020-07-14T12:46:02Z","file_size":1850530,"date_created":"2018-12-12T10:17:04Z","file_name":"IST-2018-1016-v1+1_2018_Brauns_Palladium_gates.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5256","checksum":"20af238ca4ba6491b77270be8d826bf5"}],"language":[{"iso":"eng"}],"publication_status":"published","status":"public","pubrep_id":"1016","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"317","file_date_updated":"2020-07-14T12:46:02Z","department":[{"_id":"GeKa"}],"ddc":["539"],"date_updated":"2023-09-13T09:38:00Z","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"doi":"10.1038/s41598-018-24004-y","date_published":"2018-04-09T00:00:00Z","date_created":"2018-12-11T11:45:47Z","day":"09","publication":"Scientific Reports","has_accepted_license":"1","isi":1,"year":"2018","article_number":"5690","title":"Palladium gates for reproducible quantum dots in silicon","author":[{"first_name":"Matthias","id":"33F94E3C-F248-11E8-B48F-1D18A9856A87","last_name":"Brauns","full_name":"Brauns, Matthias"},{"first_name":"Sergey","last_name":"Amitonov","full_name":"Amitonov, Sergey"},{"first_name":"Paul","last_name":"Spruijtenburg","full_name":"Spruijtenburg, Paul"},{"last_name":"Zwanenburg","full_name":"Zwanenburg, Floris","first_name":"Floris"}],"publist_id":"7548","article_processing_charge":"No","external_id":{"isi":["000429404300013"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Brauns, Matthias, Sergey Amitonov, Paul Spruijtenburg, and Floris Zwanenburg. “Palladium Gates for Reproducible Quantum Dots in Silicon.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-24004-y.","ista":"Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. 2018. Palladium gates for reproducible quantum dots in silicon. Scientific Reports. 8(1), 5690.","mla":"Brauns, Matthias, et al. “Palladium Gates for Reproducible Quantum Dots in Silicon.” Scientific Reports, vol. 8, no. 1, 5690, Nature Publishing Group, 2018, doi:10.1038/s41598-018-24004-y.","ama":"Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. Palladium gates for reproducible quantum dots in silicon. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-24004-y","apa":"Brauns, M., Amitonov, S., Spruijtenburg, P., & Zwanenburg, F. (2018). Palladium gates for reproducible quantum dots in silicon. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-24004-y","ieee":"M. Brauns, S. Amitonov, P. Spruijtenburg, and F. Zwanenburg, “Palladium gates for reproducible quantum dots in silicon,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018.","short":"M. Brauns, S. Amitonov, P. Spruijtenburg, F. Zwanenburg, Scientific Reports 8 (2018)."}},{"page":"6808-6821","date_published":"2018-11-29T00:00:00Z","doi":"10.1096/fj.201800443","date_created":"2018-12-11T11:45:08Z","isi":1,"year":"2018","day":"29","publication":"The FASEB Journal","quality_controlled":"1","publisher":"FASEB","oa":1,"publist_id":"7721","author":[{"first_name":"Zita","last_name":"Liutkeviciute","full_name":"Liutkeviciute, Zita"},{"last_name":"Gil Mansilla","full_name":"Gil Mansilla, Esther","first_name":"Esther"},{"first_name":"Thomas","last_name":"Eder","full_name":"Eder, Thomas"},{"first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","full_name":"Casillas Perez, Barbara E","last_name":"Casillas Perez"},{"full_name":"Giulia Di Giglio, Maria","last_name":"Giulia Di Giglio","first_name":"Maria"},{"last_name":"Muratspahić","full_name":"Muratspahić, Edin","first_name":"Edin"},{"first_name":"Florian","last_name":"Grebien","full_name":"Grebien, Florian"},{"last_name":"Rattei","full_name":"Rattei, Thomas","first_name":"Thomas"},{"first_name":"Markus","last_name":"Muttenthaler","full_name":"Muttenthaler, Markus"},{"last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christian","last_name":"Gruber","full_name":"Gruber, Christian"}],"article_processing_charge":"No","external_id":{"pmid":["29939785"],"isi":["000449359700035"]},"title":"Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity","citation":{"mla":"Liutkeviciute, Zita, et al. “Oxytocin-like Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.” The FASEB Journal, vol. 32, no. 12, FASEB, 2018, pp. 6808–21, doi:10.1096/fj.201800443.","apa":"Liutkeviciute, Z., Gil Mansilla, E., Eder, T., Casillas Perez, B. E., Giulia Di Giglio, M., Muratspahić, E., … Gruber, C. (2018). Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. FASEB. https://doi.org/10.1096/fj.201800443","ama":"Liutkeviciute Z, Gil Mansilla E, Eder T, et al. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. 2018;32(12):6808-6821. doi:10.1096/fj.201800443","ieee":"Z. Liutkeviciute et al., “Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity,” The FASEB Journal, vol. 32, no. 12. FASEB, pp. 6808–6821, 2018.","short":"Z. Liutkeviciute, E. Gil Mansilla, T. Eder, B.E. Casillas Perez, M. Giulia Di Giglio, E. Muratspahić, F. Grebien, T. Rattei, M. Muttenthaler, S. Cremer, C. Gruber, The FASEB Journal 32 (2018) 6808–6821.","chicago":"Liutkeviciute, Zita, Esther Gil Mansilla, Thomas Eder, Barbara E Casillas Perez, Maria Giulia Di Giglio, Edin Muratspahić, Florian Grebien, et al. “Oxytocin-like Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.” The FASEB Journal. FASEB, 2018. https://doi.org/10.1096/fj.201800443.","ista":"Liutkeviciute Z, Gil Mansilla E, Eder T, Casillas Perez BE, Giulia Di Giglio M, Muratspahić E, Grebien F, Rattei T, Muttenthaler M, Cremer S, Gruber C. 2018. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. 32(12), 6808–6821."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"25E3D34E-B435-11E9-9278-68D0E5697425","name":"Individual function and social role of oxytocin-like neuropeptides in ants"}],"issue":"12","volume":32,"publication_identifier":{"issn":["08926638"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":" https://doi.org/10.1096/fj.201800443"}],"month":"11","intvolume":" 32","abstract":[{"text":"Ants are emerging model systems to study cellular signaling because distinct castes possess different physiologic phenotypes within the same colony. Here we studied the functionality of inotocin signaling, an insect ortholog of mammalian oxytocin (OT), which was recently discovered in ants. In Lasius ants, we determined that specialization within the colony, seasonal factors, and physiologic conditions down-regulated the expression of the OT-like signaling system. Given this natural variation, we interrogated its function using RNAi knockdowns. Next-generation RNA sequencing of OT-like precursor knock-down ants highlighted its role in the regulation of genes involved in metabolism. Knock-down ants exhibited higher walking activity and increased self-grooming in the brood chamber. We propose that OT-like signaling in ants is important for regulating metabolic processes and locomotion.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"department":[{"_id":"SyCr"}],"date_updated":"2023-09-13T09:37:32Z","type":"journal_article","article_type":"original","status":"public","_id":"194"},{"department":[{"_id":"JoDa"}],"file_date_updated":"2020-07-14T12:45:03Z","ddc":["570"],"date_updated":"2023-09-13T09:36:35Z","status":"public","article_type":"original","type":"journal_article","_id":"159","volume":14,"related_material":{"link":[{"url":"https://doi.org/10.1038/s41589-021-00744-3","relation":"erratum"}]},"issue":"8","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"7832","checksum":"d42935094ec845f54a0688bf12986d62","creator":"dernst","date_updated":"2020-07-14T12:45:03Z","file_size":6321000,"date_created":"2020-05-14T12:14:09Z","file_name":"2018_NatureChemicalBiology_Fehrentz.pdf"}],"publication_status":"published","intvolume":" 14","month":"07","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"L-type Ca2+ channels (LTCCs) play a crucial role in excitation-contraction coupling and release of hormones from secretory cells. They are targets of antihypertensive and antiarrhythmic drugs such as diltiazem. Here, we present a photoswitchable diltiazem, FHU-779, which can be used to reversibly block endogenous LTCCs by light. FHU-779 is as potent as diltiazem and can be used to place pancreatic β-cell function and cardiac activity under optical control."}],"title":"Optical control of L-type Ca2+ channels using a diltiazem photoswitch","article_processing_charge":"No","external_id":{"isi":["000438970200010"]},"author":[{"first_name":"Timm","last_name":"Fehrentz","full_name":"Fehrentz, Timm"},{"full_name":"Huber, Florian","last_name":"Huber","first_name":"Florian"},{"last_name":"Hartrampf","full_name":"Hartrampf, Nina","first_name":"Nina"},{"first_name":"Tobias","full_name":"Bruegmann, Tobias","last_name":"Bruegmann"},{"first_name":"James","full_name":"Frank, James","last_name":"Frank"},{"first_name":"Nicholas","last_name":"Fine","full_name":"Fine, Nicholas"},{"full_name":"Malan, Daniela","last_name":"Malan","first_name":"Daniela"},{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl"},{"full_name":"Tikhonov, Denis","last_name":"Tikhonov","first_name":"Denis"},{"first_name":"Maritn","full_name":"Sumser, Maritn","last_name":"Sumser"},{"first_name":"Philipp","last_name":"Sasse","full_name":"Sasse, Philipp"},{"last_name":"Hodson","full_name":"Hodson, David","first_name":"David"},{"last_name":"Zhorov","full_name":"Zhorov, Boris","first_name":"Boris"},{"first_name":"Nikolaj","last_name":"Klocker","full_name":"Klocker, Nikolaj"},{"full_name":"Trauner, Dirk","last_name":"Trauner","first_name":"Dirk"}],"publist_id":"7762","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Fehrentz, Timm, Florian Huber, Nina Hartrampf, Tobias Bruegmann, James Frank, Nicholas Fine, Daniela Malan, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” Nature Chemical Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41589-018-0090-8.","ista":"Fehrentz T, Huber F, Hartrampf N, Bruegmann T, Frank J, Fine N, Malan D, Danzl JG, Tikhonov D, Sumser M, Sasse P, Hodson D, Zhorov B, Klocker N, Trauner D. 2018. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. 14(8), 764–767.","mla":"Fehrentz, Timm, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” Nature Chemical Biology, vol. 14, no. 8, Nature Publishing Group, 2018, pp. 764–67, doi:10.1038/s41589-018-0090-8.","ama":"Fehrentz T, Huber F, Hartrampf N, et al. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. 2018;14(8):764-767. doi:10.1038/s41589-018-0090-8","apa":"Fehrentz, T., Huber, F., Hartrampf, N., Bruegmann, T., Frank, J., Fine, N., … Trauner, D. (2018). Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/s41589-018-0090-8","short":"T. Fehrentz, F. Huber, N. Hartrampf, T. Bruegmann, J. Frank, N. Fine, D. Malan, J.G. Danzl, D. Tikhonov, M. Sumser, P. Sasse, D. Hodson, B. Zhorov, N. Klocker, D. Trauner, Nature Chemical Biology 14 (2018) 764–767.","ieee":"T. Fehrentz et al., “Optical control of L-type Ca2+ channels using a diltiazem photoswitch,” Nature Chemical Biology, vol. 14, no. 8. Nature Publishing Group, pp. 764–767, 2018."},"date_created":"2018-12-11T11:44:56Z","date_published":"2018-07-16T00:00:00Z","doi":"10.1038/s41589-018-0090-8","page":"764 - 767","publication":"Nature Chemical Biology","day":"16","year":"2018","isi":1,"has_accepted_license":"1","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1"},{"external_id":{"isi":["000548912200004"],"arxiv":["1806.05126"]},"article_processing_charge":"No","author":[{"first_name":"Sebastian","full_name":"Arming, Sebastian","last_name":"Arming"},{"full_name":"Bartocci, Ezio","last_name":"Bartocci","first_name":"Ezio"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"4524F760-F248-11E8-B48F-1D18A9856A87","first_name":"Joost P","last_name":"Katoen","full_name":"Katoen, Joost P"},{"full_name":"Sokolova, Ana","last_name":"Sokolova","first_name":"Ana"}],"publist_id":"7975","title":"Parameter-independent strategies for pMDPs via POMDPs","citation":{"ista":"Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. 2018. Parameter-independent strategies for pMDPs via POMDPs. QEST: Quantitative Evaluation of Systems, LNCS, vol. 11024, 53–70.","chicago":"Arming, Sebastian, Ezio Bartocci, Krishnendu Chatterjee, Joost P Katoen, and Ana Sokolova. “Parameter-Independent Strategies for PMDPs via POMDPs,” 11024:53–70. Springer, 2018. https://doi.org/10.1007/978-3-319-99154-2_4.","ama":"Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. Parameter-independent strategies for pMDPs via POMDPs. In: Vol 11024. Springer; 2018:53-70. doi:10.1007/978-3-319-99154-2_4","apa":"Arming, S., Bartocci, E., Chatterjee, K., Katoen, J. P., & Sokolova, A. (2018). Parameter-independent strategies for pMDPs via POMDPs (Vol. 11024, pp. 53–70). Presented at the QEST: Quantitative Evaluation of Systems, Beijing, China: Springer. https://doi.org/10.1007/978-3-319-99154-2_4","ieee":"S. Arming, E. Bartocci, K. Chatterjee, J. P. Katoen, and A. Sokolova, “Parameter-independent strategies for pMDPs via POMDPs,” presented at the QEST: Quantitative Evaluation of Systems, Beijing, China, 2018, vol. 11024, pp. 53–70.","short":"S. Arming, E. Bartocci, K. Chatterjee, J.P. Katoen, A. Sokolova, in:, Springer, 2018, pp. 53–70.","mla":"Arming, Sebastian, et al. Parameter-Independent Strategies for PMDPs via POMDPs. Vol. 11024, Springer, 2018, pp. 53–70, doi:10.1007/978-3-319-99154-2_4."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"53-70","date_created":"2018-12-11T11:44:31Z","date_published":"2018-08-15T00:00:00Z","doi":"10.1007/978-3-319-99154-2_4","year":"2018","isi":1,"day":"15","oa":1,"quality_controlled":"1","publisher":"Springer","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2023-09-13T09:38:28Z","conference":{"start_date":"2018-09-04","end_date":"2018-09-07","location":"Beijing, China","name":"QEST: Quantitative Evaluation of Systems"},"type":"conference","status":"public","_id":"79","volume":11024,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1806.05126","open_access":"1"}],"scopus_import":"1","alternative_title":["LNCS"],"intvolume":" 11024","month":"08","abstract":[{"text":"Markov Decision Processes (MDPs) are a popular class of models suitable for solving control decision problems in probabilistic reactive systems. We consider parametric MDPs (pMDPs) that include parameters in some of the transition probabilities to account for stochastic uncertainties of the environment such as noise or input disturbances. We study pMDPs with reachability objectives where the parameter values are unknown and impossible to measure directly during execution, but there is a probability distribution known over the parameter values. We study for the first time computing parameter-independent strategies that are expectation optimal, i.e., optimize the expected reachability probability under the probability distribution over the parameters. We present an encoding of our problem to partially observable MDPs (POMDPs), i.e., a reduction of our problem to computing optimal strategies in POMDPs. We evaluate our method experimentally on several benchmarks: a motivating (repeated) learner model; a series of benchmarks of varying configurations of a robot moving on a grid; and a consensus protocol.","lang":"eng"}],"oa_version":"Preprint"},{"project":[{"name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"title":"Persistence of translational symmetry in the BCS model with radial pair interaction","publist_id":"7429","author":[{"last_name":"Deuchert","orcid":"0000-0003-3146-6746","full_name":"Deuchert, Andreas","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"},{"first_name":"Alissa","full_name":"Geisinge, Alissa","last_name":"Geisinge"},{"first_name":"Christian","full_name":"Hainzl, Christian","last_name":"Hainzl"},{"first_name":"Michael","last_name":"Loss","full_name":"Loss, Michael"}],"external_id":{"isi":["000429799900008"]},"article_processing_charge":"Yes (via OA deal)","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Deuchert, Andreas, Alissa Geisinge, Christian Hainzl, and Michael Loss. “Persistence of Translational Symmetry in the BCS Model with Radial Pair Interaction.” Annales Henri Poincare. Springer, 2018. https://doi.org/10.1007/s00023-018-0665-7.","ista":"Deuchert A, Geisinge A, Hainzl C, Loss M. 2018. Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. 19(5), 1507–1527.","mla":"Deuchert, Andreas, et al. “Persistence of Translational Symmetry in the BCS Model with Radial Pair Interaction.” Annales Henri Poincare, vol. 19, no. 5, Springer, 2018, pp. 1507–27, doi:10.1007/s00023-018-0665-7.","ama":"Deuchert A, Geisinge A, Hainzl C, Loss M. Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. 2018;19(5):1507-1527. doi:10.1007/s00023-018-0665-7","apa":"Deuchert, A., Geisinge, A., Hainzl, C., & Loss, M. (2018). Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. Springer. https://doi.org/10.1007/s00023-018-0665-7","short":"A. Deuchert, A. Geisinge, C. Hainzl, M. Loss, Annales Henri Poincare 19 (2018) 1507–1527.","ieee":"A. Deuchert, A. Geisinge, C. Hainzl, and M. Loss, “Persistence of translational symmetry in the BCS model with radial pair interaction,” Annales Henri Poincare, vol. 19, no. 5. Springer, pp. 1507–1527, 2018."},"quality_controlled":"1","publisher":"Springer","oa":1,"date_published":"2018-05-01T00:00:00Z","doi":"10.1007/s00023-018-0665-7","date_created":"2018-12-11T11:46:15Z","page":"1507 - 1527","day":"01","publication":"Annales Henri Poincare","has_accepted_license":"1","isi":1,"year":"2018","status":"public","pubrep_id":"1011","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"400","department":[{"_id":"RoSe"}],"file_date_updated":"2020-07-14T12:46:22Z","ddc":["510"],"date_updated":"2023-09-15T12:04:15Z","month":"05","intvolume":" 19","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We consider the two-dimensional BCS functional with a radial pair interaction. We show that the translational symmetry is not broken in a certain temperature interval below the critical temperature. In the case of vanishing angular momentum, our results carry over to the three-dimensional case."}],"issue":"5","volume":19,"ec_funded":1,"file":[{"file_name":"IST-2018-1011-v1+1_2018_Deuchert_Persistence.pdf","date_created":"2018-12-12T10:12:47Z","creator":"system","file_size":582680,"date_updated":"2020-07-14T12:46:22Z","checksum":"04d2c9bd7cbf3ca1d7acaaf4e7dca3e5","file_id":"4966","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published"},{"acknowledgement":"This work was supported by the Human Frontier Science Program RGP0065/2012 (GT, ES).","oa":1,"publisher":"Public Library of Science","quality_controlled":"1","year":"2018","has_accepted_license":"1","isi":1,"publication":"PLoS One","day":"07","date_created":"2018-12-11T11:46:18Z","date_published":"2018-03-07T00:00:00Z","doi":"10.1371/journal.pone.0193049","project":[{"_id":"255008E4-B435-11E9-9278-68D0E5697425","name":"Information processing and computation in fish groups","grant_number":"RGP0065/2012"}],"citation":{"ama":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Probabilistic models of individual and collective animal behavior. PLoS One. 2018;13(3). doi:10.1371/journal.pone.0193049","apa":"Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018). Probabilistic models of individual and collective animal behavior. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0193049","ieee":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Probabilistic models of individual and collective animal behavior,” PLoS One, vol. 13, no. 3. Public Library of Science, 2018.","short":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, PLoS One 13 (2018).","mla":"Bod’Ová, Katarína, et al. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One, vol. 13, no. 3, Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.","ista":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Probabilistic models of individual and collective animal behavior. PLoS One. 13(3).","chicago":"Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper Tkačik. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One. Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0193049."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000426896800032"]},"article_processing_charge":"Yes","publist_id":"7423","author":[{"first_name":"Katarína","last_name":"Bod’Ová","full_name":"Bod’Ová, Katarína"},{"first_name":"Gabriel","id":"315BCD80-F248-11E8-B48F-1D18A9856A87","full_name":"Mitchell, Gabriel","last_name":"Mitchell"},{"first_name":"Roy","full_name":"Harpaz, Roy","last_name":"Harpaz"},{"full_name":"Schneidman, Elad","last_name":"Schneidman","first_name":"Elad"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"title":"Probabilistic models of individual and collective animal behavior","abstract":[{"lang":"eng","text":"Recent developments in automated tracking allow uninterrupted, high-resolution recording of animal trajectories, sometimes coupled with the identification of stereotyped changes of body pose or other behaviors of interest. Analysis and interpretation of such data represents a challenge: the timing of animal behaviors may be stochastic and modulated by kinematic variables, by the interaction with the environment or with the conspecifics within the animal group, and dependent on internal cognitive or behavioral state of the individual. Existing models for collective motion typically fail to incorporate the discrete, stochastic, and internal-state-dependent aspects of behavior, while models focusing on individual animal behavior typically ignore the spatial aspects of the problem. Here we propose a probabilistic modeling framework to address this gap. Each animal can switch stochastically between different behavioral states, with each state resulting in a possibly different law of motion through space. Switching rates for behavioral transitions can depend in a very general way, which we seek to identify from data, on the effects of the environment as well as the interaction between the animals. We represent the switching dynamics as a Generalized Linear Model and show that: (i) forward simulation of multiple interacting animals is possible using a variant of the Gillespie’s Stochastic Simulation Algorithm; (ii) formulated properly, the maximum likelihood inference of switching rate functions is tractably solvable by gradient descent; (iii) model selection can be used to identify factors that modulate behavioral state switching and to appropriately adjust model complexity to data. To illustrate our framework, we apply it to two synthetic models of animal motion and to real zebrafish tracking data. "}],"oa_version":"Submitted Version","scopus_import":"1","intvolume":" 13","month":"03","publication_status":"published","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"684229493db75b43e98a46cd922da497","file_id":"5165","file_size":6887358,"date_updated":"2020-07-14T12:46:22Z","creator":"system","file_name":"IST-2018-995-v1+1_2018_Bodova_Probabilistic.pdf","date_created":"2018-12-12T10:15:43Z"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9831"}]},"volume":13,"issue":"3","_id":"406","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"995","status":"public","date_updated":"2023-09-15T12:06:19Z","ddc":["530","571"],"department":[{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:46:22Z"},{"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"name":"Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems (HFSP Young investigators' grant)","grant_number":"RGY0079/2011","_id":"251BCBEC-B435-11E9-9278-68D0E5697425"},{"name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)","grant_number":"24210","_id":"251D65D8-B435-11E9-9278-68D0E5697425"}],"publist_id":"7364","author":[{"id":"4569785E-F248-11E8-B48F-1D18A9856A87","first_name":"Maros","last_name":"Pleska","full_name":"Pleska, Maros","orcid":"0000-0001-7460-7479"},{"first_name":"Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","last_name":"Lang","full_name":"Lang, Moritz"},{"first_name":"Dominik","full_name":"Refardt, Dominik","last_name":"Refardt"},{"full_name":"Levin, Bruce","last_name":"Levin","first_name":"Bruce"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"}],"article_processing_charge":"No","external_id":{"isi":["000426516400027"]},"title":"Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity","citation":{"ama":"Pleska M, Lang M, Refardt D, Levin B, Guet CC. Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. 2018;2(2):359-366. doi:10.1038/s41559-017-0424-z","apa":"Pleska, M., Lang, M., Refardt, D., Levin, B., & Guet, C. C. (2018). Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-017-0424-z","short":"M. Pleska, M. Lang, D. Refardt, B. Levin, C.C. Guet, Nature Ecology and Evolution 2 (2018) 359–366.","ieee":"M. Pleska, M. Lang, D. Refardt, B. Levin, and C. C. Guet, “Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity,” Nature Ecology and Evolution, vol. 2, no. 2. Springer Nature, pp. 359–366, 2018.","mla":"Pleska, Maros, et al. “Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with Innate Immunity.” Nature Ecology and Evolution, vol. 2, no. 2, Springer Nature, 2018, pp. 359–66, doi:10.1038/s41559-017-0424-z.","ista":"Pleska M, Lang M, Refardt D, Levin B, Guet CC. 2018. Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. 2(2), 359–366.","chicago":"Pleska, Maros, Moritz Lang, Dominik Refardt, Bruce Levin, and Calin C Guet. “Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with Innate Immunity.” Nature Ecology and Evolution. Springer Nature, 2018. https://doi.org/10.1038/s41559-017-0424-z."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","quality_controlled":"1","page":"359 - 366","date_published":"2018-02-01T00:00:00Z","doi":"10.1038/s41559-017-0424-z","date_created":"2018-12-11T11:46:35Z","isi":1,"year":"2018","day":"01","publication":"Nature Ecology and Evolution","type":"journal_article","status":"public","_id":"457","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"date_updated":"2023-09-15T12:04:57Z","scopus_import":"1","month":"02","intvolume":" 2","abstract":[{"text":"Temperate bacteriophages integrate in bacterial genomes as prophages and represent an important source of genetic variation for bacterial evolution, frequently transmitting fitness-augmenting genes such as toxins responsible for virulence of major pathogens. However, only a fraction of bacteriophage infections are lysogenic and lead to prophage acquisition, whereas the majority are lytic and kill the infected bacteria. Unless able to discriminate lytic from lysogenic infections, mechanisms of immunity to bacteriophages are expected to act as a double-edged sword and increase the odds of survival at the cost of depriving bacteria of potentially beneficial prophages. We show that although restriction-modification systems as mechanisms of innate immunity prevent both lytic and lysogenic infections indiscriminately in individual bacteria, they increase the number of prophage-acquiring individuals at the population level. We find that this counterintuitive result is a consequence of phage-host population dynamics, in which restriction-modification systems delay infection onset until bacteria reach densities at which the probability of lysogeny increases. These results underscore the importance of population-level dynamics as a key factor modulating costs and benefits of immunity to temperate bacteriophages","lang":"eng"}],"oa_version":"None","volume":2,"issue":"2","related_material":{"record":[{"relation":"dissertation_contains","id":"202","status":"public"}]},"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}]},{"issue":"19","volume":28,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2018.08.063"}],"scopus_import":"1","intvolume":" 28","month":"10","abstract":[{"lang":"eng","text":"Many animals use antimicrobials to prevent or cure disease [1,2]. For example, some animals will ingest plants with medicinal properties, both prophylactically to prevent infection and therapeutically to self-medicate when sick. Antimicrobial substances are also used as topical disinfectants, to prevent infection, protect offspring and to sanitise their surroundings [1,2]. Social insects (ants, bees, wasps and termites) build nests in environments with a high abundance and diversity of pathogenic microorganisms — such as soil and rotting wood — and colonies are often densely crowded, creating conditions that favour disease outbreaks. Consequently, social insects have evolved collective disease defences to protect their colonies from epidemics. These traits can be seen as functionally analogous to the immune system of individual organisms [3,4]. This ‘social immunity’ utilises antimicrobials to prevent and eradicate infections, and to keep the brood and nest clean. However, these antimicrobial compounds can be harmful to the insects themselves, and it is unknown how colonies prevent collateral damage when using them. Here, we demonstrate that antimicrobial acids, produced by workers to disinfect the colony, are harmful to the delicate pupal brood stage, but that the pupae are protected from the acids by the presence of a silk cocoon. Garden ants spray their nests with an antimicrobial poison to sanitize contaminated nestmates and brood. Here, Pull et al show that they also prophylactically sanitise their colonies, and that the silk cocoon serves as a barrier to protect developing pupae, thus preventing collateral damage during nest sanitation."}],"oa_version":"Published Version","department":[{"_id":"SyCr"}],"date_updated":"2023-09-15T12:06:46Z","article_type":"original","type":"journal_article","status":"public","_id":"55","page":"R1139 - R1140","date_created":"2018-12-11T11:44:23Z","date_published":"2018-10-08T00:00:00Z","doi":"10.1016/j.cub.2018.08.063","year":"2018","isi":1,"publication":"Current Biology","day":"08","oa":1,"publisher":"Cell Press","quality_controlled":"1","article_processing_charge":"No","external_id":{"isi":["000446693400008"]},"author":[{"id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher","last_name":"Pull","orcid":"0000-0003-1122-3982","full_name":"Pull, Christopher"},{"orcid":"0000-0002-9547-2494","full_name":"Metzler, Sina","last_name":"Metzler","id":"48204546-F248-11E8-B48F-1D18A9856A87","first_name":"Sina"},{"id":"31757262-F248-11E8-B48F-1D18A9856A87","first_name":"Elisabeth","full_name":"Naderlinger, Elisabeth","last_name":"Naderlinger"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer"}],"publist_id":"7999","title":"Protection against the lethal side effects of social immunity in ants","citation":{"ista":"Pull C, Metzler S, Naderlinger E, Cremer S. 2018. Protection against the lethal side effects of social immunity in ants. Current Biology. 28(19), R1139–R1140.","chicago":"Pull, Christopher, Sina Metzler, Elisabeth Naderlinger, and Sylvia Cremer. “Protection against the Lethal Side Effects of Social Immunity in Ants.” Current Biology. Cell Press, 2018. https://doi.org/10.1016/j.cub.2018.08.063.","short":"C. Pull, S. Metzler, E. Naderlinger, S. Cremer, Current Biology 28 (2018) R1139–R1140.","ieee":"C. Pull, S. Metzler, E. Naderlinger, and S. Cremer, “Protection against the lethal side effects of social immunity in ants,” Current Biology, vol. 28, no. 19. Cell Press, pp. R1139–R1140, 2018.","ama":"Pull C, Metzler S, Naderlinger E, Cremer S. Protection against the lethal side effects of social immunity in ants. Current Biology. 2018;28(19):R1139-R1140. doi:10.1016/j.cub.2018.08.063","apa":"Pull, C., Metzler, S., Naderlinger, E., & Cremer, S. (2018). Protection against the lethal side effects of social immunity in ants. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2018.08.063","mla":"Pull, Christopher, et al. “Protection against the Lethal Side Effects of Social Immunity in Ants.” Current Biology, vol. 28, no. 19, Cell Press, 2018, pp. R1139–40, doi:10.1016/j.cub.2018.08.063."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"isi":1,"year":"2018","day":"01","publication":"SIAM Journal on Mathematical Analysis","page":"3271 - 3290","doi":"10.1137/17M1143125","date_published":"2018-01-01T00:00:00Z","date_created":"2018-12-11T11:45:03Z","acknowledgement":"The work of the second author was also partially supported by the Hausdorff Center of Mathematics.","quality_controlled":"1","publisher":"Society for Industrial and Applied Mathematics ","oa":1,"citation":{"chicago":"Erdös, László, Torben H Krüger, and David T Renfrew. “Power Law Decay for Systems of Randomly Coupled Differential Equations.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/17M1143125.","ista":"Erdös L, Krüger TH, Renfrew DT. 2018. Power law decay for systems of randomly coupled differential equations. SIAM Journal on Mathematical Analysis. 50(3), 3271–3290.","mla":"Erdös, László, et al. “Power Law Decay for Systems of Randomly Coupled Differential Equations.” SIAM Journal on Mathematical Analysis, vol. 50, no. 3, Society for Industrial and Applied Mathematics , 2018, pp. 3271–90, doi:10.1137/17M1143125.","ama":"Erdös L, Krüger TH, Renfrew DT. Power law decay for systems of randomly coupled differential equations. SIAM Journal on Mathematical Analysis. 2018;50(3):3271-3290. doi:10.1137/17M1143125","apa":"Erdös, L., Krüger, T. H., & Renfrew, D. T. (2018). Power law decay for systems of randomly coupled differential equations. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/17M1143125","short":"L. Erdös, T.H. Krüger, D.T. Renfrew, SIAM Journal on Mathematical Analysis 50 (2018) 3271–3290.","ieee":"L. Erdös, T. H. Krüger, and D. T. Renfrew, “Power law decay for systems of randomly coupled differential equations,” SIAM Journal on Mathematical Analysis, vol. 50, no. 3. Society for Industrial and Applied Mathematics , pp. 3271–3290, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"last_name":"Krüger","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87","first_name":"Torben H"},{"id":"4845BF6A-F248-11E8-B48F-1D18A9856A87","first_name":"David T","last_name":"Renfrew","orcid":"0000-0003-3493-121X","full_name":"Renfrew, David T"}],"publist_id":"7740","article_processing_charge":"No","external_id":{"isi":["000437018500032"],"arxiv":["1708.01546"]},"title":"Power law decay for systems of randomly coupled differential equations","project":[{"grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"258F40A4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02080","name":"Structured Non-Hermitian Random Matrices"}],"publication_status":"published","language":[{"iso":"eng"}],"issue":"3","volume":50,"ec_funded":1,"abstract":[{"text":"We consider large random matrices X with centered, independent entries but possibly di erent variances. We compute the normalized trace of f(X)g(X∗) for f, g functions analytic on the spectrum of X. We use these results to compute the long time asymptotics for systems of coupled di erential equations with random coe cients. We show that when the coupling is critical, the norm squared of the solution decays like t−1/2.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1708.01546","open_access":"1"}],"month":"01","intvolume":" 50","date_updated":"2023-09-15T12:05:52Z","department":[{"_id":"LaEr"}],"_id":"181","type":"journal_article","status":"public"},{"project":[{"grant_number":"320593","name":"Arithmetic and physics of Higgs moduli spaces","_id":"25E549F4-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Ganev, Iordan V. “Quantizations of Multiplicative Hypertoric Varieties at a Root of Unity.” Journal of Algebra, vol. 506, World Scientific Publishing, 2018, pp. 92–128, doi:10.1016/j.jalgebra.2018.03.015.","apa":"Ganev, I. V. (2018). Quantizations of multiplicative hypertoric varieties at a root of unity. Journal of Algebra. World Scientific Publishing. https://doi.org/10.1016/j.jalgebra.2018.03.015","ama":"Ganev IV. Quantizations of multiplicative hypertoric varieties at a root of unity. Journal of Algebra. 2018;506:92-128. doi:10.1016/j.jalgebra.2018.03.015","short":"I.V. Ganev, Journal of Algebra 506 (2018) 92–128.","ieee":"I. V. Ganev, “Quantizations of multiplicative hypertoric varieties at a root of unity,” Journal of Algebra, vol. 506. World Scientific Publishing, pp. 92–128, 2018.","chicago":"Ganev, Iordan V. “Quantizations of Multiplicative Hypertoric Varieties at a Root of Unity.” Journal of Algebra. World Scientific Publishing, 2018. https://doi.org/10.1016/j.jalgebra.2018.03.015.","ista":"Ganev IV. 2018. Quantizations of multiplicative hypertoric varieties at a root of unity. Journal of Algebra. 506, 92–128."},"title":"Quantizations of multiplicative hypertoric varieties at a root of unity","publist_id":"7543","author":[{"id":"447491B8-F248-11E8-B48F-1D18A9856A87","first_name":"Iordan V","full_name":"Ganev, Iordan V","last_name":"Ganev"}],"article_processing_charge":"No","external_id":{"isi":["000433270600005"],"arxiv":["1412.7211"]},"acknowledgement":"National Science Foundation: Graduate Research Fellowship and grant No.0932078000; ERC Advanced Grant “Arithmetic and Physics of Higgs moduli spaces” No. 320593 \r\nThe author is grateful to David Jordan for suggesting this project and providing guidance throughout, particularly for the formulation of Frobenius quantum moment maps and key ideas in the proofs of Theorems 3.12 and 4.8. Special thanks to David Ben-Zvi (the author's PhD advisor) for numerous discussions and constant encouragement, and for suggesting the term ‘hypertoric quantum group.’ Many results appearing in the current paper were proven independently by Nicholas Cooney; the author is grateful to Nicholas for sharing his insight on various topics, including Proposition 3.8. The author also thanks Nicholas Proudfoot for relating the definition of multiplicative hypertoric varieties, as well as the content of Remark 2.14. The author also benefited immensely from the close reading and detailed comments of an anonymous referee, and from conversations with Justin Hilburn, Kobi Kremnitzer, Michael McBreen, Tom Nevins, Travis Schedler, and Ben Webster. \r\n\r\n\r\n\r\n","publisher":"World Scientific Publishing","quality_controlled":"1","oa":1,"day":"15","publication":"Journal of Algebra","isi":1,"year":"2018","doi":"10.1016/j.jalgebra.2018.03.015","date_published":"2018-07-15T00:00:00Z","date_created":"2018-12-11T11:45:49Z","page":"92 - 128","_id":"322","status":"public","type":"journal_article","date_updated":"2023-09-15T12:08:38Z","department":[{"_id":"TaHa"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We construct quantizations of multiplicative hypertoric varieties using an algebra of q-difference operators on affine space, where q is a root of unity in C. The quantization defines a matrix bundle (i.e. Azumaya algebra) over the multiplicative hypertoric variety and admits an explicit finite étale splitting. The global sections of this Azumaya algebra is a hypertoric quantum group, and we prove a localization theorem. We introduce a general framework of Frobenius quantum moment maps and their Hamiltonian reductions; our results shed light on an instance of this framework."}],"month":"07","intvolume":" 506","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1412.7211"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":506,"ec_funded":1},{"doi":"10.1371/journal.pone.0193049.s001","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"406"}]},"date_published":"2018-03-07T00:00:00Z","date_created":"2021-08-09T07:01:24Z","year":"2018","day":"07","publisher":"Public Library of Science","month":"03","abstract":[{"text":"Implementation of the inference method in Matlab, including three applications of the method: The first one for the model of ant motion, the second one for bacterial chemotaxis, and the third one for the motion of fish.","lang":"eng"}],"oa_version":"Published Version","author":[{"last_name":"Bod’Ová","full_name":"Bod’Ová, Katarína","first_name":"Katarína"},{"last_name":"Mitchell","full_name":"Mitchell, Gabriel","first_name":"Gabriel","id":"315BCD80-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Harpaz","full_name":"Harpaz, Roy","first_name":"Roy"},{"first_name":"Elad","last_name":"Schneidman","full_name":"Schneidman, Elad"},{"last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"}],"article_processing_charge":"No","title":"Implementation of the inference method in Matlab","department":[{"_id":"GaTk"}],"date_updated":"2023-09-15T12:06:18Z","citation":{"mla":"Bod’Ová, Katarína, et al. Implementation of the Inference Method in Matlab. Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.s001.","apa":"Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018). Implementation of the inference method in Matlab. Public Library of Science. https://doi.org/10.1371/journal.pone.0193049.s001","ama":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Implementation of the inference method in Matlab. 2018. doi:10.1371/journal.pone.0193049.s001","short":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, (2018).","ieee":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Implementation of the inference method in Matlab.” Public Library of Science, 2018.","chicago":"Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper Tkačik. “Implementation of the Inference Method in Matlab.” Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0193049.s001.","ista":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Implementation of the inference method in Matlab, Public Library of Science, 10.1371/journal.pone.0193049.s001."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","status":"public","_id":"9831"},{"volume":10981,"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"fd95e8026deacef3dc752a733bb9355f","file_id":"5718","creator":"dernst","file_size":5591566,"date_updated":"2020-07-14T12:44:53Z","file_name":"2018_LNCS_Kong.pdf","date_created":"2018-12-17T15:57:06Z"}],"language":[{"iso":"eng"}],"alternative_title":["LNCS"],"scopus_import":"1","month":"07","intvolume":" 10981","abstract":[{"text":"We address the problem of analyzing the reachable set of a polynomial nonlinear continuous system by over-approximating the flowpipe of its dynamics. The common approach to tackle this problem is to perform a numerical integration over a given time horizon based on Taylor expansion and interval arithmetic. However, this method results to be very conservative when there is a large difference in speed between trajectories as time progresses. In this paper, we propose to use combinations of barrier functions, which we call piecewise barrier tube (PBT), to over-approximate flowpipe. The basic idea of PBT is that for each segment of a flowpipe, a coarse box which is big enough to contain the segment is constructed using sampled simulation and then in the box we compute by linear programming a set of barrier functions (called barrier tube or BT for short) which work together to form a tube surrounding the flowpipe. The benefit of using PBT is that (1) BT is independent of time and hence can avoid being stretched and deformed by time; and (2) a small number of BTs can form a tight over-approximation for the flowpipe, which means that the computation required to decide whether the BTs intersect the unsafe set can be reduced significantly. We implemented a prototype called PBTS in C++. Experiments on some benchmark systems show that our approach is effective.","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:44:53Z","department":[{"_id":"ToHe"}],"date_updated":"2023-09-15T12:12:08Z","ddc":["000"],"type":"conference","conference":{"name":"CAV: Computer Aided Verification","end_date":"2018-07-17","location":"Oxford, United Kingdom","start_date":"2018-07-14"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"142","page":"449 - 467","doi":"10.1007/978-3-319-96145-3_24","date_published":"2018-07-18T00:00:00Z","date_created":"2018-12-11T11:44:51Z","isi":1,"has_accepted_license":"1","year":"2018","day":"18","quality_controlled":"1","publisher":"Springer","oa":1,"acknowledgement":"Austrian Science Fund FWF: S11402-N23, S11405-N23, Z211-N32","publist_id":"7781","author":[{"id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","first_name":"Hui","last_name":"Kong","full_name":"Kong, Hui","orcid":"0000-0002-3066-6941"},{"first_name":"Ezio","last_name":"Bartocci","full_name":"Bartocci, Ezio"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"}],"external_id":{"isi":["000491481600024"]},"article_processing_charge":"No","title":"Reachable set over-approximation for nonlinear systems using piecewise barrier tubes","citation":{"chicago":"Kong, Hui, Ezio Bartocci, and Thomas A Henzinger. “Reachable Set Over-Approximation for Nonlinear Systems Using Piecewise Barrier Tubes,” 10981:449–67. Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_24.","ista":"Kong H, Bartocci E, Henzinger TA. 2018. Reachable set over-approximation for nonlinear systems using piecewise barrier tubes. CAV: Computer Aided Verification, LNCS, vol. 10981, 449–467.","mla":"Kong, Hui, et al. Reachable Set Over-Approximation for Nonlinear Systems Using Piecewise Barrier Tubes. Vol. 10981, Springer, 2018, pp. 449–67, doi:10.1007/978-3-319-96145-3_24.","ieee":"H. Kong, E. Bartocci, and T. A. Henzinger, “Reachable set over-approximation for nonlinear systems using piecewise barrier tubes,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10981, pp. 449–467.","short":"H. Kong, E. Bartocci, T.A. Henzinger, in:, Springer, 2018, pp. 449–467.","apa":"Kong, H., Bartocci, E., & Henzinger, T. A. (2018). Reachable set over-approximation for nonlinear systems using piecewise barrier tubes (Vol. 10981, pp. 449–467). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. https://doi.org/10.1007/978-3-319-96145-3_24","ama":"Kong H, Bartocci E, Henzinger TA. Reachable set over-approximation for nonlinear systems using piecewise barrier tubes. In: Vol 10981. Springer; 2018:449-467. doi:10.1007/978-3-319-96145-3_24"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}]},{"doi":"10.1103/PhysRevA.97.022510","date_published":"2018-02-21T00:00:00Z","date_created":"2018-12-11T11:46:25Z","isi":1,"year":"2018","day":"21","publication":" Physical Review A - Atomic, Molecular, and Optical Physics","publisher":"American Physical Society","quality_controlled":"1","oa":1,"acknowledgement":"This work was funded by the Portuguese Fundação para a Ciência e a Tecnologia (FCT/MCTES/PIDDAC) under Grant No. UID/FIS/04559/2013 (LIBPhys). P.A. acknowledges the support of the FCT, under Contract No. SFRH/BPD/92329/2013. L.S. acknowledges financial support from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA Grant Agreement No. (291734). Laboratoire Kastler Brossel (LKB) is “Unité Mixte de Recherche de Sorbonne Université, de ENS-PSL Research University, du Collège de France et du CNRS No. 8552.” APPENDIX:\r\n","publist_id":"7396","author":[{"last_name":"Amaro","full_name":"Amaro, Pedro","first_name":"Pedro"},{"last_name":"Loureiro","full_name":"Loureiro, Ulisses","first_name":"Ulisses"},{"id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","first_name":"Laleh","full_name":"Safari, Laleh","last_name":"Safari"},{"full_name":"Fratini, Filippo","last_name":"Fratini","first_name":"Filippo"},{"first_name":"Paul","full_name":"Indelicato, Paul","last_name":"Indelicato"},{"first_name":"Thomas","last_name":"Stöhlker","full_name":"Stöhlker, Thomas"},{"first_name":"José","full_name":"Santos, José","last_name":"Santos"}],"article_processing_charge":"No","external_id":{"arxiv":["1802.07920"],"isi":["000425601000004"]},"title":"Quantum interference in laser spectroscopy of highly charged lithiumlike ions","citation":{"mla":"Amaro, Pedro, et al. “Quantum Interference in Laser Spectroscopy of Highly Charged Lithiumlike Ions.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 2, 022510, American Physical Society, 2018, doi:10.1103/PhysRevA.97.022510.","ieee":"P. Amaro et al., “Quantum interference in laser spectroscopy of highly charged lithiumlike ions,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 2. American Physical Society, 2018.","short":"P. Amaro, U. Loureiro, L. Safari, F. Fratini, P. Indelicato, T. Stöhlker, J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018).","apa":"Amaro, P., Loureiro, U., Safari, L., Fratini, F., Indelicato, P., Stöhlker, T., & Santos, J. (2018). Quantum interference in laser spectroscopy of highly charged lithiumlike ions. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.022510","ama":"Amaro P, Loureiro U, Safari L, et al. Quantum interference in laser spectroscopy of highly charged lithiumlike ions. Physical Review A - Atomic, Molecular, and Optical Physics. 2018;97(2). doi:10.1103/PhysRevA.97.022510","chicago":"Amaro, Pedro, Ulisses Loureiro, Laleh Safari, Filippo Fratini, Paul Indelicato, Thomas Stöhlker, and José Santos. “Quantum Interference in Laser Spectroscopy of Highly Charged Lithiumlike Ions.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.022510.","ista":"Amaro P, Loureiro U, Safari L, Fratini F, Indelicato P, Stöhlker T, Santos J. 2018. Quantum interference in laser spectroscopy of highly charged lithiumlike ions. Physical Review A - Atomic, Molecular, and Optical Physics. 97(2), 022510."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"article_number":"022510","issue":"2","volume":97,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1802.07920"}],"month":"02","intvolume":" 97","abstract":[{"text":"We investigate the quantum interference induced shifts between energetically close states in highly charged ions, with the energy structure being observed by laser spectroscopy. In this work, we focus on hyperfine states of lithiumlike heavy-Z isotopes and quantify how much quantum interference changes the observed transition frequencies. The process of photon excitation and subsequent photon decay for the transition 2s→2p→2s is implemented with fully relativistic and full-multipole frameworks, which are relevant for such relativistic atomic systems. We consider the isotopes Pb79+207 and Bi80+209 due to experimental interest, as well as other examples of isotopes with lower Z, namely Pr56+141 and Ho64+165. We conclude that quantum interference can induce shifts up to 11% of the linewidth in the measurable resonances of the considered isotopes, if interference between resonances is neglected. The inclusion of relativity decreases the cross section by 35%, mainly due to the complete retardation form of the electric dipole multipole. However, the contribution of the next higher multipoles (e.g., magnetic quadrupole) to the cross section is negligible. This makes the contribution of relativity and higher-order multipoles to the quantum interference induced shifts a minor effect, even for heavy-Z elements.","lang":"eng"}],"oa_version":"Preprint","department":[{"_id":"MiLe"}],"date_updated":"2023-09-15T12:09:35Z","article_type":"original","type":"journal_article","status":"public","_id":"427"},{"project":[{"grant_number":"M02281","name":"Eliminating intersections in drawings of graphs","_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_processing_charge":"No","external_id":{"isi":["000483921200021"],"arxiv":["1709.09209"]},"author":[{"first_name":"Hugo","last_name":"Akitaya","full_name":"Akitaya, Hugo"},{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav","last_name":"Fulek","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav"},{"last_name":"Tóth","full_name":"Tóth, Csaba","first_name":"Csaba"}],"publist_id":"7556","title":"Recognizing weak embeddings of graphs","citation":{"mla":"Akitaya, Hugo, et al. Recognizing Weak Embeddings of Graphs. ACM, 2018, pp. 274–92, doi:10.1137/1.9781611975031.20.","short":"H. Akitaya, R. Fulek, C. Tóth, in:, ACM, 2018, pp. 274–292.","ieee":"H. Akitaya, R. Fulek, and C. Tóth, “Recognizing weak embeddings of graphs,” presented at the SODA: Symposium on Discrete Algorithms, New Orleans, LA, USA, 2018, pp. 274–292.","ama":"Akitaya H, Fulek R, Tóth C. Recognizing weak embeddings of graphs. In: ACM; 2018:274-292. doi:10.1137/1.9781611975031.20","apa":"Akitaya, H., Fulek, R., & Tóth, C. (2018). Recognizing weak embeddings of graphs (pp. 274–292). Presented at the SODA: Symposium on Discrete Algorithms, New Orleans, LA, USA: ACM. https://doi.org/10.1137/1.9781611975031.20","chicago":"Akitaya, Hugo, Radoslav Fulek, and Csaba Tóth. “Recognizing Weak Embeddings of Graphs,” 274–92. ACM, 2018. https://doi.org/10.1137/1.9781611975031.20.","ista":"Akitaya H, Fulek R, Tóth C. 2018. Recognizing weak embeddings of graphs. SODA: Symposium on Discrete Algorithms, 274–292."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"quality_controlled":"1","publisher":"ACM","acknowledgement":"∗Research supported in part by the NSF awards CCF-1422311 and CCF-1423615, and the Science Without Borders program. The second author gratefully acknowledges support from Austrian Science Fund (FWF): M2281-N35.","page":"274 - 292","date_created":"2018-12-11T11:45:45Z","doi":"10.1137/1.9781611975031.20","date_published":"2018-01-01T00:00:00Z","year":"2018","isi":1,"day":"01","conference":{"start_date":"2018-01-07","end_date":"2018-01-10","location":"New Orleans, LA, USA","name":"SODA: Symposium on Discrete Algorithms"},"type":"conference","status":"public","_id":"309","department":[{"_id":"UlWa"}],"date_updated":"2023-09-15T12:19:32Z","main_file_link":[{"url":"https://arxiv.org/abs/1709.09209","open_access":"1"}],"scopus_import":"1","month":"01","abstract":[{"lang":"eng","text":"We present an efficient algorithm for a problem in the interface between clustering and graph embeddings. An embedding ' : G ! M of a graph G into a 2manifold M maps the vertices in V (G) to distinct points and the edges in E(G) to interior-disjoint Jordan arcs between the corresponding vertices. In applications in clustering, cartography, and visualization, nearby vertices and edges are often bundled to a common node or arc, due to data compression or low resolution. This raises the computational problem of deciding whether a given map ' : G ! M comes from an embedding. A map ' : G ! M is a weak embedding if it can be perturbed into an embedding ψ: G ! M with k' \"k < \" for every " > 0. A polynomial-time algorithm for recognizing weak embeddings was recently found by Fulek and Kyncl [14], which reduces to solving a system of linear equations over Z2. It runs in O(n2!) O(n4:75) time, where 2:373 is the matrix multiplication exponent and n is the number of vertices and edges of G. We improve the running time to O(n log n). Our algorithm is also conceptually simpler than [14]: We perform a sequence of local operations that gradually "untangles" the image '(G) into an embedding (G), or reports that ' is not a weak embedding. It generalizes a recent technique developed for the case that G is a cycle and the embedding is a simple polygon [1], and combines local constraints on the orientation of subgraphs directly, thereby eliminating the need for solving large systems of linear equations."}],"oa_version":"Preprint","related_material":{"record":[{"status":"public","id":"6982","relation":"later_version"}]},"publication_status":"published","language":[{"iso":"eng"}]},{"department":[{"_id":"MiLe"}],"date_updated":"2023-09-15T12:09:06Z","status":"public","type":"journal_article","article_type":"original","_id":"5794","ec_funded":1,"volume":121,"issue":"25","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00319007"]},"intvolume":" 121","month":"12","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.00222"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"We present an approach to interacting quantum many-body systems based on the notion of quantum groups, also known as q-deformed Lie algebras. In particular, we show that, if the symmetry of a free quantum particle corresponds to a Lie group G, in the presence of a many-body environment this particle can be described by a deformed group, Gq. Crucially, the single deformation parameter, q, contains all the information about the many-particle interactions in the system. We exemplify our approach by considering a quantum rotor interacting with a bath of bosons, and demonstrate that extracting the value of q from closed-form solutions in the perturbative regime allows one to predict the behavior of the system for arbitrary values of the impurity-bath coupling strength, in good agreement with nonperturbative calculations. Furthermore, the value of the deformation parameter allows one to predict at which coupling strengths rotor-bath interactions result in a formation of a stable quasiparticle. The approach based on quantum groups does not only allow for a drastic simplification of impurity problems, but also provides valuable insights into hidden symmetries of interacting many-particle systems.","lang":"eng"}],"title":"Quantum groups as hidden symmetries of quantum impurities","article_processing_charge":"No","external_id":{"arxiv":["1809.00222"],"isi":["000454178600009"]},"author":[{"first_name":"Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","full_name":"Yakaboylu, Enderalp","orcid":"0000-0001-5973-0874","last_name":"Yakaboylu"},{"id":"35084A62-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Shkolnikov","full_name":"Shkolnikov, Mikhail","orcid":"0000-0002-4310-178X"},{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Yakaboylu E, Shkolnikov M, Lemeshko M. 2018. Quantum groups as hidden symmetries of quantum impurities. Physical Review Letters. 121(25), 255302.","chicago":"Yakaboylu, Enderalp, Mikhail Shkolnikov, and Mikhail Lemeshko. “Quantum Groups as Hidden Symmetries of Quantum Impurities.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.255302.","ama":"Yakaboylu E, Shkolnikov M, Lemeshko M. Quantum groups as hidden symmetries of quantum impurities. Physical Review Letters. 2018;121(25). doi:10.1103/PhysRevLett.121.255302","apa":"Yakaboylu, E., Shkolnikov, M., & Lemeshko, M. (2018). Quantum groups as hidden symmetries of quantum impurities. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.255302","short":"E. Yakaboylu, M. Shkolnikov, M. Lemeshko, Physical Review Letters 121 (2018).","ieee":"E. Yakaboylu, M. Shkolnikov, and M. Lemeshko, “Quantum groups as hidden symmetries of quantum impurities,” Physical Review Letters, vol. 121, no. 25. American Physical Society, 2018.","mla":"Yakaboylu, Enderalp, et al. “Quantum Groups as Hidden Symmetries of Quantum Impurities.” Physical Review Letters, vol. 121, no. 25, 255302, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.255302."},"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"255302","date_created":"2019-01-06T22:59:12Z","doi":"10.1103/PhysRevLett.121.255302","date_published":"2018-12-17T00:00:00Z","publication":"Physical Review Letters","day":"17","year":"2018","isi":1,"oa":1,"quality_controlled":"1","publisher":"American Physical Society"},{"year":"2018","isi":1,"publication":"Annals of Applied Probability","day":"01","page":"3215 - 3238","date_created":"2018-12-11T11:44:33Z","doi":"10.1214/18-AAP1389","date_published":"2018-10-01T00:00:00Z","oa":1,"publisher":"Institute of Mathematical Statistics","quality_controlled":"1","citation":{"chicago":"Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes Have Similar Radius Functions as Poisson-Delaunay Mosaics.” Annals of Applied Probability. Institute of Mathematical Statistics, 2018. https://doi.org/10.1214/18-AAP1389.","ista":"Edelsbrunner H, Nikitenko A. 2018. Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability. 28(5), 3215–3238.","mla":"Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes Have Similar Radius Functions as Poisson-Delaunay Mosaics.” Annals of Applied Probability, vol. 28, no. 5, Institute of Mathematical Statistics, 2018, pp. 3215–38, doi:10.1214/18-AAP1389.","short":"H. Edelsbrunner, A. Nikitenko, Annals of Applied Probability 28 (2018) 3215–3238.","ieee":"H. Edelsbrunner and A. Nikitenko, “Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics,” Annals of Applied Probability, vol. 28, no. 5. Institute of Mathematical Statistics, pp. 3215–3238, 2018.","apa":"Edelsbrunner, H., & Nikitenko, A. (2018). Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AAP1389","ama":"Edelsbrunner H, Nikitenko A. Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability. 2018;28(5):3215-3238. doi:10.1214/18-AAP1389"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"arxiv":["1705.02870"],"isi":["000442893500018"]},"article_processing_charge":"No","publist_id":"7967","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"full_name":"Nikitenko, Anton","orcid":"0000-0002-0659-3201","last_name":"Nikitenko","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","first_name":"Anton"}],"title":"Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics","project":[{"name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","language":[{"iso":"eng"}],"volume":28,"issue":"5","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6287"}]},"abstract":[{"lang":"eng","text":"Using the geodesic distance on the n-dimensional sphere, we study the expected radius function of the Delaunay mosaic of a random set of points. Specifically, we consider the partition of the mosaic into intervals of the radius function and determine the expected number of intervals whose radii are less than or equal to a given threshold. We find that the expectations are essentially the same as for the Poisson–Delaunay mosaic in n-dimensional Euclidean space. Assuming the points are not contained in a hemisphere, the Delaunay mosaic is isomorphic to the boundary complex of the convex hull in Rn+1, so we also get the expected number of faces of a random inscribed polytope. As proved in Antonelli et al. [Adv. in Appl. Probab. 9–12 (1977–1980)], an orthant section of the n-sphere is isometric to the standard n-simplex equipped with the Fisher information metric. It follows that the latter space has similar stochastic properties as the n-dimensional Euclidean space. Our results are therefore relevant in information geometry and in population genetics."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.02870"}],"scopus_import":"1","intvolume":" 28","month":"10","date_updated":"2023-09-15T12:10:35Z","department":[{"_id":"HeEd"}],"_id":"87","article_type":"original","type":"journal_article","status":"public"},{"_id":"192","type":"journal_article","article_type":"original","status":"public","date_updated":"2023-09-15T12:11:03Z","department":[{"_id":"JiFr"},{"_id":"DaSi"},{"_id":"NanoFab"}],"abstract":[{"text":"The phytohormone auxin is the information carrier in a plethora of developmental and physiological processes in plants(1). It has been firmly established that canonical, nuclear auxin signalling acts through regulation of gene transcription(2). Here, we combined microfluidics, live imaging, genetic engineering and computational modelling to reanalyse the classical case of root growth inhibition(3) by auxin. We show that Arabidopsis roots react to addition and removal of auxin by extremely rapid adaptation of growth rate. This process requires intracellular auxin perception but not transcriptional reprogramming. The formation of the canonical TIR1/AFB-Aux/IAA co-receptor complex is required for the growth regulation, hinting to a novel, non-transcriptional branch of this signalling pathway. Our results challenge the current understanding of root growth regulation by auxin and suggest another, presumably non-transcriptional, signalling output of the canonical auxin pathway.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/29942048","open_access":"1"}],"scopus_import":"1","intvolume":" 4","month":"06","publication_status":"published","language":[{"iso":"eng"}],"volume":4,"issue":"7","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/new-mechanism-for-the-plant-hormone-auxin-discovered/"}]},"citation":{"mla":"Fendrych, Matyas, et al. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” Nature Plants, vol. 4, no. 7, Springer Nature, 2018, pp. 453–59, doi:10.1038/s41477-018-0190-1.","ieee":"M. Fendrych et al., “Rapid and reversible root growth inhibition by TIR1 auxin signalling,” Nature Plants, vol. 4, no. 7. Springer Nature, pp. 453–459, 2018.","short":"M. Fendrych, M. Akhmanova, J. Merrin, M. Glanc, S. Hagihara, K. Takahashi, N. Uchida, K.U. Torii, J. Friml, Nature Plants 4 (2018) 453–459.","ama":"Fendrych M, Akhmanova M, Merrin J, et al. Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. 2018;4(7):453-459. doi:10.1038/s41477-018-0190-1","apa":"Fendrych, M., Akhmanova, M., Merrin, J., Glanc, M., Hagihara, S., Takahashi, K., … Friml, J. (2018). Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-018-0190-1","chicago":"Fendrych, Matyas, Maria Akhmanova, Jack Merrin, Matous Glanc, Shinya Hagihara, Koji Takahashi, Naoyuki Uchida, Keiko U Torii, and Jiří Friml. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” Nature Plants. Springer Nature, 2018. https://doi.org/10.1038/s41477-018-0190-1.","ista":"Fendrych M, Akhmanova M, Merrin J, Glanc M, Hagihara S, Takahashi K, Uchida N, Torii KU, Friml J. 2018. Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. 4(7), 453–459."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000443221200017"],"pmid":["29942048"]},"article_processing_charge":"No","publist_id":"7728","author":[{"first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","last_name":"Fendrych"},{"orcid":"0000-0003-1522-3162","full_name":"Akhmanova, Maria","last_name":"Akhmanova","first_name":"Maria","id":"3425EC26-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Merrin","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"first_name":"Matous","last_name":"Glanc","full_name":"Glanc, Matous"},{"first_name":"Shinya","last_name":"Hagihara","full_name":"Hagihara, Shinya"},{"last_name":"Takahashi","full_name":"Takahashi, Koji","first_name":"Koji"},{"last_name":"Uchida","full_name":"Uchida, Naoyuki","first_name":"Naoyuki"},{"last_name":"Torii","full_name":"Torii, Keiko U","first_name":"Keiko U"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"title":"Rapid and reversible root growth inhibition by TIR1 auxin signalling","oa":1,"quality_controlled":"1","publisher":"Springer Nature","year":"2018","isi":1,"publication":"Nature Plants","day":"25","page":"453 - 459","date_created":"2018-12-11T11:45:07Z","date_published":"2018-06-25T00:00:00Z","doi":"10.1038/s41477-018-0190-1"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Hille, Sander, et al. “Relative Contribution of PIN-Containing Secretory Vesicles and Plasma Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.” International Journal of Molecular Sciences, vol. 19, no. 11, MDPI, 2018, doi:10.3390/ijms19113566.","ama":"Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. International Journal of Molecular Sciences. 2018;19(11). doi:10.3390/ijms19113566","apa":"Hille, S., Akhmanova, M., Glanc, M., Johnson, A. J., & Friml, J. (2018). Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms19113566","short":"S. Hille, M. Akhmanova, M. Glanc, A.J. Johnson, J. Friml, International Journal of Molecular Sciences 19 (2018).","ieee":"S. Hille, M. Akhmanova, M. Glanc, A. J. Johnson, and J. Friml, “Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation,” International Journal of Molecular Sciences, vol. 19, no. 11. MDPI, 2018.","chicago":"Hille, Sander, Maria Akhmanova, Matous Glanc, Alexander J Johnson, and Jiří Friml. “Relative Contribution of PIN-Containing Secretory Vesicles and Plasma Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.” International Journal of Molecular Sciences. MDPI, 2018. https://doi.org/10.3390/ijms19113566.","ista":"Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. 2018. Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. International Journal of Molecular Sciences. 19(11)."},"title":"Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation","author":[{"full_name":"Hille, Sander","last_name":"Hille","first_name":"Sander"},{"last_name":"Akhmanova","full_name":"Akhmanova, Maria","orcid":"0000-0003-1522-3162","first_name":"Maria","id":"3425EC26-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous","last_name":"Glanc","first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2"},{"last_name":"Johnson","full_name":"Johnson, Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"8042","external_id":{"isi":["000451528500282"]},"article_processing_charge":"No","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"},{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"day":"12","publication":"International Journal of Molecular Sciences","has_accepted_license":"1","isi":1,"year":"2018","doi":"10.3390/ijms19113566","date_published":"2018-11-12T00:00:00Z","date_created":"2018-12-11T11:44:09Z","acknowledgement":"European Research Council (ERC): 742985 to Jiri Friml; M.A. was supported by the Austrian Science Fund (FWF) (M2379-B28); AJ was supported by the Austria Science Fund (FWF): I03630 to Jiri Friml.","quality_controlled":"1","publisher":"MDPI","oa":1,"ddc":["580"],"date_updated":"2023-09-18T08:09:32Z","department":[{"_id":"DaSi"},{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:44:50Z","_id":"14","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_id":"5719","checksum":"e4b59c2599b0ca26ebf5b8434bcde94a","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_IJMS_Hille.pdf","date_created":"2018-12-17T16:04:11Z","file_size":2200593,"date_updated":"2020-07-14T12:44:50Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1422-0067"]},"publication_status":"published","issue":"11","volume":19,"ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"The intercellular transport of auxin is driven by PIN-formed (PIN) auxin efflux carriers. PINs are localized at the plasma membrane (PM) and on constitutively recycling endomembrane vesicles. Therefore, PINs can mediate auxin transport either by direct translocation across the PM or by pumping auxin into secretory vesicles (SVs), leading to its secretory release upon fusion with the PM. Which of these two mechanisms dominates is a matter of debate. Here, we addressed the issue with a mathematical modeling approach. We demonstrate that the efficiency of secretory transport depends on SV size, half-life of PINs on the PM, pH, exocytosis frequency and PIN density. 3D structured illumination microscopy (SIM) was used to determine PIN density on the PM. Combining this data with published values of the other parameters, we show that the transport activity of PINs in SVs would have to be at least 1000× greater than on the PM in order to produce a comparable macroscopic auxin transport. If both transport mechanisms operated simultaneously and PINs were equally active on SVs and PM, the contribution of secretion to the total auxin flux would be negligible. In conclusion, while secretory vesicle-mediated transport of auxin is an intriguing and theoretically possible model, it is unlikely to be a major mechanism of auxin transport inplanta.","lang":"eng"}],"month":"11","intvolume":" 19","scopus_import":"1"},{"citation":{"chicago":"Sachdeva, Himani, and Nicholas H Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.301429.","ista":"Sachdeva H, Barton NH. 2018. Replicability of introgression under linked, polygenic selection. Genetics. 210(4), 1411–1427.","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics, vol. 210, no. 4, Genetics Society of America, 2018, pp. 1411–27, doi:10.1534/genetics.118.301429.","short":"H. Sachdeva, N.H. Barton, Genetics 210 (2018) 1411–1427.","ieee":"H. Sachdeva and N. H. Barton, “Replicability of introgression under linked, polygenic selection,” Genetics, vol. 210, no. 4. Genetics Society of America, pp. 1411–1427, 2018.","ama":"Sachdeva H, Barton NH. Replicability of introgression under linked, polygenic selection. Genetics. 2018;210(4):1411-1427. doi:10.1534/genetics.118.301429","apa":"Sachdeva, H., & Barton, N. H. (2018). Replicability of introgression under linked, polygenic selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301429"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Sachdeva","full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"external_id":{"isi":["000452315900021"]},"article_processing_charge":"No","title":"Replicability of introgression under linked, polygenic selection","isi":1,"year":"2018","day":"04","publication":"Genetics","page":"1411-1427","doi":"10.1534/genetics.118.301429","date_published":"2018-12-04T00:00:00Z","date_created":"2018-12-11T11:44:18Z","publisher":"Genetics Society of America","quality_controlled":"1","oa":1,"date_updated":"2023-09-18T08:10:29Z","department":[{"_id":"NiBa"}],"_id":"39","article_type":"original","type":"journal_article","status":"public","publication_identifier":{"issn":["00166731"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":210,"issue":"4","abstract":[{"lang":"eng","text":"We study how a block of genome with a large number of weakly selected loci introgresses under directional selection into a genetically homogeneous population. We derive exact expressions for the expected rate of growth of any fragment of the introduced block during the initial phase of introgression, and show that the growth rate of a single-locus variant is largely insensitive to its own additive effect, but depends instead on the combined effect of all loci within a characteristic linkage scale. The expected growth rate of a fragment is highly correlated with its long-term introgression probability in populations of moderate size, and can hence identify variants that are likely to introgress across replicate populations. We clarify how the introgression probability of an individual variant is determined by the interplay between hitchhiking with relatively large fragments during the early phase of introgression and selection on fine-scale variation within these, which at longer times results in differential introgression probabilities for beneficial and deleterious loci within successful fragments. By simulating individuals, we also investigate how introgression probabilities at individual loci depend on the variance of fitness effects, the net fitness of the introduced block, and the size of the recipient population, and how this shapes the net advance under selection. Our work suggests that even highly replicable substitutions may be associated with a range of selective effects, which makes it challenging to fine map the causal loci that underlie polygenic adaptation."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/379578v1","open_access":"1"}],"month":"12","intvolume":" 210"},{"external_id":{"isi":["000438217300007"]},"article_processing_charge":"No","publist_id":"7402","author":[{"first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","last_name":"Bighin","orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo"},{"first_name":"Luca","full_name":"Salasnich, Luca","last_name":"Salasnich"}],"title":"Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover","citation":{"ista":"Bighin G, Salasnich L. 2018. Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics B. 32(17), 1840022.","chicago":"Bighin, Giacomo, and Luca Salasnich. “Renormalization of the Superfluid Density in the Two-Dimensional BCS-BEC Crossover.” International Journal of Modern Physics B. World Scientific Publishing, 2018. https://doi.org/10.1142/S0217979218400222.","ieee":"G. Bighin and L. Salasnich, “Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover,” International Journal of Modern Physics B, vol. 32, no. 17. World Scientific Publishing, p. 1840022, 2018.","short":"G. Bighin, L. Salasnich, International Journal of Modern Physics B 32 (2018) 1840022.","apa":"Bighin, G., & Salasnich, L. (2018). Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics B. World Scientific Publishing. https://doi.org/10.1142/S0217979218400222","ama":"Bighin G, Salasnich L. Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics B. 2018;32(17):1840022. doi:10.1142/S0217979218400222","mla":"Bighin, Giacomo, and Luca Salasnich. “Renormalization of the Superfluid Density in the Two-Dimensional BCS-BEC Crossover.” International Journal of Modern Physics B, vol. 32, no. 17, World Scientific Publishing, 2018, p. 1840022, doi:10.1142/S0217979218400222."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"1840022","date_created":"2018-12-11T11:46:22Z","date_published":"2018-07-10T00:00:00Z","doi":"10.1142/S0217979218400222","year":"2018","isi":1,"publication":"International Journal of Modern Physics B","day":"10","oa":1,"publisher":"World Scientific Publishing","quality_controlled":"1","department":[{"_id":"MiLe"}],"date_updated":"2023-09-18T08:09:59Z","type":"journal_article","status":"public","_id":"420","issue":"17","volume":32,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1710.11171"}],"scopus_import":"1","intvolume":" 32","month":"07","abstract":[{"lang":"eng","text":"We analyze the theoretical derivation of the beyond-mean-field equation of state for two-dimensional gas of dilute, ultracold alkali-metal atoms in the Bardeen–Cooper–Schrieffer (BCS) to Bose–Einstein condensate (BEC) crossover. We show that at zero temperature our theory — considering Gaussian fluctuations on top of the mean-field equation of state — is in very good agreement with experimental data. Subsequently, we investigate the superfluid density at finite temperature and its renormalization due to the proliferation of vortex–antivortex pairs. By doing so, we determine the Berezinskii–Kosterlitz–Thouless (BKT) critical temperature — at which the renormalized superfluid density jumps to zero — as a function of the inter-atomic potential strength. We find that the Nelson–Kosterlitz criterion overestimates the BKT temperature with respect to the renormalization group equations, this effect being particularly relevant in the intermediate regime of the crossover."}],"oa_version":"Preprint"},{"quality_controlled":"1","publisher":"National Academy of Sciences","oa":1,"acknowledgement":" ERC Grant 201252 (to N.H.B.)","page":"11006 - 11011","date_published":"2018-10-23T00:00:00Z","doi":"10.1073/pnas.1801832115","date_created":"2018-12-11T11:44:18Z","has_accepted_license":"1","isi":1,"year":"2018","day":"23","publication":"PNAS","publist_id":"8017","author":[{"first_name":"Hugo","full_name":"Tavares, Hugo","last_name":"Tavares"},{"last_name":"Whitley","full_name":"Whitley, Annabel","first_name":"Annabel"},{"last_name":"Field","orcid":"0000-0002-4014-8478","full_name":"Field, David","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Desmond","full_name":"Bradley, Desmond","last_name":"Bradley"},{"last_name":"Couchman","full_name":"Couchman, Matthew","first_name":"Matthew"},{"first_name":"Lucy","last_name":"Copsey","full_name":"Copsey, Lucy"},{"full_name":"Elleouet, Joane","last_name":"Elleouet","first_name":"Joane"},{"first_name":"Monique","last_name":"Burrus","full_name":"Burrus, Monique"},{"first_name":"Christophe","full_name":"Andalo, Christophe","last_name":"Andalo"},{"last_name":"Li","full_name":"Li, Miaomiao","first_name":"Miaomiao"},{"last_name":"Li","full_name":"Li, Qun","first_name":"Qun"},{"first_name":"Yongbiao","full_name":"Xue, Yongbiao","last_name":"Xue"},{"full_name":"Rebocho, Alexandra B","last_name":"Rebocho","first_name":"Alexandra B"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"},{"first_name":"Enrico","last_name":"Coen","full_name":"Coen, Enrico"}],"article_processing_charge":"No","external_id":{"pmid":["30297406"],"isi":["000448040500065"]},"title":"Selection and gene flow shape genomic islands that control floral guides","citation":{"ista":"Tavares H, Whitley A, Field D, Bradley D, Couchman M, Copsey L, Elleouet J, Burrus M, Andalo C, Li M, Li Q, Xue Y, Rebocho AB, Barton NH, Coen E. 2018. Selection and gene flow shape genomic islands that control floral guides. PNAS. 115(43), 11006–11011.","chicago":"Tavares, Hugo, Annabel Whitley, David Field, Desmond Bradley, Matthew Couchman, Lucy Copsey, Joane Elleouet, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1801832115.","apa":"Tavares, H., Whitley, A., Field, D., Bradley, D., Couchman, M., Copsey, L., … Coen, E. (2018). Selection and gene flow shape genomic islands that control floral guides. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1801832115","ama":"Tavares H, Whitley A, Field D, et al. Selection and gene flow shape genomic islands that control floral guides. PNAS. 2018;115(43):11006-11011. doi:10.1073/pnas.1801832115","ieee":"H. Tavares et al., “Selection and gene flow shape genomic islands that control floral guides,” PNAS, vol. 115, no. 43. National Academy of Sciences, pp. 11006–11011, 2018.","short":"H. Tavares, A. Whitley, D. Field, D. Bradley, M. Couchman, L. Copsey, J. Elleouet, M. Burrus, C. Andalo, M. Li, Q. Li, Y. Xue, A.B. Rebocho, N.H. Barton, E. Coen, PNAS 115 (2018) 11006–11011.","mla":"Tavares, Hugo, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS, vol. 115, no. 43, National Academy of Sciences, 2018, pp. 11006–11, doi:10.1073/pnas.1801832115."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","month":"10","intvolume":" 115","abstract":[{"lang":"eng","text":"Genomes of closely-related species or populations often display localized regions of enhanced relative sequence divergence, termed genomic islands. It has been proposed that these islands arise through selective sweeps and/or barriers to gene flow. Here, we genetically dissect a genomic island that controls flower color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid zone. We show that selective sweeps likely raised relative divergence at two tightly-linked MYB-like transcription factors, leading to distinct flower patterns in the two subspecies. The two patterns provide alternate floral guides and create a strong barrier to gene flow where populations come into contact. This barrier affects the selected flower color genes and tightlylinked loci, but does not extend outside of this domain, allowing gene flow to lower relative divergence for the rest of the chromosome. Thus, both selective sweeps and barriers to gene flow play a role in shaping genomic islands: sweeps cause elevation in relative divergence, while heterogeneous gene flow flattens the surrounding \"sea,\" making the island of divergence stand out. By showing how selective sweeps establish alternative adaptive phenotypes that lead to barriers to gene flow, our study sheds light on possible mechanisms leading to reproductive isolation and speciation."}],"pmid":1,"oa_version":"Published Version","issue":"43","volume":115,"publication_identifier":{"issn":["00278424"]},"publication_status":"published","file":[{"checksum":"d2305d0cc81dbbe4c1c677d64ad6f6d1","file_id":"5683","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"11006.full.pdf","date_created":"2018-12-17T08:44:03Z","file_size":1911302,"date_updated":"2020-07-14T12:46:16Z","creator":"dernst"}],"language":[{"iso":"eng"}],"type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","_id":"38","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:46:16Z","date_updated":"2023-09-18T08:36:49Z","ddc":["570"]},{"_id":"155","status":"public","conference":{"name":"SPIE: The international society for optical engineering","start_date":"2018-04-22","end_date":"2018-04-26","location":"Strasbourg, France"},"type":"conference","date_updated":"2023-09-18T08:12:24Z","department":[{"_id":"JoFi"}],"oa_version":"Preprint","abstract":[{"text":"There is currently significant interest in operating devices in the quantum regime, where their behaviour cannot be explained through classical mechanics. Quantum states, including entangled states, are fragile and easily disturbed by excessive thermal noise. Here we address the question of whether it is possible to create non-reciprocal devices that encourage the flow of thermal noise towards or away from a particular quantum device in a network. Our work makes use of the cascaded systems formalism to answer this question in the affirmative, showing how a three-port device can be used as an effective thermal transistor, and illustrates how this formalism maps onto an experimentally-realisable optomechanical system. Our results pave the way to more resilient quantum devices and to the use of thermal noise as a resource.","lang":"eng"}],"intvolume":" 10672","month":"05","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.01000"}],"scopus_import":"1","alternative_title":["Proceedings of SPIE"],"language":[{"iso":"eng"}],"publication_status":"published","volume":10672,"article_number":"106721N","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Xuereb A, Aquilina M, Barzanjeh S. 2018. Routing thermal noise through quantum networks. SPIE: The international society for optical engineering, Proceedings of SPIE, vol. 10672, 106721N.","chicago":"Xuereb, André, Matteo Aquilina, and Shabir Barzanjeh. “Routing Thermal Noise through Quantum Networks.” edited by D L Andrews, A Ostendorf, A J Bain, and J M Nunzi, Vol. 10672. SPIE, 2018. https://doi.org/10.1117/12.2309928.","ieee":"A. Xuereb, M. Aquilina, and S. Barzanjeh, “Routing thermal noise through quantum networks,” presented at the SPIE: The international society for optical engineering, Strasbourg, France, 2018, vol. 10672.","short":"A. Xuereb, M. Aquilina, S. Barzanjeh, in:, D.L. Andrews, A. Ostendorf, A.J. Bain, J.M. Nunzi (Eds.), SPIE, 2018.","ama":"Xuereb A, Aquilina M, Barzanjeh S. Routing thermal noise through quantum networks. In: Andrews DL, Ostendorf A, Bain AJ, Nunzi JM, eds. Vol 10672. SPIE; 2018. doi:10.1117/12.2309928","apa":"Xuereb, A., Aquilina, M., & Barzanjeh, S. (2018). Routing thermal noise through quantum networks. In D. L. Andrews, A. Ostendorf, A. J. Bain, & J. M. Nunzi (Eds.) (Vol. 10672). Presented at the SPIE: The international society for optical engineering, Strasbourg, France: SPIE. https://doi.org/10.1117/12.2309928","mla":"Xuereb, André, et al. Routing Thermal Noise through Quantum Networks. Edited by D L Andrews et al., vol. 10672, 106721N, SPIE, 2018, doi:10.1117/12.2309928."},"editor":[{"full_name":"Andrews, D L","last_name":"Andrews","first_name":"D L"},{"last_name":"Ostendorf","full_name":"Ostendorf, A","first_name":"A"},{"first_name":"A J","full_name":"Bain, A J","last_name":"Bain"},{"full_name":"Nunzi, J M","last_name":"Nunzi","first_name":"J M"}],"title":"Routing thermal noise through quantum networks","external_id":{"arxiv":["1806.01000"],"isi":["000453298500019"]},"article_processing_charge":"No","author":[{"first_name":"André","last_name":"Xuereb","full_name":"Xuereb, André"},{"first_name":"Matteo","full_name":"Aquilina, Matteo","last_name":"Aquilina"},{"orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir","last_name":"Barzanjeh","first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7766","oa":1,"quality_controlled":"1","publisher":"SPIE","day":"04","year":"2018","isi":1,"date_created":"2018-12-11T11:44:55Z","doi":"10.1117/12.2309928","date_published":"2018-05-04T00:00:00Z"},{"doi":"10.1126/science.aao0980","date_published":"2018-12-14T00:00:00Z","date_created":"2018-12-19T14:53:50Z","page":"1271-1275","day":"14","publication":"Science","isi":1,"year":"2018","quality_controlled":"1","publisher":"American Association for the Advancement of Science","oa":1,"acknowledgement":" M.S. was supported by the Gordon and Betty Moore Foundation s EPiQS Initiative through grant GBMF4307","title":"Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor","author":[{"last_name":"Gotlieb","full_name":"Gotlieb, Kenneth","first_name":"Kenneth"},{"full_name":"Lin, Chiu-Yun","last_name":"Lin","first_name":"Chiu-Yun"},{"orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"},{"first_name":"Wentao","last_name":"Zhang","full_name":"Zhang, Wentao"},{"first_name":"Christopher L.","full_name":"Smallwood, Christopher L.","last_name":"Smallwood"},{"last_name":"Jozwiak","full_name":"Jozwiak, Christopher","first_name":"Christopher"},{"full_name":"Eisaki, Hiroshi","last_name":"Eisaki","first_name":"Hiroshi"},{"full_name":"Hussain, Zahid","last_name":"Hussain","first_name":"Zahid"},{"first_name":"Ashvin","last_name":"Vishwanath","full_name":"Vishwanath, Ashvin"},{"last_name":"Lanzara","full_name":"Lanzara, Alessandra","first_name":"Alessandra"}],"article_processing_charge":"No","external_id":{"isi":["000452994400048"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Gotlieb K, Lin C-Y, Serbyn M, Zhang W, Smallwood CL, Jozwiak C, Eisaki H, Hussain Z, Vishwanath A, Lanzara A. 2018. Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. Science. 362(6420), 1271–1275.","chicago":"Gotlieb, Kenneth, Chiu-Yun Lin, Maksym Serbyn, Wentao Zhang, Christopher L. Smallwood, Christopher Jozwiak, Hiroshi Eisaki, Zahid Hussain, Ashvin Vishwanath, and Alessandra Lanzara. “Revealing Hidden Spin-Momentum Locking in a High-Temperature Cuprate Superconductor.” Science. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/science.aao0980.","short":"K. Gotlieb, C.-Y. Lin, M. Serbyn, W. Zhang, C.L. Smallwood, C. Jozwiak, H. Eisaki, Z. Hussain, A. Vishwanath, A. Lanzara, Science 362 (2018) 1271–1275.","ieee":"K. Gotlieb et al., “Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor,” Science, vol. 362, no. 6420. American Association for the Advancement of Science, pp. 1271–1275, 2018.","apa":"Gotlieb, K., Lin, C.-Y., Serbyn, M., Zhang, W., Smallwood, C. L., Jozwiak, C., … Lanzara, A. (2018). Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aao0980","ama":"Gotlieb K, Lin C-Y, Serbyn M, et al. Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. Science. 2018;362(6420):1271-1275. doi:10.1126/science.aao0980","mla":"Gotlieb, Kenneth, et al. “Revealing Hidden Spin-Momentum Locking in a High-Temperature Cuprate Superconductor.” Science, vol. 362, no. 6420, American Association for the Advancement of Science, 2018, pp. 1271–75, doi:10.1126/science.aao0980."},"issue":"6420","volume":362,"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"publication_status":"published","month":"12","intvolume":" 362","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1126/science.aao0980","open_access":"1"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Cuprate superconductors have long been thought of as having strong electronic correlations but negligible spin-orbit coupling. Using spin- and angle-resolved photoemission spectroscopy, we discovered that one of the most studied cuprate superconductors, Bi2212, has a nontrivial spin texture with a spin-momentum locking that circles the Brillouin zone center and a spin-layer locking that allows states of opposite spin to be localized in different parts of the unit cell. Our findings pose challenges for the vast majority of models of cuprates, such as the Hubbard model and its variants, where spin-orbit interaction has been mostly neglected, and open the intriguing question of how the high-temperature superconducting state emerges in the presence of this nontrivial spin texture. "}],"department":[{"_id":"MaSe"}],"date_updated":"2023-09-18T08:11:56Z","status":"public","article_type":"original","type":"journal_article","_id":"5767"},{"_id":"434","status":"public","type":"journal_article","date_updated":"2023-09-18T08:12:49Z","department":[{"_id":"ToHe"}],"oa_version":"None","abstract":[{"text":"In this paper, we present a formal model-driven design approach to establish a safety-assured implementation of multifunction vehicle bus controller (MVBC), which controls the data transmission among the devices of the vehicle. First, the generic models and safety requirements described in International Electrotechnical Commission Standard 61375 are formalized as time automata and timed computation tree logic formulas, respectively. With model checking tool Uppaal, we verify whether or not the constructed timed automata satisfy the formulas and several logic inconsistencies in the original standard are detected and corrected. Then, we apply the code generation tool Times to generate C code from the verified model, which is later synthesized into a real MVBC chip, with some handwriting glue code. Furthermore, the runtime verification tool RMOR is applied on the integrated code, to verify some safety requirements that cannot be formalized on the timed automata. For evaluation, we compare the proposed approach with existing MVBC design methods, such as BeagleBone, Galsblock, and Simulink. Experiments show that more ambiguousness or bugs in the standard are detected during Uppaal verification, and the generated code of Times outperforms the C code generated by others in terms of the synthesized binary code size. The errors in the standard have been confirmed and the resulting MVBC has been deployed in the real train communication network.","lang":"eng"}],"month":"01","intvolume":" 19","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","volume":19,"issue":"10","related_material":{"record":[{"id":"1205","status":"public","relation":"earlier_version"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Jiang Y, Liu H, Song H, et al. Safety-assured model-driven design of the multifunction vehicle bus controller. IEEE Transactions on Intelligent Transportation Systems. 2018;19(10):3320-3333. doi:10.1109/TITS.2017.2778077","apa":"Jiang, Y., Liu, H., Song, H., Kong, H., Wang, R., Guan, Y., & Sha, L. (2018). Safety-assured model-driven design of the multifunction vehicle bus controller. IEEE Transactions on Intelligent Transportation Systems. IEEE. https://doi.org/10.1109/TITS.2017.2778077","ieee":"Y. Jiang et al., “Safety-assured model-driven design of the multifunction vehicle bus controller,” IEEE Transactions on Intelligent Transportation Systems, vol. 19, no. 10. IEEE, pp. 3320–3333, 2018.","short":"Y. Jiang, H. Liu, H. Song, H. Kong, R. Wang, Y. Guan, L. Sha, IEEE Transactions on Intelligent Transportation Systems 19 (2018) 3320–3333.","mla":"Jiang, Yu, et al. “Safety-Assured Model-Driven Design of the Multifunction Vehicle Bus Controller.” IEEE Transactions on Intelligent Transportation Systems, vol. 19, no. 10, IEEE, 2018, pp. 3320–33, doi:10.1109/TITS.2017.2778077.","ista":"Jiang Y, Liu H, Song H, Kong H, Wang R, Guan Y, Sha L. 2018. Safety-assured model-driven design of the multifunction vehicle bus controller. IEEE Transactions on Intelligent Transportation Systems. 19(10), 3320–3333.","chicago":"Jiang, Yu, Han Liu, Huobing Song, Hui Kong, Rui Wang, Yong Guan, and Lui Sha. “Safety-Assured Model-Driven Design of the Multifunction Vehicle Bus Controller.” IEEE Transactions on Intelligent Transportation Systems. IEEE, 2018. https://doi.org/10.1109/TITS.2017.2778077."},"title":"Safety-assured model-driven design of the multifunction vehicle bus controller","publist_id":"7389","author":[{"last_name":"Jiang","full_name":"Jiang, Yu","first_name":"Yu"},{"first_name":"Han","full_name":"Liu, Han","last_name":"Liu"},{"last_name":"Song","full_name":"Song, Huobing","first_name":"Huobing"},{"full_name":"Kong, Hui","orcid":"0000-0002-3066-6941","last_name":"Kong","first_name":"Hui","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rui","full_name":"Wang, Rui","last_name":"Wang"},{"first_name":"Yong","last_name":"Guan","full_name":"Guan, Yong"},{"first_name":"Lui","full_name":"Sha, Lui","last_name":"Sha"}],"external_id":{"isi":["000446651100020"]},"article_processing_charge":"No","quality_controlled":"1","publisher":"IEEE","day":"01","publication":"IEEE Transactions on Intelligent Transportation Systems","isi":1,"year":"2018","date_published":"2018-01-01T00:00:00Z","doi":"10.1109/TITS.2017.2778077","date_created":"2018-12-11T11:46:27Z","page":"3320 - 3333"},{"_id":"162","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["571"],"date_updated":"2023-09-18T09:29:07Z","department":[{"_id":"AnKi"}],"file_date_updated":"2020-07-14T12:45:07Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here, we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts."}],"month":"06","intvolume":" 7","scopus_import":"1","file":[{"date_created":"2018-12-17T16:41:58Z","file_name":"2018_eLife_Kaucka.pdf","creator":"dernst","date_updated":"2020-07-14T12:45:07Z","file_size":9816484,"file_id":"5727","checksum":"da2378cdcf6b5461dcde194e4d608343","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"relation":"research_data","status":"public","id":"9838"}]},"volume":7,"ec_funded":1,"article_number":"e34465","project":[{"call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425","name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria Kastriti, Meng Xie, Anna Kicheva, et al. “Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.34465.","ista":"Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti M, Xie M, Kicheva A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser M, Chagin AS, Fried K, Adameyko I. 2018. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. eLife. 7, e34465.","mla":"Kaucka, Marketa, et al. “Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” ELife, vol. 7, e34465, eLife Sciences Publications, 2018, doi:10.7554/eLife.34465.","ieee":"M. Kaucka et al., “Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage,” eLife, vol. 7. eLife Sciences Publications, 2018.","short":"M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M. Kastriti, M. Xie, A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, ELife 7 (2018).","apa":"Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M., Xie, M., … Adameyko, I. (2018). Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.34465","ama":"Kaucka M, Petersen J, Tesarova M, et al. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. eLife. 2018;7. doi:10.7554/eLife.34465"},"title":"Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","author":[{"full_name":"Kaucka, Marketa","last_name":"Kaucka","first_name":"Marketa"},{"full_name":"Petersen, Julian","last_name":"Petersen","first_name":"Julian"},{"first_name":"Marketa","last_name":"Tesarova","full_name":"Tesarova, Marketa"},{"last_name":"Szarowska","full_name":"Szarowska, Bara","first_name":"Bara"},{"last_name":"Kastriti","full_name":"Kastriti, Maria","first_name":"Maria"},{"first_name":"Meng","full_name":"Xie, Meng","last_name":"Xie"},{"last_name":"Kicheva","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Annusver","full_name":"Annusver, Karl","first_name":"Karl"},{"first_name":"Maria","last_name":"Kasper","full_name":"Kasper, Maria"},{"full_name":"Symmons, Orsolya","last_name":"Symmons","first_name":"Orsolya"},{"full_name":"Pan, Leslie","last_name":"Pan","first_name":"Leslie"},{"full_name":"Spitz, Francois","last_name":"Spitz","first_name":"Francois"},{"first_name":"Jozef","last_name":"Kaiser","full_name":"Kaiser, Jozef"},{"first_name":"Maria","last_name":"Hovorakova","full_name":"Hovorakova, Maria"},{"first_name":"Tomas","last_name":"Zikmund","full_name":"Zikmund, Tomas"},{"full_name":"Sunadome, Kazunori","last_name":"Sunadome","first_name":"Kazunori"},{"full_name":"Matise, Michael P","last_name":"Matise","first_name":"Michael P"},{"first_name":"Hui","full_name":"Wang, Hui","last_name":"Wang"},{"last_name":"Marklund","full_name":"Marklund, Ulrika","first_name":"Ulrika"},{"first_name":"Hind","last_name":"Abdo","full_name":"Abdo, Hind"},{"last_name":"Ernfors","full_name":"Ernfors, Patrik","first_name":"Patrik"},{"first_name":"Pascal","last_name":"Maire","full_name":"Maire, Pascal"},{"first_name":"Maud","last_name":"Wurmser","full_name":"Wurmser, Maud"},{"first_name":"Andrei S","last_name":"Chagin","full_name":"Chagin, Andrei S"},{"first_name":"Kaj","last_name":"Fried","full_name":"Fried, Kaj"},{"first_name":"Igor","full_name":"Adameyko, Igor","last_name":"Adameyko"}],"publist_id":"7759","article_processing_charge":"No","external_id":{"isi":["000436227500001"]},"publisher":"eLife Sciences Publications","quality_controlled":"1","oa":1,"day":"13","publication":"eLife","has_accepted_license":"1","isi":1,"year":"2018","date_published":"2018-06-13T00:00:00Z","doi":"10.7554/eLife.34465","date_created":"2018-12-11T11:44:57Z"},{"date_updated":"2023-09-18T09:29:33Z","department":[{"_id":"KrPi"}],"_id":"302","conference":{"end_date":"2018-05-03","location":"Tel Aviv, Israel","start_date":"2018-04-29","name":"Eurocrypt: Advances in Cryptology"},"type":"conference","status":"public","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":10821,"abstract":[{"text":"At ITCS 2013, Mahmoody, Moran and Vadhan [MMV13] introduce and construct publicly verifiable proofs of sequential work, which is a protocol for proving that one spent sequential computational work related to some statement. The original motivation for such proofs included non-interactive time-stamping and universally verifiable CPU benchmarks. A more recent application, and our main motivation, are blockchain designs, where proofs of sequential work can be used – in combination with proofs of space – as a more ecological and economical substitute for proofs of work which are currently used to secure Bitcoin and other cryptocurrencies. The construction proposed by [MMV13] is based on a hash function and can be proven secure in the random oracle model, or assuming inherently sequential hash-functions, which is a new standard model assumption introduced in their work. In a proof of sequential work, a prover gets a “statement” χ, a time parameter N and access to a hash-function H, which for the security proof is modelled as a random oracle. Correctness requires that an honest prover can make a verifier accept making only N queries to H, while soundness requires that any prover who makes the verifier accept must have made (almost) N sequential queries to H. Thus a solution constitutes a proof that N time passed since χ was received. Solutions must be publicly verifiable in time at most polylogarithmic in N. The construction of [MMV13] is based on “depth-robust” graphs, and as a consequence has rather poor concrete parameters. But the major drawback is that the prover needs not just N time, but also N space to compute a proof. In this work we propose a proof of sequential work which is much simpler, more efficient and achieves much better concrete bounds. Most importantly, the space required can be as small as log (N) (but we get better soundness using slightly more memory than that). An open problem stated by [MMV13] that our construction does not solve either is achieving a “unique” proof, where even a cheating prover can only generate a single accepting proof. This property would be extremely useful for applications to blockchains.","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"url":"https://eprint.iacr.org/2018/183.pdf","open_access":"1"}],"alternative_title":["LNCS"],"scopus_import":"1","intvolume":" 10821","month":"05","citation":{"ista":"Cohen B, Pietrzak KZ. 2018. Simple proofs of sequential work. Eurocrypt: Advances in Cryptology, LNCS, vol. 10821, 451–467.","chicago":"Cohen, Bram, and Krzysztof Z Pietrzak. “Simple Proofs of Sequential Work,” 10821:451–67. Springer, 2018. https://doi.org/10.1007/978-3-319-78375-8_15.","apa":"Cohen, B., & Pietrzak, K. Z. (2018). Simple proofs of sequential work (Vol. 10821, pp. 451–467). Presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78375-8_15","ama":"Cohen B, Pietrzak KZ. Simple proofs of sequential work. In: Vol 10821. Springer; 2018:451-467. doi:10.1007/978-3-319-78375-8_15","ieee":"B. Cohen and K. Z. Pietrzak, “Simple proofs of sequential work,” presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel, 2018, vol. 10821, pp. 451–467.","short":"B. Cohen, K.Z. Pietrzak, in:, Springer, 2018, pp. 451–467.","mla":"Cohen, Bram, and Krzysztof Z. Pietrzak. Simple Proofs of Sequential Work. Vol. 10821, Springer, 2018, pp. 451–67, doi:10.1007/978-3-319-78375-8_15."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000517098700015"]},"author":[{"last_name":"Cohen","full_name":"Cohen, Bram","first_name":"Bram"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak"}],"publist_id":"7579","title":"Simple proofs of sequential work","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}],"year":"2018","isi":1,"day":"29","page":"451 - 467","date_created":"2018-12-11T11:45:42Z","doi":"10.1007/978-3-319-78375-8_15","date_published":"2018-05-29T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"Springer"},{"oa_version":"Preprint","abstract":[{"text":"Correlations in sensory neural networks have both extrinsic and intrinsic origins. Extrinsic or stimulus correlations arise from shared inputs to the network and, thus, depend strongly on the stimulus ensemble. Intrinsic or noise correlations reflect biophysical mechanisms of interactions between neurons, which are expected to be robust to changes in the stimulus ensemble. Despite the importance of this distinction for understanding how sensory networks encode information collectively, no method exists to reliably separate intrinsic interactions from extrinsic correlations in neural activity data, limiting our ability to build predictive models of the network response. In this paper we introduce a general strategy to infer population models of interacting neurons that collectively encode stimulus information. The key to disentangling intrinsic from extrinsic correlations is to infer the couplings between neurons separately from the encoding model and to combine the two using corrections calculated in a mean-field approximation. We demonstrate the effectiveness of this approach in retinal recordings. The same coupling network is inferred from responses to radically different stimulus ensembles, showing that these couplings indeed reflect stimulus-independent interactions between neurons. The inferred model predicts accurately the collective response of retinal ganglion cell populations as a function of the stimulus.","lang":"eng"}],"intvolume":" 98","month":"10","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/243816v2.full"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["24700045"]},"ec_funded":1,"volume":98,"issue":"4","_id":"31","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-09-18T09:18:44Z","department":[{"_id":"GaTk"}],"acknowledgement":"This work was supported by ANR Trajectory, the French State program Investissements d’Avenir managed by the Agence Nationale de la Recherche (LIFESENSES; ANR-10-LABX-65), EC Grant No. H2020-785907 from the Human Brain Project, NIH Grant No. U01NS090501, and an AVIESAN-UNADEV grant to O.M. M.C. was supported by the Agence Nationale de la Recherche Jeune Chercheur/Jeune Chercheuse grant (ANR-17-CE37-0013).","oa":1,"quality_controlled":"1","publisher":"American Physical Society","publication":"Physical Review E","day":"17","year":"2018","isi":1,"date_created":"2018-12-11T11:44:15Z","date_published":"2018-10-17T00:00:00Z","doi":"10.1103/PhysRevE.98.042410","article_number":"042410","project":[{"call_identifier":"H2020","_id":"26436750-B435-11E9-9278-68D0E5697425","grant_number":"785907","name":"Human Brain Project Specific Grant Agreement 2 (HBP SGA 2)"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Ferrari, Ulisse, et al. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” Physical Review E, vol. 98, no. 4, 042410, American Physical Society, 2018, doi:10.1103/PhysRevE.98.042410.","ama":"Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. 2018;98(4). doi:10.1103/PhysRevE.98.042410","apa":"Ferrari, U., Deny, S., Chalk, M. J., Tkačik, G., Marre, O., & Mora, T. (2018). Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.98.042410","short":"U. Ferrari, S. Deny, M.J. Chalk, G. Tkačik, O. Marre, T. Mora, Physical Review E 98 (2018).","ieee":"U. Ferrari, S. Deny, M. J. Chalk, G. Tkačik, O. Marre, and T. Mora, “Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons,” Physical Review E, vol. 98, no. 4. American Physical Society, 2018.","chicago":"Ferrari, Ulisse, Stephane Deny, Matthew J Chalk, Gašper Tkačik, Olivier Marre, and Thierry Mora. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” Physical Review E. American Physical Society, 2018. https://doi.org/10.1103/PhysRevE.98.042410.","ista":"Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. 2018. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. 98(4), 042410."},"title":"Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons","article_processing_charge":"No","external_id":{"isi":["000447486100004"]},"publist_id":"8024","author":[{"first_name":"Ulisse","full_name":"Ferrari, Ulisse","last_name":"Ferrari"},{"first_name":"Stephane","last_name":"Deny","full_name":"Deny, Stephane"},{"first_name":"Matthew J","full_name":"Chalk, Matthew J","last_name":"Chalk"},{"orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Olivier","full_name":"Marre, Olivier","last_name":"Marre"},{"full_name":"Mora, Thierry","last_name":"Mora","first_name":"Thierry"}]},{"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"title":"Self-organized criticality and pattern emergence through the lens of tropical geometry","publist_id":"7990","author":[{"last_name":"Kalinin","full_name":"Kalinin, Nikita","first_name":"Nikita"},{"last_name":"Guzmán Sáenz","full_name":"Guzmán Sáenz, Aldo","first_name":"Aldo"},{"last_name":"Prieto","full_name":"Prieto, Y","first_name":"Y"},{"id":"35084A62-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","orcid":"0000-0002-4310-178X","full_name":"Shkolnikov, Mikhail","last_name":"Shkolnikov"},{"last_name":"Kalinina","full_name":"Kalinina, V","first_name":"V"},{"full_name":"Lupercio, Ernesto","last_name":"Lupercio","first_name":"Ernesto"}],"article_processing_charge":"No","external_id":{"isi":["000442861600009"],"arxiv":["1806.09153"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E. 2018. Self-organized criticality and pattern emergence through the lens of tropical geometry. PNAS: Proceedings of the National Academy of Sciences of the United States of America. 115(35), E8135–E8142.","chicago":"Kalinin, Nikita, Aldo Guzmán Sáenz, Y Prieto, Mikhail Shkolnikov, V Kalinina, and Ernesto Lupercio. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” PNAS: Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1805847115.","short":"N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, E. Lupercio, PNAS: Proceedings of the National Academy of Sciences of the United States of America 115 (2018) E8135–E8142.","ieee":"N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, and E. Lupercio, “Self-organized criticality and pattern emergence through the lens of tropical geometry,” PNAS: Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 35. National Academy of Sciences, pp. E8135–E8142, 2018.","ama":"Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E. Self-organized criticality and pattern emergence through the lens of tropical geometry. PNAS: Proceedings of the National Academy of Sciences of the United States of America. 2018;115(35):E8135-E8142. doi:10.1073/pnas.1805847115","apa":"Kalinin, N., Guzmán Sáenz, A., Prieto, Y., Shkolnikov, M., Kalinina, V., & Lupercio, E. (2018). Self-organized criticality and pattern emergence through the lens of tropical geometry. PNAS: Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1805847115","mla":"Kalinin, Nikita, et al. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” PNAS: Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 35, National Academy of Sciences, 2018, pp. E8135–42, doi:10.1073/pnas.1805847115."},"quality_controlled":"1","publisher":"National Academy of Sciences","oa":1,"doi":"10.1073/pnas.1805847115","date_published":"2018-08-28T00:00:00Z","date_created":"2018-12-11T11:44:26Z","page":"E8135 - E8142","day":"28","publication":"PNAS: Proceedings of the National Academy of Sciences of the United States of America","isi":1,"year":"2018","status":"public","type":"journal_article","article_type":"original","_id":"64","department":[{"_id":"TaHa"}],"date_updated":"2023-09-18T08:41:16Z","month":"08","intvolume":" 115","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.09153"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Tropical geometry, an established field in pure mathematics, is a place where string theory, mirror symmetry, computational algebra, auction theory, and so forth meet and influence one another. In this paper, we report on our discovery of a tropical model with self-organized criticality (SOC) behavior. Our model is continuous, in contrast to all known models of SOC, and is a certain scaling limit of the sandpile model, the first and archetypical model of SOC. We describe how our model is related to pattern formation and proportional growth phenomena and discuss the dichotomy between continuous and discrete models in several contexts. Our aim in this context is to present an idealized tropical toy model (cf. Turing reaction-diffusion model), requiring further investigation."}],"issue":"35","volume":115,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00278424"]},"publication_status":"published"},{"author":[{"first_name":"Marketa","last_name":"Kaucka","full_name":"Kaucka, Marketa"},{"last_name":"Petersen","full_name":"Petersen, Julian","first_name":"Julian"},{"last_name":"Tesarova","full_name":"Tesarova, Marketa","first_name":"Marketa"},{"last_name":"Szarowska","full_name":"Szarowska, Bara","first_name":"Bara"},{"last_name":"Kastriti","full_name":"Kastriti, Maria Eleni","first_name":"Maria Eleni"},{"first_name":"Meng","last_name":"Xie","full_name":"Xie, Meng"},{"last_name":"Kicheva","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Annusver","full_name":"Annusver, Karl","first_name":"Karl"},{"first_name":"Maria","full_name":"Kasper, Maria","last_name":"Kasper"},{"first_name":"Orsolya","full_name":"Symmons, Orsolya","last_name":"Symmons"},{"last_name":"Pan","full_name":"Pan, Leslie","first_name":"Leslie"},{"first_name":"Francois","last_name":"Spitz","full_name":"Spitz, Francois"},{"first_name":"Jozef","last_name":"Kaiser","full_name":"Kaiser, Jozef"},{"last_name":"Hovorakova","full_name":"Hovorakova, Maria","first_name":"Maria"},{"first_name":"Tomas","full_name":"Zikmund, Tomas","last_name":"Zikmund"},{"full_name":"Sunadome, Kazunori","last_name":"Sunadome","first_name":"Kazunori"},{"full_name":"Matise, Michael P","last_name":"Matise","first_name":"Michael P"},{"last_name":"Wang","full_name":"Wang, Hui","first_name":"Hui"},{"first_name":"Ulrika","full_name":"Marklund, Ulrika","last_name":"Marklund"},{"first_name":"Hind","full_name":"Abdo, Hind","last_name":"Abdo"},{"full_name":"Ernfors, Patrik","last_name":"Ernfors","first_name":"Patrik"},{"full_name":"Maire, Pascal","last_name":"Maire","first_name":"Pascal"},{"first_name":"Maud","full_name":"Wurmser, Maud","last_name":"Wurmser"},{"last_name":"Chagin","full_name":"Chagin, Andrei S","first_name":"Andrei S"},{"first_name":"Kaj","last_name":"Fried","full_name":"Fried, Kaj"},{"first_name":"Igor","full_name":"Adameyko, Igor","last_name":"Adameyko"}],"article_processing_charge":"No","title":"Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","department":[{"_id":"AnKi"}],"date_updated":"2023-09-18T09:29:07Z","citation":{"ista":"Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti ME, Xie M, Kicheva A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser M, Chagin AS, Fried K, Adameyko I. 2018. Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage, Dryad, 10.5061/dryad.f1s76f2.","chicago":"Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria Eleni Kastriti, Meng Xie, Anna Kicheva, et al. “Data from: Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” Dryad, 2018. https://doi.org/10.5061/dryad.f1s76f2.","ieee":"M. Kaucka et al., “Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage.” Dryad, 2018.","short":"M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M.E. Kastriti, M. Xie, A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, (2018).","ama":"Kaucka M, Petersen J, Tesarova M, et al. Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. 2018. doi:10.5061/dryad.f1s76f2","apa":"Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M. E., Xie, M., … Adameyko, I. (2018). Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. Dryad. https://doi.org/10.5061/dryad.f1s76f2","mla":"Kaucka, Marketa, et al. Data from: Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage. Dryad, 2018, doi:10.5061/dryad.f1s76f2."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","status":"public","_id":"9838","doi":"10.5061/dryad.f1s76f2","related_material":{"record":[{"id":"162","status":"public","relation":"used_in_publication"}]},"date_published":"2018-06-14T00:00:00Z","date_created":"2021-08-09T12:54:35Z","year":"2018","day":"14","publisher":"Dryad","main_file_link":[{"url":"https://doi.org/10.5061/dryad.f1s76f2","open_access":"1"}],"oa":1,"month":"06","abstract":[{"text":"Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts.","lang":"eng"}],"oa_version":"Published Version"},{"quality_controlled":"1","publisher":"Frontiers Media","oa":1,"doi":"10.3389/fncel.2018.00311","date_published":"2018-09-19T00:00:00Z","date_created":"2018-12-11T11:44:19Z","day":"19","publication":"Frontiers in Cellular Neuroscience","has_accepted_license":"1","isi":1,"year":"2018","project":[{"call_identifier":"H2020","_id":"25CBA828-B435-11E9-9278-68D0E5697425","grant_number":"720270","name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)"}],"article_number":"311","title":"Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells","author":[{"last_name":"Luján","full_name":"Luján, Rafæl","first_name":"Rafæl"},{"last_name":"Aguado","full_name":"Aguado, Carolina","first_name":"Carolina"},{"last_name":"Ciruela","full_name":"Ciruela, Francisco","first_name":"Francisco"},{"last_name":"Arus","full_name":"Arus, Xavier","first_name":"Xavier"},{"first_name":"Alejandro","full_name":"Martín Belmonte, Alejandro","last_name":"Martín Belmonte"},{"first_name":"Rocío","full_name":"Alfaro Ruiz, Rocío","last_name":"Alfaro Ruiz"},{"first_name":"Jesus","last_name":"Martinez Gomez","full_name":"Martinez Gomez, Jesus"},{"full_name":"De La Ossa, Luis","last_name":"De La Ossa","first_name":"Luis"},{"last_name":"Watanabe","full_name":"Watanabe, Masahiko","first_name":"Masahiko"},{"last_name":"Adelman","full_name":"Adelman, John","first_name":"John"},{"last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yugo","last_name":"Fukazawa","full_name":"Fukazawa, Yugo"}],"publist_id":"8013","article_processing_charge":"No","external_id":{"isi":["000445090100002"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"R. Luján et al., “Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells,” Frontiers in Cellular Neuroscience, vol. 12. Frontiers Media, 2018.","short":"R. Luján, C. Aguado, F. Ciruela, X. Arus, A. Martín Belmonte, R. Alfaro Ruiz, J. Martinez Gomez, L. De La Ossa, M. Watanabe, J. Adelman, R. Shigemoto, Y. Fukazawa, Frontiers in Cellular Neuroscience 12 (2018).","ama":"Luján R, Aguado C, Ciruela F, et al. Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells. Frontiers in Cellular Neuroscience. 2018;12. doi:10.3389/fncel.2018.00311","apa":"Luján, R., Aguado, C., Ciruela, F., Arus, X., Martín Belmonte, A., Alfaro Ruiz, R., … Fukazawa, Y. (2018). Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells. Frontiers in Cellular Neuroscience. Frontiers Media. https://doi.org/10.3389/fncel.2018.00311","mla":"Luján, Rafæl, et al. “Sk2 Channels Associate with MGlu1α Receptors and CaV2.1 Channels in Purkinje Cells.” Frontiers in Cellular Neuroscience, vol. 12, 311, Frontiers Media, 2018, doi:10.3389/fncel.2018.00311.","ista":"Luján R, Aguado C, Ciruela F, Arus X, Martín Belmonte A, Alfaro Ruiz R, Martinez Gomez J, De La Ossa L, Watanabe M, Adelman J, Shigemoto R, Fukazawa Y. 2018. Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells. Frontiers in Cellular Neuroscience. 12, 311.","chicago":"Luján, Rafæl, Carolina Aguado, Francisco Ciruela, Xavier Arus, Alejandro Martín Belmonte, Rocío Alfaro Ruiz, Jesus Martinez Gomez, et al. “Sk2 Channels Associate with MGlu1α Receptors and CaV2.1 Channels in Purkinje Cells.” Frontiers in Cellular Neuroscience. Frontiers Media, 2018. https://doi.org/10.3389/fncel.2018.00311."},"month":"09","intvolume":" 12","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The small-conductance, Ca2+-activated K+ (SK) channel subtype SK2 regulates the spike rate and firing frequency, as well as Ca2+ transients in Purkinje cells (PCs). To understand the molecular basis by which SK2 channels mediate these functions, we analyzed the exact location and densities of SK2 channels along the neuronal surface of the mouse cerebellar PCs using SDS-digested freeze-fracture replica labeling (SDS-FRL) of high sensitivity combined with quantitative analyses. Immunogold particles for SK2 were observed on post- and pre-synaptic compartments showing both scattered and clustered distribution patterns. We found an axo-somato-dendritic gradient of the SK2 particle density increasing 12-fold from soma to dendritic spines. Using two different immunogold approaches, we also found that SK2 immunoparticles were frequently adjacent to, but never overlap with, the postsynaptic density of excitatory synapses in PC spines. Co-immunoprecipitation analysis demonstrated that SK2 channels form macromolecular complexes with two types of proteins that mobilize Ca2+: CaV2.1 channels and mGlu1α receptors in the cerebellum. Freeze-fracture replica double-labeling showed significant co-clustering of particles for SK2 with those for CaV2.1 channels and mGlu1α receptors. SK2 channels were also detected at presynaptic sites, mostly at the presynaptic active zone (AZ), where they are close to CaV2.1 channels, though they are not significantly co-clustered. These data demonstrate that SK2 channels located in different neuronal compartments can associate with distinct proteins mobilizing Ca2+, and suggest that the ultrastructural association of SK2 with CaV2.1 and mGlu1α provides the mechanism that ensures voltage (excitability) regulation by distinct intracellular Ca2+ transients in PCs."}],"volume":12,"ec_funded":1,"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"0bcaec8d596162af0b7fe3f31325d480","file_id":"5684","file_size":6834251,"date_updated":"2020-07-14T12:46:23Z","creator":"dernst","file_name":"fncel-12-00311.pdf","date_created":"2018-12-17T08:49:03Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["16625102"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"41","department":[{"_id":"RySh"}],"file_date_updated":"2020-07-14T12:46:23Z","ddc":["570"],"date_updated":"2023-09-18T09:31:18Z"},{"file_date_updated":"2020-07-14T12:45:37Z","department":[{"_id":"GeKa"}],"ddc":["530"],"date_updated":"2023-09-18T09:30:37Z","pubrep_id":"1065","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"23","ec_funded":1,"volume":18,"issue":"11","related_material":{"record":[{"id":"7977","relation":"popular_science"},{"status":"public","id":"69","relation":"dissertation_contains"},{"status":"public","id":"7996","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"3e6034a94c6b5335e939145d88bdb371","file_id":"5194","date_updated":"2020-07-14T12:45:37Z","file_size":1361441,"creator":"system","date_created":"2018-12-12T10:16:08Z","file_name":"IST-2018-1065-v1+1_ACS_nanoletters_8b03217.pdf"}],"publication_status":"published","publication_identifier":{"issn":["15306984"]},"intvolume":" 18","month":"10","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"The strong atomistic spin–orbit coupling of holes makes single-shot spin readout measurements difficult because it reduces the spin lifetimes. By integrating the charge sensor into a high bandwidth radio frequency reflectometry setup, we were able to demonstrate single-shot readout of a germanium quantum dot hole spin and measure the spin lifetime. Hole spin relaxation times of about 90 μs at 500 mT are reported, with a total readout visibility of about 70%. By analyzing separately the spin-to-charge conversion and charge readout fidelities, we have obtained insight into the processes limiting the visibilities of hole spins. The analyses suggest that high hole visibilities are feasible at realistic experimental conditions, underlying the potential of hole spins for the realization of viable qubit devices."}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"title":"Single-shot readout of hole spins in Ge","article_processing_charge":"No","external_id":{"isi":["000451102100064"],"pmid":["30359041"]},"publist_id":"8032","author":[{"id":"31E9F056-F248-11E8-B48F-1D18A9856A87","first_name":"Lada","last_name":"Vukušić","full_name":"Vukušić, Lada","orcid":"0000-0003-2424-8636"},{"last_name":"Kukucka","full_name":"Kukucka, Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","first_name":"Josip"},{"full_name":"Watzinger, Hannes","last_name":"Watzinger","first_name":"Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87"},{"id":"4CDE0A96-F248-11E8-B48F-1D18A9856A87","first_name":"Joshua M","last_name":"Milem","full_name":"Milem, Joshua M"},{"full_name":"Schäffler, Friedrich","last_name":"Schäffler","first_name":"Friedrich"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"L. Vukušić, J. Kukucka, H. Watzinger, J. M. Milem, F. Schäffler, and G. Katsaros, “Single-shot readout of hole spins in Ge,” Nano Letters, vol. 18, no. 11. American Chemical Society, pp. 7141–7145, 2018.","short":"L. Vukušić, J. Kukucka, H. Watzinger, J.M. Milem, F. Schäffler, G. Katsaros, Nano Letters 18 (2018) 7141–7145.","ama":"Vukušić L, Kukucka J, Watzinger H, Milem JM, Schäffler F, Katsaros G. Single-shot readout of hole spins in Ge. Nano Letters. 2018;18(11):7141-7145. doi:10.1021/acs.nanolett.8b03217","apa":"Vukušić, L., Kukucka, J., Watzinger, H., Milem, J. M., Schäffler, F., & Katsaros, G. (2018). Single-shot readout of hole spins in Ge. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.8b03217","mla":"Vukušić, Lada, et al. “Single-Shot Readout of Hole Spins in Ge.” Nano Letters, vol. 18, no. 11, American Chemical Society, 2018, pp. 7141–45, doi:10.1021/acs.nanolett.8b03217.","ista":"Vukušić L, Kukucka J, Watzinger H, Milem JM, Schäffler F, Katsaros G. 2018. Single-shot readout of hole spins in Ge. Nano Letters. 18(11), 7141–7145.","chicago":"Vukušić, Lada, Josip Kukucka, Hannes Watzinger, Joshua M Milem, Friedrich Schäffler, and Georgios Katsaros. “Single-Shot Readout of Hole Spins in Ge.” Nano Letters. American Chemical Society, 2018. https://doi.org/10.1021/acs.nanolett.8b03217."},"project":[{"call_identifier":"FP7","_id":"25517E86-B435-11E9-9278-68D0E5697425","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","grant_number":"335497"}],"date_created":"2018-12-11T11:44:13Z","doi":"10.1021/acs.nanolett.8b03217","date_published":"2018-10-25T00:00:00Z","page":"7141 - 7145","publication":"Nano Letters","day":"25","year":"2018","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"American Chemical Society"},{"file_date_updated":"2020-07-14T12:48:14Z","department":[{"_id":"DaAl"}],"ddc":["000"],"date_updated":"2023-09-18T09:32:36Z","status":"public","type":"conference","conference":{"start_date":"2018-08-27","end_date":"2018-08-31","location":"Turin, Italy","name":"Euro-Par: European Conference on Parallel Processing"},"_id":"85","volume":11014,"file":[{"date_updated":"2020-07-14T12:48:14Z","file_size":665372,"creator":"dernst","date_created":"2019-02-12T07:40:40Z","file_name":"2018_Brown.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5954","checksum":"13a3f250be8878405e791b53c19722ad"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["03029743"]},"publication_status":"published","month":"08","intvolume":" 11014","alternative_title":["LNCS"],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Concurrent accesses to shared data structures must be synchronized to avoid data races. Coarse-grained synchronization, which locks the entire data structure, is easy to implement but does not scale. Fine-grained synchronization can scale well, but can be hard to reason about. Hand-over-hand locking, in which operations are pipelined as they traverse the data structure, combines fine-grained synchronization with ease of use. However, the traditional implementation suffers from inherent overheads. This paper introduces snapshot-based synchronization (SBS), a novel hand-over-hand locking mechanism. SBS decouples the synchronization state from the data, significantly improving cache utilization. Further, it relies on guarantees provided by pipelining to minimize synchronization that requires cross-thread communication. Snapshot-based synchronization thus scales much better than traditional hand-over-hand locking, while maintaining the same ease of use."}],"title":"Snapshot based synchronization: A fast replacement for Hand-over-Hand locking","publist_id":"7969","author":[{"first_name":"Eran","full_name":"Gilad, Eran","last_name":"Gilad"},{"id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","first_name":"Trevor A","full_name":"Brown, Trevor A","last_name":"Brown"},{"first_name":"Mark","last_name":"Oskin","full_name":"Oskin, Mark"},{"first_name":"Yoav","last_name":"Etsion","full_name":"Etsion, Yoav"}],"external_id":{"isi":["000851042300031"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Gilad E, Brown TA, Oskin M, Etsion Y. 2018. Snapshot based synchronization: A fast replacement for Hand-over-Hand locking. Euro-Par: European Conference on Parallel Processing, LNCS, vol. 11014, 465–479.","chicago":"Gilad, Eran, Trevor A Brown, Mark Oskin, and Yoav Etsion. “Snapshot Based Synchronization: A Fast Replacement for Hand-over-Hand Locking,” 11014:465–79. Springer, 2018. https://doi.org/10.1007/978-3-319-96983-1_33.","ieee":"E. Gilad, T. A. Brown, M. Oskin, and Y. Etsion, “Snapshot based synchronization: A fast replacement for Hand-over-Hand locking,” presented at the Euro-Par: European Conference on Parallel Processing, Turin, Italy, 2018, vol. 11014, pp. 465–479.","short":"E. Gilad, T.A. Brown, M. Oskin, Y. Etsion, in:, Springer, 2018, pp. 465–479.","apa":"Gilad, E., Brown, T. A., Oskin, M., & Etsion, Y. (2018). Snapshot based synchronization: A fast replacement for Hand-over-Hand locking (Vol. 11014, pp. 465–479). Presented at the Euro-Par: European Conference on Parallel Processing, Turin, Italy: Springer. https://doi.org/10.1007/978-3-319-96983-1_33","ama":"Gilad E, Brown TA, Oskin M, Etsion Y. Snapshot based synchronization: A fast replacement for Hand-over-Hand locking. In: Vol 11014. Springer; 2018:465-479. doi:10.1007/978-3-319-96983-1_33","mla":"Gilad, Eran, et al. Snapshot Based Synchronization: A Fast Replacement for Hand-over-Hand Locking. Vol. 11014, Springer, 2018, pp. 465–79, doi:10.1007/978-3-319-96983-1_33."},"project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}],"doi":"10.1007/978-3-319-96983-1_33","date_published":"2018-08-01T00:00:00Z","date_created":"2018-12-11T11:44:33Z","page":"465 - 479","day":"01","has_accepted_license":"1","isi":1,"year":"2018","quality_controlled":"1","publisher":"Springer","oa":1,"acknowledgement":"Trevor Brown was supported in part by the ISF (grants 2005/17 & 1749/14) and by a NSERC post-doctoral fellowship."},{"citation":{"mla":"Michailidis, Alexios, et al. “Slow Dynamics in Translation-Invariant Quantum Lattice Models.” Physical Review B, vol. 97, no. 10, 104307, American Physical Society, 2018, doi:10.1103/PhysRevB.97.104307.","apa":"Michailidis, A., Žnidarič, M., Medvedyeva, M., Abanin, D., Prosen, T., & Papić, Z. (2018). Slow dynamics in translation-invariant quantum lattice models. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.97.104307","ama":"Michailidis A, Žnidarič M, Medvedyeva M, Abanin D, Prosen T, Papić Z. Slow dynamics in translation-invariant quantum lattice models. Physical Review B. 2018;97(10). doi:10.1103/PhysRevB.97.104307","short":"A. Michailidis, M. Žnidarič, M. Medvedyeva, D. Abanin, T. Prosen, Z. Papić, Physical Review B 97 (2018).","ieee":"A. Michailidis, M. Žnidarič, M. Medvedyeva, D. Abanin, T. Prosen, and Z. Papić, “Slow dynamics in translation-invariant quantum lattice models,” Physical Review B, vol. 97, no. 10. American Physical Society, 2018.","chicago":"Michailidis, Alexios, Marko Žnidarič, Mariya Medvedyeva, Dmitry Abanin, Tomaž Prosen, and Zlatko Papić. “Slow Dynamics in Translation-Invariant Quantum Lattice Models.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.97.104307.","ista":"Michailidis A, Žnidarič M, Medvedyeva M, Abanin D, Prosen T, Papić Z. 2018. Slow dynamics in translation-invariant quantum lattice models. Physical Review B. 97(10), 104307."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7538","author":[{"id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","first_name":"Alexios","last_name":"Michailidis","orcid":"0000-0002-8443-1064","full_name":"Michailidis, Alexios"},{"last_name":"Žnidarič","full_name":"Žnidarič, Marko","first_name":"Marko"},{"first_name":"Mariya","last_name":"Medvedyeva","full_name":"Medvedyeva, Mariya"},{"last_name":"Abanin","full_name":"Abanin, Dmitry","first_name":"Dmitry"},{"first_name":"Tomaž","last_name":"Prosen","full_name":"Prosen, Tomaž"},{"full_name":"Papić, Zlatko","last_name":"Papić","first_name":"Zlatko"}],"article_processing_charge":"No","external_id":{"isi":["000427798800005"]},"title":"Slow dynamics in translation-invariant quantum lattice models","article_number":"104307","isi":1,"year":"2018","day":"19","publication":"Physical Review B","doi":"10.1103/PhysRevB.97.104307","date_published":"2018-03-19T00:00:00Z","date_created":"2018-12-11T11:45:50Z","acknowledgement":"We thank F. Huveneers for useful discussions. Z.P. and A.M. acknowledge support by EPSRC Grant No. EP/P009409/1 and and the Royal Society Research Grant No. RG160635. Statement of compliance with EPSRC policy framework on research data: This publication is theoretical work that does not require supporting research data. D.A. acknowledges support by the Swiss National Science Foundation. M.Z., M.M. and T.P. acknowledge Grants J1-7279 (M.Z.) and N1-0025 (M.M. and T.P.) of Slovenian Research Agency, and Advanced Grant of European Research Council, Grant No. 694544 - OMNES (T.P.).","publisher":"American Physical Society","quality_controlled":"1","oa":1,"date_updated":"2023-09-18T09:31:46Z","department":[{"_id":"MaSe"}],"_id":"327","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"issue":"10","volume":97,"abstract":[{"text":"Many-body quantum systems typically display fast dynamics and ballistic spreading of information. Here we address the open problem of how slow the dynamics can be after a generic breaking of integrability by local interactions. We develop a method based on degenerate perturbation theory that reveals slow dynamical regimes and delocalization processes in general translation invariant models, along with accurate estimates of their delocalization time scales. Our results shed light on the fundamental questions of the robustness of quantum integrable systems and the possibility of many-body localization without disorder. As an example, we construct a large class of one-dimensional lattice models where, despite the absence of asymptotic localization, the transient dynamics is exceptionally slow, i.e., the dynamics is indistinguishable from that of many-body localized systems for the system sizes and time scales accessible in experiments and numerical simulations.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.05026"}],"month":"03","intvolume":" 97"},{"year":"2018","isi":1,"has_accepted_license":"1","publication":"Ecology and Evolution","day":"01","page":"11031-11070","date_created":"2018-12-11T11:44:15Z","doi":"10.1002/ece3.4573","date_published":"2018-11-01T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"Wiley","citation":{"ista":"Viljakainen L, Jurvansuu J, Holmberg I, Pamminger T, Erler S, Cremer S. 2018. Social environment affects the transcriptomic response to bacteria in ant queens. Ecology and Evolution. 8(22), 11031–11070.","chicago":"Viljakainen, Lumi, Jaana Jurvansuu, Ida Holmberg, Tobias Pamminger, Silvio Erler, and Sylvia Cremer. “Social Environment Affects the Transcriptomic Response to Bacteria in Ant Queens.” Ecology and Evolution. Wiley, 2018. https://doi.org/10.1002/ece3.4573.","short":"L. Viljakainen, J. Jurvansuu, I. Holmberg, T. Pamminger, S. Erler, S. Cremer, Ecology and Evolution 8 (2018) 11031–11070.","ieee":"L. Viljakainen, J. Jurvansuu, I. Holmberg, T. Pamminger, S. Erler, and S. Cremer, “Social environment affects the transcriptomic response to bacteria in ant queens,” Ecology and Evolution, vol. 8, no. 22. Wiley, pp. 11031–11070, 2018.","ama":"Viljakainen L, Jurvansuu J, Holmberg I, Pamminger T, Erler S, Cremer S. Social environment affects the transcriptomic response to bacteria in ant queens. Ecology and Evolution. 2018;8(22):11031-11070. doi:10.1002/ece3.4573","apa":"Viljakainen, L., Jurvansuu, J., Holmberg, I., Pamminger, T., Erler, S., & Cremer, S. (2018). Social environment affects the transcriptomic response to bacteria in ant queens. Ecology and Evolution. Wiley. https://doi.org/10.1002/ece3.4573","mla":"Viljakainen, Lumi, et al. “Social Environment Affects the Transcriptomic Response to Bacteria in Ant Queens.” Ecology and Evolution, vol. 8, no. 22, Wiley, 2018, pp. 11031–70, doi:10.1002/ece3.4573."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000451611000032"]},"article_processing_charge":"No","publist_id":"8026","author":[{"first_name":"Lumi","last_name":"Viljakainen","full_name":"Viljakainen, Lumi"},{"last_name":"Jurvansuu","full_name":"Jurvansuu, Jaana","first_name":"Jaana"},{"last_name":"Holmberg","full_name":"Holmberg, Ida","first_name":"Ida"},{"last_name":"Pamminger","full_name":"Pamminger, Tobias","first_name":"Tobias"},{"last_name":"Erler","full_name":"Erler, Silvio","first_name":"Silvio"},{"last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"title":"Social environment affects the transcriptomic response to bacteria in ant queens","publication_status":"published","publication_identifier":{"issn":["20457758"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5682","checksum":"0d1355c78627ca7210aadd9a17a01915","file_size":1272096,"date_updated":"2020-07-14T12:45:52Z","creator":"dernst","file_name":"Viljakainen_et_al-2018-Ecology_and_Evolution.pdf","date_created":"2018-12-17T08:27:04Z"}],"issue":"22","volume":8,"abstract":[{"text":"Social insects have evolved enormous capacities to collectively build nests and defend their colonies against both predators and pathogens. The latter is achieved by a combination of individual immune responses and sophisticated collective behavioral and organizational disease defenses, that is, social immunity. We investigated how the presence or absence of these social defense lines affects individual-level immunity in ant queens after bacterial infection. To this end, we injected queens of the ant Linepithema humile with a mix of gram+ and gram− bacteria or a control solution, reared them either with workers or alone and analyzed their gene expression patterns at 2, 4, 8, and 12 hr post-injection, using RNA-seq. This allowed us to test for the effect of bacterial infection, social context, as well as the interaction between the two over the course of infection and raising of an immune response. We found that social isolation per se affected queen gene expression for metabolism genes, but not for immune genes. When infected, queens reared with and without workers up-regulated similar numbers of innate immune genes revealing activation of Toll and Imd signaling pathways and melanization. Interestingly, however, they mostly regulated different genes along the pathways and showed a different pattern of overall gene up-regulation or down-regulation. Hence, we can conclude that the absence of workers does not compromise the onset of an individual immune response by the queens, but that the social environment impacts the route of the individual innate immune responses.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 8","month":"11","date_updated":"2023-09-19T09:29:12Z","ddc":["576","591"],"file_date_updated":"2020-07-14T12:45:52Z","department":[{"_id":"SyCr"}],"_id":"29","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public"},{"publication_identifier":{"issn":["1545-4487"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":63,"related_material":{"record":[{"id":"819","status":"public","relation":"dissertation_contains"}]},"abstract":[{"lang":"eng","text":"Social insect colonies have evolved many collectively performed adaptations that reduce the impact of infectious disease and that are expected to maximize their fitness. This colony-level protection is termed social immunity, and it enhances the health and survival of the colony. In this review, we address how social immunity emerges from its mechanistic components to produce colony-level disease avoidance, resistance, and tolerance. To understand the evolutionary causes and consequences of social immunity, we highlight the need for studies that evaluate the effects of social immunity on colony fitness. We discuss the role that host life history and ecology have on predicted eco-evolutionary dynamics, which differ among the social insect lineages. Throughout the review, we highlight current gaps in our knowledge and promising avenues for future research, which we hope will bring us closer to an integrated understanding of socio-eco-evo-immunology."}],"oa_version":"None","scopus_import":"1","month":"01","intvolume":" 63","date_updated":"2023-09-19T09:29:45Z","department":[{"_id":"SyCr"}],"_id":"806","type":"journal_article","status":"public","isi":1,"year":"2018","day":"07","publication":"Annual Review of Entomology","page":"105 - 123","date_published":"2018-01-07T00:00:00Z","doi":"10.1146/annurev-ento-020117-043110","date_created":"2018-12-11T11:48:36Z","publisher":"Annual Reviews","quality_controlled":"1","citation":{"short":"S. Cremer, C. Pull, M. Fürst, Annual Review of Entomology 63 (2018) 105–123.","ieee":"S. Cremer, C. Pull, and M. Fürst, “Social immunity: Emergence and evolution of colony-level disease protection,” Annual Review of Entomology, vol. 63. Annual Reviews, pp. 105–123, 2018.","apa":"Cremer, S., Pull, C., & Fürst, M. (2018). Social immunity: Emergence and evolution of colony-level disease protection. Annual Review of Entomology. Annual Reviews. https://doi.org/10.1146/annurev-ento-020117-043110","ama":"Cremer S, Pull C, Fürst M. Social immunity: Emergence and evolution of colony-level disease protection. Annual Review of Entomology. 2018;63:105-123. doi:10.1146/annurev-ento-020117-043110","mla":"Cremer, Sylvia, et al. “Social Immunity: Emergence and Evolution of Colony-Level Disease Protection.” Annual Review of Entomology, vol. 63, Annual Reviews, 2018, pp. 105–23, doi:10.1146/annurev-ento-020117-043110.","ista":"Cremer S, Pull C, Fürst M. 2018. Social immunity: Emergence and evolution of colony-level disease protection. Annual Review of Entomology. 63, 105–123.","chicago":"Cremer, Sylvia, Christopher Pull, and Matthias Fürst. “Social Immunity: Emergence and Evolution of Colony-Level Disease Protection.” Annual Review of Entomology. Annual Reviews, 2018. https://doi.org/10.1146/annurev-ento-020117-043110."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","last_name":"Cremer"},{"last_name":"Pull","full_name":"Pull, Christopher","orcid":"0000-0003-1122-3982","first_name":"Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87"},{"id":"393B1196-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","orcid":"0000-0002-3712-925X","full_name":"Fürst, Matthias","last_name":"Fürst"}],"publist_id":"6844","article_processing_charge":"No","external_id":{"isi":["000424633700008"]},"title":"Social immunity: Emergence and evolution of colony-level disease protection"},{"doi":"10.1007/978-3-319-96145-3_25","date_published":"2018-07-18T00:00:00Z","date_created":"2018-12-11T11:44:50Z","page":"468 - 486","day":"18","isi":1,"has_accepted_license":"1","year":"2018","publisher":"Springer","quality_controlled":"1","oa":1,"title":"Space-time interpolants","author":[{"last_name":"Frehse","full_name":"Frehse, Goran","first_name":"Goran"},{"id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","first_name":"Mirco","last_name":"Giacobbe","full_name":"Giacobbe, Mirco","orcid":"0000-0001-8180-0904"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7783","external_id":{"isi":["000491481600025"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Frehse, Goran, Mirco Giacobbe, and Thomas A Henzinger. “Space-Time Interpolants,” 10981:468–86. Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_25.","ista":"Frehse G, Giacobbe M, Henzinger TA. 2018. Space-time interpolants. CAV: Computer Aided Verification, LNCS, vol. 10981, 468–486.","mla":"Frehse, Goran, et al. Space-Time Interpolants. Vol. 10981, Springer, 2018, pp. 468–86, doi:10.1007/978-3-319-96145-3_25.","ieee":"G. Frehse, M. Giacobbe, and T. A. Henzinger, “Space-time interpolants,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10981, pp. 468–486.","short":"G. Frehse, M. Giacobbe, T.A. Henzinger, in:, Springer, 2018, pp. 468–486.","ama":"Frehse G, Giacobbe M, Henzinger TA. Space-time interpolants. In: Vol 10981. Springer; 2018:468-486. doi:10.1007/978-3-319-96145-3_25","apa":"Frehse, G., Giacobbe, M., & Henzinger, T. A. (2018). Space-time interpolants (Vol. 10981, pp. 468–486). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. https://doi.org/10.1007/978-3-319-96145-3_25"},"project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6894"}]},"volume":10981,"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5310","checksum":"6dca832f575d6b3f0ea9dff56f579142","file_size":563710,"date_updated":"2020-07-14T12:44:50Z","creator":"system","file_name":"IST-2018-1010-v1+1_space-time_interpolants.pdf","date_created":"2018-12-12T10:17:53Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["03029743"]},"publication_status":"published","month":"07","intvolume":" 10981","alternative_title":["LNCS"],"scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Reachability analysis is difficult for hybrid automata with affine differential equations, because the reach set needs to be approximated. Promising abstraction techniques usually employ interval methods or template polyhedra. Interval methods account for dense time and guarantee soundness, and there are interval-based tools that overapproximate affine flowpipes. But interval methods impose bounded and rigid shapes, which make refinement expensive and fixpoint detection difficult. Template polyhedra, on the other hand, can be adapted flexibly and can be unbounded, but sound template refinement for unbounded reachability analysis has been implemented only for systems with piecewise constant dynamics. We capitalize on the advantages of both techniques, combining interval arithmetic and template polyhedra, using the former to abstract time and the latter to abstract space. During a CEGAR loop, whenever a spurious error trajectory is found, we compute additional space constraints and split time intervals, and use these space-time interpolants to eliminate the counterexample. Space-time interpolation offers a lazy, flexible framework for increasing precision while guaranteeing soundness, both for error avoidance and fixpoint detection. To the best of out knowledge, this is the first abstraction refinement scheme for the reachability analysis over unbounded and dense time of affine hybrid systems, which is both sound and automatic. We demonstrate the effectiveness of our algorithm with several benchmark examples, which cannot be handled by other tools."}],"file_date_updated":"2020-07-14T12:44:50Z","department":[{"_id":"ToHe"}],"ddc":["005"],"date_updated":"2023-09-19T09:30:43Z","status":"public","pubrep_id":"1010","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"start_date":"2018-07-14","location":"Oxford, United Kingdom","end_date":"2018-07-17","name":"CAV: Computer Aided Verification"},"_id":"140"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"154","file_date_updated":"2020-07-14T12:45:01Z","department":[{"_id":"RoSe"}],"date_updated":"2023-09-19T09:31:15Z","ddc":["530"],"scopus_import":"1","intvolume":" 21","month":"09","abstract":[{"text":"We give a lower bound on the ground state energy of a system of two fermions of one species interacting with two fermions of another species via point interactions. We show that there is a critical mass ratio m2 ≈ 0.58 such that the system is stable, i.e., the energy is bounded from below, for m∈[m2,m2−1]. So far it was not known whether this 2 + 2 system exhibits a stable region at all or whether the formation of four-body bound states causes an unbounded spectrum for all mass ratios, similar to the Thomas effect. Our result gives further evidence for the stability of the more general N + M system.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"volume":21,"related_material":{"record":[{"relation":"dissertation_contains","id":"52","status":"public"}]},"issue":"3","publication_status":"published","publication_identifier":{"issn":["13850172"],"eissn":["15729656"]},"language":[{"iso":"eng"}],"file":[{"checksum":"411c4db5700d7297c9cd8ebc5dd29091","file_id":"5729","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-17T16:49:02Z","file_name":"2018_MathPhysics_Moser.pdf","date_updated":"2020-07-14T12:45:01Z","file_size":496973,"creator":"dernst"}],"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227"},{"grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425"},{"name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF"}],"article_number":"19","article_processing_charge":"No","external_id":{"isi":["000439639700001"]},"author":[{"first_name":"Thomas","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","full_name":"Moser, Thomas","last_name":"Moser"},{"last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7767","title":"Stability of the 2+2 fermionic system with point interactions","citation":{"chicago":"Moser, Thomas, and Robert Seiringer. “Stability of the 2+2 Fermionic System with Point Interactions.” Mathematical Physics Analysis and Geometry. Springer, 2018. https://doi.org/10.1007/s11040-018-9275-3.","ista":"Moser T, Seiringer R. 2018. Stability of the 2+2 fermionic system with point interactions. Mathematical Physics Analysis and Geometry. 21(3), 19.","mla":"Moser, Thomas, and Robert Seiringer. “Stability of the 2+2 Fermionic System with Point Interactions.” Mathematical Physics Analysis and Geometry, vol. 21, no. 3, 19, Springer, 2018, doi:10.1007/s11040-018-9275-3.","apa":"Moser, T., & Seiringer, R. (2018). Stability of the 2+2 fermionic system with point interactions. Mathematical Physics Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-018-9275-3","ama":"Moser T, Seiringer R. Stability of the 2+2 fermionic system with point interactions. Mathematical Physics Analysis and Geometry. 2018;21(3). doi:10.1007/s11040-018-9275-3","short":"T. Moser, R. Seiringer, Mathematical Physics Analysis and Geometry 21 (2018).","ieee":"T. Moser and R. Seiringer, “Stability of the 2+2 fermionic system with point interactions,” Mathematical Physics Analysis and Geometry, vol. 21, no. 3. Springer, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"quality_controlled":"1","publisher":"Springer","acknowledgement":"Open access funding provided by Austrian Science Fund (FWF).","date_created":"2018-12-11T11:44:55Z","doi":"10.1007/s11040-018-9275-3","date_published":"2018-09-01T00:00:00Z","year":"2018","has_accepted_license":"1","isi":1,"publication":"Mathematical Physics Analysis and Geometry","day":"01"},{"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"5787","file_date_updated":"2020-07-14T12:47:11Z","department":[{"_id":"EdHa"}],"ddc":["570"],"date_updated":"2023-09-19T09:32:49Z","intvolume":" 60","month":"12","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Branching morphogenesis remains a subject of abiding interest. Although much is \r\nknown about the gene regulatory programs and signaling pathways that operate at \r\nthe cellular scale, it has remained unclear how the macroscopic features of branched \r\norgans, including their size, network topology and spatial patterning, are encoded. \r\nLately, it has been proposed that, these features can be explained quantitatively in \r\nseveral organs within a single unifying framework. Based on large-\r\nscale organ recon\r\n-\r\nstructions and cell lineage tracing, it has been argued that morphogenesis follows \r\nfrom the collective dynamics of sublineage- \r\nrestricted self- \r\nrenewing progenitor cells, \r\nlocalized at ductal tips, that act cooperatively to drive a serial process of ductal elon\r\n-\r\ngation and stochastic tip bifurcation. By correlating differentiation or cell cycle exit \r\nwith proximity to maturing ducts, this dynamic results in the specification of a com-\r\nplex network of defined density and statistical organization. These results suggest \r\nthat, for several mammalian tissues, branched epithelial structures develop as a self- \r\norganized process, reliant upon a strikingly simple, but generic, set of local rules, \r\nwithout recourse to a rigid and deterministic sequence of genetically programmed \r\nevents. Here, we review the basis of these findings and discuss their implications.","lang":"eng"}],"issue":"9","volume":60,"language":[{"iso":"eng"}],"file":[{"file_id":"5933","checksum":"a6d30b0785db902c734a84fecb2eadd9","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_DevGrowh_Hannezo.pdf","date_created":"2019-02-06T10:40:46Z","creator":"dernst","file_size":1313606,"date_updated":"2020-07-14T12:47:11Z"}],"publication_identifier":{"issn":["00121592"]},"title":"Statistical theory of branching morphogenesis","article_processing_charge":"No","external_id":{"isi":["000453555100002"]},"author":[{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo"},{"last_name":"Simons","full_name":"Simons, Benjamin D.","first_name":"Benjamin D."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Hannezo, Edouard B, and Benjamin D. Simons. “Statistical Theory of Branching Morphogenesis.” Development Growth and Differentiation. Wiley, 2018. https://doi.org/10.1111/dgd.12570.","ista":"Hannezo EB, Simons BD. 2018. Statistical theory of branching morphogenesis. Development Growth and Differentiation. 60(9), 512–521.","mla":"Hannezo, Edouard B., and Benjamin D. Simons. “Statistical Theory of Branching Morphogenesis.” Development Growth and Differentiation, vol. 60, no. 9, Wiley, 2018, pp. 512–21, doi:10.1111/dgd.12570.","apa":"Hannezo, E. B., & Simons, B. D. (2018). Statistical theory of branching morphogenesis. Development Growth and Differentiation. Wiley. https://doi.org/10.1111/dgd.12570","ama":"Hannezo EB, Simons BD. Statistical theory of branching morphogenesis. Development Growth and Differentiation. 2018;60(9):512-521. doi:10.1111/dgd.12570","short":"E.B. Hannezo, B.D. Simons, Development Growth and Differentiation 60 (2018) 512–521.","ieee":"E. B. Hannezo and B. D. Simons, “Statistical theory of branching morphogenesis,” Development Growth and Differentiation, vol. 60, no. 9. Wiley, pp. 512–521, 2018."},"oa":1,"quality_controlled":"1","publisher":"Wiley","date_created":"2018-12-30T22:59:14Z","date_published":"2018-12-09T00:00:00Z","doi":"10.1111/dgd.12570","page":"512-521","publication":"Development Growth and Differentiation","day":"09","year":"2018","isi":1,"has_accepted_license":"1"},{"day":"12","has_accepted_license":"1","isi":1,"year":"2018","doi":"10.1007/978-3-319-89960-2_21","date_published":"2018-04-12T00:00:00Z","date_created":"2018-12-11T11:45:41Z","page":"385 - 407","publisher":"Springer","quality_controlled":"1","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Jan Kretinsky, and Viktor Toman. “Strategy Representation by Decision Trees in Reactive Synthesis,” 10805:385–407. Springer, 2018. https://doi.org/10.1007/978-3-319-89960-2_21.","ista":"Brázdil T, Chatterjee K, Kretinsky J, Toman V. 2018. Strategy representation by decision trees in reactive synthesis. TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10805, 385–407.","mla":"Brázdil, Tomáš, et al. Strategy Representation by Decision Trees in Reactive Synthesis. Vol. 10805, Springer, 2018, pp. 385–407, doi:10.1007/978-3-319-89960-2_21.","apa":"Brázdil, T., Chatterjee, K., Kretinsky, J., & Toman, V. (2018). Strategy representation by decision trees in reactive synthesis (Vol. 10805, pp. 385–407). Presented at the TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece: Springer. https://doi.org/10.1007/978-3-319-89960-2_21","ama":"Brázdil T, Chatterjee K, Kretinsky J, Toman V. Strategy representation by decision trees in reactive synthesis. In: Vol 10805. Springer; 2018:385-407. doi:10.1007/978-3-319-89960-2_21","short":"T. Brázdil, K. Chatterjee, J. Kretinsky, V. Toman, in:, Springer, 2018, pp. 385–407.","ieee":"T. Brázdil, K. Chatterjee, J. Kretinsky, and V. Toman, “Strategy representation by decision trees in reactive synthesis,” presented at the TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece, 2018, vol. 10805, pp. 385–407."},"title":"Strategy representation by decision trees in reactive synthesis","publist_id":"7584","author":[{"last_name":"Brázdil","full_name":"Brázdil, Tomáš","first_name":"Tomáš"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881"},{"full_name":"Toman, Viktor","orcid":"0000-0001-9036-063X","last_name":"Toman","first_name":"Viktor","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000546326300021"]},"project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"file":[{"file_size":1829940,"date_updated":"2020-07-14T12:45:57Z","creator":"dernst","file_name":"2018_LNCS_Brazdil.pdf","date_created":"2018-12-17T16:29:08Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5723","checksum":"b13874ffb114932ad9cc2586b7469db4"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":10805,"ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"Graph games played by two players over finite-state graphs are central in many problems in computer science. In particular, graph games with ω -regular winning conditions, specified as parity objectives, which can express properties such as safety, liveness, fairness, are the basic framework for verification and synthesis of reactive systems. The decisions for a player at various states of the graph game are represented as strategies. While the algorithmic problem for solving graph games with parity objectives has been widely studied, the most prominent data-structure for strategy representation in graph games has been binary decision diagrams (BDDs). However, due to the bit-level representation, BDDs do not retain the inherent flavor of the decisions of strategies, and are notoriously hard to minimize to obtain succinct representation. In this work we propose decision trees for strategy representation in graph games. Decision trees retain the flavor of decisions of strategies and allow entropy-based minimization to obtain succinct trees. However, decision trees work in settings (e.g., probabilistic models) where errors are allowed, and overfitting of data is typically avoided. In contrast, for strategies in graph games no error is allowed, and the decision tree must represent the entire strategy. We develop new techniques to extend decision trees to overcome the above obstacles, while retaining the entropy-based techniques to obtain succinct trees. We have implemented our techniques to extend the existing decision tree solvers. We present experimental results for problems in reactive synthesis to show that decision trees provide a much more efficient data-structure for strategy representation as compared to BDDs.","lang":"eng"}],"month":"04","intvolume":" 10805","scopus_import":"1","alternative_title":["LNCS"],"ddc":["000"],"date_updated":"2023-09-19T09:57:08Z","file_date_updated":"2020-07-14T12:45:57Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"_id":"297","status":"public","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems","start_date":"2018-04-14","location":"Thessaloniki, Greece","end_date":"2018-04-20"}},{"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"K. Chatterjee, M. H. Henzinger, V. Loitzenbauer, S. Oraee, and V. Toman, “Symbolic algorithms for graphs and Markov decision processes with fairness objectives,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10982, pp. 178–197.","short":"K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, S. Oraee, V. Toman, in:, Springer, 2018, pp. 178–197.","ama":"Chatterjee K, Henzinger MH, Loitzenbauer V, Oraee S, Toman V. Symbolic algorithms for graphs and Markov decision processes with fairness objectives. In: Vol 10982. Springer; 2018:178-197. doi:10.1007/978-3-319-96142-2_13","apa":"Chatterjee, K., Henzinger, M. H., Loitzenbauer, V., Oraee, S., & Toman, V. (2018). Symbolic algorithms for graphs and Markov decision processes with fairness objectives (Vol. 10982, pp. 178–197). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. https://doi.org/10.1007/978-3-319-96142-2_13","mla":"Chatterjee, Krishnendu, et al. Symbolic Algorithms for Graphs and Markov Decision Processes with Fairness Objectives. Vol. 10982, Springer, 2018, pp. 178–97, doi:10.1007/978-3-319-96142-2_13.","ista":"Chatterjee K, Henzinger MH, Loitzenbauer V, Oraee S, Toman V. 2018. Symbolic algorithms for graphs and Markov decision processes with fairness objectives. CAV: Computer Aided Verification, LNCS, vol. 10982, 178–197.","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, Veronika Loitzenbauer, Simin Oraee, and Viktor Toman. “Symbolic Algorithms for Graphs and Markov Decision Processes with Fairness Objectives,” 10982:178–97. Springer, 2018. https://doi.org/10.1007/978-3-319-96142-2_13."},"title":"Symbolic algorithms for graphs and Markov decision processes with fairness objectives","publist_id":"7782","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger"},{"first_name":"Veronika","last_name":"Loitzenbauer","full_name":"Loitzenbauer, Veronika"},{"first_name":"Simin","full_name":"Oraee, Simin","last_name":"Oraee"},{"orcid":"0000-0001-9036-063X","full_name":"Toman, Viktor","last_name":"Toman","first_name":"Viktor","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000491469700013"]},"acknowledgement":"Acknowledgements. K. C. and M. H. are partially supported by the Vienna Science and Technology Fund (WWTF) grant ICT15-003. K. C. is partially supported by the Austrian Science Fund (FWF): S11407-N23 (RiSE/SHiNE), and an ERC Start Grant (279307: Graph Games). V. T. is partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie Grant Agreement No. 665385.","quality_controlled":"1","publisher":"Springer","oa":1,"day":"18","isi":1,"has_accepted_license":"1","year":"2018","doi":"10.1007/978-3-319-96142-2_13","date_published":"2018-07-18T00:00:00Z","date_created":"2018-12-11T11:44:51Z","page":"178-197","_id":"141","status":"public","type":"conference","conference":{"start_date":"2018-07-14","location":"Oxford, United Kingdom","end_date":"2018-07-17","name":"CAV: Computer Aided Verification"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["000"],"date_updated":"2023-09-19T09:59:55Z","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:44:53Z","oa_version":"Published Version","abstract":[{"text":"Given a model and a specification, the fundamental model-checking problem asks for algorithmic verification of whether the model satisfies the specification. We consider graphs and Markov decision processes (MDPs), which are fundamental models for reactive systems. One of the very basic specifications that arise in verification of reactive systems is the strong fairness (aka Streett) objective. Given different types of requests and corresponding grants, the objective requires that for each type, if the request event happens infinitely often, then the corresponding grant event must also happen infinitely often. All ω -regular objectives can be expressed as Streett objectives and hence they are canonical in verification. To handle the state-space explosion, symbolic algorithms are required that operate on a succinct implicit representation of the system rather than explicitly accessing the system. While explicit algorithms for graphs and MDPs with Streett objectives have been widely studied, there has been no improvement of the basic symbolic algorithms. The worst-case numbers of symbolic steps required for the basic symbolic algorithms are as follows: quadratic for graphs and cubic for MDPs. In this work we present the first sub-quadratic symbolic algorithm for graphs with Streett objectives, and our algorithm is sub-quadratic even for MDPs. Based on our algorithmic insights we present an implementation of the new symbolic approach and show that it improves the existing approach on several academic benchmark examples.","lang":"eng"}],"month":"07","intvolume":" 10982","alternative_title":["LNCS"],"scopus_import":"1","file":[{"file_size":675606,"date_updated":"2020-07-14T12:44:53Z","creator":"dernst","file_name":"2018_LNCS_Chatterjee.pdf","date_created":"2018-12-18T08:52:38Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"1a6ffa4febe8bb8ac28be3adb3eafebc","file_id":"5737"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10199"}]},"volume":10982,"ec_funded":1},{"oa":1,"publisher":"Springer","quality_controlled":"1","page":"99 - 130","date_created":"2018-12-11T11:45:41Z","doi":"10.1007/978-3-319-78375-8_4","date_published":"2018-03-31T00:00:00Z","year":"2018","isi":1,"day":"31","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","grant_number":"682815"}],"article_processing_charge":"No","external_id":{"isi":["000517098700004"],"arxiv":["1705.05313"]},"author":[{"id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F","full_name":"Alwen, Joel F","last_name":"Alwen"},{"last_name":"Blocki","full_name":"Blocki, Jeremiah","first_name":"Jeremiah"},{"orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7583","title":"Sustained space complexity","citation":{"chicago":"Alwen, Joel F, Jeremiah Blocki, and Krzysztof Z Pietrzak. “Sustained Space Complexity,” 10821:99–130. Springer, 2018. https://doi.org/10.1007/978-3-319-78375-8_4.","ista":"Alwen JF, Blocki J, Pietrzak KZ. 2018. Sustained space complexity. Eurocrypt 2018: Advances in Cryptology, LNCS, vol. 10821, 99–130.","mla":"Alwen, Joel F., et al. Sustained Space Complexity. Vol. 10821, Springer, 2018, pp. 99–130, doi:10.1007/978-3-319-78375-8_4.","short":"J.F. Alwen, J. Blocki, K.Z. Pietrzak, in:, Springer, 2018, pp. 99–130.","ieee":"J. F. Alwen, J. Blocki, and K. Z. Pietrzak, “Sustained space complexity,” presented at the Eurocrypt 2018: Advances in Cryptology, Tel Aviv, Israel, 2018, vol. 10821, pp. 99–130.","apa":"Alwen, J. F., Blocki, J., & Pietrzak, K. Z. (2018). Sustained space complexity (Vol. 10821, pp. 99–130). Presented at the Eurocrypt 2018: Advances in Cryptology, Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78375-8_4","ama":"Alwen JF, Blocki J, Pietrzak KZ. Sustained space complexity. In: Vol 10821. Springer; 2018:99-130. doi:10.1007/978-3-319-78375-8_4"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","main_file_link":[{"url":"https://arxiv.org/abs/1705.05313","open_access":"1"}],"scopus_import":"1","alternative_title":["LNCS"],"intvolume":" 10821","month":"03","abstract":[{"lang":"eng","text":"Memory-hard functions (MHF) are functions whose evaluation cost is dominated by memory cost. MHFs are egalitarian, in the sense that evaluating them on dedicated hardware (like FPGAs or ASICs) is not much cheaper than on off-the-shelf hardware (like x86 CPUs). MHFs have interesting cryptographic applications, most notably to password hashing and securing blockchains.\r\n\r\nAlwen and Serbinenko [STOC’15] define the cumulative memory complexity (cmc) of a function as the sum (over all time-steps) of the amount of memory required to compute the function. They advocate that a good MHF must have high cmc. Unlike previous notions, cmc takes into account that dedicated hardware might exploit amortization and parallelism. Still, cmc has been critizised as insufficient, as it fails to capture possible time-memory trade-offs; as memory cost doesn’t scale linearly, functions with the same cmc could still have very different actual hardware cost.\r\n\r\nIn this work we address this problem, and introduce the notion of sustained-memory complexity, which requires that any algorithm evaluating the function must use a large amount of memory for many steps. We construct functions (in the parallel random oracle model) whose sustained-memory complexity is almost optimal: our function can be evaluated using n steps and O(n/log(n)) memory, in each step making one query to the (fixed-input length) random oracle, while any algorithm that can make arbitrary many parallel queries to the random oracle, still needs Ω(n/log(n)) memory for Ω(n) steps.\r\n\r\nAs has been done for various notions (including cmc) before, we reduce the task of constructing an MHFs with high sustained-memory complexity to proving pebbling lower bounds on DAGs. Our main technical contribution is the construction is a family of DAGs on n nodes with constant indegree with high “sustained-space complexity”, meaning that any parallel black-pebbling strategy requires Ω(n/log(n)) pebbles for at least Ω(n) steps.\r\n\r\nAlong the way we construct a family of maximally “depth-robust” DAGs with maximum indegree O(logn) , improving upon the construction of Mahmoody et al. [ITCS’13] which had maximum indegree O(log2n⋅"}],"oa_version":"Preprint","ec_funded":1,"volume":10821,"publication_status":"published","language":[{"iso":"eng"}],"conference":{"end_date":"2018-05-03","location":"Tel Aviv, Israel","start_date":"2018-04-29","name":"Eurocrypt 2018: Advances in Cryptology"},"type":"conference","status":"public","_id":"298","department":[{"_id":"KrPi"}],"date_updated":"2023-09-19T09:59:30Z"},{"citation":{"ieee":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, and I. De Smet, “Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms,” Journal of Experimental Botany, vol. 69, no. 19. Oxford University Press, pp. 4609–4624, 2018.","short":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, I. De Smet, Journal of Experimental Botany 69 (2018) 4609–4624.","apa":"Vu, L., Zhu, T., Verstraeten, I., Van De Cotte, B., Gevaert, K., & De Smet, I. (2018). Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/ery204","ama":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. 2018;69(19):4609-4624. doi:10.1093/jxb/ery204","mla":"Vu, Lam, et al. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental Botany, vol. 69, no. 19, Oxford University Press, 2018, pp. 4609–24, doi:10.1093/jxb/ery204.","ista":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. 2018. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. 69(19), 4609–4624.","chicago":"Vu, Lam, Tingting Zhu, Inge Verstraeten, Brigitte Van De Cotte, Kris Gevaert, and Ive De Smet. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental Botany. Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery204."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000443568700010"]},"article_processing_charge":"No","publist_id":"8019","author":[{"last_name":"Vu","full_name":"Vu, Lam","first_name":"Lam"},{"first_name":"Tingting","full_name":"Zhu, Tingting","last_name":"Zhu"},{"last_name":"Verstraeten","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge"},{"first_name":"Brigitte","full_name":"Van De Cotte, Brigitte","last_name":"Van De Cotte"},{"last_name":"Gevaert","full_name":"Gevaert, Kris","first_name":"Kris"},{"first_name":"Ive","last_name":"De Smet","full_name":"De Smet, Ive"}],"title":"Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms","acknowledgement":"TZ is supported by a grant from the Chinese Scholarship Council.","oa":1,"quality_controlled":"1","publisher":"Oxford University Press","year":"2018","isi":1,"has_accepted_license":"1","publication":"Journal of Experimental Botany","day":"31","page":"4609 - 4624","date_created":"2018-12-11T11:44:17Z","date_published":"2018-08-31T00:00:00Z","doi":"10.1093/jxb/ery204","_id":"36","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","date_updated":"2023-09-19T10:00:46Z","ddc":["581"],"department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:46:13Z","abstract":[{"lang":"eng","text":"Wheat (Triticum ssp.) is one of the most important human food sources. However, this crop is very sensitive to temperature changes. Specifically, processes during wheat leaf, flower, and seed development and photosynthesis, which all contribute to the yield of this crop, are affected by high temperature. While this has to some extent been investigated on physiological, developmental, and molecular levels, very little is known about early signalling events associated with an increase in temperature. Phosphorylation-mediated signalling mechanisms, which are quick and dynamic, are associated with plant growth and development, also under abiotic stress conditions. Therefore, we probed the impact of a short-term and mild increase in temperature on the wheat leaf and spikelet phosphoproteome. In total, 3822 (containing 5178 phosphosites) and 5581 phosphopeptides (containing 7023 phosphosites) were identified in leaf and spikelet samples, respectively. Following statistical analysis, the resulting data set provides the scientific community with a first large-scale plant phosphoproteome under the control of higher ambient temperature. This community resource on the high temperature-mediated wheat phosphoproteome will be valuable for future studies. Our analyses also revealed a core set of common proteins between leaf and spikelet, suggesting some level of conserved regulatory mechanisms. Furthermore, we observed temperature-regulated interconversion of phosphoforms, which probably impacts protein activity."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 69","month":"08","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-18T09:47:51Z","file_name":"2018_JournalExperimBotany_Vu.pdf","creator":"dernst","date_updated":"2020-07-14T12:46:13Z","file_size":3359316,"file_id":"5741","checksum":"34cb0a1611588b75bd6f4913fb4e30f1","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"volume":69,"issue":"19"},{"_id":"326","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"journal_article","ddc":["570"],"date_updated":"2023-09-19T09:58:40Z","department":[{"_id":"RySh"}],"file_date_updated":"2020-07-14T12:46:06Z","oa_version":"Published Version","abstract":[{"text":"Three-dimensional (3D) super-resolution microscopy technique structured illumination microscopy (SIM) imaging of dendritic spines along the dendrite has not been previously performed in fixed tissues, mainly due to deterioration of the stripe pattern of the excitation laser induced by light scattering and optical aberrations. To address this issue and solve these optical problems, we applied a novel clearing reagent, LUCID, to fixed brains. In SIM imaging, the penetration depth and the spatial resolution were improved in LUCID-treated slices, and 160-nm spatial resolution was obtained in a large portion of the imaging volume on a single apical dendrite. Furthermore, in a morphological analysis of spine heads of layer V pyramidal neurons (L5PNs) in the medial prefrontal cortex (mPFC) of chronic dexamethasone (Dex)-treated mice, SIM imaging revealed an altered distribution of spine forms that could not be detected by high-NA confocal imaging. Thus, super-resolution SIM imaging represents a promising high-throughput method for revealing spine morphologies in single dendrites.","lang":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"intvolume":" 47","month":"03","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"98e901d8229e44aa8f3b51d248dedd09","file_id":"5721","file_size":4850261,"date_updated":"2020-07-14T12:46:06Z","creator":"dernst","file_name":"2018_EJN_Sawada.pdf","date_created":"2018-12-17T16:16:50Z"}],"publication_status":"published","volume":47,"issue":"9","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Sawada, Kazuaki, Ryosuke Kawakami, Ryuichi Shigemoto, and Tomomi Nemoto. “Super Resolution Structural Analysis of Dendritic Spines Using Three-Dimensional Structured Illumination Microscopy in Cleared Mouse Brain Slices.” European Journal of Neuroscience. Wiley, 2018. https://doi.org/10.1111/ejn.13901.","ista":"Sawada K, Kawakami R, Shigemoto R, Nemoto T. 2018. Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. European Journal of Neuroscience. 47(9), 1033–1042.","mla":"Sawada, Kazuaki, et al. “Super Resolution Structural Analysis of Dendritic Spines Using Three-Dimensional Structured Illumination Microscopy in Cleared Mouse Brain Slices.” European Journal of Neuroscience, vol. 47, no. 9, Wiley, 2018, pp. 1033–42, doi:10.1111/ejn.13901.","apa":"Sawada, K., Kawakami, R., Shigemoto, R., & Nemoto, T. (2018). Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. European Journal of Neuroscience. Wiley. https://doi.org/10.1111/ejn.13901","ama":"Sawada K, Kawakami R, Shigemoto R, Nemoto T. Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. European Journal of Neuroscience. 2018;47(9):1033-1042. doi:10.1111/ejn.13901","short":"K. Sawada, R. Kawakami, R. Shigemoto, T. Nemoto, European Journal of Neuroscience 47 (2018) 1033–1042.","ieee":"K. Sawada, R. Kawakami, R. Shigemoto, and T. Nemoto, “Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices,” European Journal of Neuroscience, vol. 47, no. 9. Wiley, pp. 1033–1042, 2018."},"title":"Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices","article_processing_charge":"No","external_id":{"isi":["000431496400001"]},"publist_id":"7539","author":[{"last_name":"Sawada","full_name":"Sawada, Kazuaki","first_name":"Kazuaki"},{"last_name":"Kawakami","full_name":"Kawakami, Ryosuke","first_name":"Ryosuke"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nemoto, Tomomi","last_name":"Nemoto","first_name":"Tomomi"}],"oa":1,"quality_controlled":"1","publisher":"Wiley","publication":"European Journal of Neuroscience","day":"07","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:45:50Z","doi":"10.1111/ejn.13901","date_published":"2018-03-07T00:00:00Z","page":"1033 - 1042"},{"external_id":{"pmid":["30478053"],"isi":["000452866000022"]},"article_processing_charge":"No","author":[{"first_name":"Kun","full_name":"Qu, Kun","last_name":"Qu"},{"last_name":"Glass","full_name":"Glass, Bärbel","first_name":"Bärbel"},{"full_name":"Doležal, Michal","last_name":"Doležal","first_name":"Michal"},{"last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian","first_name":"Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Murciano, Brice","last_name":"Murciano","first_name":"Brice"},{"full_name":"Rein, Alan","last_name":"Rein","first_name":"Alan"},{"full_name":"Rumlová, Michaela","last_name":"Rumlová","first_name":"Michaela"},{"last_name":"Ruml","full_name":"Ruml, Tomáš","first_name":"Tomáš"},{"first_name":"Hans-Georg","last_name":"Kräusslich","full_name":"Kräusslich, Hans-Georg"},{"full_name":"Briggs, John A. G.","last_name":"Briggs","first_name":"John A. G."}],"title":"Structure and architecture of immature and mature murine leukemia virus capsids","citation":{"chicago":"Qu, Kun, Bärbel Glass, Michal Doležal, Florian KM Schur, Brice Murciano, Alan Rein, Michaela Rumlová, Tomáš Ruml, Hans-Georg Kräusslich, and John A. G. Briggs. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1811580115.","ista":"Qu K, Glass B, Doležal M, Schur FK, Murciano B, Rein A, Rumlová M, Ruml T, Kräusslich H-G, Briggs JAG. 2018. Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. 115(50), E11751–E11760.","mla":"Qu, Kun, et al. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” Proceedings of the National Academy of Sciences, vol. 115, no. 50, Proceedings of the National Academy of Sciences, 2018, pp. E11751–60, doi:10.1073/pnas.1811580115.","ama":"Qu K, Glass B, Doležal M, et al. Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. 2018;115(50):E11751-E11760. doi:10.1073/pnas.1811580115","apa":"Qu, K., Glass, B., Doležal, M., Schur, F. K., Murciano, B., Rein, A., … Briggs, J. A. G. (2018). Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1811580115","short":"K. Qu, B. Glass, M. Doležal, F.K. Schur, B. Murciano, A. Rein, M. Rumlová, T. Ruml, H.-G. Kräusslich, J.A.G. Briggs, Proceedings of the National Academy of Sciences 115 (2018) E11751–E11760.","ieee":"K. Qu et al., “Structure and architecture of immature and mature murine leukemia virus capsids,” Proceedings of the National Academy of Sciences, vol. 115, no. 50. Proceedings of the National Academy of Sciences, pp. E11751–E11760, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"E11751-E11760","date_created":"2018-12-20T21:09:37Z","doi":"10.1073/pnas.1811580115","date_published":"2018-12-11T00:00:00Z","year":"2018","isi":1,"publication":"Proceedings of the National Academy of Sciences","day":"11","oa":1,"publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","department":[{"_id":"FlSc"}],"date_updated":"2023-09-19T09:57:45Z","type":"journal_article","status":"public","_id":"5770","volume":115,"issue":"50","publication_status":"published","publication_identifier":{"issn":["00278424"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30478053","open_access":"1"}],"scopus_import":"1","intvolume":" 115","month":"12","abstract":[{"lang":"eng","text":"Retroviruses assemble and bud from infected cells in an immature form and require proteolytic maturation for infectivity. The CA (capsid) domains of the Gag polyproteins assemble a protein lattice as a truncated sphere in the immature virion. Proteolytic cleavage of Gag induces dramatic structural rearrangements; a subset of cleaved CA subsequently assembles into the mature core, whose architecture varies among retroviruses. Murine leukemia virus (MLV) is the prototypical γ-retrovirus and serves as the basis of retroviral vectors, but the structure of the MLV CA layer is unknown. Here we have combined X-ray crystallography with cryoelectron tomography to determine the structures of immature and mature MLV CA layers within authentic viral particles. This reveals the structural changes associated with maturation, and, by comparison with HIV-1, uncovers conserved and variable features. In contrast to HIV-1, most MLV CA is used for assembly of the mature core, which adopts variable, multilayered morphologies and does not form a closed structure. Unlike in HIV-1, there is similarity between protein–protein interfaces in the immature MLV CA layer and those in the mature CA layer, and structural maturation of MLV could be achieved through domain rotations that largely maintain hexameric interactions. Nevertheless, the dramatic architectural change on maturation indicates that extensive disassembly and reassembly are required for mature core growth. The core morphology suggests that wrapping of the genome in CA sheets may be sufficient to protect the MLV ribonucleoprotein during cell entry."}],"oa_version":"Submitted Version","pmid":1},{"citation":{"ista":"Avni G, Kupferman O. 2018. Synthesis from component libraries with costs. Theoretical Computer Science. 712, 50–72.","chicago":"Avni, Guy, and Orna Kupferman. “Synthesis from Component Libraries with Costs.” Theoretical Computer Science. Elsevier, 2018. https://doi.org/10.1016/j.tcs.2017.11.001.","apa":"Avni, G., & Kupferman, O. (2018). Synthesis from component libraries with costs. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2017.11.001","ama":"Avni G, Kupferman O. Synthesis from component libraries with costs. Theoretical Computer Science. 2018;712:50-72. doi:10.1016/j.tcs.2017.11.001","ieee":"G. Avni and O. Kupferman, “Synthesis from component libraries with costs,” Theoretical Computer Science, vol. 712. Elsevier, pp. 50–72, 2018.","short":"G. Avni, O. Kupferman, Theoretical Computer Science 712 (2018) 50–72.","mla":"Avni, Guy, and Orna Kupferman. “Synthesis from Component Libraries with Costs.” Theoretical Computer Science, vol. 712, Elsevier, 2018, pp. 50–72, doi:10.1016/j.tcs.2017.11.001."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7197","author":[{"full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","last_name":"Avni","first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Orna","last_name":"Kupferman","full_name":"Kupferman, Orna"}],"article_processing_charge":"No","external_id":{"isi":["000424959200003"]},"title":"Synthesis from component libraries with costs","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"isi":1,"year":"2018","day":"15","publication":"Theoretical Computer Science","page":"50 - 72","doi":"10.1016/j.tcs.2017.11.001","date_published":"2018-02-15T00:00:00Z","date_created":"2018-12-11T11:47:28Z","publisher":"Elsevier","quality_controlled":"1","oa":1,"date_updated":"2023-09-19T10:00:21Z","department":[{"_id":"ToHe"}],"_id":"608","article_type":"original","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":712,"ec_funded":1,"abstract":[{"lang":"eng","text":"Synthesis is the automated construction of a system from its specification. In real life, hardware and software systems are rarely constructed from scratch. Rather, a system is typically constructed from a library of components. Lustig and Vardi formalized this intuition and studied LTL synthesis from component libraries. In real life, designers seek optimal systems. In this paper we add optimality considerations to the setting. We distinguish between quality considerations (for example, size - the smaller a system is, the better it is), and pricing (for example, the payment to the company who manufactured the component). We study the problem of designing systems with minimal quality-cost and price. A key point is that while the quality cost is individual - the choices of a designer are independent of choices made by other designers that use the same library, pricing gives rise to a resource-allocation game - designers that use the same component share its price, with the share being proportional to the number of uses (a component can be used several times in a design). We study both closed and open settings, and in both we solve the problem of finding an optimal design. In a setting with multiple designers, we also study the game-theoretic problems of the induced resource-allocation game."}],"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.636.4529","open_access":"1"}],"month":"02","intvolume":" 712"},{"_id":"705","status":"public","type":"journal_article","date_updated":"2023-09-19T09:58:11Z","department":[{"_id":"RySh"}],"oa_version":"None","abstract":[{"lang":"eng","text":"Although dopamine receptors D1 and D2 play key roles in hippocampal function, their synaptic localization within the hippocampus has not been fully elucidated. In order to understand precise functions of pre- or postsynaptic dopamine receptors (DRs), the development of protocols to differentiate pre- and postsynaptic DRs is essential. So far, most studies on determination and quantification of DRs did not discriminate between subsynaptic localization. Therefore, the aim of the study was to generate a robust workflow for the localization of DRs. This work provides the basis for future work on hippocampal DRs, in light that DRs may have different functions at pre- or postsynaptic sites. Synaptosomes from rat hippocampi isolated by a sucrose gradient protocol were prepared for super-resolution direct stochastic optical reconstruction microscopy (dSTORM) using Bassoon as a presynaptic zone and Homer1 as postsynaptic density marker. Direct labeling of primary validated antibodies against dopamine receptors D1 (D1R) and D2 (D2R) with Alexa Fluor 594 enabled unequivocal assignment of D1R and D2R to both, pre- and postsynaptic sites. D1R immunoreactivity clusters were observed within the presynaptic active zone as well as at perisynaptic sites at the edge of the presynaptic active zone. The results may be useful for the interpretation of previous studies and the design of future work on DRs in the hippocampus. Moreover, the reduction of the complexity of brain tissue by the use of synaptosomal preparations and dSTORM technology may represent a useful tool for synaptic localization of brain proteins."}],"intvolume":" 55","month":"06","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","volume":55,"issue":"6","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"A. Miklosi, G. Del Favero, T. Bulat, H. Höger, R. Shigemoto, D. Marko, G. Lubec, Molecular Neurobiology 55 (2018) 4857 – 4869.","ieee":"A. Miklosi et al., “Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes,” Molecular Neurobiology, vol. 55, no. 6. Springer, pp. 4857 – 4869, 2018.","ama":"Miklosi A, Del Favero G, Bulat T, et al. Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. Molecular Neurobiology. 2018;55(6):4857 – 4869. doi:10.1007/s12035-017-0688-y","apa":"Miklosi, A., Del Favero, G., Bulat, T., Höger, H., Shigemoto, R., Marko, D., & Lubec, G. (2018). Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. Molecular Neurobiology. Springer. https://doi.org/10.1007/s12035-017-0688-y","mla":"Miklosi, Andras, et al. “Super Resolution Microscopical Localization of Dopamine Receptors 1 and 2 in Rat Hippocampal Synaptosomes.” Molecular Neurobiology, vol. 55, no. 6, Springer, 2018, pp. 4857 – 4869, doi:10.1007/s12035-017-0688-y.","ista":"Miklosi A, Del Favero G, Bulat T, Höger H, Shigemoto R, Marko D, Lubec G. 2018. Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. Molecular Neurobiology. 55(6), 4857 – 4869.","chicago":"Miklosi, Andras, Giorgia Del Favero, Tanja Bulat, Harald Höger, Ryuichi Shigemoto, Doris Marko, and Gert Lubec. “Super Resolution Microscopical Localization of Dopamine Receptors 1 and 2 in Rat Hippocampal Synaptosomes.” Molecular Neurobiology. Springer, 2018. https://doi.org/10.1007/s12035-017-0688-y."},"title":"Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes","article_processing_charge":"No","external_id":{"isi":["000431991500025"]},"author":[{"first_name":"Andras","full_name":"Miklosi, Andras","last_name":"Miklosi"},{"full_name":"Del Favero, Giorgia","last_name":"Del Favero","first_name":"Giorgia"},{"first_name":"Tanja","full_name":"Bulat, Tanja","last_name":"Bulat"},{"first_name":"Harald","full_name":"Höger, Harald","last_name":"Höger"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444"},{"first_name":"Doris","last_name":"Marko","full_name":"Marko, Doris"},{"first_name":"Gert","full_name":"Lubec, Gert","last_name":"Lubec"}],"publist_id":"6991","quality_controlled":"1","publisher":"Springer","publication":"Molecular Neurobiology","day":"01","year":"2018","isi":1,"date_created":"2018-12-11T11:48:02Z","doi":"10.1007/s12035-017-0688-y","date_published":"2018-06-01T00:00:00Z","page":"4857 – 4869"},{"publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":174,"issue":"2","abstract":[{"text":"Land plants evolved from charophytic algae, among which Charophyceae possess the most complex body plans. We present the genome of Chara braunii; comparison of the genome to those of land plants identified evolutionary novelties for plant terrestrialization and land plant heritage genes. C. braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C. braunii plastids are controlled via land-plant-like retrograde signaling, and transcriptional regulation is more elaborate than in other algae. The morphological complexity of this organism may result from expanded gene families, with three cases of particular note: genes effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases, and transcription factors (TFs). Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30007417"}],"scopus_import":"1","intvolume":" 174","month":"07","date_updated":"2023-09-19T10:02:47Z","department":[{"_id":"JiFr"}],"_id":"148","type":"journal_article","status":"public","year":"2018","isi":1,"publication":"Cell","day":"12","page":"448 - 464.e24","date_created":"2018-12-11T11:44:53Z","date_published":"2018-07-12T00:00:00Z","doi":"10.1016/j.cell.2018.06.033","acknowledgement":"In-Data-Review","oa":1,"quality_controlled":"1","publisher":"Cell Press","citation":{"mla":"Nishiyama, Tomoaki, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” Cell, vol. 174, no. 2, Cell Press, 2018, p. 448–464.e24, doi:10.1016/j.cell.2018.06.033.","apa":"Nishiyama, T., Sakayama, H., De Vries, J., Buschmann, H., Saint Marcoux, D., Ullrich, K., … Rensing, S. (2018). The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. Cell Press. https://doi.org/10.1016/j.cell.2018.06.033","ama":"Nishiyama T, Sakayama H, De Vries J, et al. The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. 2018;174(2):448-464.e24. doi:10.1016/j.cell.2018.06.033","short":"T. Nishiyama, H. Sakayama, J. De Vries, H. Buschmann, D. Saint Marcoux, K. Ullrich, F. Haas, L. Vanderstraeten, D. Becker, D. Lang, S. Vosolsobě, S. Rombauts, P. Wilhelmsson, P. Janitza, R. Kern, A. Heyl, F. Rümpler, L. Calderón Villalobos, J. Clay, R. Skokan, A. Toyoda, Y. Suzuki, H. Kagoshima, E. Schijlen, N. Tajeshwar, B. Catarino, A. Hetherington, A. Saltykova, C. Bonnot, H. Breuninger, A. Symeonidi, G. Radhakrishnan, F. Van Nieuwerburgh, D. Deforce, C. Chang, K. Karol, R. Hedrich, P. Ulvskov, G. Glöckner, C. Delwiche, J. Petrášek, Y. Van De Peer, J. Friml, M. Beilby, L. Dolan, Y. Kohara, S. Sugano, A. Fujiyama, P.M. Delaux, M. Quint, G. Theissen, M. Hagemann, J. Harholt, C. Dunand, S. Zachgo, J. Langdale, F. Maumus, D. Van Der Straeten, S.B. Gould, S. Rensing, Cell 174 (2018) 448–464.e24.","ieee":"T. Nishiyama et al., “The Chara genome: Secondary complexity and implications for plant terrestrialization,” Cell, vol. 174, no. 2. Cell Press, p. 448–464.e24, 2018.","chicago":"Nishiyama, Tomoaki, Hidetoshi Sakayama, Jan De Vries, Henrik Buschmann, Denis Saint Marcoux, Kristian Ullrich, Fabian Haas, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” Cell. Cell Press, 2018. https://doi.org/10.1016/j.cell.2018.06.033.","ista":"Nishiyama T, Sakayama H, De Vries J, Buschmann H, Saint Marcoux D, Ullrich K, Haas F, Vanderstraeten L, Becker D, Lang D, Vosolsobě S, Rombauts S, Wilhelmsson P, Janitza P, Kern R, Heyl A, Rümpler F, Calderón Villalobos L, Clay J, Skokan R, Toyoda A, Suzuki Y, Kagoshima H, Schijlen E, Tajeshwar N, Catarino B, Hetherington A, Saltykova A, Bonnot C, Breuninger H, Symeonidi A, Radhakrishnan G, Van Nieuwerburgh F, Deforce D, Chang C, Karol K, Hedrich R, Ulvskov P, Glöckner G, Delwiche C, Petrášek J, Van De Peer Y, Friml J, Beilby M, Dolan L, Kohara Y, Sugano S, Fujiyama A, Delaux PM, Quint M, Theissen G, Hagemann M, Harholt J, Dunand C, Zachgo S, Langdale J, Maumus F, Van Der Straeten D, Gould SB, Rensing S. 2018. The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. 174(2), 448–464.e24."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000438482800019"],"pmid":["30007417"]},"article_processing_charge":"No","publist_id":"7774","author":[{"first_name":"Tomoaki","full_name":"Nishiyama, Tomoaki","last_name":"Nishiyama"},{"full_name":"Sakayama, Hidetoshi","last_name":"Sakayama","first_name":"Hidetoshi"},{"full_name":"De Vries, Jan","last_name":"De Vries","first_name":"Jan"},{"last_name":"Buschmann","full_name":"Buschmann, Henrik","first_name":"Henrik"},{"first_name":"Denis","last_name":"Saint Marcoux","full_name":"Saint Marcoux, Denis"},{"first_name":"Kristian","full_name":"Ullrich, Kristian","last_name":"Ullrich"},{"first_name":"Fabian","last_name":"Haas","full_name":"Haas, Fabian"},{"first_name":"Lisa","full_name":"Vanderstraeten, Lisa","last_name":"Vanderstraeten"},{"last_name":"Becker","full_name":"Becker, Dirk","first_name":"Dirk"},{"first_name":"Daniel","full_name":"Lang, Daniel","last_name":"Lang"},{"full_name":"Vosolsobě, Stanislav","last_name":"Vosolsobě","first_name":"Stanislav"},{"full_name":"Rombauts, Stephane","last_name":"Rombauts","first_name":"Stephane"},{"first_name":"Per","last_name":"Wilhelmsson","full_name":"Wilhelmsson, Per"},{"first_name":"Philipp","last_name":"Janitza","full_name":"Janitza, Philipp"},{"last_name":"Kern","full_name":"Kern, Ramona","first_name":"Ramona"},{"last_name":"Heyl","full_name":"Heyl, Alexander","first_name":"Alexander"},{"full_name":"Rümpler, Florian","last_name":"Rümpler","first_name":"Florian"},{"last_name":"Calderón Villalobos","full_name":"Calderón Villalobos, Luz","first_name":"Luz"},{"first_name":"John","full_name":"Clay, John","last_name":"Clay"},{"last_name":"Skokan","full_name":"Skokan, Roman","first_name":"Roman"},{"first_name":"Atsushi","full_name":"Toyoda, Atsushi","last_name":"Toyoda"},{"first_name":"Yutaka","last_name":"Suzuki","full_name":"Suzuki, Yutaka"},{"last_name":"Kagoshima","full_name":"Kagoshima, Hiroshi","first_name":"Hiroshi"},{"full_name":"Schijlen, Elio","last_name":"Schijlen","first_name":"Elio"},{"first_name":"Navindra","full_name":"Tajeshwar, Navindra","last_name":"Tajeshwar"},{"full_name":"Catarino, Bruno","last_name":"Catarino","first_name":"Bruno"},{"full_name":"Hetherington, Alexander","last_name":"Hetherington","first_name":"Alexander"},{"full_name":"Saltykova, Assia","last_name":"Saltykova","first_name":"Assia"},{"first_name":"Clemence","last_name":"Bonnot","full_name":"Bonnot, Clemence"},{"full_name":"Breuninger, Holger","last_name":"Breuninger","first_name":"Holger"},{"last_name":"Symeonidi","full_name":"Symeonidi, Aikaterini","first_name":"Aikaterini"},{"first_name":"Guru","last_name":"Radhakrishnan","full_name":"Radhakrishnan, Guru"},{"first_name":"Filip","last_name":"Van Nieuwerburgh","full_name":"Van Nieuwerburgh, Filip"},{"first_name":"Dieter","last_name":"Deforce","full_name":"Deforce, Dieter"},{"first_name":"Caren","last_name":"Chang","full_name":"Chang, Caren"},{"first_name":"Kenneth","full_name":"Karol, Kenneth","last_name":"Karol"},{"last_name":"Hedrich","full_name":"Hedrich, Rainer","first_name":"Rainer"},{"first_name":"Peter","full_name":"Ulvskov, Peter","last_name":"Ulvskov"},{"last_name":"Glöckner","full_name":"Glöckner, Gernot","first_name":"Gernot"},{"first_name":"Charles","full_name":"Delwiche, Charles","last_name":"Delwiche"},{"last_name":"Petrášek","full_name":"Petrášek, Jan","first_name":"Jan"},{"first_name":"Yves","last_name":"Van De Peer","full_name":"Van De Peer, Yves"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"full_name":"Beilby, Mary","last_name":"Beilby","first_name":"Mary"},{"last_name":"Dolan","full_name":"Dolan, Liam","first_name":"Liam"},{"full_name":"Kohara, Yuji","last_name":"Kohara","first_name":"Yuji"},{"first_name":"Sumio","full_name":"Sugano, Sumio","last_name":"Sugano"},{"first_name":"Asao","full_name":"Fujiyama, Asao","last_name":"Fujiyama"},{"full_name":"Delaux, Pierre Marc","last_name":"Delaux","first_name":"Pierre Marc"},{"first_name":"Marcel","last_name":"Quint","full_name":"Quint, Marcel"},{"full_name":"Theissen, Gunter","last_name":"Theissen","first_name":"Gunter"},{"last_name":"Hagemann","full_name":"Hagemann, Martin","first_name":"Martin"},{"first_name":"Jesper","full_name":"Harholt, Jesper","last_name":"Harholt"},{"first_name":"Christophe","full_name":"Dunand, Christophe","last_name":"Dunand"},{"first_name":"Sabine","full_name":"Zachgo, Sabine","last_name":"Zachgo"},{"first_name":"Jane","last_name":"Langdale","full_name":"Langdale, Jane"},{"last_name":"Maumus","full_name":"Maumus, Florian","first_name":"Florian"},{"first_name":"Dominique","last_name":"Van Der Straeten","full_name":"Van Der Straeten, Dominique"},{"last_name":"Gould","full_name":"Gould, Sven B","first_name":"Sven B"},{"first_name":"Stefan","full_name":"Rensing, Stefan","last_name":"Rensing"}],"title":"The Chara genome: Secondary complexity and implications for plant terrestrialization","project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985"}]},{"date_updated":"2023-09-19T10:07:08Z","ddc":["580"],"file_date_updated":"2020-07-14T12:46:22Z","department":[{"_id":"EvBe"}],"_id":"403","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_status":"published","file":[{"file_size":1543354,"date_updated":"2020-07-14T12:46:22Z","creator":"dernst","file_name":"2018_PlantJourn_Cavallari.pdf","date_created":"2019-02-06T11:40:54Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"d9d3ad3215ac0e581731443fca312266","file_id":"5934"}],"language":[{"iso":"eng"}],"volume":94,"issue":"6","abstract":[{"lang":"eng","text":"The ability to adapt growth and development to temperature variations is crucial to generate plant varieties resilient to predicted temperature changes. However, the mechanisms underlying plant response to progressive increases in temperature have just started to be elucidated. Here, we report that the Cyclin-dependent Kinase G1 (CDKG1) is a central element in a thermo-sensitive mRNA splicing cascade that transduces changes in ambient temperature into differential expression of the fundamental spliceosome component, ATU2AF65A. CDKG1 is alternatively spliced in a temperature-dependent manner. We found that this process is partly dependent on both the Cyclin-dependent Kinase G2 (CDKG2) and the interacting co-factor CYCLIN L1 resulting in two distinct messenger RNAs. Relative abundance of both CDKG1 transcripts correlates with ambient temperature and possibly with different expression levels of the associated protein isoforms. Both CDKG1 alternative transcripts are necessary to fully complement the expression of ATU2AF65A across the temperature range. Our data support a previously unidentified temperature-dependent mechanism based on the alternative splicing of CDKG1 and regulated by CDKG2 and CYCLIN L1. We propose that changes in ambient temperature affect the relative abundance of CDKG1 transcripts and this in turn translates into differential CDKG1 protein expression coordinating the alternative splicing of ATU2AF65A. This article is protected by copyright. All rights reserved."}],"oa_version":"Published Version","scopus_import":"1","month":"06","intvolume":" 94","citation":{"ama":"Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan J. The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. 2018;94(6):1010-1022. doi:10.1111/tpj.13914","apa":"Cavallari, N., Nibau, C., Fuchs, A., Dadarou, D., Barta, A., & Doonan, J. (2018). The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. Wiley. https://doi.org/10.1111/tpj.13914","short":"N. Cavallari, C. Nibau, A. Fuchs, D. Dadarou, A. Barta, J. Doonan, The Plant Journal 94 (2018) 1010–1022.","ieee":"N. Cavallari, C. Nibau, A. Fuchs, D. Dadarou, A. Barta, and J. Doonan, “The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A,” The Plant Journal, vol. 94, no. 6. Wiley, pp. 1010–1022, 2018.","mla":"Cavallari, Nicola, et al. “The Cyclin‐dependent Kinase G Group Defines a Thermo‐sensitive Alternative Splicing Circuit Modulating the Expression of Arabidopsis ATU 2AF 65A.” The Plant Journal, vol. 94, no. 6, Wiley, 2018, pp. 1010–22, doi:10.1111/tpj.13914.","ista":"Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan J. 2018. The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. 94(6), 1010–1022.","chicago":"Cavallari, Nicola, Candida Nibau, Armin Fuchs, Despoina Dadarou, Andrea Barta, and John Doonan. “The Cyclin‐dependent Kinase G Group Defines a Thermo‐sensitive Alternative Splicing Circuit Modulating the Expression of Arabidopsis ATU 2AF 65A.” The Plant Journal. Wiley, 2018. https://doi.org/10.1111/tpj.13914."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola","full_name":"Cavallari, Nicola","last_name":"Cavallari"},{"first_name":"Candida","last_name":"Nibau","full_name":"Nibau, Candida"},{"last_name":"Fuchs","full_name":"Fuchs, Armin","first_name":"Armin"},{"first_name":"Despoina","last_name":"Dadarou","full_name":"Dadarou, Despoina"},{"first_name":"Andrea","last_name":"Barta","full_name":"Barta, Andrea"},{"full_name":"Doonan, John","last_name":"Doonan","first_name":"John"}],"publist_id":"7426","article_processing_charge":"No","external_id":{"isi":["000434365500008"]},"title":"The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A","isi":1,"has_accepted_license":"1","year":"2018","day":"01","publication":"The Plant Journal","page":"1010 - 1022","doi":"10.1111/tpj.13914","date_published":"2018-06-01T00:00:00Z","date_created":"2018-12-11T11:46:17Z","acknowledgement":"CN, DD and JHD were funded by the BBSRC (grant number BB/M009459/1). NC was funded by the VIPS Program of the Austrian Federal Ministry of Science and Research and the City of Vienna. AB and AF were supported by the Austrian Science Fund (FWF) [DK W1207; SFB RNAreg F43-P10]","publisher":"Wiley","quality_controlled":"1","oa":1}]