[{"month":"09","author":[{"orcid":"0000-0003-1109-5511","full_name":"Virosztek, Daniel","first_name":"Daniel","last_name":"Virosztek","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87"}],"article_type":"original","arxiv":1,"citation":{"ista":"Virosztek D. 2019. Jointly convex quantum Jensen divergences. Linear Algebra and Its Applications. 576, 67–78.","apa":"Virosztek, D. (2019). Jointly convex quantum Jensen divergences. <i>Linear Algebra and Its Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.laa.2018.03.002\">https://doi.org/10.1016/j.laa.2018.03.002</a>","ama":"Virosztek D. Jointly convex quantum Jensen divergences. <i>Linear Algebra and Its Applications</i>. 2019;576:67-78. doi:<a href=\"https://doi.org/10.1016/j.laa.2018.03.002\">10.1016/j.laa.2018.03.002</a>","mla":"Virosztek, Daniel. “Jointly Convex Quantum Jensen Divergences.” <i>Linear Algebra and Its Applications</i>, vol. 576, Elsevier, 2019, pp. 67–78, doi:<a href=\"https://doi.org/10.1016/j.laa.2018.03.002\">10.1016/j.laa.2018.03.002</a>.","short":"D. Virosztek, Linear Algebra and Its Applications 576 (2019) 67–78.","chicago":"Virosztek, Daniel. “Jointly Convex Quantum Jensen Divergences.” <i>Linear Algebra and Its Applications</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.laa.2018.03.002\">https://doi.org/10.1016/j.laa.2018.03.002</a>.","ieee":"D. Virosztek, “Jointly convex quantum Jensen divergences,” <i>Linear Algebra and Its Applications</i>, vol. 576. Elsevier, pp. 67–78, 2019."},"page":"67-78","acknowledgement":"The author was supported by the ISTFELLOW program of the Institute of Science and Technology Austria (project code IC1027FELL01) and partially supported by the Hungarian National Research, Development and Innovation Office – NKFIH (grant no. K124152)","language":[{"iso":"eng"}],"_id":"405","title":"Jointly convex quantum Jensen divergences","doi":"10.1016/j.laa.2018.03.002","isi":1,"external_id":{"isi":["000470955300005"],"arxiv":["1712.05324"]},"day":"01","date_updated":"2023-08-24T14:31:47Z","ec_funded":1,"year":"2019","article_processing_charge":"No","oa":1,"oa_version":"Preprint","scopus_import":"1","date_created":"2018-12-11T11:46:17Z","abstract":[{"lang":"eng","text":"We investigate the quantum Jensen divergences from the viewpoint of joint convexity. It turns out that the set of the functions which generate jointly convex quantum Jensen divergences on positive matrices coincides with the Matrix Entropy Class which has been introduced by Chen and Tropp quite recently."}],"status":"public","date_published":"2019-09-01T00:00:00Z","publication":"Linear Algebra and Its Applications","publist_id":"7424","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"       576","department":[{"_id":"LaEr"}],"project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"}],"quality_controlled":"1","publication_status":"published","publisher":"Elsevier","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.05324"}],"volume":576,"type":"journal_article"},{"publisher":"Springer","publication_status":"published","project":[{"call_identifier":"FP7","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"quality_controlled":"1","department":[{"_id":"LaEr"}],"volume":173,"type":"journal_article","date_created":"2018-12-11T11:46:25Z","scopus_import":"1","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"license":"https://creativecommons.org/licenses/by/4.0/","intvolume":"       173","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","date_published":"2019-02-01T00:00:00Z","publist_id":"7394","publication":"Probability Theory and Related Fields","abstract":[{"lang":"eng","text":"We consider real symmetric or complex hermitian random matrices with correlated entries. We prove local laws for the resolvent and universality of the local eigenvalue statistics in the bulk of the spectrum. The correlations have fast decay but are otherwise of general form. The key novelty is the detailed stability analysis of the corresponding matrix valued Dyson equation whose solution is the deterministic limit of the resolvent."}],"date_updated":"2023-08-24T14:39:00Z","publication_identifier":{"issn":["01788051"],"eissn":["14322064"]},"day":"01","isi":1,"external_id":{"isi":["000459396500007"]},"title":"Stability of the matrix Dyson equation and random matrices with correlations","doi":"10.1007/s00440-018-0835-z","oa":1,"article_processing_charge":"Yes (via OA deal)","ec_funded":1,"year":"2019","has_accepted_license":"1","citation":{"ieee":"O. H. Ajanki, L. Erdös, and T. H. Krüger, “Stability of the matrix Dyson equation and random matrices with correlations,” <i>Probability Theory and Related Fields</i>, vol. 173, no. 1–2. Springer, pp. 293–373, 2019.","chicago":"Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Stability of the Matrix Dyson Equation and Random Matrices with Correlations.” <i>Probability Theory and Related Fields</i>. Springer, 2019. <a href=\"https://doi.org/10.1007/s00440-018-0835-z\">https://doi.org/10.1007/s00440-018-0835-z</a>.","mla":"Ajanki, Oskari H., et al. “Stability of the Matrix Dyson Equation and Random Matrices with Correlations.” <i>Probability Theory and Related Fields</i>, vol. 173, no. 1–2, Springer, 2019, pp. 293–373, doi:<a href=\"https://doi.org/10.1007/s00440-018-0835-z\">10.1007/s00440-018-0835-z</a>.","short":"O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields 173 (2019) 293–373.","ama":"Ajanki OH, Erdös L, Krüger TH. Stability of the matrix Dyson equation and random matrices with correlations. <i>Probability Theory and Related Fields</i>. 2019;173(1-2):293–373. doi:<a href=\"https://doi.org/10.1007/s00440-018-0835-z\">10.1007/s00440-018-0835-z</a>","apa":"Ajanki, O. H., Erdös, L., &#38; Krüger, T. H. (2019). Stability of the matrix Dyson equation and random matrices with correlations. <i>Probability Theory and Related Fields</i>. Springer. <a href=\"https://doi.org/10.1007/s00440-018-0835-z\">https://doi.org/10.1007/s00440-018-0835-z</a>","ista":"Ajanki OH, Erdös L, Krüger TH. 2019. Stability of the matrix Dyson equation and random matrices with correlations. Probability Theory and Related Fields. 173(1–2), 293–373."},"ddc":["510"],"article_type":"original","month":"02","file_date_updated":"2020-07-14T12:46:26Z","file":[{"access_level":"open_access","date_updated":"2020-07-14T12:46:26Z","date_created":"2018-12-17T16:12:08Z","file_size":1201840,"file_id":"5720","relation":"main_file","file_name":"2018_ProbTheory_Ajanki.pdf","checksum":"f9354fa5c71f9edd17132588f0dc7d01","creator":"dernst","content_type":"application/pdf"}],"author":[{"full_name":"Ajanki, Oskari H","id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87","first_name":"Oskari H","last_name":"Ajanki"},{"last_name":"Erdös","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","first_name":"Torben H","last_name":"Krüger"}],"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).\r\n","language":[{"iso":"eng"}],"_id":"429","issue":"1-2","page":"293–373"},{"language":[{"iso":"eng"}],"_id":"439","page":"2995-3052","issue":"10","article_type":"original","arxiv":1,"citation":{"mla":"Hausel, Tamás, et al. “Arithmetic and Representation Theory of Wild Character Varieties.” <i>Journal of the European Mathematical Society</i>, vol. 21, no. 10, European Mathematical Society, 2019, pp. 2995–3052, doi:<a href=\"https://doi.org/10.4171/JEMS/896\">10.4171/JEMS/896</a>.","short":"T. Hausel, M. Mereb, M. Wong, Journal of the European Mathematical Society 21 (2019) 2995–3052.","ieee":"T. Hausel, M. Mereb, and M. Wong, “Arithmetic and representation theory of wild character varieties,” <i>Journal of the European Mathematical Society</i>, vol. 21, no. 10. European Mathematical Society, pp. 2995–3052, 2019.","chicago":"Hausel, Tamás, Martin Mereb, and Michael Wong. “Arithmetic and Representation Theory of Wild Character Varieties.” <i>Journal of the European Mathematical Society</i>. European Mathematical Society, 2019. <a href=\"https://doi.org/10.4171/JEMS/896\">https://doi.org/10.4171/JEMS/896</a>.","apa":"Hausel, T., Mereb, M., &#38; Wong, M. (2019). Arithmetic and representation theory of wild character varieties. <i>Journal of the European Mathematical Society</i>. European Mathematical Society. <a href=\"https://doi.org/10.4171/JEMS/896\">https://doi.org/10.4171/JEMS/896</a>","ista":"Hausel T, Mereb M, Wong M. 2019. Arithmetic and representation theory of wild character varieties. Journal of the European Mathematical Society. 21(10), 2995–3052.","ama":"Hausel T, Mereb M, Wong M. Arithmetic and representation theory of wild character varieties. <i>Journal of the European Mathematical Society</i>. 2019;21(10):2995-3052. doi:<a href=\"https://doi.org/10.4171/JEMS/896\">10.4171/JEMS/896</a>"},"author":[{"full_name":"Hausel, Tamas","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel","first_name":"Tamas"},{"first_name":"Martin","last_name":"Mereb","id":"43D735EE-F248-11E8-B48F-1D18A9856A87","full_name":"Mereb, Martin"},{"first_name":"Michael","last_name":"Wong","full_name":"Wong, Michael"}],"month":"10","oa":1,"article_processing_charge":"No","ec_funded":1,"year":"2019","day":"01","publication_identifier":{"eissn":["1435-9855"]},"date_updated":"2023-08-24T14:24:49Z","doi":"10.4171/JEMS/896","title":"Arithmetic and representation theory of wild character varieties","external_id":{"arxiv":["1604.03382"],"isi":["000480413600002"]},"isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"        21","abstract":[{"text":"We count points over a finite field on wild character varieties,of Riemann surfaces for singularities with regular semisimple leading term. The new feature in our counting formulas is the appearance of characters of Yokonuma–Hecke algebras. Our result leads to the conjecture that the mixed Hodge polynomials of these character varieties agree with previously conjectured perverse Hodge polynomials of certain twisted parabolic Higgs moduli spaces, indicating the\r\npossibility of a P = W conjecture for a suitable wild Hitchin system.","lang":"eng"}],"publist_id":"7384","publication":"Journal of the European Mathematical Society","status":"public","date_published":"2019-10-01T00:00:00Z","scopus_import":"1","date_created":"2018-12-11T11:46:29Z","oa_version":"Preprint","type":"journal_article","volume":21,"main_file_link":[{"url":"https://arxiv.org/abs/1604.03382","open_access":"1"}],"publication_status":"published","publisher":"European Mathematical Society","department":[{"_id":"TaHa"}],"quality_controlled":"1","project":[{"name":"Arithmetic and physics of Higgs moduli spaces","_id":"25E549F4-B435-11E9-9278-68D0E5697425","grant_number":"320593","call_identifier":"FP7"}]},{"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","intvolume":"         5","date_published":"2019-09-15T00:00:00Z","status":"public","publist_id":"7382","publication":"European Journal of Mathematics","scopus_import":1,"date_created":"2018-12-11T11:46:29Z","oa_version":"Preprint","volume":5,"type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1711.02089","open_access":"1"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"TaHa"}],"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","language":[{"iso":"eng"}],"_id":"441","page":"909–928","issue":"3","article_type":"original","arxiv":1,"citation":{"ieee":"N. Kalinin and M. Shkolnikov, “Tropical formulae for summation over a part of SL(2,Z),” <i>European Journal of Mathematics</i>, vol. 5, no. 3. Springer Nature, pp. 909–928, 2019.","chicago":"Kalinin, Nikita, and Mikhail Shkolnikov. “Tropical Formulae for Summation over a Part of SL(2,Z).” <i>European Journal of Mathematics</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/s40879-018-0218-0\">https://doi.org/10.1007/s40879-018-0218-0</a>.","short":"N. Kalinin, M. Shkolnikov, European Journal of Mathematics 5 (2019) 909–928.","mla":"Kalinin, Nikita, and Mikhail Shkolnikov. “Tropical Formulae for Summation over a Part of SL(2,Z).” <i>European Journal of Mathematics</i>, vol. 5, no. 3, Springer Nature, 2019, pp. 909–928, doi:<a href=\"https://doi.org/10.1007/s40879-018-0218-0\">10.1007/s40879-018-0218-0</a>.","ama":"Kalinin N, Shkolnikov M. Tropical formulae for summation over a part of SL(2,Z). <i>European Journal of Mathematics</i>. 2019;5(3):909–928. doi:<a href=\"https://doi.org/10.1007/s40879-018-0218-0\">10.1007/s40879-018-0218-0</a>","apa":"Kalinin, N., &#38; Shkolnikov, M. (2019). Tropical formulae for summation over a part of SL(2,Z). <i>European Journal of Mathematics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s40879-018-0218-0\">https://doi.org/10.1007/s40879-018-0218-0</a>","ista":"Kalinin N, Shkolnikov M. 2019. Tropical formulae for summation over a part of SL(2,Z). European Journal of Mathematics. 5(3), 909–928."},"month":"09","author":[{"last_name":"Kalinin","first_name":"Nikita","full_name":"Kalinin, Nikita"},{"id":"35084A62-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Shkolnikov","orcid":"0000-0002-4310-178X","full_name":"Shkolnikov, Mikhail"}],"article_processing_charge":"No","oa":1,"ec_funded":1,"year":"2019","publication_identifier":{"issn":["2199-675X"],"eissn":["2199-6768"]},"day":"15","date_updated":"2021-01-12T07:56:46Z","title":"Tropical formulae for summation over a part of SL(2,Z)","doi":"10.1007/s40879-018-0218-0","external_id":{"arxiv":["1711.02089"]}},{"file_date_updated":"2020-07-14T12:46:35Z","month":"06","author":[{"first_name":"Iordan V","last_name":"Ganev","id":"447491B8-F248-11E8-B48F-1D18A9856A87","full_name":"Ganev, Iordan V"}],"file":[{"file_id":"7238","file_size":431754,"date_updated":"2020-07-14T12:46:35Z","date_created":"2020-01-07T13:31:53Z","access_level":"open_access","content_type":"application/pdf","checksum":"1be56239b2cd740a0e9a084f773c22f6","creator":"kschuh","relation":"main_file","file_name":"2019_Wiley_Ganev.pdf"}],"citation":{"short":"I.V. Ganev, Journal of the London Mathematical Society 99 (2019) 778–806.","mla":"Ganev, Iordan V. “The Wonderful Compactification for Quantum Groups.” <i>Journal of the London Mathematical Society</i>, vol. 99, no. 3, Wiley, 2019, pp. 778–806, doi:<a href=\"https://doi.org/10.1112/jlms.12193\">10.1112/jlms.12193</a>.","chicago":"Ganev, Iordan V. “The Wonderful Compactification for Quantum Groups.” <i>Journal of the London Mathematical Society</i>. Wiley, 2019. <a href=\"https://doi.org/10.1112/jlms.12193\">https://doi.org/10.1112/jlms.12193</a>.","ieee":"I. V. Ganev, “The wonderful compactification for quantum groups,” <i>Journal of the London Mathematical Society</i>, vol. 99, no. 3. Wiley, pp. 778–806, 2019.","ista":"Ganev IV. 2019. The wonderful compactification for quantum groups. Journal of the London Mathematical Society. 99(3), 778–806.","apa":"Ganev, I. V. (2019). The wonderful compactification for quantum groups. <i>Journal of the London Mathematical Society</i>. Wiley. <a href=\"https://doi.org/10.1112/jlms.12193\">https://doi.org/10.1112/jlms.12193</a>","ama":"Ganev IV. The wonderful compactification for quantum groups. <i>Journal of the London Mathematical Society</i>. 2019;99(3):778-806. doi:<a href=\"https://doi.org/10.1112/jlms.12193\">10.1112/jlms.12193</a>"},"ddc":["510"],"issue":"3","page":"778-806","language":[{"iso":"eng"}],"_id":"5","isi":1,"external_id":{"isi":["000470025900008"]},"title":"The wonderful compactification for quantum groups","doi":"10.1112/jlms.12193","date_updated":"2023-09-19T10:13:08Z","day":"01","year":"2019","has_accepted_license":"1","oa":1,"article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","date_created":"2018-12-11T11:44:06Z","scopus_import":"1","date_published":"2019-06-01T00:00:00Z","status":"public","publication":"Journal of the London Mathematical Society","publist_id":"8052","abstract":[{"text":"In this paper, we introduce a quantum version of the wonderful compactification of a group as a certain noncommutative projective scheme. Our approach stems from the fact that the wonderful compactification encodes the asymptotics of matrix coefficients, and from its realization as a GIT quotient of the Vinberg semigroup. In order to define the wonderful compactification for a quantum group, we adopt a generalized formalism of Proj categories in the spirit of Artin and Zhang. Key to our construction is a quantum version of the Vinberg semigroup, which we define as a q-deformation of a certain Rees algebra, compatible with a standard Poisson structure. Furthermore, we discuss quantum analogues of the stratification of the wonderful compactification by orbits for a certain group action, and provide explicit computations in the case of SL2.","lang":"eng"}],"intvolume":"        99","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","department":[{"_id":"TaHa"}],"publisher":"Wiley","publication_status":"published","volume":99,"type":"journal_article"},{"day":"01","date_updated":"2021-01-12T06:49:09Z","title":"Infinite-dimensional calculus under weak spatial regularity of the processes","doi":"10.1007/s10959-016-0724-2","oa":1,"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","year":"2018","citation":{"chicago":"Flandoli, Franco, Francesco Russo, and Giovanni A Zanco. “Infinite-Dimensional Calculus under Weak Spatial Regularity of the Processes.” <i>Journal of Theoretical Probability</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s10959-016-0724-2\">https://doi.org/10.1007/s10959-016-0724-2</a>.","ieee":"F. Flandoli, F. Russo, and G. A. Zanco, “Infinite-dimensional calculus under weak spatial regularity of the processes,” <i>Journal of Theoretical Probability</i>, vol. 31, no. 2. Springer, pp. 789–826, 2018.","mla":"Flandoli, Franco, et al. “Infinite-Dimensional Calculus under Weak Spatial Regularity of the Processes.” <i>Journal of Theoretical Probability</i>, vol. 31, no. 2, Springer, 2018, pp. 789–826, doi:<a href=\"https://doi.org/10.1007/s10959-016-0724-2\">10.1007/s10959-016-0724-2</a>.","short":"F. Flandoli, F. Russo, G.A. Zanco, Journal of Theoretical Probability 31 (2018) 789–826.","ama":"Flandoli F, Russo F, Zanco GA. Infinite-dimensional calculus under weak spatial regularity of the processes. <i>Journal of Theoretical Probability</i>. 2018;31(2):789-826. doi:<a href=\"https://doi.org/10.1007/s10959-016-0724-2\">10.1007/s10959-016-0724-2</a>","ista":"Flandoli F, Russo F, Zanco GA. 2018. Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. 31(2), 789–826.","apa":"Flandoli, F., Russo, F., &#38; Zanco, G. A. (2018). Infinite-dimensional calculus under weak spatial regularity of the processes. <i>Journal of Theoretical Probability</i>. Springer. <a href=\"https://doi.org/10.1007/s10959-016-0724-2\">https://doi.org/10.1007/s10959-016-0724-2</a>"},"ddc":["519"],"month":"06","file_date_updated":"2020-07-14T12:44:39Z","file":[{"date_updated":"2020-07-14T12:44:39Z","date_created":"2018-12-12T10:17:13Z","access_level":"open_access","file_id":"5266","file_size":671125,"checksum":"47686d58ec21c164540f1a980ff2163f","creator":"system","relation":"main_file","file_name":"IST-2016-712-v1+1_s10959-016-0724-2.pdf","content_type":"application/pdf"}],"author":[{"first_name":"Franco","last_name":"Flandoli","full_name":"Flandoli, Franco"},{"first_name":"Francesco","last_name":"Russo","full_name":"Russo, Francesco"},{"id":"47491882-F248-11E8-B48F-1D18A9856A87","last_name":"Zanco","first_name":"Giovanni A","full_name":"Zanco, Giovanni A"}],"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The second named author benefited partially from the support of the “FMJH Program Gaspard Monge in Optimization and Operations Research” (Project 2014-1607H). He is also grateful for the invitation to the Department of Mathematics of the University of Pisa. The third named author is grateful for the invitation to ENSTA.","_id":"1215","pubrep_id":"712","language":[{"iso":"eng"}],"page":"789-826","issue":"2","publication_status":"published","publisher":"Springer","department":[{"_id":"JaMa"}],"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"quality_controlled":"1","volume":31,"type":"journal_article","scopus_import":1,"date_created":"2018-12-11T11:50:45Z","oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"        31","abstract":[{"text":"Two generalizations of Itô formula to infinite-dimensional spaces are given.\r\nThe first one, in Hilbert spaces, extends the classical one by taking advantage of\r\ncancellations when they occur in examples and it is applied to the case of a group\r\ngenerator. The second one, based on the previous one and a limit procedure, is an Itô\r\nformula in a special class of Banach spaces having a product structure with the noise\r\nin a Hilbert component; again the key point is the extension due to a cancellation. This\r\nextension to Banach spaces and in particular the specific cancellation are motivated\r\nby path-dependent Itô calculus.","lang":"eng"}],"status":"public","date_published":"2018-06-01T00:00:00Z","publist_id":"6119","publication":"Journal of Theoretical Probability"},{"date_updated":"2023-09-13T08:56:07Z","day":"04","external_id":{"isi":["000448185000097"]},"isi":1,"doi":"10.1145/3197517.3201381","title":"Metamolds: Computational design of silicone molds","article_processing_charge":"No","oa":1,"ec_funded":1,"year":"2018","has_accepted_license":"1","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/metamolds-molding-a-mold/"}]},"ddc":["004"],"citation":{"ista":"Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. 2018. Metamolds: Computational design of silicone molds. ACM Trans. Graph. 37(4), 136.","apa":"Alderighi, T., Malomo, L., Giorgi, D., Pietroni, N., Bickel, B., &#38; Cignoni, P. (2018). Metamolds: Computational design of silicone molds. <i>ACM Trans. Graph.</i> ACM. <a href=\"https://doi.org/10.1145/3197517.3201381\">https://doi.org/10.1145/3197517.3201381</a>","ama":"Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. Metamolds: Computational design of silicone molds. <i>ACM Trans Graph</i>. 2018;37(4). doi:<a href=\"https://doi.org/10.1145/3197517.3201381\">10.1145/3197517.3201381</a>","short":"T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, P. Cignoni, ACM Trans. Graph. 37 (2018).","mla":"Alderighi, Thomas, et al. “Metamolds: Computational Design of Silicone Molds.” <i>ACM Trans. Graph.</i>, vol. 37, no. 4, 136, ACM, 2018, doi:<a href=\"https://doi.org/10.1145/3197517.3201381\">10.1145/3197517.3201381</a>.","chicago":"Alderighi, Thomas, Luigi Malomo, Daniela Giorgi, Nico Pietroni, Bernd Bickel, and Paolo Cignoni. “Metamolds: Computational Design of Silicone Molds.” <i>ACM Trans. Graph.</i> ACM, 2018. <a href=\"https://doi.org/10.1145/3197517.3201381\">https://doi.org/10.1145/3197517.3201381</a>.","ieee":"T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, and P. Cignoni, “Metamolds: Computational design of silicone molds,” <i>ACM Trans. Graph.</i>, vol. 37, no. 4. ACM, 2018."},"file":[{"file_size":91939066,"file_id":"5374","access_level":"open_access","date_updated":"2020-07-14T12:44:43Z","date_created":"2018-12-12T10:18:52Z","content_type":"application/pdf","relation":"main_file","file_name":"IST-2018-1038-v1+1_metamolds_authorversion.pdf","checksum":"61d46273dca4de626accef1d17a0aaad","creator":"system"}],"author":[{"full_name":"Alderighi, Thomas","last_name":"Alderighi","first_name":"Thomas"},{"first_name":"Luigi","last_name":"Malomo","full_name":"Malomo, Luigi"},{"first_name":"Daniela","last_name":"Giorgi","full_name":"Giorgi, Daniela"},{"first_name":"Nico","last_name":"Pietroni","full_name":"Pietroni, Nico"},{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Paolo","last_name":"Cignoni","full_name":"Cignoni, Paolo"}],"month":"08","file_date_updated":"2020-07-14T12:44:43Z","article_number":"136","pubrep_id":"1038","_id":"13","language":[{"iso":"eng"}],"issue":"4","publisher":"ACM","publication_status":"published","quality_controlled":"1","project":[{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"}],"department":[{"_id":"BeBi"}],"type":"journal_article","volume":37,"date_created":"2018-12-11T11:44:09Z","scopus_import":"1","oa_version":"Submitted Version","intvolume":"        37","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"ACM Trans. Graph.","publist_id":"8043","date_published":"2018-08-04T00:00:00Z","status":"public","abstract":[{"text":"We propose a new method for fabricating digital objects through reusable silicone molds. Molds are generated by casting liquid silicone into custom 3D printed containers called metamolds. Metamolds automatically define the cuts that are needed to extract the cast object from the silicone mold. The shape of metamolds is designed through a novel segmentation technique, which takes into account both geometric and topological constraints involved in the process of mold casting. Our technique is simple, does not require changing the shape or topology of the input objects, and only requires off-the- shelf materials and technologies. We successfully tested our method on a set of challenging examples with complex shapes and rich geometric detail. © 2018 Association for Computing Machinery.","lang":"eng"}]},{"date_created":"2023-05-23T13:24:51Z","citation":{"short":"N. Stroeymeyt, A.V. Grasse, A. Crespi, D. Mersch, S. Cremer, L. Keller, (2018).","mla":"Stroeymeyt, Nathalie, et al. <i>Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect</i>. Zenodo, 2018, doi:<a href=\"https://doi.org/10.5281/ZENODO.1322669\">10.5281/ZENODO.1322669</a>.","ieee":"N. Stroeymeyt, A. V. Grasse, A. Crespi, D. Mersch, S. Cremer, and L. Keller, “Social network plasticity decreases disease transmission in a eusocial insect.” Zenodo, 2018.","chicago":"Stroeymeyt, Nathalie, Anna V Grasse, Alessandro Crespi, Danielle Mersch, Sylvia Cremer, and Laurent Keller. “Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect.” Zenodo, 2018. <a href=\"https://doi.org/10.5281/ZENODO.1322669\">https://doi.org/10.5281/ZENODO.1322669</a>.","apa":"Stroeymeyt, N., Grasse, A. V., Crespi, A., Mersch, D., Cremer, S., &#38; Keller, L. (2018). Social network plasticity decreases disease transmission in a eusocial insect. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.1322669\">https://doi.org/10.5281/ZENODO.1322669</a>","ista":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. 2018. Social network plasticity decreases disease transmission in a eusocial insect, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.1322669\">10.5281/ZENODO.1322669</a>.","ama":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. Social network plasticity decreases disease transmission in a eusocial insect. 2018. doi:<a href=\"https://doi.org/10.5281/ZENODO.1322669\">10.5281/ZENODO.1322669</a>"},"ddc":["570"],"month":"10","oa_version":"Published Version","author":[{"last_name":"Stroeymeyt","first_name":"Nathalie","full_name":"Stroeymeyt, Nathalie"},{"full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","first_name":"Anna V"},{"full_name":"Crespi, Alessandro","first_name":"Alessandro","last_name":"Crespi"},{"first_name":"Danielle","last_name":"Mersch","full_name":"Mersch, Danielle"},{"first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"},{"first_name":"Laurent","last_name":"Keller","full_name":"Keller, Laurent"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"_id":"13055","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2018-10-23T00:00:00Z","status":"public","abstract":[{"lang":"eng","text":"Dataset for manuscript 'Social network plasticity decreases disease transmission in a eusocial insect'\r\nCompared to previous versions: - raw image files added\r\n                                                     - correction of URLs within README.txt file\r\n"}],"publisher":"Zenodo","date_updated":"2023-10-17T11:50:04Z","day":"23","department":[{"_id":"SyCr"}],"title":"Social network plasticity decreases disease transmission in a eusocial insect","doi":"10.5281/ZENODO.1322669","article_processing_charge":"No","oa":1,"type":"research_data_reference","year":"2018","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.1480665","open_access":"1"}],"related_material":{"record":[{"relation":"used_in_publication","id":"7","status":"public"}]}},{"day":"07","date_updated":"2023-09-06T14:32:51Z","publisher":"Zenodo","doi":"10.5281/ZENODO.2025846","title":"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method","department":[{"_id":"FyKo"}],"type":"research_data_reference","article_processing_charge":"No","oa":1,"related_material":{"record":[{"relation":"used_in_publication","id":"7181","status":"public"}]},"year":"2018","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.3271452","open_access":"1"}],"ddc":["570"],"citation":{"ama":"Garriga E, di Tommaso P, Magis C, et al. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. 2018. doi:<a href=\"https://doi.org/10.5281/ZENODO.2025846\">10.5281/ZENODO.2025846</a>","apa":"Garriga, E., di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2018). Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.2025846\">https://doi.org/10.5281/ZENODO.2025846</a>","ista":"Garriga E, di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2018. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.2025846\">10.5281/ZENODO.2025846</a>.","ieee":"E. Garriga <i>et al.</i>, “Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method.” Zenodo, 2018.","chicago":"Garriga, Edgar, Paolo di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Zenodo, 2018. <a href=\"https://doi.org/10.5281/ZENODO.2025846\">https://doi.org/10.5281/ZENODO.2025846</a>.","short":"E. Garriga, P. di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, (2018).","mla":"Garriga, Edgar, et al. <i>Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method</i>. Zenodo, 2018, doi:<a href=\"https://doi.org/10.5281/ZENODO.2025846\">10.5281/ZENODO.2025846</a>."},"date_created":"2023-05-23T16:08:20Z","author":[{"first_name":"Edgar","last_name":"Garriga","full_name":"Garriga, Edgar"},{"full_name":"di Tommaso, Paolo","last_name":"di Tommaso","first_name":"Paolo"},{"first_name":"Cedrik","last_name":"Magis","full_name":"Magis, Cedrik"},{"full_name":"Erb, Ionas","last_name":"Erb","first_name":"Ionas"},{"last_name":"Mansouri","first_name":"Leila","full_name":"Mansouri, Leila"},{"full_name":"Baltzis, Athanasios","first_name":"Athanasios","last_name":"Baltzis"},{"first_name":"Hafid","last_name":"Laayouni","full_name":"Laayouni, Hafid"},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor"},{"full_name":"Floden, Evan","last_name":"Floden","first_name":"Evan"},{"first_name":"Cedric","last_name":"Notredame","full_name":"Notredame, Cedric"}],"oa_version":"Published Version","month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"_id":"13059","abstract":[{"text":"This dataset contains a GitHub repository containing all the data, analysis, Nextflow workflows and Jupyter notebooks to replicate the manuscript titled \"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method\".\r\nIt also contains the Multiple Sequence Alignments (MSAs) generated and well as the main figures and tables from the manuscript.\r\nThe repository is also available at GitHub (https://github.com/cbcrg/dpa-analysis) release `v1.2`.\r\nFor details on how to use the regressive alignment algorithm, see the T-Coffee software suite (https://github.com/cbcrg/tcoffee).","lang":"eng"}],"date_published":"2018-12-07T00:00:00Z","status":"public"},{"date_created":"2018-12-11T11:44:47Z","scopus_import":"1","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"         7","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7792","publication":"eLife","date_published":"2018-08-13T00:00:00Z","status":"public","abstract":[{"text":"XY systems usually show chromosome-wide compensation of X-linked genes, while in many ZW systems, compensation is restricted to a minority of dosage-sensitive genes. Why such differences arose is still unclear. Here, we combine comparative genomics, transcriptomics and proteomics to obtain a complete overview of the evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium) and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary strata. We use these to assess gene expression evolution following sex-linkage. The resulting patterns suggest a reduction in expression of Z-linked genes in females, combined with upregulation of the Z in both sexes, in line with the first step of Ohno’s classic model of dosage compensation evolution. Quantitative proteomics suggest that post-transcriptional mechanisms do not play a major role in balancing the expression of Z-linked genes. ","lang":"eng"}],"publisher":"eLife Sciences Publications","publication_status":"published","quality_controlled":"1","project":[{"grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety","_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"department":[{"_id":"BeVi"}],"type":"journal_article","volume":7,"ddc":["570"],"citation":{"ama":"Picard MAL, Cosseau C, Ferré S, et al. Evolution of gene dosage on the Z-chromosome of schistosome parasites. <i>eLife</i>. 2018;7. doi:<a href=\"https://doi.org/10.7554/eLife.35684\">10.7554/eLife.35684</a>","apa":"Picard, M. A. L., Cosseau, C., Ferré, S., Quack, T., Grevelding, C., Couté, Y., &#38; Vicoso, B. (2018). Evolution of gene dosage on the Z-chromosome of schistosome parasites. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.35684\">https://doi.org/10.7554/eLife.35684</a>","ista":"Picard MAL, Cosseau C, Ferré S, Quack T, Grevelding C, Couté Y, Vicoso B. 2018. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife. 7, e35684.","ieee":"M. A. L. Picard <i>et al.</i>, “Evolution of gene dosage on the Z-chromosome of schistosome parasites,” <i>eLife</i>, vol. 7. eLife Sciences Publications, 2018.","chicago":"Picard, Marion A L, Celine Cosseau, Sabrina Ferré, Thomas Quack, Christoph Grevelding, Yohann Couté, and Beatriz Vicoso. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” <i>ELife</i>. eLife Sciences Publications, 2018. <a href=\"https://doi.org/10.7554/eLife.35684\">https://doi.org/10.7554/eLife.35684</a>.","mla":"Picard, Marion A. L., et al. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” <i>ELife</i>, vol. 7, e35684, eLife Sciences Publications, 2018, doi:<a href=\"https://doi.org/10.7554/eLife.35684\">10.7554/eLife.35684</a>.","short":"M.A.L. Picard, C. Cosseau, S. Ferré, T. Quack, C. Grevelding, Y. Couté, B. Vicoso, ELife 7 (2018)."},"article_type":"original","file":[{"date_updated":"2020-07-14T12:44:43Z","date_created":"2018-12-17T11:55:05Z","access_level":"open_access","file_id":"5695","file_size":3158125,"checksum":"d6331d4385b1fffd6b47b45d5949d841","creator":"dernst","file_name":"2018_eLife_Picard.pdf","relation":"main_file","content_type":"application/pdf"}],"author":[{"id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","last_name":"Picard","first_name":"Marion A","full_name":"Picard, Marion A","orcid":"0000-0002-8101-2518"},{"last_name":"Cosseau","first_name":"Celine","full_name":"Cosseau, Celine"},{"full_name":"Ferré, Sabrina","last_name":"Ferré","first_name":"Sabrina"},{"full_name":"Quack, Thomas","last_name":"Quack","first_name":"Thomas"},{"full_name":"Grevelding, Christoph","last_name":"Grevelding","first_name":"Christoph"},{"full_name":"Couté, Yohann","first_name":"Yohann","last_name":"Couté"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:44:43Z","month":"08","article_number":"e35684","_id":"131","language":[{"iso":"eng"}],"acknowledgement":"We are grateful to Lu Dabing (Soochow University, Suzhou, China) for providing Schistosoma japonicum samples, to Ariana Macon (IST Austria) and Georgette Stovall (JLU Giessen) for technical assistance, to IT support at IST Austria for providing optimal environment to bioinformatic analyses, and to the Vicoso lab for comments on the manuscript.","date_updated":"2024-02-21T13:45:12Z","day":"13","external_id":{"isi":["000441388200001"]},"isi":1,"doi":"10.7554/eLife.35684","title":"Evolution of gene dosage on the Z-chromosome of schistosome parasites","article_processing_charge":"No","oa":1,"year":"2018","related_material":{"record":[{"relation":"popular_science","id":"5586","status":"public"}]},"has_accepted_license":"1"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"        46","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"Developmental Cell","publist_id":"7791","status":"public","date_published":"2018-08-06T00:00:00Z","abstract":[{"lang":"eng","text":"Pancreas development involves a coordinated process in which an early phase of cell segregation is followed by a longer phase of lineage restriction, expansion, and tissue remodeling. By combining clonal tracing and whole-mount reconstruction with proliferation kinetics and single-cell transcriptional profiling, we define the functional basis of pancreas morphogenesis. We show that the large-scale organization of mouse pancreas can be traced to the activity of self-renewing precursors positioned at the termini of growing ducts, which act collectively to drive serial rounds of stochastic ductal bifurcation balanced by termination. During this phase of branching morphogenesis, multipotent precursors become progressively fate-restricted, giving rise to self-renewing acinar-committed precursors that are conveyed with growing ducts, as well as ductal progenitors that expand the trailing ducts and give rise to delaminating endocrine cells. These findings define quantitatively how the functional behavior and lineage progression of precursor pools determine the large-scale patterning of pancreatic sub-compartments."}],"date_created":"2018-12-11T11:44:48Z","scopus_import":"1","oa_version":"Published Version","type":"journal_article","volume":46,"publisher":"Cell Press","publication_status":"published","quality_controlled":"1","department":[{"_id":"EdHa"}],"_id":"132","language":[{"iso":"eng"}],"acknowledgement":"E.H. is funded by a Junior Research Fellowship from Trinity College, Cam-bridge, a Sir Henry Wellcome Fellowship from the Wellcome Trust, and theBettencourt-Schueller Young Researcher Prize for support.","issue":"3","page":"360 - 375","ddc":["570"],"citation":{"apa":"Sznurkowska, M., Hannezo, E. B., Azzarelli, R., Rulands, S., Nestorowa, S., Hindley, C., … Simons, B. (2018). Defining lineage potential and fate behavior of precursors during pancreas development. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2018.06.028\">https://doi.org/10.1016/j.devcel.2018.06.028</a>","ista":"Sznurkowska M, Hannezo EB, Azzarelli R, Rulands S, Nestorowa S, Hindley C, Nichols J, Göttgens B, Huch M, Philpott A, Simons B. 2018. Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. 46(3), 360–375.","ama":"Sznurkowska M, Hannezo EB, Azzarelli R, et al. Defining lineage potential and fate behavior of precursors during pancreas development. <i>Developmental Cell</i>. 2018;46(3):360-375. doi:<a href=\"https://doi.org/10.1016/j.devcel.2018.06.028\">10.1016/j.devcel.2018.06.028</a>","mla":"Sznurkowska, Magdalena, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” <i>Developmental Cell</i>, vol. 46, no. 3, Cell Press, 2018, pp. 360–75, doi:<a href=\"https://doi.org/10.1016/j.devcel.2018.06.028\">10.1016/j.devcel.2018.06.028</a>.","short":"M. Sznurkowska, E.B. Hannezo, R. Azzarelli, S. Rulands, S. Nestorowa, C. Hindley, J. Nichols, B. Göttgens, M. Huch, A. Philpott, B. Simons, Developmental Cell 46 (2018) 360–375.","ieee":"M. Sznurkowska <i>et al.</i>, “Defining lineage potential and fate behavior of precursors during pancreas development,” <i>Developmental Cell</i>, vol. 46, no. 3. Cell Press, pp. 360–375, 2018.","chicago":"Sznurkowska, Magdalena, Edouard B Hannezo, Roberta Azzarelli, Steffen Rulands, Sonia Nestorowa, Christopher Hindley, Jennifer Nichols, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” <i>Developmental Cell</i>. Cell Press, 2018. <a href=\"https://doi.org/10.1016/j.devcel.2018.06.028\">https://doi.org/10.1016/j.devcel.2018.06.028</a>."},"article_type":"original","author":[{"first_name":"Magdalena","last_name":"Sznurkowska","full_name":"Sznurkowska, Magdalena"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Azzarelli","first_name":"Roberta","full_name":"Azzarelli, Roberta"},{"last_name":"Rulands","first_name":"Steffen","full_name":"Rulands, Steffen"},{"first_name":"Sonia","last_name":"Nestorowa","full_name":"Nestorowa, Sonia"},{"first_name":"Christopher","last_name":"Hindley","full_name":"Hindley, Christopher"},{"full_name":"Nichols, Jennifer","last_name":"Nichols","first_name":"Jennifer"},{"first_name":"Berthold","last_name":"Göttgens","full_name":"Göttgens, Berthold"},{"last_name":"Huch","first_name":"Meritxell","full_name":"Huch, Meritxell"},{"first_name":"Anna","last_name":"Philpott","full_name":"Philpott, Anna"},{"first_name":"Benjamin","last_name":"Simons","full_name":"Simons, Benjamin"}],"file":[{"content_type":"application/pdf","file_name":"2018_DevelopmentalCell_Sznurkowska.pdf","relation":"main_file","checksum":"78d2062b9e3c3b90fe71545aeb6d2f65","creator":"dernst","file_size":8948384,"file_id":"5694","access_level":"open_access","date_created":"2018-12-17T10:49:49Z","date_updated":"2020-07-14T12:44:43Z"}],"file_date_updated":"2020-07-14T12:44:43Z","month":"08","oa":1,"article_processing_charge":"No","year":"2018","has_accepted_license":"1","date_updated":"2023-09-11T12:52:41Z","day":"06","external_id":{"isi":["000441327300012"]},"isi":1,"doi":"10.1016/j.devcel.2018.06.028","title":"Defining lineage potential and fate behavior of precursors during pancreas development"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"       118","abstract":[{"lang":"eng","text":"Synchronous programs are easy to specify because the side effects of an operation are finished by the time the invocation of the operation returns to the caller. Asynchronous programs, on the other hand, are difficult to specify because there are side effects due to pending computation scheduled as a result of the invocation of an operation. They are also difficult to verify because of the large number of possible interleavings of concurrent computation threads. We present synchronization, a new proof rule that simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Modular verification is enabled via pending asynchronous calls in atomic summaries, and a complementary proof rule that eliminates pending asynchronous calls when components and their specifications are composed. We evaluate synchronization in the context of a multi-layer refinement verification methodology on a collection of benchmark programs."}],"publist_id":"7790","date_published":"2018-08-13T00:00:00Z","status":"public","scopus_import":1,"alternative_title":["LIPIcs"],"date_created":"2018-12-11T11:44:48Z","oa_version":"Published Version","type":"conference","volume":118,"publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"ToHe"}],"quality_controlled":"1","project":[{"grant_number":"S11402-N23","name":"Rigorous Systems Engineering","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","call_identifier":"FWF"}],"_id":"133","language":[{"iso":"eng"}],"pubrep_id":"1039","ddc":["000"],"citation":{"ama":"Kragl B, Qadeer S, Henzinger TA. Synchronizing the asynchronous. In: Vol 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.21\">10.4230/LIPIcs.CONCUR.2018.21</a>","ista":"Kragl B, Qadeer S, Henzinger TA. 2018. Synchronizing the asynchronous. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 118, 21.","apa":"Kragl, B., Qadeer, S., &#38; Henzinger, T. A. (2018). Synchronizing the asynchronous (Vol. 118). Presented at the CONCUR: International Conference on Concurrency Theory, Beijing, China: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.21\">https://doi.org/10.4230/LIPIcs.CONCUR.2018.21</a>","chicago":"Kragl, Bernhard, Shaz Qadeer, and Thomas A Henzinger. “Synchronizing the Asynchronous,” Vol. 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.21\">https://doi.org/10.4230/LIPIcs.CONCUR.2018.21</a>.","ieee":"B. Kragl, S. Qadeer, and T. A. Henzinger, “Synchronizing the asynchronous,” presented at the CONCUR: International Conference on Concurrency Theory, Beijing, China, 2018, vol. 118.","short":"B. Kragl, S. Qadeer, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","mla":"Kragl, Bernhard, et al. <i>Synchronizing the Asynchronous</i>. Vol. 118, 21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.21\">10.4230/LIPIcs.CONCUR.2018.21</a>."},"author":[{"last_name":"Kragl","first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87","full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117"},{"first_name":"Shaz","last_name":"Qadeer","full_name":"Qadeer, Shaz"},{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"}],"file":[{"date_created":"2018-12-12T10:18:46Z","date_updated":"2020-07-14T12:44:44Z","access_level":"open_access","file_id":"5368","file_size":745438,"creator":"system","checksum":"c90895f4c5fafc18ddc54d1c8848077e","file_name":"IST-2018-853-v2+2_concur2018.pdf","relation":"main_file","content_type":"application/pdf"}],"file_date_updated":"2020-07-14T12:44:44Z","month":"08","article_number":"21","oa":1,"conference":{"location":"Beijing, China","name":"CONCUR: International Conference on Concurrency Theory","start_date":"2018-09-04","end_date":"2018-09-07"},"related_material":{"record":[{"status":"public","id":"6426","relation":"earlier_version"},{"status":"public","id":"8332","relation":"dissertation_contains"}]},"has_accepted_license":"1","year":"2018","day":"13","publication_identifier":{"issn":["18688969"]},"date_updated":"2023-09-07T13:18:00Z","doi":"10.4230/LIPIcs.CONCUR.2018.21","title":"Synchronizing the asynchronous"},{"isi":1,"external_id":{"isi":["000443383300024"]},"title":"Leaky resistance and the conditions for the existence of lytic bacteriophage","doi":"10.1371/journal.pbio.2005971","date_updated":"2023-09-13T08:45:41Z","day":"16","year":"2018","has_accepted_license":"1","related_material":{"record":[{"status":"public","id":"9810","relation":"research_data"}]},"article_processing_charge":"Yes","oa":1,"month":"08","file_date_updated":"2020-07-14T12:48:10Z","article_number":"2005971","file":[{"file_size":4007095,"file_id":"5706","access_level":"open_access","date_updated":"2020-07-14T12:48:10Z","date_created":"2018-12-17T12:55:31Z","content_type":"application/pdf","relation":"main_file","file_name":"2018_Plos_Chaudhry.pdf","checksum":"527076f78265cd4ea192cd1569851587","creator":"dernst"}],"author":[{"full_name":"Chaudhry, Waqas","first_name":"Waqas","last_name":"Chaudhry"},{"id":"4569785E-F248-11E8-B48F-1D18A9856A87","first_name":"Maros","last_name":"Pleska","orcid":"0000-0001-7460-7479","full_name":"Pleska, Maros"},{"first_name":"Nilang","last_name":"Shah","full_name":"Shah, Nilang"},{"first_name":"Howard","last_name":"Weiss","full_name":"Weiss, Howard"},{"first_name":"Ingrid","last_name":"Mccall","full_name":"Mccall, Ingrid"},{"full_name":"Meyer, Justin","last_name":"Meyer","first_name":"Justin"},{"full_name":"Gupta, Animesh","last_name":"Gupta","first_name":"Animesh"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Levin, Bruce","last_name":"Levin","first_name":"Bruce"}],"citation":{"short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, PLoS Biology 16 (2018).","mla":"Chaudhry, Waqas, et al. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” <i>PLoS Biology</i>, vol. 16, no. 8, 2005971, Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005971\">10.1371/journal.pbio.2005971</a>.","ieee":"W. Chaudhry <i>et al.</i>, “Leaky resistance and the conditions for the existence of lytic bacteriophage,” <i>PLoS Biology</i>, vol. 16, no. 8. Public Library of Science, 2018.","chicago":"Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” <i>PLoS Biology</i>. Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pbio.2005971\">https://doi.org/10.1371/journal.pbio.2005971</a>.","apa":"Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin, B. (2018). Leaky resistance and the conditions for the existence of lytic bacteriophage. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2005971\">https://doi.org/10.1371/journal.pbio.2005971</a>","ista":"Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC, Levin B. 2018. Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. 16(8), 2005971.","ama":"Chaudhry W, Pleska M, Shah N, et al. Leaky resistance and the conditions for the existence of lytic bacteriophage. <i>PLoS Biology</i>. 2018;16(8). doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005971\">10.1371/journal.pbio.2005971</a>"},"ddc":["570"],"issue":"8","language":[{"iso":"eng"}],"_id":"82","quality_controlled":"1","department":[{"_id":"CaGu"}],"publisher":"Public Library of Science","publication_status":"published","volume":16,"type":"journal_article","oa_version":"Published Version","date_created":"2018-12-11T11:44:32Z","scopus_import":"1","status":"public","date_published":"2018-08-16T00:00:00Z","publist_id":"7972","publication":"PLoS Biology","abstract":[{"lang":"eng","text":"In experimental cultures, when bacteria are mixed with lytic (virulent) bacteriophage, bacterial cells resistant to the phage commonly emerge and become the dominant population of bacteria. Following the ascent of resistant mutants, the densities of bacteria in these simple communities become limited by resources rather than the phage. Despite the evolution of resistant hosts, upon which the phage cannot replicate, the lytic phage population is most commonly maintained in an apparently stable state with the resistant bacteria. Several mechanisms have been put forward to account for this result. Here we report the results of population dynamic/evolution experiments with a virulent mutant of phage Lambda, λVIR, and Escherichia coli in serial transfer cultures. We show that, following the ascent of λVIR-resistant bacteria, λVIRis maintained in the majority of cases in maltose-limited minimal media and in all cases in nutrient-rich broth. Using mathematical models and experiments, we show that the dominant mechanism responsible for maintenance of λVIRin these resource-limited populations dominated by resistant E. coli is a high rate of either phenotypic or genetic transition from resistance to susceptibility—a hitherto undemonstrated mechanism we term &quot;leaky resistance.&quot; We discuss the implications of leaky resistance to our understanding of the conditions for the maintenance of phage in populations of bacteria—their “existence conditions.”."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"        16","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"type":"dissertation","project":[{"call_identifier":"FP7","name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668"},{"grant_number":"682815","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"department":[{"_id":"KrPi"}],"supervisor":[{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","status":"public","date_published":"2018-09-05T00:00:00Z","publist_id":"7971","abstract":[{"lang":"eng","text":"A proof system is a protocol between a prover and a verifier over a common input in which an honest prover convinces the verifier of the validity of true statements. Motivated by the success of decentralized cryptocurrencies, exemplified by Bitcoin, the focus of this thesis will be on proof systems which found applications in some sustainable alternatives to Bitcoin, such as the Spacemint and Chia cryptocurrencies. In particular, we focus on proofs of space and proofs of sequential work.\r\nProofs of space (PoSpace) were suggested as more ecological, economical, and egalitarian alternative to the energy-wasteful proof-of-work mining of Bitcoin. However, the state-of-the-art constructions of PoSpace are based on sophisticated graph pebbling lower bounds, and are therefore complex. Moreover, when these PoSpace are used in cryptocurrencies like Spacemint, miners can only start mining after ensuring that a commitment to their space is already added in a special transaction to the blockchain. Proofs of sequential work (PoSW) are proof systems in which a prover, upon receiving a statement x and a time parameter T, computes a proof which convinces the verifier that T time units had passed since x was received. Whereas Spacemint assumes synchrony to retain some interesting Bitcoin dynamics, Chia requires PoSW with unique proofs, i.e., PoSW in which it is hard to come up with more than one accepting proof for any true statement. In this thesis we construct simple and practically-efficient PoSpace and PoSW. When using our PoSpace in cryptocurrencies, miners can start mining on the fly, like in Bitcoin, and unlike current constructions of PoSW, which either achieve efficient verification of sequential work, or faster-than-recomputing verification of correctness of proofs, but not both at the same time, ours achieve the best of these two worlds."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","date_created":"2018-12-11T11:44:32Z","alternative_title":["ISTA Thesis"],"ec_funded":1,"year":"2018","has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1229"},{"status":"public","id":"1235","relation":"part_of_dissertation"},{"status":"public","id":"1236","relation":"part_of_dissertation"},{"id":"559","relation":"part_of_dissertation","status":"public"}]},"oa":1,"article_processing_charge":"No","title":"Proof systems for sustainable decentralized cryptocurrencies","doi":"10.15479/AT:ISTA:TH_1046","date_updated":"2023-09-07T12:30:23Z","publication_identifier":{"issn":["2663-337X"]},"day":"05","page":"59","_id":"83","language":[{"iso":"eng"}],"pubrep_id":"1046","degree_awarded":"PhD","file_date_updated":"2020-07-14T12:48:11Z","month":"09","author":[{"last_name":"Abusalah","first_name":"Hamza M","id":"40297222-F248-11E8-B48F-1D18A9856A87","full_name":"Abusalah, Hamza M"}],"file":[{"content_type":"application/pdf","file_name":"2018_Thesis_Abusalah.pdf","relation":"main_file","creator":"dernst","checksum":"c4b5f7d111755d1396787f41886fc674","file_size":876241,"file_id":"6245","access_level":"open_access","date_updated":"2020-07-14T12:48:11Z","date_created":"2019-04-09T06:43:41Z"},{"date_updated":"2020-07-14T12:48:11Z","date_created":"2019-04-09T06:43:41Z","access_level":"closed","file_id":"6246","file_size":2029190,"creator":"dernst","checksum":"0f382ac56b471c48fd907d63eb87dafe","file_name":"2018_Thesis_Abusalah_source.tar.gz","relation":"source_file","content_type":"application/x-gzip"}],"citation":{"short":"H.M. Abusalah, Proof Systems for Sustainable Decentralized Cryptocurrencies, Institute of Science and Technology Austria, 2018.","mla":"Abusalah, Hamza M. <i>Proof Systems for Sustainable Decentralized Cryptocurrencies</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1046\">10.15479/AT:ISTA:TH_1046</a>.","chicago":"Abusalah, Hamza M. “Proof Systems for Sustainable Decentralized Cryptocurrencies.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1046\">https://doi.org/10.15479/AT:ISTA:TH_1046</a>.","ieee":"H. M. Abusalah, “Proof systems for sustainable decentralized cryptocurrencies,” Institute of Science and Technology Austria, 2018.","ista":"Abusalah HM. 2018. Proof systems for sustainable decentralized cryptocurrencies. Institute of Science and Technology Austria.","apa":"Abusalah, H. M. (2018). <i>Proof systems for sustainable decentralized cryptocurrencies</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1046\">https://doi.org/10.15479/AT:ISTA:TH_1046</a>","ama":"Abusalah HM. Proof systems for sustainable decentralized cryptocurrencies. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1046\">10.15479/AT:ISTA:TH_1046</a>"},"ddc":["004"]},{"publication_identifier":{"issn":["03029743"]},"day":"01","date_updated":"2023-09-18T09:32:36Z","title":"Snapshot based synchronization: A fast replacement for Hand-over-Hand locking","doi":"10.1007/978-3-319-96983-1_33","isi":1,"external_id":{"isi":["000851042300031"]},"oa":1,"article_processing_charge":"No","has_accepted_license":"1","conference":{"name":"Euro-Par: European Conference on Parallel Processing","location":"Turin, Italy","end_date":"2018-08-31","start_date":"2018-08-27"},"year":"2018","citation":{"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:<a href=\"https://doi.org/10.1007/978-3-319-96983-1_33\">10.1007/978-3-319-96983-1_33</a>","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.","apa":"Gilad, E., Brown, T. A., Oskin, M., &#38; 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. <a href=\"https://doi.org/10.1007/978-3-319-96983-1_33\">https://doi.org/10.1007/978-3-319-96983-1_33</a>","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. <a href=\"https://doi.org/10.1007/978-3-319-96983-1_33\">https://doi.org/10.1007/978-3-319-96983-1_33</a>.","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.","mla":"Gilad, Eran, et al. <i>Snapshot Based Synchronization: A Fast Replacement for Hand-over-Hand Locking</i>. Vol. 11014, Springer, 2018, pp. 465–79, doi:<a href=\"https://doi.org/10.1007/978-3-319-96983-1_33\">10.1007/978-3-319-96983-1_33</a>.","short":"E. Gilad, T.A. Brown, M. Oskin, Y. Etsion, in:, Springer, 2018, pp. 465–479."},"ddc":["000"],"month":"08","file_date_updated":"2020-07-14T12:48:14Z","file":[{"content_type":"application/pdf","creator":"dernst","checksum":"13a3f250be8878405e791b53c19722ad","relation":"main_file","file_name":"2018_Brown.pdf","file_id":"5954","file_size":665372,"date_created":"2019-02-12T07:40:40Z","date_updated":"2020-07-14T12:48:14Z","access_level":"open_access"}],"author":[{"full_name":"Gilad, Eran","last_name":"Gilad","first_name":"Eran"},{"last_name":"Brown","first_name":"Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Trevor A"},{"full_name":"Oskin, Mark","last_name":"Oskin","first_name":"Mark"},{"full_name":"Etsion, Yoav","last_name":"Etsion","first_name":"Yoav"}],"acknowledgement":"Trevor Brown was supported in part by the ISF (grants 2005/17 & 1749/14) and by a NSERC post-doctoral fellowship.","_id":"85","language":[{"iso":"eng"}],"page":"465 - 479","publication_status":"published","publisher":"Springer","department":[{"_id":"DaAl"}],"project":[{"_id":"26450934-B435-11E9-9278-68D0E5697425","name":"NSERC Postdoctoral fellowship"}],"quality_controlled":"1","volume":11014,"type":"conference","alternative_title":["LNCS"],"scopus_import":"1","date_created":"2018-12-11T11:44:33Z","oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"     11014","abstract":[{"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.","lang":"eng"}],"date_published":"2018-08-01T00:00:00Z","status":"public","publist_id":"7969"},{"abstract":[{"lang":"eng","text":"The cerebral cortex contains multiple hierarchically organized areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have quantitatively investigated the neuronal output of individual progenitor cells in the ventricular zone of the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. We found that individual cortical progenitor cells show a high degree of stochasticity and generate pyramidal cell lineages that adopt a wide range of laminar configurations. Mathematical modelling these lineage data suggests that a small number of progenitor cell populations, each generating pyramidal cells following different stochastic developmental programs, suffice to generate the heterogenous complement of pyramidal cell lineages that collectively build the complex cytoarchitecture of the neocortex."}],"date_published":"2018-12-13T00:00:00Z","status":"public","publication":"bioRxiv","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank I. Andrew and S.E. Bae for excellent technical assistance, F. Gage for plasmids, and K. Nave (Nex-Cre) for mouse colonies. We thank members of the Marín and Rico laboratories for stimulating discussions and ideas. Our research on this topic is supported by grants from the European Research Council (ERC-2017-AdG 787355 to O.M and ERC2016-CoG 725780 to S.H.) and Wellcome Trust (103714MA) to O.M. L.L. was the recipient of an EMBO long-term postdoctoral fellowship, R.B. received support from FWF Lise-Meitner program (M 2416) and F.K.W. was supported by an EMBO postdoctoral fellowship and is currently a Marie Skłodowska-Curie Fellow from the European Commission under the H2020 Programme.","language":[{"iso":"eng"}],"_id":"8547","month":"12","oa_version":"Preprint","author":[{"full_name":"Llorca, Alfredo","first_name":"Alfredo","last_name":"Llorca"},{"last_name":"Ciceri","first_name":"Gabriele","full_name":"Ciceri, Gabriele"},{"id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","last_name":"Beattie","first_name":"Robert J","full_name":"Beattie, Robert J","orcid":"0000-0002-8483-8753"},{"first_name":"Fong K.","last_name":"Wong","full_name":"Wong, Fong K."},{"first_name":"Giovanni","last_name":"Diana","full_name":"Diana, Giovanni"},{"last_name":"Serafeimidou","first_name":"Eleni","full_name":"Serafeimidou, Eleni"},{"full_name":"Fernández-Otero, Marian","first_name":"Marian","last_name":"Fernández-Otero"},{"full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher","first_name":"Carmen"},{"last_name":"Arnold","first_name":"Sebastian J.","full_name":"Arnold, Sebastian J."},{"full_name":"Meyer, Martin","last_name":"Meyer","first_name":"Martin"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Maravall, Miguel","last_name":"Maravall","first_name":"Miguel"},{"first_name":"Oscar","last_name":"Marín","full_name":"Marín, Oscar"}],"citation":{"ista":"Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv, <a href=\"https://doi.org/10.1101/494088\">10.1101/494088</a>.","apa":"Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou, E., … Marín, O. (n.d.). Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/494088\">https://doi.org/10.1101/494088</a>","ama":"Llorca A, Ciceri G, Beattie RJ, et al. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/494088\">10.1101/494088</a>","short":"A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou, M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall, O. Marín, BioRxiv (n.d.).","mla":"Llorca, Alfredo, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/494088\">10.1101/494088</a>.","chicago":"Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong K. Wong, Giovanni Diana, Eleni Serafeimidou, Marian Fernández-Otero, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/494088\">https://doi.org/10.1101/494088</a>.","ieee":"A. Llorca <i>et al.</i>, “Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory."},"date_created":"2020-09-21T12:01:50Z","year":"2018","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/494088"}],"ec_funded":1,"type":"preprint","oa":1,"article_processing_charge":"No","department":[{"_id":"SiHi"}],"title":"Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture","doi":"10.1101/494088","project":[{"call_identifier":"H2020","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"},{"call_identifier":"FWF","grant_number":"M02416","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","_id":"264E56E2-B435-11E9-9278-68D0E5697425"}],"publication_status":"submitted","day":"13","publisher":"Cold Spring Harbor Laboratory","date_updated":"2021-01-12T08:20:00Z"},{"date_created":"2018-12-11T11:44:33Z","scopus_import":1,"alternative_title":["LNCS"],"oa_version":"Submitted Version","intvolume":"     10760","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7968","publication":"Principles of Modeling","date_published":"2018-07-20T00:00:00Z","status":"public","abstract":[{"lang":"eng","text":"Responsiveness—the requirement that every request to a system be eventually handled—is one of the fundamental liveness properties of a reactive system. Average response time is a quantitative measure for the responsiveness requirement used commonly in performance evaluation. We show how average response time can be computed on state-transition graphs, on Markov chains, and on game graphs. In all three cases, we give polynomial-time algorithms."}],"publisher":"Springer","publication_status":"published","quality_controlled":"1","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"}],"editor":[{"last_name":"Lohstroh","first_name":"Marten","full_name":"Lohstroh, Marten"},{"full_name":"Derler, Patricia","last_name":"Derler","first_name":"Patricia"},{"first_name":"Marjan","last_name":"Sirjani","full_name":"Sirjani, Marjan"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"type":"book_chapter","volume":10760,"ddc":["000"],"citation":{"mla":"Chatterjee, Krishnendu, et al. “Computing Average Response Time.” <i>Principles of Modeling</i>, edited by Marten Lohstroh et al., vol. 10760, Springer, 2018, pp. 143–61, doi:<a href=\"https://doi.org/10.1007/978-3-319-95246-8_9\">10.1007/978-3-319-95246-8_9</a>.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, M. Lohstroh, P. Derler, M. Sirjani (Eds.), Principles of Modeling, Springer, 2018, pp. 143–161.","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Computing average response time,” in <i>Principles of Modeling</i>, vol. 10760, M. Lohstroh, P. Derler, and M. Sirjani, Eds. Springer, 2018, pp. 143–161.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Computing Average Response Time.” In <i>Principles of Modeling</i>, edited by Marten Lohstroh, Patricia Derler, and Marjan Sirjani, 10760:143–61. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-95246-8_9\">https://doi.org/10.1007/978-3-319-95246-8_9</a>.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2018). Computing average response time. In M. Lohstroh, P. Derler, &#38; M. Sirjani (Eds.), <i>Principles of Modeling</i> (Vol. 10760, pp. 143–161). Springer. <a href=\"https://doi.org/10.1007/978-3-319-95246-8_9\">https://doi.org/10.1007/978-3-319-95246-8_9</a>","ista":"Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time. In: Principles of Modeling. LNCS, vol. 10760, 143–161.","ama":"Chatterjee K, Henzinger TA, Otop J. Computing average response time. In: Lohstroh M, Derler P, Sirjani M, eds. <i>Principles of Modeling</i>. Vol 10760. Springer; 2018:143-161. doi:<a href=\"https://doi.org/10.1007/978-3-319-95246-8_9\">10.1007/978-3-319-95246-8_9</a>"},"author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Otop","full_name":"Otop, Jan"}],"file":[{"content_type":"application/pdf","checksum":"9995c6ce6957333baf616fc4f20be597","creator":"dernst","file_name":"2018_PrinciplesModeling_Chatterjee.pdf","relation":"main_file","file_id":"7053","file_size":516307,"date_updated":"2020-07-14T12:48:14Z","date_created":"2019-11-19T08:22:18Z","access_level":"open_access"}],"month":"07","file_date_updated":"2020-07-14T12:48:14Z","_id":"86","language":[{"iso":"eng"}],"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23, S11407-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund (WWTF) through project ICT15-003 and by the National Science Centre (NCN), Poland under grant 2014/15/D/ST6/04543.","page":"143 - 161","date_updated":"2021-01-12T08:20:14Z","day":"20","doi":"10.1007/978-3-319-95246-8_9","title":"Computing average response time","oa":1,"year":"2018","ec_funded":1,"has_accepted_license":"1"},{"_id":"8618","language":[{"iso":"eng"}],"file_date_updated":"2020-10-06T16:35:16Z","month":"02","article_number":"2724","author":[{"last_name":"Gregor","first_name":"Carola","full_name":"Gregor, Carola"},{"last_name":"Sidenstein","first_name":"Sven C.","full_name":"Sidenstein, Sven C."},{"last_name":"Andresen","first_name":"Martin","full_name":"Andresen, Martin"},{"first_name":"Steffen J.","last_name":"Sahl","full_name":"Sahl, Steffen J."},{"last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"},{"last_name":"Hell","first_name":"Stefan W.","full_name":"Hell, Stefan W."}],"file":[{"creator":"dernst","checksum":"e642080fcbde9584c63544f587c74f03","relation":"main_file","file_name":"2018_ScientificReports_Gregor.pdf","content_type":"application/pdf","date_created":"2020-10-06T16:35:16Z","date_updated":"2020-10-06T16:35:16Z","access_level":"open_access","file_id":"8619","success":1,"file_size":2818077}],"article_type":"original","keyword":["Multidisciplinary"],"citation":{"ama":"Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. <i>Scientific Reports</i>. 2018;8. doi:<a href=\"https://doi.org/10.1038/s41598-018-19947-1\">10.1038/s41598-018-19947-1</a>","apa":"Gregor, C., Sidenstein, S. C., Andresen, M., Sahl, S. J., Danzl, J. G., &#38; Hell, S. W. (2018). Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-018-19947-1\">https://doi.org/10.1038/s41598-018-19947-1</a>","ista":"Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. 2018. Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. Scientific Reports. 8, 2724.","ieee":"C. Gregor, S. C. Sidenstein, M. Andresen, S. J. Sahl, J. G. Danzl, and S. W. Hell, “Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA,” <i>Scientific Reports</i>, vol. 8. Springer Nature, 2018.","chicago":"Gregor, Carola, Sven C. Sidenstein, Martin Andresen, Steffen J. Sahl, Johann G Danzl, and Stefan W. Hell. “Novel Reversibly Switchable Fluorescent Proteins for RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.” <i>Scientific Reports</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41598-018-19947-1\">https://doi.org/10.1038/s41598-018-19947-1</a>.","mla":"Gregor, Carola, et al. “Novel Reversibly Switchable Fluorescent Proteins for RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.” <i>Scientific Reports</i>, vol. 8, 2724, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s41598-018-19947-1\">10.1038/s41598-018-19947-1</a>.","short":"C. Gregor, S.C. Sidenstein, M. Andresen, S.J. Sahl, J.G. Danzl, S.W. Hell, Scientific Reports 8 (2018)."},"ddc":["570"],"has_accepted_license":"1","year":"2018","article_processing_charge":"No","oa":1,"title":"Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA","doi":"10.1038/s41598-018-19947-1","isi":1,"external_id":{"pmid":["29426833"],"isi":["000424630400037"]},"publication_identifier":{"issn":["2045-2322"]},"day":"09","date_updated":"2023-09-19T15:04:49Z","abstract":[{"lang":"eng","text":"The reversibly switchable fluorescent proteins (RSFPs) commonly used for RESOLFT nanoscopy have been developed from fluorescent proteins of the GFP superfamily. These proteins are bright, but exhibit several drawbacks such as relatively large size, oxygen-dependence, sensitivity to low pH, and limited switching speed. Therefore, RSFPs from other origins with improved properties need to be explored. Here, we report the development of two RSFPs based on the LOV domain of the photoreceptor protein YtvA from Bacillus subtilis. LOV domains obtain their fluorescence by association with the abundant cellular cofactor flavin mononucleotide (FMN). Under illumination with blue and ultraviolet light, they undergo a photocycle, making these proteins inherently photoswitchable. Our first improved variant, rsLOV1, can be used for RESOLFT imaging, whereas rsLOV2 proved useful for STED nanoscopy of living cells with a resolution of down to 50 nm. In addition to their smaller size compared to GFP-related proteins (17 kDa instead of 27 kDa) and their usability at low pH, rsLOV1 and rsLOV2 exhibit faster switching kinetics, switching on and off 3 times faster than rsEGFP2, the fastest-switching RSFP reported to date. Therefore, LOV-domain-based RSFPs have potential for applications where the switching speed of GFP-based proteins is limiting."}],"status":"public","date_published":"2018-02-09T00:00:00Z","publication":"Scientific Reports","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"         8","oa_version":"Published Version","date_created":"2020-10-06T16:33:37Z","volume":8,"type":"journal_article","department":[{"_id":"JoDa"}],"pmid":1,"quality_controlled":"1","publication_status":"published","publisher":"Springer Nature"},{"year":"2018","related_material":{"record":[{"status":"public","id":"6287","relation":"dissertation_contains"}]},"article_processing_charge":"No","oa":1,"isi":1,"external_id":{"arxiv":["1705.02870"],"isi":["000442893500018"]},"title":"Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics","doi":"10.1214/18-AAP1389","date_updated":"2023-09-15T12:10:35Z","day":"01","issue":"5","page":"3215 - 3238","language":[{"iso":"eng"}],"_id":"87","month":"10","author":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0659-3201","full_name":"Nikitenko, Anton","first_name":"Anton","last_name":"Nikitenko","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87"}],"arxiv":1,"citation":{"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.","apa":"Edelsbrunner, H., &#38; Nikitenko, A. (2018). Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/18-AAP1389\">https://doi.org/10.1214/18-AAP1389</a>","ama":"Edelsbrunner H, Nikitenko A. Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. <i>Annals of Applied Probability</i>. 2018;28(5):3215-3238. doi:<a href=\"https://doi.org/10.1214/18-AAP1389\">10.1214/18-AAP1389</a>","mla":"Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes Have Similar Radius Functions as Poisson-Delaunay Mosaics.” <i>Annals of Applied Probability</i>, vol. 28, no. 5, Institute of Mathematical Statistics, 2018, pp. 3215–38, doi:<a href=\"https://doi.org/10.1214/18-AAP1389\">10.1214/18-AAP1389</a>.","short":"H. Edelsbrunner, A. Nikitenko, Annals of Applied Probability 28 (2018) 3215–3238.","chicago":"Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes Have Similar Radius Functions as Poisson-Delaunay Mosaics.” <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2018. <a href=\"https://doi.org/10.1214/18-AAP1389\">https://doi.org/10.1214/18-AAP1389</a>.","ieee":"H. Edelsbrunner and A. Nikitenko, “Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics,” <i>Annals of Applied Probability</i>, vol. 28, no. 5. Institute of Mathematical Statistics, pp. 3215–3238, 2018."},"article_type":"original","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.02870"}],"volume":28,"type":"journal_article","project":[{"call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"}],"quality_controlled":"1","department":[{"_id":"HeEd"}],"publisher":"Institute of Mathematical Statistics","publication_status":"published","status":"public","date_published":"2018-10-01T00:00:00Z","publist_id":"7967","publication":"Annals of Applied Probability","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."}],"intvolume":"        28","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","date_created":"2018-12-11T11:44:33Z","scopus_import":"1"},{"ddc":["570"],"citation":{"chicago":"Belyaeva, Vera. “Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo .” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th1064\">https://doi.org/10.15479/AT:ISTA:th1064</a>.","ieee":"V. Belyaeva, “Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo ,” Institute of Science and Technology Austria, 2018.","mla":"Belyaeva, Vera. <i>Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo </i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1064\">10.15479/AT:ISTA:th1064</a>.","short":"V. Belyaeva, Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo , Institute of Science and Technology Austria, 2018.","ama":"Belyaeva V. Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1064\">10.15479/AT:ISTA:th1064</a>","ista":"Belyaeva V. 2018. Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . Institute of Science and Technology Austria.","apa":"Belyaeva, V. (2018). <i>Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th1064\">https://doi.org/10.15479/AT:ISTA:th1064</a>"},"author":[{"full_name":"Belyaeva, Vera","id":"47F080FE-F248-11E8-B48F-1D18A9856A87","last_name":"Belyaeva","first_name":"Vera"}],"file":[{"file_size":102737483,"file_id":"6243","access_level":"closed","embargo_to":"open_access","date_updated":"2020-07-14T12:48:14Z","date_created":"2019-04-08T14:13:12Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"2018_Thesis_Belyaeva_source.docx","relation":"source_file","checksum":"d27b2465cb70d0c9678a0381b9b6ced1","creator":"dernst"},{"embargo":"2019-11-19","relation":"main_file","file_name":"2018_Thesis_Belyaeva.pdf","creator":"dernst","checksum":"a2939b61bde2de7b8ced77bbae0eaaed","content_type":"application/pdf","access_level":"open_access","date_updated":"2021-02-11T11:17:16Z","date_created":"2019-04-08T14:14:08Z","file_size":88077843,"file_id":"6244"}],"file_date_updated":"2021-02-11T11:17:16Z","month":"07","degree_awarded":"PhD","language":[{"iso":"eng"}],"_id":"9","pubrep_id":"1064","page":"96","day":"01","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2023-09-07T12:43:10Z","doi":"10.15479/AT:ISTA:th1064","title":"Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo ","article_processing_charge":"No","oa":1,"has_accepted_license":"1","year":"2018","alternative_title":["ISTA Thesis"],"date_created":"2018-12-11T11:44:08Z","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Immune cells migrating to the sites of infection navigate through diverse tissue architectures and switch their migratory mechanisms upon demand. However, little is known about systemic regulators that could allow the acquisition of these mechanisms. We performed a genetic screen in Drosophila melanogaster to identify regulators of germband invasion by embryonic macrophages into the confined space between the ectoderm and mesoderm. We have found that bZIP circadian transcription factors (TFs) Kayak (dFos) and Vrille (dNFIL3) have opposite effects on macrophage germband infiltration: Kayak facilitated and Vrille inhibited it. These TFs are enriched in the macrophages during migration and genetically interact to control it. Kayak sets a less coordinated mode of migration of the macrophage group and increases the probability and length of Levy walks. Intriguingly, the motility of kayak mutant macrophages was also strongly affected during initial germband invasion but not along another less confined route. Inhibiting Rho1 signaling within the tail ectoderm partially rescued the Kayak mutant phenotype, strongly suggesting that migrating macrophages have to overcome a barrier imposed by the stiffness of the ectoderm. Also, Kayak appeared to be important for the maintenance of the round cell shape and the rear edge translocation of the macrophages invading the germband. Complementary to this, the cortical actin cytoskeleton of Kayak- deficient macrophages was strongly affected. RNA sequencing revealed the filamin Cheerio and tetraspanin TM4SF to be downstream of Kayak. Chromatin immunoprecipitation and immunostaining revealed that the formin Diaphanous is another downstream target of Kayak. Immunostaining revealed that the formin Diaphanous is another downstream target of Kayak. Indeed, Cheerio, TM4SF and Diaphanous are required within macrophages for germband invasion, and expression of constitutively active Diaphanous in macrophages was able to rescue the kayak mutant phenotype. Moreover, Cher and Diaphanous are also reduced in the macrophages overexpressing Vrille. We hypothesize that Kayak, through its targets, increases actin polymerization and cortical tension in macrophages and thus allows extra force generation necessary for macrophage dissemination and migration through confined stiff tissues, while Vrille counterbalances it."}],"publist_id":"8047","status":"public","date_published":"2018-07-01T00:00:00Z","publication_status":"published","publisher":"Institute of Science and Technology Austria","supervisor":[{"first_name":"Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E"}],"department":[{"_id":"DaSi"}],"type":"dissertation"}]