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This chapter also presents detailed protocols for utilizing the main technical advantages provided by such a preparation, namely, labeling and imaging of synaptic organelles and electrophysiological recordings directly from presynaptic terminals.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"alternative_title":["Methods in Molecular Biology"],"scopus_import":1,"month":"01","intvolume":" 1727","citation":{"short":"D. Dimitrov, L. Guillaud, K. Eguchi, T. Takahashi, in:, S.D. Skaper (Ed.), Neurotrophic Factors, Springer, 2018, pp. 201–215.","ieee":"D. Dimitrov, L. Guillaud, K. Eguchi, and T. Takahashi, “Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses,” in Neurotrophic Factors, vol. 1727, S. D. Skaper, Ed. Springer, 2018, pp. 201–215.","apa":"Dimitrov, D., Guillaud, L., Eguchi, K., & Takahashi, T. (2018). Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In S. D. Skaper (Ed.), Neurotrophic Factors (Vol. 1727, pp. 201–215). Springer. https://doi.org/10.1007/978-1-4939-7571-6_15","ama":"Dimitrov D, Guillaud L, Eguchi K, Takahashi T. Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In: Skaper SD, ed. Neurotrophic Factors. Vol 1727. Springer; 2018:201-215. doi:10.1007/978-1-4939-7571-6_15","mla":"Dimitrov, Dimitar, et al. “Culture of Mouse Giant Central Nervous System Synapses and Application for Imaging and Electrophysiological Analyses.” Neurotrophic Factors, edited by Stephen D. Skaper, vol. 1727, Springer, 2018, pp. 201–15, doi:10.1007/978-1-4939-7571-6_15.","ista":"Dimitrov D, Guillaud L, Eguchi K, Takahashi T. 2018.Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In: Neurotrophic Factors. Methods in Molecular Biology, vol. 1727, 201–215.","chicago":"Dimitrov, Dimitar, Laurent Guillaud, Kohgaku Eguchi, and Tomoyuki Takahashi. “Culture of Mouse Giant Central Nervous System Synapses and Application for Imaging and Electrophysiological Analyses.” In Neurotrophic Factors, edited by Stephen D. Skaper, 1727:201–15. Springer, 2018. https://doi.org/10.1007/978-1-4939-7571-6_15."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Dimitrov","full_name":"Dimitrov, Dimitar","first_name":"Dimitar"},{"last_name":"Guillaud","full_name":"Guillaud, Laurent","first_name":"Laurent"},{"id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","first_name":"Kohgaku","full_name":"Eguchi, Kohgaku","orcid":"0000-0002-6170-2546","last_name":"Eguchi"},{"last_name":"Takahashi","full_name":"Takahashi, Tomoyuki","first_name":"Tomoyuki"}],"publist_id":"7252","article_processing_charge":"No","external_id":{"pmid":["29222783"]},"editor":[{"first_name":"Stephen D.","full_name":"Skaper, Stephen D.","last_name":"Skaper"}],"title":"Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses","has_accepted_license":"1","year":"2018","day":"01","publication":"Neurotrophic Factors","page":"201 - 215","doi":"10.1007/978-1-4939-7571-6_15","date_published":"2018-01-01T00:00:00Z","date_created":"2018-12-11T11:47:11Z","quality_controlled":"1","publisher":"Springer","oa":1},{"citation":{"short":"R. Bloem, K. Chatterjee, B. Jobstmann, in:, T.A. Henzinger, E.M. Clarke, H. Veith, R. Bloem (Eds.), Handbook of Model Checking, 1st ed., Springer, 2018, pp. 921–962.","ieee":"R. Bloem, K. Chatterjee, and B. Jobstmann, “Graph games and reactive synthesis,” in Handbook of Model Checking, 1st ed., T. A. Henzinger, E. M. Clarke, H. Veith, and R. Bloem, Eds. Springer, 2018, pp. 921–962.","ama":"Bloem R, Chatterjee K, Jobstmann B. Graph games and reactive synthesis. In: Henzinger TA, Clarke EM, Veith H, Bloem R, eds. Handbook of Model Checking. 1st ed. Springer; 2018:921-962. doi:10.1007/978-3-319-10575-8_27","apa":"Bloem, R., Chatterjee, K., & Jobstmann, B. (2018). Graph games and reactive synthesis. In T. A. Henzinger, E. M. Clarke, H. Veith, & R. Bloem (Eds.), Handbook of Model Checking (1st ed., pp. 921–962). Springer. https://doi.org/10.1007/978-3-319-10575-8_27","mla":"Bloem, Roderick, et al. “Graph Games and Reactive Synthesis.” Handbook of Model Checking, edited by Thomas A Henzinger et al., 1st ed., Springer, 2018, pp. 921–62, doi:10.1007/978-3-319-10575-8_27.","ista":"Bloem R, Chatterjee K, Jobstmann B. 2018.Graph games and reactive synthesis. In: Handbook of Model Checking. , 921–962.","chicago":"Bloem, Roderick, Krishnendu Chatterjee, and Barbara Jobstmann. “Graph Games and Reactive Synthesis.” In Handbook of Model Checking, edited by Thomas A Henzinger, Edmund M. Clarke, Helmut Veith, and Roderick Bloem, 1st ed., 921–62. Springer, 2018. https://doi.org/10.1007/978-3-319-10575-8_27."},"date_updated":"2021-01-12T08:05:10Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Roderick","last_name":"Bloem","full_name":"Bloem, Roderick"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jobstmann, Barbara","last_name":"Jobstmann","first_name":"Barbara"}],"publist_id":"7995","title":"Graph games and reactive synthesis","department":[{"_id":"KrCh"}],"editor":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"first_name":"Edmund M.","full_name":"Clarke, Edmund M.","last_name":"Clarke"},{"first_name":"Helmut","last_name":"Veith","full_name":"Veith, Helmut"},{"first_name":"Roderick","last_name":"Bloem","full_name":"Bloem, Roderick"}],"_id":"59","type":"book_chapter","status":"public","year":"2018","publication_status":"published","publication_identifier":{"isbn":["978-3-319-10574-1"]},"language":[{"iso":"eng"}],"publication":"Handbook of Model Checking","day":"19","page":"921 - 962","date_created":"2018-12-11T11:44:24Z","date_published":"2018-05-19T00:00:00Z","doi":"10.1007/978-3-319-10575-8_27","abstract":[{"lang":"eng","text":"Graph-based games are an important tool in computer science. They have applications in synthesis, verification, refinement, and far beyond. We review graphbased games with objectives on infinite plays. We give definitions and algorithms to solve the games and to give a winning strategy. The objectives we consider are mostly Boolean, but we also look at quantitative graph-based games and their objectives. Synthesis aims to turn temporal logic specifications into correct reactive systems. We explain the reduction of synthesis to graph-based games (or equivalently tree automata) using synthesis of LTL specifications as an example. We treat the classical approach that uses determinization of parity automata and more modern approaches."}],"oa_version":"None","edition":"1","publisher":"Springer","quality_controlled":"1","scopus_import":1,"month":"05"},{"_id":"60","series_title":"Handbook of Model Checking","type":"book_chapter","status":"public","citation":{"ama":"Clarke E, Henzinger TA, Veith H. Introduction to model checking. In: Henzinger TA, ed. Handbook of Model Checking. Handbook of Model Checking. Springer; 2018:1-26. doi:10.1007/978-3-319-10575-8_1","apa":"Clarke, E., Henzinger, T. A., & Veith, H. (2018). Introduction to model checking. In T. A. Henzinger (Ed.), Handbook of Model Checking (pp. 1–26). Springer. https://doi.org/10.1007/978-3-319-10575-8_1","ieee":"E. Clarke, T. A. Henzinger, and H. Veith, “Introduction to model checking,” in Handbook of Model Checking, T. A. Henzinger, Ed. Springer, 2018, pp. 1–26.","short":"E. Clarke, T.A. Henzinger, H. Veith, in:, T.A. Henzinger (Ed.), Handbook of Model Checking, Springer, 2018, pp. 1–26.","mla":"Clarke, Edmund, et al. “Introduction to Model Checking.” Handbook of Model Checking, edited by Thomas A Henzinger, Springer, 2018, pp. 1–26, doi:10.1007/978-3-319-10575-8_1.","ista":"Clarke E, Henzinger TA, Veith H. 2018.Introduction to model checking. In: Handbook of Model Checking. , 1–26.","chicago":"Clarke, Edmund, Thomas A Henzinger, and Helmut Veith. “Introduction to Model Checking.” In Handbook of Model Checking, edited by Thomas A Henzinger, 1–26. Handbook of Model Checking. Springer, 2018. https://doi.org/10.1007/978-3-319-10575-8_1."},"date_updated":"2021-01-12T08:05:35Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"7994","author":[{"last_name":"Clarke","full_name":"Clarke, Edmund","first_name":"Edmund"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"full_name":"Veith, Helmut","last_name":"Veith","first_name":"Helmut"}],"title":"Introduction to model checking","editor":[{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A"}],"department":[{"_id":"ToHe"}],"abstract":[{"text":"Model checking is a computer-assisted method for the analysis of dynamical systems that can be modeled by state-transition systems. Drawing from research traditions in mathematical logic, programming languages, hardware design, and theoretical computer science, model checking is now widely used for the verification of hardware and software in industry. This chapter is an introduction and short survey of model checking. The chapter aims to motivate and link the individual chapters of the handbook, and to provide context for readers who are not familiar with model checking.","lang":"eng"}],"oa_version":"None","publisher":"Springer","scopus_import":1,"quality_controlled":"1","month":"05","publication_status":"published","year":"2018","language":[{"iso":"eng"}],"publication":"Handbook of Model Checking","day":"19","page":"1 - 26","date_created":"2018-12-11T11:44:25Z","date_published":"2018-05-19T00:00:00Z","doi":"10.1007/978-3-319-10575-8_1"},{"date_created":"2018-12-11T11:44:25Z","date_published":"2018-05-23T00:00:00Z","doi":"10.1007/978-3-319-72456-0_7","page":"131 - 134","publication":"Contemporary Computational Mathematics","language":[{"iso":"eng"}],"day":"23","publication_status":"published","year":"2018","month":"05","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1509.06286"}],"publisher":"Springer","quality_controlled":"1","oa_version":"Preprint","abstract":[{"text":"We prove that there is no strongly regular graph (SRG) with parameters (460; 153; 32; 60). The proof is based on a recent lower bound on the number of 4-cliques in a SRG and some applications of Euclidean representation of SRGs. ","lang":"eng"}],"department":[{"_id":"TaHa"}],"title":"There is no strongly regular graph with parameters (460; 153; 32; 60)","external_id":{"arxiv":["1509.06286"]},"article_processing_charge":"No","author":[{"first_name":"Andriy","last_name":"Bondarenko","full_name":"Bondarenko, Andriy"},{"id":"388D3134-F248-11E8-B48F-1D18A9856A87","first_name":"Anton","full_name":"Mellit, Anton","last_name":"Mellit"},{"last_name":"Prymak","full_name":"Prymak, Andriy","first_name":"Andriy"},{"first_name":"Danylo","last_name":"Radchenko","full_name":"Radchenko, Danylo"},{"last_name":"Viazovska","full_name":"Viazovska, Maryna","first_name":"Maryna"}],"publist_id":"7993","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2021-01-12T08:06:06Z","citation":{"chicago":"Bondarenko, Andriy, Anton Mellit, Andriy Prymak, Danylo Radchenko, and Maryna Viazovska. “There Is No Strongly Regular Graph with Parameters (460; 153; 32; 60).” In Contemporary Computational Mathematics, 131–34. Springer, 2018. https://doi.org/10.1007/978-3-319-72456-0_7.","ista":"Bondarenko A, Mellit A, Prymak A, Radchenko D, Viazovska M. 2018.There is no strongly regular graph with parameters (460; 153; 32; 60). In: Contemporary Computational Mathematics. , 131–134.","mla":"Bondarenko, Andriy, et al. “There Is No Strongly Regular Graph with Parameters (460; 153; 32; 60).” Contemporary Computational Mathematics, Springer, 2018, pp. 131–34, doi:10.1007/978-3-319-72456-0_7.","ama":"Bondarenko A, Mellit A, Prymak A, Radchenko D, Viazovska M. There is no strongly regular graph with parameters (460; 153; 32; 60). In: Contemporary Computational Mathematics. Springer; 2018:131-134. doi:10.1007/978-3-319-72456-0_7","apa":"Bondarenko, A., Mellit, A., Prymak, A., Radchenko, D., & Viazovska, M. (2018). There is no strongly regular graph with parameters (460; 153; 32; 60). In Contemporary Computational Mathematics (pp. 131–134). Springer. https://doi.org/10.1007/978-3-319-72456-0_7","short":"A. Bondarenko, A. Mellit, A. Prymak, D. Radchenko, M. Viazovska, in:, Contemporary Computational Mathematics, Springer, 2018, pp. 131–134.","ieee":"A. Bondarenko, A. Mellit, A. Prymak, D. Radchenko, and M. Viazovska, “There is no strongly regular graph with parameters (460; 153; 32; 60),” in Contemporary Computational Mathematics, Springer, 2018, pp. 131–134."},"status":"public","type":"book_chapter","_id":"61"},{"has_accepted_license":"1","year":"2018","day":"20","publication":"Bio-Protocol","doi":"10.21769/bioprotoc.3018","date_published":"2018-09-20T00:00:00Z","date_created":"2019-04-29T09:40:33Z","acknowledgement":" FöFoLe project 947 (F.G.), the Friedrich-Baur-Stiftung project 41/16 (F.G.)","quality_controlled":"1","publisher":"Bio-Protocol","oa":1,"citation":{"chicago":"Fan, Shuxia, Michael Lorenz, Steffen Massberg, and Florian R Gärtner. “Platelet Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol. Bio-Protocol, 2018. https://doi.org/10.21769/bioprotoc.3018.","ista":"Fan S, Lorenz M, Massberg S, Gärtner FR. 2018. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 8(18), e3018.","mla":"Fan, Shuxia, et al. “Platelet Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol, vol. 8, no. 18, e3018, Bio-Protocol, 2018, doi:10.21769/bioprotoc.3018.","ieee":"S. Fan, M. Lorenz, S. Massberg, and F. R. Gärtner, “Platelet migration and bacterial trapping assay under flow,” Bio-Protocol, vol. 8, no. 18. Bio-Protocol, 2018.","short":"S. Fan, M. Lorenz, S. Massberg, F.R. Gärtner, Bio-Protocol 8 (2018).","apa":"Fan, S., Lorenz, M., Massberg, S., & Gärtner, F. R. (2018). Platelet migration and bacterial trapping assay under flow. Bio-Protocol. Bio-Protocol. https://doi.org/10.21769/bioprotoc.3018","ama":"Fan S, Lorenz M, Massberg S, Gärtner FR. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 2018;8(18). doi:10.21769/bioprotoc.3018"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Shuxia","last_name":"Fan","full_name":"Fan, Shuxia"},{"first_name":"Michael","full_name":"Lorenz, Michael","last_name":"Lorenz"},{"first_name":"Steffen","full_name":"Massberg, Steffen","last_name":"Massberg"},{"last_name":"Gärtner","orcid":"0000-0001-6120-3723","full_name":"Gärtner, Florian R","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","first_name":"Florian R"}],"title":"Platelet migration and bacterial trapping assay under flow","article_number":"e3018","project":[{"call_identifier":"H2020","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","grant_number":"747687","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells"}],"publication_identifier":{"issn":["2331-8325"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"6360","checksum":"d4588377e789da7f360b553ae02c5119","creator":"dernst","date_updated":"2020-07-14T12:47:28Z","file_size":2928337,"date_created":"2019-04-30T08:04:33Z","file_name":"2018_BioProtocol_Fan.pdf"}],"language":[{"iso":"eng"}],"volume":8,"issue":"18","ec_funded":1,"abstract":[{"lang":"eng","text":"Blood platelets are critical for hemostasis and thrombosis, but also play diverse roles during immune responses. We have recently reported that platelets migrate at sites of infection in vitro and in vivo. Importantly, platelets use their ability to migrate to collect and bundle fibrin (ogen)-bound bacteria accomplishing efficient intravascular bacterial trapping. Here, we describe a method that allows analyzing platelet migration in vitro, focusing on their ability to collect bacteria and trap bacteria under flow."}],"oa_version":"Published Version","month":"09","intvolume":" 8","date_updated":"2021-01-12T08:07:12Z","ddc":["570"],"department":[{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:47:28Z","_id":"6354","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Platelets","Cell migration","Bacteria","Shear flow","Fibrinogen","E. coli"]},{"date_updated":"2020-07-14T23:06:21Z","citation":{"short":"B. Petritsch, Open Access at IST Austria 2009-2017, IST Austria, 2018.","ieee":"B. Petritsch, Open Access at IST Austria 2009-2017. IST Austria, 2018.","apa":"Petritsch, B. (2018). Open Access at IST Austria 2009-2017. Presented at the Open-Access-Tage, Graz, Austria: IST Austria. https://doi.org/10.5281/zenodo.1410279","ama":"Petritsch B. Open Access at IST Austria 2009-2017. IST Austria; 2018. doi:10.5281/zenodo.1410279","mla":"Petritsch, Barbara. Open Access at IST Austria 2009-2017. IST Austria, 2018, doi:10.5281/zenodo.1410279.","ista":"Petritsch B. 2018. Open Access at IST Austria 2009-2017, IST Austria,p.","chicago":"Petritsch, Barbara. Open Access at IST Austria 2009-2017. IST Austria, 2018. https://doi.org/10.5281/zenodo.1410279."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["020"],"author":[{"id":"406048EC-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara","full_name":"Petritsch, Barbara","orcid":"0000-0003-2724-4614","last_name":"Petritsch"}],"department":[{"_id":"E-Lib"}],"file_date_updated":"2020-07-14T12:47:30Z","title":"Open Access at IST Austria 2009-2017","_id":"6459","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"Open-Access-Tage","start_date":"2018-09-24","end_date":"2018-09-26","location":"Graz, Austria"},"type":"conference_poster","keyword":["Open Access","Publication Analysis"],"status":"public","publication_status":"published","year":"2018","has_accepted_license":"1","language":[{"iso":"eng"}],"day":"24","file":[{"file_name":"Poster_Beitrag_125_Petritsch.pdf","date_created":"2019-05-16T07:26:25Z","creator":"dernst","file_size":1967778,"date_updated":"2020-07-14T12:47:30Z","checksum":"9063ab4d10ea93353c3a03bbf53fbcf1","file_id":"6460","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"date_created":"2019-05-16T07:27:14Z","doi":"10.5281/zenodo.1410279","date_published":"2018-09-24T00:00:00Z","oa_version":"Published Version","oa":1,"publisher":"IST Austria","month":"09"},{"type":"book_chapter","status":"public","_id":"6525","author":[{"first_name":"Tamás","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","full_name":"Hausel, Tamás","last_name":"Hausel"},{"full_name":"Mellit, Anton","last_name":"Mellit","first_name":"Anton","id":"388D3134-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pei","full_name":"Pei, Du","first_name":"Du"}],"title":"Mirror symmetry with branes by equivariant verlinde formulas","department":[{"_id":"TaHa"}],"citation":{"ista":"Hausel T, Mellit A, Pei D. 2018.Mirror symmetry with branes by equivariant verlinde formulas. In: Geometry and Physics: Volume I. , 189–218.","chicago":"Hausel, Tamás, Anton Mellit, and Du Pei. “Mirror Symmetry with Branes by Equivariant Verlinde Formulas.” In Geometry and Physics: Volume I, 189–218. Oxford University Press, 2018. https://doi.org/10.1093/oso/9780198802013.003.0009.","short":"T. Hausel, A. Mellit, D. Pei, in:, Geometry and Physics: Volume I, Oxford University Press, 2018, pp. 189–218.","ieee":"T. Hausel, A. Mellit, and D. Pei, “Mirror symmetry with branes by equivariant verlinde formulas,” in Geometry and Physics: Volume I, Oxford University Press, 2018, pp. 189–218.","apa":"Hausel, T., Mellit, A., & Pei, D. (2018). Mirror symmetry with branes by equivariant verlinde formulas. In Geometry and Physics: Volume I (pp. 189–218). Oxford University Press. https://doi.org/10.1093/oso/9780198802013.003.0009","ama":"Hausel T, Mellit A, Pei D. Mirror symmetry with branes by equivariant verlinde formulas. In: Geometry and Physics: Volume I. Oxford University Press; 2018:189-218. doi:10.1093/oso/9780198802013.003.0009","mla":"Hausel, Tamás, et al. “Mirror Symmetry with Branes by Equivariant Verlinde Formulas.” Geometry and Physics: Volume I, Oxford University Press, 2018, pp. 189–218, doi:10.1093/oso/9780198802013.003.0009."},"date_updated":"2021-01-12T08:07:52Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"quality_controlled":"1","publisher":"Oxford University Press","month":"01","abstract":[{"text":"This chapter finds an agreement of equivariant indices of semi-classical homomorphisms between pairwise mirror branes in the GL2 Higgs moduli space on a Riemann surface. On one side of the agreement, components of the Lagrangian brane of U(1,1) Higgs bundles, whose mirror was proposed by Hitchin to be certain even exterior powers of the hyperholomorphic Dirac bundle on the SL2 Higgs moduli space, are present. The agreement arises from a mysterious functional equation. This gives strong computational evidence for Hitchin’s proposal.","lang":"eng"}],"oa_version":"None","page":"189-218","date_published":"2018-01-01T00:00:00Z","doi":"10.1093/oso/9780198802013.003.0009","date_created":"2019-06-06T12:42:01Z","publication_identifier":{"isbn":["9780198802013","9780191840500"]},"year":"2018","publication_status":"published","day":"01","publication":"Geometry and Physics: Volume I","language":[{"iso":"eng"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random Matrices.” Probability Theory and Related Fields. Springer, 2018. https://doi.org/10.1007/s00440-017-0787-8.","ista":"Lee J, Schnelli K. 2018. Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. 171(1–2), 543–616.","mla":"Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random Matrices.” Probability Theory and Related Fields, vol. 171, no. 1–2, 543–616, Springer, 2018, doi:10.1007/s00440-017-0787-8.","ieee":"J. Lee and K. Schnelli, “Local law and Tracy–Widom limit for sparse random matrices,” Probability Theory and Related Fields, vol. 171, no. 1–2. Springer, 2018.","short":"J. Lee, K. Schnelli, Probability Theory and Related Fields 171 (2018).","ama":"Lee J, Schnelli K. Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. 2018;171(1-2). doi:10.1007/s00440-017-0787-8","apa":"Lee, J., & Schnelli, K. (2018). Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-017-0787-8"},"title":"Local law and Tracy–Widom limit for sparse random matrices","publist_id":"7017","author":[{"first_name":"Jii","full_name":"Lee, Jii","last_name":"Lee"},{"last_name":"Schnelli","full_name":"Schnelli, Kevin","orcid":"0000-0003-0954-3231","first_name":"Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["1605.08767"]},"article_number":"543-616","project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"day":"14","publication":"Probability Theory and Related Fields","year":"2018","doi":"10.1007/s00440-017-0787-8","date_published":"2018-06-14T00:00:00Z","date_created":"2018-12-11T11:47:56Z","quality_controlled":"1","publisher":"Springer","oa":1,"date_updated":"2021-01-12T08:09:33Z","department":[{"_id":"LaEr"}],"_id":"690","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","volume":171,"issue":"1-2","ec_funded":1,"oa_version":"Preprint","abstract":[{"text":"We consider spectral properties and the edge universality of sparse random matrices, the class of random matrices that includes the adjacency matrices of the Erdős–Rényi graph model G(N, p). We prove a local law for the eigenvalue density up to the spectral edges. Under a suitable condition on the sparsity, we also prove that the rescaled extremal eigenvalues exhibit GOE Tracy–Widom fluctuations if a deterministic shift of the spectral edge due to the sparsity is included. For the adjacency matrix of the Erdős–Rényi graph this establishes the Tracy–Widom fluctuations of the second largest eigenvalue when p is much larger than N−2/3 with a deterministic shift of order (Np)−1.","lang":"eng"}],"month":"06","intvolume":" 171","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1605.08767","open_access":"1"}]},{"department":[{"_id":"VlKo"}],"date_updated":"2021-01-12T08:11:32Z","type":"journal_article","status":"public","_id":"703","volume":40,"issue":"7","publication_status":"published","publication_identifier":{"issn":["01628828"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1508.07902","open_access":"1"}],"scopus_import":1,"intvolume":" 40","month":"07","abstract":[{"text":"We consider the NP-hard problem of MAP-inference for undirected discrete graphical models. We propose a polynomial time and practically efficient algorithm for finding a part of its optimal solution. Specifically, our algorithm marks some labels of the considered graphical model either as (i) optimal, meaning that they belong to all optimal solutions of the inference problem; (ii) non-optimal if they provably do not belong to any solution. With access to an exact solver of a linear programming relaxation to the MAP-inference problem, our algorithm marks the maximal possible (in a specified sense) number of labels. We also present a version of the algorithm, which has access to a suboptimal dual solver only and still can ensure the (non-)optimality for the marked labels, although the overall number of the marked labels may decrease. We propose an efficient implementation, which runs in time comparable to a single run of a suboptimal dual solver. Our method is well-scalable and shows state-of-the-art results on computational benchmarks from machine learning and computer vision.","lang":"eng"}],"oa_version":"Preprint","external_id":{"arxiv":["1508.07902"]},"publist_id":"6992","author":[{"first_name":"Alexander","last_name":"Shekhovtsov","full_name":"Shekhovtsov, Alexander"},{"full_name":"Swoboda, Paul","last_name":"Swoboda","id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul"},{"first_name":"Bogdan","last_name":"Savchynskyy","full_name":"Savchynskyy, Bogdan"}],"title":"Maximum persistency via iterative relaxed inference with graphical models","citation":{"ista":"Shekhovtsov A, Swoboda P, Savchynskyy B. 2018. Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. 40(7), 1668–1682.","chicago":"Shekhovtsov, Alexander, Paul Swoboda, and Bogdan Savchynskyy. “Maximum Persistency via Iterative Relaxed Inference with Graphical Models.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2018. https://doi.org/10.1109/TPAMI.2017.2730884.","short":"A. Shekhovtsov, P. Swoboda, B. Savchynskyy, IEEE Transactions on Pattern Analysis and Machine Intelligence 40 (2018) 1668–1682.","ieee":"A. Shekhovtsov, P. Swoboda, and B. Savchynskyy, “Maximum persistency via iterative relaxed inference with graphical models,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40, no. 7. IEEE, pp. 1668–1682, 2018.","ama":"Shekhovtsov A, Swoboda P, Savchynskyy B. Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2018;40(7):1668-1682. doi:10.1109/TPAMI.2017.2730884","apa":"Shekhovtsov, A., Swoboda, P., & Savchynskyy, B. (2018). Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2017.2730884","mla":"Shekhovtsov, Alexander, et al. “Maximum Persistency via Iterative Relaxed Inference with Graphical Models.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40, no. 7, IEEE, 2018, pp. 1668–82, doi:10.1109/TPAMI.2017.2730884."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"1668-1682","date_created":"2018-12-11T11:48:01Z","doi":"10.1109/TPAMI.2017.2730884","date_published":"2018-07-01T00:00:00Z","year":"2018","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","day":"01","oa":1,"publisher":"IEEE","quality_controlled":"1"},{"_id":"7116","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"conference":{"name":"EDBT: Conference on Extending Database Technology","start_date":"2018-03-26","end_date":"2018-03-29","location":"Vienna, Austria"},"type":"conference","ddc":["000"],"date_updated":"2023-02-23T12:59:17Z","department":[{"_id":"DaAl"}],"file_date_updated":"2020-07-14T12:47:49Z","oa_version":"Published Version","abstract":[{"text":"Training deep learning models has received tremendous research interest recently. In particular, there has been intensive research on reducing the communication cost of training when using multiple computational devices, through reducing the precision of the underlying data representation. Naturally, such methods induce system trade-offs—lowering communication precision could de-crease communication overheads and improve scalability; but, on the other hand, it can also reduce the accuracy of training. In this paper, we study this trade-off space, and ask:Can low-precision communication consistently improve the end-to-end performance of training modern neural networks, with no accuracy loss?From the performance point of view, the answer to this question may appear deceptively easy: compressing communication through low precision should help when the ratio between communication and computation is high. However, this answer is less straightforward when we try to generalize this principle across various neural network architectures (e.g., AlexNet vs. ResNet),number of GPUs (e.g., 2 vs. 8 GPUs), machine configurations(e.g., EC2 instances vs. NVIDIA DGX-1), communication primitives (e.g., MPI vs. NCCL), and even different GPU architectures(e.g., Kepler vs. Pascal). Currently, it is not clear how a realistic realization of all these factors maps to the speed up provided by low-precision communication. In this paper, we conduct an empirical study to answer this question and report the insights.","lang":"eng"}],"month":"03","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"date_created":"2019-11-26T14:23:04Z","file_name":"2018_OpenProceedings_Grubic.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:49Z","file_size":1603204,"checksum":"ec979b56abc71016d6e6adfdadbb4afe","file_id":"7118","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"isbn":["9783893180783"],"issn":["2367-2005"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Grubic, Demjan, et al. “Synchronous Multi-GPU Training for Deep Learning with Low-Precision Communications: An Empirical Study.” Proceedings of the 21st International Conference on Extending Database Technology, OpenProceedings, 2018, pp. 145–56, doi:10.5441/002/EDBT.2018.14.","short":"D. Grubic, L. Tam, D.-A. Alistarh, C. Zhang, in:, Proceedings of the 21st International Conference on Extending Database Technology, OpenProceedings, 2018, pp. 145–156.","ieee":"D. Grubic, L. Tam, D.-A. Alistarh, and C. Zhang, “Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study,” in Proceedings of the 21st International Conference on Extending Database Technology, Vienna, Austria, 2018, pp. 145–156.","apa":"Grubic, D., Tam, L., Alistarh, D.-A., & Zhang, C. (2018). Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. In Proceedings of the 21st International Conference on Extending Database Technology (pp. 145–156). Vienna, Austria: OpenProceedings. https://doi.org/10.5441/002/EDBT.2018.14","ama":"Grubic D, Tam L, Alistarh D-A, Zhang C. Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. In: Proceedings of the 21st International Conference on Extending Database Technology. OpenProceedings; 2018:145-156. doi:10.5441/002/EDBT.2018.14","chicago":"Grubic, Demjan, Leo Tam, Dan-Adrian Alistarh, and Ce Zhang. “Synchronous Multi-GPU Training for Deep Learning with Low-Precision Communications: An Empirical Study.” In Proceedings of the 21st International Conference on Extending Database Technology, 145–56. OpenProceedings, 2018. https://doi.org/10.5441/002/EDBT.2018.14.","ista":"Grubic D, Tam L, Alistarh D-A, Zhang C. 2018. Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. Proceedings of the 21st International Conference on Extending Database Technology. EDBT: Conference on Extending Database Technology, 145–156."},"title":"Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study","article_processing_charge":"No","author":[{"first_name":"Demjan","last_name":"Grubic","full_name":"Grubic, Demjan"},{"first_name":"Leo","full_name":"Tam, Leo","last_name":"Tam"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"full_name":"Zhang, Ce","last_name":"Zhang","first_name":"Ce"}],"oa":1,"quality_controlled":"1","publisher":"OpenProceedings","publication":"Proceedings of the 21st International Conference on Extending Database Technology","day":"26","year":"2018","has_accepted_license":"1","date_created":"2019-11-26T14:19:11Z","doi":"10.5441/002/EDBT.2018.14","date_published":"2018-03-26T00:00:00Z","page":"145-156"},{"project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}],"citation":{"chicago":"Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” In 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), 124:59:1-59:25. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.ITCS.2019.59.","ista":"Pietrzak KZ. 2018. Proofs of catalytic space. 10th Innovations in Theoretical Computer Science Conference (ITCS 2019). ITCS: Innovations in theoretical Computer Science Conference, LIPIcs, vol. 124, 59:1-59:25.","mla":"Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), vol. 124, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 59:1-59:25, doi:10.4230/LIPICS.ITCS.2019.59.","ama":"Pietrzak KZ. Proofs of catalytic space. In: 10th Innovations in Theoretical Computer Science Conference (ITCS 2019). Vol 124. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:59:1-59:25. doi:10.4230/LIPICS.ITCS.2019.59","apa":"Pietrzak, K. Z. (2018). Proofs of catalytic space. In 10th Innovations in Theoretical Computer Science Conference (ITCS 2019) (Vol. 124, p. 59:1-59:25). San Diego, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ITCS.2019.59","ieee":"K. Z. Pietrzak, “Proofs of catalytic space,” in 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), San Diego, CA, United States, 2018, vol. 124, p. 59:1-59:25.","short":"K.Z. Pietrzak, in:, 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 59:1-59:25."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"}],"title":"Proofs of catalytic space","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","year":"2018","has_accepted_license":"1","publication":"10th Innovations in Theoretical Computer Science Conference (ITCS 2019)","day":"31","page":"59:1-59:25","date_created":"2020-01-30T09:16:05Z","doi":"10.4230/LIPICS.ITCS.2019.59","date_published":"2018-12-31T00:00:00Z","_id":"7407","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"end_date":"2019-01-12","location":"San Diego, CA, United States","start_date":"2019-01-10","name":"ITCS: Innovations in theoretical Computer Science Conference"},"type":"conference","status":"public","date_updated":"2021-01-12T08:13:26Z","ddc":["000"],"file_date_updated":"2020-07-14T12:47:57Z","department":[{"_id":"KrPi"}],"abstract":[{"lang":"eng","text":"Proofs of space (PoS) [Dziembowski et al., CRYPTO'15] are proof systems where a prover can convince a verifier that he \"wastes\" disk space. PoS were introduced as a more ecological and economical replacement for proofs of work which are currently used to secure blockchains like Bitcoin. In this work we investigate extensions of PoS which allow the prover to embed useful data into the dedicated space, which later can be recovered. Our first contribution is a security proof for the original PoS from CRYPTO'15 in the random oracle model (the original proof only applied to a restricted class of adversaries which can store a subset of the data an honest prover would store). When this PoS is instantiated with recent constructions of maximally depth robust graphs, our proof implies basically optimal security. As a second contribution we show three different extensions of this PoS where useful data can be embedded into the space required by the prover. Our security proof for the PoS extends (non-trivially) to these constructions. We discuss how some of these variants can be used as proofs of catalytic space (PoCS), a notion we put forward in this work, and which basically is a PoS where most of the space required by the prover can be used to backup useful data. Finally we discuss how one of the extensions is a candidate construction for a proof of replication (PoR), a proof system recently suggested in the Filecoin whitepaper. "}],"oa_version":"Published Version","main_file_link":[{"url":"https://eprint.iacr.org/2018/194","open_access":"1"}],"scopus_import":1,"alternative_title":["LIPIcs"],"intvolume":" 124","month":"12","publication_status":"published","publication_identifier":{"isbn":["978-3-95977-095-8"],"issn":["1868-8969"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"7443","checksum":"5cebb7f7849a3beda898f697d755dd96","creator":"dernst","file_size":822884,"date_updated":"2020-07-14T12:47:57Z","file_name":"2018_LIPIcs_Pietrzak.pdf","date_created":"2020-02-04T08:17:52Z"}],"ec_funded":1,"volume":124},{"article_number":"18","_id":"6001","status":"public","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T13:17:54Z","citation":{"mla":"Alistarh, Dan-Adrian, et al. “ThreadScan: Automatic and Scalable Memory Reclamation.” ACM Transactions on Parallel Computing, vol. 4, no. 4, 18, Association for Computing Machinery, 2018, doi:10.1145/3201897.","apa":"Alistarh, D.-A., Leiserson, W., Matveev, A., & Shavit, N. (2018). ThreadScan: Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing. Association for Computing Machinery. https://doi.org/10.1145/3201897","ama":"Alistarh D-A, Leiserson W, Matveev A, Shavit N. ThreadScan: Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing. 2018;4(4). doi:10.1145/3201897","ieee":"D.-A. Alistarh, W. Leiserson, A. Matveev, and N. Shavit, “ThreadScan: Automatic and scalable memory reclamation,” ACM Transactions on Parallel Computing, vol. 4, no. 4. Association for Computing Machinery, 2018.","short":"D.-A. Alistarh, W. Leiserson, A. Matveev, N. Shavit, ACM Transactions on Parallel Computing 4 (2018).","chicago":"Alistarh, Dan-Adrian, William Leiserson, Alexander Matveev, and Nir Shavit. “ThreadScan: Automatic and Scalable Memory Reclamation.” ACM Transactions on Parallel Computing. Association for Computing Machinery, 2018. https://doi.org/10.1145/3201897.","ista":"Alistarh D-A, Leiserson W, Matveev A, Shavit N. 2018. ThreadScan: Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing. 4(4), 18."},"title":"ThreadScan: Automatic and scalable memory reclamation","department":[{"_id":"DaAl"}],"author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh"},{"first_name":"William","full_name":"Leiserson, William","last_name":"Leiserson"},{"first_name":"Alexander","last_name":"Matveev","full_name":"Matveev, Alexander"},{"first_name":"Nir","full_name":"Shavit, Nir","last_name":"Shavit"}],"oa_version":"None","abstract":[{"text":"The concurrent memory reclamation problem is that of devising a way for a deallocating thread to verify that no other concurrent threads hold references to a memory block being deallocated. To date, in the absence of automatic garbage collection, there is no satisfactory solution to this problem; existing tracking methods like hazard pointers, reference counters, or epoch-based techniques like RCU are either prohibitively expensive or require significant programming expertise to the extent that implementing them efficiently can be worthy of a publication. None of the existing techniques are automatic or even semi-automated.\r\nIn this article, we take a new approach to concurrent memory reclamation. Instead of manually tracking access to memory locations as done in techniques like hazard pointers, or restricting shared accesses to specific epoch boundaries as in RCU, our algorithm, called ThreadScan, leverages operating system signaling to automatically detect which memory locations are being accessed by concurrent threads.\r\nInitial empirical evidence shows that ThreadScan scales surprisingly well and requires negligible programming effort beyond the standard use of Malloc and Free.","lang":"eng"}],"month":"09","intvolume":" 4","publisher":"Association for Computing Machinery","scopus_import":1,"quality_controlled":"1","day":"01","publication":"ACM Transactions on Parallel Computing","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2329-4949"]},"publication_status":"published","year":"2018","date_published":"2018-09-01T00:00:00Z","issue":"4","doi":"10.1145/3201897","related_material":{"record":[{"id":"779","status":"public","relation":"earlier_version"}]},"volume":4,"date_created":"2019-02-14T13:24:11Z"},{"file":[{"file_size":308339,"date_updated":"2020-07-14T12:48:03Z","creator":"dernst","file_name":"2018_ICLR_Polino.pdf","date_created":"2020-05-26T13:02:00Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"a4336c167978e81891970e4e4517a8c3","file_id":"7894"}],"day":"01","language":[{"iso":"eng"}],"publication":"6th International Conference on Learning Representations","has_accepted_license":"1","publication_status":"published","year":"2018","date_published":"2018-05-01T00:00:00Z","date_created":"2020-05-10T22:00:51Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Deep neural networks (DNNs) continue to make significant advances, solving tasks from image classification to translation or reinforcement learning. One aspect of the field receiving considerable attention is efficiently executing deep models in resource-constrained environments, such as mobile or embedded devices. This paper focuses on this problem, and proposes two new compression methods, which jointly leverage weight quantization and distillation of larger teacher networks into smaller student networks. The first method we propose is called quantized distillation and leverages distillation during the training process, by incorporating distillation loss, expressed with respect to the teacher, into the training of a student network whose weights are quantized to a limited set of levels. The second method, differentiable quantization, optimizes the location of quantization points through stochastic gradient descent, to better fit the behavior of the teacher model. We validate both methods through experiments on convolutional and recurrent architectures. We show that quantized shallow students can reach similar accuracy levels to full-precision teacher models, while providing order of magnitude compression, and inference speedup that is linear in the depth reduction. In sum, our results enable DNNs for resource-constrained environments to leverage architecture and accuracy advances developed on more powerful devices."}],"month":"05","quality_controlled":"1","scopus_import":1,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"date_updated":"2023-02-23T13:18:41Z","citation":{"mla":"Polino, Antonio, et al. “Model Compression via Distillation and Quantization.” 6th International Conference on Learning Representations, 2018.","ama":"Polino A, Pascanu R, Alistarh D-A. Model compression via distillation and quantization. In: 6th International Conference on Learning Representations. ; 2018.","apa":"Polino, A., Pascanu, R., & Alistarh, D.-A. (2018). Model compression via distillation and quantization. In 6th International Conference on Learning Representations. Vancouver, Canada.","ieee":"A. Polino, R. Pascanu, and D.-A. Alistarh, “Model compression via distillation and quantization,” in 6th International Conference on Learning Representations, Vancouver, Canada, 2018.","short":"A. Polino, R. Pascanu, D.-A. Alistarh, in:, 6th International Conference on Learning Representations, 2018.","chicago":"Polino, Antonio, Razvan Pascanu, and Dan-Adrian Alistarh. “Model Compression via Distillation and Quantization.” In 6th International Conference on Learning Representations, 2018.","ista":"Polino A, Pascanu R, Alistarh D-A. 2018. Model compression via distillation and quantization. 6th International Conference on Learning Representations. ICLR: International Conference on Learning Representations."},"title":"Model compression via distillation and quantization","file_date_updated":"2020-07-14T12:48:03Z","department":[{"_id":"DaAl"}],"author":[{"last_name":"Polino","full_name":"Polino, Antonio","first_name":"Antonio"},{"last_name":"Pascanu","full_name":"Pascanu, Razvan","first_name":"Razvan"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["1802.05668"]},"article_processing_charge":"No","_id":"7812","status":"public","type":"conference","conference":{"start_date":"2018-04-30","location":"Vancouver, Canada","end_date":"2018-05-03","name":"ICLR: International Conference on Learning Representations"}},{"department":[{"_id":"SiHi"}],"title":"Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture","author":[{"first_name":"Alfredo","last_name":"Llorca","full_name":"Llorca, Alfredo"},{"first_name":"Gabriele","full_name":"Ciceri, Gabriele","last_name":"Ciceri"},{"orcid":"0000-0002-8483-8753","full_name":"Beattie, Robert J","last_name":"Beattie","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","first_name":"Robert J"},{"first_name":"Fong K.","last_name":"Wong","full_name":"Wong, Fong K."},{"first_name":"Giovanni","full_name":"Diana, Giovanni","last_name":"Diana"},{"last_name":"Serafeimidou","full_name":"Serafeimidou, Eleni","first_name":"Eleni"},{"first_name":"Marian","last_name":"Fernández-Otero","full_name":"Fernández-Otero, Marian"},{"full_name":"Streicher, Carmen","last_name":"Streicher","first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sebastian J.","last_name":"Arnold","full_name":"Arnold, Sebastian J."},{"full_name":"Meyer, Martin","last_name":"Meyer","first_name":"Martin"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"first_name":"Miguel","last_name":"Maravall","full_name":"Maravall, Miguel"},{"full_name":"Marín, Oscar","last_name":"Marín","first_name":"Oscar"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Llorca, Alfredo, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/494088.","ieee":"A. Llorca et al., “Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture,” bioRxiv. Cold Spring Harbor Laboratory.","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.).","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. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/494088","ama":"Llorca A, Ciceri G, Beattie RJ, et al. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv. doi:10.1101/494088","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.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/494088.","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, 10.1101/494088."},"date_updated":"2021-01-12T08:20:00Z","status":"public","project":[{"grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"264E56E2-B435-11E9-9278-68D0E5697425","grant_number":"M02416","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex"}],"type":"preprint","_id":"8547","date_published":"2018-12-13T00:00:00Z","doi":"10.1101/494088","ec_funded":1,"date_created":"2020-09-21T12:01:50Z","day":"13","language":[{"iso":"eng"}],"publication":"bioRxiv","publication_status":"submitted","year":"2018","month":"12","publisher":"Cold Spring Harbor Laboratory","oa":1,"main_file_link":[{"url":"https://doi.org/10.1101/494088","open_access":"1"}],"oa_version":"Preprint","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.","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."}]},{"project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"editor":[{"last_name":"Lohstroh","full_name":"Lohstroh, Marten","first_name":"Marten"},{"first_name":"Patricia","full_name":"Derler, Patricia","last_name":"Derler"},{"first_name":"Marjan","full_name":"Sirjani, Marjan","last_name":"Sirjani"}],"title":"Computing average response time","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"last_name":"Otop","full_name":"Otop, Jan","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7968","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Computing Average Response Time.” In Principles of Modeling, edited by Marten Lohstroh, Patricia Derler, and Marjan Sirjani, 10760:143–61. Springer, 2018. https://doi.org/10.1007/978-3-319-95246-8_9.","ista":"Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time. In: Principles of Modeling. LNCS, vol. 10760, 143–161.","mla":"Chatterjee, Krishnendu, et al. “Computing Average Response Time.” Principles of Modeling, edited by Marten Lohstroh et al., vol. 10760, Springer, 2018, pp. 143–61, doi:10.1007/978-3-319-95246-8_9.","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 Principles of Modeling, vol. 10760, M. Lohstroh, P. Derler, and M. Sirjani, Eds. Springer, 2018, pp. 143–161.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2018). Computing average response time. In M. Lohstroh, P. Derler, & M. Sirjani (Eds.), Principles of Modeling (Vol. 10760, pp. 143–161). Springer. https://doi.org/10.1007/978-3-319-95246-8_9","ama":"Chatterjee K, Henzinger TA, Otop J. Computing average response time. In: Lohstroh M, Derler P, Sirjani M, eds. Principles of Modeling. Vol 10760. Springer; 2018:143-161. doi:10.1007/978-3-319-95246-8_9"},"publisher":"Springer","quality_controlled":"1","oa":1,"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.","date_published":"2018-07-20T00:00:00Z","doi":"10.1007/978-3-319-95246-8_9","date_created":"2018-12-11T11:44:33Z","page":"143 - 161","day":"20","publication":"Principles of Modeling","has_accepted_license":"1","year":"2018","status":"public","type":"book_chapter","_id":"86","file_date_updated":"2020-07-14T12:48:14Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"ddc":["000"],"date_updated":"2021-01-12T08:20:14Z","month":"07","intvolume":" 10760","scopus_import":1,"alternative_title":["LNCS"],"oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"volume":10760,"ec_funded":1,"file":[{"file_id":"7053","checksum":"9995c6ce6957333baf616fc4f20be597","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_PrinciplesModeling_Chatterjee.pdf","date_created":"2019-11-19T08:22:18Z","creator":"dernst","file_size":516307,"date_updated":"2020-07-14T12:48:14Z"}],"language":[{"iso":"eng"}],"publication_status":"published"},{"citation":{"chicago":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod, 2018. https://doi.org/10.20388/omp2018.00s1.001.","ista":"Danzl JG. 2018. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 4(S1), 11.","mla":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” Opera Medica et Physiologica, vol. 4, no. S1, Lobachevsky State University of Nizhny Novgorod, 2018, p. 11, doi:10.20388/omp2018.00s1.001.","ieee":"J. G. Danzl, “Diffraction-unlimited optical imaging for synaptic physiology,” Opera Medica et Physiologica, vol. 4, no. S1. Lobachevsky State University of Nizhny Novgorod, p. 11, 2018.","short":"J.G. Danzl, Opera Medica et Physiologica 4 (2018) 11.","apa":"Danzl, J. G. (2018). Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod. https://doi.org/10.20388/omp2018.00s1.001","ama":"Danzl JG. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 2018;4(S1):11. doi:10.20388/omp2018.00s1.001"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G"}],"article_processing_charge":"No","title":"Diffraction-unlimited optical imaging for synaptic physiology","year":"2018","day":"30","publication":"Opera Medica et Physiologica","page":"11","doi":"10.20388/omp2018.00s1.001","date_published":"2018-06-30T00:00:00Z","date_created":"2021-03-07T23:01:25Z","publisher":"Lobachevsky State University of Nizhny Novgorod","quality_controlled":"1","oa":1,"date_updated":"2021-12-03T07:31:05Z","department":[{"_id":"JoDa"}],"_id":"9229","type":"journal_article","article_type":"letter_note","status":"public","publication_identifier":{"issn":["2500-2287"],"eissn":["2500-2295"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":4,"issue":"S1","oa_version":"Published Version","scopus_import":"1","alternative_title":["Molecular and cellular neuroscience"],"main_file_link":[{"open_access":"1","url":"http://operamedphys.org/content/molecular-and-cellular-neuroscience"}],"month":"06","intvolume":" 4"},{"oa_version":"Published Version","abstract":[{"text":"Network games are widely used as a model for selfish resource-allocation problems. In the classicalmodel, each player selects a path connecting her source and target vertices. The cost of traversingan edge depends on theload; namely, number of players that traverse it. Thus, it abstracts the factthat different users may use a resource at different times and for different durations, which playsan important role in determining the costs of the users in reality. For example, when transmittingpackets in a communication network, routing traffic in a road network, or processing a task in aproduction system, actual sharing and congestion of resources crucially depends on time.In [13], we introducedtimed network games, which add a time component to network games.Each vertexvin the network is associated with a cost function, mapping the load onvto theprice that a player pays for staying invfor one time unit with this load. Each edge in thenetwork is guarded by the time intervals in which it can be traversed, which forces the players tospend time in the vertices. In this work we significantly extend the way time can be referred toin timed network games. In the model we study, the network is equipped withclocks, and, as intimed automata, edges are guarded by constraints on the values of the clocks, and their traversalmay involve a reset of some clocks. We argue that the stronger model captures many realisticnetworks. The addition of clocks breaks the techniques we developed in [13] and we developnew techniques in order to show that positive results on classic network games carry over to thestronger timed setting.","lang":"eng"}],"intvolume":" 117","month":"08","alternative_title":["LIPIcs"],"scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_size":542889,"date_updated":"2020-07-14T12:47:15Z","creator":"dernst","file_name":"2018_LIPIcs_Avni.pdf","date_created":"2019-02-14T14:22:04Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"41ab2ae9b63f5eb49fa995250c0ba128","file_id":"6007"}],"publication_status":"published","publication_identifier":{"issn":["1868-8969"]},"related_material":{"record":[{"relation":"earlier_version","id":"963","status":"public"}]},"volume":117,"_id":"6005","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"MFCS: Mathematical Foundations of Computer Science","end_date":"2018-08-31","location":"Liverpool, United Kingdom","start_date":"2018-08-27"},"type":"conference","ddc":["000"],"date_updated":"2023-02-23T14:02:58Z","file_date_updated":"2020-07-14T12:47:15Z","department":[{"_id":"ToHe"}],"oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","day":"01","year":"2018","has_accepted_license":"1","date_created":"2019-02-14T14:12:09Z","date_published":"2018-08-01T00:00:00Z","doi":"10.4230/LIPICS.MFCS.2018.23","article_number":"23","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"},{"name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369","call_identifier":"FWF","_id":"264B3912-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","ieee":"G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom, 2018, vol. 117.","apa":"Avni, G., Guha, S., & Kupferman, O. (2018). Timed network games with clocks (Vol. 117). Presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.MFCS.2018.23","ama":"Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.MFCS.2018.23","mla":"Avni, Guy, et al. Timed Network Games with Clocks. Vol. 117, 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.MFCS.2018.23.","ista":"Avni G, Guha S, Kupferman O. 2018. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 117, 23.","chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with Clocks,” Vol. 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.MFCS.2018.23."},"title":"Timed network games with clocks","article_processing_charge":"No","author":[{"id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy","last_name":"Avni","full_name":"Avni, Guy","orcid":"0000-0001-5588-8287"},{"first_name":"Shibashis","full_name":"Guha, Shibashis","last_name":"Guha"},{"last_name":"Kupferman","full_name":"Kupferman, Orna","first_name":"Orna"}]},{"month":"06","intvolume":" 16","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range.","lang":"eng"}],"volume":16,"issue":"6","related_material":{"record":[{"status":"public","id":"9839","relation":"research_data"}]},"file":[{"file_id":"5870","checksum":"908c52751bba30c55ed36789e5e4c84d","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-01-22T08:30:03Z","file_name":"2017_PLOS_Polechova.pdf","creator":"dernst","date_updated":"2020-07-14T12:46:01Z","file_size":6968201}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["15449173"]},"publication_status":"published","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"315","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:46:01Z","ddc":["576"],"date_updated":"2023-02-23T14:10:16Z","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"date_published":"2018-06-15T00:00:00Z","doi":"10.1371/journal.pbio.2005372","date_created":"2018-12-11T11:45:46Z","day":"15","publication":"PLoS Biology","has_accepted_license":"1","year":"2018","article_number":"e2005372","title":"Is the sky the limit? On the expansion threshold of a species’ range","publist_id":"7550","author":[{"first_name":"Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112","last_name":"Polechova"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology, vol. 16, no. 6, e2005372, Public Library of Science, 2018, doi:10.1371/journal.pbio.2005372.","apa":"Polechova, J. (2018). Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005372","ama":"Polechova J. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 2018;16(6). doi:10.1371/journal.pbio.2005372","ieee":"J. Polechova, “Is the sky the limit? On the expansion threshold of a species’ range,” PLoS Biology, vol. 16, no. 6. Public Library of Science, 2018.","short":"J. Polechova, PLoS Biology 16 (2018).","chicago":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005372.","ista":"Polechova J. 2018. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 16(6), e2005372."}},{"title":"FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis","article_processing_charge":"No","external_id":{"pmid":["29712855"]},"author":[{"full_name":"Frost, Jennifer M.","last_name":"Frost","first_name":"Jennifer M."},{"full_name":"Kim, M. Yvonne","last_name":"Kim","first_name":"M. Yvonne"},{"first_name":"Guen Tae","full_name":"Park, Guen Tae","last_name":"Park"},{"first_name":"Ping-Hung","full_name":"Hsieh, Ping-Hung","last_name":"Hsieh"},{"last_name":"Nakamura","full_name":"Nakamura, Miyuki","first_name":"Miyuki"},{"full_name":"Lin, Samuel J. H.","last_name":"Lin","first_name":"Samuel J. H."},{"last_name":"Yoo","full_name":"Yoo, Hyunjin","first_name":"Hyunjin"},{"first_name":"Jaemyung","full_name":"Choi, Jaemyung","last_name":"Choi"},{"first_name":"Yoko","last_name":"Ikeda","full_name":"Ikeda, Yoko"},{"last_name":"Kinoshita","full_name":"Kinoshita, Tetsu","first_name":"Tetsu"},{"last_name":"Choi","full_name":"Choi, Yeonhee","first_name":"Yeonhee"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"},{"full_name":"Fischer, Robert L.","last_name":"Fischer","first_name":"Robert L."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Frost, Jennifer M., M. Yvonne Kim, Guen Tae Park, Ping-Hung Hsieh, Miyuki Nakamura, Samuel J. H. Lin, Hyunjin Yoo, et al. “FACT Complex Is Required for DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1713333115.","ista":"Frost JM, Kim MY, Park GT, Hsieh P-H, Nakamura M, Lin SJH, Yoo H, Choi J, Ikeda Y, Kinoshita T, Choi Y, Zilberman D, Fischer RL. 2018. FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences. 115(20), E4720–E4729.","mla":"Frost, Jennifer M., et al. “FACT Complex Is Required for DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” Proceedings of the National Academy of Sciences, vol. 115, no. 20, National Academy of Sciences, 2018, pp. E4720–29, doi:10.1073/pnas.1713333115.","ama":"Frost JM, Kim MY, Park GT, et al. FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences. 2018;115(20):E4720-E4729. doi:10.1073/pnas.1713333115","apa":"Frost, J. M., Kim, M. Y., Park, G. T., Hsieh, P.-H., Nakamura, M., Lin, S. J. H., … Fischer, R. L. (2018). FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1713333115","ieee":"J. M. Frost et al., “FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis,” Proceedings of the National Academy of Sciences, vol. 115, no. 20. National Academy of Sciences, pp. E4720–E4729, 2018.","short":"J.M. Frost, M.Y. Kim, G.T. Park, P.-H. Hsieh, M. Nakamura, S.J.H. Lin, H. Yoo, J. Choi, Y. Ikeda, T. Kinoshita, Y. Choi, D. Zilberman, R.L. Fischer, Proceedings of the National Academy of Sciences 115 (2018) E4720–E4729."},"date_created":"2021-06-07T06:11:28Z","doi":"10.1073/pnas.1713333115","date_published":"2018-05-15T00:00:00Z","page":"E4720-E4729","publication":"Proceedings of the National Academy of Sciences","day":"15","year":"2018","has_accepted_license":"1","oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","file_date_updated":"2021-06-07T06:16:38Z","department":[{"_id":"DaZi"}],"ddc":["580"],"extern":"1","date_updated":"2021-12-14T07:53:40Z","keyword":["Multidisciplinary"],"status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","_id":"9471","volume":115,"related_material":{"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/187674 "}]},"issue":"20","language":[{"iso":"eng"}],"file":[{"file_size":3045260,"date_updated":"2021-06-07T06:16:38Z","creator":"asandaue","file_name":"2018_PNAS_Frost.pdf","date_created":"2021-06-07T06:16:38Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"9472","checksum":"810260dc0e3cc3033e15c19ad0dc123e"}],"publication_status":"published","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"intvolume":" 115","month":"05","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons and at the boundaries of large transposons, but how DME interacts with these diverse chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) subunit of the chromatin remodeler FACT (facilitates chromatin transactions), was previously shown to be involved in the DME-dependent regulation of genomic imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction between DME and chromatin, we focused on the activity of the two FACT subunits, SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of target sites, the first being euchromatic and accessible to DME, but the second, representing over half of DME targets, requiring the action of FACT for DME-mediated DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets are GC-rich heterochromatin domains with high nucleosome occupancy enriched with H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated linker histone H1 specifically mediates the requirement for FACT at a subset of DME-target loci. Overall, our results demonstrate that FACT is required for DME targeting by facilitating its access to heterochromatin.","lang":"eng"}]},{"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"day":"11","year":"2018","doi":"10.4230/LIPIcs.SoCG.2018.40","date_published":"2018-06-11T00:00:00Z","date_created":"2018-12-11T11:45:05Z","page":"40.1 - 40.14","project":[{"_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs","grant_number":"M02281"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Fulek, Radoslav, and Jan Kynčl. The ℤ2-Genus of Kuratowski Minors. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14, doi:10.4230/LIPIcs.SoCG.2018.40.","ieee":"R. Fulek and J. Kynčl, “The ℤ2-Genus of Kuratowski minors,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 40.1-40.14.","short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14.","apa":"Fulek, R., & Kynčl, J. (2018). The ℤ2-Genus of Kuratowski minors (Vol. 99, p. 40.1-40.14). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.40","ama":"Fulek R, Kynčl J. The ℤ2-Genus of Kuratowski minors. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:40.1-40.14. doi:10.4230/LIPIcs.SoCG.2018.40","chicago":"Fulek, Radoslav, and Jan Kynčl. “The ℤ2-Genus of Kuratowski Minors,” 99:40.1-40.14. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.40.","ista":"Fulek R, Kynčl J. 2018. The ℤ2-Genus of Kuratowski minors. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 40.1-40.14."},"title":"The ℤ2-Genus of Kuratowski minors","publist_id":"7734","author":[{"full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav"},{"first_name":"Jan","full_name":"Kynčl, Jan","last_name":"Kynčl"}],"external_id":{"arxiv":["1803.05085"]},"article_processing_charge":"No","oa_version":"Submitted Version","abstract":[{"text":"A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The ℤ2-genus of a graph G is the minimum g such that G has an independently even drawing on the orientable surface of genus g. An unpublished result by Robertson and Seymour implies that for every t, every graph of sufficiently large genus contains as a minor a projective t × t grid or one of the following so-called t-Kuratowski graphs: K3, t, or t copies of K5 or K3,3 sharing at most 2 common vertices. We show that the ℤ2-genus of graphs in these families is unbounded in t; in fact, equal to their genus. Together, this implies that the genus of a graph is bounded from above by a function of its ℤ2-genus, solving a problem posed by Schaefer and Štefankovič, and giving an approximate version of the Hanani-Tutte theorem on orientable surfaces.","lang":"eng"}],"month":"06","intvolume":" 99","alternative_title":["LIPIcs"],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1803.05085","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":99,"related_material":{"record":[{"id":"11593","status":"public","relation":"later_version"}]},"_id":"186","status":"public","type":"conference","conference":{"name":"SoCG: Symposium on Computational Geometry","end_date":"2018-06-14","location":"Budapest, Hungary","start_date":"2018-06-11"},"date_updated":"2023-08-14T12:43:51Z","department":[{"_id":"UlWa"}]},{"conference":{"location":"Boston, MA, United States","end_date":"2017-09-27","start_date":"201-09-25","name":"GD 2017: Graph Drawing and Network Visualization"},"type":"conference","status":"public","_id":"433","department":[{"_id":"UlWa"}],"date_updated":"2023-08-24T14:39:32Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.08037"}],"scopus_import":1,"alternative_title":["LNCS"],"intvolume":" 10692","month":"01","abstract":[{"text":"A thrackle is a graph drawn in the plane so that every pair of its edges meet exactly once: either at a common end vertex or in a proper crossing. We prove that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are defined similarly, except that every pair of edges that do not share a vertex are allowed to cross an odd number of times. It is also shown that the maximum number of edges of a quasi-thrackle on n vertices is 3/2(n-1), and that this bound is best possible for infinitely many values of n.","lang":"eng"}],"oa_version":"Submitted Version","volume":10692,"related_material":{"record":[{"status":"public","id":"5857","relation":"later_version"}]},"publication_status":"published","language":[{"iso":"eng"}],"external_id":{"arxiv":["1708.08037"]},"author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav","last_name":"Fulek","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774"},{"first_name":"János","full_name":"Pach, János","last_name":"Pach"}],"publist_id":"7390","title":"Thrackles: An improved upper bound","citation":{"ista":"Fulek R, Pach J. 2018. Thrackles: An improved upper bound. GD 2017: Graph Drawing and Network Visualization, LNCS, vol. 10692, 160–166.","chicago":"Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound,” 10692:160–66. Springer, 2018. https://doi.org/10.1007/978-3-319-73915-1_14.","ieee":"R. Fulek and J. Pach, “Thrackles: An improved upper bound,” presented at the GD 2017: Graph Drawing and Network Visualization, Boston, MA, United States, 2018, vol. 10692, pp. 160–166.","short":"R. Fulek, J. Pach, in:, Springer, 2018, pp. 160–166.","ama":"Fulek R, Pach J. Thrackles: An improved upper bound. In: Vol 10692. Springer; 2018:160-166. doi:10.1007/978-3-319-73915-1_14","apa":"Fulek, R., & Pach, J. (2018). Thrackles: An improved upper bound (Vol. 10692, pp. 160–166). Presented at the GD 2017: Graph Drawing and Network Visualization, Boston, MA, United States: Springer. https://doi.org/10.1007/978-3-319-73915-1_14","mla":"Fulek, Radoslav, and János Pach. Thrackles: An Improved Upper Bound. Vol. 10692, Springer, 2018, pp. 160–66, doi:10.1007/978-3-319-73915-1_14."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"Springer","page":"160 - 166","date_created":"2018-12-11T11:46:27Z","doi":"10.1007/978-3-319-73915-1_14","date_published":"2018-01-21T00:00:00Z","year":"2018","day":"21"},{"type":"research_data_reference","status":"public","_id":"9837","article_processing_charge":"No","author":[{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"first_name":"Pragya","last_name":"Chaube","full_name":"Chaube, Pragya"},{"first_name":"Hernán E.","last_name":"Morales","full_name":"Morales, Hernán E."},{"full_name":"Larsson, Tomas","last_name":"Larsson","first_name":"Tomas"},{"last_name":"Lemmon","full_name":"Lemmon, Alan R.","first_name":"Alan R."},{"first_name":"Emily M.","last_name":"Lemmon","full_name":"Lemmon, Emily M."},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"last_name":"Panova","full_name":"Panova, Marina","first_name":"Marina"},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"},{"last_name":"Johannesson","full_name":"Johannesson, Kerstin","first_name":"Kerstin"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969"},{"last_name":"Butlin","full_name":"Butlin, Roger K.","first_name":"Roger K."}],"department":[{"_id":"NiBa"}],"title":"Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","citation":{"mla":"Faria, Rui, et al. Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes. Dryad, 2018, doi:10.5061/dryad.72cg113.","ama":"Faria R, Chaube P, Morales HE, et al. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. 2018. doi:10.5061/dryad.72cg113","apa":"Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2018). Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Dryad. https://doi.org/10.5061/dryad.72cg113","short":"R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, (2018).","ieee":"R. Faria et al., “Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.","chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Dryad, 2018. https://doi.org/10.5061/dryad.72cg113.","ista":"Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2018. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes, Dryad, 10.5061/dryad.72cg113."},"date_updated":"2023-08-24T14:50:26Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.72cg113"}],"oa":1,"publisher":"Dryad","month":"10","abstract":[{"text":"Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients.","lang":"eng"}],"oa_version":"Published Version","date_created":"2021-08-09T12:46:39Z","doi":"10.5061/dryad.72cg113","related_material":{"record":[{"status":"public","id":"6095","relation":"used_in_publication"}]},"date_published":"2018-10-09T00:00:00Z","year":"2018","day":"09"},{"volume":16,"publication_identifier":{"eisbn":["9783319747729"],"isbn":["9783319747712"],"eissn":["2211-2766"],"issn":["2211-2758"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1502.01072"}],"month":"03","place":"Cham","intvolume":" 16","abstract":[{"lang":"eng","text":"We prove that every congruence distributive variety has directed Jónsson terms, and every congruence modular variety has directed Gumm terms. The directed terms we construct witness every case of absorption witnessed by the original Jónsson or Gumm terms. This result is equivalent to a pair of claims about absorption for admissible preorders in congruence distributive and congruence modular varieties, respectively. For finite algebras, these absorption theorems have already seen significant applications, but until now, it was not clear if the theorems hold for general algebras as well. Our method also yields a novel proof of a result by P. Lipparini about the existence of a chain of terms (which we call Pixley terms) in varieties that are at the same time congruence distributive and k-permutable for some k."}],"oa_version":"Preprint","department":[{"_id":"VlKo"}],"date_updated":"2023-09-05T15:37:18Z","type":"book_chapter","status":"public","series_title":"OCTR","_id":"10864","page":"203-220","doi":"10.1007/978-3-319-74772-9_7","date_published":"2018-03-21T00:00:00Z","date_created":"2022-03-18T10:30:32Z","year":"2018","day":"21","publication":"Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"The second author was supported by National Science Center grant DEC-2011-/01/B/ST6/01006.","author":[{"id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandr","full_name":"Kazda, Alexandr","last_name":"Kazda"},{"first_name":"Marcin","full_name":"Kozik, Marcin","last_name":"Kozik"},{"last_name":"McKenzie","full_name":"McKenzie, Ralph","first_name":"Ralph"},{"full_name":"Moore, Matthew","last_name":"Moore","first_name":"Matthew"}],"external_id":{"arxiv":["1502.01072"]},"article_processing_charge":"No","title":"Absorption and directed Jónsson terms","editor":[{"first_name":"J","full_name":"Czelakowski, J","last_name":"Czelakowski"}],"citation":{"mla":"Kazda, Alexandr, et al. “Absorption and Directed Jónsson Terms.” Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, edited by J Czelakowski, vol. 16, Springer Nature, 2018, pp. 203–20, doi:10.1007/978-3-319-74772-9_7.","ama":"Kazda A, Kozik M, McKenzie R, Moore M. Absorption and directed Jónsson terms. In: Czelakowski J, ed. Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science. Vol 16. OCTR. Cham: Springer Nature; 2018:203-220. doi:10.1007/978-3-319-74772-9_7","apa":"Kazda, A., Kozik, M., McKenzie, R., & Moore, M. (2018). Absorption and directed Jónsson terms. In J. Czelakowski (Ed.), Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science (Vol. 16, pp. 203–220). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-74772-9_7","ieee":"A. Kazda, M. Kozik, R. McKenzie, and M. Moore, “Absorption and directed Jónsson terms,” in Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, vol. 16, J. Czelakowski, Ed. Cham: Springer Nature, 2018, pp. 203–220.","short":"A. Kazda, M. Kozik, R. McKenzie, M. Moore, in:, J. Czelakowski (Ed.), Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, Springer Nature, Cham, 2018, pp. 203–220.","chicago":"Kazda, Alexandr, Marcin Kozik, Ralph McKenzie, and Matthew Moore. “Absorption and Directed Jónsson Terms.” In Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, edited by J Czelakowski, 16:203–20. OCTR. Cham: Springer Nature, 2018. https://doi.org/10.1007/978-3-319-74772-9_7.","ista":"Kazda A, Kozik M, McKenzie R, Moore M. 2018.Absorption and directed Jónsson terms. In: Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science. vol. 16, 203–220."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial complex is shellable is NP-hard, hence NP-complete. This resolves a question raised, e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d ≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible pure d-dimensional complexes."}],"month":"06","intvolume":" 99","scopus_import":1,"alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"file":[{"file_name":"2018_LIPIcs_Goaoc.pdf","date_created":"2018-12-17T16:35:02Z","file_size":718414,"date_updated":"2020-07-14T12:45:18Z","creator":"dernst","checksum":"d12bdd60f04a57307867704b5f930afd","file_id":"5725","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":99,"related_material":{"record":[{"id":"7108","status":"public","relation":"later_version"}]},"_id":"184","status":"public","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"start_date":"2018-06-11","end_date":"2018-06-14","location":"Budapest, Hungary","name":"SoCG: Symposium on Computational Geometry"},"ddc":["516","000"],"date_updated":"2023-09-06T11:10:57Z","file_date_updated":"2020-07-14T12:45:18Z","department":[{"_id":"UlWa"}],"acknowledgement":"Partially supported by the project EMBEDS II (CZ: 7AMB17FR029, FR: 38087RM) of Czech-French collaboration.","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"day":"11","has_accepted_license":"1","year":"2018","date_published":"2018-06-11T00:00:00Z","doi":"10.4230/LIPIcs.SoCG.2018.41","date_created":"2018-12-11T11:45:04Z","page":"41:1 - 41:16","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Goaoc, Xavier, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Shellability Is NP-Complete,” 99:41:1-41:16. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.41.","ista":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. 2018. Shellability is NP-complete. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 41:1-41:16.","mla":"Goaoc, Xavier, et al. Shellability Is NP-Complete. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 41:1-41:16, doi:10.4230/LIPIcs.SoCG.2018.41.","apa":"Goaoc, X., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2018). Shellability is NP-complete (Vol. 99, p. 41:1-41:16). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.41","ama":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:41:1-41:16. doi:10.4230/LIPIcs.SoCG.2018.41","ieee":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “Shellability is NP-complete,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 41:1-41:16.","short":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 41:1-41:16."},"title":"Shellability is NP-complete","publist_id":"7736","author":[{"full_name":"Goaoc, Xavier","last_name":"Goaoc","first_name":"Xavier"},{"last_name":"Paták","full_name":"Paták, Pavel","first_name":"Pavel"},{"full_name":"Patakova, Zuzana","orcid":"0000-0002-3975-1683","last_name":"Patakova","id":"48B57058-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana"},{"id":"38AC689C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Tancer","orcid":"0000-0002-1191-6714","full_name":"Tancer, Martin"},{"orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"}]},{"date_updated":"2023-09-06T11:13:41Z","ddc":["516","000"],"file_date_updated":"2020-07-14T12:45:51Z","department":[{"_id":"UlWa"}],"_id":"285","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"location":"Budapest, Hungary","end_date":"2018-06-14","start_date":"2018-06-11","name":"SoCG: Symposium on Computational Geometry"},"type":"conference","status":"public","publication_status":"published","publication_identifier":{"issn":["18688969"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":642522,"date_updated":"2020-07-14T12:45:51Z","file_name":"2018_LIPIcs_Huszar.pdf","date_created":"2018-12-17T15:32:38Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5713","checksum":"530d084116778135d5bffaa317479cac"}],"volume":99,"related_material":{"record":[{"relation":"later_version","status":"public","id":"7093"}]},"abstract":[{"text":"In graph theory, as well as in 3-manifold topology, there exist several width-type parameters to describe how "simple" or "thin" a given graph or 3-manifold is. These parameters, such as pathwidth or treewidth for graphs, or the concept of thin position for 3-manifolds, play an important role when studying algorithmic problems; in particular, there is a variety of problems in computational 3-manifold topology - some of them known to be computationally hard in general - that become solvable in polynomial time as soon as the dual graph of the input triangulation has bounded treewidth. In view of these algorithmic results, it is natural to ask whether every 3-manifold admits a triangulation of bounded treewidth. We show that this is not the case, i.e., that there exists an infinite family of closed 3-manifolds not admitting triangulations of bounded pathwidth or treewidth (the latter implies the former, but we present two separate proofs). We derive these results from work of Agol and of Scharlemann and Thompson, by exhibiting explicit connections between the topology of a 3-manifold M on the one hand and width-type parameters of the dual graphs of triangulations of M on the other hand, answering a question that had been raised repeatedly by researchers in computational 3-manifold topology. In particular, we show that if a closed, orientable, irreducible, non-Haken 3-manifold M has a triangulation of treewidth (resp. pathwidth) k then the Heegaard genus of M is at most 48(k+1) (resp. 4(3k+1)).","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":1,"alternative_title":["LIPIcs"],"intvolume":" 99","month":"06","citation":{"chicago":"Huszár, Kristóf, Jonathan Spreer, and Uli Wagner. “On the Treewidth of Triangulated 3-Manifolds,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.46.","ista":"Huszár K, Spreer J, Wagner U. 2018. On the treewidth of triangulated 3-manifolds. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 46.","mla":"Huszár, Kristóf, et al. On the Treewidth of Triangulated 3-Manifolds. Vol. 99, 46, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.SoCG.2018.46.","apa":"Huszár, K., Spreer, J., & Wagner, U. (2018). On the treewidth of triangulated 3-manifolds (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.46","ama":"Huszár K, Spreer J, Wagner U. On the treewidth of triangulated 3-manifolds. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.SoCG.2018.46","short":"K. Huszár, J. Spreer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","ieee":"K. Huszár, J. Spreer, and U. Wagner, “On the treewidth of triangulated 3-manifolds,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1712.00434"]},"article_processing_charge":"No","publist_id":"7614","author":[{"last_name":"Huszár","full_name":"Huszár, Kristóf","orcid":"0000-0002-5445-5057","first_name":"Kristóf","id":"33C26278-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jonathan","full_name":"Spreer, Jonathan","last_name":"Spreer"},{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"}],"title":"On the treewidth of triangulated 3-manifolds","article_number":"46","year":"2018","has_accepted_license":"1","day":"01","date_created":"2018-12-11T11:45:37Z","doi":"10.4230/LIPIcs.SoCG.2018.46","date_published":"2018-06-01T00:00:00Z","acknowledgement":"Research of the second author was supported by the Einstein Foundation (project “Einstein Visiting Fellow Santos”) and by the Simons Foundation (“Simons Visiting Professors” program).","oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik"},{"title":"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method","department":[{"_id":"FyKo"}],"article_processing_charge":"No","author":[{"first_name":"Edgar","last_name":"Garriga","full_name":"Garriga, Edgar"},{"full_name":"di Tommaso, Paolo","last_name":"di Tommaso","first_name":"Paolo"},{"last_name":"Magis","full_name":"Magis, Cedrik","first_name":"Cedrik"},{"first_name":"Ionas","full_name":"Erb, Ionas","last_name":"Erb"},{"last_name":"Mansouri","full_name":"Mansouri, Leila","first_name":"Leila"},{"full_name":"Baltzis, Athanasios","last_name":"Baltzis","first_name":"Athanasios"},{"full_name":"Laayouni, Hafid","last_name":"Laayouni","first_name":"Hafid"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694"},{"full_name":"Floden, Evan","last_name":"Floden","first_name":"Evan"},{"last_name":"Notredame","full_name":"Notredame, Cedric","first_name":"Cedric"}],"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-06T14:32:51Z","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:10.5281/ZENODO.2025846","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. https://doi.org/10.5281/ZENODO.2025846","short":"E. Garriga, P. di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, (2018).","ieee":"E. Garriga et al., “Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method.” Zenodo, 2018.","mla":"Garriga, Edgar, et al. Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method. Zenodo, 2018, doi:10.5281/ZENODO.2025846.","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, 10.5281/ZENODO.2025846.","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. https://doi.org/10.5281/ZENODO.2025846."},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data_reference","_id":"13059","date_created":"2023-05-23T16:08:20Z","date_published":"2018-12-07T00:00:00Z","doi":"10.5281/ZENODO.2025846","related_material":{"record":[{"id":"7181","status":"public","relation":"used_in_publication"}]},"day":"07","year":"2018","month":"12","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.3271452","open_access":"1"}],"oa":1,"publisher":"Zenodo","oa_version":"Published Version","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"}]},{"_id":"49","status":"public","pubrep_id":"1033","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["530"],"supervisor":[{"first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros"}],"date_updated":"2023-09-07T12:27:43Z","file_date_updated":"2020-07-14T12:46:35Z","department":[{"_id":"GeKa"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Nowadays, quantum computation is receiving more and more attention as an alternative to the classical way of computing. For realizing a quantum computer, different devices are investigated as potential quantum bits. In this thesis, the focus is on Ge hut wires, which turned out to be promising candidates for implementing hole spin quantum bits. The advantages of Ge as a material system are the low hyperfine interaction for holes and the strong spin orbit coupling, as well as the compatibility with the highly developed CMOS processes in industry. In addition, Ge can also be isotopically purified which is expected to boost the spin coherence times. The strong spin orbit interaction for holes in Ge on the one hand enables the full electrical control of the quantum bit and on the other hand should allow short spin manipulation times. Starting with a bare Si wafer, this work covers the entire process reaching from growth over the fabrication and characterization of hut wire devices up to the demonstration of hole spin resonance. From experiments with single quantum dots, a large g-factor anisotropy between the in-plane and the out-of-plane direction was found. A comparison to a theoretical model unveiled the heavy-hole character of the lowest energy states. The second part of the thesis addresses double quantum dot devices, which were realized by adding two gate electrodes to a hut wire. In such devices, Pauli spin blockade was observed, which can serve as a read-out mechanism for spin quantum bits. Applying oscillating electric fields in spin blockade allowed the demonstration of continuous spin rotations and the extraction of a lower bound for the spin dephasing time. Despite the strong spin orbit coupling in Ge, the obtained value for the dephasing time is comparable to what has been recently reported for holes in Si. All in all, the presented results point out the high potential of Ge hut wires as a platform for long-lived, fast and fully electrically tunable hole spin quantum bits."}],"month":"07","alternative_title":["ISTA Thesis"],"file":[{"file_size":85539748,"date_updated":"2020-07-14T12:46:35Z","creator":"dernst","file_name":"2018_Thesis_Watzinger.pdf","date_created":"2019-04-09T07:13:28Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"b653b5216251f938ddbeafd1de88667c","file_id":"6249"},{"creator":"dernst","date_updated":"2020-07-14T12:46:35Z","file_size":21830697,"date_created":"2019-04-09T07:13:27Z","file_name":"2018_Thesis_Watzinger_source.zip","access_level":"closed","relation":"source_file","content_type":"application/zip","file_id":"6250","checksum":"39bcf8de7ac5b1bb516b11ce2f966785"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"H. Watzinger, Ge Hut Wires - from Growth to Hole Spin Resonance, Institute of Science and Technology Austria, 2018.","ieee":"H. Watzinger, “Ge hut wires - from growth to hole spin resonance,” Institute of Science and Technology Austria, 2018.","ama":"Watzinger H. Ge hut wires - from growth to hole spin resonance. 2018. doi:10.15479/AT:ISTA:th_1033","apa":"Watzinger, H. (2018). Ge hut wires - from growth to hole spin resonance. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1033","mla":"Watzinger, Hannes. Ge Hut Wires - from Growth to Hole Spin Resonance. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1033.","ista":"Watzinger H. 2018. Ge hut wires - from growth to hole spin resonance. Institute of Science and Technology Austria.","chicago":"Watzinger, Hannes. “Ge Hut Wires - from Growth to Hole Spin Resonance.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1033."},"title":"Ge hut wires - from growth to hole spin resonance","author":[{"full_name":"Watzinger, Hannes","last_name":"Watzinger","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","first_name":"Hannes"}],"publist_id":"8005","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","oa":1,"day":"30","has_accepted_license":"1","year":"2018","date_published":"2018-07-30T00:00:00Z","doi":"10.15479/AT:ISTA:th_1033","date_created":"2018-12-11T11:44:21Z","page":"77"},{"file_date_updated":"2020-07-14T12:45:24Z","department":[{"_id":"HeEd"}],"supervisor":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T12:25:32Z","ddc":["514","516"],"type":"dissertation","status":"public","pubrep_id":"1026","_id":"201","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"access_level":"closed","relation":"source_file","content_type":"application/zip","checksum":"dd699303623e96d1478a6ae07210dd05","file_id":"5918","creator":"kschuh","date_updated":"2020-07-14T12:45:24Z","file_size":11827713,"date_created":"2019-02-05T07:43:31Z","file_name":"IST-2018-1025-v2+5_ist-thesis-iglesias-11June2018(1).zip"},{"file_name":"IST-2018-1025-v2+4_ThesisIglesiasFinal11June2018.pdf","date_created":"2019-02-05T07:43:45Z","file_size":4783846,"date_updated":"2020-07-14T12:45:24Z","creator":"kschuh","checksum":"ba163849a190d2b41d66fef0e4983294","file_id":"5919","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"06","abstract":[{"text":"We describe arrangements of three-dimensional spheres from a geometrical and topological point of view. Real data (fitting this setup) often consist of soft spheres which show certain degree of deformation while strongly packing against each other. In this context, we answer the following questions: If we model a soft packing of spheres by hard spheres that are allowed to overlap, can we measure the volume in the overlapped areas? Can we be more specific about the overlap volume, i.e. quantify how much volume is there covered exactly twice, three times, or k times? What would be a good optimization criteria that rule the arrangement of soft spheres while making a good use of the available space? Fixing a particular criterion, what would be the optimal sphere configuration? The first result of this thesis are short formulas for the computation of volumes covered by at least k of the balls. The formulas exploit information contained in the order-k Voronoi diagrams and its closely related Level-k complex. The used complexes lead to a natural generalization into poset diagrams, a theoretical formalism that contains the order-k and degree-k diagrams as special cases. In parallel, we define different criteria to determine what could be considered an optimal arrangement from a geometrical point of view. Fixing a criterion, we find optimal soft packing configurations in 2D and 3D where the ball centers lie on a lattice. As a last step, we use tools from computational topology on real physical data, to show the potentials of higher-order diagrams in the description of melting crystals. The results of the experiments leaves us with an open window to apply the theories developed in this thesis in real applications.","lang":"eng"}],"oa_version":"Published Version","author":[{"id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","first_name":"Mabel","last_name":"Iglesias Ham","full_name":"Iglesias Ham, Mabel"}],"publist_id":"7712","article_processing_charge":"No","title":"Multiple covers with balls","citation":{"chicago":"Iglesias Ham, Mabel. “Multiple Covers with Balls.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1026.","ista":"Iglesias Ham M. 2018. Multiple covers with balls. Institute of Science and Technology Austria.","mla":"Iglesias Ham, Mabel. Multiple Covers with Balls. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1026.","ieee":"M. Iglesias Ham, “Multiple covers with balls,” Institute of Science and Technology Austria, 2018.","short":"M. Iglesias Ham, Multiple Covers with Balls, Institute of Science and Technology Austria, 2018.","ama":"Iglesias Ham M. Multiple covers with balls. 2018. doi:10.15479/AT:ISTA:th_1026","apa":"Iglesias Ham, M. (2018). Multiple covers with balls. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1026"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"171","doi":"10.15479/AT:ISTA:th_1026","date_published":"2018-06-11T00:00:00Z","date_created":"2018-12-11T11:45:10Z","has_accepted_license":"1","year":"2018","day":"11","publisher":"Institute of Science and Technology Austria","oa":1},{"project":[{"name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Zimin, Alexander. Learning from Dependent Data. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH1048.","short":"A. Zimin, Learning from Dependent Data, Institute of Science and Technology Austria, 2018.","ieee":"A. Zimin, “Learning from dependent data,” Institute of Science and Technology Austria, 2018.","apa":"Zimin, A. (2018). Learning from dependent data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH1048","ama":"Zimin A. Learning from dependent data. 2018. doi:10.15479/AT:ISTA:TH1048","chicago":"Zimin, Alexander. “Learning from Dependent Data.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH1048.","ista":"Zimin A. 2018. Learning from dependent data. Institute of Science and Technology Austria."},"title":"Learning from dependent data","article_processing_charge":"No","publist_id":"7986","author":[{"id":"37099E9C-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander","full_name":"Zimin, Alexander","last_name":"Zimin"}],"oa":1,"publisher":"Institute of Science and Technology Austria","day":"01","year":"2018","has_accepted_license":"1","date_created":"2018-12-11T11:44:27Z","date_published":"2018-09-01T00:00:00Z","doi":"10.15479/AT:ISTA:TH1048","page":"92","_id":"68","pubrep_id":"1048","status":"public","type":"dissertation","ddc":["004","519"],"date_updated":"2023-09-07T12:29:07Z","supervisor":[{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:47:40Z","department":[{"_id":"ChLa"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The most common assumption made in statistical learning theory is the assumption of the independent and identically distributed (i.i.d.) data. While being very convenient mathematically, it is often very clearly violated in practice. This disparity between the machine learning theory and applications underlies a growing demand in the development of algorithms that learn from dependent data and theory that can provide generalization guarantees similar to the independent situations. This thesis is dedicated to two variants of dependencies that can arise in practice. One is a dependence on the level of samples in a single learning task. Another dependency type arises in the multi-task setting when the tasks are dependent on each other even though the data for them can be i.i.d. In both cases we model the data (samples or tasks) as stochastic processes and introduce new algorithms for both settings that take into account and exploit the resulting dependencies. We prove the theoretical guarantees on the performance of the introduced algorithms under different evaluation criteria and, in addition, we compliment the theoretical study by the empirical one, where we evaluate some of the algorithms on two real world datasets to highlight their practical applicability."}],"month":"09","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"6253","checksum":"e849dd40a915e4d6c5572b51b517f098","creator":"dernst","file_size":1036137,"date_updated":"2020-07-14T12:47:40Z","file_name":"2018_Thesis_Zimin.pdf","date_created":"2019-04-09T07:32:47Z"},{"file_id":"6254","checksum":"da092153cec55c97461bd53c45c5d139","content_type":"application/zip","relation":"source_file","access_level":"closed","file_name":"2018_Thesis_Zimin_Source.zip","date_created":"2019-04-09T07:32:47Z","file_size":637490,"date_updated":"2020-07-14T12:47:40Z","creator":"dernst"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1},{"status":"public","pubrep_id":"1046","type":"dissertation","_id":"83","file_date_updated":"2020-07-14T12:48:11Z","department":[{"_id":"KrPi"}],"ddc":["004"],"supervisor":[{"last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"}],"date_updated":"2023-09-07T12:30:23Z","month":"09","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","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."}],"related_material":{"record":[{"id":"1229","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"1235","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"1236"},{"status":"public","id":"559","relation":"part_of_dissertation"}]},"ec_funded":1,"file":[{"date_created":"2019-04-09T06:43:41Z","file_name":"2018_Thesis_Abusalah.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:11Z","file_size":876241,"checksum":"c4b5f7d111755d1396787f41886fc674","file_id":"6245","access_level":"open_access","relation":"main_file","content_type":"application/pdf"},{"file_name":"2018_Thesis_Abusalah_source.tar.gz","date_created":"2019-04-09T06:43:41Z","file_size":2029190,"date_updated":"2020-07-14T12:48:11Z","creator":"dernst","checksum":"0f382ac56b471c48fd907d63eb87dafe","file_id":"6246","content_type":"application/x-gzip","relation":"source_file","access_level":"closed"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","project":[{"name":"Provable Security for Physical Cryptography","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","grant_number":"682815"}],"title":"Proof systems for sustainable decentralized cryptocurrencies","publist_id":"7971","author":[{"full_name":"Abusalah, Hamza M","last_name":"Abusalah","first_name":"Hamza M","id":"40297222-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Abusalah, Hamza M. Proof Systems for Sustainable Decentralized Cryptocurrencies. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1046.","ama":"Abusalah HM. Proof systems for sustainable decentralized cryptocurrencies. 2018. doi:10.15479/AT:ISTA:TH_1046","apa":"Abusalah, H. M. (2018). Proof systems for sustainable decentralized cryptocurrencies. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1046","ieee":"H. M. Abusalah, “Proof systems for sustainable decentralized cryptocurrencies,” Institute of Science and Technology Austria, 2018.","short":"H.M. Abusalah, Proof Systems for Sustainable Decentralized Cryptocurrencies, Institute of Science and Technology Austria, 2018.","chicago":"Abusalah, Hamza M. “Proof Systems for Sustainable Decentralized Cryptocurrencies.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1046.","ista":"Abusalah HM. 2018. Proof systems for sustainable decentralized cryptocurrencies. Institute of Science and Technology Austria."},"publisher":"Institute of Science and Technology Austria","oa":1,"doi":"10.15479/AT:ISTA:TH_1046","date_published":"2018-09-05T00:00:00Z","date_created":"2018-12-11T11:44:32Z","page":"59","day":"05","has_accepted_license":"1","year":"2018"},{"date_created":"2018-12-11T11:45:09Z","doi":"10.15479/AT:ISTA:th_1021","date_published":"2018-05-25T00:00:00Z","page":"113","day":"25","year":"2018","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","acknowledgement":"I also gratefully acknowledge the support of NVIDIA Corporation with the donation of the GPUs used for this research.","title":"Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images","article_processing_charge":"No","author":[{"id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander","last_name":"Kolesnikov","full_name":"Kolesnikov, Alexander"}],"publist_id":"7718","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Kolesnikov A. 2018. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria.","chicago":"Kolesnikov, Alexander. “Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1021.","ama":"Kolesnikov A. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. 2018. doi:10.15479/AT:ISTA:th_1021","apa":"Kolesnikov, A. (2018). Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1021","short":"A. Kolesnikov, Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images, Institute of Science and Technology Austria, 2018.","ieee":"A. Kolesnikov, “Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images,” Institute of Science and Technology Austria, 2018.","mla":"Kolesnikov, Alexander. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1021."},"project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036"}],"ec_funded":1,"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:45:22Z","file_size":12918758,"creator":"system","date_created":"2018-12-12T10:14:57Z","file_name":"IST-2018-1021-v1+1_thesis-unsigned-pdfa.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"bc678e02468d8ebc39dc7267dfb0a1c4","file_id":"5113"},{"file_id":"6225","checksum":"bc66973b086da5a043f1162dcfb1fde4","content_type":"application/zip","relation":"source_file","access_level":"closed","file_name":"2018_Thesis_Kolesnikov_source.zip","date_created":"2019-04-05T09:34:49Z","file_size":55973760,"date_updated":"2020-07-14T12:45:22Z","creator":"dernst"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"05","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"Modern computer vision systems heavily rely on statistical machine learning models, which typically require large amounts of labeled data to be learned reliably. Moreover, very recently computer vision research widely adopted techniques for representation learning, which further increase the demand for labeled data. However, for many important practical problems there is relatively small amount of labeled data available, so it is problematic to leverage full potential of the representation learning methods. One way to overcome this obstacle is to invest substantial resources into producing large labelled datasets. Unfortunately, this can be prohibitively expensive in practice. In this thesis we focus on the alternative way of tackling the aforementioned issue. We concentrate on methods, which make use of weakly-labeled or even unlabeled data. Specifically, the first half of the thesis is dedicated to the semantic image segmentation task. We develop a technique, which achieves competitive segmentation performance and only requires annotations in a form of global image-level labels instead of dense segmentation masks. Subsequently, we present a new methodology, which further improves segmentation performance by leveraging tiny additional feedback from a human annotator. By using our methods practitioners can greatly reduce the amount of data annotation effort, which is required to learn modern image segmentation models. In the second half of the thesis we focus on methods for learning from unlabeled visual data. We study a family of autoregressive models for modeling structure of natural images and discuss potential applications of these models. Moreover, we conduct in-depth study of one of these applications, where we develop the state-of-the-art model for the probabilistic image colorization task.","lang":"eng"}],"file_date_updated":"2020-07-14T12:45:22Z","department":[{"_id":"ChLa"}],"ddc":["004"],"date_updated":"2023-09-07T12:51:46Z","supervisor":[{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert"}],"pubrep_id":"1021","status":"public","type":"dissertation","_id":"197"},{"file_date_updated":"2020-07-14T12:47:40Z","department":[{"_id":"UlWa"}],"ddc":["514"],"date_updated":"2023-09-07T13:10:36Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"6774","volume":2,"issue":"3-4","related_material":{"record":[{"relation":"dissertation_contains","id":"6681","status":"public"}]},"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"cf9e7fcd2a113dd4828774fc75cdb7e8","file_id":"6775","file_size":1056278,"date_updated":"2020-07-14T12:47:40Z","creator":"dernst","file_name":"2018_JourAppliedComputTopology_Filakovsky.pdf","date_created":"2019-08-08T06:55:21Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2367-1726"],"eissn":["2367-1734"]},"publication_status":"published","month":"12","intvolume":" 2","oa_version":"Published Version","abstract":[{"lang":"eng","text":"A central problem of algebraic topology is to understand the homotopy groups 𝜋𝑑(𝑋) of a topological space X. For the computational version of the problem, it is well known that there is no algorithm to decide whether the fundamental group 𝜋1(𝑋) of a given finite simplicial complex X is trivial. On the other hand, there are several algorithms that, given a finite simplicial complex X that is simply connected (i.e., with 𝜋1(𝑋) trivial), compute the higher homotopy group 𝜋𝑑(𝑋) for any given 𝑑≥2 . However, these algorithms come with a caveat: They compute the isomorphism type of 𝜋𝑑(𝑋) , 𝑑≥2 as an abstract finitely generated abelian group given by generators and relations, but they work with very implicit representations of the elements of 𝜋𝑑(𝑋) . Converting elements of this abstract group into explicit geometric maps from the d-dimensional sphere 𝑆𝑑 to X has been one of the main unsolved problems in the emerging field of computational homotopy theory. Here we present an algorithm that, given a simply connected space X, computes 𝜋𝑑(𝑋) and represents its elements as simplicial maps from a suitable triangulation of the d-sphere 𝑆𝑑 to X. For fixed d, the algorithm runs in time exponential in size(𝑋) , the number of simplices of X. Moreover, we prove that this is optimal: For every fixed 𝑑≥2 , we construct a family of simply connected spaces X such that for any simplicial map representing a generator of 𝜋𝑑(𝑋) , the size of the triangulation of 𝑆𝑑 on which the map is defined, is exponential in size(𝑋) ."}],"title":"Computing simplicial representatives of homotopy group elements","author":[{"full_name":"Filakovský, Marek","last_name":"Filakovský","first_name":"Marek","id":"3E8AF77E-F248-11E8-B48F-1D18A9856A87"},{"id":"473294AE-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Franek","orcid":"0000-0001-8878-8397","full_name":"Franek, Peter"},{"last_name":"Wagner","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"},{"last_name":"Zhechev","full_name":"Zhechev, Stephan Y","first_name":"Stephan Y","id":"3AA52972-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Filakovský M, Franek P, Wagner U, Zhechev SY. 2018. Computing simplicial representatives of homotopy group elements. Journal of Applied and Computational Topology. 2(3–4), 177–231.","chicago":"Filakovský, Marek, Peter Franek, Uli Wagner, and Stephan Y Zhechev. “Computing Simplicial Representatives of Homotopy Group Elements.” Journal of Applied and Computational Topology. Springer, 2018. https://doi.org/10.1007/s41468-018-0021-5.","short":"M. Filakovský, P. Franek, U. Wagner, S.Y. Zhechev, Journal of Applied and Computational Topology 2 (2018) 177–231.","ieee":"M. Filakovský, P. Franek, U. Wagner, and S. Y. Zhechev, “Computing simplicial representatives of homotopy group elements,” Journal of Applied and Computational Topology, vol. 2, no. 3–4. Springer, pp. 177–231, 2018.","ama":"Filakovský M, Franek P, Wagner U, Zhechev SY. Computing simplicial representatives of homotopy group elements. Journal of Applied and Computational Topology. 2018;2(3-4):177-231. doi:10.1007/s41468-018-0021-5","apa":"Filakovský, M., Franek, P., Wagner, U., & Zhechev, S. Y. (2018). Computing simplicial representatives of homotopy group elements. Journal of Applied and Computational Topology. Springer. https://doi.org/10.1007/s41468-018-0021-5","mla":"Filakovský, Marek, et al. “Computing Simplicial Representatives of Homotopy Group Elements.” Journal of Applied and Computational Topology, vol. 2, no. 3–4, Springer, 2018, pp. 177–231, doi:10.1007/s41468-018-0021-5."},"project":[{"name":"Robust invariants of Nonlinear Systems","grant_number":"M01980","_id":"25F8B9BC-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF"}],"doi":"10.1007/s41468-018-0021-5","date_published":"2018-12-01T00:00:00Z","date_created":"2019-08-08T06:47:40Z","page":"177-231","day":"01","publication":"Journal of Applied and Computational Topology","has_accepted_license":"1","year":"2018","publisher":"Springer","quality_controlled":"1","oa":1},{"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:44:44Z","date_updated":"2023-09-07T13:18:00Z","ddc":["000"],"conference":{"name":"CONCUR: International Conference on Concurrency Theory","start_date":"2018-09-04","end_date":"2018-09-07","location":"Beijing, China"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","pubrep_id":"1039","status":"public","_id":"133","volume":118,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"6426"},{"relation":"dissertation_contains","status":"public","id":"8332"}]},"publication_status":"published","publication_identifier":{"issn":["18688969"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5368","checksum":"c90895f4c5fafc18ddc54d1c8848077e","file_size":745438,"date_updated":"2020-07-14T12:44:44Z","creator":"system","file_name":"IST-2018-853-v2+2_concur2018.pdf","date_created":"2018-12-12T10:18:46Z"}],"alternative_title":["LIPIcs"],"scopus_import":1,"intvolume":" 118","month":"08","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."}],"oa_version":"Published Version","author":[{"first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87","full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117","last_name":"Kragl"},{"last_name":"Qadeer","full_name":"Qadeer, Shaz","first_name":"Shaz"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"}],"publist_id":"7790","title":"Synchronizing the asynchronous","citation":{"ista":"Kragl B, Qadeer S, Henzinger TA. 2018. Synchronizing the asynchronous. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 118, 21.","chicago":"Kragl, Bernhard, Shaz Qadeer, and Thomas A Henzinger. “Synchronizing the Asynchronous,” Vol. 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.CONCUR.2018.21.","short":"B. Kragl, S. Qadeer, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","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.","apa":"Kragl, B., Qadeer, S., & 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. https://doi.org/10.4230/LIPIcs.CONCUR.2018.21","ama":"Kragl B, Qadeer S, Henzinger TA. Synchronizing the asynchronous. In: Vol 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.CONCUR.2018.21","mla":"Kragl, Bernhard, et al. Synchronizing the Asynchronous. Vol. 118, 21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.CONCUR.2018.21."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Rigorous Systems Engineering","grant_number":"S11402-N23","call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"},{"name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"}],"article_number":"21","date_created":"2018-12-11T11:44:48Z","date_published":"2018-08-13T00:00:00Z","doi":"10.4230/LIPIcs.CONCUR.2018.21","year":"2018","has_accepted_license":"1","day":"13","oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik"},{"file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"HeEd"}],"ddc":["516"],"date_updated":"2023-09-07T13:29:00Z","status":"public","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"location":"Budapest, Hungary","end_date":"2018-06-14","start_date":"2018-06-11","name":"SoCG: Symposium on Computational Geometry"},"_id":"187","volume":99,"related_material":{"record":[{"status":"public","id":"9317","relation":"later_version"},{"status":"public","id":"9056","relation":"dissertation_contains"}]},"file":[{"file_name":"2018_LIPIcs_Edelsbrunner_Osang.pdf","date_created":"2018-12-18T09:27:22Z","creator":"dernst","file_size":528018,"date_updated":"2020-07-14T12:45:19Z","checksum":"d8c0533ad0018eb4ed1077475eb8fc18","file_id":"5738","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"06","intvolume":" 99","scopus_import":1,"alternative_title":["LIPIcs"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Given a locally finite X ⊆ ℝd and a radius r ≥ 0, the k-fold cover of X and r consists of all points in ℝd that have k or more points of X within distance r. We consider two filtrations - one in scale obtained by fixing k and increasing r, and the other in depth obtained by fixing r and decreasing k - and we compute the persistence diagrams of both. While standard methods suffice for the filtration in scale, we need novel geometric and topological concepts for the filtration in depth. In particular, we introduce a rhomboid tiling in ℝd+1 whose horizontal integer slices are the order-k Delaunay mosaics of X, and construct a zigzag module from Delaunay mosaics that is isomorphic to the persistence module of the multi-covers. "}],"title":"The multi-cover persistence of Euclidean balls","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"full_name":"Osang, Georg F","orcid":"0000-0002-8882-5116","last_name":"Osang","first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7732","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Edelsbrunner H, Osang GF. 2018. The multi-cover persistence of Euclidean balls. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 34.","chicago":"Edelsbrunner, Herbert, and Georg F Osang. “The Multi-Cover Persistence of Euclidean Balls,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.34.","short":"H. Edelsbrunner, G.F. Osang, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","ieee":"H. Edelsbrunner and G. F. Osang, “The multi-cover persistence of Euclidean balls,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","apa":"Edelsbrunner, H., & Osang, G. F. (2018). The multi-cover persistence of Euclidean balls (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.34","ama":"Edelsbrunner H, Osang GF. The multi-cover persistence of Euclidean balls. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.SoCG.2018.34","mla":"Edelsbrunner, Herbert, and Georg F. Osang. The Multi-Cover Persistence of Euclidean Balls. Vol. 99, 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.SoCG.2018.34."},"project":[{"name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"34","date_published":"2018-06-11T00:00:00Z","doi":"10.4230/LIPIcs.SoCG.2018.34","date_created":"2018-12-11T11:45:05Z","day":"11","has_accepted_license":"1","year":"2018","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"acknowledgement":"This work is partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF)."},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We consider families of confocal conics and two pencils of Apollonian circles having the same foci. We will show that these families of curves generate trivial 3-webs and find the exact formulas describing them."}],"month":"06","intvolume":" 194","scopus_import":"1","file":[{"file_name":"2018_Springer_Akopyan.pdf","date_created":"2020-01-03T11:35:08Z","creator":"kschuh","file_size":1140860,"date_updated":"2020-07-14T12:47:44Z","file_id":"7222","checksum":"1febcfc1266486053a069e3425ea3713","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":194,"issue":"1","ec_funded":1,"_id":"692","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["510"],"date_updated":"2023-09-08T11:40:29Z","department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:47:44Z","quality_controlled":"1","publisher":"Springer","oa":1,"day":"01","publication":"Geometriae Dedicata","isi":1,"has_accepted_license":"1","year":"2018","doi":"10.1007/s10711-017-0265-6","date_published":"2018-06-01T00:00:00Z","date_created":"2018-12-11T11:47:57Z","page":"55 - 64","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Akopyan, Arseniy. “3-Webs Generated by Confocal Conics and Circles.” Geometriae Dedicata. Springer, 2018. https://doi.org/10.1007/s10711-017-0265-6.","ista":"Akopyan A. 2018. 3-Webs generated by confocal conics and circles. Geometriae Dedicata. 194(1), 55–64.","mla":"Akopyan, Arseniy. “3-Webs Generated by Confocal Conics and Circles.” Geometriae Dedicata, vol. 194, no. 1, Springer, 2018, pp. 55–64, doi:10.1007/s10711-017-0265-6.","short":"A. Akopyan, Geometriae Dedicata 194 (2018) 55–64.","ieee":"A. Akopyan, “3-Webs generated by confocal conics and circles,” Geometriae Dedicata, vol. 194, no. 1. Springer, pp. 55–64, 2018.","apa":"Akopyan, A. (2018). 3-Webs generated by confocal conics and circles. Geometriae Dedicata. Springer. https://doi.org/10.1007/s10711-017-0265-6","ama":"Akopyan A. 3-Webs generated by confocal conics and circles. Geometriae Dedicata. 2018;194(1):55-64. doi:10.1007/s10711-017-0265-6"},"title":"3-Webs generated by confocal conics and circles","author":[{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","last_name":"Akopyan","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X"}],"publist_id":"7014","external_id":{"isi":["000431418800004"]},"article_processing_charge":"Yes (via OA deal)"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Watzinger, Hannes, et al. “A Germanium Hole Spin Qubit.” Nature Communications, vol. 9, no. 3902, Nature Publishing Group, 2018, doi:10.1038/s41467-018-06418-4.","ama":"Watzinger H, Kukucka J, Vukušić L, et al. A germanium hole spin qubit. Nature Communications. 2018;9(3902). doi:10.1038/s41467-018-06418-4","apa":"Watzinger, H., Kukucka, J., Vukušić, L., Gao, F., Wang, T., Schäffler, F., … Katsaros, G. (2018). A germanium hole spin qubit. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-018-06418-4","ieee":"H. Watzinger et al., “A germanium hole spin qubit,” Nature Communications, vol. 9, no. 3902. Nature Publishing Group, 2018.","short":"H. Watzinger, J. Kukucka, L. Vukušić, F. Gao, T. Wang, F. Schäffler, J. Zhang, G. Katsaros, Nature Communications 9 (2018).","chicago":"Watzinger, Hannes, Josip Kukucka, Lada Vukušić, Fei Gao, Ting Wang, Friedrich Schäffler, Jian Zhang, and Georgios Katsaros. “A Germanium Hole Spin Qubit.” Nature Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-018-06418-4.","ista":"Watzinger H, Kukucka J, Vukušić L, Gao F, Wang T, Schäffler F, Zhang J, Katsaros G. 2018. A germanium hole spin qubit. Nature Communications. 9(3902)."},"title":"A germanium hole spin qubit","author":[{"full_name":"Watzinger, Hannes","last_name":"Watzinger","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","first_name":"Hannes"},{"full_name":"Kukucka, Josip","last_name":"Kukucka","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","first_name":"Josip"},{"first_name":"Lada","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2424-8636","full_name":"Vukusic, Lada","last_name":"Vukusic"},{"full_name":"Gao, Fei","last_name":"Gao","first_name":"Fei"},{"full_name":"Wang, Ting","last_name":"Wang","first_name":"Ting"},{"first_name":"Friedrich","full_name":"Schäffler, Friedrich","last_name":"Schäffler"},{"first_name":"Jian","last_name":"Zhang","full_name":"Zhang, Jian"},{"full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"}],"external_id":{"isi":["000445560800010"]},"article_processing_charge":"Yes","project":[{"name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","grant_number":"335497","call_identifier":"FP7","_id":"25517E86-B435-11E9-9278-68D0E5697425"},{"_id":"2552F888-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Y00715","name":"Loch Spin-Qubits und Majorana-Fermionen in Germanium"}],"day":"25","publication":"Nature Communications","has_accepted_license":"1","isi":1,"year":"2018","date_published":"2018-09-25T00:00:00Z","doi":"10.1038/s41467-018-06418-4","date_created":"2018-12-11T11:44:30Z","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"ddc":["530"],"date_updated":"2023-09-08T11:44:02Z","file_date_updated":"2020-07-14T12:48:02Z","department":[{"_id":"GeKa"}],"_id":"77","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_id":"5687","checksum":"e7148c10a64497e279c4de570b6cc544","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_NatureComm_Watzinger.pdf","date_created":"2018-12-17T10:28:30Z","creator":"dernst","file_size":1063469,"date_updated":"2020-07-14T12:48:02Z"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"3902 ","volume":9,"related_material":{"record":[{"relation":"popular_science","id":"7977"},{"id":"7996","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"Holes confined in quantum dots have gained considerable interest in the past few years due to their potential as spin qubits. Here we demonstrate two-axis control of a spin 3/2 qubit in natural Ge. The qubit is formed in a hut wire double quantum dot device. The Pauli spin blockade principle allowed us to demonstrate electric dipole spin resonance by applying a radio frequency electric field to one of the electrodes defining the double quantum dot. Coherent hole spin oscillations with Rabi frequencies reaching 140 MHz are demonstrated and dephasing times of 130 ns are measured. The reported results emphasize the potential of Ge as a platform for fast and electrically tunable hole spin qubit devices.","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"month":"09","intvolume":" 9","scopus_import":"1"},{"article_number":"1210","title":"A biochemical network controlling basal myosin oscillation","publist_id":"7427","author":[{"first_name":"Xiang","full_name":"Qin, Xiang","last_name":"Qin"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"first_name":"Thomas","last_name":"Mangeat","full_name":"Mangeat, Thomas"},{"last_name":"Liu","full_name":"Liu, Chang","first_name":"Chang"},{"first_name":"Pralay","last_name":"Majumder","full_name":"Majumder, Pralay"},{"last_name":"Liu","full_name":"Liu, Jjiaying","first_name":"Jjiaying"},{"last_name":"Choesmel Cadamuro","full_name":"Choesmel Cadamuro, Valerie","first_name":"Valerie"},{"first_name":"Jocelyn","last_name":"Mcdonald","full_name":"Mcdonald, Jocelyn"},{"full_name":"Liu, Yinyao","last_name":"Liu","first_name":"Yinyao"},{"full_name":"Yi, Bin","last_name":"Yi","first_name":"Bin"},{"first_name":"Xiaobo","full_name":"Wang, Xiaobo","last_name":"Wang"}],"article_processing_charge":"No","external_id":{"isi":["000428165400009"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"X. Qin et al., “A biochemical network controlling basal myosin oscillation,” Nature Communications, vol. 9, no. 1. Nature Publishing Group, 2018.","short":"X. Qin, E.B. Hannezo, T. Mangeat, C. Liu, P. Majumder, J. Liu, V. Choesmel Cadamuro, J. Mcdonald, Y. Liu, B. Yi, X. Wang, Nature Communications 9 (2018).","apa":"Qin, X., Hannezo, E. B., Mangeat, T., Liu, C., Majumder, P., Liu, J., … Wang, X. (2018). A biochemical network controlling basal myosin oscillation. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-018-03574-5","ama":"Qin X, Hannezo EB, Mangeat T, et al. A biochemical network controlling basal myosin oscillation. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-03574-5","mla":"Qin, Xiang, et al. “A Biochemical Network Controlling Basal Myosin Oscillation.” Nature Communications, vol. 9, no. 1, 1210, Nature Publishing Group, 2018, doi:10.1038/s41467-018-03574-5.","ista":"Qin X, Hannezo EB, Mangeat T, Liu C, Majumder P, Liu J, Choesmel Cadamuro V, Mcdonald J, Liu Y, Yi B, Wang X. 2018. A biochemical network controlling basal myosin oscillation. Nature Communications. 9(1), 1210.","chicago":"Qin, Xiang, Edouard B Hannezo, Thomas Mangeat, Chang Liu, Pralay Majumder, Jjiaying Liu, Valerie Choesmel Cadamuro, et al. “A Biochemical Network Controlling Basal Myosin Oscillation.” Nature Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-018-03574-5."},"publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"date_published":"2018-03-23T00:00:00Z","doi":"10.1038/s41467-018-03574-5","date_created":"2018-12-11T11:46:16Z","day":"23","publication":"Nature Communications","isi":1,"has_accepted_license":"1","year":"2018","status":"public","pubrep_id":"996","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"401","file_date_updated":"2020-07-14T12:46:22Z","department":[{"_id":"EdHa"}],"ddc":["539","570"],"date_updated":"2023-09-08T11:41:45Z","month":"03","intvolume":" 9","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"The actomyosin cytoskeleton, a key stress-producing unit in epithelial cells, oscillates spontaneously in a wide variety of systems. Although much of the signal cascade regulating myosin activity has been characterized, the origin of such oscillatory behavior is still unclear. Here, we show that basal myosin II oscillation in Drosophila ovarian epithelium is not controlled by actomyosin cortical tension, but instead relies on a biochemical oscillator involving ROCK and myosin phosphatase. Key to this oscillation is a diffusive ROCK flow, linking junctional Rho1 to medial actomyosin cortex, and dynamically maintained by a self-activation loop reliant on ROCK kinase activity. In response to the resulting myosin II recruitment, myosin phosphatase is locally enriched and shuts off ROCK and myosin II signals. Coupling Drosophila genetics, live imaging, modeling, and optogenetics, we uncover an intrinsic biochemical oscillator at the core of myosin II regulatory network, shedding light on the spatio-temporal dynamics of force generation.","lang":"eng"}],"issue":"1","volume":9,"file":[{"date_created":"2018-12-12T10:11:45Z","file_name":"IST-2018-996-v1+1_2018_Hannezo_A-biochemical.pdf","creator":"system","date_updated":"2020-07-14T12:46:22Z","file_size":3780491,"file_id":"4902","checksum":"87a427bc2e8724be3dd22a4efdd21a33","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published"},{"month":"02","intvolume":" 44","scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/29486189","open_access":"1"}],"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The insect’s fat body combines metabolic and immunological functions. In this issue of Developmental Cell, Franz et al. (2018) show that in Drosophila, cells of the fat body are not static, but can actively “swim” toward sites of epithelial injury, where they physically clog the wound and locally secrete antimicrobial peptides."}],"volume":44,"issue":"4","language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","_id":"318","department":[{"_id":"MiSi"}],"date_updated":"2023-09-08T11:42:28Z","quality_controlled":"1","publisher":"Cell Press","oa":1,"acknowledgement":"Short Survey","doi":"10.1016/j.devcel.2018.02.009","date_published":"2018-02-26T00:00:00Z","date_created":"2018-12-11T11:45:47Z","page":"405 - 406","day":"26","publication":"Developmental Cell","isi":1,"year":"2018","title":"A fat lot of good for wound healing","author":[{"full_name":"Casano, Alessandra M","orcid":"0000-0002-6009-6804","last_name":"Casano","id":"3DBA3F4E-F248-11E8-B48F-1D18A9856A87","first_name":"Alessandra M"},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7547","article_processing_charge":"No","external_id":{"isi":["000426150700002"],"pmid":["29486189"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Casano, A. M., & Sixt, M. K. (2018). A fat lot of good for wound healing. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2018.02.009","ama":"Casano AM, Sixt MK. A fat lot of good for wound healing. Developmental Cell. 2018;44(4):405-406. doi:10.1016/j.devcel.2018.02.009","ieee":"A. M. Casano and M. K. Sixt, “A fat lot of good for wound healing,” Developmental Cell, vol. 44, no. 4. Cell Press, pp. 405–406, 2018.","short":"A.M. Casano, M.K. Sixt, Developmental Cell 44 (2018) 405–406.","mla":"Casano, Alessandra M., and Michael K. Sixt. “A Fat Lot of Good for Wound Healing.” Developmental Cell, vol. 44, no. 4, Cell Press, 2018, pp. 405–06, doi:10.1016/j.devcel.2018.02.009.","ista":"Casano AM, Sixt MK. 2018. A fat lot of good for wound healing. Developmental Cell. 44(4), 405–406.","chicago":"Casano, Alessandra M, and Michael K Sixt. “A Fat Lot of Good for Wound Healing.” Developmental Cell. Cell Press, 2018. https://doi.org/10.1016/j.devcel.2018.02.009."}},{"isi":1,"has_accepted_license":"1","year":"2018","day":"26","publication":"Scientific Reports","doi":"10.1038/s41598-018-23247-z","date_published":"2018-03-26T00:00:00Z","date_created":"2018-12-11T11:46:19Z","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"citation":{"ieee":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M. A. Jösch, and D. Cox, “A micro-CT-based method for quantitative brain lesion characterization and electrode localization,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018.","short":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M.A. Jösch, D. Cox, Scientific Reports 8 (2018).","apa":"Masís, J., Mankus, D., Wolff, S., Guitchounts, G., Jösch, M. A., & Cox, D. (2018). A micro-CT-based method for quantitative brain lesion characterization and electrode localization. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-23247-z","ama":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. A micro-CT-based method for quantitative brain lesion characterization and electrode localization. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-23247-z","mla":"Masís, Javier, et al. “A Micro-CT-Based Method for Quantitative Brain Lesion Characterization and Electrode Localization.” Scientific Reports, vol. 8, no. 1, 5184, Nature Publishing Group, 2018, doi:10.1038/s41598-018-23247-z.","ista":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. 2018. A micro-CT-based method for quantitative brain lesion characterization and electrode localization. Scientific Reports. 8(1), 5184.","chicago":"Masís, Javier, David Mankus, Steffen Wolff, Grigori Guitchounts, Maximilian A Jösch, and David Cox. “A Micro-CT-Based Method for Quantitative Brain Lesion Characterization and Electrode Localization.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-23247-z."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Javier","full_name":"Masís, Javier","last_name":"Masís"},{"full_name":"Mankus, David","last_name":"Mankus","first_name":"David"},{"last_name":"Wolff","full_name":"Wolff, Steffen","first_name":"Steffen"},{"last_name":"Guitchounts","full_name":"Guitchounts, Grigori","first_name":"Grigori"},{"last_name":"Jösch","full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","full_name":"Cox, David","last_name":"Cox"}],"publist_id":"7419","external_id":{"isi":["000428234100005"]},"article_processing_charge":"No","title":"A micro-CT-based method for quantitative brain lesion characterization and electrode localization","article_number":"5184","publication_status":"published","file":[{"file_id":"4831","checksum":"653fcb852f899c75b00ceee2a670d738","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:10:42Z","file_name":"IST-2018-994-v1+1_2018_Joesch_A-micro-CT-based.pdf","creator":"system","date_updated":"2020-07-14T12:46:23Z","file_size":2359430}],"language":[{"iso":"eng"}],"volume":8,"issue":"1","abstract":[{"text":"Lesion verification and quantification is traditionally done via histological examination of sectioned brains, a time-consuming process that relies heavily on manual estimation. Such methods are particularly problematic in posterior cortical regions (e.g. visual cortex), where sectioning leads to significant damage and distortion of tissue. Even more challenging is the post hoc localization of micro-electrodes, which relies on the same techniques, suffers from similar drawbacks and requires even higher precision. Here, we propose a new, simple method for quantitative lesion characterization and electrode localization that is less labor-intensive and yields more detailed results than conventional methods. We leverage staining techniques standard in electron microscopy with the use of commodity micro-CT imaging. We stain whole rat and zebra finch brains in osmium tetroxide, embed these in resin and scan entire brains in a micro-CT machine. The scans result in 3D reconstructions of the brains with section thickness dependent on sample size (12–15 and 5–6 microns for rat and zebra finch respectively) that can be segmented manually or automatically. Because the method captures the entire intact brain volume, comparisons within and across studies are more tractable, and the extent of lesions and electrodes may be studied with higher accuracy than with current methods.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"03","intvolume":" 8","date_updated":"2023-09-08T11:48:39Z","ddc":["571","572"],"department":[{"_id":"MaJö"}],"file_date_updated":"2020-07-14T12:46:23Z","_id":"410","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"994"},{"oa":1,"publisher":"Springer","quality_controlled":"1","publication":"Plant Molecular Biology","day":"12","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:45:34Z","doi":"10.1007/s11103-018-0747-4","date_published":"2018-06-12T00:00:00Z","page":"407 - 420","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Dokládal L, Benková E, Honys D, Dupláková N, Lee L, Gelvin S, Sýkorová E. 2018. An armadillo-domain protein participates in a telomerase interaction network. Plant Molecular Biology. 97(5), 407–420.","chicago":"Dokládal, Ladislav, Eva Benková, David Honys, Nikoleta Dupláková, Lan Lee, Stanton Gelvin, and Eva Sýkorová. “An Armadillo-Domain Protein Participates in a Telomerase Interaction Network.” Plant Molecular Biology. Springer, 2018. https://doi.org/10.1007/s11103-018-0747-4.","short":"L. Dokládal, E. Benková, D. Honys, N. Dupláková, L. Lee, S. Gelvin, E. Sýkorová, Plant Molecular Biology 97 (2018) 407–420.","ieee":"L. Dokládal et al., “An armadillo-domain protein participates in a telomerase interaction network,” Plant Molecular Biology, vol. 97, no. 5. Springer, pp. 407–420, 2018.","apa":"Dokládal, L., Benková, E., Honys, D., Dupláková, N., Lee, L., Gelvin, S., & Sýkorová, E. (2018). An armadillo-domain protein participates in a telomerase interaction network. Plant Molecular Biology. Springer. https://doi.org/10.1007/s11103-018-0747-4","ama":"Dokládal L, Benková E, Honys D, et al. An armadillo-domain protein participates in a telomerase interaction network. Plant Molecular Biology. 2018;97(5):407-420. doi:10.1007/s11103-018-0747-4","mla":"Dokládal, Ladislav, et al. “An Armadillo-Domain Protein Participates in a Telomerase Interaction Network.” Plant Molecular Biology, vol. 97, no. 5, Springer, 2018, pp. 407–20, doi:10.1007/s11103-018-0747-4."},"title":"An armadillo-domain protein participates in a telomerase interaction network","external_id":{"isi":["000438981700009"]},"article_processing_charge":"No","author":[{"first_name":"Ladislav","last_name":"Dokládal","full_name":"Dokládal, Ladislav"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"},{"last_name":"Honys","full_name":"Honys, David","first_name":"David"},{"full_name":"Dupláková, Nikoleta","last_name":"Dupláková","first_name":"Nikoleta"},{"full_name":"Lee, Lan","last_name":"Lee","first_name":"Lan"},{"first_name":"Stanton","last_name":"Gelvin","full_name":"Gelvin, Stanton"},{"last_name":"Sýkorová","full_name":"Sýkorová, Eva","first_name":"Eva"}],"publist_id":"7625","oa_version":"Submitted Version","abstract":[{"text":"Arabidopsis and human ARM protein interact with telomerase. Deregulated mRNA levels of DNA repair and ribosomal protein genes in an Arabidopsis arm mutant suggest non-telomeric ARM function. The human homolog ARMC6 interacts with hTRF2. Abstract: Telomerase maintains telomeres and has proposed non-telomeric functions. We previously identified interaction of the C-terminal domain of Arabidopsis telomerase reverse transcriptase (AtTERT) with an armadillo/β-catenin-like repeat (ARM) containing protein. Here we explore protein–protein interactions of the ARM protein, AtTERT domains, POT1a, TRF-like family and SMH family proteins, and the chromatin remodeling protein CHR19 using bimolecular fluorescence complementation (BiFC), yeast two-hybrid (Y2H) analysis, and co-immunoprecipitation. The ARM protein interacts with both the N- and C-terminal domains of AtTERT in different cellular compartments. ARM interacts with CHR19 and TRF-like I family proteins that also bind AtTERT directly or through interaction with POT1a. The putative human ARM homolog co-precipitates telomerase activity and interacts with hTRF2 protein in vitro. Analysis of Arabidopsis arm mutants shows no obvious changes in telomere length or telomerase activity, suggesting that ARM is not essential for telomere maintenance. The observed interactions with telomerase and Myb-like domain proteins (TRF-like family I) may therefore reflect possible non-telomeric functions. Transcript levels of several DNA repair and ribosomal genes are affected in arm mutants, and ARM, likely in association with other proteins, suppressed expression of XRCC3 and RPSAA promoter constructs in luciferase reporter assays. In conclusion, ARM can participate in non-telomeric functions of telomerase, and can also perform its own telomerase-independent functions.","lang":"eng"}],"intvolume":" 97","month":"06","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_size":1150679,"date_updated":"2020-07-14T12:45:45Z","creator":"dernst","file_name":"2018_PlantMolecBio_Dokladal.pdf","date_created":"2020-05-14T12:23:08Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"7834","checksum":"451ae47616e6af2533099f596b2a47fb"}],"publication_status":"published","issue":"5","volume":97,"_id":"277","status":"public","type":"journal_article","article_type":"original","ddc":["580"],"date_updated":"2023-09-08T13:21:05Z","department":[{"_id":"EvBe"}],"file_date_updated":"2020-07-14T12:45:45Z"},{"page":"303 - 319","doi":"10.1007/978-3-319-89963-3_18","date_published":"2018-04-14T00:00:00Z","date_created":"2018-12-11T11:45:41Z","has_accepted_license":"1","isi":1,"year":"2018","day":"14","publisher":"Springer","quality_controlled":"1","oa":1,"author":[{"full_name":"Nickovic, Dejan","last_name":"Nickovic","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","first_name":"Dejan"},{"first_name":"Olivier","last_name":"Lebeltel","full_name":"Lebeltel, Olivier"},{"full_name":"Maler, Oded","last_name":"Maler","first_name":"Oded"},{"first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas"},{"first_name":"Dogan","last_name":"Ulus","full_name":"Ulus, Dogan"}],"publist_id":"7582","article_processing_charge":"No","external_id":{"isi":["00445822600018"]},"title":"AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic","editor":[{"last_name":"Beyer","full_name":"Beyer, Dirk","first_name":"Dirk"},{"first_name":"Marieke","full_name":"Huisman, Marieke","last_name":"Huisman"}],"citation":{"chicago":"Nickovic, Dejan, Olivier Lebeltel, Oded Maler, Thomas Ferrere, and Dogan Ulus. “AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic.” edited by Dirk Beyer and Marieke Huisman, 10806:303–19. Springer, 2018. https://doi.org/10.1007/978-3-319-89963-3_18.","ista":"Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. 2018. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10806, 303–319.","mla":"Nickovic, Dejan, et al. AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic. Edited by Dirk Beyer and Marieke Huisman, vol. 10806, Springer, 2018, pp. 303–19, doi:10.1007/978-3-319-89963-3_18.","ieee":"D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, and D. Ulus, “AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece, 2018, vol. 10806, pp. 303–319.","short":"D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, D. Ulus, in:, D. Beyer, M. Huisman (Eds.), Springer, 2018, pp. 303–319.","apa":"Nickovic, D., Lebeltel, O., Maler, O., Ferrere, T., & Ulus, D. (2018). AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. In D. Beyer & M. Huisman (Eds.) (Vol. 10806, pp. 303–319). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece: Springer. https://doi.org/10.1007/978-3-319-89963-3_18","ama":"Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. In: Beyer D, Huisman M, eds. Vol 10806. Springer; 2018:303-319. doi:10.1007/978-3-319-89963-3_18"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":10806,"related_material":{"record":[{"relation":"later_version","status":"public","id":"10861"}]},"publication_status":"published","file":[{"file_size":3267209,"date_updated":"2020-07-14T12:45:58Z","creator":"dernst","file_name":"2018_LNCS_Nickovic.pdf","date_created":"2019-02-06T07:33:05Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"e11db3b9c8e27a1c7d1c738cc5e4d25a","file_id":"5928"}],"language":[{"iso":"eng"}],"scopus_import":"1","alternative_title":["LNCS"],"month":"04","intvolume":" 10806","abstract":[{"lang":"eng","text":"We introduce in this paper AMT 2.0 , a tool for qualitative and quantitative analysis of hybrid continuous and Boolean signals that combine numerical values and discrete events. The evaluation of the signals is based on rich temporal specifications expressed in extended Signal Temporal Logic (xSTL), which integrates Timed Regular Expressions (TRE) within Signal Temporal Logic (STL). The tool features qualitative monitoring (property satisfaction checking), trace diagnostics for explaining and justifying property violations and specification-driven measurement of quantitative features of the signal."}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:45:58Z","department":[{"_id":"ToHe"}],"date_updated":"2023-09-08T11:52:02Z","ddc":["000"],"type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"end_date":"2018-04-20","location":"Thessaloniki, Greece","start_date":"2018-04-14","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"status":"public","_id":"299"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Konrad, Matthias, Christopher Pull, Sina Metzler, Katharina Seif, Elisabeth Naderlinger, Anna V Grasse, and Sylvia Cremer. “Ants Avoid Superinfections by Performing Risk-Adjusted Sanitary Care.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1713501115.","ista":"Konrad M, Pull C, Metzler S, Seif K, Naderlinger E, Grasse AV, Cremer S. 2018. Ants avoid superinfections by performing risk-adjusted sanitary care. PNAS. 115(11), 2782–2787.","mla":"Konrad, Matthias, et al. “Ants Avoid Superinfections by Performing Risk-Adjusted Sanitary Care.” PNAS, vol. 115, no. 11, National Academy of Sciences, 2018, pp. 2782–87, doi:10.1073/pnas.1713501115.","short":"M. Konrad, C. Pull, S. Metzler, K. Seif, E. Naderlinger, A.V. Grasse, S. Cremer, PNAS 115 (2018) 2782–2787.","ieee":"M. Konrad et al., “Ants avoid superinfections by performing risk-adjusted sanitary care,” PNAS, vol. 115, no. 11. National Academy of Sciences, pp. 2782–2787, 2018.","ama":"Konrad M, Pull C, Metzler S, et al. Ants avoid superinfections by performing risk-adjusted sanitary care. PNAS. 2018;115(11):2782-2787. doi:10.1073/pnas.1713501115","apa":"Konrad, M., Pull, C., Metzler, S., Seif, K., Naderlinger, E., Grasse, A. V., & Cremer, S. (2018). Ants avoid superinfections by performing risk-adjusted sanitary care. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1713501115"},"title":"Ants avoid superinfections by performing risk-adjusted sanitary care","article_processing_charge":"No","external_id":{"isi":["000427245400069"],"pmid":["29463746"]},"author":[{"last_name":"Konrad","full_name":"Konrad, Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias"},{"full_name":"Pull, Christopher","orcid":"0000-0003-1122-3982","last_name":"Pull","first_name":"Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sina","id":"48204546-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9547-2494","full_name":"Metzler, Sina","last_name":"Metzler"},{"full_name":"Seif, Katharina","last_name":"Seif","first_name":"Katharina","id":"90F7894A-02CF-11E9-976E-E38CFE5CBC1D"},{"full_name":"Naderlinger, Elisabeth","last_name":"Naderlinger","id":"31757262-F248-11E8-B48F-1D18A9856A87","first_name":"Elisabeth"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","full_name":"Grasse, Anna V","last_name":"Grasse"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","last_name":"Cremer"}],"publist_id":"7416","project":[{"call_identifier":"FP7","_id":"25DC711C-B435-11E9-9278-68D0E5697425","grant_number":"243071","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects"}],"publication":"PNAS","day":"13","year":"2018","isi":1,"date_created":"2018-12-11T11:46:20Z","doi":"10.1073/pnas.1713501115","date_published":"2018-03-13T00:00:00Z","page":"2782 - 2787","oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","date_updated":"2023-09-08T13:22:21Z","department":[{"_id":"SyCr"}],"_id":"413","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":115,"issue":"11","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/helping-in-spite-of-risk-ants-perform-risk-averse-sanitary-care-of-infectious-nest-mates/","relation":"press_release"}]},"pmid":1,"oa_version":"Published Version","abstract":[{"text":"Being cared for when sick is a benefit of sociality that can reduce disease and improve survival of group members. However, individuals providing care risk contracting infectious diseases themselves. If they contract a low pathogen dose, they may develop low-level infections that do not cause disease but still affect host immunity by either decreasing or increasing the host’s vulnerability to subsequent infections. Caring for contagious individuals can thus significantly alter the future disease susceptibility of caregivers. Using ants and their fungal pathogens as a model system, we tested if the altered disease susceptibility of experienced caregivers, in turn, affects their expression of sanitary care behavior. We found that low-level infections contracted during sanitary care had protective or neutral effects on secondary exposure to the same (homologous) pathogen but consistently caused high mortality on superinfection with a different (heterologous) pathogen. In response to this risk, the ants selectively adjusted the expression of their sanitary care. Specifically, the ants performed less grooming and more antimicrobial disinfection when caring for nestmates contaminated with heterologous pathogens compared with homologous ones. By modulating the components of sanitary care in this way the ants acquired less infectious particles of the heterologous pathogens, resulting in reduced superinfection. The performance of risk-adjusted sanitary care reveals the remarkable capacity of ants to react to changes in their disease susceptibility, according to their own infection history and to flexibly adjust collective care to individual risk.","lang":"eng"}],"intvolume":" 115","month":"03","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29463746"}],"scopus_import":"1"},{"oa":1,"publisher":"American Physical Society","quality_controlled":"1","publication":"Physical Review B - Condensed Matter and Materials Physics","day":"15","year":"2018","isi":1,"date_created":"2018-12-11T11:45:08Z","date_published":"2018-07-15T00:00:00Z","doi":"10.1103/PhysRevB.98.045402","article_number":"045402","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anyonic Statistics of Quantum Impurities in Two Dimensions.” Physical Review B - Condensed Matter and Materials Physics, vol. 98, no. 4, 045402, American Physical Society, 2018, doi:10.1103/PhysRevB.98.045402.","ama":"Yakaboylu E, Lemeshko M. Anyonic statistics of quantum impurities in two dimensions. Physical Review B - Condensed Matter and Materials Physics. 2018;98(4). doi:10.1103/PhysRevB.98.045402","apa":"Yakaboylu, E., & Lemeshko, M. (2018). Anyonic statistics of quantum impurities in two dimensions. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.98.045402","ieee":"E. Yakaboylu and M. Lemeshko, “Anyonic statistics of quantum impurities in two dimensions,” Physical Review B - Condensed Matter and Materials Physics, vol. 98, no. 4. American Physical Society, 2018.","short":"E. Yakaboylu, M. Lemeshko, Physical Review B - Condensed Matter and Materials Physics 98 (2018).","chicago":"Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anyonic Statistics of Quantum Impurities in Two Dimensions.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.98.045402.","ista":"Yakaboylu E, Lemeshko M. 2018. Anyonic statistics of quantum impurities in two dimensions. Physical Review B - Condensed Matter and Materials Physics. 98(4), 045402."},"title":"Anyonic statistics of quantum impurities in two dimensions","article_processing_charge":"No","external_id":{"isi":["000436939100007"],"arxiv":["1712.00308"]},"author":[{"id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","first_name":"Enderalp","last_name":"Yakaboylu","full_name":"Yakaboylu, Enderalp","orcid":"0000-0001-5973-0874"},{"last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Submitted Version","abstract":[{"text":"We demonstrate that identical impurities immersed in a two-dimensional many-particle bath can be viewed as flux-tube-charged-particle composites described by fractional statistics. In particular, we find that the bath manifests itself as an external magnetic flux tube with respect to the impurities, and hence the time-reversal symmetry is broken for the effective Hamiltonian describing the impurities. The emerging flux tube acts as a statistical gauge field after a certain critical coupling. This critical coupling corresponds to the intersection point between the quasiparticle state and the phonon wing, where the angular momentum is transferred from the impurity to the bath. This amounts to a novel configuration with emerging anyons. The proposed setup paves the way to realizing anyons using electrons interacting with superfluid helium or lattice phonons, as well as using atomic impurities in ultracold gases.","lang":"eng"}],"intvolume":" 98","month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.00308"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"issue":"4","volume":98,"_id":"195","status":"public","type":"journal_article","date_updated":"2023-09-08T13:22:57Z","department":[{"_id":"MiLe"}]},{"abstract":[{"text":"The task of a monitor is to watch, at run-time, the execution of a reactive system, and signal the occurrence of a safety violation in the observed sequence of events. While finite-state monitors have been studied extensively, in practice, monitoring software also makes use of unbounded memory. We define a model of automata equipped with integer-valued registers which can execute only a bounded number of instructions between consecutive events, and thus can form the theoretical basis for the study of infinite-state monitors. We classify these register monitors according to the number k of available registers, and the type of register instructions. In stark contrast to the theory of computability for register machines, we prove that for every k 1, monitors with k + 1 counters (with instruction set 〈+1, =〉) are strictly more expressive than monitors with k counters. We also show that adder monitors (with instruction set 〈1, +, =〉) are strictly more expressive than counter monitors, but are complete for monitoring all computable safety -languages for k = 6. Real-time monitors are further required to signal the occurrence of a safety violation as soon as it occurs. The expressiveness hierarchy for counter monitors carries over to real-time monitors. We then show that 2 adders cannot simulate 3 counters in real-time. Finally, we show that real-time adder monitors with inequalities are as expressive as real-time Turing machines.","lang":"eng"}],"oa_version":"None","publisher":"IEEE","alternative_title":["ACM/IEEE Symposium on Logic in Computer Science"],"quality_controlled":"1","scopus_import":"1","month":"07","year":"2018","publication_status":"published","isi":1,"language":[{"iso":"eng"}],"day":"09","page":"394 - 403","date_created":"2018-12-11T11:44:52Z","volume":"Part F138033","date_published":"2018-07-09T00:00:00Z","doi":"10.1145/3209108.3209194","_id":"144","conference":{"name":"LICS: Logic in Computer Science","end_date":"2018-07-12","location":"Oxford, UK","start_date":"2018-07-09"},"type":"conference","status":"public","citation":{"ista":"Ferrere T, Henzinger TA, Saraç E. 2018. A theory of register monitors. LICS: Logic in Computer Science, ACM/IEEE Symposium on Logic in Computer Science, vol. Part F138033, 394–403.","chicago":"Ferrere, Thomas, Thomas A Henzinger, and Ege Saraç. “A Theory of Register Monitors,” Part F138033:394–403. IEEE, 2018. https://doi.org/10.1145/3209108.3209194.","ama":"Ferrere T, Henzinger TA, Saraç E. A theory of register monitors. In: Vol Part F138033. IEEE; 2018:394-403. doi:10.1145/3209108.3209194","apa":"Ferrere, T., Henzinger, T. A., & Saraç, E. (2018). A theory of register monitors (Vol. Part F138033, pp. 394–403). Presented at the LICS: Logic in Computer Science, Oxford, UK: IEEE. https://doi.org/10.1145/3209108.3209194","short":"T. Ferrere, T.A. Henzinger, E. Saraç, in:, IEEE, 2018, pp. 394–403.","ieee":"T. Ferrere, T. A. Henzinger, and E. Saraç, “A theory of register monitors,” presented at the LICS: Logic in Computer Science, Oxford, UK, 2018, vol. Part F138033, pp. 394–403.","mla":"Ferrere, Thomas, et al. A Theory of Register Monitors. Vol. Part F138033, IEEE, 2018, pp. 394–403, doi:10.1145/3209108.3209194."},"date_updated":"2023-09-08T11:49:13Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000545262800041"]},"publist_id":"7779","author":[{"id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","last_name":"Ferrere"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"first_name":"Ege","last_name":"Saraç","full_name":"Saraç, Ege"}],"title":"A theory of register monitors","department":[{"_id":"ToHe"}]},{"_id":"203","type":"journal_article","status":"public","date_updated":"2023-09-08T13:24:40Z","department":[{"_id":"JiFr"}],"abstract":[{"text":"Asymmetric auxin distribution is instrumental for the differential growth that causes organ bending on tropic stimuli and curvatures during plant development. Local differences in auxin concentrations are achieved mainly by polarized cellular distribution of PIN auxin transporters, but whether other mechanisms involving auxin homeostasis are also relevant for the formation of auxin gradients is not clear. Here we show that auxin methylation is required for asymmetric auxin distribution across the hypocotyl, particularly during its response to gravity. We found that loss-of-function mutants in Arabidopsis IAA CARBOXYL METHYLTRANSFERASE1 (IAMT1) prematurely unfold the apical hook, and that their hypocotyls are impaired in gravitropic reorientation. This defect is linked to an auxin-dependent increase in PIN gene expression, leading to an increased polar auxin transport and lack of asymmetric distribution of PIN3 in the iamt1 mutant. Gravitropic reorientation in the iamt1 mutant could be restored with either endodermis-specific expression of IAMT1 or partial inhibition of polar auxin transport, which also results in normal PIN gene expression levels. We propose that IAA methylation is necessary in gravity-sensing cells to restrict polar auxin transport within the range of auxin levels that allow for differential responses.","lang":"eng"}],"oa_version":"None","main_file_link":[{"open_access":"1","url":"http://eprints.nottingham.ac.uk/52388/"}],"scopus_import":"1","intvolume":" 115","month":"06","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"issue":"26","volume":115,"project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"citation":{"ieee":"M. Abbas et al., “Auxin methylation is required for differential growth in Arabidopsis,” PNAS, vol. 115, no. 26. National Academy of Sciences, pp. 6864–6869, 2018.","short":"M. Abbas, G.J. Hernández, S. Pollmann, S.L. Samodelov, M. Kolb, J. Friml, U.Z. Hammes, M.D. Zurbriggen, M. Blázquez, D. Alabadí, PNAS 115 (2018) 6864–6869.","ama":"Abbas M, Hernández GJ, Pollmann S, et al. Auxin methylation is required for differential growth in Arabidopsis. PNAS. 2018;115(26):6864-6869. doi:10.1073/pnas.1806565115","apa":"Abbas, M., Hernández, G. J., Pollmann, S., Samodelov, S. L., Kolb, M., Friml, J., … Alabadí, D. (2018). Auxin methylation is required for differential growth in Arabidopsis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1806565115","mla":"Abbas, Mohamad, et al. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” PNAS, vol. 115, no. 26, National Academy of Sciences, 2018, pp. 6864–69, doi:10.1073/pnas.1806565115.","ista":"Abbas M, Hernández GJ, Pollmann S, Samodelov SL, Kolb M, Friml J, Hammes UZ, Zurbriggen MD, Blázquez M, Alabadí D. 2018. Auxin methylation is required for differential growth in Arabidopsis. PNAS. 115(26), 6864–6869.","chicago":"Abbas, Mohamad, García J Hernández, Stephan Pollmann, Sophia L Samodelov, Martina Kolb, Jiří Friml, Ulrich Z Hammes, Matias D Zurbriggen, Miguel Blázquez, and David Alabadí. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1806565115."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000436245000096"]},"publist_id":"7710","author":[{"last_name":"Abbas","full_name":"Abbas, Mohamad","id":"47E8FC1C-F248-11E8-B48F-1D18A9856A87","first_name":"Mohamad"},{"full_name":"Hernández, García J","last_name":"Hernández","first_name":"García J"},{"full_name":"Pollmann, Stephan","last_name":"Pollmann","first_name":"Stephan"},{"last_name":"Samodelov","full_name":"Samodelov, Sophia L","first_name":"Sophia L"},{"first_name":"Martina","last_name":"Kolb","full_name":"Kolb, Martina"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"last_name":"Hammes","full_name":"Hammes, Ulrich Z","first_name":"Ulrich Z"},{"first_name":"Matias D","last_name":"Zurbriggen","full_name":"Zurbriggen, Matias D"},{"full_name":"Blázquez, Miguel","last_name":"Blázquez","first_name":"Miguel"},{"first_name":"David","last_name":"Alabadí","full_name":"Alabadí, David"}],"title":"Auxin methylation is required for differential growth in Arabidopsis","oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","year":"2018","isi":1,"publication":"PNAS","day":"26","page":"6864-6869","date_created":"2018-12-11T11:45:11Z","doi":"10.1073/pnas.1806565115","date_published":"2018-06-26T00:00:00Z"},{"_id":"399","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-09-08T13:30:51Z","department":[{"_id":"RoSe"}],"oa_version":"Preprint","abstract":[{"text":"Following an earlier calculation in 3D, we calculate the 2D critical temperature of a dilute, translation-invariant Bose gas using a variational formulation of the Bogoliubov approximation introduced by Critchley and Solomon in 1976. This provides the first analytical calculation of the Kosterlitz-Thouless transition temperature that includes the constant in the logarithm.","lang":"eng"}],"month":"01","intvolume":" 121","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1706.01822","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"1","volume":121,"article_number":"10007","project":[{"call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Napiórkowski MM, Reuvers R, Solovej J. 2018. Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. 121(1), 10007.","chicago":"Napiórkowski, Marcin M, Robin Reuvers, and Jan Solovej. “Calculation of the Critical Temperature of a Dilute Bose Gas in the Bogoliubov Approximation.” EPL. IOP Publishing Ltd., 2018. https://doi.org/10.1209/0295-5075/121/10007.","short":"M.M. Napiórkowski, R. Reuvers, J. Solovej, EPL 121 (2018).","ieee":"M. M. Napiórkowski, R. Reuvers, and J. Solovej, “Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation,” EPL, vol. 121, no. 1. IOP Publishing Ltd., 2018.","apa":"Napiórkowski, M. M., Reuvers, R., & Solovej, J. (2018). Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. IOP Publishing Ltd. https://doi.org/10.1209/0295-5075/121/10007","ama":"Napiórkowski MM, Reuvers R, Solovej J. Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. 2018;121(1). doi:10.1209/0295-5075/121/10007","mla":"Napiórkowski, Marcin M., et al. “Calculation of the Critical Temperature of a Dilute Bose Gas in the Bogoliubov Approximation.” EPL, vol. 121, no. 1, 10007, IOP Publishing Ltd., 2018, doi:10.1209/0295-5075/121/10007."},"title":"Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation","author":[{"first_name":"Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87","last_name":"Napiórkowski","full_name":"Napiórkowski, Marcin M"},{"first_name":"Robin","full_name":"Reuvers, Robin","last_name":"Reuvers"},{"first_name":"Jan","full_name":"Solovej, Jan","last_name":"Solovej"}],"publist_id":"7432","external_id":{"isi":["000460003000003"],"arxiv":["1706.01822"]},"article_processing_charge":"No","acknowledgement":"We thank Robert Seiringer and Daniel Ueltschi for bringing the issue of the change in critical temperature to our attention. We also thank the Erwin Schrödinger Institute (all authors) and the Department of Mathematics, University of Copenhagen (MN) for the hospitality during the period this work was carried out. We gratefully acknowledge the financial support by the European Unions Seventh Framework Programme under the ERC Grant Agreement Nos. 321029 (JPS and RR) and 337603 (RR) as well as support by the VIL-LUM FONDEN via the QMATH Centre of Excellence (Grant No. 10059) (JPS and RR), by the National Science Center (NCN) under grant No. 2016/21/D/ST1/02430 and the Austrian Science Fund (FWF) through project No. P 27533-N27 (MN).","quality_controlled":"1","publisher":"IOP Publishing Ltd.","oa":1,"day":"01","publication":"EPL","isi":1,"year":"2018","date_published":"2018-01-01T00:00:00Z","doi":"10.1209/0295-5075/121/10007","date_created":"2018-12-11T11:46:15Z"},{"type":"journal_article","status":"public","_id":"5830","author":[{"first_name":"Luosha","last_name":"Zhang","full_name":"Zhang, Luosha"},{"first_name":"Xiong","last_name":"Shi","full_name":"Shi, Xiong"},{"last_name":"Zhang","full_name":"Zhang, Yutao","first_name":"Yutao"},{"first_name":"Jiajing","full_name":"Wang, Jiajing","last_name":"Wang"},{"last_name":"Yang","full_name":"Yang, Jingwei","first_name":"Jingwei"},{"last_name":"Ishida","full_name":"Ishida, Takashi","first_name":"Takashi"},{"full_name":"Jiang, Wenqian","last_name":"Jiang","first_name":"Wenqian"},{"first_name":"Xiangyu","last_name":"Han","full_name":"Han, Xiangyu"},{"first_name":"Jingke","full_name":"Kang, Jingke","last_name":"Kang"},{"last_name":"Wang","full_name":"Wang, Xuening","first_name":"Xuening"},{"full_name":"Pan, Lixia","last_name":"Pan","first_name":"Lixia"},{"first_name":"Shuo","last_name":"Lv","full_name":"Lv, Shuo"},{"first_name":"Bing","full_name":"Cao, Bing","last_name":"Cao"},{"full_name":"Zhang, Yonghong","last_name":"Zhang","first_name":"Yonghong"},{"full_name":"Wu, Jinbin","last_name":"Wu","first_name":"Jinbin"},{"last_name":"Han","full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin"},{"full_name":"Hu, Zhubing","last_name":"Hu","first_name":"Zhubing"},{"first_name":"Langjun","last_name":"Cui","full_name":"Cui, Langjun"},{"first_name":"Shinichiro","full_name":"Sawa, Shinichiro","last_name":"Sawa"},{"first_name":"Junmin","last_name":"He","full_name":"He, Junmin"},{"full_name":"Wang, Guodong","last_name":"Wang","first_name":"Guodong"}],"external_id":{"isi":["000459014800021"],"pmid":["30378140"]},"article_processing_charge":"No","department":[{"_id":"JiFr"}],"title":"CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana","citation":{"chicago":"Zhang, Luosha, Xiong Shi, Yutao Zhang, Jiajing Wang, Jingwei Yang, Takashi Ishida, Wenqian Jiang, et al. “CLE9 Peptide-Induced Stomatal Closure Is Mediated by Abscisic Acid, Hydrogen Peroxide, and Nitric Oxide in Arabidopsis Thaliana.” Plant Cell and Environment. Wiley, 2018. https://doi.org/10.1111/pce.13475.","ista":"Zhang L, Shi X, Zhang Y, Wang J, Yang J, Ishida T, Jiang W, Han X, Kang J, Wang X, Pan L, Lv S, Cao B, Zhang Y, Wu J, Han H, Hu Z, Cui L, Sawa S, He J, Wang G. 2018. CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment.","mla":"Zhang, Luosha, et al. “CLE9 Peptide-Induced Stomatal Closure Is Mediated by Abscisic Acid, Hydrogen Peroxide, and Nitric Oxide in Arabidopsis Thaliana.” Plant Cell and Environment, Wiley, 2018, doi:10.1111/pce.13475.","short":"L. Zhang, X. Shi, Y. Zhang, J. Wang, J. Yang, T. Ishida, W. Jiang, X. Han, J. Kang, X. Wang, L. Pan, S. Lv, B. Cao, Y. Zhang, J. Wu, H. Han, Z. Hu, L. Cui, S. Sawa, J. He, G. Wang, Plant Cell and Environment (2018).","ieee":"L. Zhang et al., “CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana,” Plant Cell and Environment. Wiley, 2018.","apa":"Zhang, L., Shi, X., Zhang, Y., Wang, J., Yang, J., Ishida, T., … Wang, G. (2018). CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment. Wiley. https://doi.org/10.1111/pce.13475","ama":"Zhang L, Shi X, Zhang Y, et al. CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment. 2018. doi:10.1111/pce.13475"},"date_updated":"2023-09-11T12:43:31Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","publisher":"Wiley","scopus_import":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30378140"}],"month":"10","abstract":[{"lang":"eng","text":"CLE peptides have been implicated in various developmental processes of plants and mediate their responses to environmental stimuli. However, the biological relevance of most CLE genes remains to be functionally characterized. Here, we report that CLE9, which is expressed in stomata, acts as an essential regulator in the induction of stomatal closure. Exogenous application of CLE9 peptides or overexpression of CLE9 effectively led to stomatal closure and enhanced drought tolerance, whereas CLE9 loss-of-function mutants were sensitivity to drought stress. CLE9-induced stomatal closure was impaired in abscisic acid (ABA)-deficient mutants, indicating that ABA is required for CLE9-medaited guard cell signalling. We further deciphered that two guard cell ABA-signalling components, OST1 and SLAC1, were responsible for CLE9-induced stomatal closure. MPK3 and MPK6 were activated by the CLE9 peptide, and CLE9 peptides failed to close stomata in mpk3 and mpk6 mutants. In addition, CLE9 peptides stimulated the induction of hydrogen peroxide (H2O2) and nitric oxide (NO) synthesis associated with stomatal closure, which was abolished in the NADPH oxidase-deficient mutants or nitric reductase mutants, respectively. Collectively, our results reveal a novel ABA-dependent function of CLE9 in the regulation of stomatal apertures, thereby suggesting a potential role of CLE9 in the stress acclimatization of plants."}],"oa_version":"Published Version","pmid":1,"doi":"10.1111/pce.13475","date_published":"2018-10-31T00:00:00Z","date_created":"2019-01-13T22:59:11Z","publication_identifier":{"issn":["01407791"]},"isi":1,"year":"2018","publication_status":"epub_ahead","day":"31","publication":"Plant Cell and Environment","language":[{"iso":"eng"}]},{"year":"2018","isi":1,"publication":"Nature Cell Biology","day":"21","page":"677 - 687","date_created":"2018-12-11T11:45:38Z","doi":"10.1038/s41556-018-0108-1","date_published":"2018-05-21T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","citation":{"short":"A. Lilja, V. Rodilla, M. Huyghe, E.B. Hannezo, C. Landragin, O. Renaud, O. Leroy, S. Rulands, B. Simons, S. Fré, Nature Cell Biology 20 (2018) 677–687.","ieee":"A. Lilja et al., “Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland,” Nature Cell Biology, vol. 20, no. 6. Nature Publishing Group, pp. 677–687, 2018.","ama":"Lilja A, Rodilla V, Huyghe M, et al. Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. Nature Cell Biology. 2018;20(6):677-687. doi:10.1038/s41556-018-0108-1","apa":"Lilja, A., Rodilla, V., Huyghe, M., Hannezo, E. B., Landragin, C., Renaud, O., … Fré, S. (2018). Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/s41556-018-0108-1","mla":"Lilja, Anna, et al. “Clonal Analysis of Notch1-Expressing Cells Reveals the Existence of Unipotent Stem Cells That Retain Long-Term Plasticity in the Embryonic Mammary Gland.” Nature Cell Biology, vol. 20, no. 6, Nature Publishing Group, 2018, pp. 677–87, doi:10.1038/s41556-018-0108-1.","ista":"Lilja A, Rodilla V, Huyghe M, Hannezo EB, Landragin C, Renaud O, Leroy O, Rulands S, Simons B, Fré S. 2018. Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. Nature Cell Biology. 20(6), 677–687.","chicago":"Lilja, Anna, Veronica Rodilla, Mathilde Huyghe, Edouard B Hannezo, Camille Landragin, Olivier Renaud, Olivier Leroy, Steffen Rulands, Benjamin Simons, and Silvia Fré. “Clonal Analysis of Notch1-Expressing Cells Reveals the Existence of Unipotent Stem Cells That Retain Long-Term Plasticity in the Embryonic Mammary Gland.” Nature Cell Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41556-018-0108-1."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000433237300003"],"pmid":["29784917"]},"author":[{"last_name":"Lilja","full_name":"Lilja, Anna","first_name":"Anna"},{"last_name":"Rodilla","full_name":"Rodilla, Veronica","first_name":"Veronica"},{"first_name":"Mathilde","last_name":"Huyghe","full_name":"Huyghe, Mathilde"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"full_name":"Landragin, Camille","last_name":"Landragin","first_name":"Camille"},{"last_name":"Renaud","full_name":"Renaud, Olivier","first_name":"Olivier"},{"last_name":"Leroy","full_name":"Leroy, Olivier","first_name":"Olivier"},{"full_name":"Rulands, Steffen","last_name":"Rulands","first_name":"Steffen"},{"full_name":"Simons, Benjamin","last_name":"Simons","first_name":"Benjamin"},{"last_name":"Fré","full_name":"Fré, Silvia","first_name":"Silvia"}],"publist_id":"7594","title":"Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland","publication_status":"published","language":[{"iso":"eng"}],"issue":"6","volume":20,"abstract":[{"lang":"eng","text":"Recent lineage tracing studies have revealed that mammary gland homeostasis relies on unipotent stem cells. However, whether and when lineage restriction occurs during embryonic mammary development, and which signals orchestrate cell fate specification, remain unknown. Using a combination of in vivo clonal analysis with whole mount immunofluorescence and mathematical modelling of clonal dynamics, we found that embryonic multipotent mammary cells become lineage-restricted surprisingly early in development, with evidence for unipotency as early as E12.5 and no statistically discernable bipotency after E15.5. To gain insights into the mechanisms governing the switch from multipotency to unipotency, we used gain-of-function Notch1 mice and demonstrated that Notch activation cell autonomously dictates luminal cell fate specification to both embryonic and basally committed mammary cells. These functional studies have important implications for understanding the signals underlying cell plasticity and serve to clarify how reactivation of embryonic programs in adult cells can lead to cancer."}],"pmid":1,"oa_version":"Submitted Version","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6984964","open_access":"1"}],"scopus_import":"1","intvolume":" 20","month":"05","date_updated":"2023-09-11T12:44:08Z","department":[{"_id":"EdHa"}],"_id":"288","type":"journal_article","article_type":"original","status":"public"},{"department":[{"_id":"BeBi"}],"file_date_updated":"2020-07-14T12:45:59Z","ddc":["000","535","680"],"date_updated":"2023-09-11T12:46:13Z","status":"public","pubrep_id":"1028","type":"journal_article","_id":"304","related_material":{"link":[{"url":"https://ist.ac.at/en/news/color-effects-from-transparent-3d-printed-nanostructures/","relation":"press_release","description":"News on IST 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scale.\r\n \r\nWe show initial results of material samples fabricated based on our designs.\r\nWhile these suffer from the prototype character of state-of-the-art fabrication hardware, we believe they clearly demonstrate the potential of additive nanofabrication for structural colors and other graphics applications.","lang":"eng"}],"title":"Computational design of nanostructural color for additive manufacturing","author":[{"id":"4718F954-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","orcid":"0000-0002-1546-3265","full_name":"Auzinger, Thomas","last_name":"Auzinger"},{"first_name":"Wolfgang","last_name":"Heidrich","full_name":"Heidrich, Wolfgang"},{"last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"}],"article_processing_charge":"No","external_id":{"isi":["000448185000120"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"T. Auzinger, W. Heidrich, and B. Bickel, “Computational design of nanostructural color for additive manufacturing,” ACM Transactions on Graphics, vol. 37, no. 4. ACM, 2018.","short":"T. Auzinger, W. Heidrich, B. Bickel, ACM Transactions on Graphics 37 (2018).","apa":"Auzinger, T., Heidrich, W., & Bickel, B. (2018). Computational design of nanostructural color for additive manufacturing. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3197517.3201376","ama":"Auzinger T, Heidrich W, Bickel B. Computational design of nanostructural color for additive manufacturing. ACM Transactions on Graphics. 2018;37(4). doi:10.1145/3197517.3201376","mla":"Auzinger, Thomas, et al. “Computational Design of Nanostructural Color for Additive Manufacturing.” ACM Transactions on Graphics, vol. 37, no. 4, 159, ACM, 2018, doi:10.1145/3197517.3201376.","ista":"Auzinger T, Heidrich W, Bickel B. 2018. Computational design of nanostructural color for additive manufacturing. ACM Transactions on Graphics. 37(4), 159.","chicago":"Auzinger, Thomas, Wolfgang Heidrich, and Bernd Bickel. “Computational Design of Nanostructural Color for Additive Manufacturing.” ACM Transactions on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201376."},"project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"159","date_published":"2018-08-01T00:00:00Z","doi":"10.1145/3197517.3201376","date_created":"2018-12-11T11:45:43Z","day":"01","publication":"ACM Transactions on Graphics","has_accepted_license":"1","isi":1,"year":"2018","quality_controlled":"1","publisher":"ACM","oa":1,"acknowledgement":"This work was in part supported by King Abdullah University of Science and Technology Baseline Funding."},{"month":"08","intvolume":" 37","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Molding is a popular mass production method, in which the initial expenses for the mold are offset by the low per-unit production cost. However, the physical fabrication constraints of the molding technique commonly restrict the shape of moldable objects. For a complex shape, a decomposition of the object into moldable parts is a common strategy to address these constraints, with plastic model kits being a popular and illustrative example. However, conducting such a decomposition requires considerable expertise, and it depends on the technical aspects of the fabrication technique, as well as aesthetic considerations. We present an interactive technique to create such decompositions for two-piece molding, in which each part of the object is cast between two rigid mold pieces. Given the surface description of an object, we decompose its thin-shell equivalent into moldable parts by first performing a coarse decomposition and then utilizing an active contour model for the boundaries between individual parts. Formulated as an optimization problem, the movement of the contours is guided by an energy reflecting fabrication constraints to ensure the moldability of each part. Simultaneously, the user is provided with editing capabilities to enforce aesthetic guidelines. Our interactive interface provides control of the contour positions by allowing, for example, the alignment of part boundaries with object features. Our technique enables a novel workflow, as it empowers novice users to explore the design space, and it generates fabrication-ready two-piece molds that can be used either for casting or industrial injection molding of free-form objects."}],"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/interactive-software-tool-makes-complex-mold-design-simple/","description":"News on IST Homepage"}]},"volume":37,"issue":"4","ec_funded":1,"file":[{"checksum":"6a5368bc86c4e1a9fcfe588fd1f14ee8","file_id":"5360","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2018-1037-v1+1_CoreCavity-AuthorVersion.pdf","date_created":"2018-12-12T10:18:38Z","file_size":104225664,"date_updated":"2020-07-14T12:44:38Z","creator":"system"},{"creator":"system","file_size":377743553,"date_updated":"2020-07-14T12:44:38Z","file_name":"IST-2018-1037-v1+2_CoreCavity-Supplemental.zip","date_created":"2018-12-12T10:18:39Z","relation":"main_file","access_level":"open_access","content_type":"application/zip","checksum":"3861e693ba47c51f3ec7b7867d573a61","file_id":"5361"},{"creator":"system","date_updated":"2020-07-14T12:44:38Z","file_size":162634396,"date_created":"2018-12-12T10:18:41Z","file_name":"IST-2018-1037-v1+3_CoreCavity-Video.mp4","access_level":"open_access","relation":"main_file","content_type":"video/vnd.objectvideo","checksum":"490040c685ed869536e2a18f5a906b94","file_id":"5362"},{"content_type":"image/jpeg","relation":"main_file","access_level":"open_access","file_id":"5363","checksum":"be7fc8b229adda727419b6504b3b9352","file_size":527972,"date_updated":"2020-07-14T12:44:38Z","creator":"system","file_name":"IST-2018-1037-v1+4_CoreCavity-RepresentativeImage.jpg","date_created":"2018-12-12T10:18:42Z"}],"language":[{"iso":"eng"}],"publication_status":"published","status":"public","pubrep_id":"1037","type":"journal_article","_id":"12","file_date_updated":"2020-07-14T12:44:38Z","department":[{"_id":"BeBi"}],"ddc":["004","516","670"],"date_updated":"2023-09-11T12:48:09Z","publisher":"ACM","quality_controlled":"1","oa":1,"doi":"10.1145/3197517.3201341","date_published":"2018-08-04T00:00:00Z","date_created":"2018-12-11T11:44:09Z","day":"04","publication":"ACM Transaction on Graphics","has_accepted_license":"1","isi":1,"year":"2018","project":[{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"},{"_id":"2508E324-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Distributed 3D Object Design","grant_number":"642841"}],"article_number":"135","title":"CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds","publist_id":"8044","author":[{"first_name":"Kazutaka","full_name":"Nakashima, Kazutaka","last_name":"Nakashima"},{"last_name":"Auzinger","full_name":"Auzinger, Thomas","orcid":"0000-0002-1546-3265","first_name":"Thomas","id":"4718F954-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Emmanuel","id":"33F19F16-F248-11E8-B48F-1D18A9856A87","last_name":"Iarussi","full_name":"Iarussi, Emmanuel"},{"id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","first_name":"Ran","orcid":"0000-0002-3808-281X","full_name":"Zhang, Ran","last_name":"Zhang"},{"last_name":"Igarashi","full_name":"Igarashi, Takeo","first_name":"Takeo"},{"last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000448185000096"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. 2018. CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. ACM Transaction on Graphics. 37(4), 135.","chicago":"Nakashima, Kazutaka, Thomas Auzinger, Emmanuel Iarussi, Ran Zhang, Takeo Igarashi, and Bernd Bickel. “CoreCavity: Interactive Shell Decomposition for Fabrication with Two-Piece Rigid Molds.” ACM Transaction on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201341.","ama":"Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. ACM Transaction on Graphics. 2018;37(4). doi:10.1145/3197517.3201341","apa":"Nakashima, K., Auzinger, T., Iarussi, E., Zhang, R., Igarashi, T., & Bickel, B. (2018). CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. ACM Transaction on Graphics. ACM. https://doi.org/10.1145/3197517.3201341","ieee":"K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, and B. Bickel, “CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds,” ACM Transaction on Graphics, vol. 37, no. 4. ACM, 2018.","short":"K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, B. Bickel, ACM Transaction on Graphics 37 (2018).","mla":"Nakashima, Kazutaka, et al. “CoreCavity: Interactive Shell Decomposition for Fabrication with Two-Piece Rigid Molds.” ACM Transaction on Graphics, vol. 37, no. 4, 135, ACM, 2018, doi:10.1145/3197517.3201341."}}]