[{"publisher":"American Physical Society","quality_controlled":"1","oa":1,"acknowledgement":"The authors are grateful to Florian Gebhard and Mikhail Lemeshko for discussions and critical reading of the manuscript. The work was supported by the Ministry of Science and Higher Education in Poland through the Iuventus Plus Grant No. IP2012 017172, as well as by the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA Grant Agreement No. 291734. J.K. acknowledges hospitality of the Leibniz Universität in Hannover where a large part of the work was performed.","doi":"10.1103/PhysRevB.94.085152","date_published":"2016-08-30T00:00:00Z","date_created":"2018-12-11T11:51:32Z","year":"2016","day":"30","publication":"Physical Review B - Condensed Matter and Materials Physics","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"article_number":"085152","publist_id":"5897","author":[{"last_name":"Kaczmarczyk","orcid":"0000-0002-1629-3675","full_name":"Kaczmarczyk, Jan","first_name":"Jan","id":"46C405DE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tobias","last_name":"Schickling","full_name":"Schickling, Tobias"},{"first_name":"Jörg","last_name":"Bünemann","full_name":"Bünemann, Jörg"}],"title":"Coexistence of nematic order and superconductivity in the Hubbard model","citation":{"ama":"Kaczmarczyk J, Schickling T, Bünemann J. Coexistence of nematic order and superconductivity in the Hubbard model. Physical Review B - Condensed Matter and Materials Physics. 2016;94(8). doi:10.1103/PhysRevB.94.085152","apa":"Kaczmarczyk, J., Schickling, T., & Bünemann, J. (2016). Coexistence of nematic order and superconductivity in the Hubbard model. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.94.085152","ieee":"J. Kaczmarczyk, T. Schickling, and J. Bünemann, “Coexistence of nematic order and superconductivity in the Hubbard model,” Physical Review B - Condensed Matter and Materials Physics, vol. 94, no. 8. American Physical Society, 2016.","short":"J. Kaczmarczyk, T. Schickling, J. Bünemann, Physical Review B - Condensed Matter and Materials Physics 94 (2016).","mla":"Kaczmarczyk, Jan, et al. “Coexistence of Nematic Order and Superconductivity in the Hubbard Model.” Physical Review B - Condensed Matter and Materials Physics, vol. 94, no. 8, 085152, American Physical Society, 2016, doi:10.1103/PhysRevB.94.085152.","ista":"Kaczmarczyk J, Schickling T, Bünemann J. 2016. Coexistence of nematic order and superconductivity in the Hubbard model. Physical Review B - Condensed Matter and Materials Physics. 94(8), 085152.","chicago":"Kaczmarczyk, Jan, Tobias Schickling, and Jörg Bünemann. “Coexistence of Nematic Order and Superconductivity in the Hubbard Model.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2016. https://doi.org/10.1103/PhysRevB.94.085152."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1512.06688"}],"month":"08","intvolume":" 94","abstract":[{"text":"We study the interplay of nematic and superconducting order in the two-dimensional Hubbard model and show that they can coexist, especially when superconductivity is not the energetically dominant phase. Due to a breaking of the C4 symmetry, the coexisting phase inherently contains admixture of the s-wave pairing components. As a result, the superconducting gap exhibits nonstandard features including changed nodal directions. Our results also show that in the optimally doped regime the pure superconducting phase is typically unstable towards developing nematicity (breaking of the C4 symmetry). This has implications for the cuprate high-Tc superconductors, for which in this regime the so-called intertwined orders have recently been observed. Namely, the coexisting phase may be viewed as a precursor to such more involved patterns of symmetry breaking.","lang":"eng"}],"oa_version":"Preprint","volume":94,"issue":"8","ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"1352","department":[{"_id":"MiLe"}],"date_updated":"2021-01-12T06:50:05Z"},{"publist_id":"5892","author":[{"first_name":"Paul","last_name":"Dieterle","full_name":"Dieterle, Paul"},{"first_name":"Mahmoud","last_name":"Kalaee","full_name":"Kalaee, Mahmoud"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Oskar","full_name":"Painter, Oskar","last_name":"Painter"}],"title":"Superconducting cavity electromechanics on a silicon-on-insulator platform","department":[{"_id":"JoFi"}],"citation":{"chicago":"Dieterle, Paul, Mahmoud Kalaee, Johannes M Fink, and Oskar Painter. “Superconducting Cavity Electromechanics on a Silicon-on-Insulator Platform.” Physical Review Applied. American Physical Society, 2016. https://doi.org/10.1103/PhysRevApplied.6.014013.","ista":"Dieterle P, Kalaee M, Fink JM, Painter O. 2016. Superconducting cavity electromechanics on a silicon-on-insulator platform. Physical Review Applied. 6(1), 014013.","mla":"Dieterle, Paul, et al. “Superconducting Cavity Electromechanics on a Silicon-on-Insulator Platform.” Physical Review Applied, vol. 6, no. 1, 014013, American Physical Society, 2016, doi:10.1103/PhysRevApplied.6.014013.","ieee":"P. Dieterle, M. Kalaee, J. M. Fink, and O. Painter, “Superconducting cavity electromechanics on a silicon-on-insulator platform,” Physical Review Applied, vol. 6, no. 1. American Physical Society, 2016.","short":"P. Dieterle, M. Kalaee, J.M. Fink, O. Painter, Physical Review Applied 6 (2016).","apa":"Dieterle, P., Kalaee, M., Fink, J. M., & Painter, O. (2016). Superconducting cavity electromechanics on a silicon-on-insulator platform. Physical Review Applied. 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Using this fabrication process, a high-impedance 8.9-GHz coil resonator is coupled capacitively with a large participation ratio to a 9.7-MHz micromechanical resonator. Two-tone microwave spectroscopy and radiation pressure backaction are used to characterize the coupled system in a dilution refrigerator down to temperatures of Tf=11 mK, yielding a measured electromechanical vacuum coupling rate of g0/2π=24.6 Hz and a mechanical resonator Q factor of Qm=1.7×107. Microwave backaction cooling of the mechanical resonator is also studied, with a minimum phonon occupancy of nm≈16 phonons being realized at an elevated fridge temperature of Tf=211 mK.","lang":"eng"}],"oa_version":"Preprint"},{"scopus_import":1,"intvolume":" 202","month":"01","oa_version":"Submitted Version","volume":202,"issue":"1","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_size":112674,"date_updated":"2020-07-14T12:44:46Z","creator":"system","file_name":"IST-2017-769-v1+1_SewallWright1931.pdf","date_created":"2018-12-12T10:08:26Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"4687","checksum":"3562b89c821a4be84edf2b6ebd870cf5"}],"type":"journal_article","pubrep_id":"769","status":"public","_id":"1356","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:44:46Z","date_updated":"2021-01-12T06:50:07Z","ddc":["570"],"oa":1,"publisher":"Genetics Society of America","quality_controlled":"1","page":"3 - 4","date_created":"2018-12-11T11:51:33Z","date_published":"2016-01-05T00:00:00Z","doi":"10.1534/genetics.115.184796","year":"2016","has_accepted_license":"1","publication":"Genetics","day":"05","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"publist_id":"5889","title":"Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”","citation":{"mla":"Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations and the ‘Shifting Balance.’” Genetics, vol. 202, no. 1, Genetics Society of America, 2016, pp. 3–4, doi:10.1534/genetics.115.184796.","ama":"Barton NH. Sewall Wright on evolution in Mendelian populations and the “Shifting Balance.” Genetics. 2016;202(1):3-4. doi:10.1534/genetics.115.184796","apa":"Barton, N. H. (2016). Sewall Wright on evolution in Mendelian populations and the “Shifting Balance.” Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.184796","short":"N.H. Barton, Genetics 202 (2016) 3–4.","ieee":"N. H. Barton, “Sewall Wright on evolution in Mendelian populations and the ‘Shifting Balance,’” Genetics, vol. 202, no. 1. Genetics Society of America, pp. 3–4, 2016.","chicago":"Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations and the ‘Shifting Balance.’” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.184796.","ista":"Barton NH. 2016. Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”. 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Genetics. 2016;202(3):865-866. doi:10.1534/genetics.116.187542"}},{"title":"Deciding absorption","publist_id":"5893","author":[{"full_name":"Barto, Libor","last_name":"Barto","first_name":"Libor"},{"first_name":"Alexandr","id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87","full_name":"Kazda, Alexandr","last_name":"Kazda"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"L. Barto, A. Kazda, International Journal of Algebra and Computation 26 (2016) 1033–1060.","ieee":"L. Barto and A. Kazda, “Deciding absorption,” International Journal of Algebra and Computation, vol. 26, no. 5. World Scientific Publishing, pp. 1033–1060, 2016.","ama":"Barto L, Kazda A. Deciding absorption. International Journal of Algebra and Computation. 2016;26(5):1033-1060. doi:10.1142/S0218196716500430","apa":"Barto, L., & Kazda, A. (2016). Deciding absorption. International Journal of Algebra and Computation. World Scientific Publishing. https://doi.org/10.1142/S0218196716500430","mla":"Barto, Libor, and Alexandr Kazda. “Deciding Absorption.” International Journal of Algebra and Computation, vol. 26, no. 5, World Scientific Publishing, 2016, pp. 1033–60, doi:10.1142/S0218196716500430.","ista":"Barto L, Kazda A. 2016. Deciding absorption. International Journal of Algebra and Computation. 26(5), 1033–1060.","chicago":"Barto, Libor, and Alexandr Kazda. “Deciding Absorption.” International Journal of Algebra and Computation. World Scientific Publishing, 2016. https://doi.org/10.1142/S0218196716500430."},"doi":"10.1142/S0218196716500430","date_published":"2016-07-20T00:00:00Z","date_created":"2018-12-11T11:51:32Z","page":"1033 - 1060","day":"20","publication":"International Journal of Algebra and Computation","year":"2016","publisher":"World Scientific Publishing","quality_controlled":"1","oa":1,"acknowledgement":"Libor Barto and Alexandr Kazda were supported by the the Grant Agency of the Czech Republic, grant GACR 13-01832S. ","department":[{"_id":"VlKo"}],"date_updated":"2021-01-12T06:50:06Z","status":"public","type":"journal_article","_id":"1353","volume":26,"issue":"5","language":[{"iso":"eng"}],"publication_status":"published","month":"07","intvolume":" 26","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1512.07009","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":"We characterize absorption in finite idempotent algebras by means of Jónsson absorption and cube term blockers. As an application we show that it is decidable whether a given subset is an absorbing subuniverse of an algebra given by the tables of its basic operations.","lang":"eng"}]},{"acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"When aiming to seamlessly integrate a fluid simulation into a larger scenario (like an open ocean), careful attention must be paid to boundary conditions. In particular, one must implement special "non-reflecting" boundary conditions, which dissipate out-going waves as they exit the simulation. Unfortunately, the state of the art in non-reflecting boundary conditions (perfectly-matched layers, or PMLs) only permits trivially simple inflow/outflow conditions, so there is no reliable way to integrate a fluid simulation into a more complicated environment like a stormy ocean or a turbulent river. This paper introduces the first method for combining nonreflecting boundary conditions based on PMLs with inflow/outflow boundary conditions that vary arbitrarily throughout space and time. Our algorithm is a generalization of stateof- the-art mean-flow boundary conditions in the computational fluid dynamics literature, and it allows for seamless integration of a fluid simulation into much more complicated environments. Our method also opens the door for previously-unseen postprocess effects like retroactively changing the location of solid obstacles, and locally increasing the visual detail of a pre-existing simulation.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ACM Transactions on Graphics"],"intvolume":" 35","month":"07","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_name":"IST-2016-631-v1+2_a96-bojsen-hansen.pdf","date_created":"2018-12-12T10:13:00Z","creator":"system","file_size":12422760,"date_updated":"2020-07-14T12:44:47Z","file_id":"4981","checksum":"140b5532f0a2a006a0149cab7c73c17c","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"volume":35,"issue":"4","_id":"1363","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":"2016-07-24","end_date":"2016-07-28","location":"Anaheim, CA, USA","name":"ACM SIGGRAPH"},"type":"conference","pubrep_id":"631","status":"public","date_updated":"2023-02-21T10:36:12Z","ddc":["000"],"file_date_updated":"2020-07-14T12:44:47Z","department":[{"_id":"ChWo"}],"acknowledgement":"We thank the IST Austria Visual Computing group for helpful feedback throughout the project. 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Bojsen-Hansen, C. Wojtan, in:, ACM, 2016.","mla":"Bojsen-Hansen, Morten, and Chris Wojtan. Generalized Non-Reflecting Boundaries for Fluid Re-Simulation. Vol. 35, no. 4, 96, ACM, 2016, doi:10.1145/2897824.2925963.","ista":"Bojsen-Hansen M, Wojtan C. 2016. Generalized non-reflecting boundaries for fluid re-simulation. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 96.","chicago":"Bojsen-Hansen, Morten, and Chris Wojtan. “Generalized Non-Reflecting Boundaries for Fluid Re-Simulation,” Vol. 35. 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Computational Design of Stable Planar-Rod Structures. Vol. 35, no. 4, 86, ACM, 2016, doi:10.1145/2897824.2925978.","short":"E. Miguel Villalba, M. Lepoutre, B. Bickel, in:, ACM, 2016.","ieee":"E. Miguel Villalba, M. Lepoutre, and B. Bickel, “Computational design of stable planar-rod structures,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4.","apa":"Miguel Villalba, E., Lepoutre, M., & Bickel, B. (2016). Computational design of stable planar-rod structures (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM. https://doi.org/10.1145/2897824.2925978","ama":"Miguel Villalba E, Lepoutre M, Bickel B. Computational design of stable planar-rod structures. In: Vol 35. ACM; 2016. doi:10.1145/2897824.2925978","chicago":"Miguel Villalba, Eder, Mathias Lepoutre, and Bernd Bickel. “Computational Design of Stable Planar-Rod Structures,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2897824.2925978.","ista":"Miguel Villalba E, Lepoutre M, Bickel B. 2016. Computational design of stable planar-rod structures. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 86."},"title":"Computational design of stable planar-rod structures","publist_id":"5878","author":[{"full_name":"Miguel Villalba, Eder","last_name":"Miguel Villalba","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","first_name":"Eder"},{"first_name":"Mathias","full_name":"Lepoutre, Mathias","last_name":"Lepoutre"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"}],"oa_version":"Preprint","abstract":[{"text":"We present a computational method for designing wire sculptures consisting of interlocking wires. Our method allows the computation of aesthetically pleasing structures that are structurally stable, efficiently fabricatable with a 2D wire bending machine, and assemblable without the need of additional connectors. Starting from a set of planar contours provided by the user, our method automatically tests for the feasibility of a design, determines a discrete ordering of wires at intersection points, and optimizes for the rest shape of the individual wires to maximize structural stability under frictional contact. In addition to their application to art, wire sculptures present an extremely efficient and fast alternative for low-fidelity rapid prototyping because manufacturing time and required material linearly scales with the physical size of objects. We demonstrate the effectiveness of our approach on a varied set of examples, all of which we fabricated.","lang":"eng"}],"month":"07","intvolume":" 35","alternative_title":["ACM Transactions on Graphics"],"scopus_import":1,"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"d00c2664a43d945df8876ea0193734e3","file_id":"4853","date_updated":"2020-07-14T12:44:47Z","file_size":44766392,"creator":"system","date_created":"2018-12-12T10:11:01Z","file_name":"IST-2017-763-v1+1_wirebending.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"4","volume":35,"ec_funded":1,"_id":"1364","status":"public","pubrep_id":"763","type":"conference","conference":{"name":"ACM SIGGRAPH","start_date":"2016-07-24","end_date":"2016-07-28","location":"Anaheim, CA, USA"},"ddc":["006"],"date_updated":"2021-01-12T06:50:10Z","file_date_updated":"2020-07-14T12:44:47Z","department":[{"_id":"BeBi"}]},{"conference":{"start_date":"2016-07-24","end_date":"2016-07-28","location":"Anaheim, CA, USA","name":"ACM SIGGRAPH"},"type":"conference","pubrep_id":"637","status":"public","_id":"1361","file_date_updated":"2020-07-14T12:44:46Z","department":[{"_id":"ChWo"}],"date_updated":"2023-02-21T10:36:07Z","ddc":["000"],"scopus_import":1,"alternative_title":["ACM Transactions on Graphics"],"intvolume":" 35","month":"07","abstract":[{"text":"We propose a novel surface-only technique for simulating incompressible, inviscid and uniform-density liquids with surface tension in three dimensions. The liquid surface is captured by a triangle mesh on which a Lagrangian velocity field is stored. Because advection of the velocity field may violate the incompressibility condition, we devise an orthogonal projection technique to remove the divergence while requiring the evaluation of only two boundary integrals. The forces of surface tension, gravity, and solid contact are all treated by a boundary element solve, allowing us to perform detailed simulations of a wide range of liquid phenomena, including waterbells, droplet and jet collisions, fluid chains, and crown splashes.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"volume":35,"issue":"4","publication_status":"published","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"4660","checksum":"6d662893bd447d4f575b4961a2247811","creator":"system","date_updated":"2020-07-14T12:44:46Z","file_size":10561865,"date_created":"2018-12-12T10:08:01Z","file_name":"IST-2016-637-v1+1_2016_Da_SOL.pdf"}],"project":[{"call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"article_number":"a78","author":[{"full_name":"Da, Fang","last_name":"Da","first_name":"Fang"},{"last_name":"Hahn","full_name":"Hahn, David","first_name":"David","id":"357A6A66-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Batty, Christopher","last_name":"Batty","first_name":"Christopher"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Eitan","last_name":"Grinspun","full_name":"Grinspun, Eitan"}],"publist_id":"5881","title":"Surface only liquids","citation":{"short":"F. Da, D. Hahn, C. Batty, C. Wojtan, E. Grinspun, in:, ACM, 2016.","ieee":"F. Da, D. Hahn, C. Batty, C. Wojtan, and E. Grinspun, “Surface only liquids,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4.","ama":"Da F, Hahn D, Batty C, Wojtan C, Grinspun E. Surface only liquids. In: Vol 35. ACM; 2016. doi:10.1145/2897824.2925899","apa":"Da, F., Hahn, D., Batty, C., Wojtan, C., & Grinspun, E. (2016). Surface only liquids (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM. https://doi.org/10.1145/2897824.2925899","mla":"Da, Fang, et al. Surface Only Liquids. Vol. 35, no. 4, a78, ACM, 2016, doi:10.1145/2897824.2925899.","ista":"Da F, Hahn D, Batty C, Wojtan C, Grinspun E. 2016. Surface only liquids. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, a78.","chicago":"Da, Fang, David Hahn, Christopher Batty, Chris Wojtan, and Eitan Grinspun. “Surface Only Liquids,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2897824.2925899."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"ACM","quality_controlled":"1","date_created":"2018-12-11T11:51:35Z","doi":"10.1145/2897824.2925899","date_published":"2016-07-11T00:00:00Z","year":"2016","has_accepted_license":"1","day":"11"},{"author":[{"id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F","full_name":"Alwen, Joel F","last_name":"Alwen"},{"first_name":"Jeremiah","last_name":"Blocki","full_name":"Blocki, Jeremiah"}],"publist_id":"5876","department":[{"_id":"KrPi"}],"title":"Efficiently computing data-independent memory-hard functions","citation":{"ista":"Alwen JF, Blocki J. 2016. Efficiently computing data-independent memory-hard functions. CRYPTO: International Cryptology Conference, LNCS, vol. 9815, 241–271.","chicago":"Alwen, Joel F, and Jeremiah Blocki. “Efficiently Computing Data-Independent Memory-Hard Functions,” 9815:241–71. Springer, 2016. https://doi.org/10.1007/978-3-662-53008-5_9.","ama":"Alwen JF, Blocki J. Efficiently computing data-independent memory-hard functions. In: Vol 9815. Springer; 2016:241-271. doi:10.1007/978-3-662-53008-5_9","apa":"Alwen, J. F., & Blocki, J. (2016). Efficiently computing data-independent memory-hard functions (Vol. 9815, pp. 241–271). Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, USA: Springer. https://doi.org/10.1007/978-3-662-53008-5_9","short":"J.F. Alwen, J. Blocki, in:, Springer, 2016, pp. 241–271.","ieee":"J. F. Alwen and J. Blocki, “Efficiently computing data-independent memory-hard functions,” presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, USA, 2016, vol. 9815, pp. 241–271.","mla":"Alwen, Joel F., and Jeremiah Blocki. Efficiently Computing Data-Independent Memory-Hard Functions. Vol. 9815, Springer, 2016, pp. 241–71, doi:10.1007/978-3-662-53008-5_9."},"date_updated":"2021-01-12T06:50:11Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","conference":{"name":"CRYPTO: International Cryptology Conference","start_date":"2016-08-14","location":"Santa Barbara, CA, USA","end_date":"2016-08-18"},"type":"conference","status":"public","_id":"1365","page":"241 - 271","date_created":"2018-12-11T11:51:36Z","date_published":"2016-08-01T00:00:00Z","doi":"10.1007/978-3-662-53008-5_9","volume":9815,"publication_status":"published","year":"2016","language":[{"iso":"eng"}],"day":"01","oa":1,"main_file_link":[{"url":"http://eprint.iacr.org/2016/115","open_access":"1"}],"publisher":"Springer","scopus_import":1,"alternative_title":["LNCS"],"quality_controlled":"1","intvolume":" 9815","month":"08","abstract":[{"text":"A memory-hard function (MHF) f is equipped with a space cost σ and time cost τ parameter such that repeatedly computing fσ,τ on an application specific integrated circuit (ASIC) is not economically advantageous relative to a general purpose computer. Technically we would like that any (generalized) circuit for evaluating an iMHF fσ,τ has area × time (AT) complexity at Θ(σ2 ∗ τ). A data-independent MHF (iMHF) has the added property that it can be computed with almost optimal memory and time complexity by an algorithm which accesses memory in a pattern independent of the input value. Such functions can be specified by fixing a directed acyclic graph (DAG) G on n = Θ(σ ∗ τ) nodes representing its computation graph. In this work we develop new tools for analyzing iMHFs. First we define and motivate a new complexity measure capturing the amount of energy (i.e. electricity) required to compute a function. We argue that, in practice, this measure is at least as important as the more traditional AT-complexity. Next we describe an algorithm A for repeatedly evaluating an iMHF based on an arbitrary DAG G. We upperbound both its energy and AT complexities per instance evaluated in terms of a certain combinatorial property of G. Next we instantiate our attack for several general classes of DAGs which include those underlying many of the most important iMHF candidates in the literature. In particular, we obtain the following results which hold for all choices of parameters σ and τ (and thread-count) such that n = σ ∗ τ. -The Catena-Dragonfly function of [FLW13] has AT and energy complexities O(n1.67). -The Catena-Butterfly function of [FLW13] has complexities is O(n1.67). -The Double-Buffer and the Linear functions of [CGBS16] both have complexities in O(n1.67). -The Argon2i function of [BDK15] (winner of the Password Hashing Competition [PHC]) has complexities O(n7/4 log(n)). -The Single-Buffer function of [CGBS16] has complexities O(n7/4 log(n)). -Any iMHF can be computed by an algorithm with complexities O(n2/ log1 −ε(n)) for all ε > 0. In particular when τ = 1 this shows that the goal of constructing an iMHF with AT-complexity Θ(σ2 ∗ τ ) is unachievable. Along the way we prove a lemma upper-bounding the depth-robustness of any DAG which may prove to be of independent interest.","lang":"eng"}],"oa_version":"Preprint"},{"type":"conference","conference":{"start_date":"2016-05-08","location":"Vienna, Austria","end_date":"2016-05-12","name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques"},"status":"public","_id":"1366","department":[{"_id":"KrPi"}],"date_updated":"2021-01-12T06:50:11Z","alternative_title":["LNCS"],"scopus_import":1,"main_file_link":[{"url":"https://eprint.iacr.org/2016/169/20160219:201940","open_access":"1"}],"month":"05","intvolume":" 9665","abstract":[{"lang":"eng","text":"We study the problem of devising provably secure PRNGs with input based on the sponge paradigm. Such constructions are very appealing, as efficient software/hardware implementations of SHA-3 can easily be translated into a PRNG in a nearly black-box way. The only existing sponge-based construction, proposed by Bertoni et al. (CHES 2010), fails to achieve the security notion of robustness recently considered by Dodis et al. (CCS 2013), for two reasons: (1) The construction is deterministic, and thus there are high-entropy input distributions on which the construction fails to extract random bits, and (2) The construction is not forward secure, and presented solutions aiming at restoring forward security have not been rigorously analyzed. We propose a seeded variant of Bertoni et al.’s PRNG with input which we prove secure in the sense of robustness, delivering in particular concrete security bounds. On the way, we make what we believe to be an important conceptual contribution, developing a variant of the security framework of Dodis et al. tailored at the ideal permutation model that captures PRNG security in settings where the weakly random inputs are provided from a large class of possible adversarial samplers which are also allowed to query the random permutation. As a further application of our techniques, we also present an efficient sponge-based key-derivation function (which can be instantiated from SHA-3 in a black-box fashion), which we also prove secure when fed with samples from permutation-dependent distributions."}],"oa_version":"Preprint","volume":9665,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"project":[{"name":"Provable Security for Physical Cryptography","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"author":[{"first_name":"Peter","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","last_name":"Gazi","full_name":"Gazi, Peter"},{"first_name":"Stefano","full_name":"Tessaro, Stefano","last_name":"Tessaro"}],"publist_id":"5872","title":"Provably robust sponge-based PRNGs and KDFs","citation":{"short":"P. Gazi, S. Tessaro, in:, Springer, 2016, pp. 87–116.","ieee":"P. Gazi and S. Tessaro, “Provably robust sponge-based PRNGs and KDFs,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Vienna, Austria, 2016, vol. 9665, pp. 87–116.","apa":"Gazi, P., & Tessaro, S. (2016). Provably robust sponge-based PRNGs and KDFs (Vol. 9665, pp. 87–116). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Vienna, Austria: Springer. https://doi.org/10.1007/978-3-662-49890-3_4","ama":"Gazi P, Tessaro S. Provably robust sponge-based PRNGs and KDFs. In: Vol 9665. Springer; 2016:87-116. doi:10.1007/978-3-662-49890-3_4","mla":"Gazi, Peter, and Stefano Tessaro. Provably Robust Sponge-Based PRNGs and KDFs. Vol. 9665, Springer, 2016, pp. 87–116, doi:10.1007/978-3-662-49890-3_4.","ista":"Gazi P, Tessaro S. 2016. Provably robust sponge-based PRNGs and KDFs. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 9665, 87–116.","chicago":"Gazi, Peter, and Stefano Tessaro. “Provably Robust Sponge-Based PRNGs and KDFs,” 9665:87–116. Springer, 2016. https://doi.org/10.1007/978-3-662-49890-3_4."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","quality_controlled":"1","oa":1,"page":"87 - 116","date_published":"2016-05-01T00:00:00Z","doi":"10.1007/978-3-662-49890-3_4","date_created":"2018-12-11T11:51:36Z","year":"2016","day":"01"},{"title":"Elementary approach to closed billiard trajectories in asymmetric normed spaces","article_processing_charge":"No","publist_id":"5885","author":[{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","last_name":"Akopyan","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X"},{"last_name":"Balitskiy","full_name":"Balitskiy, Alexey","first_name":"Alexey"},{"last_name":"Karasev","full_name":"Karasev, Roman","first_name":"Roman"},{"first_name":"Anastasia","full_name":"Sharipova, Anastasia","last_name":"Sharipova"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Akopyan, Arseniy, et al. “Elementary Approach to Closed Billiard Trajectories in Asymmetric Normed Spaces.” Proceedings of the American Mathematical Society, vol. 144, no. 10, American Mathematical Society, 2016, pp. 4501–13, doi:10.1090/proc/13062.","ieee":"A. Akopyan, A. Balitskiy, R. Karasev, and A. Sharipova, “Elementary approach to closed billiard trajectories in asymmetric normed spaces,” Proceedings of the American Mathematical Society, vol. 144, no. 10. American Mathematical Society, pp. 4501–4513, 2016.","short":"A. Akopyan, A. Balitskiy, R. Karasev, A. Sharipova, Proceedings of the American Mathematical Society 144 (2016) 4501–4513.","ama":"Akopyan A, Balitskiy A, Karasev R, Sharipova A. Elementary approach to closed billiard trajectories in asymmetric normed spaces. Proceedings of the American Mathematical Society. 2016;144(10):4501-4513. doi:10.1090/proc/13062","apa":"Akopyan, A., Balitskiy, A., Karasev, R., & Sharipova, A. (2016). Elementary approach to closed billiard trajectories in asymmetric normed spaces. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/13062","chicago":"Akopyan, Arseniy, Alexey Balitskiy, Roman Karasev, and Anastasia Sharipova. “Elementary Approach to Closed Billiard Trajectories in Asymmetric Normed Spaces.” Proceedings of the American Mathematical Society. American Mathematical Society, 2016. https://doi.org/10.1090/proc/13062.","ista":"Akopyan A, Balitskiy A, Karasev R, Sharipova A. 2016. Elementary approach to closed billiard trajectories in asymmetric normed spaces. Proceedings of the American Mathematical Society. 144(10), 4501–4513."},"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"date_created":"2018-12-11T11:51:34Z","doi":"10.1090/proc/13062","date_published":"2016-10-01T00:00:00Z","page":"4501 - 4513","publication":"Proceedings of the American Mathematical Society","day":"01","year":"2016","oa":1,"quality_controlled":"1","publisher":"American Mathematical Society","acknowledgement":"The first and third authors were supported by the Dynasty Foundation. The first, second and third authors were supported by the Russian Foundation for Basic Re- search grant 15-31-20403 (mol a ved).","department":[{"_id":"HeEd"}],"date_updated":"2021-01-12T06:50:09Z","status":"public","type":"journal_article","_id":"1360","ec_funded":1,"issue":"10","volume":144,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 144","month":"10","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1401.0442"}],"scopus_import":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We apply the technique of Károly Bezdek and Daniel Bezdek to study billiard trajectories in convex bodies, when the length is measured with a (possibly asymmetric) norm. We prove a lower bound for the length of the shortest closed billiard trajectory, related to the non-symmetric Mahler problem. With this technique we are able to give short and elementary proofs to some known results. "}]},{"author":[{"first_name":"Markéta","full_name":"Pernisová, Markéta","last_name":"Pernisová"},{"full_name":"Prat, Tomas","last_name":"Prat","first_name":"Tomas","id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Grones","full_name":"Grones, Peter","first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Danka","last_name":"Haruštiaková","full_name":"Haruštiaková, Danka"},{"first_name":"Martina","full_name":"Matonohova, Martina","last_name":"Matonohova"},{"full_name":"Spíchal, Lukáš","last_name":"Spíchal","first_name":"Lukáš"},{"last_name":"Nodzyński","full_name":"Nodzyński, Tomasz","first_name":"Tomasz"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hejátko, Jan","last_name":"Hejátko","first_name":"Jan"}],"publist_id":"5839","title":"Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis","citation":{"chicago":"Pernisová, Markéta, Tomas Prat, Peter Grones, Danka Haruštiaková, Martina Matonohova, Lukáš Spíchal, Tomasz Nodzyński, Jiří Friml, and Jan Hejátko. “Cytokinins Influence Root Gravitropism via Differential Regulation of Auxin Transporter Expression and Localization in Arabidopsis.” New Phytologist. Wiley-Blackwell, 2016. https://doi.org/10.1111/nph.14049.","ista":"Pernisová M, Prat T, Grones P, Haruštiaková D, Matonohova M, Spíchal L, Nodzyński T, Friml J, Hejátko J. 2016. Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. New Phytologist. 212(2), 497–509.","mla":"Pernisová, Markéta, et al. “Cytokinins Influence Root Gravitropism via Differential Regulation of Auxin Transporter Expression and Localization in Arabidopsis.” New Phytologist, vol. 212, no. 2, Wiley-Blackwell, 2016, pp. 497–509, doi:10.1111/nph.14049.","ama":"Pernisová M, Prat T, Grones P, et al. Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. New Phytologist. 2016;212(2):497-509. doi:10.1111/nph.14049","apa":"Pernisová, M., Prat, T., Grones, P., Haruštiaková, D., Matonohova, M., Spíchal, L., … Hejátko, J. (2016). Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. New Phytologist. Wiley-Blackwell. https://doi.org/10.1111/nph.14049","ieee":"M. Pernisová et al., “Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis,” New Phytologist, vol. 212, no. 2. Wiley-Blackwell, pp. 497–509, 2016.","short":"M. Pernisová, T. Prat, P. Grones, D. Haruštiaková, M. Matonohova, L. Spíchal, T. Nodzyński, J. Friml, J. Hejátko, New Phytologist 212 (2016) 497–509."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Wiley-Blackwell","oa":1,"acknowledgement":"Funded by Ministry of Education, Youth and Sports Czech Republic. Grant Numbers: CEITEC 2020, LQ1601, LO1204, LH14104 and The European Research Council. Grant Number: ERC-2011-StG-20101109-PSDP and The Czech Science Foundation. Grant Numbers: GAP501/11/1150, GA13-40637S, GP14-30004P","page":"497 - 509","doi":"10.1111/nph.14049","date_published":"2016-10-01T00:00:00Z","date_created":"2018-12-11T11:51:38Z","has_accepted_license":"1","year":"2016","day":"01","publication":"New Phytologist","type":"journal_article","status":"public","pubrep_id":"1006","_id":"1372","file_date_updated":"2020-07-14T12:44:47Z","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T06:50:13Z","ddc":["581"],"scopus_import":1,"month":"10","intvolume":" 212","abstract":[{"lang":"eng","text":"Redirection of intercellular auxin fluxes via relocalization of the PIN-FORMED 3 (PIN3) and PIN7 auxin efflux carriers has been suggested to be necessary for the root gravitropic response. Cytokinins have also been proposed to play a role in controlling root gravitropism, but conclusive evidence is lacking. We present a detailed study of the dynamics of root bending early after gravistimulation, which revealed a delayed gravitropic response in transgenic lines with depleted endogenous cytokinins (Pro35S:AtCKX) and cytokinin signaling mutants. Pro35S:AtCKX lines, as well as a cytokinin receptor mutant ahk3, showed aberrations in the auxin response distribution in columella cells consistent with defects in the auxin transport machinery. Using in vivo real-time imaging of PIN3-GFP and PIN7-GFP in AtCKX3 overexpression and ahk3 backgrounds, we observed wild-type-like relocalization of PIN proteins in the columella early after gravistimulation, with gravity-induced relocalization of PIN7 faster than that of PIN3. Nonetheless, the cellular distribution of PIN3 and PIN7 and expression of PIN7 and the auxin influx carrier AUX1 was affected in AtCKX overexpression lines. Based on the retained cytokinin sensitivity in pin3 pin4 pin7 mutant, we propose the AUX1-mediated auxin transport rather than columella-located PIN proteins as a target of endogenous cytokinins in the control of root gravitropism."}],"oa_version":"Submitted Version","issue":"2","volume":212,"publication_status":"published","file":[{"checksum":"27fd841ceaf0403559d7048ef51500f9","file_id":"5108","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:14:53Z","file_name":"IST-2018-1006-v1+1_Pernisova_NewPhytol_2016_peer_review.pdf","date_updated":"2020-07-14T12:44:47Z","file_size":972763,"creator":"system"}],"language":[{"iso":"eng"}]},{"date_updated":"2021-01-12T06:50:12Z","department":[{"_id":"ChLa"}],"_id":"1369","status":"public","conference":{"name":"ECCV: European Conference on Computer Vision","end_date":"2016-10-14","location":"Amsterdam, The Netherlands","start_date":"2016-10-11"},"type":"conference","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":9908,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We introduce a new loss function for the weakly-supervised training of semantic image segmentation models based on three guiding principles: to seed with weak localization cues, to expand objects based on the information about which classes can occur in an image, and to constrain the segmentations to coincide with object boundaries. We show experimentally that training a deep convolutional neural network using the proposed loss function leads to substantially better segmentations than previous state-of-the-art methods on the challenging PASCAL VOC 2012 dataset. We furthermore give insight into the working mechanism of our method by a detailed experimental study that illustrates how the segmentation quality is affected by each term of the proposed loss function as well as their combinations."}],"intvolume":" 9908","month":"09","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1603.06098"}],"alternative_title":["LNCS"],"scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kolesnikov, Alexander, and Christoph Lampert. “Seed, Expand and Constrain: Three Principles for Weakly-Supervised Image Segmentation,” 9908:695–711. Springer, 2016. https://doi.org/10.1007/978-3-319-46493-0_42.","ista":"Kolesnikov A, Lampert C. 2016. Seed, expand and constrain: Three principles for weakly-supervised image segmentation. ECCV: European Conference on Computer Vision, LNCS, vol. 9908, 695–711.","mla":"Kolesnikov, Alexander, and Christoph Lampert. Seed, Expand and Constrain: Three Principles for Weakly-Supervised Image Segmentation. Vol. 9908, Springer, 2016, pp. 695–711, doi:10.1007/978-3-319-46493-0_42.","short":"A. Kolesnikov, C. Lampert, in:, Springer, 2016, pp. 695–711.","ieee":"A. Kolesnikov and C. Lampert, “Seed, expand and constrain: Three principles for weakly-supervised image segmentation,” presented at the ECCV: European Conference on Computer Vision, Amsterdam, The Netherlands, 2016, vol. 9908, pp. 695–711.","ama":"Kolesnikov A, Lampert C. Seed, expand and constrain: Three principles for weakly-supervised image segmentation. In: Vol 9908. Springer; 2016:695-711. doi:10.1007/978-3-319-46493-0_42","apa":"Kolesnikov, A., & Lampert, C. (2016). Seed, expand and constrain: Three principles for weakly-supervised image segmentation (Vol. 9908, pp. 695–711). Presented at the ECCV: European Conference on Computer Vision, Amsterdam, The Netherlands: Springer. https://doi.org/10.1007/978-3-319-46493-0_42"},"title":"Seed, expand and constrain: Three principles for weakly-supervised image segmentation","publist_id":"5842","author":[{"first_name":"Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","full_name":"Kolesnikov, Alexander","last_name":"Kolesnikov"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert"}],"project":[{"grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"day":"15","year":"2016","date_created":"2018-12-11T11:51:37Z","doi":"10.1007/978-3-319-46493-0_42","date_published":"2016-09-15T00:00:00Z","page":"695 - 711","oa":1,"publisher":"Springer","quality_controlled":"1"},{"date_updated":"2021-01-12T06:50:12Z","department":[{"_id":"MiLe"}],"_id":"1368","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":94,"issue":"2","ec_funded":1,"abstract":[{"text":"Superconductivity in heavy-fermion systems has an unconventional nature and is considered to originate from the universal features of the electronic structure. Here, the Anderson lattice model is studied by means of the full variational Gutzwiller wave function incorporating nonlocal effects of the on-site interaction. We show that the d-wave superconducting ground state can be driven solely by interelectronic correlations. The proposed microscopic mechanism leads to a multigap superconductivity with the dominant contribution due to f electrons and in the dx2−y2-wave channel. Our results rationalize several important observations for CeCoIn5.","lang":"eng"}],"oa_version":"Preprint","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1510.00224"}],"month":"07","intvolume":" 94","citation":{"ieee":"M. Wysokiński, J. Kaczmarczyk, and J. Spałek, “Correlation driven d wave superconductivity in Anderson lattice model: Two gaps,” Physical Review B - Condensed Matter and Materials Physics, vol. 94, no. 2. American Physical Society, 2016.","short":"M. Wysokiński, J. Kaczmarczyk, J. Spałek, Physical Review B - Condensed Matter and Materials Physics 94 (2016).","ama":"Wysokiński M, Kaczmarczyk J, Spałek J. Correlation driven d wave superconductivity in Anderson lattice model: Two gaps. Physical Review B - Condensed Matter and Materials Physics. 2016;94(2). doi:10.1103/PhysRevB.94.024517","apa":"Wysokiński, M., Kaczmarczyk, J., & Spałek, J. (2016). Correlation driven d wave superconductivity in Anderson lattice model: Two gaps. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.94.024517","mla":"Wysokiński, Marcin, et al. “Correlation Driven d Wave Superconductivity in Anderson Lattice Model: Two Gaps.” Physical Review B - Condensed Matter and Materials Physics, vol. 94, no. 2, 024517, American Physical Society, 2016, doi:10.1103/PhysRevB.94.024517.","ista":"Wysokiński M, Kaczmarczyk J, Spałek J. 2016. Correlation driven d wave superconductivity in Anderson lattice model: Two gaps. Physical Review B - Condensed Matter and Materials Physics. 94(2), 024517.","chicago":"Wysokiński, Marcin, Jan Kaczmarczyk, and Jozef Spałek. “Correlation Driven d Wave Superconductivity in Anderson Lattice Model: Two Gaps.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2016. https://doi.org/10.1103/PhysRevB.94.024517."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5844","author":[{"full_name":"Wysokiński, Marcin","last_name":"Wysokiński","first_name":"Marcin"},{"last_name":"Kaczmarczyk","full_name":"Kaczmarczyk, Jan","orcid":"0000-0002-1629-3675","id":"46C405DE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"full_name":"Spałek, Jozef","last_name":"Spałek","first_name":"Jozef"}],"title":"Correlation driven d wave superconductivity in Anderson lattice model: Two gaps","article_number":"024517","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"year":"2016","day":"01","publication":"Physical Review B - Condensed Matter and Materials Physics","doi":"10.1103/PhysRevB.94.024517","date_published":"2016-07-01T00:00:00Z","date_created":"2018-12-11T11:51:37Z","acknowledgement":"The work has been supported by the National Science Center (NCN) under the Grant MAESTRO, No.\r\nDEC-2012/04/A/ST3/00342. ","publisher":"American Physical Society","quality_controlled":"1","oa":1},{"title":"Phonon Josephson junction with nanomechanical resonators","publist_id":"5841","author":[{"last_name":"Barzanjeh","orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir"},{"first_name":"David","last_name":"Vitali","full_name":"Vitali, David"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Barzanjeh S, Vitali D. 2016. Phonon Josephson junction with nanomechanical resonators. Physical Review A - Atomic, Molecular, and Optical Physics. 93(3), 033846.","chicago":"Barzanjeh, Shabir, and David Vitali. “Phonon Josephson Junction with Nanomechanical Resonators.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2016. https://doi.org/10.1103/PhysRevA.93.033846.","short":"S. Barzanjeh, D. Vitali, Physical Review A - Atomic, Molecular, and Optical Physics 93 (2016).","ieee":"S. Barzanjeh and D. Vitali, “Phonon Josephson junction with nanomechanical resonators,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 93, no. 3. American Physical Society, 2016.","ama":"Barzanjeh S, Vitali D. Phonon Josephson junction with nanomechanical resonators. Physical Review A - Atomic, Molecular, and Optical Physics. 2016;93(3). doi:10.1103/PhysRevA.93.033846","apa":"Barzanjeh, S., & Vitali, D. (2016). Phonon Josephson junction with nanomechanical resonators. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.93.033846","mla":"Barzanjeh, Shabir, and David Vitali. “Phonon Josephson Junction with Nanomechanical Resonators.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 93, no. 3, 033846, American Physical Society, 2016, doi:10.1103/PhysRevA.93.033846."},"article_number":"033846","date_created":"2018-12-11T11:51:38Z","date_published":"2016-03-28T00:00:00Z","doi":"10.1103/PhysRevA.93.033846","publication":"Physical Review A - Atomic, Molecular, and Optical Physics","day":"28","year":"2016","oa":1,"publisher":"American Physical Society","quality_controlled":"1","acknowledgement":"The work of S.B. has been supported by the European Commission (Belgium) via the SCALEQIT program and by the Alexander von Humboldt Foundation. ","department":[{"_id":"JoFi"}],"date_updated":"2023-02-21T10:36:32Z","status":"public","type":"journal_article","_id":"1370","volume":93,"issue":"3","language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 93","month":"03","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1601.01818"}],"scopus_import":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We study coherent phonon oscillations and tunneling between two coupled nonlinear nanomechanical resonators. We show that the coupling between two nanomechanical resonators creates an effective phonon Josephson junction, which exhibits two different dynamical behaviors: Josephson oscillation (phonon-Rabi oscillation) and macroscopic self-trapping (phonon blockade). Self-trapping originates from mechanical nonlinearities, meaning that when the nonlinearity exceeds its critical value, the energy exchange between the two resonators is suppressed, and phonon Josephson oscillations between them are completely blocked. An effective classical Hamiltonian for the phonon Josephson junction is derived and its mean-field dynamics is studied in phase space. Finally, we study the phonon-phonon coherence quantified by the mean fringe visibility, and show that the interaction between the two resonators may lead to the loss of coherence in the phononic junction."}]},{"publisher":"Elsevier","quality_controlled":"1","scopus_import":"1","main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-01531698","open_access":"1"}],"oa":1,"month":"07","intvolume":" 17","oa_version":"Preprint","page":"168 - 171","doi":"10.1016/j.plrev.2016.06.006","date_published":"2016-07-01T00:00:00Z","volume":17,"date_created":"2018-12-11T11:51:39Z","year":"2016","publication_status":"published","day":"01","publication":"Physics of Life Reviews","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"1373","author":[{"last_name":"Martin","full_name":"Martin, Olivier","first_name":"Olivier"},{"last_name":"Zagórski","orcid":"0000-0001-7896-7762","full_name":"Zagórski, Marcin P","first_name":"Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5838","article_processing_charge":"No","department":[{"_id":"AnKi"}],"title":"Network architectures and operating principles. Reply to comments on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function"","date_updated":"2022-08-26T09:39:27Z","citation":{"ama":"Martin O, Zagórski MP. Network architectures and operating principles. Reply to comments on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" Physics of Life Reviews. 2016;17:168-171. doi:10.1016/j.plrev.2016.06.006","apa":"Martin, O., & Zagórski, M. P. (2016). Network architectures and operating principles. Reply to comments on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" Physics of Life Reviews. Elsevier. https://doi.org/10.1016/j.plrev.2016.06.006","ieee":"O. Martin and M. P. Zagórski, “Network architectures and operating principles. Reply to comments on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function",” Physics of Life Reviews, vol. 17. Elsevier, pp. 168–171, 2016.","short":"O. Martin, M.P. Zagórski, Physics of Life Reviews 17 (2016) 168–171.","mla":"Martin, Olivier, and Marcin P. Zagórski. “Network Architectures and Operating Principles. Reply to Comments on "Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function"” Physics of Life Reviews, vol. 17, Elsevier, 2016, pp. 168–71, doi:10.1016/j.plrev.2016.06.006.","ista":"Martin O, Zagórski MP. 2016. Network architectures and operating principles. Reply to comments on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" Physics of Life Reviews. 17, 168–171.","chicago":"Martin, Olivier, and Marcin P Zagórski. “Network Architectures and Operating Principles. Reply to Comments on "Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function"” Physics of Life Reviews. Elsevier, 2016. https://doi.org/10.1016/j.plrev.2016.06.006."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"quality_controlled":"1","publisher":"Society for Industrial and Applied Mathematics ","oa":1,"year":"2016","day":"03","publication":"SIAM Journal on Imaging Sciences","page":"605 - 636","doi":"10.1137/15M1010257","date_published":"2016-05-03T00:00:00Z","date_created":"2018-12-11T11:51:40Z","project":[{"call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"citation":{"mla":"Kolmogorov, Vladimir, et al. “Total Variation on a Tree.” SIAM Journal on Imaging Sciences, vol. 9, no. 2, Society for Industrial and Applied Mathematics , 2016, pp. 605–36, doi:10.1137/15M1010257.","apa":"Kolmogorov, V., Pock, T., & Rolinek, M. (2016). Total variation on a tree. SIAM Journal on Imaging Sciences. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/15M1010257","ama":"Kolmogorov V, Pock T, Rolinek M. Total variation on a tree. SIAM Journal on Imaging Sciences. 2016;9(2):605-636. doi:10.1137/15M1010257","short":"V. Kolmogorov, T. Pock, M. Rolinek, SIAM Journal on Imaging Sciences 9 (2016) 605–636.","ieee":"V. Kolmogorov, T. Pock, and M. Rolinek, “Total variation on a tree,” SIAM Journal on Imaging Sciences, vol. 9, no. 2. Society for Industrial and Applied Mathematics , pp. 605–636, 2016.","chicago":"Kolmogorov, Vladimir, Thomas Pock, and Michal Rolinek. “Total Variation on a Tree.” SIAM Journal on Imaging Sciences. Society for Industrial and Applied Mathematics , 2016. https://doi.org/10.1137/15M1010257.","ista":"Kolmogorov V, Pock T, Rolinek M. 2016. Total variation on a tree. SIAM Journal on Imaging Sciences. 9(2), 605–636."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir"},{"full_name":"Pock, Thomas","last_name":"Pock","first_name":"Thomas"},{"first_name":"Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","full_name":"Rolinek, Michal","last_name":"Rolinek"}],"publist_id":"5834","title":"Total variation on a tree","abstract":[{"lang":"eng","text":"We consider the problem of minimizing the continuous valued total variation subject to different unary terms on trees and propose fast direct algorithms based on dynamic programming to solve these problems. We treat both the convex and the nonconvex case and derive worst-case complexities that are equal to or better than existing methods. We show applications to total variation based two dimensional image processing and computer vision problems based on a Lagrangian decomposition approach. The resulting algorithms are very effcient, offer a high degree of parallelism, and come along with memory requirements which are only in the order of the number of image pixels."}],"oa_version":"Preprint","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1502.07770","open_access":"1"}],"month":"05","intvolume":" 9","publication_status":"published","language":[{"iso":"eng"}],"volume":9,"issue":"2","ec_funded":1,"_id":"1377","type":"journal_article","status":"public","date_updated":"2021-01-12T06:50:15Z","department":[{"_id":"VlKo"}]},{"title":"Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range","author":[{"last_name":"Mabillard","full_name":"Mabillard, Isaac","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","first_name":"Isaac"},{"last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"}],"publist_id":"5830","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Mabillard I, Wagner U. 2016. Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 51, 51.1-51.12.","chicago":"Mabillard, Isaac, and Uli Wagner. “Eliminating Higher-Multiplicity Intersections, II. The Deleted Product Criterion in the r-Metastable Range,” 51:51.1-51.12. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, 2016. https://doi.org/10.4230/LIPIcs.SoCG.2016.51.","ama":"Mabillard I, Wagner U. Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range. In: Vol 51. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH; 2016:51.1-51.12. doi:10.4230/LIPIcs.SoCG.2016.51","apa":"Mabillard, I., & Wagner, U. (2016). Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range (Vol. 51, p. 51.1-51.12). Presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH. https://doi.org/10.4230/LIPIcs.SoCG.2016.51","short":"I. Mabillard, U. Wagner, in:, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, 2016, p. 51.1-51.12.","ieee":"I. Mabillard and U. Wagner, “Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range,” presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA, 2016, vol. 51, p. 51.1-51.12.","mla":"Mabillard, Isaac, and Uli Wagner. Eliminating Higher-Multiplicity Intersections, II. The Deleted Product Criterion in the r-Metastable Range. Vol. 51, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, 2016, p. 51.1-51.12, doi:10.4230/LIPIcs.SoCG.2016.51."},"project":[{"_id":"25FA3206-B435-11E9-9278-68D0E5697425","name":"Embeddings in Higher Dimensions: Algorithms and Combinatorics","grant_number":"PP00P2_138948"}],"date_created":"2018-12-11T11:51:41Z","date_published":"2016-06-01T00:00:00Z","doi":"10.4230/LIPIcs.SoCG.2016.51","page":"51.1 - 51.12","day":"01","year":"2016","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH","file_date_updated":"2020-07-14T12:44:47Z","department":[{"_id":"UlWa"}],"ddc":["510"],"date_updated":"2021-01-12T06:50:17Z","pubrep_id":"621","status":"public","conference":{"name":"SoCG: Symposium on Computational Geometry","start_date":"2016-06-14","location":"Medford, MA, USA","end_date":"2016-06-17"},"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","_id":"1381","volume":51,"language":[{"iso":"eng"}],"file":[{"file_id":"4791","checksum":"92c0c3735fe908f8ded6e484005cb3b1","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-621-v1+1_LIPIcs-SoCG-2016-51.pdf","date_created":"2018-12-12T10:10:06Z","creator":"system","file_size":622969,"date_updated":"2020-07-14T12:44:47Z"}],"publication_status":"published","intvolume":" 51","month":"06","alternative_title":["LIPIcs"],"scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Motivated by Tverberg-type problems in topological combinatorics and by classical results about embeddings (maps without double points), we study the question whether a finite simplicial complex K can be mapped into double-struck Rd without higher-multiplicity intersections. We focus on conditions for the existence of almost r-embeddings, i.e., maps f : K → double-struck Rd such that f(σ1) ∩ ⋯ ∩ f(σr) = ∅ whenever σ1, ..., σr are pairwise disjoint simplices of K. Generalizing the classical Haefliger-Weber embeddability criterion, we show that a well-known necessary deleted product condition for the existence of almost r-embeddings is sufficient in a suitable r-metastable range of dimensions: If rd ≥ (r + 1) dim K + 3, then there exists an almost r-embedding K → double-struck Rd if and only if there exists an equivariant map (K)Δ r → Sr Sd(r-1)-1, where (K)Δ r is the deleted r-fold product of K, the target Sd(r-1)-1 is the sphere of dimension d(r - 1) - 1, and Sr is the symmetric group. This significantly extends one of the main results of our previous paper (which treated the special case where d = rk and dim K = (r - 1)k for some k ≥ 3), and settles an open question raised there."}]},{"intvolume":" 63","month":"06","main_file_link":[{"url":"http://arxiv.org/abs/1303.2981","open_access":"1"}],"oa":1,"quality_controlled":"1","publisher":"ACM","scopus_import":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider higher-dimensional versions of Kannan and Lipton's Orbit Problem - determining whether a target vector space V may be reached from a starting point x under repeated applications of a linear transformation A. Answering two questions posed by Kannan and Lipton in the 1980s, we show that when V has dimension one, this problem is solvable in polynomial time, and when V has dimension two or three, the problem is in NPRP."}],"date_created":"2018-12-11T11:51:41Z","volume":63,"date_published":"2016-06-01T00:00:00Z","doi":"10.1145/2857050","issue":"3","language":[{"iso":"eng"}],"publication":"Journal of the ACM","day":"01","publication_status":"published","year":"2016","status":"public","type":"journal_article","article_number":"23","_id":"1380","title":"On the complexity of the orbit problem","department":[{"_id":"KrCh"}],"publist_id":"5831","author":[{"id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Ventsislav K","last_name":"Chonev","full_name":"Chonev, Ventsislav K"},{"last_name":"Ouaknine","full_name":"Ouaknine, Joël","first_name":"Joël"},{"first_name":"James","last_name":"Worrell","full_name":"Worrell, James"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:50:17Z","citation":{"ama":"Chonev VK, Ouaknine J, Worrell J. On the complexity of the orbit problem. Journal of the ACM. 2016;63(3). doi:10.1145/2857050","apa":"Chonev, V. K., Ouaknine, J., & Worrell, J. (2016). On the complexity of the orbit problem. Journal of the ACM. ACM. https://doi.org/10.1145/2857050","ieee":"V. K. Chonev, J. Ouaknine, and J. Worrell, “On the complexity of the orbit problem,” Journal of the ACM, vol. 63, no. 3. ACM, 2016.","short":"V.K. Chonev, J. Ouaknine, J. Worrell, Journal of the ACM 63 (2016).","mla":"Chonev, Ventsislav K., et al. “On the Complexity of the Orbit Problem.” Journal of the ACM, vol. 63, no. 3, 23, ACM, 2016, doi:10.1145/2857050.","ista":"Chonev VK, Ouaknine J, Worrell J. 2016. On the complexity of the orbit problem. Journal of the ACM. 63(3), 23.","chicago":"Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On the Complexity of the Orbit Problem.” Journal of the ACM. ACM, 2016. https://doi.org/10.1145/2857050."}},{"ec_funded":1,"date_created":"2018-12-11T11:51:44Z","date_published":"2016-07-05T00:00:00Z","doi":"10.1145/2933575.2934548","page":"515 - 524","language":[{"iso":"eng"}],"publication":"LICS '16","day":"05","publication_status":"published","year":"2016","month":"07","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1507.03632","open_access":"1"}],"scopus_import":1,"publisher":"IEEE","quality_controlled":"1","oa_version":"Preprint","abstract":[{"text":"The continuous evolution of a wide variety of systems, including continous-time Markov chains and linear hybrid automata, can be\r\ndescribed in terms of linear differential equations. In this paper we study the decision problem of whether the solution x(t) of a system of linear differential equations dx/dt = Ax reaches a target halfspace infinitely often. This recurrent reachability problem can\r\nequivalently be formulated as the following Infinite Zeros Problem: does a real-valued function f:R≥0 --> R satisfying a given linear\r\ndifferential equation have infinitely many zeros? Our main decidability result is that if the differential equation has order at most 7, then the Infinite Zeros Problem is decidable. On the other hand, we show that a decision procedure for the Infinite Zeros Problem at order 9 (and above) would entail a major breakthrough in Diophantine Approximation, specifically an algorithm for computing the Lagrange constants of arbitrary real algebraic numbers to arbitrary precision.","lang":"eng"}],"department":[{"_id":"KrCh"}],"title":"On recurrent reachability for continuous linear dynamical systems","author":[{"id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Ventsislav K","full_name":"Chonev, Ventsislav K","last_name":"Chonev"},{"last_name":"Ouaknine","full_name":"Ouaknine, Joël","first_name":"Joël"},{"full_name":"Worrell, James","last_name":"Worrell","first_name":"James"}],"publist_id":"5820","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:50:20Z","citation":{"short":"V.K. Chonev, J. Ouaknine, J. Worrell, in:, LICS ’16, IEEE, 2016, pp. 515–524.","ieee":"V. K. Chonev, J. Ouaknine, and J. Worrell, “On recurrent reachability for continuous linear dynamical systems,” in LICS ’16, New York, NY, USA, 2016, pp. 515–524.","apa":"Chonev, V. K., Ouaknine, J., & Worrell, J. (2016). On recurrent reachability for continuous linear dynamical systems. In LICS ’16 (pp. 515–524). New York, NY, USA: IEEE. https://doi.org/10.1145/2933575.2934548","ama":"Chonev VK, Ouaknine J, Worrell J. On recurrent reachability for continuous linear dynamical systems. In: LICS ’16. IEEE; 2016:515-524. doi:10.1145/2933575.2934548","mla":"Chonev, Ventsislav K., et al. “On Recurrent Reachability for Continuous Linear Dynamical Systems.” LICS ’16, IEEE, 2016, pp. 515–24, doi:10.1145/2933575.2934548.","ista":"Chonev VK, Ouaknine J, Worrell J. 2016. On recurrent reachability for continuous linear dynamical systems. LICS ’16. LICS: Logic in Computer Science, 515–524.","chicago":"Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On Recurrent Reachability for Continuous Linear Dynamical Systems.” In LICS ’16, 515–24. IEEE, 2016. https://doi.org/10.1145/2933575.2934548."},"status":"public","project":[{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"}],"conference":{"name":"LICS: Logic in Computer Science","start_date":"2018-07-05","end_date":"2018-07-08","location":"New York, NY, USA"},"type":"conference","_id":"1389"},{"month":"05","intvolume":" 13","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1601.03243"}],"oa_version":"Preprint","abstract":[{"text":"The solution space of genome-scale models of cellular metabolism provides a map between physically\r\nviable flux configurations and cellular metabolic phenotypes described, at the most basic level, by the\r\ncorresponding growth rates. By sampling the solution space of E. coliʼs metabolic network, we show\r\nthat empirical growth rate distributions recently obtained in experiments at single-cell resolution can\r\nbe explained in terms of a trade-off between the higher fitness of fast-growing phenotypes and the\r\nhigher entropy of slow-growing ones. Based on this, we propose a minimal model for the evolution of\r\na large bacterial population that captures this trade-off. The scaling relationships observed in\r\nexperiments encode, in such frameworks, for the same distance from the maximum achievable growth\r\nrate, the same degree of growth rate maximization, and/or the same rate of phenotypic change. Being\r\ngrounded on genome-scale metabolic network reconstructions, these results allow for multiple\r\nimplications and extensions in spite of the underlying conceptual simplicity.","lang":"eng"}],"volume":13,"issue":"3","ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","_id":"1394","department":[{"_id":"GaTk"}],"date_updated":"2021-01-12T06:50:23Z","publisher":"IOP Publishing Ltd.","quality_controlled":"1","oa":1,"acknowledgement":"The research leading to these results has received funding from the from the Marie\r\nCurie Action ITN NETADIS, grant agreement no. 290038.","date_published":"2016-05-27T00:00:00Z","doi":"10.1088/1478-3975/13/3/036005","date_created":"2018-12-11T11:51:46Z","day":"27","publication":"Physical Biology","year":"2016","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"article_number":"036005","title":"Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli","author":[{"last_name":"De Martino","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Fabrizio","last_name":"Capuani","full_name":"Capuani, Fabrizio"},{"first_name":"Andrea","full_name":"De Martino, Andrea","last_name":"De Martino"}],"publist_id":"5815","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"D. De Martino, F. Capuani, A. De Martino, Physical Biology 13 (2016).","ieee":"D. De Martino, F. Capuani, and A. De Martino, “Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli,” Physical Biology, vol. 13, no. 3. IOP Publishing Ltd., 2016.","apa":"De Martino, D., Capuani, F., & De Martino, A. (2016). Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli. Physical Biology. IOP Publishing Ltd. https://doi.org/10.1088/1478-3975/13/3/036005","ama":"De Martino D, Capuani F, De Martino A. Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli. Physical Biology. 2016;13(3). doi:10.1088/1478-3975/13/3/036005","mla":"De Martino, Daniele, et al. “Growth against Entropy in Bacterial Metabolism: The Phenotypic Trade-off behind Empirical Growth Rate Distributions in E. Coli.” Physical Biology, vol. 13, no. 3, 036005, IOP Publishing Ltd., 2016, doi:10.1088/1478-3975/13/3/036005.","ista":"De Martino D, Capuani F, De Martino A. 2016. Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli. Physical Biology. 13(3), 036005.","chicago":"De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Growth against Entropy in Bacterial Metabolism: The Phenotypic Trade-off behind Empirical Growth Rate Distributions in E. Coli.” Physical Biology. IOP Publishing Ltd., 2016. https://doi.org/10.1088/1478-3975/13/3/036005."}},{"project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"citation":{"apa":"Goldade, R., Batty, C., & Wojtan, C. (2016). A practical method for high-resolution embedded liquid surfaces. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12826","ama":"Goldade R, Batty C, Wojtan C. A practical method for high-resolution embedded liquid surfaces. Computer Graphics Forum. 2016;35(2):233-242. doi:10.1111/cgf.12826","short":"R. Goldade, C. Batty, C. Wojtan, Computer Graphics Forum 35 (2016) 233–242.","ieee":"R. Goldade, C. Batty, and C. Wojtan, “A practical method for high-resolution embedded liquid surfaces,” Computer Graphics Forum, vol. 35, no. 2. Wiley-Blackwell, pp. 233–242, 2016.","mla":"Goldade, Ryan, et al. “A Practical Method for High-Resolution Embedded Liquid Surfaces.” Computer Graphics Forum, vol. 35, no. 2, Wiley-Blackwell, 2016, pp. 233–42, doi:10.1111/cgf.12826.","ista":"Goldade R, Batty C, Wojtan C. 2016. A practical method for high-resolution embedded liquid surfaces. Computer Graphics Forum. 35(2), 233–242.","chicago":"Goldade, Ryan, Christopher Batty, and Chris Wojtan. “A Practical Method for High-Resolution Embedded Liquid Surfaces.” Computer Graphics Forum. Wiley-Blackwell, 2016. https://doi.org/10.1111/cgf.12826."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5795","author":[{"full_name":"Goldade, Ryan","last_name":"Goldade","first_name":"Ryan"},{"first_name":"Christopher","last_name":"Batty","full_name":"Batty, Christopher"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"}],"title":"A practical method for high-resolution embedded liquid surfaces","acknowledgement":"This research was supported by NSERC (RGPIN-04360-2014) and IST Austria. ","quality_controlled":"1","publisher":"Wiley-Blackwell","oa":1,"has_accepted_license":"1","year":"2016","day":"27","publication":"Computer Graphics Forum","page":"233 - 242","doi":"10.1111/cgf.12826","date_published":"2016-05-27T00:00:00Z","date_created":"2018-12-11T11:51:52Z","_id":"1412","type":"journal_article","status":"public","pubrep_id":"612","date_updated":"2023-02-21T10:38:30Z","ddc":["000"],"file_date_updated":"2020-07-14T12:44:53Z","department":[{"_id":"ChWo"}],"abstract":[{"text":"Combining high-resolution level set surface tracking with lower resolution physics is an inexpensive method for achieving highly detailed liquid animations. Unfortunately, the inherent resolution mismatch introduces several types of disturbing visual artifacts. We identify the primary sources of these artifacts and present simple, efficient, and practical solutions to address them. First, we propose an unconditionally stable filtering method that selectively removes sub-grid surface artifacts not seen by the fluid physics, while preserving fine detail in dynamic splashing regions. It provides comparable results to recent error-correction techniques at lower cost, without substepping, and with better scaling behavior. Second, we show how a modified narrow-band scheme can ensure accurate free surface boundary conditions in the presence of large resolution mismatches. Our scheme preserves the efficiency of the narrow-band methodology, while eliminating objectionable stairstep artifacts observed in prior work. Third, we demonstrate that the use of linear interpolation of velocity during advection of the high-resolution level set surface is responsible for visible grid-aligned kinks; we therefore advocate higher-order velocity interpolation, and show that it dramatically reduces this artifact. While these three contributions are orthogonal, our results demonstrate that taken together they efficiently address the dominant sources of visual artifacts arising with high-resolution embedded liquid surfaces; the proposed approach offers improved visual quality, a straightforward implementation, and substantially greater scalability than competing methods.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":1,"month":"05","intvolume":" 35","publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5000","checksum":"8e61387ee2e3bd0e776fbe301629bfd9","date_updated":"2020-07-14T12:44:53Z","file_size":15873858,"creator":"system","date_created":"2018-12-12T10:13:18Z","file_name":"IST-2016-612-v1+2_Wojtan_APracticalMethod_PostPrint_2016.pdf"}],"language":[{"iso":"eng"}],"issue":"2","volume":35,"ec_funded":1},{"_id":"1410","type":"journal_article","status":"public","pubrep_id":"1005","date_updated":"2021-01-12T06:50:33Z","ddc":["581"],"department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:44:53Z","abstract":[{"text":"The pollen grains arise after meiosis of pollen mother cells within the anthers. A series of complex structural changes follows, generating mature pollen grains capable of performing the double fertilization of the female megasporophyte. Several signaling molecules, including hormones and lipids, have been involved in the regulation and appropriate control of pollen development. Phosphatidylinositol 4-phophate 5-kinases (PIP5K), which catalyze the biosynthesis of the phosphoinositide PtdIns(4,5)P2, are important for tip polar growth of root hairs and pollen tubes, embryo development, vegetative plant growth, and responses to the environment. Here, we report a role of PIP5Ks during microgametogenesis. PIP5K1 and PIP5K2 are expressed during early stages of pollen development and their transcriptional activity respond to auxin in pollen grains. Early male gametophytic lethality to certain grade was observed in both pip5k1-/- and pip5k2-/- single mutants. The number of pip5k mutant alleles is directly related to the frequency of aborted pollen grains suggesting the two genes are involved in the same function. Indeed PIP5K1 and PIP5K2 are functionally redundant since homozygous double mutants did not render viable pollen grains. The loss of function of PIP5K1 and PIP5K2results in defects in vacuole morphology in pollen at the later stages and epidermal root cells. Our results show that PIP5K1, PIP5K2 and phosphoinositide signaling are important cues for early developmental stages and vacuole formation during microgametogenesis.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"scopus_import":1,"month":"09","intvolume":" 250","publication_status":"published","file":[{"creator":"dernst","date_updated":"2020-07-14T12:44:53Z","file_size":4338545,"date_created":"2019-04-17T07:41:57Z","file_name":"2016_PlantScience_Ugalde.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"6331","checksum":"ca08de036e6ddc81e6f760e0ccdebd3f"}],"language":[{"iso":"eng"}],"volume":250,"citation":{"ama":"Ugalde J, Rodríguez Furlán C, De Rycke R, et al. Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development. Plant Science. 2016;250:10-19. doi:10.1016/j.plantsci.2016.05.014","apa":"Ugalde, J., Rodríguez Furlán, C., De Rycke, R., Norambuena, L., Friml, J., León, G., & Tejos, R. (2016). Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development. Plant Science. Elsevier. https://doi.org/10.1016/j.plantsci.2016.05.014","short":"J. Ugalde, C. Rodríguez Furlán, R. De Rycke, L. Norambuena, J. Friml, G. León, R. Tejos, Plant Science 250 (2016) 10–19.","ieee":"J. Ugalde et al., “Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development,” Plant Science, vol. 250. Elsevier, pp. 10–19, 2016.","mla":"Ugalde, José, et al. “Phosphatidylinositol 4-Phosphate 5-Kinases 1 and 2 Are Involved in the Regulation of Vacuole Morphology during Arabidopsis Thaliana Pollen Development.” Plant Science, vol. 250, Elsevier, 2016, pp. 10–19, doi:10.1016/j.plantsci.2016.05.014.","ista":"Ugalde J, Rodríguez Furlán C, De Rycke R, Norambuena L, Friml J, León G, Tejos R. 2016. Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development. Plant Science. 250, 10–19.","chicago":"Ugalde, José, Cecilia Rodríguez Furlán, Riet De Rycke, Lorena Norambuena, Jiří Friml, Gabriel León, and Ricardo Tejos. “Phosphatidylinositol 4-Phosphate 5-Kinases 1 and 2 Are Involved in the Regulation of Vacuole Morphology during Arabidopsis Thaliana Pollen Development.” Plant Science. Elsevier, 2016. https://doi.org/10.1016/j.plantsci.2016.05.014."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Ugalde, José","last_name":"Ugalde","first_name":"José"},{"full_name":"Rodríguez Furlán, Cecilia","last_name":"Rodríguez Furlán","first_name":"Cecilia"},{"first_name":"Riet","full_name":"De Rycke, Riet","last_name":"De Rycke"},{"first_name":"Lorena","full_name":"Norambuena, Lorena","last_name":"Norambuena"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"full_name":"León, Gabriel","last_name":"León","first_name":"Gabriel"},{"full_name":"Tejos, Ricardo","last_name":"Tejos","first_name":"Ricardo"}],"publist_id":"5797","external_id":{"pmid":["27457979"]},"title":"Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development","acknowledgement":"the Odysseus Program of the Research Foundation-Flanders [G091608] to JF.","quality_controlled":"1","publisher":"Elsevier","oa":1,"has_accepted_license":"1","year":"2016","day":"01","publication":"Plant Science","page":"10 - 19","date_published":"2016-09-01T00:00:00Z","doi":"10.1016/j.plantsci.2016.05.014","date_created":"2018-12-11T11:51:51Z"},{"oa_version":"Submitted Version","scopus_import":1,"intvolume":" 25","month":"06","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_name":"IST-2017-772-v1+1_AbbotEtAl2016-3.pdf","date_created":"2018-12-12T10:10:12Z","creator":"system","file_size":226137,"date_updated":"2020-07-14T12:44:53Z","checksum":"ede7d0b8a471754f71f17e2b20f3135b","file_id":"4797","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"issue":"11","volume":25,"_id":"1409","type":"journal_article","pubrep_id":"772","status":"public","date_updated":"2021-01-12T06:50:33Z","ddc":["576"],"file_date_updated":"2020-07-14T12:44:53Z","department":[{"_id":"NiBa"}],"oa":1,"publisher":"Wiley-Blackwell","quality_controlled":"1","year":"2016","has_accepted_license":"1","publication":"Molecular Ecology","day":"08","page":"2325 - 2332","date_created":"2018-12-11T11:51:51Z","date_published":"2016-06-08T00:00:00Z","doi":"10.1111/mec.13685","citation":{"ista":"Abbott R, Barton NH, Good J. 2016. Genomics of hybridization and its evolutionary consequences. Molecular Ecology. 25(11), 2325–2332.","chicago":"Abbott, Richard, Nicholas H Barton, and Jeffrey Good. “Genomics of Hybridization and Its Evolutionary Consequences.” Molecular Ecology. Wiley-Blackwell, 2016. https://doi.org/10.1111/mec.13685.","ama":"Abbott R, Barton NH, Good J. Genomics of hybridization and its evolutionary consequences. Molecular Ecology. 2016;25(11):2325-2332. doi:10.1111/mec.13685","apa":"Abbott, R., Barton, N. H., & Good, J. (2016). Genomics of hybridization and its evolutionary consequences. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.13685","short":"R. Abbott, N.H. Barton, J. Good, Molecular Ecology 25 (2016) 2325–2332.","ieee":"R. Abbott, N. H. Barton, and J. Good, “Genomics of hybridization and its evolutionary consequences,” Molecular Ecology, vol. 25, no. 11. Wiley-Blackwell, pp. 2325–2332, 2016.","mla":"Abbott, Richard, et al. “Genomics of Hybridization and Its Evolutionary Consequences.” Molecular Ecology, vol. 25, no. 11, Wiley-Blackwell, 2016, pp. 2325–32, doi:10.1111/mec.13685."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Abbott, Richard","last_name":"Abbott","first_name":"Richard"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Good, Jeffrey","last_name":"Good","first_name":"Jeffrey"}],"publist_id":"5798","title":"Genomics of hybridization and its evolutionary consequences"},{"abstract":[{"lang":"eng","text":"Plant development mediated by the phytohormone auxin depends on tightly controlled cellular auxin levels at its target tissue that are largely established by intercellular and intracellular auxin transport mediated by PIN auxin transporters. Among the eight members of the Arabidopsis PIN family, PIN6 is the least characterized candidate. In this study we generated functional, fluorescent protein-tagged PIN6 proteins and performed comprehensive analysis of their subcellular localization and also performed a detailed functional characterization of PIN6 and its developmental roles. The localization study of PIN6 revealed a dual localization at the plasma membrane (PM) and endoplasmic reticulum (ER). Transport and metabolic profiling assays in cultured cells and Arabidopsis strongly suggest that PIN6 mediates both auxin transport across the PM and intracellular auxin homeostasis, including the regulation of free auxin and auxin conjugates levels. As evidenced by the loss- and gain-of-function analysis, the complex function of PIN6 in auxin transport and homeostasis is required for auxin distribution during lateral and adventitious root organogenesis and for progression of these developmental processes. These results illustrate a unique position of PIN6 within the family of PIN auxin transporters and further add complexity to the developmentally crucial process of auxin transport."}],"oa_version":"Submitted Version","scopus_import":1,"month":"07","intvolume":" 211","publication_status":"published","file":[{"date_created":"2018-12-12T10:13:32Z","file_name":"IST-2018-1004-v1+1_Simon_NewPhytol_2016_proof.pdf","date_updated":"2020-07-14T12:44:53Z","file_size":3828383,"creator":"system","file_id":"5016","checksum":"23522ced3508ffe7a4f247c4230e6493","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"issue":"1","volume":211,"_id":"1417","type":"journal_article","status":"public","pubrep_id":"1004","date_updated":"2021-01-12T06:50:36Z","ddc":["581"],"file_date_updated":"2020-07-14T12:44:53Z","department":[{"_id":"JiFr"}],"acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP, project CEITEC (CZ.1.05/1.1.00/02.0068) and the Czech Science Foundation GACR (project no. 13-4063 7S to J.F.)","publisher":"Wiley-Blackwell","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2016","day":"01","publication":"New Phytologist","page":"65 - 74","date_published":"2016-07-01T00:00:00Z","doi":"10.1111/nph.14019","date_created":"2018-12-11T11:51:54Z","citation":{"mla":"Simon, Sibu, et al. “PIN6 Auxin Transporter at Endoplasmic Reticulum and Plasma Membrane Mediates Auxin Homeostasis and Organogenesis in Arabidopsis.” New Phytologist, vol. 211, no. 1, Wiley-Blackwell, 2016, pp. 65–74, doi:10.1111/nph.14019.","apa":"Simon, S., Skůpa, P., Viaene, T., Zwiewka, M., Tejos, R., Klíma, P., … Friml, J. (2016). PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist. Wiley-Blackwell. https://doi.org/10.1111/nph.14019","ama":"Simon S, Skůpa P, Viaene T, et al. PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist. 2016;211(1):65-74. doi:10.1111/nph.14019","ieee":"S. Simon et al., “PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis,” New Phytologist, vol. 211, no. 1. Wiley-Blackwell, pp. 65–74, 2016.","short":"S. Simon, P. Skůpa, T. Viaene, M. Zwiewka, R. Tejos, P. Klíma, M. Čarná, J. Rolčík, R. De Rycke, I. Moreno, P. Dobrev, A. Orellana, E. Zažímalová, J. Friml, New Phytologist 211 (2016) 65–74.","chicago":"Simon, Sibu, Petr Skůpa, Tom Viaene, Marta Zwiewka, Ricardo Tejos, Petr Klíma, Mária Čarná, et al. “PIN6 Auxin Transporter at Endoplasmic Reticulum and Plasma Membrane Mediates Auxin Homeostasis and Organogenesis in Arabidopsis.” New Phytologist. Wiley-Blackwell, 2016. https://doi.org/10.1111/nph.14019.","ista":"Simon S, Skůpa P, Viaene T, Zwiewka M, Tejos R, Klíma P, Čarná M, Rolčík J, De Rycke R, Moreno I, Dobrev P, Orellana A, Zažímalová E, Friml J. 2016. PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist. 211(1), 65–74."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5790","author":[{"last_name":"Simon","full_name":"Simon, Sibu","orcid":"0000-0002-1998-6741","first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Skůpa, Petr","last_name":"Skůpa","first_name":"Petr"},{"first_name":"Tom","last_name":"Viaene","full_name":"Viaene, Tom"},{"full_name":"Zwiewka, Marta","last_name":"Zwiewka","first_name":"Marta"},{"first_name":"Ricardo","last_name":"Tejos","full_name":"Tejos, Ricardo"},{"first_name":"Petr","last_name":"Klíma","full_name":"Klíma, Petr"},{"first_name":"Mária","full_name":"Čarná, Mária","last_name":"Čarná"},{"first_name":"Jakub","full_name":"Rolčík, Jakub","last_name":"Rolčík"},{"full_name":"De Rycke, Riet","last_name":"De Rycke","first_name":"Riet"},{"first_name":"Ignacio","last_name":"Moreno","full_name":"Moreno, Ignacio"},{"last_name":"Dobrev","full_name":"Dobrev, Petre","first_name":"Petre"},{"last_name":"Orellana","full_name":"Orellana, Ariel","first_name":"Ariel"},{"first_name":"Eva","last_name":"Zažímalová","full_name":"Zažímalová, Eva"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"title":"PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis"},{"ddc":["000"],"date_updated":"2023-02-21T10:38:38Z","file_date_updated":"2020-07-14T12:44:53Z","department":[{"_id":"ChWo"}],"_id":"1415","pubrep_id":"611","status":"public","type":"journal_article","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:12:22Z","file_name":"IST-2016-611-v1+3_CW_nbflip_postprint_2016.pdf","creator":"system","date_updated":"2020-07-14T12:44:53Z","file_size":5938324,"checksum":"984afbe510ed48019025dff1dcc7baad","file_id":"4940","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","volume":35,"issue":"2","oa_version":"Submitted Version","abstract":[{"text":"The Fluid Implicit Particle method (FLIP) for liquid simulations uses particles to reduce numerical dissipation and provide important visual cues for events like complex splashes and small-scale features near the liquid surface. Unfortunately, FLIP simulations can be computationally expensive, because they require a dense sampling of particles to fill the entire liquid volume. Furthermore, the vast majority of these FLIP particles contribute nothing to the fluid's visual appearance, especially for larger volumes of liquid. We present a method that only uses FLIP particles within a narrow band of the liquid surface, while efficiently representing the remaining inner volume on a regular grid. We show that a naïve realization of this idea introduces unstable and uncontrollable energy fluctuations, and we propose a novel coupling scheme between FLIP particles and regular grid which overcomes this problem. Our method drastically reduces the particle count and simulation times while yielding results that are nearly indistinguishable from regular FLIP simulations. Our approach is easy to integrate into any existing FLIP implementation.","lang":"eng"}],"intvolume":" 35","month":"05","scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Ferstl, Florian, et al. “Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum, vol. 35, no. 2, Wiley-Blackwell, 2016, pp. 225–32, doi:10.1111/cgf.12825.","ieee":"F. Ferstl, R. Ando, C. Wojtan, R. Westermann, and N. Thuerey, “Narrow band FLIP for liquid simulations,” Computer Graphics Forum, vol. 35, no. 2. Wiley-Blackwell, pp. 225–232, 2016.","short":"F. Ferstl, R. Ando, C. Wojtan, R. Westermann, N. Thuerey, Computer Graphics Forum 35 (2016) 225–232.","ama":"Ferstl F, Ando R, Wojtan C, Westermann R, Thuerey N. Narrow band FLIP for liquid simulations. Computer Graphics Forum. 2016;35(2):225-232. doi:10.1111/cgf.12825","apa":"Ferstl, F., Ando, R., Wojtan, C., Westermann, R., & Thuerey, N. (2016). Narrow band FLIP for liquid simulations. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12825","chicago":"Ferstl, Florian, Ryoichi Ando, Chris Wojtan, Rüdiger Westermann, and Nils Thuerey. “Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum. Wiley-Blackwell, 2016. https://doi.org/10.1111/cgf.12825.","ista":"Ferstl F, Ando R, Wojtan C, Westermann R, Thuerey N. 2016. Narrow band FLIP for liquid simulations. Computer Graphics Forum. 35(2), 225–232."},"title":"Narrow band FLIP for liquid simulations","author":[{"first_name":"Florian","full_name":"Ferstl, Florian","last_name":"Ferstl"},{"first_name":"Ryoichi","full_name":"Ando, Ryoichi","last_name":"Ando"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan"},{"first_name":"Rüdiger","last_name":"Westermann","full_name":"Westermann, Rüdiger"},{"last_name":"Thuerey","full_name":"Thuerey, Nils","first_name":"Nils"}],"publist_id":"5793","publication":"Computer Graphics Forum","day":"01","year":"2016","has_accepted_license":"1","date_created":"2018-12-11T11:51:53Z","doi":"10.1111/cgf.12825","date_published":"2016-05-01T00:00:00Z","page":"225 - 232","oa":1,"publisher":"Wiley-Blackwell","quality_controlled":"1"},{"intvolume":" 93","month":"05","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1603.09358"}],"scopus_import":1,"publisher":"American Physical Society","quality_controlled":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Anisotropic dipole-dipole interactions between ultracold dipolar fermions break the symmetry of the Fermi surface and thereby deform it. Here we demonstrate that such a Fermi surface deformation induces a topological phase transition - the so-called Lifshitz transition - in the regime accessible to present-day experiments. We describe the impact of the Lifshitz transition on observable quantities such as the Fermi surface topology, the density-density correlation function, and the excitation spectrum of the system. The Lifshitz transition in ultracold atoms can be controlled by tuning the dipole orientation and, in contrast to the transition studied in crystalline solids, is completely interaction driven."}],"date_created":"2018-12-11T11:51:54Z","issue":"19","date_published":"2016-05-15T00:00:00Z","doi":"10.1103/PhysRevB.93.195145","volume":93,"language":[{"iso":"eng"}],"publication":"Physical Review B - Condensed Matter and Materials Physics","day":"15","year":"2016","publication_status":"published","status":"public","type":"journal_article","article_number":"195145","_id":"1416","department":[{"_id":"MiLe"}],"title":"Interaction-driven Lifshitz transition with dipolar fermions in optical lattices","author":[{"full_name":"Van Loon, Erik","last_name":"Van Loon","first_name":"Erik"},{"first_name":"Mikhail","full_name":"Katsnelson, Mikhail","last_name":"Katsnelson"},{"first_name":"Lauriane","full_name":"Chomaz, Lauriane","last_name":"Chomaz"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko"}],"publist_id":"5791","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"E. Van Loon, M. Katsnelson, L. Chomaz, and M. Lemeshko, “Interaction-driven Lifshitz transition with dipolar fermions in optical lattices,” Physical Review B - Condensed Matter and Materials Physics, vol. 93, no. 19. American Physical Society, 2016.","short":"E. Van Loon, M. Katsnelson, L. Chomaz, M. Lemeshko, Physical Review B - Condensed Matter and Materials Physics 93 (2016).","ama":"Van Loon E, Katsnelson M, Chomaz L, Lemeshko M. Interaction-driven Lifshitz transition with dipolar fermions in optical lattices. Physical Review B - Condensed Matter and Materials Physics. 2016;93(19). doi:10.1103/PhysRevB.93.195145","apa":"Van Loon, E., Katsnelson, M., Chomaz, L., & Lemeshko, M. (2016). Interaction-driven Lifshitz transition with dipolar fermions in optical lattices. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.93.195145","mla":"Van Loon, Erik, et al. “Interaction-Driven Lifshitz Transition with Dipolar Fermions in Optical Lattices.” Physical Review B - Condensed Matter and Materials Physics, vol. 93, no. 19, 195145, American Physical Society, 2016, doi:10.1103/PhysRevB.93.195145.","ista":"Van Loon E, Katsnelson M, Chomaz L, Lemeshko M. 2016. Interaction-driven Lifshitz transition with dipolar fermions in optical lattices. Physical Review B - Condensed Matter and Materials Physics. 93(19), 195145.","chicago":"Van Loon, Erik, Mikhail Katsnelson, Lauriane Chomaz, and Mikhail Lemeshko. “Interaction-Driven Lifshitz Transition with Dipolar Fermions in Optical Lattices.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2016. https://doi.org/10.1103/PhysRevB.93.195145."},"date_updated":"2021-01-12T06:50:36Z"},{"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Lagator M, Igler C, Moreno A, Guet CC, Bollback JP. 2016. Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution. 33(3), 761–769.","chicago":"Lagator, Mato, Claudia Igler, Anaisa Moreno, Calin C Guet, and Jonathan P Bollback. “Epistatic Interactions in the Arabinose Cis-Regulatory Element.” Molecular Biology and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/molbev/msv269.","ieee":"M. Lagator, C. Igler, A. Moreno, C. C. Guet, and J. P. Bollback, “Epistatic interactions in the arabinose cis-regulatory element,” Molecular Biology and Evolution, vol. 33, no. 3. Oxford University Press, pp. 761–769, 2016.","short":"M. Lagator, C. Igler, A. Moreno, C.C. Guet, J.P. Bollback, Molecular Biology and Evolution 33 (2016) 761–769.","apa":"Lagator, M., Igler, C., Moreno, A., Guet, C. C., & Bollback, J. P. (2016). Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msv269","ama":"Lagator M, Igler C, Moreno A, Guet CC, Bollback JP. Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution. 2016;33(3):761-769. doi:10.1093/molbev/msv269","mla":"Lagator, Mato, et al. “Epistatic Interactions in the Arabinose Cis-Regulatory Element.” Molecular Biology and Evolution, vol. 33, no. 3, Oxford University Press, 2016, pp. 761–69, doi:10.1093/molbev/msv269."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5772","author":[{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato","full_name":"Lagator, Mato","last_name":"Lagator"},{"first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","full_name":"Igler, Claudia","last_name":"Igler"},{"first_name":"Anaisa","last_name":"Moreno","full_name":"Moreno, Anaisa"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","last_name":"Bollback"}],"title":"Epistatic interactions in the arabinose cis-regulatory element","quality_controlled":"1","publisher":"Oxford University Press","oa":1,"has_accepted_license":"1","year":"2016","day":"01","publication":"Molecular Biology and Evolution","page":"761 - 769","date_published":"2016-03-01T00:00:00Z","doi":"10.1093/molbev/msv269","date_created":"2018-12-11T11:51:57Z","_id":"1427","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":"588","date_updated":"2021-01-12T06:50:39Z","ddc":["570","576"],"department":[{"_id":"CaGu"},{"_id":"JoBo"}],"file_date_updated":"2020-07-14T12:44:53Z","abstract":[{"text":"Changes in gene expression are an important mode of evolution; however, the proximate mechanism of these changes is poorly understood. In particular, little is known about the effects of mutations within cis binding sites for transcription factors, or the nature of epistatic interactions between these mutations. Here, we tested the effects of single and double mutants in two cis binding sites involved in the transcriptional regulation of the Escherichia coli araBAD operon, a component of arabinose metabolism, using a synthetic system. This system decouples transcriptional control from any posttranslational effects on fitness, allowing a precise estimate of the effect of single and double mutations, and hence epistasis, on gene expression. We found that epistatic interactions between mutations in the araBAD cis-regulatory element are common, and that the predominant form of epistasis is negative. The magnitude of the interactions depended on whether the mutations are located in the same or in different operator sites. Importantly, these epistatic interactions were dependent on the presence of arabinose, a native inducer of the araBAD operon in vivo, with some interactions changing in sign (e.g., from negative to positive) in its presence. This study thus reveals that mutations in even relatively simple cis-regulatory elements interact in complex ways such that selection on the level of gene expression in one environment might perturb regulation in the other environment in an unpredictable and uncorrelated manner.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"month":"03","intvolume":" 33","publication_status":"published","file":[{"date_updated":"2020-07-14T12:44:53Z","file_size":648115,"creator":"system","date_created":"2018-12-12T10:09:27Z","file_name":"IST-2016-588-v1+1_Mol_Biol_Evol-2016-Lagator-761-9.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"4751","checksum":"1f456ce1d2aa2f67176a1709f9702ecf"}],"language":[{"iso":"eng"}],"issue":"3","volume":33,"ec_funded":1},{"article_number":"012016","project":[{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Könenberg, Martin, et al. “Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential.” Journal of Physics: Conference Series, vol. 691, no. 1, 012016, IOP Publishing Ltd., 2016, doi:10.1088/1742-6596/691/1/012016.","apa":"Könenberg, M., Moser, T., Seiringer, R., & Yngvason, J. (2016). Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential. In Journal of Physics: Conference Series (Vol. 691). Shanghai, China: IOP Publishing Ltd. https://doi.org/10.1088/1742-6596/691/1/012016","ama":"Könenberg M, Moser T, Seiringer R, Yngvason J. Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential. In: Journal of Physics: Conference Series. Vol 691. IOP Publishing Ltd.; 2016. doi:10.1088/1742-6596/691/1/012016","ieee":"M. Könenberg, T. Moser, R. Seiringer, and J. Yngvason, “Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential,” in Journal of Physics: Conference Series, Shanghai, China, 2016, vol. 691, no. 1.","short":"M. Könenberg, T. Moser, R. Seiringer, J. Yngvason, in:, Journal of Physics: Conference Series, IOP Publishing Ltd., 2016.","chicago":"Könenberg, Martin, Thomas Moser, Robert Seiringer, and Jakob Yngvason. “Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential.” In Journal of Physics: Conference Series, Vol. 691. IOP Publishing Ltd., 2016. https://doi.org/10.1088/1742-6596/691/1/012016.","ista":"Könenberg M, Moser T, Seiringer R, Yngvason J. 2016. Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential. Journal of Physics: Conference Series. 24th International Laser Physics Workshop (LPHYS’15) vol. 691, 012016."},"title":"Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential","publist_id":"5770","author":[{"first_name":"Martin","full_name":"Könenberg, Martin","last_name":"Könenberg"},{"last_name":"Moser","full_name":"Moser, Thomas","first_name":"Thomas","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer"},{"last_name":"Yngvason","full_name":"Yngvason, Jakob","first_name":"Jakob"}],"quality_controlled":"1","publisher":"IOP Publishing Ltd.","oa":1,"day":"07","publication":"Journal of Physics: Conference Series","has_accepted_license":"1","year":"2016","doi":"10.1088/1742-6596/691/1/012016","date_published":"2016-03-07T00:00:00Z","date_created":"2018-12-11T11:51:58Z","_id":"1428","status":"public","pubrep_id":"585","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"24th International Laser Physics Workshop (LPHYS'15)","end_date":"2015-08-25","location":"Shanghai, China","start_date":"2015-08-21"},"ddc":["510","530"],"date_updated":"2021-01-12T06:50:40Z","department":[{"_id":"RoSe"}],"file_date_updated":"2020-07-14T12:44:53Z","oa_version":"Published Version","abstract":[{"text":"We report on a mathematically rigorous analysis of the superfluid properties of a Bose- Einstein condensate in the many-body ground state of a one-dimensional model of interacting bosons in a random potential.","lang":"eng"}],"month":"03","intvolume":" 691","scopus_import":1,"file":[{"checksum":"109db801749072c3f6c8f1a1848700fa","file_id":"4847","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:10:55Z","file_name":"IST-2016-585-v1+1_JPCS_691_1_012016.pdf","date_updated":"2020-07-14T12:44:53Z","file_size":1434688,"creator":"system"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":691,"issue":"1"},{"year":"2016","has_accepted_license":"1","publication":"Royal Society Open Science","day":"01","date_created":"2018-12-11T11:51:57Z","doi":"10.1098/rsos.160036","date_published":"2016-05-01T00:00:00Z","acknowledgement":"C.H. gratefully acknowledges funding by the Schrödinger scholarship of the Austrian Science Fund (FWF) J3475.","oa":1,"publisher":"Royal Society, The","quality_controlled":"1","citation":{"mla":"Chakra, Maria, et al. “Coevolutionary Interactions between Farmers and Mafia Induce Host Acceptance of Avian Brood Parasites.” Royal Society Open Science, vol. 3, no. 5, 160036, Royal Society, The, 2016, doi:10.1098/rsos.160036.","ama":"Chakra M, Hilbe C, Traulsen A. Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites. Royal Society Open Science. 2016;3(5). doi:10.1098/rsos.160036","apa":"Chakra, M., Hilbe, C., & Traulsen, A. (2016). Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites. Royal Society Open Science. Royal Society, The. https://doi.org/10.1098/rsos.160036","short":"M. Chakra, C. Hilbe, A. Traulsen, Royal Society Open Science 3 (2016).","ieee":"M. Chakra, C. Hilbe, and A. Traulsen, “Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites,” Royal Society Open Science, vol. 3, no. 5. Royal Society, The, 2016.","chicago":"Chakra, Maria, Christian Hilbe, and Arne Traulsen. “Coevolutionary Interactions between Farmers and Mafia Induce Host Acceptance of Avian Brood Parasites.” Royal Society Open Science. Royal Society, The, 2016. https://doi.org/10.1098/rsos.160036.","ista":"Chakra M, Hilbe C, Traulsen A. 2016. Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites. Royal Society Open Science. 3(5), 160036."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Maria","full_name":"Chakra, Maria","last_name":"Chakra"},{"full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"},{"last_name":"Traulsen","full_name":"Traulsen, Arne","first_name":"Arne"}],"publist_id":"5776","title":"Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites","article_number":"160036","publication_status":"published","language":[{"iso":"eng"}],"file":[{"checksum":"bf84211b31fe87451e738ba301d729c3","file_id":"5104","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:14:49Z","file_name":"IST-2016-589-v1+1_160036.full.pdf","date_updated":"2020-07-14T12:44:53Z","file_size":937002,"creator":"system"}],"volume":3,"issue":"5","abstract":[{"lang":"eng","text":"Brood parasites exploit their host in order to increase their own fitness. Typically, this results in an arms race between parasite trickery and host defence. Thus, it is puzzling to observe hosts that accept parasitism without any resistance. The ‘mafia’ hypothesis suggests that these hosts accept parasitism to avoid retaliation. Retaliation has been shown to evolve when the hosts condition their response to mafia parasites, who use depredation as a targeted response to rejection. However, it is unclear if acceptance would also emerge when ‘farming’ parasites are present in the population. Farming parasites use depredation to synchronize the timing with the host, destroying mature clutches to force the host to re-nest. Herein, we develop an evolutionary model to analyse the interaction between depredatory parasites and their hosts. We show that coevolutionary cycles between farmers and mafia can still induce host acceptance of brood parasites. However, this equilibrium is unstable and in the long-run the dynamics of this host–parasite interaction exhibits strong oscillations: when farmers are the majority, accepters conditional to mafia (the host will reject first and only accept after retaliation by the parasite) have a higher fitness than unconditional accepters (the host always accepts parasitism). This leads to an increase in mafia parasites’ fitness and in turn induce an optimal environment for accepter hosts."}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 3","month":"05","date_updated":"2021-01-12T06:50:39Z","ddc":["000"],"file_date_updated":"2020-07-14T12:44:53Z","department":[{"_id":"KrCh"}],"_id":"1426","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"589","status":"public"},{"status":"public","pubrep_id":"590","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":"1423","file_date_updated":"2020-07-14T12:44:53Z","department":[{"_id":"KrCh"}],"ddc":["000"],"date_updated":"2021-01-12T06:50:38Z","month":"05","intvolume":" 6","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"Direct reciprocity is a mechanism for the evolution of cooperation based on repeated interactions. When individuals meet repeatedly, they can use conditional strategies to enforce cooperative outcomes that would not be feasible in one-shot social dilemmas. Direct reciprocity requires that individuals keep track of their past interactions and find the right response. However, there are natural bounds on strategic complexity: Humans find it difficult to remember past interactions accurately, especially over long timespans. Given these limitations, it is natural to ask how complex strategies need to be for cooperation to evolve. Here, we study stochastic evolutionary game dynamics in finite populations to systematically compare the evolutionary performance of reactive strategies, which only respond to the co-player's previous move, and memory-one strategies, which take into account the own and the co-player's previous move. In both cases, we compare deterministic strategy and stochastic strategy spaces. For reactive strategies and small costs, we find that stochasticity benefits cooperation, because it allows for generous-tit-for-tat. For memory one strategies and small costs, we find that stochasticity does not increase the propensity for cooperation, because the deterministic rule of win-stay, lose-shift works best. For memory one strategies and large costs, however, stochasticity can augment cooperation.","lang":"eng"}],"volume":6,"file":[{"checksum":"ee17c482370d2e1b3add393710d3c696","file_id":"5327","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-590-v1+1_srep25676.pdf","date_created":"2018-12-12T10:18:08Z","creator":"system","file_size":1349915,"date_updated":"2020-07-14T12:44:53Z"}],"language":[{"iso":"eng"}],"publication_status":"published","article_number":"25676","title":"Comparing reactive and memory-one strategies of direct reciprocity","publist_id":"5784","author":[{"full_name":"Baek, Seung","last_name":"Baek","first_name":"Seung"},{"first_name":"Hyeongchai","last_name":"Jeong","full_name":"Jeong, Hyeongchai"},{"first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","last_name":"Hilbe"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Baek, Seung, Hyeongchai Jeong, Christian Hilbe, and Martin Nowak. “Comparing Reactive and Memory-One Strategies of Direct Reciprocity.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep25676.","ista":"Baek S, Jeong H, Hilbe C, Nowak M. 2016. Comparing reactive and memory-one strategies of direct reciprocity. Scientific Reports. 6, 25676.","mla":"Baek, Seung, et al. “Comparing Reactive and Memory-One Strategies of Direct Reciprocity.” Scientific Reports, vol. 6, 25676, Nature Publishing Group, 2016, doi:10.1038/srep25676.","ama":"Baek S, Jeong H, Hilbe C, Nowak M. Comparing reactive and memory-one strategies of direct reciprocity. Scientific Reports. 2016;6. doi:10.1038/srep25676","apa":"Baek, S., Jeong, H., Hilbe, C., & Nowak, M. (2016). Comparing reactive and memory-one strategies of direct reciprocity. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep25676","short":"S. Baek, H. Jeong, C. Hilbe, M. Nowak, Scientific Reports 6 (2016).","ieee":"S. Baek, H. Jeong, C. Hilbe, and M. Nowak, “Comparing reactive and memory-one strategies of direct reciprocity,” Scientific Reports, vol. 6. Nature Publishing Group, 2016."},"quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"acknowledgement":"C.H. acknowledges generous funding from the Schrödinger scholarship of the Austrian Science Fund (FWF), J3475.","date_published":"2016-05-10T00:00:00Z","doi":"10.1038/srep25676","date_created":"2018-12-11T11:51:56Z","day":"10","publication":"Scientific Reports","has_accepted_license":"1","year":"2016"},{"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":"591","_id":"1422","department":[{"_id":"RoSe"}],"file_date_updated":"2020-07-14T12:44:53Z","date_updated":"2021-01-12T06:50:38Z","ddc":["510","530"],"scopus_import":1,"month":"07","intvolume":" 106","abstract":[{"text":"We study the time-dependent Bogoliubov–de-Gennes equations for generic translation-invariant fermionic many-body systems. For initial states that are close to thermal equilibrium states at temperatures near the critical temperature, we show that the magnitude of the order parameter stays approximately constant in time and, in particular, does not follow a time-dependent Ginzburg–Landau equation, which is often employed as a phenomenological description and predicts a decay of the order parameter in time. The full non-linear structure of the equations is necessary to understand this behavior.","lang":"eng"}],"oa_version":"Published Version","issue":"7","volume":106,"publication_status":"published","file":[{"file_size":458968,"date_updated":"2020-07-14T12:44:53Z","creator":"system","file_name":"IST-2016-591-v1+1_s11005-016-0847-5.pdf","date_created":"2018-12-12T10:15:57Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"fb404923d8ca9a1faeb949561f26cbea","file_id":"5181"}],"language":[{"iso":"eng"}],"project":[{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"author":[{"last_name":"Frank","full_name":"Frank, Rupert","first_name":"Rupert"},{"full_name":"Hainzl, Christian","last_name":"Hainzl","first_name":"Christian"},{"first_name":"Benjamin","full_name":"Schlein, Benjamin","last_name":"Schlein"},{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"publist_id":"5785","article_processing_charge":"Yes (via OA deal)","title":"Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations","citation":{"mla":"Frank, Rupert, et al. “Incompatibility of Time-Dependent Bogoliubov–de-Gennes and Ginzburg–Landau Equations.” Letters in Mathematical Physics, vol. 106, no. 7, Springer, 2016, pp. 913–23, doi:10.1007/s11005-016-0847-5.","apa":"Frank, R., Hainzl, C., Schlein, B., & Seiringer, R. (2016). Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-016-0847-5","ama":"Frank R, Hainzl C, Schlein B, Seiringer R. Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations. Letters in Mathematical Physics. 2016;106(7):913-923. doi:10.1007/s11005-016-0847-5","ieee":"R. Frank, C. Hainzl, B. Schlein, and R. Seiringer, “Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations,” Letters in Mathematical Physics, vol. 106, no. 7. Springer, pp. 913–923, 2016.","short":"R. Frank, C. Hainzl, B. Schlein, R. Seiringer, Letters in Mathematical Physics 106 (2016) 913–923.","chicago":"Frank, Rupert, Christian Hainzl, Benjamin Schlein, and Robert Seiringer. “Incompatibility of Time-Dependent Bogoliubov–de-Gennes and Ginzburg–Landau Equations.” Letters in Mathematical Physics. Springer, 2016. https://doi.org/10.1007/s11005-016-0847-5.","ista":"Frank R, Hainzl C, Schlein B, Seiringer R. 2016. Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations. Letters in Mathematical Physics. 106(7), 913–923."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","quality_controlled":"1","oa":1,"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). ","page":"913 - 923","doi":"10.1007/s11005-016-0847-5","date_published":"2016-07-01T00:00:00Z","date_created":"2018-12-11T11:51:56Z","has_accepted_license":"1","year":"2016","day":"01","publication":"Letters in Mathematical Physics"},{"department":[{"_id":"GaTk"},{"_id":"NiBa"}],"date_updated":"2022-08-01T10:49:55Z","type":"journal_article","status":"public","_id":"1420","issue":"4","volume":202,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1510.08344"}],"month":"04","intvolume":" 202","abstract":[{"text":"Selection, mutation, and random drift affect the dynamics of allele frequencies and consequently of quantitative traits. While the macroscopic dynamics of quantitative traits can be measured, the underlying allele frequencies are typically unobserved. Can we understand how the macroscopic observables evolve without following these microscopic processes? This problem has been studied previously by analogy with statistical mechanics: the allele frequency distribution at each time point is approximated by the stationary form, which maximizes entropy. We explore the limitations of this method when mutation is small (4Nμ < 1) so that populations are typically close to fixation, and we extend the theory in this regime to account for changes in mutation strength. We consider a single diallelic locus either under directional selection or with overdominance and then generalize to multiple unlinked biallelic loci with unequal effects. We find that the maximum-entropy approximation is remarkably accurate, even when mutation and selection change rapidly. ","lang":"eng"}],"oa_version":"Preprint","publist_id":"5787","author":[{"last_name":"Bod'ová","full_name":"Bod'ová, Katarína","orcid":"0000-0002-7214-0171","first_name":"Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"article_processing_charge":"No","external_id":{"arxiv":["1510.08344"]},"title":"A general approximation for the dynamics of quantitative traits","citation":{"mla":"Bodova, Katarina, et al. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics, vol. 202, no. 4, Genetics Society of America, 2016, pp. 1523–48, doi:10.1534/genetics.115.184127.","ieee":"K. Bodova, G. Tkačik, and N. H. Barton, “A general approximation for the dynamics of quantitative traits,” Genetics, vol. 202, no. 4. Genetics Society of America, pp. 1523–1548, 2016.","short":"K. Bodova, G. Tkačik, N.H. Barton, Genetics 202 (2016) 1523–1548.","ama":"Bodova K, Tkačik G, Barton NH. A general approximation for the dynamics of quantitative traits. Genetics. 2016;202(4):1523-1548. doi:10.1534/genetics.115.184127","apa":"Bodova, K., Tkačik, G., & Barton, N. H. (2016). A general approximation for the dynamics of quantitative traits. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.184127","chicago":"Bodova, Katarina, Gašper Tkačik, and Nicholas H Barton. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.184127.","ista":"Bodova K, Tkačik G, Barton NH. 2016. A general approximation for the dynamics of quantitative traits. Genetics. 202(4), 1523–1548."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"255008E4-B435-11E9-9278-68D0E5697425","name":"Information processing and computation in fish groups","grant_number":"RGP0065/2012"}],"page":"1523 - 1548","doi":"10.1534/genetics.115.184127","date_published":"2016-04-06T00:00:00Z","date_created":"2018-12-11T11:51:55Z","year":"2016","day":"06","publication":"Genetics","publisher":"Genetics Society of America","quality_controlled":"1","oa":1},{"article_number":"11332 (2016)","publist_id":"5769","author":[{"first_name":"Chad","full_name":"Husko, Chad","last_name":"Husko"},{"first_name":"Matthias","id":"45598606-F248-11E8-B48F-1D18A9856A87","full_name":"Wulf, Matthias","orcid":"0000-0001-6613-1378","last_name":"Wulf"},{"first_name":"Simon","full_name":"Lefrançois, Simon","last_name":"Lefrançois"},{"full_name":"Combrié, Sylvain","last_name":"Combrié","first_name":"Sylvain"},{"first_name":"Gaëlle","last_name":"Lehoucq","full_name":"Lehoucq, Gaëlle"},{"first_name":"Alfredo","last_name":"De Rossi","full_name":"De Rossi, Alfredo"},{"first_name":"Benjamin","last_name":"Eggleton","full_name":"Eggleton, Benjamin"},{"first_name":"Laurens","last_name":"Kuipers","full_name":"Kuipers, Laurens"}],"title":"Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides","citation":{"ista":"Husko C, Wulf M, Lefrançois S, Combrié S, Lehoucq G, De Rossi A, Eggleton B, Kuipers L. 2016. Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides. Nature Communications. 7, 11332 (2016).","chicago":"Husko, Chad, Matthias Wulf, Simon Lefrançois, Sylvain Combrié, Gaëlle Lehoucq, Alfredo De Rossi, Benjamin Eggleton, and Laurens Kuipers. “Free-Carrier-Induced Soliton Fission Unveiled by in Situ Measurements in Nanophotonic Waveguides.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms11332.","ama":"Husko C, Wulf M, Lefrançois S, et al. Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides. Nature Communications. 2016;7. doi:10.1038/ncomms11332","apa":"Husko, C., Wulf, M., Lefrançois, S., Combrié, S., Lehoucq, G., De Rossi, A., … Kuipers, L. (2016). Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms11332","ieee":"C. Husko et al., “Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides,” Nature Communications, vol. 7. Nature Publishing Group, 2016.","short":"C. Husko, M. Wulf, S. Lefrançois, S. Combrié, G. Lehoucq, A. De Rossi, B. Eggleton, L. Kuipers, Nature Communications 7 (2016).","mla":"Husko, Chad, et al. “Free-Carrier-Induced Soliton Fission Unveiled by in Situ Measurements in Nanophotonic Waveguides.” Nature Communications, vol. 7, 11332 (2016), Nature Publishing Group, 2016, doi:10.1038/ncomms11332."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","acknowledgement":"This research was supported by the Australian Research Council (ARC) Center of Excellence CUDOS (CE110001018), ARC Laureate Fellowship (FL120100029), ARC Discovery Early Career Researcher Award (DECRA DE120102069), the Netherlands Foundation for Fundamental Research on Matter (FOM) and the Netherlands Organization for Scientific Research (NWO). L.K. acknowledges funding from ERC Advanced Investigator Grant (no. 240438-CONSTANS). A.D.R, S.C., and G.L. acknowledge financial support from the ERC-Pharos programme lead by A. P. Mosk.","date_created":"2018-12-11T11:51:58Z","date_published":"2016-04-15T00:00:00Z","doi":"10.1038/ncomms11332","year":"2016","has_accepted_license":"1","publication":"Nature Communications","day":"15","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"583","status":"public","_id":"1429","file_date_updated":"2020-07-14T12:44:53Z","department":[{"_id":"JoFi"}],"date_updated":"2021-01-12T06:50:40Z","ddc":["530"],"scopus_import":1,"intvolume":" 7","month":"04","abstract":[{"lang":"eng","text":"Solitons are localized waves formed by a balance of focusing and defocusing effects. These nonlinear waves exist in diverse forms of matter yet exhibit similar properties including stability, periodic recurrence and particle-like trajectories. One important property is soliton fission, a process by which an energetic higher-order soliton breaks apart due to dispersive or nonlinear perturbations. Here we demonstrate through both experiment and theory that nonlinear photocarrier generation can induce soliton fission. Using near-field measurements, we directly observe the nonlinear spatial and temporal evolution of optical pulses in situ in a nanophotonic semiconductor waveguide. We develop an analytic formalism describing the free-carrier dispersion (FCD) perturbation and show the experiment exceeds the minimum threshold by an order of magnitude. We confirm these observations with a numerical nonlinear Schrödinger equation model. These results provide a fundamental explanation and physical scaling of optical pulse evolution in free-carrier media and could enable improved supercontinuum sources in gas based and integrated semiconductor waveguides."}],"oa_version":"Published Version","volume":7,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:15:53Z","file_name":"IST-2016-583-v1+1_ncomms11332.pdf","creator":"system","date_updated":"2020-07-14T12:44:53Z","file_size":965176,"checksum":"6484fa81a2e52e4fdd7935e1ae6091d4","file_id":"5177","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}]},{"intvolume":" 2016","month":"01","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The rare socially parasitic butterfly Maculinea alcon occurs in two forms, which are characteristic of hygric or xeric habitats and which exploit different host plants and host ants. The status of these two forms has been the subject of considerable controversy. Populations of the two forms are usually spatially distinct, but at Răscruci in Romania both forms occur on the same site (syntopically). We examined the genetic differentiation between the two forms using eight microsatellite markers, and compared with a nearby hygric site, Şardu. Our results showed that while the two forms are strongly differentiated at Răscruci, it is the xeric form there that is most similar to the hygric form at Şardu, and Bayesian clustering algorithms suggest that these two populations have exchanged genes relatively recently. We found strong evidence for population substructuring, caused by high within host ant nest relatedness, indicating very limited dispersal of most ovipositing females, but not association with particular host ant species. Our results are consistent with the results of larger scale phylogeographic studies that suggest that the two forms represent local ecotypes specialising on different host plants, each with a distinct flowering phenology, providing a temporal rather than spatial barrier to gene flow."}],"volume":2016,"issue":"3","language":[{"iso":"eng"}],"file":[{"file_id":"5272","checksum":"c27d898598a1e3d7f629607a309254e1","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:17:19Z","file_name":"IST-2016-584-v1+1_peerj-1865.pdf","date_updated":"2020-07-14T12:44:53Z","file_size":1216360,"creator":"system"}],"publication_status":"published","pubrep_id":"584","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"1431","department":[{"_id":"SyCr"}],"file_date_updated":"2020-07-14T12:44:53Z","ddc":["570"],"date_updated":"2021-01-12T06:50:41Z","oa":1,"publisher":"PeerJ","quality_controlled":"1","date_created":"2018-12-11T11:51:59Z","date_published":"2016-01-01T00:00:00Z","doi":"10.7717/peerj.1865","publication":"PeerJ","day":"01","year":"2016","has_accepted_license":"1","article_number":"1865","title":"Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon","author":[{"first_name":"András","full_name":"Tartally, András","last_name":"Tartally"},{"first_name":"Andreas","full_name":"Kelager, Andreas","last_name":"Kelager"},{"orcid":"0000-0002-3712-925X","full_name":"Fürst, Matthias","last_name":"Fürst","id":"393B1196-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias"},{"full_name":"Nash, David","last_name":"Nash","first_name":"David"}],"publist_id":"5767","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"A. Tartally, A. Kelager, M. Fürst, D. Nash, PeerJ 2016 (2016).","ieee":"A. Tartally, A. Kelager, M. Fürst, and D. Nash, “Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon,” PeerJ, vol. 2016, no. 3. PeerJ, 2016.","ama":"Tartally A, Kelager A, Fürst M, Nash D. Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon. PeerJ. 2016;2016(3). doi:10.7717/peerj.1865","apa":"Tartally, A., Kelager, A., Fürst, M., & Nash, D. (2016). Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon. PeerJ. PeerJ. https://doi.org/10.7717/peerj.1865","mla":"Tartally, András, et al. “Host Plant Use Drives Genetic Differentiation in Syntopic Populations of Maculinea Alcon.” PeerJ, vol. 2016, no. 3, 1865, PeerJ, 2016, doi:10.7717/peerj.1865.","ista":"Tartally A, Kelager A, Fürst M, Nash D. 2016. Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon. PeerJ. 2016(3), 1865.","chicago":"Tartally, András, Andreas Kelager, Matthias Fürst, and David Nash. “Host Plant Use Drives Genetic Differentiation in Syntopic Populations of Maculinea Alcon.” PeerJ. PeerJ, 2016. https://doi.org/10.7717/peerj.1865."}},{"author":[{"last_name":"Bao","orcid":"0000-0003-3036-1475","full_name":"Bao, Zhigang","first_name":"Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schnelli","full_name":"Schnelli, Kevin","orcid":"0000-0003-0954-3231","first_name":"Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5764","title":"Local stability of the free additive convolution","citation":{"chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Stability of the Free Additive Convolution.” Journal of Functional Analysis. Academic Press, 2016. https://doi.org/10.1016/j.jfa.2016.04.006.","ista":"Bao Z, Erdös L, Schnelli K. 2016. Local stability of the free additive convolution. Journal of Functional Analysis. 271(3), 672–719.","mla":"Bao, Zhigang, et al. “Local Stability of the Free Additive Convolution.” Journal of Functional Analysis, vol. 271, no. 3, Academic Press, 2016, pp. 672–719, doi:10.1016/j.jfa.2016.04.006.","short":"Z. Bao, L. Erdös, K. Schnelli, Journal of Functional Analysis 271 (2016) 672–719.","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Local stability of the free additive convolution,” Journal of Functional Analysis, vol. 271, no. 3. Academic Press, pp. 672–719, 2016.","apa":"Bao, Z., Erdös, L., & Schnelli, K. (2016). Local stability of the free additive convolution. Journal of Functional Analysis. Academic Press. https://doi.org/10.1016/j.jfa.2016.04.006","ama":"Bao Z, Erdös L, Schnelli K. Local stability of the free additive convolution. Journal of Functional Analysis. 2016;271(3):672-719. doi:10.1016/j.jfa.2016.04.006"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"}],"page":"672 - 719","date_published":"2016-08-01T00:00:00Z","doi":"10.1016/j.jfa.2016.04.006","date_created":"2018-12-11T11:52:00Z","year":"2016","day":"01","publication":"Journal of Functional Analysis","quality_controlled":"1","publisher":"Academic Press","oa":1,"department":[{"_id":"LaEr"}],"date_updated":"2021-01-12T06:50:42Z","type":"journal_article","status":"public","_id":"1434","issue":"3","volume":271,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1508.05905","open_access":"1"}],"month":"08","intvolume":" 271","abstract":[{"text":"We prove that the system of subordination equations, defining the free additive convolution of two probability measures, is stable away from the edges of the support and blow-up singularities by showing that the recent smoothness condition of Kargin is always satisfied. As an application, we consider the local spectral statistics of the random matrix ensemble A+UBU⁎A+UBU⁎, where U is a Haar distributed random unitary or orthogonal matrix, and A and B are deterministic matrices. In the bulk regime, we prove that the empirical spectral distribution of A+UBU⁎A+UBU⁎ concentrates around the free additive convolution of the spectral distributions of A and B on scales down to N−2/3N−2/3.","lang":"eng"}],"oa_version":"Preprint"},{"quality_controlled":"1","publisher":"Elsevier","oa":1,"has_accepted_license":"1","year":"2016","day":"01","publication":"Journal de Mathématiques Pures et Appliquées","page":"1 - 30","doi":"10.1016/j.matpur.2015.09.003","date_published":"2016-01-01T00:00:00Z","date_created":"2018-12-11T11:52:00Z","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"citation":{"apa":"Bach, V., Breteaux, S., Petrat, S. P., Pickl, P., & Tzaneteas, T. (2016). Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. Journal de Mathématiques Pures et Appliquées. Elsevier. https://doi.org/10.1016/j.matpur.2015.09.003","ama":"Bach V, Breteaux S, Petrat SP, Pickl P, Tzaneteas T. Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. Journal de Mathématiques Pures et Appliquées. 2016;105(1):1-30. doi:10.1016/j.matpur.2015.09.003","short":"V. Bach, S. Breteaux, S.P. Petrat, P. Pickl, T. Tzaneteas, Journal de Mathématiques Pures et Appliquées 105 (2016) 1–30.","ieee":"V. Bach, S. Breteaux, S. P. Petrat, P. Pickl, and T. Tzaneteas, “Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction,” Journal de Mathématiques Pures et Appliquées, vol. 105, no. 1. Elsevier, pp. 1–30, 2016.","mla":"Bach, Volker, et al. “Kinetic Energy Estimates for the Accuracy of the Time-Dependent Hartree-Fock Approximation with Coulomb Interaction.” Journal de Mathématiques Pures et Appliquées, vol. 105, no. 1, Elsevier, 2016, pp. 1–30, doi:10.1016/j.matpur.2015.09.003.","ista":"Bach V, Breteaux S, Petrat SP, Pickl P, Tzaneteas T. 2016. Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. Journal de Mathématiques Pures et Appliquées. 105(1), 1–30.","chicago":"Bach, Volker, Sébastien Breteaux, Sören P Petrat, Peter Pickl, and Tim Tzaneteas. “Kinetic Energy Estimates for the Accuracy of the Time-Dependent Hartree-Fock Approximation with Coulomb Interaction.” Journal de Mathématiques Pures et Appliquées. Elsevier, 2016. https://doi.org/10.1016/j.matpur.2015.09.003."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5763","author":[{"last_name":"Bach","full_name":"Bach, Volker","first_name":"Volker"},{"last_name":"Breteaux","full_name":"Breteaux, Sébastien","first_name":"Sébastien"},{"id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","first_name":"Sören P","orcid":"0000-0002-9166-5889","full_name":"Petrat, Sören P","last_name":"Petrat"},{"first_name":"Peter","last_name":"Pickl","full_name":"Pickl, Peter"},{"last_name":"Tzaneteas","full_name":"Tzaneteas, Tim","first_name":"Tim"}],"title":"Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction","abstract":[{"lang":"eng","text":"We study the time evolution of a system of N spinless fermions in R3 which interact through a pair potential, e.g., the Coulomb potential. We compare the dynamics given by the solution to Schrödinger's equation with the time-dependent Hartree-Fock approximation, and we give an estimate for the accuracy of this approximation in terms of the kinetic energy of the system. This leads, in turn, to bounds in terms of the initial total energy of the system."}],"oa_version":"Published Version","scopus_import":1,"month":"01","intvolume":" 105","publication_status":"published","file":[{"file_name":"IST-2016-581-v1+1_1-s2.0-S0021782415001191-main.pdf","date_created":"2018-12-12T10:10:36Z","file_size":658491,"date_updated":"2020-07-14T12:44:54Z","creator":"system","file_id":"4825","checksum":"c5afe1f6935bc7f2b546adbde1d31a35","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"volume":105,"issue":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ec_funded":1,"_id":"1436","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","pubrep_id":"581","date_updated":"2021-01-12T06:50:43Z","ddc":["510","530"],"file_date_updated":"2020-07-14T12:44:54Z","department":[{"_id":"RoSe"}]},{"_id":"1435","pubrep_id":"580","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["570"],"date_updated":"2021-01-12T06:50:43Z","department":[{"_id":"PeJo"}],"file_date_updated":"2020-07-14T12:44:54Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"ATP released from neurons and astrocytes during neuronal activity or under pathophysiological circumstances is able to influence information flow in neuronal circuits by activation of ionotropic P2X and metabotropic P2Y receptors and subsequent modulation of cellular excitability, synaptic strength, and plasticity. In the present paper we review cellular and network effects of P2Y receptors in the brain. We show that P2Y receptors inhibit the release of neurotransmitters, modulate voltage- and ligand-gated ion channels, and differentially influence the induction of synaptic plasticity in the prefrontal cortex, hippocampus, and cerebellum. The findings discussed here may explain how P2Y1 receptor activation during brain injury, hypoxia, inflammation, schizophrenia, or Alzheimer's disease leads to an impairment of cognitive processes. Hence, it is suggested that the blockade of P2Y1 receptors may have therapeutic potential against cognitive disturbances in these states."}],"intvolume":" 2016","month":"01","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"checksum":"8dc5c2f3d44d4775a6e7e3edb0d7a0da","file_id":"4740","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-580-v1+1_1207393.pdf","date_created":"2018-12-12T10:09:17Z","creator":"system","file_size":1395180,"date_updated":"2020-07-14T12:44:54Z"}],"publication_status":"published","volume":2016,"article_number":"1207393","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"J. Guzmán and Z. Gerevich, “P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction,” Neural Plasticity, vol. 2016. Hindawi Publishing Corporation, 2016.","short":"J. Guzmán, Z. Gerevich, Neural Plasticity 2016 (2016).","apa":"Guzmán, J., & Gerevich, Z. (2016). P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. Neural Plasticity. Hindawi Publishing Corporation. https://doi.org/10.1155/2016/1207393","ama":"Guzmán J, Gerevich Z. P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. Neural Plasticity. 2016;2016. doi:10.1155/2016/1207393","mla":"Guzmán, José, and Zoltan Gerevich. “P2Y Receptors in Synaptic Transmission and Plasticity: Therapeutic Potential in Cognitive Dysfunction.” Neural Plasticity, vol. 2016, 1207393, Hindawi Publishing Corporation, 2016, doi:10.1155/2016/1207393.","ista":"Guzmán J, Gerevich Z. 2016. P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. Neural Plasticity. 2016, 1207393.","chicago":"Guzmán, José, and Zoltan Gerevich. “P2Y Receptors in Synaptic Transmission and Plasticity: Therapeutic Potential in Cognitive Dysfunction.” Neural Plasticity. Hindawi Publishing Corporation, 2016. https://doi.org/10.1155/2016/1207393."},"title":"P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction","publist_id":"5762","author":[{"id":"30CC5506-F248-11E8-B48F-1D18A9856A87","first_name":"José","full_name":"Guzmán, José","last_name":"Guzmán"},{"full_name":"Gerevich, Zoltan","last_name":"Gerevich","first_name":"Zoltan"}],"oa":1,"publisher":"Hindawi Publishing Corporation","quality_controlled":"1","publication":"Neural Plasticity","day":"01","year":"2016","has_accepted_license":"1","date_created":"2018-12-11T11:52:00Z","date_published":"2016-01-01T00:00:00Z","doi":"10.1155/2016/1207393"},{"month":"01","main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-01251199/"}],"scopus_import":1,"alternative_title":["ACM SIGPLAN Notices"],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Fault-tolerant distributed algorithms play an important role in many critical/high-availability applications. These algorithms are notoriously difficult to implement correctly, due to asynchronous communication and the occurrence of faults, such as the network dropping messages or computers crashing. We introduce PSYNC, a domain specific language based on the Heard-Of model, which views asynchronous faulty systems as synchronous ones with an adversarial environment that simulates asynchrony and faults by dropping messages. We define a runtime system for PSYNC that efficiently executes on asynchronous networks. We formalize the relation between the runtime system and PSYNC in terms of observational refinement. The high-level lockstep abstraction introduced by PSYNC simplifies the design and implementation of fault-tolerant distributed algorithms and enables automated formal verification. We have implemented an embedding of PSYNC in the SCALA programming language with a runtime system for asynchronous networks. We show the applicability of PSYNC by implementing several important fault-tolerant distributed algorithms and we compare the implementation of consensus algorithms in PSYNC against implementations in other languages in terms of code size, runtime efficiency, and verification."}],"ec_funded":1,"volume":"20-22","language":[{"iso":"eng"}],"publication_status":"published","status":"public","conference":{"end_date":"2016-01-22","location":"St. Petersburg, FL, USA","start_date":"2016-01-20","name":"POPL: Principles of Programming Languages"},"type":"conference","_id":"1439","department":[{"_id":"ToHe"}],"date_updated":"2021-01-12T06:50:45Z","oa":1,"quality_controlled":"1","publisher":"ACM","acknowledgement":"Damien Zufferey was supported by DARPA (Grants FA8650-11-C-7192 and FA8650-15-C-7564) and NSF (Grant CCF-1138967). ","date_created":"2018-12-11T11:52:01Z","date_published":"2016-01-11T00:00:00Z","doi":"10.1145/2837614.2837650","page":"400 - 415","day":"11","year":"2016","project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"title":"PSYNC: A partially synchronous language for fault-tolerant distributed algorithms","author":[{"id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","first_name":"Cezara","full_name":"Dragoi, Cezara","last_name":"Dragoi"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"last_name":"Zufferey","full_name":"Zufferey, Damien","orcid":"0000-0002-3197-8736","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","first_name":"Damien"}],"publist_id":"5759","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Dragoi, C., Henzinger, T. A., & Zufferey, D. (2016). PSYNC: A partially synchronous language for fault-tolerant distributed algorithms (Vol. 20–22, pp. 400–415). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. https://doi.org/10.1145/2837614.2837650","ama":"Dragoi C, Henzinger TA, Zufferey D. PSYNC: A partially synchronous language for fault-tolerant distributed algorithms. In: Vol 20-22. ACM; 2016:400-415. doi:10.1145/2837614.2837650","ieee":"C. Dragoi, T. A. Henzinger, and D. Zufferey, “PSYNC: A partially synchronous language for fault-tolerant distributed algorithms,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 400–415.","short":"C. Dragoi, T.A. Henzinger, D. Zufferey, in:, ACM, 2016, pp. 400–415.","mla":"Dragoi, Cezara, et al. PSYNC: A Partially Synchronous Language for Fault-Tolerant Distributed Algorithms. Vol. 20–22, ACM, 2016, pp. 400–15, doi:10.1145/2837614.2837650.","ista":"Dragoi C, Henzinger TA, Zufferey D. 2016. PSYNC: A partially synchronous language for fault-tolerant distributed algorithms. POPL: Principles of Programming Languages, ACM SIGPLAN Notices, vol. 20–22, 400–415.","chicago":"Dragoi, Cezara, Thomas A Henzinger, and Damien Zufferey. “PSYNC: A Partially Synchronous Language for Fault-Tolerant Distributed Algorithms,” 20–22:400–415. ACM, 2016. https://doi.org/10.1145/2837614.2837650."}},{"year":"2016","has_accepted_license":"1","publication":"Scientometrics","day":"01","page":"213 - 232","date_created":"2018-12-11T11:52:04Z","doi":"10.1007/s11192-016-1842-4","date_published":"2016-04-01T00:00:00Z","oa":1,"publisher":"Springer","quality_controlled":"1","citation":{"mla":"Calatrava Moreno, Maria, et al. “On the Uncertainty of Interdisciplinarity Measurements Due to Incomplete Bibliographic Data.” Scientometrics, vol. 107, no. 1, Springer, 2016, pp. 213–32, doi:10.1007/s11192-016-1842-4.","ieee":"M. Calatrava Moreno, T. Auzinger, and H. Werthner, “On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data,” Scientometrics, vol. 107, no. 1. Springer, pp. 213–232, 2016.","short":"M. Calatrava Moreno, T. Auzinger, H. Werthner, Scientometrics 107 (2016) 213–232.","apa":"Calatrava Moreno, M., Auzinger, T., & Werthner, H. (2016). On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data. Scientometrics. Springer. https://doi.org/10.1007/s11192-016-1842-4","ama":"Calatrava Moreno M, Auzinger T, Werthner H. On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data. Scientometrics. 2016;107(1):213-232. doi:10.1007/s11192-016-1842-4","chicago":"Calatrava Moreno, Maria, Thomas Auzinger, and Hannes Werthner. “On the Uncertainty of Interdisciplinarity Measurements Due to Incomplete Bibliographic Data.” Scientometrics. Springer, 2016. https://doi.org/10.1007/s11192-016-1842-4.","ista":"Calatrava Moreno M, Auzinger T, Werthner H. 2016. On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data. Scientometrics. 107(1), 213–232."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","author":[{"first_name":"Maria","last_name":"Calatrava Moreno","full_name":"Calatrava Moreno, Maria"},{"full_name":"Auzinger, Thomas","orcid":"0000-0002-1546-3265","last_name":"Auzinger","id":"4718F954-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"full_name":"Werthner, Hannes","last_name":"Werthner","first_name":"Hannes"}],"publist_id":"5750","title":"On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data","publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_id":"4848","checksum":"32d46268588b87d9b686492018e6a2b2","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:10:56Z","file_name":"IST-2016-530-v1+1_s11192-016-1842-4.pdf","creator":"system","date_updated":"2020-07-14T12:44:55Z","file_size":806035}],"issue":"1","volume":107,"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1007/s11192-016-1902-9"}]},"abstract":[{"lang":"eng","text":"The accuracy of interdisciplinarity measurements is directly related to the quality of the underlying bibliographic data. Existing indicators of interdisciplinarity are not capable of reflecting the inaccuracies introduced by incorrect and incomplete records because correct and complete bibliographic data can rarely be obtained. This is the case for the Rao–Stirling index, which cannot handle references that are not categorized into disciplinary fields. We introduce a method that addresses this problem. It extends the Rao–Stirling index to acknowledge missing data by calculating its interval of uncertainty using computational optimization. The evaluation of our method indicates that the uncertainty interval is not only useful for estimating the inaccuracy of interdisciplinarity measurements, but it also delivers slightly more accurate aggregated interdisciplinarity measurements than the Rao–Stirling index."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 107","month":"04","date_updated":"2021-11-16T08:29:11Z","ddc":["000"],"department":[{"_id":"BeBi"}],"file_date_updated":"2020-07-14T12:44:55Z","_id":"1446","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"530","status":"public"},{"_id":"1448","type":"journal_article","status":"public","date_updated":"2021-01-12T06:50:49Z","department":[{"_id":"JaMa"}],"abstract":[{"lang":"eng","text":"We develop a new and systematic method for proving entropic Ricci curvature lower bounds for Markov chains on discrete sets. Using different methods, such bounds have recently been obtained in several examples (e.g., 1-dimensional birth and death chains, product chains, Bernoulli–Laplace models, and random transposition models). However, a general method to obtain discrete Ricci bounds had been lacking. Our method covers all of the examples above. In addition we obtain new Ricci curvature bounds for zero-range processes on the complete graph. The method is inspired by recent work of Caputo, Dai Pra and Posta on discrete functional inequalities."}],"oa_version":"Preprint","main_file_link":[{"url":"http://arxiv.org/abs/1501.00562","open_access":"1"}],"scopus_import":1,"intvolume":" 26","month":"06","publication_status":"published","language":[{"iso":"eng"}],"issue":"3","volume":26,"citation":{"mla":"Fathi, Max, and Jan Maas. “Entropic Ricci Curvature Bounds for Discrete Interacting Systems.” The Annals of Applied Probability, vol. 26, no. 3, Institute of Mathematical Statistics, 2016, pp. 1774–806, doi:10.1214/15-AAP1133.","apa":"Fathi, M., & Maas, J. (2016). Entropic Ricci curvature bounds for discrete interacting systems. The Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/15-AAP1133","ama":"Fathi M, Maas J. Entropic Ricci curvature bounds for discrete interacting systems. The Annals of Applied Probability. 2016;26(3):1774-1806. doi:10.1214/15-AAP1133","short":"M. Fathi, J. Maas, The Annals of Applied Probability 26 (2016) 1774–1806.","ieee":"M. Fathi and J. Maas, “Entropic Ricci curvature bounds for discrete interacting systems,” The Annals of Applied Probability, vol. 26, no. 3. Institute of Mathematical Statistics, pp. 1774–1806, 2016.","chicago":"Fathi, Max, and Jan Maas. “Entropic Ricci Curvature Bounds for Discrete Interacting Systems.” The Annals of Applied Probability. Institute of Mathematical Statistics, 2016. https://doi.org/10.1214/15-AAP1133.","ista":"Fathi M, Maas J. 2016. Entropic Ricci curvature bounds for discrete interacting systems. The Annals of Applied Probability. 26(3), 1774–1806."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5748","author":[{"last_name":"Fathi","full_name":"Fathi, Max","first_name":"Max"},{"first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338"}],"title":"Entropic Ricci curvature bounds for discrete interacting systems","acknowledgement":"Supported by the German Research Foundation through the Collaborative Research Center 1060\r\nThe Mathematics of Emergent Effects and the Hausdorff Center for Mathematics. Part of this work has been done while M. Fathi visited J. Maas at the University of Bonn in July 2014.We would like to thank the referees for their careful reading of the manuscript. ","oa":1,"quality_controlled":"1","publisher":"Institute of Mathematical Statistics","year":"2016","publication":"The Annals of Applied Probability","day":"01","page":"1774 - 1806","date_created":"2018-12-11T11:52:05Z","doi":"10.1214/15-AAP1133","date_published":"2016-06-01T00:00:00Z"},{"page":"367 - 379","date_published":"2016-01-15T00:00:00Z","doi":"10.1242/jcs.176651","date_created":"2018-12-11T11:52:14Z","has_accepted_license":"1","year":"2016","day":"15","publication":"Journal of Cell Science","publisher":"Company of Biologists","quality_controlled":"1","oa":1,"acknowledgement":"We are grateful to Anthony Bretscher (Cornell University, NY) for providing the bni1-12 bnr1Δ (Y4135) strain. J.Y.T. was supported by a Japan Society for the Promotion of Science (JSPS) KAKENHI grant [grant number 26440067]; the Takeda Science Foundation; and the Novartis Foundation (Japan). J.T. was supported by a JSPS KAKENHI grant [grant number 25440054]; the Takeda Science Foundation; and the Kurata Memorial Hitachi Science and Technology Foundation. D.E.S. was supported by the European Union [grant number PCIG12-GA-2012-334077].","publist_id":"5720","author":[{"full_name":"Toshima, Junko","last_name":"Toshima","first_name":"Junko"},{"full_name":"Horikomi, Chika","last_name":"Horikomi","first_name":"Chika"},{"last_name":"Okada","full_name":"Okada, Asuka","first_name":"Asuka"},{"first_name":"Makiko","full_name":"Hatori, Makiko","last_name":"Hatori"},{"last_name":"Nagano","full_name":"Nagano, Makoto","first_name":"Makoto"},{"last_name":"Masuda","full_name":"Masuda, Atsushi","first_name":"Atsushi"},{"first_name":"Wataru","full_name":"Yamamoto, Wataru","last_name":"Yamamoto"},{"last_name":"Siekhaus","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E"},{"last_name":"Toshima","full_name":"Toshima, Jiro","first_name":"Jiro"}],"title":"Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis","citation":{"ista":"Toshima J, Horikomi C, Okada A, Hatori M, Nagano M, Masuda A, Yamamoto W, Siekhaus DE, Toshima J. 2016. Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis. Journal of Cell Science. 129(2), 367–379.","chicago":"Toshima, Junko, Chika Horikomi, Asuka Okada, Makiko Hatori, Makoto Nagano, Atsushi Masuda, Wataru Yamamoto, Daria E Siekhaus, and Jiro Toshima. “Srv2/CAP Is Required for Polarized Actin Cable Assembly and Patch Internalization during Clathrin-Mediated Endocytosis.” Journal of Cell Science. Company of Biologists, 2016. https://doi.org/10.1242/jcs.176651.","short":"J. Toshima, C. Horikomi, A. Okada, M. Hatori, M. Nagano, A. Masuda, W. Yamamoto, D.E. Siekhaus, J. Toshima, Journal of Cell Science 129 (2016) 367–379.","ieee":"J. Toshima et al., “Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis,” Journal of Cell Science, vol. 129, no. 2. Company of Biologists, pp. 367–379, 2016.","ama":"Toshima J, Horikomi C, Okada A, et al. Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis. Journal of Cell Science. 2016;129(2):367-379. doi:10.1242/jcs.176651","apa":"Toshima, J., Horikomi, C., Okada, A., Hatori, M., Nagano, M., Masuda, A., … Toshima, J. (2016). Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.176651","mla":"Toshima, Junko, et al. “Srv2/CAP Is Required for Polarized Actin Cable Assembly and Patch Internalization during Clathrin-Mediated Endocytosis.” Journal of Cell Science, vol. 129, no. 2, Company of Biologists, 2016, pp. 367–79, doi:10.1242/jcs.176651."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"2536F660-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Investigating the role of transporters in invasive migration through junctions","grant_number":"334077"}],"volume":129,"issue":"2","ec_funded":1,"publication_status":"published","file":[{"creator":"system","date_updated":"2020-07-14T12:44:56Z","file_size":7176912,"date_created":"2018-12-12T10:11:08Z","file_name":"IST-2017-767-v1+1_367.full.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"4861","checksum":"2da0a09149a9ed956cdf79a95c17f08a"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"01","intvolume":" 129","abstract":[{"text":"The dynamic assembly and disassembly of actin filaments is essential for the formation and transport of vesicles during endocytosis. In yeast, two types of actin structures, namely cortical patches and cytoplasmic cables, play a direct role in endocytosis, but how their interaction is regulated remains unclear. Here, we show that Srv2/CAP, an evolutionarily conserved actin regulator, is required for efficient endocytosis owing to its role in the formation of the actin patches that aid initial vesicle invagination and of the actin cables that these move along. Deletion of the SRV2 gene resulted in the appearance of aberrant fragmented actin cables that frequently moved past actin patches, the sites of endocytosis. We find that the C-terminal CARP domain of Srv2p is vitally important for the proper assembly of actin patches and cables; we also demonstrate that the N-terminal helical folded domain of Srv2 is required for its localization to actin patches, specifically to the ADP-actin rich region through an interaction with cofilin. These results demonstrate the in vivo roles of Srv2p in the regulation of the actin cytoskeleton during clathrin-mediated endocytosis","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"DaSi"}],"file_date_updated":"2020-07-14T12:44:56Z","date_updated":"2021-01-12T06:51:00Z","ddc":["570","576"],"type":"journal_article","status":"public","pubrep_id":"767","_id":"1476"},{"oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","publication":"eLife","day":"25","year":"2016","has_accepted_license":"1","date_created":"2018-12-11T11:52:14Z","date_published":"2016-02-25T00:00:00Z","doi":"10.7554/eLife.10276","article_number":"e10276","project":[{"grant_number":"334077","name":"Investigating the role of transporters in invasive migration through junctions","call_identifier":"FP7","_id":"2536F660-B435-11E9-9278-68D0E5697425"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Toshima J, Furuya E, Nagano M, Kanno C, Sakamoto Y, Ebihara M, Siekhaus DE, Toshima J. 2016. Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton. eLife. 5(February 2016), e10276.","chicago":"Toshima, Junko, Eri Furuya, Makoto Nagano, Chisa Kanno, Yuta Sakamoto, Masashi Ebihara, Daria E Siekhaus, and Jiro Toshima. “Yeast Eps15-like Endocytic Protein Pan1p Regulates the Interaction between Endocytic Vesicles, Endosomes and the Actin Cytoskeleton.” ELife. eLife Sciences Publications, 2016. https://doi.org/10.7554/eLife.10276.","apa":"Toshima, J., Furuya, E., Nagano, M., Kanno, C., Sakamoto, Y., Ebihara, M., … Toshima, J. (2016). Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.10276","ama":"Toshima J, Furuya E, Nagano M, et al. Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton. eLife. 2016;5(February 2016). doi:10.7554/eLife.10276","short":"J. Toshima, E. Furuya, M. Nagano, C. Kanno, Y. Sakamoto, M. Ebihara, D.E. Siekhaus, J. Toshima, ELife 5 (2016).","ieee":"J. Toshima et al., “Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton,” eLife, vol. 5, no. February 2016. eLife Sciences Publications, 2016.","mla":"Toshima, Junko, et al. “Yeast Eps15-like Endocytic Protein Pan1p Regulates the Interaction between Endocytic Vesicles, Endosomes and the Actin Cytoskeleton.” ELife, vol. 5, no. February 2016, e10276, eLife Sciences Publications, 2016, doi:10.7554/eLife.10276."},"title":"Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton","author":[{"last_name":"Toshima","full_name":"Toshima, Junko","first_name":"Junko"},{"last_name":"Furuya","full_name":"Furuya, Eri","first_name":"Eri"},{"full_name":"Nagano, Makoto","last_name":"Nagano","first_name":"Makoto"},{"first_name":"Chisa","last_name":"Kanno","full_name":"Kanno, Chisa"},{"last_name":"Sakamoto","full_name":"Sakamoto, Yuta","first_name":"Yuta"},{"first_name":"Masashi","last_name":"Ebihara","full_name":"Ebihara, Masashi"},{"last_name":"Siekhaus","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Toshima, Jiro","last_name":"Toshima","first_name":"Jiro"}],"publist_id":"5721","oa_version":"Published Version","abstract":[{"text":"The actin cytoskeleton plays important roles in the formation and internalization of endocytic vesicles. In yeast, endocytic vesicles move towards early endosomes along actin cables, however, the molecular machinery regulating interaction between endocytic vesicles and actin cables is poorly understood. The Eps15-like protein Pan1p plays a key role in actin-mediated endocytosis and is negatively regulated by Ark1 and Prk1 kinases. Here we show that pan1 mutated to prevent phosphorylation at all 18 threonines, pan1-18TA, displayed almost the same endocytic defect as ark1Δ prk1Δ cells, and contained abnormal actin concentrations including several endocytic compartments. Early endosomes were highly localized in the actin concentrations and displayed movement along actin cables. The dephosphorylated form of Pan1p also caused stable associations between endocytic vesicles and actin cables, and between endocytic vesicles and endosomes. Thus Pan1 phosphorylation is part of a novel mechanism that regulates endocytic compartment interactions with each other and with actin cables.","lang":"eng"}],"intvolume":" 5","month":"02","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"file_id":"4793","checksum":"d1cc44870580756ba8badd8e41adfdb5","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2016-529-v1+1_elife-10276-v1.pdf","date_created":"2018-12-12T10:10:08Z","file_size":5198001,"date_updated":"2020-07-14T12:44:56Z","creator":"system"}],"publication_status":"published","ec_funded":1,"issue":"February 2016","volume":5,"_id":"1475","pubrep_id":"529","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["570"],"date_updated":"2021-01-12T06:50:59Z","department":[{"_id":"DaSi"}],"file_date_updated":"2020-07-14T12:44:56Z"},{"publisher":"IOP Publishing Ltd.","quality_controlled":"1","oa":1,"date_published":"2016-02-29T00:00:00Z","doi":"10.1088/1367-2630/18/3/035002","date_created":"2018-12-11T11:52:15Z","day":"29","publication":"New Journal of Physics","has_accepted_license":"1","year":"2016","project":[{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"article_number":"035002","title":"Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas","publist_id":"5716","author":[{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Warzel, Simone","last_name":"Warzel","first_name":"Simone"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Seiringer, Robert, and Simone Warzel. “Decay of Correlations and Absence of Superfluidity in the Disordered Tonks-Girardeau Gas.” New Journal of Physics. IOP Publishing Ltd., 2016. https://doi.org/10.1088/1367-2630/18/3/035002.","ista":"Seiringer R, Warzel S. 2016. Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas. New Journal of Physics. 18(3), 035002.","mla":"Seiringer, Robert, and Simone Warzel. “Decay of Correlations and Absence of Superfluidity in the Disordered Tonks-Girardeau Gas.” New Journal of Physics, vol. 18, no. 3, 035002, IOP Publishing Ltd., 2016, doi:10.1088/1367-2630/18/3/035002.","apa":"Seiringer, R., & Warzel, S. (2016). Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas. New Journal of Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/18/3/035002","ama":"Seiringer R, Warzel S. Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas. New Journal of Physics. 2016;18(3). doi:10.1088/1367-2630/18/3/035002","short":"R. Seiringer, S. Warzel, New Journal of Physics 18 (2016).","ieee":"R. Seiringer and S. Warzel, “Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas,” New Journal of Physics, vol. 18, no. 3. IOP Publishing Ltd., 2016."},"month":"02","intvolume":" 18","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We consider the Tonks-Girardeau gas subject to a random external potential. If the disorder is such that the underlying one-particle Hamiltonian displays localization (which is known to be generically the case), we show that there is exponential decay of correlations in the many-body eigenstates. Moreover, there is no Bose-Einstein condensation and no superfluidity, even at zero temperature."}],"volume":18,"issue":"3","file":[{"date_created":"2018-12-12T10:17:22Z","file_name":"IST-2016-579-v1+1_njp_18_3_035002.pdf","date_updated":"2020-07-14T12:44:56Z","file_size":965607,"creator":"system","file_id":"5276","checksum":"4f959eabc19d2a2f518318a450a4d424","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_status":"published","status":"public","pubrep_id":"579","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":"1478","file_date_updated":"2020-07-14T12:44:56Z","department":[{"_id":"RoSe"}],"ddc":["510","530"],"date_updated":"2021-01-12T06:51:01Z"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Michałek M, Sturmfels B, Uhler C, Zwiernik P. 2016. Exponential varieties. Proceedings of the London Mathematical Society. 112(1), 27–56.","chicago":"Michałek, Mateusz, Bernd Sturmfels, Caroline Uhler, and Piotr Zwiernik. “Exponential Varieties.” Proceedings of the London Mathematical Society. Oxford University Press, 2016. https://doi.org/10.1112/plms/pdv066.","ieee":"M. Michałek, B. Sturmfels, C. Uhler, and P. Zwiernik, “Exponential varieties,” Proceedings of the London Mathematical Society, vol. 112, no. 1. Oxford University Press, pp. 27–56, 2016.","short":"M. Michałek, B. Sturmfels, C. Uhler, P. Zwiernik, Proceedings of the London Mathematical Society 112 (2016) 27–56.","ama":"Michałek M, Sturmfels B, Uhler C, Zwiernik P. Exponential varieties. Proceedings of the London Mathematical Society. 2016;112(1):27-56. doi:10.1112/plms/pdv066","apa":"Michałek, M., Sturmfels, B., Uhler, C., & Zwiernik, P. (2016). Exponential varieties. Proceedings of the London Mathematical Society. Oxford University Press. https://doi.org/10.1112/plms/pdv066","mla":"Michałek, Mateusz, et al. “Exponential Varieties.” Proceedings of the London Mathematical Society, vol. 112, no. 1, Oxford University Press, 2016, pp. 27–56, doi:10.1112/plms/pdv066."},"date_updated":"2021-01-12T06:51:02Z","department":[{"_id":"CaUh"}],"title":"Exponential varieties","author":[{"full_name":"Michałek, Mateusz","last_name":"Michałek","first_name":"Mateusz"},{"first_name":"Bernd","last_name":"Sturmfels","full_name":"Sturmfels, Bernd"},{"full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","last_name":"Uhler","first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zwiernik","full_name":"Zwiernik, Piotr","first_name":"Piotr"}],"publist_id":"5714","_id":"1480","status":"public","type":"journal_article","publication":"Proceedings of the London Mathematical Society","language":[{"iso":"eng"}],"day":"07","year":"2016","publication_status":"published","date_created":"2018-12-11T11:52:16Z","doi":"10.1112/plms/pdv066","volume":112,"date_published":"2016-01-07T00:00:00Z","issue":"1","page":"27 - 56","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Exponential varieties arise from exponential families in statistics. These real algebraic varieties have strong positivity and convexity properties, familiar from toric varieties and their moment maps. Among them are varieties of inverses of symmetric matrices satisfying linear constraints. This class includes Gaussian graphical models. We develop a general theory of exponential varieties. These are derived from hyperbolic polynomials and their integral representations. We compare the multidegrees and ML degrees of the gradient map for hyperbolic polynomials. "}],"intvolume":" 112","month":"01","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1412.6185"}],"oa":1,"publisher":"Oxford University Press","scopus_import":1,"quality_controlled":"1"},{"file_date_updated":"2020-07-14T12:44:57Z","department":[{"_id":"JoCs"}],"date_updated":"2021-01-12T06:51:05Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"518","status":"public","_id":"1487","issue":"2","volume":14,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"checksum":"3a5ce0d4e4e36bd6ceb4be761f85644a","file_id":"5129","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:15:11Z","file_name":"IST-2016-518-v1+1_journal.pbio.1002384.PDF","creator":"system","date_updated":"2020-07-14T12:44:57Z","file_size":2879899}],"scopus_import":1,"intvolume":" 14","month":"02","abstract":[{"text":"Rhythms with time scales of multiple cycles per second permeate the mammalian brain, yet neuroscientists are not certain of their functional roles. One leading idea is that coherent oscillation between two brain regions facilitates the exchange of information between them. In rats, the hippocampus and the vibrissal sensorimotor system both are characterized by rhythmic oscillation in the theta range, 5–12 Hz. Previous work has been divided as to whether the two rhythms are independent or coherent. To resolve this question, we acquired three measures from rats—whisker motion, hippocampal local field potential (LFP), and barrel cortex unit firing—during a whisker-mediated texture discrimination task and during control conditions (not engaged in a whisker-mediated memory task). Compared to control conditions, the theta band of hippocampal LFP showed a marked increase in power as the rats approached and then palpated the texture. Phase synchronization between whisking and hippocampal LFP increased by almost 50% during approach and texture palpation. In addition, a greater proportion of barrel cortex neurons showed firing that was phase-locked to hippocampal theta while rats were engaged in the discrimination task. Consistent with a behavioral consequence of phase synchronization, the rats identified the texture more rapidly and with lower error likelihood on trials in which there was an increase in theta-whisking coherence at the moment of texture palpation. These results suggest that coherence between the whisking rhythm, barrel cortex firing, and hippocampal LFP is augmented selectively during epochs in which the rat collects sensory information and that such coherence enhances the efficiency of integration of stimulus information into memory and decision-making centers.","lang":"eng"}],"oa_version":"Published Version","publist_id":"5700","author":[{"last_name":"Grion","full_name":"Grion, Natalia","first_name":"Natalia"},{"last_name":"Akrami","full_name":"Akrami, Athena","first_name":"Athena"},{"first_name":"Yangfang","last_name":"Zuo","full_name":"Zuo, Yangfang"},{"id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","first_name":"Federico","orcid":"0000-0001-9439-3148","full_name":"Stella, Federico","last_name":"Stella"},{"first_name":"Mathew","full_name":"Diamond, Mathew","last_name":"Diamond"}],"title":"Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination","citation":{"chicago":"Grion, Natalia, Athena Akrami, Yangfang Zuo, Federico Stella, and Mathew Diamond. “Coherence between Rat Sensorimotor System and Hippocampus Is Enhanced during Tactile Discrimination.” PLoS Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.1002384.","ista":"Grion N, Akrami A, Zuo Y, Stella F, Diamond M. 2016. Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination. PLoS Biology. 14(2), e1002384.","mla":"Grion, Natalia, et al. “Coherence between Rat Sensorimotor System and Hippocampus Is Enhanced during Tactile Discrimination.” PLoS Biology, vol. 14, no. 2, e1002384, Public Library of Science, 2016, doi:10.1371/journal.pbio.1002384.","apa":"Grion, N., Akrami, A., Zuo, Y., Stella, F., & Diamond, M. (2016). Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002384","ama":"Grion N, Akrami A, Zuo Y, Stella F, Diamond M. Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination. PLoS Biology. 2016;14(2). doi:10.1371/journal.pbio.1002384","short":"N. Grion, A. Akrami, Y. Zuo, F. Stella, M. Diamond, PLoS Biology 14 (2016).","ieee":"N. Grion, A. Akrami, Y. Zuo, F. Stella, and M. Diamond, “Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination,” PLoS Biology, vol. 14, no. 2. Public Library of Science, 2016."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_number":"e1002384","date_created":"2018-12-11T11:52:18Z","date_published":"2016-02-18T00:00:00Z","doi":"10.1371/journal.pbio.1002384","year":"2016","has_accepted_license":"1","publication":"PLoS Biology","day":"18","oa":1,"quality_controlled":"1","publisher":"Public Library of Science","acknowledgement":"We thank Eric Maris, Demian Battaglia, and Rodrigo Quian Quiroga for useful discussions. We are grateful to Fabrizio Manzino and Marco Gigante for construction of the behavioral apparatus, Igor Perkon for developing custom whisker tracking software and to Francesca Pulecchi for animal care and histological processing."},{"status":"public","pubrep_id":"521","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":"1482","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:44:57Z","ddc":["570"],"date_updated":"2021-01-12T06:51:03Z","month":"02","intvolume":" 11","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Plants have the ability to continously generate new organs by maintaining populations of stem cells throught their lives. The shoot apical meristem (SAM) provides a stable environment for the maintenance of stem cells. All cells inside the SAM divide, yet boundaries and patterns are maintained. Experimental evidence indicates that patterning is independent of cell lineage, thus a dynamic self-regulatory mechanism is required. A pivotal role in the organization of the SAM is played by the WUSCHEL gene (WUS). An important question in this regard is that how WUS expression is positioned in the SAM via a cell-lineage independent signaling mechanism. In this study we demonstrate via mathematical modeling that a combination of an inhibitor of the Cytokinin (CK) receptor, Arabidopsis histidine kinase 4 (AHK4) and two morphogens originating from the top cell layer, can plausibly account for the cell lineage-independent centering of WUS expression within SAM. Furthermore, our laser ablation and microsurgical experiments support the hypothesis that patterning in SAM occurs at the level of CK reception and signaling. The model suggests that the interplay between CK signaling, WUS/CLV feedback loop and boundary signals can account for positioning of the WUS expression, and provides directions for further experimental investigation."}],"volume":11,"issue":"2","file":[{"date_updated":"2020-07-14T12:44:57Z","file_size":4297148,"creator":"system","date_created":"2018-12-12T10:14:16Z","file_name":"IST-2016-521-v1+1_journal.pone.0147830.PDF","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"6066146e527335030f83aa5924ab72a6","file_id":"5066"}],"language":[{"iso":"eng"}],"publication_status":"published","article_number":"e0147830","title":"Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization","author":[{"first_name":"Milad","last_name":"Adibi","full_name":"Adibi, Milad"},{"id":"2E46069C-F248-11E8-B48F-1D18A9856A87","first_name":"Saiko","last_name":"Yoshida","full_name":"Yoshida, Saiko"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"first_name":"Christian","full_name":"Fleck, Christian","last_name":"Fleck"}],"publist_id":"5711","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Adibi M, Yoshida S, Weijers D, Fleck C. Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. PLoS One. 2016;11(2). doi:10.1371/journal.pone.0147830","apa":"Adibi, M., Yoshida, S., Weijers, D., & Fleck, C. (2016). Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0147830","short":"M. Adibi, S. Yoshida, D. Weijers, C. Fleck, PLoS One 11 (2016).","ieee":"M. Adibi, S. Yoshida, D. Weijers, and C. Fleck, “Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization,” PLoS One, vol. 11, no. 2. Public Library of Science, 2016.","mla":"Adibi, Milad, et al. “Centering the Organizing Center in the Arabidopsis Thaliana Shoot Apical Meristem by a Combination of Cytokinin Signaling and Self-Organization.” PLoS One, vol. 11, no. 2, e0147830, Public Library of Science, 2016, doi:10.1371/journal.pone.0147830.","ista":"Adibi M, Yoshida S, Weijers D, Fleck C. 2016. Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. PLoS One. 11(2), e0147830.","chicago":"Adibi, Milad, Saiko Yoshida, Dolf Weijers, and Christian Fleck. “Centering the Organizing Center in the Arabidopsis Thaliana Shoot Apical Meristem by a Combination of Cytokinin Signaling and Self-Organization.” PLoS One. Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0147830."},"publisher":"Public Library of Science","quality_controlled":"1","oa":1,"acknowledgement":"We thank J. Traas, B. Müller and V. Reddy for providing seed materials and Y. Deb for advice regarding the laser ablation experiments. We specially thank Thomas Laux for stimulating discussions and support in the initial phase of this project.","doi":"10.1371/journal.pone.0147830","date_published":"2016-02-01T00:00:00Z","date_created":"2018-12-11T11:52:17Z","day":"01","publication":"PLoS One","has_accepted_license":"1","year":"2016"},{"scopus_import":1,"intvolume":" 26","month":"06","oa_version":"Submitted Version","volume":26,"issue":"6","publication_status":"published","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"b229e5bb4676ec3e27b7b9ea603b3a63","file_id":"5155","file_size":2329117,"date_updated":"2020-07-14T12:44:57Z","creator":"system","file_name":"IST-2018-1002-v1+1_Chen_TICB_2016_proofs.pdf","date_created":"2018-12-12T10:15:34Z"}],"article_type":"review","type":"journal_article","pubrep_id":"1002","status":"public","_id":"1484","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:44:57Z","date_updated":"2021-01-12T06:51:04Z","ddc":["581"],"oa":1,"publisher":"Cell Press","quality_controlled":"1","acknowledgement":"We thank Maciek Adamowski for helpful discussions and Qiang Zhu and Israel Ausin for critical reading of the manuscript. We sincerely apologize to colleagues whose work we could not include owing to space limitations.","page":"409 - 419","date_created":"2018-12-11T11:52:17Z","doi":"10.1016/j.tcb.2016.02.003","date_published":"2016-06-01T00:00:00Z","year":"2016","has_accepted_license":"1","publication":"Trends in Cell Biology","day":"01","publist_id":"5704","author":[{"first_name":"Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","full_name":"Chen, Xu"},{"full_name":"Wu, Shuang","last_name":"Wu","first_name":"Shuang"},{"last_name":"Liu","full_name":"Liu, Zengyu","first_name":"Zengyu"},{"first_name":"Jiřĺ","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiřĺ","last_name":"Friml"}],"title":"Environmental and endogenous control of cortical microtubule orientation","citation":{"chicago":"Chen, Xu, Shuang Wu, Zengyu Liu, and Jiří Friml. “Environmental and Endogenous Control of Cortical Microtubule Orientation.” Trends in Cell Biology. Cell Press, 2016. https://doi.org/10.1016/j.tcb.2016.02.003.","ista":"Chen X, Wu S, Liu Z, Friml J. 2016. Environmental and endogenous control of cortical microtubule orientation. Trends in Cell Biology. 26(6), 409–419.","mla":"Chen, Xu, et al. “Environmental and Endogenous Control of Cortical Microtubule Orientation.” Trends in Cell Biology, vol. 26, no. 6, Cell Press, 2016, pp. 409–19, doi:10.1016/j.tcb.2016.02.003.","ieee":"X. Chen, S. Wu, Z. Liu, and J. Friml, “Environmental and endogenous control of cortical microtubule orientation,” Trends in Cell Biology, vol. 26, no. 6. Cell Press, pp. 409–419, 2016.","short":"X. Chen, S. Wu, Z. Liu, J. Friml, Trends in Cell Biology 26 (2016) 409–419.","ama":"Chen X, Wu S, Liu Z, Friml J. Environmental and endogenous control of cortical microtubule orientation. Trends in Cell Biology. 2016;26(6):409-419. doi:10.1016/j.tcb.2016.02.003","apa":"Chen, X., Wu, S., Liu, Z., & Friml, J. (2016). Environmental and endogenous control of cortical microtubule orientation. Trends in Cell Biology. Cell Press. https://doi.org/10.1016/j.tcb.2016.02.003"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"article_number":"016003","publist_id":"5702","author":[{"last_name":"De Martino","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87"}],"title":"Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis","citation":{"chicago":"De Martino, Daniele. “Genome-Scale Estimate of the Metabolic Turnover of E. Coli from the Energy Balance Analysis.” Physical Biology. IOP Publishing Ltd., 2016. https://doi.org/10.1088/1478-3975/13/1/016003.","ista":"De Martino D. 2016. Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis. Physical Biology. 13(1), 016003.","mla":"De Martino, Daniele. “Genome-Scale Estimate of the Metabolic Turnover of E. Coli from the Energy Balance Analysis.” Physical Biology, vol. 13, no. 1, 016003, IOP Publishing Ltd., 2016, doi:10.1088/1478-3975/13/1/016003.","short":"D. De Martino, Physical Biology 13 (2016).","ieee":"D. De Martino, “Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis,” Physical Biology, vol. 13, no. 1. IOP Publishing Ltd., 2016.","ama":"De Martino D. Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis. Physical Biology. 2016;13(1). doi:10.1088/1478-3975/13/1/016003","apa":"De Martino, D. (2016). Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis. Physical Biology. IOP Publishing Ltd. https://doi.org/10.1088/1478-3975/13/1/016003"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"IOP Publishing Ltd.","oa":1,"doi":"10.1088/1478-3975/13/1/016003","date_published":"2016-01-29T00:00:00Z","date_created":"2018-12-11T11:52:18Z","year":"2016","day":"29","publication":"Physical Biology","type":"journal_article","status":"public","_id":"1485","department":[{"_id":"GaTk"}],"date_updated":"2021-01-12T06:51:04Z","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1505.04613","open_access":"1"}],"month":"01","intvolume":" 13","abstract":[{"text":"In this article the notion of metabolic turnover is revisited in the light of recent results of out-of-equilibrium thermodynamics. By means of Monte Carlo methods we perform an exact sampling of the enzymatic fluxes in a genome scale metabolic network of E. Coli in stationary growth conditions from which we infer the metabolites turnover times. However the latter are inferred from net fluxes, and we argue that this approximation is not valid for enzymes working nearby thermodynamic equilibrium. We recalculate turnover times from total fluxes by performing an energy balance analysis of the network and recurring to the fluctuation theorem. We find in many cases values one of order of magnitude lower, implying a faster picture of intermediate metabolism.","lang":"eng"}],"oa_version":"Preprint","volume":13,"issue":"1","ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}]},{"status":"public","type":"journal_article","article_number":"021101","_id":"1486","department":[{"_id":"RoSe"}],"title":"The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties","publist_id":"5701","author":[{"last_name":"Hainzl","full_name":"Hainzl, Christian","first_name":"Christian"},{"last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Hainzl, Christian, and Robert Seiringer. “The Bardeen–Cooper–Schrieffer Functional of Superconductivity and Its Mathematical Properties.” Journal of Mathematical Physics. American Institute of Physics, 2016. https://doi.org/10.1063/1.4941723.","ista":"Hainzl C, Seiringer R. 2016. The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties. Journal of Mathematical Physics. 57(2), 021101.","mla":"Hainzl, Christian, and Robert Seiringer. “The Bardeen–Cooper–Schrieffer Functional of Superconductivity and Its Mathematical Properties.” Journal of Mathematical Physics, vol. 57, no. 2, 021101, American Institute of Physics, 2016, doi:10.1063/1.4941723.","ama":"Hainzl C, Seiringer R. The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties. Journal of Mathematical Physics. 2016;57(2). doi:10.1063/1.4941723","apa":"Hainzl, C., & Seiringer, R. (2016). The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4941723","short":"C. Hainzl, R. Seiringer, Journal of Mathematical Physics 57 (2016).","ieee":"C. Hainzl and R. Seiringer, “The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties,” Journal of Mathematical Physics, vol. 57, no. 2. American Institute of Physics, 2016."},"date_updated":"2021-01-12T06:51:04Z","month":"02","intvolume":" 57","quality_controlled":"1","scopus_import":1,"publisher":"American Institute of Physics","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1511.01995"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We review recent results concerning the mathematical properties of the Bardeen-Cooper-Schrieffer (BCS) functional of superconductivity, which were obtained in a series of papers, partly in collaboration with R. Frank, E. Hamza, S. Naboko, and J. P. Solovej. Our discussion includes, in particular, an investigation of the critical temperature for a general class of interaction potentials, as well as a study of its dependence on external fields. We shall explain how the Ginzburg-Landau model can be derived from the BCS theory in a suitable parameter regime."}],"date_published":"2016-02-24T00:00:00Z","volume":57,"doi":"10.1063/1.4941723","issue":"2","date_created":"2018-12-11T11:52:18Z","day":"24","publication":"Journal of Mathematical Physics","language":[{"iso":"eng"}],"publication_status":"published","year":"2016"},{"_id":"1488","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":"517","date_updated":"2023-02-23T10:01:08Z","ddc":["570"],"department":[{"_id":"SiHi"}],"file_date_updated":"2020-07-14T12:44:57Z","abstract":[{"text":"Branching morphogenesis of the epithelial ureteric bud forms the renal collecting duct system and is critical for normal nephron number, while low nephron number is implicated in hypertension and renal disease. Ureteric bud growth and branching requires GDNF signaling from the surrounding mesenchyme to cells at the ureteric bud tips, via the Ret receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling up-regulates transcription factors Etv4 and Etv5, which are also critical for branching. Despite extensive knowledge of the genetic control of these events, it is not understood, at the cellular level, how renal branching morphogenesis is achieved or how Ret signaling influences epithelial cell behaviors to promote this process. Analysis of chimeric embryos previously suggested a role for Ret signaling in promoting cell rearrangements in the nephric duct, but this method was unsuited to study individual cell behaviors during ureteric bud branching. Here, we use Mosaic Analysis with Double Markers (MADM), combined with organ culture and time-lapse imaging, to trace the movements and divisions of individual ureteric bud tip cells. We first examine wild-type clones and then Ret or Etv4 mutant/wild-type clones in which the mutant and wild-type sister cells are differentially and heritably marked by green and red fluorescent proteins. We find that, in normal kidneys, most individual tip cells behave as self-renewing progenitors, some of whose progeny remain at the tips while others populate the growing UB trunks. In Ret or Etv4 MADM clones, the wild-type cells generated at a UB tip are much more likely to remain at, or move to, the new tips during branching and elongation, while their Ret−/− or Etv4−/− sister cells tend to lag behind and contribute only to the trunks. By tracking successive mitoses in a cell lineage, we find that Ret signaling has little effect on proliferation, in contrast to its effects on cell movement. Our results show that Ret/Etv4 signaling promotes directed cell movements in the ureteric bud tips, and suggest a model in which these cell movements mediate branching morphogenesis.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"month":"02","intvolume":" 14","publication_status":"published","file":[{"creator":"system","file_size":5904773,"date_updated":"2020-07-14T12:44:57Z","file_name":"IST-2016-517-v1+1_journal.pbio.1002382_1_.PDF","date_created":"2018-12-12T10:13:42Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"7f8fa1b3a29f94c0a14dd4465278cdbc","file_id":"5027"}],"language":[{"iso":"eng"}],"volume":14,"issue":"2","related_material":{"record":[{"relation":"research_data","id":"9703","status":"deleted"}]},"article_number":"e1002382","citation":{"short":"P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, F. Costantini, PLoS Biology 14 (2016).","ieee":"P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, and F. Costantini, “Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis,” PLoS Biology, vol. 14, no. 2. Public Library of Science, 2016.","ama":"Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. PLoS Biology. 2016;14(2). doi:10.1371/journal.pbio.1002382","apa":"Riccio, P., Cebrián, C., Zong, H., Hippenmeyer, S., & Costantini, F. (2016). Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002382","mla":"Riccio, Paul, et al. “Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis.” PLoS Biology, vol. 14, no. 2, e1002382, Public Library of Science, 2016, doi:10.1371/journal.pbio.1002382.","ista":"Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. 2016. Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. PLoS Biology. 14(2), e1002382.","chicago":"Riccio, Paul, Cristina Cebrián, Hui Zong, Simon Hippenmeyer, and Frank Costantini. “Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis.” PLoS Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.1002382."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Paul","full_name":"Riccio, Paul","last_name":"Riccio"},{"last_name":"Cebrián","full_name":"Cebrián, Cristina","first_name":"Cristina"},{"full_name":"Zong, Hui","last_name":"Zong","first_name":"Hui"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Costantini","full_name":"Costantini, Frank","first_name":"Frank"}],"publist_id":"5699","title":"Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis","acknowledgement":"We thank Silvia Arber, Thomas Jessell, Kenneth M. Murphy, Carlton Bates, Hideki Enomoto, Liqun Luo and Andrew McMahon for mouse strains; Thomas Jessell for antibodies; and Laura Martinez Prat for experimental assistance.","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2016","day":"19","publication":"PLoS Biology","doi":"10.1371/journal.pbio.1002382","date_published":"2016-02-19T00:00:00Z","date_created":"2018-12-11T11:52:19Z"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"516","status":"public","_id":"1489","file_date_updated":"2020-07-14T12:44:57Z","department":[{"_id":"LaEr"}],"date_updated":"2021-01-12T06:51:05Z","ddc":["510"],"scopus_import":1,"intvolume":" 163","month":"04","abstract":[{"text":"We prove optimal local law, bulk universality and non-trivial decay for the off-diagonal elements of the resolvent for a class of translation invariant Gaussian random matrix ensembles with correlated entries. ","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"issue":"2","volume":163,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"creator":"system","file_size":660602,"date_updated":"2020-07-14T12:44:57Z","file_name":"IST-2016-516-v1+1_s10955-016-1479-y.pdf","date_created":"2018-12-12T10:11:16Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"4869","checksum":"7139598dcb1cafbe6866bd2bfd732b33"}],"project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"article_processing_charge":"Yes (via OA deal)","publist_id":"5698","author":[{"id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87","first_name":"Oskari H","last_name":"Ajanki","full_name":"Ajanki, Oskari H"},{"last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297","last_name":"Krüger","first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87"}],"title":"Local spectral statistics of Gaussian matrices with correlated entries","citation":{"ama":"Ajanki OH, Erdös L, Krüger TH. Local spectral statistics of Gaussian matrices with correlated entries. Journal of Statistical Physics. 2016;163(2):280-302. doi:10.1007/s10955-016-1479-y","apa":"Ajanki, O. H., Erdös, L., & Krüger, T. H. (2016). Local spectral statistics of Gaussian matrices with correlated entries. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-016-1479-y","short":"O.H. Ajanki, L. Erdös, T.H. Krüger, Journal of Statistical Physics 163 (2016) 280–302.","ieee":"O. H. Ajanki, L. Erdös, and T. H. Krüger, “Local spectral statistics of Gaussian matrices with correlated entries,” Journal of Statistical Physics, vol. 163, no. 2. Springer, pp. 280–302, 2016.","mla":"Ajanki, Oskari H., et al. “Local Spectral Statistics of Gaussian Matrices with Correlated Entries.” Journal of Statistical Physics, vol. 163, no. 2, Springer, 2016, pp. 280–302, doi:10.1007/s10955-016-1479-y.","ista":"Ajanki OH, Erdös L, Krüger TH. 2016. Local spectral statistics of Gaussian matrices with correlated entries. Journal of Statistical Physics. 163(2), 280–302.","chicago":"Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Local Spectral Statistics of Gaussian Matrices with Correlated Entries.” Journal of Statistical Physics. Springer, 2016. https://doi.org/10.1007/s10955-016-1479-y."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"Springer","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). Oskari H. Ajanki was Partially supported by ERC Advanced Grant RANMAT No. 338804, and SFB-TR 12 Grant of the German Research Council. László Erdős was Partially supported by ERC Advanced Grant RANMAT No. 338804. Torben Krüger was Partially supported by ERC Advanced Grant RANMAT No. 338804, and SFB-TR 12 Grant of the German Research Council.","page":"280 - 302","date_created":"2018-12-11T11:52:19Z","date_published":"2016-04-01T00:00:00Z","doi":"10.1007/s10955-016-1479-y","year":"2016","has_accepted_license":"1","publication":"Journal of Statistical Physics","day":"01"},{"date_published":"2016-02-23T00:00:00Z","doi":"10.1016/j.celrep.2016.01.048","date_created":"2018-12-11T11:52:19Z","page":"1723 - 1734","day":"23","publication":"Cell Reports","has_accepted_license":"1","year":"2016","publisher":"Cell Press","quality_controlled":"1","oa":1,"title":"Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent lymphatic vessels","author":[{"full_name":"Russo, Erica","last_name":"Russo","first_name":"Erica"},{"last_name":"Teijeira","full_name":"Teijeira, Alvaro","first_name":"Alvaro"},{"first_name":"Kari","id":"368EE576-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7829-3518","full_name":"Vaahtomeri, Kari","last_name":"Vaahtomeri"},{"first_name":"Ann","full_name":"Willrodt, Ann","last_name":"Willrodt"},{"last_name":"Bloch","full_name":"Bloch, Joël","first_name":"Joël"},{"full_name":"Nitschké, Maximilian","last_name":"Nitschké","first_name":"Maximilian"},{"first_name":"Laura","full_name":"Santambrogio, Laura","last_name":"Santambrogio"},{"full_name":"Kerjaschki, Dontscho","last_name":"Kerjaschki","first_name":"Dontscho"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"},{"full_name":"Halin, Cornelia","last_name":"Halin","first_name":"Cornelia"}],"publist_id":"5697","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Russo, Erica, et al. “Intralymphatic CCL21 Promotes Tissue Egress of Dendritic Cells through Afferent Lymphatic Vessels.” Cell Reports, vol. 14, no. 7, Cell Press, 2016, pp. 1723–34, doi:10.1016/j.celrep.2016.01.048.","ieee":"E. Russo et al., “Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent lymphatic vessels,” Cell Reports, vol. 14, no. 7. Cell Press, pp. 1723–1734, 2016.","short":"E. Russo, A. Teijeira, K. Vaahtomeri, A. Willrodt, J. Bloch, M. Nitschké, L. Santambrogio, D. Kerjaschki, M.K. Sixt, C. Halin, Cell Reports 14 (2016) 1723–1734.","apa":"Russo, E., Teijeira, A., Vaahtomeri, K., Willrodt, A., Bloch, J., Nitschké, M., … Halin, C. (2016). Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent lymphatic vessels. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2016.01.048","ama":"Russo E, Teijeira A, Vaahtomeri K, et al. Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent lymphatic vessels. Cell Reports. 2016;14(7):1723-1734. doi:10.1016/j.celrep.2016.01.048","chicago":"Russo, Erica, Alvaro Teijeira, Kari Vaahtomeri, Ann Willrodt, Joël Bloch, Maximilian Nitschké, Laura Santambrogio, Dontscho Kerjaschki, Michael K Sixt, and Cornelia Halin. “Intralymphatic CCL21 Promotes Tissue Egress of Dendritic Cells through Afferent Lymphatic Vessels.” Cell Reports. Cell Press, 2016. https://doi.org/10.1016/j.celrep.2016.01.048.","ista":"Russo E, Teijeira A, Vaahtomeri K, Willrodt A, Bloch J, Nitschké M, Santambrogio L, Kerjaschki D, Sixt MK, Halin C. 2016. Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent lymphatic vessels. Cell Reports. 14(7), 1723–1734."},"issue":"7","volume":14,"file":[{"date_created":"2018-12-12T10:12:30Z","file_name":"IST-2016-515-v1+1_1-s2.0-S2211124716300262-main.pdf","creator":"system","date_updated":"2020-07-14T12:44:58Z","file_size":5489897,"file_id":"4948","checksum":"c98c1151d5f1e5ce1643a83d8d7f3c29","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"02","intvolume":" 14","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"To induce adaptive immunity, dendritic cells (DCs) migrate through afferent lymphatic vessels (LVs) to draining lymph nodes (dLNs). This process occurs in several consecutive steps. Upon entry into lymphatic capillaries, DCs first actively crawl into downstream collecting vessels. From there, they are next passively and rapidly transported to the dLN by lymph flow. Here, we describe a role for the chemokine CCL21 in intralymphatic DC crawling. Performing time-lapse imaging in murine skin, we found that blockade of CCL21-but not the absence of lymph flow-completely abolished DC migration from capillaries toward collecting vessels and reduced the ability of intralymphatic DCs to emigrate from skin. Moreover, we found that in vitro low laminar flow established a CCL21 gradient along lymphatic endothelial monolayers, thereby inducing downstream-directed DC migration. These findings reveal a role for intralymphatic CCL21 in promoting DC trafficking to dLNs, through the formation of a flow-induced gradient.","lang":"eng"}],"department":[{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:44:58Z","ddc":["570"],"date_updated":"2021-01-12T06:51:07Z","status":"public","pubrep_id":"515","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"_id":"1490"},{"oa_version":"Published Version","abstract":[{"text":"We introduce a new method for deriving the time-dependent Hartree or Hartree-Fock equations as an effective mean-field dynamics from the microscopic Schrödinger equation for fermionic many-particle systems in quantum mechanics. The method is an adaption of the method used in Pickl (Lett. Math. Phys. 97 (2) 151–164 2011) for bosonic systems to fermionic systems. It is based on a Gronwall type estimate for a suitable measure of distance between the microscopic solution and an antisymmetrized product state. We use this method to treat a new mean-field limit for fermions with long-range interactions in a large volume. Some of our results hold for singular attractive or repulsive interactions. We can also treat Coulomb interaction assuming either a mild singularity cutoff or certain regularity conditions on the solutions to the Hartree(-Fock) equations. In the considered limit, the kinetic and interaction energy are of the same order, while the average force is subleading. For some interactions, we prove that the Hartree(-Fock) dynamics is a more accurate approximation than a simpler dynamics that one would expect from the subleading force. With our method we also treat the mean-field limit coupled to a semiclassical limit, which was discussed in the literature before, and we recover some of the previous results. All results hold for initial data close (but not necessarily equal) to antisymmetrized product states and we always provide explicit rates of convergence.","lang":"eng"}],"month":"03","intvolume":" 19","scopus_import":1,"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"eb5d2145ef0d377c4f78bf06e18f4529","file_id":"5246","creator":"system","file_size":911310,"date_updated":"2020-07-14T12:44:58Z","file_name":"IST-2016-514-v1+1_s11040-016-9204-2.pdf","date_created":"2018-12-12T10:16:55Z"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"1","volume":19,"ec_funded":1,"_id":"1493","status":"public","pubrep_id":"514","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","530"],"date_updated":"2021-01-12T06:51:08Z","department":[{"_id":"RoSe"}],"file_date_updated":"2020-07-14T12:44:58Z","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). ","quality_controlled":"1","publisher":"Springer","oa":1,"day":"01","publication":"Mathematical Physics, Analysis and Geometry","has_accepted_license":"1","year":"2016","date_published":"2016-03-01T00:00:00Z","doi":"10.1007/s11040-016-9204-2","date_created":"2018-12-11T11:52:20Z","article_number":"3","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Petrat, Sören P., and Peter Pickl. “A New Method and a New Scaling for Deriving Fermionic Mean-Field Dynamics.” Mathematical Physics, Analysis and Geometry, vol. 19, no. 1, 3, Springer, 2016, doi:10.1007/s11040-016-9204-2.","ieee":"S. P. Petrat and P. Pickl, “A new method and a new scaling for deriving fermionic mean-field dynamics,” Mathematical Physics, Analysis and Geometry, vol. 19, no. 1. Springer, 2016.","short":"S.P. Petrat, P. Pickl, Mathematical Physics, Analysis and Geometry 19 (2016).","apa":"Petrat, S. P., & Pickl, P. (2016). A new method and a new scaling for deriving fermionic mean-field dynamics. Mathematical Physics, Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-016-9204-2","ama":"Petrat SP, Pickl P. A new method and a new scaling for deriving fermionic mean-field dynamics. Mathematical Physics, Analysis and Geometry. 2016;19(1). doi:10.1007/s11040-016-9204-2","chicago":"Petrat, Sören P, and Peter Pickl. “A New Method and a New Scaling for Deriving Fermionic Mean-Field Dynamics.” Mathematical Physics, Analysis and Geometry. Springer, 2016. https://doi.org/10.1007/s11040-016-9204-2.","ista":"Petrat SP, Pickl P. 2016. A new method and a new scaling for deriving fermionic mean-field dynamics. Mathematical Physics, Analysis and Geometry. 19(1), 3."},"title":"A new method and a new scaling for deriving fermionic mean-field dynamics","author":[{"first_name":"Sören P","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","full_name":"Petrat, Sören P","orcid":"0000-0002-9166-5889","last_name":"Petrat"},{"last_name":"Pickl","full_name":"Pickl, Peter","first_name":"Peter"}],"publist_id":"5690","article_processing_charge":"Yes (via OA deal)"},{"_id":"1492","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"ddc":["570"],"date_updated":"2021-01-12T06:51:08Z","department":[{"_id":"EvBe"}],"file_date_updated":"2020-07-14T12:44:58Z","oa_version":"Published Version","pmid":1,"acknowledged_ssus":[{"_id":"LifeSc"}],"abstract":[{"text":"To sustain a lifelong ability to initiate organs, plants retain pools of undifferentiated cells with a preserved prolif eration capacity. The root pericycle represents a unique tissue with conditional meristematic activity, and its tight control determines initiation of lateral organs. Here we show that the meristematic activity of the pericycle is constrained by the interaction with the adjacent endodermis. Release of these restraints by elimination of endo dermal cells by single-cell ablation triggers the pericycle to re-enter the cell cycle. We found that endodermis removal substitutes for the phytohormone auxin-dependent initiation of the pericycle meristematic activity. However, auxin is indispensable to steer the cell division plane orientation of new organ-defining divisions. We propose a dual, spatiotemporally distinct role for auxin during lateral root initiation. In the endodermis, auxin releases constraints arising from cell-to-cell interactions that compromise the pericycle meristematic activity, whereas, in the pericycle, auxin defines the orientation of the cell division plane to initiate lateral roots.","lang":"eng"}],"month":"03","intvolume":" 30","scopus_import":1,"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"ea394498ee56270e021d1028a29358a0","file_id":"5883","creator":"kschuh","file_size":2757636,"date_updated":"2020-07-14T12:44:58Z","file_name":"2016_GeneDev_Marhavy.pdf","date_created":"2019-01-25T09:56:11Z"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":30,"issue":"4","license":"https://creativecommons.org/licenses/by-nc/4.0/","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Marhavý, Peter, et al. “Targeted Cell Elimination Reveals an Auxin-Guided Biphasic Mode of Lateral Root Initiation.” Genes and Development, vol. 30, no. 4, Cold Spring Harbor Laboratory Press, 2016, pp. 471–83, doi:10.1101/gad.276964.115.","ama":"Marhavý P, Montesinos López JC, Abuzeineh A, et al. Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation. Genes and Development. 2016;30(4):471-483. doi:10.1101/gad.276964.115","apa":"Marhavý, P., Montesinos López, J. C., Abuzeineh, A., Van Damme, D., Vermeer, J., Duclercq, J., … Benková, E. (2016). Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation. Genes and Development. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/gad.276964.115","ieee":"P. Marhavý et al., “Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation,” Genes and Development, vol. 30, no. 4. Cold Spring Harbor Laboratory Press, pp. 471–483, 2016.","short":"P. Marhavý, J.C. Montesinos López, A. Abuzeineh, D. Van Damme, J. Vermeer, J. Duclercq, H. Rakusova, P. Marhavá, J. Friml, N. Geldner, E. Benková, Genes and Development 30 (2016) 471–483.","chicago":"Marhavý, Peter, Juan C Montesinos López, Anas Abuzeineh, Daniël Van Damme, Joop Vermeer, Jérôme Duclercq, Hana Rakusova, et al. “Targeted Cell Elimination Reveals an Auxin-Guided Biphasic Mode of Lateral Root Initiation.” Genes and Development. Cold Spring Harbor Laboratory Press, 2016. https://doi.org/10.1101/gad.276964.115.","ista":"Marhavý P, Montesinos López JC, Abuzeineh A, Van Damme D, Vermeer J, Duclercq J, Rakusova H, Marhavá P, Friml J, Geldner N, Benková E. 2016. Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation. Genes and Development. 30(4), 471–483."},"title":"Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation","author":[{"id":"3F45B078-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Marhavy","full_name":"Marhavy, Peter","orcid":"0000-0001-5227-5741"},{"last_name":"Montesinos López","orcid":"0000-0001-9179-6099","full_name":"Montesinos López, Juan C","first_name":"Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anas","last_name":"Abuzeineh","full_name":"Abuzeineh, Anas"},{"last_name":"Van Damme","full_name":"Van Damme, Daniël","first_name":"Daniël"},{"first_name":"Joop","last_name":"Vermeer","full_name":"Vermeer, Joop"},{"last_name":"Duclercq","full_name":"Duclercq, Jérôme","first_name":"Jérôme"},{"full_name":"Rakusova, Hana","last_name":"Rakusova","first_name":"Hana"},{"id":"44E59624-F248-11E8-B48F-1D18A9856A87","first_name":"Petra","last_name":"Marhavá","full_name":"Marhavá, Petra"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"first_name":"Niko","full_name":"Geldner, Niko","last_name":"Geldner"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"}],"publist_id":"5691","external_id":{"pmid":[" 26883363"]},"acknowledgement":"This work was supported by a European Research Council Starting Inde-pendent Research grant (ERC-2007-Stg-207362-HCPO to J.D.), Research Foundation-Flanders (G033711N to A.A.), and the Austrian Science Fund (FWF01_I1774S to E.B.). P.M. is indebted to the Federation of European Biochemical Sciences for a Long-Term Fellowship. ","quality_controlled":"1","publisher":"Cold Spring Harbor Laboratory Press","oa":1,"day":"01","publication":"Genes and Development","has_accepted_license":"1","year":"2016","doi":"10.1101/gad.276964.115","date_published":"2016-03-01T00:00:00Z","date_created":"2018-12-11T11:52:20Z","page":"471 - 483"},{"acknowledgement":"This research was supported in part by FCT, Portugal, through Project No. PTDC/FIS/117606/2010, financed by the European Community Fund FEDER through the COMPETE. ","oa":1,"quality_controlled":"1","publisher":"American Physical Society","publication":"Physical Review A - Atomic, Molecular, and Optical Physics","day":"07","year":"2016","date_created":"2018-12-11T11:52:21Z","date_published":"2016-03-07T00:00:00Z","doi":"10.1103/PhysRevA.93.032502","article_number":"032502","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Amaro P, Fratini F, Safari L, Machado J, Guerra M, Indelicato P, Santos J. 2016. Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model. Physical Review A - Atomic, Molecular, and Optical Physics. 93(3), 032502.","chicago":"Amaro, Pedro, Filippo Fratini, Laleh Safari, Jorge Machado, Mauro Guerra, Paul Indelicato, and José Santos. “Relativistic Evaluation of the Two-Photon Decay of the Metastable 1s22s2p3P0 State in Berylliumlike Ions with an Effective-Potential Model.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2016. https://doi.org/10.1103/PhysRevA.93.032502.","apa":"Amaro, P., Fratini, F., Safari, L., Machado, J., Guerra, M., Indelicato, P., & Santos, J. (2016). Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.93.032502","ama":"Amaro P, Fratini F, Safari L, et al. Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model. Physical Review A - Atomic, Molecular, and Optical Physics. 2016;93(3). doi:10.1103/PhysRevA.93.032502","short":"P. Amaro, F. Fratini, L. Safari, J. Machado, M. Guerra, P. Indelicato, J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 93 (2016).","ieee":"P. Amaro et al., “Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 93, no. 3. American Physical Society, 2016.","mla":"Amaro, Pedro, et al. “Relativistic Evaluation of the Two-Photon Decay of the Metastable 1s22s2p3P0 State in Berylliumlike Ions with an Effective-Potential Model.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 93, no. 3, 032502, American Physical Society, 2016, doi:10.1103/PhysRevA.93.032502."},"title":"Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model","publist_id":"5683","author":[{"last_name":"Amaro","full_name":"Amaro, Pedro","first_name":"Pedro"},{"last_name":"Fratini","full_name":"Fratini, Filippo","first_name":"Filippo"},{"id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","first_name":"Laleh","last_name":"Safari","full_name":"Safari, Laleh"},{"first_name":"Jorge","full_name":"Machado, Jorge","last_name":"Machado"},{"last_name":"Guerra","full_name":"Guerra, Mauro","first_name":"Mauro"},{"first_name":"Paul","full_name":"Indelicato, Paul","last_name":"Indelicato"},{"last_name":"Santos","full_name":"Santos, José","first_name":"José"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The two-photon 1s2 2s 2p 3P0 1s22s2 1S0 transition in berylliumlike ions is theoretically investigated within a fully relativistic framework and a second-order perturbation theory. We focus our analysis on how electron correlation, as well as the negative-energy spectrum, can affect the forbidden E1M1 decay rate. For this purpose, we include the electronic correlation via an effective local potential and within a single configuration-state model. Due to its experimental interest, evaluations of decay rates are performed for berylliumlike xenon and uranium. We find that the negative-energy contribution can be neglected at the present level of accuracy in the evaluation of the decay rate. On the other hand, if contributions of electronic correlation are not carefully taken into account, it may change the lifetime of the metastable state by up to 20%. By performing a full-relativistic jj-coupling calculation, we found a decrease of the decay rate by two orders of magnitude compared to non-relativistic LS-coupling calculations, for the selected heavy ions."}],"intvolume":" 93","month":"03","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1508.06169"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":93,"issue":"3","_id":"1496","status":"public","type":"journal_article","date_updated":"2021-01-12T06:51:09Z","department":[{"_id":"MiLe"}]},{"date_updated":"2021-01-12T06:51:07Z","department":[{"_id":"RoSe"}],"_id":"1491","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","volume":368,"issue":"9","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We study the ground state of a trapped Bose gas, starting from the full many-body Schrödinger Hamiltonian, and derive the non-linear Schrödinger energy functional in the limit of a large particle number, when the interaction potential converges slowly to a Dirac delta function. Our method is based on quantitative estimates on the discrepancy between the full many-body energy and its mean-field approximation using Hartree states. These are proved using finite dimensional localization and a quantitative version of the quantum de Finetti theorem. Our approach covers the case of attractive interactions in the regime of stability. In particular, our main new result is a derivation of the 2D attractive non-linear Schrödinger ground state."}],"month":"01","intvolume":" 368","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1405.3220"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Lewin M, Nam P, Rougerie N. 2016. The mean-field approximation and the non-linear Schrödinger functional for trapped Bose gases. Transactions of the American Mathematical Society. 368(9), 6131–6157.","chicago":"Lewin, Mathieu, Phan Nam, and Nicolas Rougerie. “The Mean-Field Approximation and the Non-Linear Schrödinger Functional for Trapped Bose Gases.” Transactions of the American Mathematical Society. American Mathematical Society, 2016. https://doi.org/10.1090/tran/6537.","ama":"Lewin M, Nam P, Rougerie N. The mean-field approximation and the non-linear Schrödinger functional for trapped Bose gases. Transactions of the American Mathematical Society. 2016;368(9):6131-6157. doi:10.1090/tran/6537","apa":"Lewin, M., Nam, P., & Rougerie, N. (2016). The mean-field approximation and the non-linear Schrödinger functional for trapped Bose gases. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/6537","short":"M. Lewin, P. Nam, N. Rougerie, Transactions of the American Mathematical Society 368 (2016) 6131–6157.","ieee":"M. Lewin, P. Nam, and N. Rougerie, “The mean-field approximation and the non-linear Schrödinger functional for trapped Bose gases,” Transactions of the American Mathematical Society, vol. 368, no. 9. American Mathematical Society, pp. 6131–6157, 2016.","mla":"Lewin, Mathieu, et al. “The Mean-Field Approximation and the Non-Linear Schrödinger Functional for Trapped Bose Gases.” Transactions of the American Mathematical Society, vol. 368, no. 9, American Mathematical Society, 2016, pp. 6131–57, doi:10.1090/tran/6537."},"title":"The mean-field approximation and the non-linear Schrödinger functional for trapped Bose gases","author":[{"first_name":"Mathieu","last_name":"Lewin","full_name":"Lewin, Mathieu"},{"id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan","last_name":"Nam","full_name":"Nam, Phan"},{"first_name":"Nicolas","full_name":"Rougerie, Nicolas","last_name":"Rougerie"}],"publist_id":"5692","day":"01","publication":"Transactions of the American Mathematical Society","year":"2016","doi":"10.1090/tran/6537","date_published":"2016-01-01T00:00:00Z","date_created":"2018-12-11T11:52:20Z","page":"6131 - 6157","acknowledgement":"The authors acknowledge financial support from the European Research Council (FP7/2007-2013 Grant Agreement MNIQS 258023) and the ANR (Mathostaq project, ANR-13-JS01-0005-01). The second and third authors have benefited from the hospitality of the Institute for Mathematical Science of the National University of Singapore.","publisher":"American Mathematical Society","quality_controlled":"1","oa":1},{"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). ","oa":1,"publisher":"Springer","quality_controlled":"1","year":"2016","has_accepted_license":"1","publication":"Discrete & Computational Geometry","day":"01","page":"126 - 164","date_created":"2018-12-11T11:51:51Z","date_published":"2016-07-01T00:00:00Z","doi":"10.1007/s00454-016-9794-2","project":[{"_id":"25F8B9BC-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M01980","name":"Robust invariants of Nonlinear Systems"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"citation":{"ista":"Franek P, Krcál M. 2016. On computability and triviality of well groups. Discrete & Computational Geometry. 56(1), 126–164.","chicago":"Franek, Peter, and Marek Krcál. “On Computability and Triviality of Well Groups.” Discrete & Computational Geometry. Springer, 2016. https://doi.org/10.1007/s00454-016-9794-2.","ama":"Franek P, Krcál M. On computability and triviality of well groups. Discrete & Computational Geometry. 2016;56(1):126-164. doi:10.1007/s00454-016-9794-2","apa":"Franek, P., & Krcál, M. (2016). On computability and triviality of well groups. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-016-9794-2","ieee":"P. Franek and M. Krcál, “On computability and triviality of well groups,” Discrete & Computational Geometry, vol. 56, no. 1. Springer, pp. 126–164, 2016.","short":"P. Franek, M. Krcál, Discrete & Computational Geometry 56 (2016) 126–164.","mla":"Franek, Peter, and Marek Krcál. “On Computability and Triviality of Well Groups.” Discrete & Computational Geometry, vol. 56, no. 1, Springer, 2016, pp. 126–64, doi:10.1007/s00454-016-9794-2."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","author":[{"id":"473294AE-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Franek","full_name":"Franek, Peter"},{"full_name":"Krcál, Marek","last_name":"Krcál","id":"33E21118-F248-11E8-B48F-1D18A9856A87","first_name":"Marek"}],"publist_id":"5799","title":"On computability and triviality of well groups","abstract":[{"lang":"eng","text":"The concept of well group in a special but important case captures homological properties of the zero set of a continuous map (Formula presented.) on a compact space K that are invariant with respect to perturbations of f. The perturbations are arbitrary continuous maps within (Formula presented.) distance r from f for a given (Formula presented.). The main drawback of the approach is that the computability of well groups was shown only when (Formula presented.) or (Formula presented.). Our contribution to the theory of well groups is twofold: on the one hand we improve on the computability issue, but on the other hand we present a range of examples where the well groups are incomplete invariants, that is, fail to capture certain important robust properties of the zero set. For the first part, we identify a computable subgroup of the well group that is obtained by cap product with the pullback of the orientation of (Formula presented.) by f. In other words, well groups can be algorithmically approximated from below. When f is smooth and (Formula presented.), our approximation of the (Formula presented.)th well group is exact. For the second part, we find examples of maps (Formula presented.) with all well groups isomorphic but whose perturbations have different zero sets. We discuss on a possible replacement of the well groups of vector valued maps by an invariant of a better descriptive power and computability status."}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 56","month":"07","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:10:55Z","file_name":"IST-2016-614-v1+1_s00454-016-9794-2.pdf","creator":"system","date_updated":"2020-07-14T12:44:53Z","file_size":905303,"checksum":"e0da023abf6b72abd8c6a8c76740d53c","file_id":"4846","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"ec_funded":1,"related_material":{"record":[{"relation":"earlier_version","id":"1510","status":"public"}]},"issue":"1","volume":56,"_id":"1408","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"614","status":"public","date_updated":"2023-02-23T10:02:11Z","ddc":["510"],"file_date_updated":"2020-07-14T12:44:53Z","department":[{"_id":"UlWa"},{"_id":"HeEd"}]},{"day":"01","publication":"Genetics","has_accepted_license":"1","year":"2016","date_published":"2016-02-01T00:00:00Z","doi":"10.1534/genetics.115.183814","date_created":"2018-12-11T11:52:29Z","page":"775 - 786","acknowledgement":"We thank Lynsey Bunnefeld for discussions throughout the project and Joshua Schraiber and one anonymous reviewer\r\nfor constructive comments on an earlier version of this manuscript. This work was supported by funding from the\r\nUnited Kingdom Natural Environment Research Council (to K.L.) (NE/I020288/1) and a grant from the European\r\nResearch Council (250152) (to N.H.B.).","quality_controlled":"1","publisher":"Genetics Society of America","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Lohse, Konrad, et al. “Efficient Strategies for Calculating Blockwise Likelihoods under the Coalescent.” Genetics, vol. 202, no. 2, Genetics Society of America, 2016, pp. 775–86, doi:10.1534/genetics.115.183814.","short":"K. Lohse, M. Chmelik, S. Martin, N.H. Barton, Genetics 202 (2016) 775–786.","ieee":"K. Lohse, M. Chmelik, S. Martin, and N. H. Barton, “Efficient strategies for calculating blockwise likelihoods under the coalescent,” Genetics, vol. 202, no. 2. Genetics Society of America, pp. 775–786, 2016.","ama":"Lohse K, Chmelik M, Martin S, Barton NH. Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics. 2016;202(2):775-786. doi:10.1534/genetics.115.183814","apa":"Lohse, K., Chmelik, M., Martin, S., & Barton, N. H. (2016). Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.183814","chicago":"Lohse, Konrad, Martin Chmelik, Simon Martin, and Nicholas H Barton. “Efficient Strategies for Calculating Blockwise Likelihoods under the Coalescent.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.183814.","ista":"Lohse K, Chmelik M, Martin S, Barton NH. 2016. Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics. 202(2), 775–786."},"title":"Efficient strategies for calculating blockwise likelihoods under the coalescent","publist_id":"5658","author":[{"first_name":"Konrad","full_name":"Lohse, Konrad","last_name":"Lohse"},{"id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Chmelik, Martin","last_name":"Chmelik"},{"full_name":"Martin, Simon","last_name":"Martin","first_name":"Simon"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"pmid":["26715666"]},"project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"41c9b5d72e7fe4624dd22dfe622337d5","file_id":"5241","date_updated":"2020-07-14T12:45:00Z","file_size":957466,"creator":"system","date_created":"2018-12-12T10:16:51Z","file_name":"IST-2016-561-v1+1_Lohse_et_al_Genetics_2015.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":202,"issue":"2","ec_funded":1,"pmid":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The inference of demographic history from genome data is hindered by a lack of efficient computational approaches. In particular, it has proved difficult to exploit the information contained in the distribution of genealogies across the genome. We have previously shown that the generating function (GF) of genealogies can be used to analytically compute likelihoods of demographic models from configurations of mutations in short sequence blocks (Lohse et al. 2011). Although the GF has a simple, recursive form, the size of such likelihood calculations explodes quickly with the number of individuals and applications of this framework have so far been mainly limited to small samples (pairs and triplets) for which the GF can be written by hand. Here we investigate several strategies for exploiting the inherent symmetries of the coalescent. In particular, we show that the GF of genealogies can be decomposed into a set of equivalence classes that allows likelihood calculations from nontrivial samples. Using this strategy, we automated blockwise likelihood calculations for a general set of demographic scenarios in Mathematica. These histories may involve population size changes, continuous migration, discrete divergence, and admixture between multiple populations. To give a concrete example, we calculate the likelihood for a model of isolation with migration (IM), assuming two diploid samples without phase and outgroup information. We demonstrate the new inference scheme with an analysis of two individual butterfly genomes from the sister species Heliconius melpomene rosina and H. cydno."}],"month":"02","intvolume":" 202","scopus_import":"1","ddc":["570"],"date_updated":"2022-05-24T09:16:22Z","department":[{"_id":"KrCh"},{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:45:00Z","_id":"1518","status":"public","pubrep_id":"561","article_type":"original","type":"journal_article"},{"page":"173 - 191","date_published":"2016-01-10T00:00:00Z","doi":"10.1007/978-3-319-26916-0_10","date_created":"2018-12-11T11:52:31Z","year":"2016","day":"10","publisher":"Springer","quality_controlled":"1","oa":1,"acknowledgement":"This research was supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734, and the SNSF Early Postdoc.Mobility Fellowship, the grant number P2EZP2_148797.","publist_id":"5649","author":[{"full_name":"Beica, Andreea","last_name":"Beica","first_name":"Andreea"},{"last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"},{"last_name":"Petrov","full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905","first_name":"Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87"}],"title":"Efficient reduction of kappa models by static inspection of the rule-set","citation":{"chicago":"Beica, Andreea, Calin C Guet, and Tatjana Petrov. “Efficient Reduction of Kappa Models by Static Inspection of the Rule-Set,” 9271:173–91. Springer, 2016. https://doi.org/10.1007/978-3-319-26916-0_10.","ista":"Beica A, Guet CC, Petrov T. 2016. Efficient reduction of kappa models by static inspection of the rule-set. HSB: Hybrid Systems Biology, LNCS, vol. 9271, 173–191.","mla":"Beica, Andreea, et al. Efficient Reduction of Kappa Models by Static Inspection of the Rule-Set. Vol. 9271, Springer, 2016, pp. 173–91, doi:10.1007/978-3-319-26916-0_10.","apa":"Beica, A., Guet, C. C., & Petrov, T. (2016). Efficient reduction of kappa models by static inspection of the rule-set (Vol. 9271, pp. 173–191). Presented at the HSB: Hybrid Systems Biology, Madrid, Spain: Springer. https://doi.org/10.1007/978-3-319-26916-0_10","ama":"Beica A, Guet CC, Petrov T. Efficient reduction of kappa models by static inspection of the rule-set. In: Vol 9271. Springer; 2016:173-191. doi:10.1007/978-3-319-26916-0_10","ieee":"A. Beica, C. C. Guet, and T. Petrov, “Efficient reduction of kappa models by static inspection of the rule-set,” presented at the HSB: Hybrid Systems Biology, Madrid, Spain, 2016, vol. 9271, pp. 173–191.","short":"A. Beica, C.C. Guet, T. Petrov, in:, Springer, 2016, pp. 173–191."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"volume":9271,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1501.00440","open_access":"1"}],"month":"01","intvolume":" 9271","abstract":[{"text":"When designing genetic circuits, the typical primitives used in major existing modelling formalisms are gene interaction graphs, where edges between genes denote either an activation or inhibition relation. However, when designing experiments, it is important to be precise about the low-level mechanistic details as to how each such relation is implemented. The rule-based modelling language Kappa allows to unambiguously specify mechanistic details such as DNA binding sites, dimerisation of transcription factors, or co-operative interactions. Such a detailed description comes with complexity and computationally costly executions. We propose a general method for automatically transforming a rule-based program, by eliminating intermediate species and adjusting the rate constants accordingly. To the best of our knowledge, we show the first automated reduction of rule-based models based on equilibrium approximations.\r\nOur algorithm is an adaptation of an existing algorithm, which was designed for reducing reaction-based programs; our version of the algorithm scans the rule-based Kappa model in search for those interaction patterns known to be amenable to equilibrium approximations (e.g. Michaelis-Menten scheme). Additional checks are then performed in order to verify if the reduction is meaningful in the context of the full model. The reduced model is efficiently obtained by static inspection over the rule-set. The tool is tested on a detailed rule-based model of a λ-phage switch, which lists 92 rules and 13 agents. The reduced model has 11 rules and 5 agents, and provides a dramatic reduction in simulation time of several orders of magnitude.","lang":"eng"}],"oa_version":"Preprint","department":[{"_id":"CaGu"},{"_id":"ToHe"}],"date_updated":"2021-01-12T06:51:22Z","type":"conference","conference":{"start_date":"2015-09-04","location":"Madrid, Spain","end_date":"2015-09-05","name":"HSB: Hybrid Systems Biology"},"status":"public","_id":"1524"},{"citation":{"ista":"Avvakumov S. 2016. The classification of certain linked 3-manifolds in 6-space. Moscow Mathematical Journal. 16(1), 1–25.","chicago":"Avvakumov, Sergey. “The Classification of Certain Linked 3-Manifolds in 6-Space.” Moscow Mathematical Journal. Independent University of Moscow, 2016. https://doi.org/10.17323/1609-4514-2016-16-1-1-25.","ieee":"S. Avvakumov, “The classification of certain linked 3-manifolds in 6-space,” Moscow Mathematical Journal, vol. 16, no. 1. Independent University of Moscow, pp. 1–25, 2016.","short":"S. Avvakumov, Moscow Mathematical Journal 16 (2016) 1–25.","ama":"Avvakumov S. The classification of certain linked 3-manifolds in 6-space. Moscow Mathematical Journal. 2016;16(1):1-25. doi:10.17323/1609-4514-2016-16-1-1-25","apa":"Avvakumov, S. (2016). The classification of certain linked 3-manifolds in 6-space. Moscow Mathematical Journal. Independent University of Moscow. https://doi.org/10.17323/1609-4514-2016-16-1-1-25","mla":"Avvakumov, Sergey. “The Classification of Certain Linked 3-Manifolds in 6-Space.” Moscow Mathematical Journal, vol. 16, no. 1, Independent University of Moscow, 2016, pp. 1–25, doi:10.17323/1609-4514-2016-16-1-1-25."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["1408.3918"]},"publist_id":"5652","author":[{"first_name":"Serhii","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","full_name":"Avvakumov, Serhii","last_name":"Avvakumov"}],"title":"The classification of certain linked 3-manifolds in 6-space","acknowledgement":"I thank A. Skopenkov for telling me about the problem and for his useful remarks. I also thank A. Sossinsky,\r\nA. Zhubr, M. Skopenkov, P. Akhmetiev, and an anonymous referee for their feedback. Author was partially\r\nsupported by Dobrushin fellowship, 2013, and by RFBR grant 15-01-06302.","oa":1,"publisher":"Independent University of Moscow","quality_controlled":"1","year":"2016","publication":"Moscow Mathematical Journal","day":"01","page":"1 - 25","date_created":"2018-12-11T11:52:30Z","date_published":"2016-01-01T00:00:00Z","doi":"10.17323/1609-4514-2016-16-1-1-25","_id":"1522","type":"journal_article","article_type":"original","status":"public","date_updated":"2022-02-25T10:15:57Z","department":[{"_id":"UlWa"}],"abstract":[{"text":"We classify smooth Brunnian (i.e., unknotted on both components) embeddings (S2 × S1) ⊔ S3 → ℝ6. Any Brunnian embedding (S2 × S1) ⊔ S3 → ℝ6 is isotopic to an explicitly constructed embedding fk,m,n for some integers k, m, n such that m ≡ n (mod 2). Two embeddings fk,m,n and fk′ ,m′,n′ are isotopic if and only if k = k′, m ≡ m′ (mod 2k) and n ≡ n′ (mod 2k). We use Haefliger’s classification of embeddings S3 ⊔ S3 → ℝ6 in our proof. The relation between the embeddings (S2 × S1) ⊔ S3 → ℝ6 and S3 ⊔ S3 → ℝ6 is not trivial, however. For example, we show that there exist embeddings f: (S2 ×S1) ⊔ S3 → ℝ6 and g, g′ : S3 ⊔ S3 → ℝ6 such that the componentwise embedded connected sum f # g is isotopic to f # g′ but g is not isotopic to g′.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1408.3918"}],"scopus_import":"1","intvolume":" 16","month":"01","publication_status":"published","publication_identifier":{"eissn":["1609-4514"]},"language":[{"iso":"eng"}],"issue":"1","volume":16},{"acknowledgement":"This research was supported by the Swiss National Science Foundation (SNF Projects 200021-125309 and 200020-138230","oa":1,"quality_controlled":"1","publisher":"American Mathematical Society","publication":"Proceedings of the American Mathematical Society","day":"01","year":"2016","date_created":"2018-12-11T11:52:30Z","doi":"10.1090/proc/12824","date_published":"2016-04-01T00:00:00Z","page":"1815 - 1828","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Gundert, Anna, and Uli Wagner. “On Topological Minors in Random Simplicial Complexes.” Proceedings of the American Mathematical Society, vol. 144, no. 4, American Mathematical Society, 2016, pp. 1815–28, doi:10.1090/proc/12824.","ieee":"A. Gundert and U. Wagner, “On topological minors in random simplicial complexes,” Proceedings of the American Mathematical Society, vol. 144, no. 4. American Mathematical Society, pp. 1815–1828, 2016.","short":"A. Gundert, U. Wagner, Proceedings of the American Mathematical Society 144 (2016) 1815–1828.","apa":"Gundert, A., & Wagner, U. (2016). On topological minors in random simplicial complexes. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/12824","ama":"Gundert A, Wagner U. On topological minors in random simplicial complexes. Proceedings of the American Mathematical Society. 2016;144(4):1815-1828. doi:10.1090/proc/12824","chicago":"Gundert, Anna, and Uli Wagner. “On Topological Minors in Random Simplicial Complexes.” Proceedings of the American Mathematical Society. American Mathematical Society, 2016. https://doi.org/10.1090/proc/12824.","ista":"Gundert A, Wagner U. 2016. On topological minors in random simplicial complexes. Proceedings of the American Mathematical Society. 144(4), 1815–1828."},"title":"On topological minors in random simplicial complexes","author":[{"last_name":"Gundert","full_name":"Gundert, Anna","first_name":"Anna"},{"first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner"}],"publist_id":"5650","oa_version":"Preprint","abstract":[{"text":"For random graphs, the containment problem considers the probability that a binomial random graph G(n, p) contains a given graph as a substructure. When asking for the graph as a topological minor, i.e., for a copy of a subdivision of the given graph, it is well known that the (sharp) threshold is at p = 1/n. We consider a natural analogue of this question for higher-dimensional random complexes Xk(n, p), first studied by Cohen, Costa, Farber and Kappeler for k = 2. Improving previous results, we show that p = Θ(1/ √n) is the (coarse) threshold for containing a subdivision of any fixed complete 2-complex. For higher dimensions k > 2, we get that p = O(n−1/k) is an upper bound for the threshold probability of containing a subdivision of a fixed k-dimensional complex.","lang":"eng"}],"intvolume":" 144","month":"04","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.2106"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","issue":"4","volume":144,"_id":"1523","status":"public","type":"journal_article","date_updated":"2021-01-12T06:51:22Z","department":[{"_id":"UlWa"}]},{"project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Henzinger TA, Otop J, Samanta R. Lipschitz robustness of timed I/O systems. In: Vol 9583. Springer; 2016:250-267. doi:10.1007/978-3-662-49122-5_12","apa":"Henzinger, T. A., Otop, J., & Samanta, R. (2016). Lipschitz robustness of timed I/O systems (Vol. 9583, pp. 250–267). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, St. Petersburg, FL, USA: Springer. https://doi.org/10.1007/978-3-662-49122-5_12","ieee":"T. A. Henzinger, J. Otop, and R. Samanta, “Lipschitz robustness of timed I/O systems,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, St. Petersburg, FL, USA, 2016, vol. 9583, pp. 250–267.","short":"T.A. Henzinger, J. Otop, R. Samanta, in:, Springer, 2016, pp. 250–267.","mla":"Henzinger, Thomas A., et al. Lipschitz Robustness of Timed I/O Systems. Vol. 9583, Springer, 2016, pp. 250–67, doi:10.1007/978-3-662-49122-5_12.","ista":"Henzinger TA, Otop J, Samanta R. 2016. Lipschitz robustness of timed I/O systems. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 9583, 250–267.","chicago":"Henzinger, Thomas A, Jan Otop, and Roopsha Samanta. “Lipschitz Robustness of Timed I/O Systems,” 9583:250–67. Springer, 2016. https://doi.org/10.1007/978-3-662-49122-5_12."},"title":"Lipschitz robustness of timed I/O systems","publist_id":"5647","author":[{"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"},{"first_name":"Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","full_name":"Samanta, Roopsha","last_name":"Samanta"}],"acknowledgement":"This research was supported in part by the European Research Council (ERC) under grant 267989 (QUAREM), by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), and by the National Science Centre (NCN), Poland under grant 2014/15/D/ST6/04543.","oa":1,"quality_controlled":"1","publisher":"Springer","day":"01","year":"2016","date_created":"2018-12-11T11:52:32Z","date_published":"2016-01-01T00:00:00Z","doi":"10.1007/978-3-662-49122-5_12","page":"250 - 267","_id":"1526","status":"public","conference":{"name":"VMCAI: Verification, Model Checking and Abstract Interpretation","location":"St. Petersburg, FL, USA","end_date":"2016-01-19","start_date":"2016-01-17"},"type":"conference","date_updated":"2021-01-12T06:51:23Z","department":[{"_id":"ToHe"}],"oa_version":"Preprint","abstract":[{"text":"We present the first study of robustness of systems that are both timed as well as reactive (I/O). We study the behavior of such timed I/O systems in the presence of uncertain inputs and formalize their robustness using the analytic notion of Lipschitz continuity: a timed I/O system is K-(Lipschitz) robust if the perturbation in its output is at most K times the perturbation in its input. We quantify input and output perturbation using similarity functions over timed words such as the timed version of the Manhattan distance and the Skorokhod distance. We consider two models of timed I/O systems — timed transducers and asynchronous sequential circuits. We show that K-robustness of timed transducers can be decided in polynomial space under certain conditions. For asynchronous sequential circuits, we reduce K-robustness w.r.t. timed Manhattan distances to K-robustness of discrete letter-to-letter transducers and show PSpace-completeness of the problem.","lang":"eng"}],"intvolume":" 9583","month":"01","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1506.01233"}],"scopus_import":1,"alternative_title":["LNCS"],"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":9583},{"_id":"1545","status":"public","type":"journal_article","date_updated":"2021-01-12T06:51:30Z","department":[{"_id":"RoSe"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We provide general conditions for which bosonic quadratic Hamiltonians on Fock spaces can be diagonalized by Bogoliubov transformations. Our results cover the case when quantum systems have infinite degrees of freedom and the associated one-body kinetic and paring operators are unbounded. Our sufficient conditions are optimal in the sense that they become necessary when the relevant one-body operators commute."}],"intvolume":" 270","month":"06","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1508.07321"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":270,"issue":"11","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Nam, Phan, Marcin M Napiórkowski, and Jan Solovej. “Diagonalization of Bosonic Quadratic Hamiltonians by Bogoliubov Transformations.” Journal of Functional Analysis. Academic Press, 2016. https://doi.org/10.1016/j.jfa.2015.12.007.","ista":"Nam P, Napiórkowski MM, Solovej J. 2016. Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations. Journal of Functional Analysis. 270(11), 4340–4368.","mla":"Nam, Phan, et al. “Diagonalization of Bosonic Quadratic Hamiltonians by Bogoliubov Transformations.” Journal of Functional Analysis, vol. 270, no. 11, Academic Press, 2016, pp. 4340–68, doi:10.1016/j.jfa.2015.12.007.","apa":"Nam, P., Napiórkowski, M. M., & Solovej, J. (2016). Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations. Journal of Functional Analysis. Academic Press. https://doi.org/10.1016/j.jfa.2015.12.007","ama":"Nam P, Napiórkowski MM, Solovej J. Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations. Journal of Functional Analysis. 2016;270(11):4340-4368. doi:10.1016/j.jfa.2015.12.007","short":"P. Nam, M.M. Napiórkowski, J. Solovej, Journal of Functional Analysis 270 (2016) 4340–4368.","ieee":"P. Nam, M. M. Napiórkowski, and J. Solovej, “Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations,” Journal of Functional Analysis, vol. 270, no. 11. Academic Press, pp. 4340–4368, 2016."},"title":"Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations","author":[{"last_name":"Nam","full_name":"Nam, Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan"},{"full_name":"Napiórkowski, Marcin M","last_name":"Napiórkowski","first_name":"Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","last_name":"Solovej","full_name":"Solovej, Jan"}],"publist_id":"5626","acknowledgement":"We thank Jan Dereziński for several inspiring discussions and useful remarks. We thank the referee for helpful comments. J.P.S. thanks the Erwin Schrödinger Institute for the hospitality during the thematic programme “Quantum many-body systems, random matrices, and disorder”. We gratefully acknowledge the financial supports by the European Union's Seventh Framework Programme under the ERC Advanced Grant ERC-2012-AdG 321029 (J.P.S.) and the REA grant agreement No. 291734 (P.T.N.), as well as the support of the National Science Center (NCN) grant No. 2012/07/N/ST1/03185 and the Austrian Science Fund (FWF) project No. P 27533-N27 (M.N.).","oa":1,"quality_controlled":"1","publisher":"Academic Press","publication":"Journal of Functional Analysis","day":"01","year":"2016","date_created":"2018-12-11T11:52:38Z","doi":"10.1016/j.jfa.2015.12.007","date_published":"2016-06-01T00:00:00Z","page":"4340 - 4368"},{"_id":"1552","pubrep_id":"488","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["570"],"date_updated":"2021-01-12T06:51:33Z","file_date_updated":"2020-07-14T12:45:02Z","department":[{"_id":"ToBo"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Antibiotic resistance carries a fitness cost that must be overcome in order for resistance to persist over the long term. Compensatory mutations that recover the functional defects associated with resistance mutations have been argued to play a key role in overcoming the cost of resistance, but compensatory mutations are expected to be rare relative to generally beneficial mutations that increase fitness, irrespective of antibiotic resistance. Given this asymmetry, population genetics theory predicts that populations should adapt by compensatory mutations when the cost of resistance is large, whereas generally beneficial mutations should drive adaptation when the cost of resistance is small. We tested this prediction by determining the genomic mechanisms underpinning adaptation to antibiotic-free conditions in populations of the pathogenic bacterium Pseudomonas aeruginosa that carry costly antibiotic resistance mutations. Whole-genome sequencing revealed that populations founded by high-cost rifampicin-resistant mutants adapted via compensatory mutations in three genes of the RNA polymerase core enzyme, whereas populations founded by low-cost mutants adapted by generally beneficial mutations, predominantly in the quorum-sensing transcriptional regulator gene lasR. Even though the importance of compensatory evolution in maintaining resistance has been widely recognized, our study shows that the roles of general adaptation in maintaining resistance should not be underestimated and highlights the need to understand how selection at other sites in the genome influences the dynamics of resistance alleles in clinical settings."}],"intvolume":" 283","month":"01","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:11:43Z","file_name":"IST-2016-488-v1+1_20152452.full.pdf","creator":"system","date_updated":"2020-07-14T12:45:02Z","file_size":626804,"file_id":"4899","checksum":"78ffe70c1c88af3856d31ca6b7195a27","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","issue":"1822","volume":283,"article_number":"20152452","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Qi, Qin, Macarena Toll Riera, Karl Heilbron, Gail Preston, and R Craig Maclean. “The Genomic Basis of Adaptation to the Fitness Cost of Rifampicin Resistance in Pseudomonas Aeruginosa.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2016. https://doi.org/10.1098/rspb.2015.2452.","ista":"Qi Q, Toll Riera M, Heilbron K, Preston G, Maclean RC. 2016. The genomic basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa. Proceedings of the Royal Society of London Series B Biological Sciences. 283(1822), 20152452.","mla":"Qi, Qin, et al. “The Genomic Basis of Adaptation to the Fitness Cost of Rifampicin Resistance in Pseudomonas Aeruginosa.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 283, no. 1822, 20152452, Royal Society, The, 2016, doi:10.1098/rspb.2015.2452.","apa":"Qi, Q., Toll Riera, M., Heilbron, K., Preston, G., & Maclean, R. C. (2016). The genomic basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2015.2452","ama":"Qi Q, Toll Riera M, Heilbron K, Preston G, Maclean RC. The genomic basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa. Proceedings of the Royal Society of London Series B Biological Sciences. 2016;283(1822). doi:10.1098/rspb.2015.2452","ieee":"Q. Qi, M. Toll Riera, K. Heilbron, G. Preston, and R. C. Maclean, “The genomic basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 283, no. 1822. Royal Society, The, 2016.","short":"Q. Qi, M. Toll Riera, K. Heilbron, G. Preston, R.C. Maclean, Proceedings of the Royal Society of London Series B Biological Sciences 283 (2016)."},"title":"The genomic basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa","author":[{"first_name":"Qin","id":"3B22D412-F248-11E8-B48F-1D18A9856A87","last_name":"Qi","orcid":"0000-0002-6148-2416","full_name":"Qi, Qin"},{"first_name":"Macarena","last_name":"Toll Riera","full_name":"Toll Riera, Macarena"},{"last_name":"Heilbron","full_name":"Heilbron, Karl","first_name":"Karl"},{"first_name":"Gail","last_name":"Preston","full_name":"Preston, Gail"},{"first_name":"R Craig","last_name":"Maclean","full_name":"Maclean, R Craig"}],"publist_id":"5619","acknowledgement":"We thank the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics funded by Wellcome\r\nTrust grant reference 090532/Z/09/Z and Medical Research Council Hub grant no. G0900747 91070 for generation of the high-throughput sequencing data. We thank Wook Kim and two anonymous reviewers for their constructive feedback on previous versions of our manuscript.","oa":1,"quality_controlled":"1","publisher":"Royal Society, The","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","day":"13","year":"2016","has_accepted_license":"1","date_created":"2018-12-11T11:52:40Z","doi":"10.1098/rspb.2015.2452","date_published":"2016-01-13T00:00:00Z"},{"author":[{"last_name":"Dunaeva","full_name":"Dunaeva, Olga","first_name":"Olga"},{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lukyanov","full_name":"Lukyanov, Anton","first_name":"Anton"},{"full_name":"Machin, Michael","last_name":"Machin","first_name":"Michael"},{"full_name":"Malkova, Daria","last_name":"Malkova","first_name":"Daria"},{"first_name":"Roman","full_name":"Kuvaev, Roman","last_name":"Kuvaev"},{"first_name":"Sergey","full_name":"Kashin, Sergey","last_name":"Kashin"}],"publist_id":"6027","article_processing_charge":"No","title":"The classification of endoscopy images with persistent homology","citation":{"chicago":"Dunaeva, Olga, Herbert Edelsbrunner, Anton Lukyanov, Michael Machin, Daria Malkova, Roman Kuvaev, and Sergey Kashin. “The Classification of Endoscopy Images with Persistent Homology.” Pattern Recognition Letters. Elsevier, 2016. https://doi.org/10.1016/j.patrec.2015.12.012.","ista":"Dunaeva O, Edelsbrunner H, Lukyanov A, Machin M, Malkova D, Kuvaev R, Kashin S. 2016. The classification of endoscopy images with persistent homology. Pattern Recognition Letters. 83(1), 13–22.","mla":"Dunaeva, Olga, et al. “The Classification of Endoscopy Images with Persistent Homology.” Pattern Recognition Letters, vol. 83, no. 1, Elsevier, 2016, pp. 13–22, doi:10.1016/j.patrec.2015.12.012.","short":"O. Dunaeva, H. Edelsbrunner, A. Lukyanov, M. Machin, D. Malkova, R. Kuvaev, S. Kashin, Pattern Recognition Letters 83 (2016) 13–22.","ieee":"O. Dunaeva et al., “The classification of endoscopy images with persistent homology,” Pattern Recognition Letters, vol. 83, no. 1. Elsevier, pp. 13–22, 2016.","apa":"Dunaeva, O., Edelsbrunner, H., Lukyanov, A., Machin, M., Malkova, D., Kuvaev, R., & Kashin, S. (2016). The classification of endoscopy images with persistent homology. Pattern Recognition Letters. Elsevier. https://doi.org/10.1016/j.patrec.2015.12.012","ama":"Dunaeva O, Edelsbrunner H, Lukyanov A, et al. The classification of endoscopy images with persistent homology. Pattern Recognition Letters. 2016;83(1):13-22. doi:10.1016/j.patrec.2015.12.012"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"13 - 22","date_published":"2016-11-01T00:00:00Z","doi":"10.1016/j.patrec.2015.12.012","date_created":"2018-12-11T11:51:10Z","has_accepted_license":"1","year":"2016","day":"01","publication":"Pattern Recognition Letters","quality_controlled":"1","publisher":"Elsevier","oa":1,"department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:44:42Z","date_updated":"2023-02-23T10:04:40Z","ddc":["004","514"],"type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","pubrep_id":"975","_id":"1289","volume":83,"issue":"1","related_material":{"record":[{"id":"1568","status":"public","relation":"earlier_version"}]},"publication_status":"published","file":[{"file_size":1921113,"date_updated":"2020-07-14T12:44:42Z","creator":"dernst","file_name":"2016-Edelsbrunner_The_classification.pdf","date_created":"2019-04-17T07:55:51Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"6334","checksum":"33458bbb8c32a339e1adeca6d5a1112d"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"11","intvolume":" 83","abstract":[{"text":"Aiming at the automatic diagnosis of tumors using narrow band imaging (NBI) magnifying endoscopic (ME) images of the stomach, we combine methods from image processing, topology, geometry, and machine learning to classify patterns into three classes: oval, tubular and irregular. Training the algorithm on a small number of images of each type, we achieve a high rate of correct classifications. The analysis of the learning algorithm reveals that a handful of geometric and topological features are responsible for the overwhelming majority of decisions.","lang":"eng"}],"oa_version":"Submitted Version"},{"day":"08","year":"2016","date_created":"2018-12-11T11:50:29Z","date_published":"2016-12-08T00:00:00Z","doi":"10.1007/978-3-319-50106-2_36","page":"468 - 481","oa":1,"quality_controlled":"1","publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Fulek R, Pelsmajer M, Schaefer M. 2016. Hanani-Tutte for radial planarity II. GD: Graph Drawing and Network Visualization, LNCS, vol. 9801, 468–481.","chicago":"Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte for Radial Planarity II,” 9801:468–81. Springer, 2016. https://doi.org/10.1007/978-3-319-50106-2_36.","ieee":"R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity II,” presented at the GD: Graph Drawing and Network Visualization, Athens, Greece, 2016, vol. 9801, pp. 468–481.","short":"R. Fulek, M. Pelsmajer, M. Schaefer, in:, Springer, 2016, pp. 468–481.","apa":"Fulek, R., Pelsmajer, M., & Schaefer, M. (2016). Hanani-Tutte for radial planarity II (Vol. 9801, pp. 468–481). Presented at the GD: Graph Drawing and Network Visualization, Athens, Greece: Springer. https://doi.org/10.1007/978-3-319-50106-2_36","ama":"Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity II. In: Vol 9801. Springer; 2016:468-481. doi:10.1007/978-3-319-50106-2_36","mla":"Fulek, Radoslav, et al. Hanani-Tutte for Radial Planarity II. Vol. 9801, Springer, 2016, pp. 468–81, doi:10.1007/978-3-319-50106-2_36."},"title":"Hanani-Tutte for radial planarity II","article_processing_charge":"No","external_id":{"arxiv":["1608.08662"]},"publist_id":"6193","author":[{"full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","last_name":"Fulek","first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael","last_name":"Pelsmajer","full_name":"Pelsmajer, Michael"},{"first_name":"Marcus","last_name":"Schaefer","full_name":"Schaefer, Marcus"}],"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"related_material":{"record":[{"relation":"later_version","status":"public","id":"1113"},{"relation":"earlier_version","id":"1595","status":"public"}]},"volume":9801,"oa_version":"Preprint","abstract":[{"text":"A drawing of a graph G is radial if the vertices of G are placed on concentric circles C1, … , Ck with common center c, and edges are drawn radially: every edge intersects every circle centered at c at most once. G is radial planar if it has a radial embedding, that is, a crossing-free radial drawing. If the vertices of G are ordered or partitioned into ordered levels (as they are for leveled graphs), we require that the assignment of vertices to circles corresponds to the given ordering or leveling. A pair of edges e and f in a graph is independent if e and f do not share a vertex. We show that a graph G is radial planar if G has a radial drawing in which every two independent edges cross an even number of times; the radial embedding has the same leveling as the radial drawing. In other words, we establish the strong Hanani-Tutte theorem for radial planarity. This characterization yields a very simple algorithm for radial planarity testing.","lang":"eng"}],"intvolume":" 9801","month":"12","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1608.08662"}],"alternative_title":["LNCS"],"scopus_import":1,"date_updated":"2023-02-23T10:05:57Z","department":[{"_id":"UlWa"}],"_id":"1164","status":"public","conference":{"name":"GD: Graph Drawing and Network Visualization","end_date":"2016-09-21","location":"Athens, Greece","start_date":"2016-09-19"},"type":"conference"},{"project":[{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)"},{"name":"Stromal Cell-immune Cell Interactions in Health and Disease","grant_number":"289720","_id":"25A76F58-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","grant_number":"Y 564-B12"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Kiermaier, Eva, et al. “Polysialylation Controls Dendritic Cell Trafficking by Regulating Chemokine Recognition.” Science, vol. 351, no. 6269, American Association for the Advancement of Science, 2016, pp. 186–90, doi:10.1126/science.aad0512.","apa":"Kiermaier, E., Moussion, C., Veldkamp, C., Gerardy Schahn, R., de Vries, I., Williams, L., … Sixt, M. K. (2016). Polysialylation controls dendritic cell trafficking by regulating chemokine recognition. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aad0512","ama":"Kiermaier E, Moussion C, Veldkamp C, et al. Polysialylation controls dendritic cell trafficking by regulating chemokine recognition. Science. 2016;351(6269):186-190. doi:10.1126/science.aad0512","short":"E. Kiermaier, C. Moussion, C. Veldkamp, R. Gerardy Schahn, I. de Vries, L. Williams, G. Chaffee, A. Phillips, F. Freiberger, R. Imre, D. Taleski, R. Payne, A. Braun, R. Förster, K. Mechtler, M. Mühlenhoff, B. Volkman, M.K. Sixt, Science 351 (2016) 186–190.","ieee":"E. Kiermaier et al., “Polysialylation controls dendritic cell trafficking by regulating chemokine recognition,” Science, vol. 351, no. 6269. American Association for the Advancement of Science, pp. 186–190, 2016.","chicago":"Kiermaier, Eva, Christine Moussion, Christopher Veldkamp, Rita Gerardy Schahn, Ingrid de Vries, Larry Williams, Gary Chaffee, et al. “Polysialylation Controls Dendritic Cell Trafficking by Regulating Chemokine Recognition.” Science. American Association for the Advancement of Science, 2016. https://doi.org/10.1126/science.aad0512.","ista":"Kiermaier E, Moussion C, Veldkamp C, Gerardy Schahn R, de Vries I, Williams L, Chaffee G, Phillips A, Freiberger F, Imre R, Taleski D, Payne R, Braun A, Förster R, Mechtler K, Mühlenhoff M, Volkman B, Sixt MK. 2016. Polysialylation controls dendritic cell trafficking by regulating chemokine recognition. Science. 351(6269), 186–190."},"title":"Polysialylation controls dendritic cell trafficking by regulating chemokine recognition","publist_id":"5570","author":[{"id":"3EB04B78-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0001-6165-5738","full_name":"Kiermaier, Eva","last_name":"Kiermaier"},{"first_name":"Christine","id":"3356F664-F248-11E8-B48F-1D18A9856A87","full_name":"Moussion, Christine","last_name":"Moussion"},{"full_name":"Veldkamp, Christopher","last_name":"Veldkamp","first_name":"Christopher"},{"first_name":"Rita","last_name":"Gerardy Schahn","full_name":"Gerardy Schahn, Rita"},{"full_name":"De Vries, Ingrid","last_name":"De Vries","first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Williams","full_name":"Williams, Larry","first_name":"Larry"},{"first_name":"Gary","last_name":"Chaffee","full_name":"Chaffee, Gary"},{"first_name":"Andrew","full_name":"Phillips, Andrew","last_name":"Phillips"},{"full_name":"Freiberger, Friedrich","last_name":"Freiberger","first_name":"Friedrich"},{"last_name":"Imre","full_name":"Imre, Richard","first_name":"Richard"},{"first_name":"Deni","last_name":"Taleski","full_name":"Taleski, Deni"},{"last_name":"Payne","full_name":"Payne, Richard","first_name":"Richard"},{"first_name":"Asolina","full_name":"Braun, Asolina","last_name":"Braun"},{"first_name":"Reinhold","full_name":"Förster, Reinhold","last_name":"Förster"},{"first_name":"Karl","last_name":"Mechtler","full_name":"Mechtler, Karl"},{"first_name":"Martina","last_name":"Mühlenhoff","full_name":"Mühlenhoff, Martina"},{"last_name":"Volkman","full_name":"Volkman, Brian","first_name":"Brian"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"external_id":{"pmid":["26657283"]},"article_processing_charge":"No","acknowledgement":"We thank S. Schüchner and E. Ogris for kindly providing the antibody to GFP, M. Helmbrecht and A. Huber for providing Nrp2−/− mice, the IST Scientific Support Facilities for excellent services, and J. Renkawitz and K. Vaahtomeri for critically reading the manuscript. ","quality_controlled":"1","publisher":"American Association for the Advancement of Science","oa":1,"day":"08","publication":"Science","year":"2016","doi":"10.1126/science.aad0512","date_published":"2016-01-08T00:00:00Z","date_created":"2018-12-11T11:52:57Z","page":"186 - 190","_id":"1599","status":"public","type":"journal_article","article_type":"original","date_updated":"2021-01-12T06:51:52Z","department":[{"_id":"MiSi"}],"oa_version":"Submitted Version","pmid":1,"acknowledged_ssus":[{"_id":"SSU"}],"abstract":[{"lang":"eng","text":"The addition of polysialic acid to N- and/or O-linked glycans, referred to as polysialylation, is a rare posttranslational modification that is mainly known to control the developmental plasticity of the nervous system. Here we show that CCR7, the central chemokine receptor controlling immune cell trafficking to secondary lymphatic organs, carries polysialic acid. This modification is essential for the recognition of the CCR7 ligand CCL21. As a consequence, dendritic cell trafficking is abrogated in polysialyltransferase-deficient mice, manifesting as disturbed lymph node homeostasis and unresponsiveness to inflammatory stimuli. Structure-function analysis of chemokine-receptor interactions reveals that CCL21 adopts an autoinhibited conformation, which is released upon interaction with polysialic acid. Thus, we describe a glycosylation-mediated immune cell trafficking disorder and its mechanistic basis.\r\n"}],"month":"01","intvolume":" 351","scopus_import":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5583642/","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":351,"issue":"6269","ec_funded":1},{"date_created":"2018-12-11T11:53:00Z","doi":"10.1007/s00023-015-0456-3","date_published":"2016-07-01T00:00:00Z","page":"1631 - 1675","publication":"Annales Henri Poincare","day":"01","year":"2016","oa":1,"publisher":"Birkhäuser","quality_controlled":"1","title":"Anderson transition at 2 dimensional growth rate on antitrees and spectral theory for operators with one propagating channel","author":[{"last_name":"Sadel","full_name":"Sadel, Christian","orcid":"0000-0001-8255-3968","first_name":"Christian","id":"4760E9F8-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5558","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Sadel C. 2016. Anderson transition at 2 dimensional growth rate on antitrees and spectral theory for operators with one propagating channel. Annales Henri Poincare. 17(7), 1631–1675.","chicago":"Sadel, Christian. “Anderson Transition at 2 Dimensional Growth Rate on Antitrees and Spectral Theory for Operators with One Propagating Channel.” Annales Henri Poincare. Birkhäuser, 2016. https://doi.org/10.1007/s00023-015-0456-3.","ama":"Sadel C. Anderson transition at 2 dimensional growth rate on antitrees and spectral theory for operators with one propagating channel. Annales Henri Poincare. 2016;17(7):1631-1675. doi:10.1007/s00023-015-0456-3","apa":"Sadel, C. (2016). Anderson transition at 2 dimensional growth rate on antitrees and spectral theory for operators with one propagating channel. Annales Henri Poincare. Birkhäuser. https://doi.org/10.1007/s00023-015-0456-3","ieee":"C. Sadel, “Anderson transition at 2 dimensional growth rate on antitrees and spectral theory for operators with one propagating channel,” Annales Henri Poincare, vol. 17, no. 7. Birkhäuser, pp. 1631–1675, 2016.","short":"C. Sadel, Annales Henri Poincare 17 (2016) 1631–1675.","mla":"Sadel, Christian. “Anderson Transition at 2 Dimensional Growth Rate on Antitrees and Spectral Theory for Operators with One Propagating Channel.” Annales Henri Poincare, vol. 17, no. 7, Birkhäuser, 2016, pp. 1631–75, doi:10.1007/s00023-015-0456-3."},"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"ec_funded":1,"issue":"7","volume":17,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 17","month":"07","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1501.04287"}],"scopus_import":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We show that the Anderson model has a transition from localization to delocalization at exactly 2 dimensional growth rate on antitrees with normalized edge weights which are certain discrete graphs. The kinetic part has a one-dimensional structure allowing a description through transfer matrices which involve some Schur complement. For such operators we introduce the notion of having one propagating channel and extend theorems from the theory of one-dimensional Jacobi operators that relate the behavior of transfer matrices with the spectrum. These theorems are then applied to the considered model. In essence, in a certain energy region the kinetic part averages the random potentials along shells and the transfer matrices behave similar as for a one-dimensional operator with random potential of decaying variance. At d dimensional growth for d>2 this effective decay is strong enough to obtain absolutely continuous spectrum, whereas for some uniform d dimensional growth with d<2 one has pure point spectrum in this energy region. At exactly uniform 2 dimensional growth also some singular continuous spectrum appears, at least at small disorder. As a corollary we also obtain a change from singular spectrum (d≤2) to absolutely continuous spectrum (d≥3) for random operators of the type rΔdr+λ on ℤd, where r is an orthogonal radial projection, Δd the discrete adjacency operator (Laplacian) on ℤd and λ a random potential. "}],"department":[{"_id":"LaEr"}],"date_updated":"2021-01-12T06:51:58Z","status":"public","type":"journal_article","_id":"1608"},{"_id":"1612","type":"journal_article","status":"public","date_updated":"2021-01-12T06:52:00Z","citation":{"ama":"Kazda A. CSP for binary conservative relational structures. Algebra Universalis. 2016;75(1):75-84. doi:10.1007/s00012-015-0358-8","apa":"Kazda, A. (2016). CSP for binary conservative relational structures. Algebra Universalis. Springer. https://doi.org/10.1007/s00012-015-0358-8","ieee":"A. Kazda, “CSP for binary conservative relational structures,” Algebra Universalis, vol. 75, no. 1. Springer, pp. 75–84, 2016.","short":"A. Kazda, Algebra Universalis 75 (2016) 75–84.","mla":"Kazda, Alexandr. “CSP for Binary Conservative Relational Structures.” Algebra Universalis, vol. 75, no. 1, Springer, 2016, pp. 75–84, doi:10.1007/s00012-015-0358-8.","ista":"Kazda A. 2016. CSP for binary conservative relational structures. Algebra Universalis. 75(1), 75–84.","chicago":"Kazda, Alexandr. “CSP for Binary Conservative Relational Structures.” Algebra Universalis. Springer, 2016. https://doi.org/10.1007/s00012-015-0358-8."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5554","author":[{"id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandr","full_name":"Kazda, Alexandr","last_name":"Kazda"}],"department":[{"_id":"VlKo"}],"title":"CSP for binary conservative relational structures","abstract":[{"text":"We prove that whenever A is a 3-conservative relational structure with only binary and unary relations,then the algebra of polymorphisms of A either has no Taylor operation (i.e.,CSP(A)is NP-complete),or it generates an SD(∧) variety (i.e.,CSP(A)has bounded width).","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1112.1099"}],"oa":1,"scopus_import":1,"publisher":"Springer","quality_controlled":"1","intvolume":" 75","month":"02","year":"2016","publication_status":"published","language":[{"iso":"eng"}],"publication":"Algebra Universalis","day":"01","page":"75 - 84","date_created":"2018-12-11T11:53:01Z","issue":"1","date_published":"2016-02-01T00:00:00Z","doi":"10.1007/s00012-015-0358-8","volume":75},{"title":"On the discrepancy of jittered sampling","department":[{"_id":"HeEd"}],"publist_id":"5549","author":[{"id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","orcid":"0000-0002-8379-3768","full_name":"Pausinger, Florian","last_name":"Pausinger"},{"first_name":"Stefan","full_name":"Steinerberger, Stefan","last_name":"Steinerberger"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Pausinger F, Steinerberger S. 2016. On the discrepancy of jittered sampling. Journal of Complexity. 33, 199–216.","chicago":"Pausinger, Florian, and Stefan Steinerberger. “On the Discrepancy of Jittered Sampling.” Journal of Complexity. Academic Press, 2016. https://doi.org/10.1016/j.jco.2015.11.003.","ama":"Pausinger F, Steinerberger S. On the discrepancy of jittered sampling. Journal of Complexity. 2016;33:199-216. doi:10.1016/j.jco.2015.11.003","apa":"Pausinger, F., & Steinerberger, S. (2016). On the discrepancy of jittered sampling. Journal of Complexity. Academic Press. https://doi.org/10.1016/j.jco.2015.11.003","short":"F. Pausinger, S. Steinerberger, Journal of Complexity 33 (2016) 199–216.","ieee":"F. Pausinger and S. Steinerberger, “On the discrepancy of jittered sampling,” Journal of Complexity, vol. 33. Academic Press, pp. 199–216, 2016.","mla":"Pausinger, Florian, and Stefan Steinerberger. “On the Discrepancy of Jittered Sampling.” Journal of Complexity, vol. 33, Academic Press, 2016, pp. 199–216, doi:10.1016/j.jco.2015.11.003."},"date_updated":"2021-01-12T06:52:02Z","status":"public","type":"journal_article","_id":"1617","volume":33,"doi":"10.1016/j.jco.2015.11.003","date_published":"2016-04-01T00:00:00Z","date_created":"2018-12-11T11:53:03Z","page":"199 - 216","day":"01","publication":"Journal of Complexity","language":[{"iso":"eng"}],"publication_status":"published","year":"2016","month":"04","intvolume":" 33","quality_controlled":"1","scopus_import":1,"publisher":"Academic Press","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1510.00251"}],"oa":1,"oa_version":"Submitted Version","acknowledgement":"We are grateful to the referee whose suggestions greatly improved the quality and clarity of the exposition.","abstract":[{"text":"We study the discrepancy of jittered sampling sets: such a set P⊂ [0,1]d is generated for fixed m∈ℕ by partitioning [0,1]d into md axis aligned cubes of equal measure and placing a random point inside each of the N=md cubes. We prove that, for N sufficiently large, 1/10 d/N1/2+1/2d ≤EDN∗(P)≤ √d(log N) 1/2/N1/2+1/2d, where the upper bound with an unspecified constant Cd was proven earlier by Beck. Our proof makes crucial use of the sharp Dvoretzky-Kiefer-Wolfowitz inequality and a suitably taylored Bernstein inequality; we have reasons to believe that the upper bound has the sharp scaling in N. Additional heuristics suggest that jittered sampling should be able to improve known bounds on the inverse of the star-discrepancy in the regime N≳dd. We also prove a partition principle showing that every partition of [0,1]d combined with a jittered sampling construction gives rise to a set whose expected squared L2-discrepancy is smaller than that of purely random points.","lang":"eng"}]},{"citation":{"apa":"Frank, R., Hainzl, C., Seiringer, R., & Solovej, J. (2016). The external field dependence of the BCS critical temperature. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-015-2526-2","ama":"Frank R, Hainzl C, Seiringer R, Solovej J. The external field dependence of the BCS critical temperature. Communications in Mathematical Physics. 2016;342(1):189-216. doi:10.1007/s00220-015-2526-2","short":"R. Frank, C. Hainzl, R. Seiringer, J. Solovej, Communications in Mathematical Physics 342 (2016) 189–216.","ieee":"R. Frank, C. Hainzl, R. Seiringer, and J. Solovej, “The external field dependence of the BCS critical temperature,” Communications in Mathematical Physics, vol. 342, no. 1. Springer, pp. 189–216, 2016.","mla":"Frank, Rupert, et al. “The External Field Dependence of the BCS Critical Temperature.” Communications in Mathematical Physics, vol. 342, no. 1, Springer, 2016, pp. 189–216, doi:10.1007/s00220-015-2526-2.","ista":"Frank R, Hainzl C, Seiringer R, Solovej J. 2016. The external field dependence of the BCS critical temperature. Communications in Mathematical Physics. 342(1), 189–216.","chicago":"Frank, Rupert, Christian Hainzl, Robert Seiringer, and Jan Solovej. “The External Field Dependence of the BCS Critical Temperature.” Communications in Mathematical Physics. Springer, 2016. https://doi.org/10.1007/s00220-015-2526-2."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Rupert","last_name":"Frank","full_name":"Frank, Rupert"},{"last_name":"Hainzl","full_name":"Hainzl, Christian","first_name":"Christian"},{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"first_name":"Jan","last_name":"Solovej","full_name":"Solovej, Jan"}],"publist_id":"5546","title":"The external field dependence of the BCS critical temperature","acknowledgement":"The authors are grateful to I. M. Sigal for useful discussions. Financial support from the US National Science Foundation through Grants PHY-1347399 and DMS-1363432 (R.L.F.), from the Danish council for independent research and from ERC Advanced Grant 321029 (J.P.S.) is acknowledged.","quality_controlled":"1","publisher":"Springer","oa":1,"year":"2016","day":"01","publication":"Communications in Mathematical Physics","page":"189 - 216","date_published":"2016-02-01T00:00:00Z","doi":"10.1007/s00220-015-2526-2","date_created":"2018-12-11T11:53:04Z","_id":"1620","type":"journal_article","status":"public","date_updated":"2021-01-12T06:52:03Z","department":[{"_id":"RoSe"}],"abstract":[{"text":"We consider the Bardeen–Cooper–Schrieffer free energy functional for particles interacting via a two-body potential on a microscopic scale and in the presence of weak external fields varying on a macroscopic scale. We study the influence of the external fields on the critical temperature. We show that in the limit where the ratio between the microscopic and macroscopic scale tends to zero, the next to leading order of the critical temperature is determined by the lowest eigenvalue of the linearization of the Ginzburg–Landau equation.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1410.2352"}],"month":"02","intvolume":" 342","publication_status":"published","language":[{"iso":"eng"}],"volume":342,"issue":"1"},{"status":"public","type":"journal_article","_id":"1622","department":[{"_id":"RoSe"}],"date_updated":"2021-01-12T06:52:04Z","intvolume":" 219","month":"03","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1501.04570"}],"scopus_import":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We prove analogues of the Lieb–Thirring and Hardy–Lieb–Thirring inequalities for many-body quantum systems with fractional kinetic operators and homogeneous interaction potentials, where no anti-symmetry on the wave functions is assumed. These many-body inequalities imply interesting one-body interpolation inequalities, and we show that the corresponding one- and many-body inequalities are actually equivalent in certain cases."}],"ec_funded":1,"volume":219,"issue":"3","language":[{"iso":"eng"}],"publication_status":"published","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"title":"Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems","publist_id":"5542","author":[{"last_name":"Lundholm","full_name":"Lundholm, Douglas","first_name":"Douglas"},{"id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan","last_name":"Nam","full_name":"Nam, Phan"},{"full_name":"Portmann, Fabian","last_name":"Portmann","first_name":"Fabian"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Lundholm, Douglas, et al. “Fractional Hardy–Lieb–Thirring and Related Inequalities for Interacting Systems.” Archive for Rational Mechanics and Analysis, vol. 219, no. 3, Springer, 2016, pp. 1343–82, doi:10.1007/s00205-015-0923-5.","apa":"Lundholm, D., Nam, P., & Portmann, F. (2016). Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems. Archive for Rational Mechanics and Analysis. Springer. https://doi.org/10.1007/s00205-015-0923-5","ama":"Lundholm D, Nam P, Portmann F. Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems. Archive for Rational Mechanics and Analysis. 2016;219(3):1343-1382. doi:10.1007/s00205-015-0923-5","ieee":"D. Lundholm, P. Nam, and F. Portmann, “Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems,” Archive for Rational Mechanics and Analysis, vol. 219, no. 3. Springer, pp. 1343–1382, 2016.","short":"D. Lundholm, P. Nam, F. Portmann, Archive for Rational Mechanics and Analysis 219 (2016) 1343–1382.","chicago":"Lundholm, Douglas, Phan Nam, and Fabian Portmann. “Fractional Hardy–Lieb–Thirring and Related Inequalities for Interacting Systems.” Archive for Rational Mechanics and Analysis. Springer, 2016. https://doi.org/10.1007/s00205-015-0923-5.","ista":"Lundholm D, Nam P, Portmann F. 2016. Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems. Archive for Rational Mechanics and Analysis. 219(3), 1343–1382."},"oa":1,"quality_controlled":"1","publisher":"Springer","acknowledgement":"We thank Jan Philip Solovej, Robert Seiringer and Vladimir Maz’ya for helpful discussions, as well as Rupert Frank\r\nand the anonymous referee for useful comments. Part of this work has been carried out during a visit at the Institut Mittag-Leffler (Stockholm). D.L. acknowledges financial support by the grant KAW 2010.0063 from the Knut and Alice Wallenberg Foundation and the Swedish Research Council grant no. 2013-4734. P.T.N. is supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734. F.P. acknowledges support from the ERC project no. 321029 “The\r\nmathematics of the structure of matter”.","date_created":"2018-12-11T11:53:05Z","date_published":"2016-03-01T00:00:00Z","doi":"10.1007/s00205-015-0923-5","page":"1343 - 1382","publication":"Archive for Rational Mechanics and Analysis","day":"01","year":"2016"},{"citation":{"apa":"Kelleher, J., Etheridge, A., Véber, A., & Barton, N. H. (2016). Spread of pedigree versus genetic ancestry in spatially distributed populations. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2015.10.008","ama":"Kelleher J, Etheridge A, Véber A, Barton NH. Spread of pedigree versus genetic ancestry in spatially distributed populations. Theoretical Population Biology. 2016;108:1-12. doi:10.1016/j.tpb.2015.10.008","ieee":"J. Kelleher, A. Etheridge, A. Véber, and N. H. Barton, “Spread of pedigree versus genetic ancestry in spatially distributed populations,” Theoretical Population Biology, vol. 108. Academic Press, pp. 1–12, 2016.","short":"J. Kelleher, A. Etheridge, A. Véber, N.H. Barton, Theoretical Population Biology 108 (2016) 1–12.","mla":"Kelleher, Jerome, et al. “Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.” Theoretical Population Biology, vol. 108, Academic Press, 2016, pp. 1–12, doi:10.1016/j.tpb.2015.10.008.","ista":"Kelleher J, Etheridge A, Véber A, Barton NH. 2016. Spread of pedigree versus genetic ancestry in spatially distributed populations. Theoretical Population Biology. 108, 1–12.","chicago":"Kelleher, Jerome, Alison Etheridge, Amandine Véber, and Nicholas H Barton. “Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.” Theoretical Population Biology. Academic Press, 2016. https://doi.org/10.1016/j.tpb.2015.10.008."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5524","author":[{"full_name":"Kelleher, Jerome","last_name":"Kelleher","first_name":"Jerome"},{"first_name":"Alison","full_name":"Etheridge, Alison","last_name":"Etheridge"},{"full_name":"Véber, Amandine","last_name":"Véber","first_name":"Amandine"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"title":"Spread of pedigree versus genetic ancestry in spatially distributed populations","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"has_accepted_license":"1","year":"2016","day":"01","publication":"Theoretical Population Biology","page":"1 - 12","date_published":"2016-04-01T00:00:00Z","doi":"10.1016/j.tpb.2015.10.008","date_created":"2018-12-11T11:53:08Z","quality_controlled":"1","publisher":"Academic Press","oa":1,"date_updated":"2021-01-12T06:52:07Z","ddc":["576"],"department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:45:07Z","_id":"1631","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":"465","publication_status":"published","file":[{"date_created":"2018-12-12T10:11:12Z","file_name":"IST-2016-465-v1+1_1-s2.0-S0040580915001094-main.pdf","creator":"system","date_updated":"2020-07-14T12:45:07Z","file_size":1684043,"file_id":"4865","checksum":"6a65ba187994d4ad86c1c509e0ff482a","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":108,"ec_funded":1,"abstract":[{"lang":"eng","text":"Ancestral processes are fundamental to modern population genetics and spatial structure has been the subject of intense interest for many years. Despite this interest, almost nothing is known about the distribution of the locations of pedigree or genetic ancestors. Using both spatially continuous and stepping-stone models, we show that the distribution of pedigree ancestors approaches a travelling wave, for which we develop two alternative approximations. The speed and width of the wave are sensitive to the local details of the model. After a short time, genetic ancestors spread far more slowly than pedigree ancestors, ultimately diffusing out with radius ## rather than spreading at constant speed. In contrast to the wave of pedigree ancestors, the spread of genetic ancestry is insensitive to the local details of the models."}],"oa_version":"Published Version","scopus_import":1,"month":"04","intvolume":" 108"},{"title":"A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana","author":[{"first_name":"Radka","full_name":"Zemová, Radka","last_name":"Zemová"},{"full_name":"Zwiewka, Marta","last_name":"Zwiewka","first_name":"Marta"},{"last_name":"Bielach","full_name":"Bielach, Agnieszka","first_name":"Agnieszka"},{"last_name":"Robert","full_name":"Robert, Hélène","first_name":"Hélène"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596"}],"publist_id":"5512","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Zemová, Radka, et al. “A Forward Genetic Screen for New Regulators of Auxin Mediated Degradation of Auxin Transport Proteins in Arabidopsis Thaliana.” Journal of Plant Growth Regulation, vol. 35, no. 2, Springer, 2016, pp. 465–76, doi:10.1007/s00344-015-9553-2.","apa":"Zemová, R., Zwiewka, M., Bielach, A., Robert, H., & Friml, J. (2016). A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana. Journal of Plant Growth Regulation. Springer. https://doi.org/10.1007/s00344-015-9553-2","ama":"Zemová R, Zwiewka M, Bielach A, Robert H, Friml J. A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana. Journal of Plant Growth Regulation. 2016;35(2):465-476. doi:10.1007/s00344-015-9553-2","short":"R. Zemová, M. Zwiewka, A. Bielach, H. Robert, J. Friml, Journal of Plant Growth Regulation 35 (2016) 465–476.","ieee":"R. Zemová, M. Zwiewka, A. Bielach, H. Robert, and J. Friml, “A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana,” Journal of Plant Growth Regulation, vol. 35, no. 2. Springer, pp. 465–476, 2016.","chicago":"Zemová, Radka, Marta Zwiewka, Agnieszka Bielach, Hélène Robert, and Jiří Friml. “A Forward Genetic Screen for New Regulators of Auxin Mediated Degradation of Auxin Transport Proteins in Arabidopsis Thaliana.” Journal of Plant Growth Regulation. Springer, 2016. https://doi.org/10.1007/s00344-015-9553-2.","ista":"Zemová R, Zwiewka M, Bielach A, Robert H, Friml J. 2016. A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana. Journal of Plant Growth Regulation. 35(2), 465–476."},"date_published":"2016-06-01T00:00:00Z","doi":"10.1007/s00344-015-9553-2","date_created":"2018-12-11T11:53:12Z","page":"465 - 476","day":"01","publication":"Journal of Plant Growth Regulation","has_accepted_license":"1","year":"2016","publisher":"Springer","quality_controlled":"1","oa":1,"acknowledgement":"European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation GAČR (GA13-40637S) to JF. ","file_date_updated":"2020-07-14T12:45:08Z","department":[{"_id":"JiFr"}],"ddc":["581"],"date_updated":"2021-01-12T06:52:11Z","status":"public","pubrep_id":"1001","type":"journal_article","_id":"1641","issue":"2","volume":35,"file":[{"file_id":"4695","checksum":"0dc6a300cde6536ceedd2bcdd2060efb","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:08:34Z","file_name":"IST-2018-1001-v1+1_Zemova_JPlantGrowthRegul_2016_proofs.pdf","date_updated":"2020-07-14T12:45:08Z","file_size":5637591,"creator":"system"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"06","intvolume":" 35","scopus_import":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The plant hormone auxin (indole-3-acetic acid) is a major regulator of plant growth and development including embryo and root patterning, lateral organ formation and growth responses to environmental stimuli. Auxin is directionally transported from cell to cell by the action of specific auxin influx [AUXIN-RESISTANT1 (AUX1)] and efflux [PIN-FORMED (PIN)] transport regulators, whose polar, subcellular localizations are aligned with the direction of the auxin flow. Auxin itself regulates its own transport by modulation of the expression and subcellular localization of the auxin transporters. Increased auxin levels promote the transcription of PIN2 and AUX1 genes as well as stabilize PIN proteins at the plasma membrane, whereas prolonged auxin exposure increases the turnover of PIN proteins and their degradation in the vacuole. In this study, we applied a forward genetic approach, to identify molecular components playing a role in the auxin-mediated degradation. We generated EMS-mutagenized Arabidopsis PIN2::PIN2:GFP, AUX1::AUX1:YFP eir1aux1 populations and designed a screen for mutants with persistently strong fluorescent signals of the tagged PIN2 and AUX1 after prolonged treatment with the synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D). This approach yielded novel auxin degradation mutants defective in trafficking and degradation of PIN2 and AUX1 proteins and established a role for auxin-mediated degradation in plant development."}]},{"project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"259668","name":"Provable Security for Physical Cryptography"},{"grant_number":"682815","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"title":"Practical round-optimal blind signatures in the standard model from weaker assumptions","author":[{"first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","last_name":"Fuchsbauer","full_name":"Fuchsbauer, Georg"},{"full_name":"Hanser, Christian","last_name":"Hanser","first_name":"Christian"},{"id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan","full_name":"Kamath Hosdurg, Chethan","last_name":"Kamath Hosdurg"},{"last_name":"Slamanig","full_name":"Slamanig, Daniel","first_name":"Daniel"}],"publist_id":"6109","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Fuchsbauer, G., Hanser, C., Kamath Hosdurg, C., & Slamanig, D. (2016). Practical round-optimal blind signatures in the standard model from weaker assumptions (Vol. 9841, pp. 391–408). Presented at the SCN: Security and Cryptography for Networks, Amalfi, Italy: Springer. https://doi.org/10.1007/978-3-319-44618-9_21","ama":"Fuchsbauer G, Hanser C, Kamath Hosdurg C, Slamanig D. Practical round-optimal blind signatures in the standard model from weaker assumptions. In: Vol 9841. Springer; 2016:391-408. doi:10.1007/978-3-319-44618-9_21","ieee":"G. Fuchsbauer, C. Hanser, C. Kamath Hosdurg, and D. Slamanig, “Practical round-optimal blind signatures in the standard model from weaker assumptions,” presented at the SCN: Security and Cryptography for Networks, Amalfi, Italy, 2016, vol. 9841, pp. 391–408.","short":"G. Fuchsbauer, C. Hanser, C. Kamath Hosdurg, D. Slamanig, in:, Springer, 2016, pp. 391–408.","mla":"Fuchsbauer, Georg, et al. Practical Round-Optimal Blind Signatures in the Standard Model from Weaker Assumptions. Vol. 9841, Springer, 2016, pp. 391–408, doi:10.1007/978-3-319-44618-9_21.","ista":"Fuchsbauer G, Hanser C, Kamath Hosdurg C, Slamanig D. 2016. Practical round-optimal blind signatures in the standard model from weaker assumptions. SCN: Security and Cryptography for Networks, LNCS, vol. 9841, 391–408.","chicago":"Fuchsbauer, Georg, Christian Hanser, Chethan Kamath Hosdurg, and Daniel Slamanig. “Practical Round-Optimal Blind Signatures in the Standard Model from Weaker Assumptions,” 9841:391–408. Springer, 2016. https://doi.org/10.1007/978-3-319-44618-9_21."},"publisher":"Springer","quality_controlled":"1","oa":1,"date_published":"2016-08-11T00:00:00Z","doi":"10.1007/978-3-319-44618-9_21","date_created":"2018-12-11T11:50:49Z","page":"391 - 408","day":"11","year":"2016","status":"public","type":"conference","conference":{"name":"SCN: Security and Cryptography for Networks","start_date":"2016-08-31","end_date":"2016-09-02","location":"Amalfi, Italy"},"_id":"1225","department":[{"_id":"KrPi"}],"date_updated":"2023-02-23T10:08:16Z","month":"08","intvolume":" 9841","alternative_title":["LNCS"],"scopus_import":1,"main_file_link":[{"url":"https://eprint.iacr.org/2016/662","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"At Crypto 2015 Fuchsbauer, Hanser and Slamanig (FHS) presented the first standard-model construction of efficient roundoptimal blind signatures that does not require complexity leveraging. It is conceptually simple and builds on the primitive of structure-preserving signatures on equivalence classes (SPS-EQ). FHS prove the unforgeability of their scheme assuming EUF-CMA security of the SPS-EQ scheme and hardness of a version of the DH inversion problem. Blindness under adversarially chosen keys is proven under an interactive variant of the DDH assumption. We propose a variant of their scheme whose blindness can be proven under a non-interactive assumption, namely a variant of the bilinear DDH assumption. We moreover prove its unforgeability assuming only unforgeability of the underlying SPS-EQ but no additional assumptions as needed for the FHS scheme."}],"related_material":{"record":[{"relation":"earlier_version","id":"1647","status":"public"}]},"volume":9841,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published"},{"project":[{"call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","grant_number":"259668"}],"citation":{"chicago":"Okamoto, Tatsuaki, Krzysztof Z Pietrzak, Brent Waters, and Daniel Wichs. “New Realizations of Somewhere Statistically Binding Hashing and Positional Accumulators,” 9452:121–45. Springer, 2016. https://doi.org/10.1007/978-3-662-48797-6_6.","ista":"Okamoto T, Pietrzak KZ, Waters B, Wichs D. 2016. New realizations of somewhere statistically binding hashing and positional accumulators. ASIACRYPT: Theory and Application of Cryptology and Information Security, LNCS, vol. 9452, 121–145.","mla":"Okamoto, Tatsuaki, et al. New Realizations of Somewhere Statistically Binding Hashing and Positional Accumulators. Vol. 9452, Springer, 2016, pp. 121–45, doi:10.1007/978-3-662-48797-6_6.","ieee":"T. Okamoto, K. Z. Pietrzak, B. Waters, and D. Wichs, “New realizations of somewhere statistically binding hashing and positional accumulators,” presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Auckland, New Zealand, 2016, vol. 9452, pp. 121–145.","short":"T. Okamoto, K.Z. Pietrzak, B. Waters, D. Wichs, in:, Springer, 2016, pp. 121–145.","apa":"Okamoto, T., Pietrzak, K. Z., Waters, B., & Wichs, D. (2016). New realizations of somewhere statistically binding hashing and positional accumulators (Vol. 9452, pp. 121–145). Presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Auckland, New Zealand: Springer. https://doi.org/10.1007/978-3-662-48797-6_6","ama":"Okamoto T, Pietrzak KZ, Waters B, Wichs D. New realizations of somewhere statistically binding hashing and positional accumulators. In: Vol 9452. Springer; 2016:121-145. doi:10.1007/978-3-662-48797-6_6"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Okamoto","full_name":"Okamoto, Tatsuaki","first_name":"Tatsuaki"},{"last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Waters, Brent","last_name":"Waters","first_name":"Brent"},{"last_name":"Wichs","full_name":"Wichs, Daniel","first_name":"Daniel"}],"publist_id":"5497","title":"New realizations of somewhere statistically binding hashing and positional accumulators","quality_controlled":"1","publisher":"Springer","oa":1,"has_accepted_license":"1","year":"2016","day":"08","page":"121 - 145","date_published":"2016-01-08T00:00:00Z","doi":"10.1007/978-3-662-48797-6_6","date_created":"2018-12-11T11:53:16Z","_id":"1653","type":"conference","conference":{"start_date":"2015-11-29","location":"Auckland, New Zealand","end_date":"2015-12-03","name":"ASIACRYPT: Theory and Application of Cryptology and Information Security"},"status":"public","pubrep_id":"677","date_updated":"2021-01-12T06:52:16Z","ddc":["000"],"department":[{"_id":"KrPi"}],"file_date_updated":"2020-07-14T12:45:08Z","abstract":[{"text":"A somewhere statistically binding (SSB) hash, introduced by Hubáček and Wichs (ITCS ’15), can be used to hash a long string x to a short digest y = H hk (x) using a public hashing-key hk. Furthermore, there is a way to set up the hash key hk to make it statistically binding on some arbitrary hidden position i, meaning that: (1) the digest y completely determines the i’th bit (or symbol) of x so that all pre-images of y have the same value in the i’th position, (2) it is computationally infeasible to distinguish the position i on which hk is statistically binding from any other position i’. Lastly, the hash should have a local opening property analogous to Merkle-Tree hashing, meaning that given x and y = H hk (x) it should be possible to create a short proof π that certifies the value of the i’th bit (or symbol) of x without having to provide the entire input x. A similar primitive called a positional accumulator, introduced by Koppula, Lewko and Waters (STOC ’15) further supports dynamic updates of the hashed value. These tools, which are interesting in their own right, also serve as one of the main technical components in several recent works building advanced applications from indistinguishability obfuscation (iO).\r\n\r\nThe prior constructions of SSB hashing and positional accumulators required fully homomorphic encryption (FHE) and iO respectively. In this work, we give new constructions of these tools based on well studied number-theoretic assumptions such as DDH, Phi-Hiding and DCR, as well as a general construction from lossy/injective functions.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":1,"alternative_title":["LNCS"],"month":"01","intvolume":" 9452","publication_status":"published","file":[{"creator":"system","date_updated":"2020-07-14T12:45:08Z","file_size":580088,"date_created":"2018-12-12T10:12:05Z","file_name":"IST-2016-677-v1+1_869.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"a57711cb660c5b17b42bb47275a00180","file_id":"4923"}],"language":[{"iso":"eng"}],"volume":9452,"ec_funded":1},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"457","status":"public","_id":"1705","file_date_updated":"2020-07-14T12:45:13Z","department":[{"_id":"ToHe"}],"date_updated":"2021-01-12T06:52:38Z","ddc":["000"],"scopus_import":1,"intvolume":" 18","month":"08","abstract":[{"lang":"eng","text":"Hybrid systems represent an important and powerful formalism for modeling real-world applications such as embedded systems. A verification tool like SpaceEx is based on the exploration of a symbolic search space (the region space). As a verification tool, it is typically optimized towards proving the absence of errors. In some settings, e.g., when the verification tool is employed in a feedback-directed design cycle, one would like to have the option to call a version that is optimized towards finding an error trajectory in the region space. A recent approach in this direction is based on guided search. Guided search relies on a cost function that indicates which states are promising to be explored, and preferably explores more promising states first. In this paper, we propose an abstraction-based cost function based on coarse-grained space abstractions for guiding the reachability analysis. For this purpose, a suitable abstraction technique that exploits the flexible granularity of modern reachability analysis algorithms is introduced. The new cost function is an effective extension of pattern database approaches that have been successfully applied in other areas. The approach has been implemented in the SpaceEx model checker. The evaluation shows its practical potential."}],"oa_version":"Published Version","ec_funded":1,"volume":18,"issue":"4","publication_status":"published","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5146","checksum":"31561d7705599a9bd4ea816accc0752e","creator":"system","file_size":2296522,"date_updated":"2020-07-14T12:45:13Z","file_name":"IST-2016-457-v1+1_s10009-015-0393-y.pdf","date_created":"2018-12-12T10:15:26Z"}],"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"article_processing_charge":"Yes (via OA deal)","publist_id":"5431","author":[{"id":"369D9A44-F248-11E8-B48F-1D18A9856A87","first_name":"Sergiy","orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy","last_name":"Bogomolov"},{"first_name":"Alexandre","full_name":"Donzé, Alexandre","last_name":"Donzé"},{"first_name":"Goran","full_name":"Frehse, Goran","last_name":"Frehse"},{"first_name":"Radu","full_name":"Grosu, Radu","last_name":"Grosu"},{"first_name":"Taylor","full_name":"Johnson, Taylor","last_name":"Johnson"},{"last_name":"Ladan","full_name":"Ladan, Hamed","first_name":"Hamed"},{"full_name":"Podelski, Andreas","last_name":"Podelski","first_name":"Andreas"},{"first_name":"Martin","full_name":"Wehrle, Martin","last_name":"Wehrle"}],"title":"Guided search for hybrid systems based on coarse-grained space abstractions","citation":{"mla":"Bogomolov, Sergiy, et al. “Guided Search for Hybrid Systems Based on Coarse-Grained Space Abstractions.” International Journal on Software Tools for Technology Transfer, vol. 18, no. 4, Springer, 2016, pp. 449–67, doi:10.1007/s10009-015-0393-y.","ama":"Bogomolov S, Donzé A, Frehse G, et al. Guided search for hybrid systems based on coarse-grained space abstractions. International Journal on Software Tools for Technology Transfer. 2016;18(4):449-467. doi:10.1007/s10009-015-0393-y","apa":"Bogomolov, S., Donzé, A., Frehse, G., Grosu, R., Johnson, T., Ladan, H., … Wehrle, M. (2016). Guided search for hybrid systems based on coarse-grained space abstractions. International Journal on Software Tools for Technology Transfer. Springer. https://doi.org/10.1007/s10009-015-0393-y","ieee":"S. Bogomolov et al., “Guided search for hybrid systems based on coarse-grained space abstractions,” International Journal on Software Tools for Technology Transfer, vol. 18, no. 4. Springer, pp. 449–467, 2016.","short":"S. Bogomolov, A. Donzé, G. Frehse, R. Grosu, T. Johnson, H. Ladan, A. Podelski, M. Wehrle, International Journal on Software Tools for Technology Transfer 18 (2016) 449–467.","chicago":"Bogomolov, Sergiy, Alexandre Donzé, Goran Frehse, Radu Grosu, Taylor Johnson, Hamed Ladan, Andreas Podelski, and Martin Wehrle. “Guided Search for Hybrid Systems Based on Coarse-Grained Space Abstractions.” International Journal on Software Tools for Technology Transfer. Springer, 2016. https://doi.org/10.1007/s10009-015-0393-y.","ista":"Bogomolov S, Donzé A, Frehse G, Grosu R, Johnson T, Ladan H, Podelski A, Wehrle M. 2016. Guided search for hybrid systems based on coarse-grained space abstractions. International Journal on Software Tools for Technology Transfer. 18(4), 449–467."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Springer","quality_controlled":"1","page":"449 - 467","date_created":"2018-12-11T11:53:34Z","doi":"10.1007/s10009-015-0393-y","date_published":"2016-08-01T00:00:00Z","year":"2016","has_accepted_license":"1","publication":"International Journal on Software Tools for Technology Transfer","day":"01"},{"publication":"Journal of Multivariate Analysis","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2016","date_created":"2018-12-11T11:54:15Z","volume":143,"doi":"10.1016/j.jmva.2015.10.005","date_published":"2016-01-01T00:00:00Z","page":"440 - 452","oa_version":"Preprint","abstract":[{"text":"Relational models for contingency tables are generalizations of log-linear models, allowing effects associated with arbitrary subsets of cells in the table, and not necessarily containing the overall effect, that is, a common parameter in every cell. Similarly to log-linear models, relational models can be extended to non-negative distributions, but the extension requires more complex methods. An extended relational model is defined as an algebraic variety, and it turns out to be the closure of the original model with respect to the Bregman divergence. In the extended relational model, the MLE of the cell parameters always exists and is unique, but some of its properties may be different from those of the MLE under log-linear models. The MLE can be computed using a generalized iterative scaling procedure based on Bregman projections. ","lang":"eng"}],"intvolume":" 143","month":"01","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1501.00600"}],"quality_controlled":"1","scopus_import":1,"publisher":"Elsevier","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Klimova, Anna, and Tamás Rudas. “On the Closure of Relational Models.” Journal of Multivariate Analysis. Elsevier, 2016. https://doi.org/10.1016/j.jmva.2015.10.005.","ista":"Klimova A, Rudas T. 2016. On the closure of relational models. Journal of Multivariate Analysis. 143, 440–452.","mla":"Klimova, Anna, and Tamás Rudas. “On the Closure of Relational Models.” Journal of Multivariate Analysis, vol. 143, Elsevier, 2016, pp. 440–52, doi:10.1016/j.jmva.2015.10.005.","ieee":"A. Klimova and T. Rudas, “On the closure of relational models,” Journal of Multivariate Analysis, vol. 143. Elsevier, pp. 440–452, 2016.","short":"A. Klimova, T. Rudas, Journal of Multivariate Analysis 143 (2016) 440–452.","apa":"Klimova, A., & Rudas, T. (2016). On the closure of relational models. Journal of Multivariate Analysis. Elsevier. https://doi.org/10.1016/j.jmva.2015.10.005","ama":"Klimova A, Rudas T. On the closure of relational models. Journal of Multivariate Analysis. 2016;143:440-452. doi:10.1016/j.jmva.2015.10.005"},"date_updated":"2021-01-12T06:53:30Z","department":[{"_id":"CaUh"}],"title":"On the closure of relational models","publist_id":"5270","author":[{"id":"31934120-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","full_name":"Klimova, Anna","last_name":"Klimova"},{"full_name":"Rudas, Tamás","last_name":"Rudas","first_name":"Tamás"}],"_id":"1833","status":"public","type":"journal_article"},{"_id":"1881","type":"journal_article","status":"public","date_updated":"2021-01-12T06:53:49Z","department":[{"_id":"LaEr"}],"abstract":[{"lang":"eng","text":"We consider random matrices of the form H=W+λV, λ∈ℝ+, where W is a real symmetric or complex Hermitian Wigner matrix of size N and V is a real bounded diagonal random matrix of size N with i.i.d.\\ entries that are independent of W. We assume subexponential decay for the matrix entries of W and we choose λ∼1, so that the eigenvalues of W and λV are typically of the same order. Further, we assume that the density of the entries of V is supported on a single interval and is convex near the edges of its support. In this paper we prove that there is λ+∈ℝ+ such that the largest eigenvalues of H are in the limit of large N determined by the order statistics of V for λ>λ+. In particular, the largest eigenvalue of H has a Weibull distribution in the limit N→∞ if λ>λ+. Moreover, for N sufficiently large, we show that the eigenvectors associated to the largest eigenvalues are partially localized for λ>λ+, while they are completely delocalized for λ<λ+. Similar results hold for the lowest eigenvalues. "}],"oa_version":"Preprint","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1310.7057","open_access":"1"}],"month":"02","intvolume":" 164","publication_status":"published","language":[{"iso":"eng"}],"issue":"1-2","volume":164,"ec_funded":1,"project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Lee, Jioon, and Kevin Schnelli. “Extremal Eigenvalues and Eigenvectors of Deformed Wigner Matrices.” Probability Theory and Related Fields, vol. 164, no. 1–2, Springer, 2016, pp. 165–241, doi:10.1007/s00440-014-0610-8.","short":"J. Lee, K. Schnelli, Probability Theory and Related Fields 164 (2016) 165–241.","ieee":"J. Lee and K. Schnelli, “Extremal eigenvalues and eigenvectors of deformed Wigner matrices,” Probability Theory and Related Fields, vol. 164, no. 1–2. Springer, pp. 165–241, 2016.","ama":"Lee J, Schnelli K. Extremal eigenvalues and eigenvectors of deformed Wigner matrices. Probability Theory and Related Fields. 2016;164(1-2):165-241. doi:10.1007/s00440-014-0610-8","apa":"Lee, J., & Schnelli, K. (2016). Extremal eigenvalues and eigenvectors of deformed Wigner matrices. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-014-0610-8","chicago":"Lee, Jioon, and Kevin Schnelli. “Extremal Eigenvalues and Eigenvectors of Deformed Wigner Matrices.” Probability Theory and Related Fields. Springer, 2016. https://doi.org/10.1007/s00440-014-0610-8.","ista":"Lee J, Schnelli K. 2016. Extremal eigenvalues and eigenvectors of deformed Wigner matrices. Probability Theory and Related Fields. 164(1–2), 165–241."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5215","author":[{"first_name":"Jioon","last_name":"Lee","full_name":"Lee, Jioon"},{"id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","first_name":"Kevin","orcid":"0000-0003-0954-3231","full_name":"Schnelli, Kevin","last_name":"Schnelli"}],"title":"Extremal eigenvalues and eigenvectors of deformed Wigner matrices","acknowledgement":"Most of the presented work was obtained while Kevin Schnelli was staying at the IAS with the support of\r\nThe Fund For Math.","quality_controlled":"1","publisher":"Springer","oa":1,"year":"2016","day":"01","publication":"Probability Theory and Related Fields","page":"165 - 241","date_published":"2016-02-01T00:00:00Z","doi":"10.1007/s00440-014-0610-8","date_created":"2018-12-11T11:54:31Z"},{"date_updated":"2023-02-23T10:34:31Z","department":[{"_id":"UlWa"}],"_id":"1411","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"earlier_version","id":"2244","status":"public"}]},"issue":"1","volume":212,"abstract":[{"text":"We consider two systems (α1, …, αm) and (β1, …,βn) of simple curves drawn on a compact two-dimensional surface M with boundary. Each αi and each βj is either an arc meeting the boundary of M at its two endpoints, or a closed curve. The αi are pairwise disjoint except for possibly sharing endpoints, and similarly for the βj. We want to “untangle” the βj from the ai by a self-homeomorphism of M; more precisely, we seek a homeomorphism φ:M→M fixing the boundary of M pointwise such that the total number of crossings of the ai with the φ(βj) is as small as possible. This problem is motivated by an application in the algorithmic theory of embeddings and 3-manifolds. We prove that if M is planar, i.e., a sphere with h ≥ 0 boundary components (“holes”), then O(mn) crossings can be achieved (independently of h), which is asymptotically tight, as an easy lower bound shows. In general, for an arbitrary (orientable or nonorientable) surface M with h holes and of (orientable or nonorientable) genus g ≥ 0, we obtain an O((m + n)4) upper bound, again independent of h and g. The proofs rely, among other things, on a result concerning simultaneous planar drawings of graphs by Erten and Kobourov.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1302.6475"}],"scopus_import":1,"intvolume":" 212","month":"05","citation":{"ista":"Matoušek J, Sedgwick E, Tancer M, Wagner U. 2016. Untangling two systems of noncrossing curves. Israel Journal of Mathematics. 212(1), 37–79.","chicago":"Matoušek, Jiří, Eric Sedgwick, Martin Tancer, and Uli Wagner. “Untangling Two Systems of Noncrossing Curves.” Israel Journal of Mathematics. Springer, 2016. https://doi.org/10.1007/s11856-016-1294-9.","short":"J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, Israel Journal of Mathematics 212 (2016) 37–79.","ieee":"J. Matoušek, E. Sedgwick, M. Tancer, and U. Wagner, “Untangling two systems of noncrossing curves,” Israel Journal of Mathematics, vol. 212, no. 1. Springer, pp. 37–79, 2016.","apa":"Matoušek, J., Sedgwick, E., Tancer, M., & Wagner, U. (2016). Untangling two systems of noncrossing curves. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-016-1294-9","ama":"Matoušek J, Sedgwick E, Tancer M, Wagner U. Untangling two systems of noncrossing curves. Israel Journal of Mathematics. 2016;212(1):37-79. doi:10.1007/s11856-016-1294-9","mla":"Matoušek, Jiří, et al. “Untangling Two Systems of Noncrossing Curves.” Israel Journal of Mathematics, vol. 212, no. 1, Springer, 2016, pp. 37–79, doi:10.1007/s11856-016-1294-9."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5796","author":[{"last_name":"Matoušek","full_name":"Matoušek, Jiří","first_name":"Jiří"},{"first_name":"Eric","full_name":"Sedgwick, Eric","last_name":"Sedgwick"},{"last_name":"Tancer","orcid":"0000-0002-1191-6714","full_name":"Tancer, Martin","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"title":"Untangling two systems of noncrossing curves","project":[{"grant_number":"PP00P2_138948","name":"Embeddings in Higher Dimensions: Algorithms and Combinatorics","_id":"25FA3206-B435-11E9-9278-68D0E5697425"}],"year":"2016","publication":"Israel Journal of Mathematics","day":"01","page":"37 - 79","date_created":"2018-12-11T11:51:52Z","date_published":"2016-05-01T00:00:00Z","doi":"10.1007/s11856-016-1294-9","acknowledgement":"Supported by the ERC Adv anced Grant No. 267165. ","oa":1,"quality_controlled":"1","publisher":"Springer"},{"doi":"10.1007/s00037-015-0120-9","date_published":"2016-09-01T00:00:00Z","date_created":"2018-12-11T11:52:16Z","page":"567 - 605","day":"01","publication":"Computational Complexity","has_accepted_license":"1","year":"2016","quality_controlled":"1","publisher":"Springer","oa":1,"acknowledgement":"This work was partly funded by the European Research Council under ERC Starting Grant 259668-PSPC and ERC Advanced Grant 321310-PERCY.\r\n","title":"A counterexample to the chain rule for conditional HILL entropy","publist_id":"5715","author":[{"last_name":"Krenn","orcid":"0000-0003-2835-9093","full_name":"Krenn, Stephan","id":"329FCCF0-F248-11E8-B48F-1D18A9856A87","first_name":"Stephan"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654"},{"first_name":"Akshay","full_name":"Wadia, Akshay","last_name":"Wadia"},{"first_name":"Daniel","full_name":"Wichs, Daniel","last_name":"Wichs"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Krenn S, Pietrzak KZ, Wadia A, Wichs D. 2016. A counterexample to the chain rule for conditional HILL entropy. Computational Complexity. 25(3), 567–605.","chicago":"Krenn, Stephan, Krzysztof Z Pietrzak, Akshay Wadia, and Daniel Wichs. “A Counterexample to the Chain Rule for Conditional HILL Entropy.” Computational Complexity. Springer, 2016. https://doi.org/10.1007/s00037-015-0120-9.","ama":"Krenn S, Pietrzak KZ, Wadia A, Wichs D. A counterexample to the chain rule for conditional HILL entropy. Computational Complexity. 2016;25(3):567-605. doi:10.1007/s00037-015-0120-9","apa":"Krenn, S., Pietrzak, K. Z., Wadia, A., & Wichs, D. (2016). A counterexample to the chain rule for conditional HILL entropy. Computational Complexity. Springer. https://doi.org/10.1007/s00037-015-0120-9","short":"S. Krenn, K.Z. Pietrzak, A. Wadia, D. Wichs, Computational Complexity 25 (2016) 567–605.","ieee":"S. Krenn, K. Z. Pietrzak, A. Wadia, and D. Wichs, “A counterexample to the chain rule for conditional HILL entropy,” Computational Complexity, vol. 25, no. 3. Springer, pp. 567–605, 2016.","mla":"Krenn, Stephan, et al. “A Counterexample to the Chain Rule for Conditional HILL Entropy.” Computational Complexity, vol. 25, no. 3, Springer, 2016, pp. 567–605, doi:10.1007/s00037-015-0120-9."},"project":[{"grant_number":"259668","name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"volume":25,"issue":"3","related_material":{"record":[{"relation":"earlier_version","id":"2940","status":"public"}]},"ec_funded":1,"file":[{"file_id":"5012","checksum":"7659296174fa75f5f0364f31f46f4bcf","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-766-v1+1_678.pdf","date_created":"2018-12-12T10:13:29Z","creator":"system","file_size":483258,"date_updated":"2020-07-14T12:44:56Z"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"09","intvolume":" 25","scopus_import":1,"oa_version":"Submitted Version","abstract":[{"text":"Most entropy notions H(.) like Shannon or min-entropy satisfy a chain rule stating that for random variables X,Z, and A we have H(X|Z,A)≥H(X|Z)−|A|. That is, by conditioning on A the entropy of X can decrease by at most the bitlength |A| of A. Such chain rules are known to hold for some computational entropy notions like Yao’s and unpredictability-entropy. For HILL entropy, the computational analogue of min-entropy, the chain rule is of special interest and has found many applications, including leakage-resilient cryptography, deterministic encryption, and memory delegation. These applications rely on restricted special cases of the chain rule. Whether the chain rule for conditional HILL entropy holds in general was an open problem for which we give a strong negative answer: we construct joint distributions (X,Z,A), where A is a distribution over a single bit, such that the HILL entropy H HILL (X|Z) is large but H HILL (X|Z,A) is basically zero.\r\n\r\nOur counterexample just makes the minimal assumption that NP⊈P/poly. Under the stronger assumption that injective one-way function exist, we can make all the distributions efficiently samplable.\r\n\r\nFinally, we show that some more sophisticated cryptographic objects like lossy functions can be used to sample a distribution constituting a counterexample to the chain rule making only a single invocation to the underlying object.","lang":"eng"}],"file_date_updated":"2020-07-14T12:44:56Z","department":[{"_id":"KrPi"}],"ddc":["004"],"date_updated":"2023-02-23T11:05:09Z","status":"public","pubrep_id":"766","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":"1479"},{"_id":"478","type":"conference","conference":{"name":"ECAI: European Conference on Artificial Intelligence","start_date":"2016-08-29","location":"The Hague, Netherlands","end_date":"2016-09-02"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"status":"public","pubrep_id":"950","date_updated":"2021-01-12T08:00:54Z","ddc":["004"],"department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:46:35Z","abstract":[{"lang":"eng","text":"Magic: the Gathering is a game about magical combat for any number of players. Formally it is a zero-sum, imperfect information stochastic game that consists of a potentially unbounded number of steps. We consider the problem of deciding if a move is legal in a given single step of Magic. We show that the problem is (a) coNP-complete in general; and (b) in P if either of two small sets of cards are not used. Our lower bound holds even for single-player Magic games. The significant aspects of our results are as follows: First, in most real-life game problems, the task of deciding whether a given move is legal in a single step is trivial, and the computationally hard task is to find the best sequence of legal moves in the presence of multiple players. In contrast, quite uniquely our hardness result holds for single step and with only one-player. Second, we establish efficient algorithms for important special cases of Magic."}],"oa_version":"Published Version","alternative_title":["Frontiers in Artificial Intelligence and Applications"],"scopus_import":1,"month":"01","intvolume":" 285","publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"4658","checksum":"848043c812ace05e459579c923f3d3cf","creator":"system","file_size":2116225,"date_updated":"2020-07-14T12:46:35Z","file_name":"IST-2018-950-v1+1_2016_Chatterjee_The_complexity.pdf","date_created":"2018-12-12T10:07:59Z"}],"language":[{"iso":"eng"}],"volume":285,"citation":{"ieee":"K. Chatterjee and R. Ibsen-Jensen, “The complexity of deciding legality of a single step of magic: The gathering,” presented at the ECAI: European Conference on Artificial Intelligence, The Hague, Netherlands, 2016, vol. 285, pp. 1432–1439.","short":"K. Chatterjee, R. Ibsen-Jensen, in:, IOS Press, 2016, pp. 1432–1439.","ama":"Chatterjee K, Ibsen-Jensen R. The complexity of deciding legality of a single step of magic: The gathering. In: Vol 285. IOS Press; 2016:1432-1439. doi:10.3233/978-1-61499-672-9-1432","apa":"Chatterjee, K., & Ibsen-Jensen, R. (2016). The complexity of deciding legality of a single step of magic: The gathering (Vol. 285, pp. 1432–1439). Presented at the ECAI: European Conference on Artificial Intelligence, The Hague, Netherlands: IOS Press. https://doi.org/10.3233/978-1-61499-672-9-1432","mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. The Complexity of Deciding Legality of a Single Step of Magic: The Gathering. Vol. 285, IOS Press, 2016, pp. 1432–39, doi:10.3233/978-1-61499-672-9-1432.","ista":"Chatterjee K, Ibsen-Jensen R. 2016. The complexity of deciding legality of a single step of magic: The gathering. ECAI: European Conference on Artificial Intelligence, Frontiers in Artificial Intelligence and Applications, vol. 285, 1432–1439.","chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Complexity of Deciding Legality of a Single Step of Magic: The Gathering,” 285:1432–39. IOS Press, 2016. https://doi.org/10.3233/978-1-61499-672-9-1432."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"7342","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87"}],"title":"The complexity of deciding legality of a single step of magic: The gathering","quality_controlled":"1","publisher":"IOS Press","oa":1,"has_accepted_license":"1","year":"2016","day":"01","page":"1432 - 1439","date_published":"2016-01-01T00:00:00Z","doi":"10.3233/978-1-61499-672-9-1432","date_created":"2018-12-11T11:46:41Z"},{"oa":1,"publisher":"IEEE","quality_controlled":"1","page":"247 - 256","date_created":"2018-12-11T11:46:42Z","doi":"10.1145/2933575.2934513","date_published":"2016-07-05T00:00:00Z","year":"2016","day":"05","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"publist_id":"7340","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Laurent","full_name":"Doyen, Laurent","last_name":"Doyen"}],"title":"Perfect-information stochastic games with generalized mean-payoff objectives","citation":{"apa":"Chatterjee, K., & Doyen, L. (2016). Perfect-information stochastic games with generalized mean-payoff objectives (Vol. 05-08-July-2016, pp. 247–256). Presented at the LICS: Logic in Computer Science, New York, NY, USA: IEEE. https://doi.org/10.1145/2933575.2934513","ama":"Chatterjee K, Doyen L. Perfect-information stochastic games with generalized mean-payoff objectives. In: Vol 05-08-July-2016. IEEE; 2016:247-256. doi:10.1145/2933575.2934513","short":"K. Chatterjee, L. Doyen, in:, IEEE, 2016, pp. 247–256.","ieee":"K. Chatterjee and L. Doyen, “Perfect-information stochastic games with generalized mean-payoff objectives,” presented at the LICS: Logic in Computer Science, New York, NY, USA, 2016, vol. 05-08-July-2016, pp. 247–256.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. Perfect-Information Stochastic Games with Generalized Mean-Payoff Objectives. Vol. 05-08-July-2016, IEEE, 2016, pp. 247–56, doi:10.1145/2933575.2934513.","ista":"Chatterjee K, Doyen L. 2016. Perfect-information stochastic games with generalized mean-payoff objectives. LICS: Logic in Computer Science, Proceedings Symposium on Logic in Computer Science, vol. 05-08-July-2016, 247–256.","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Perfect-Information Stochastic Games with Generalized Mean-Payoff Objectives,” 05-08-July-2016:247–56. IEEE, 2016. https://doi.org/10.1145/2933575.2934513."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.06376"}],"alternative_title":["Proceedings Symposium on Logic in Computer Science"],"scopus_import":1,"month":"07","abstract":[{"lang":"eng","text":"Graph games provide the foundation for modeling and synthesizing reactive processes. In the synthesis of stochastic reactive processes, the traditional model is perfect-information stochastic games, where some transitions of the game graph are controlled by two adversarial players, and the other transitions are executed probabilistically. We consider such games where the objective is the conjunction of several quantitative objectives (specified as mean-payoff conditions), which we refer to as generalized mean-payoff objectives. The basic decision problem asks for the existence of a finite-memory strategy for a player that ensures the generalized mean-payoff objective be satisfied with a desired probability against all strategies of the opponent. A special case of the decision problem is the almost-sure problem where the desired probability is 1. Previous results presented a semi-decision procedure for -approximations of the almost-sure problem. In this work, we show that both the almost-sure problem as well as the general basic decision problem are coNP-complete, significantly improving the previous results. Moreover, we show that in the case of 1-player stochastic games, randomized memoryless strategies are sufficient and the problem can be solved in polynomial time. In contrast, in two-player stochastic games, we show that even with randomized strategies exponential memory is required in general, and present a matching exponential upper bound. We also study the basic decision problem with infinite-memory strategies and present computational complexity results for the problem. Our results are relevant in the synthesis of stochastic reactive systems with multiple quantitative requirements."}],"oa_version":"Preprint","ec_funded":1,"volume":"05-08-July-2016","publication_status":"published","language":[{"iso":"eng"}],"conference":{"start_date":"2016-07-05","end_date":"2016-07-08","location":"New York, NY, USA","name":"LICS: Logic in Computer Science"},"type":"conference","status":"public","_id":"480","department":[{"_id":"KrCh"}],"date_updated":"2021-01-12T08:00:56Z"},{"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"f04248a61c24297cfabd30c5f8e0deb9","file_id":"4930","creator":"system","file_size":574770,"date_updated":"2020-07-14T12:44:47Z","file_name":"IST-2016-622-v1+1_LIPIcs-SoCG-2016-24.pdf","date_created":"2018-12-12T10:12:12Z"}],"publication_status":"published","related_material":{"record":[{"relation":"later_version","id":"534","status":"public"}]},"volume":51,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We investigate the complexity of finding an embedded non-orientable surface of Euler genus g in a triangulated 3-manifold. This problem occurs both as a natural question in low-dimensional topology, and as a first non-trivial instance of embeddability of complexes into 3-manifolds. We prove that the problem is NP-hard, thus adding to the relatively few hardness results that are currently known in 3-manifold topology. In addition, we show that the problem lies in NP when the Euler genus g is odd, and we give an explicit algorithm in this case."}],"intvolume":" 51","month":"06","scopus_import":1,"alternative_title":["LIPIcs"],"ddc":["510"],"date_updated":"2023-02-23T12:23:20Z","file_date_updated":"2020-07-14T12:44:47Z","department":[{"_id":"UlWa"}],"_id":"1379","pubrep_id":"622","status":"public","conference":{"end_date":"2016-06-17","location":"Medford, MA, USA","start_date":"2016-06-14","name":"SoCG: Symposium on Computational Geometry"},"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","day":"01","year":"2016","has_accepted_license":"1","date_created":"2018-12-11T11:51:41Z","date_published":"2016-06-01T00:00:00Z","doi":"10.4230/LIPIcs.SoCG.2016.24","page":"24.1 - 24.15","oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Burton, Benjamin, et al. Finding Non-Orientable Surfaces in 3-Manifolds. Vol. 51, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2016, p. 24.1-24.15, doi:10.4230/LIPIcs.SoCG.2016.24.","ieee":"B. Burton, A. N. de Mesmay, and U. Wagner, “Finding non-orientable surfaces in 3-manifolds,” presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA, 2016, vol. 51, p. 24.1-24.15.","short":"B. Burton, A.N. de Mesmay, U. Wagner, in:, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2016, p. 24.1-24.15.","apa":"Burton, B., de Mesmay, A. N., & Wagner, U. (2016). Finding non-orientable surfaces in 3-manifolds (Vol. 51, p. 24.1-24.15). Presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. https://doi.org/10.4230/LIPIcs.SoCG.2016.24","ama":"Burton B, de Mesmay AN, Wagner U. Finding non-orientable surfaces in 3-manifolds. In: Vol 51. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing; 2016:24.1-24.15. doi:10.4230/LIPIcs.SoCG.2016.24","chicago":"Burton, Benjamin, Arnaud N de Mesmay, and Uli Wagner. “Finding Non-Orientable Surfaces in 3-Manifolds,” 51:24.1-24.15. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2016. https://doi.org/10.4230/LIPIcs.SoCG.2016.24.","ista":"Burton B, de Mesmay AN, Wagner U. 2016. Finding non-orientable surfaces in 3-manifolds. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 51, 24.1-24.15."},"title":"Finding non-orientable surfaces in 3-manifolds","publist_id":"5832","author":[{"last_name":"Burton","full_name":"Burton, Benjamin","first_name":"Benjamin"},{"first_name":"Arnaud N","id":"3DB2F25C-F248-11E8-B48F-1D18A9856A87","full_name":"De Mesmay, Arnaud N","last_name":"De Mesmay"},{"orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}]},{"date_updated":"2023-02-23T12:24:38Z","department":[{"_id":"KrCh"}],"_id":"1477","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":82,"issue":"5","related_material":{"record":[{"status":"public","id":"2295","relation":"earlier_version"},{"status":"public","id":"5400","relation":"earlier_version"}]},"ec_funded":1,"abstract":[{"lang":"eng","text":"We consider partially observable Markov decision processes (POMDPs) with ω-regular conditions specified as parity objectives. The class of ω-regular languages provides a robust specification language to express properties in verification, and parity objectives are canonical forms to express them. The qualitative analysis problem given a POMDP and a parity objective asks whether there is a strategy to ensure that the objective is satisfied with probability 1 (resp. positive probability). While the qualitative analysis problems are undecidable even for special cases of parity objectives, we establish decidability (with optimal complexity) for POMDPs with all parity objectives under finite-memory strategies. We establish optimal (exponential) memory bounds and EXPTIME-completeness of the qualitative analysis problems under finite-memory strategies for POMDPs with parity objectives. We also present a practical approach, where we design heuristics to deal with the exponential complexity, and have applied our implementation on a number of POMDP examples."}],"oa_version":"Preprint","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1309.2802","open_access":"1"}],"month":"08","intvolume":" 82","citation":{"chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Mathieu Tracol. “What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives.” Journal of Computer and System Sciences. Elsevier, 2016. https://doi.org/10.1016/j.jcss.2016.02.009.","ista":"Chatterjee K, Chmelik M, Tracol M. 2016. What is decidable about partially observable Markov decision processes with ω-regular objectives. Journal of Computer and System Sciences. 82(5), 878–911.","mla":"Chatterjee, Krishnendu, et al. “What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives.” Journal of Computer and System Sciences, vol. 82, no. 5, Elsevier, 2016, pp. 878–911, doi:10.1016/j.jcss.2016.02.009.","ieee":"K. Chatterjee, M. Chmelik, and M. Tracol, “What is decidable about partially observable Markov decision processes with ω-regular objectives,” Journal of Computer and System Sciences, vol. 82, no. 5. Elsevier, pp. 878–911, 2016.","short":"K. Chatterjee, M. Chmelik, M. Tracol, Journal of Computer and System Sciences 82 (2016) 878–911.","ama":"Chatterjee K, Chmelik M, Tracol M. What is decidable about partially observable Markov decision processes with ω-regular objectives. Journal of Computer and System Sciences. 2016;82(5):878-911. doi:10.1016/j.jcss.2016.02.009","apa":"Chatterjee, K., Chmelik, M., & Tracol, M. (2016). What is decidable about partially observable Markov decision processes with ω-regular objectives. Journal of Computer and System Sciences. Elsevier. https://doi.org/10.1016/j.jcss.2016.02.009"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5718","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Chmelik","full_name":"Chmelik, Martin"},{"id":"3F54FA38-F248-11E8-B48F-1D18A9856A87","first_name":"Mathieu","full_name":"Tracol, Mathieu","last_name":"Tracol"}],"external_id":{"arxiv":["1309.2802"]},"title":"What is decidable about partially observable Markov decision processes with ω-regular objectives","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory","grant_number":"S11407"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"year":"2016","day":"01","publication":"Journal of Computer and System Sciences","page":"878 - 911","date_published":"2016-08-01T00:00:00Z","doi":"10.1016/j.jcss.2016.02.009","date_created":"2018-12-11T11:52:15Z","quality_controlled":"1","publisher":"Elsevier","oa":1},{"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"related_material":{"record":[{"relation":"earlier_version","id":"1820","status":"public"},{"status":"public","id":"5425","relation":"earlier_version"}]},"volume":234,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider partially observable Markov decision processes (POMDPs) with a set of target states and an integer cost associated with every transition. The optimization objective we study asks to minimize the expected total cost of reaching a state in the target set, while ensuring that the target set is reached almost surely (with probability 1). We show that for integer costs approximating the optimal cost is undecidable. For positive costs, our results are as follows: (i) we establish matching lower and upper bounds for the optimal cost, both double exponential in the POMDP state space size; (ii) we show that the problem of approximating the optimal cost is decidable and present approximation algorithms developing on the existing algorithms for POMDPs with finite-horizon objectives. While the worst-case running time of our algorithm is double exponential, we also present efficient stopping criteria for the algorithm and show experimentally that it performs well in many examples of interest."}],"intvolume":" 234","month":"05","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1411.3880"}],"scopus_import":1,"date_updated":"2023-02-23T12:25:49Z","department":[{"_id":"KrCh"}],"_id":"1529","status":"public","type":"journal_article","publication":"Artificial Intelligence","day":"01","year":"2016","date_created":"2018-12-11T11:52:33Z","date_published":"2016-05-01T00:00:00Z","doi":"10.1016/j.artint.2016.01.007","page":"26 - 48","acknowledgement":"We thank Blai Bonet for helping us with RTDP-Bel. The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","oa":1,"publisher":"Elsevier","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2016. Optimal cost almost-sure reachability in POMDPs. Artificial Intelligence. 234, 26–48.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. “Optimal Cost Almost-Sure Reachability in POMDPs.” Artificial Intelligence. Elsevier, 2016. https://doi.org/10.1016/j.artint.2016.01.007.","short":"K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, Artificial Intelligence 234 (2016) 26–48.","ieee":"K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Optimal cost almost-sure reachability in POMDPs,” Artificial Intelligence, vol. 234. Elsevier, pp. 26–48, 2016.","ama":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. Optimal cost almost-sure reachability in POMDPs. Artificial Intelligence. 2016;234:26-48. doi:10.1016/j.artint.2016.01.007","apa":"Chatterjee, K., Chmelik, M., Gupta, R., & Kanodia, A. (2016). Optimal cost almost-sure reachability in POMDPs. Artificial Intelligence. Elsevier. https://doi.org/10.1016/j.artint.2016.01.007","mla":"Chatterjee, Krishnendu, et al. “Optimal Cost Almost-Sure Reachability in POMDPs.” Artificial Intelligence, vol. 234, Elsevier, 2016, pp. 26–48, doi:10.1016/j.artint.2016.01.007."},"title":"Optimal cost almost-sure reachability in POMDPs","external_id":{"arxiv":["1411.3880"]},"article_processing_charge":"No","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Chmelik, Martin","last_name":"Chmelik"},{"full_name":"Gupta, Raghav","last_name":"Gupta","first_name":"Raghav"},{"first_name":"Ayush","last_name":"Kanodia","full_name":"Kanodia, Ayush"}],"publist_id":"5642","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}]},{"abstract":[{"lang":"eng","text":"We consider the quantitative analysis problem for interprocedural control-flow graphs (ICFGs). The input consists of an ICFG, a positive weight function that assigns every transition a positive integer-valued number, and a labelling of the transitions (events) as good, bad, and neutral events. The weight function assigns to each transition a numerical value that represents ameasure of how good or bad an event is. The quantitative analysis problem asks whether there is a run of the ICFG where the ratio of the sum of the numerical weights of good events versus the sum of weights of bad events in the long-run is at least a given threshold (or equivalently, to compute the maximal ratio among all valid paths in the ICFG). The quantitative analysis problem for ICFGs can be solved in polynomial time, and we present an efficient and practical algorithm for the problem. We show that several problems relevant for static program analysis, such as estimating the worst-case execution time of a program or the average energy consumption of a mobile application, can be modeled in our framework. We have implemented our algorithm as a tool in the Java Soot framework. We demonstrate the effectiveness of our approach with two case studies. First, we show that our framework provides a sound approach (no false positives) for the analysis of inefficiently-used containers. Second, we show that our approach can also be used for static profiling of programs which reasons about methods that are frequently invoked. Our experimental results show that our tool scales to relatively large benchmarks, and discovers relevant and useful information that can be used to optimize performance of the programs. "}],"oa_version":"Published Version","publisher":"IST Austria","alternative_title":["IST Austria Technical Report"],"oa":1,"month":"03","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","year":"2016","publication_status":"published","day":"31","file":[{"checksum":"cef516fa091925b5868813e355268fb4","file_id":"5513","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-523-v1+1_main.pdf","date_created":"2018-12-12T11:53:52Z","creator":"system","file_size":1012204,"date_updated":"2020-07-14T12:46:58Z"}],"language":[{"iso":"eng"}],"page":"33","related_material":{"record":[{"id":"1604","status":"public","relation":"later_version"}]},"doi":"10.15479/AT:IST-2016-523-v1-1","date_published":"2016-03-31T00:00:00Z","date_created":"2018-12-12T11:39:22Z","_id":"5445","type":"technical_report","status":"public","pubrep_id":"523","date_updated":"2023-02-23T10:06:22Z","citation":{"mla":"Chatterjee, Krishnendu, et al. Quantitative Interprocedural Analysis. IST Austria, 2016, doi:10.15479/AT:IST-2016-523-v1-1.","ieee":"K. Chatterjee, A. Pavlogiannis, and Y. Velner, Quantitative interprocedural analysis. IST Austria, 2016.","short":"K. Chatterjee, A. Pavlogiannis, Y. Velner, Quantitative Interprocedural Analysis, IST Austria, 2016.","apa":"Chatterjee, K., Pavlogiannis, A., & Velner, Y. (2016). Quantitative interprocedural analysis. IST Austria. https://doi.org/10.15479/AT:IST-2016-523-v1-1","ama":"Chatterjee K, Pavlogiannis A, Velner Y. Quantitative Interprocedural Analysis. IST Austria; 2016. doi:10.15479/AT:IST-2016-523-v1-1","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, and Yaron Velner. Quantitative Interprocedural Analysis. IST Austria, 2016. https://doi.org/10.15479/AT:IST-2016-523-v1-1.","ista":"Chatterjee K, Pavlogiannis A, Velner Y. 2016. Quantitative interprocedural analysis, IST Austria, 33p."},"ddc":["005"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yaron","full_name":"Velner, Yaron","last_name":"Velner"}],"title":"Quantitative interprocedural analysis","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:46:58Z"},{"month":"11","oa":1,"publisher":"IST Austria","alternative_title":["IST Austria Technical Report"],"oa_version":"Updated Version","abstract":[{"text":"The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population.\r\nThe fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure.\r\nAmplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade.\r\nIn this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Comet-swarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively.","lang":"eng"}],"date_created":"2018-12-12T11:39:24Z","doi":"10.15479/AT:IST-2016-648-v1-1","date_published":"2016-11-09T00:00:00Z","related_material":{"record":[{"relation":"later_version","id":"512","status":"public"}]},"page":"22","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5529","checksum":"8345a8c1e7d7f0cd92516d182b7fc59e","date_updated":"2020-07-14T12:46:58Z","file_size":1264221,"creator":"system","date_created":"2018-12-12T11:54:07Z","file_name":"IST-2016-648-v1+1_tr.pdf"}],"day":"09","publication_status":"published","year":"2016","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"pubrep_id":"648","status":"public","type":"technical_report","_id":"5449","file_date_updated":"2020-07-14T12:46:58Z","title":"Amplification on undirected population structures: Comets beat stars","department":[{"_id":"KrCh"}],"author":[{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis"},{"id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","last_name":"Tkadlec"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"ddc":["519"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T12:22:21Z","citation":{"chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. Amplification on Undirected Population Structures: Comets Beat Stars. IST Austria, 2016. https://doi.org/10.15479/AT:IST-2016-648-v1-1.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Amplification on undirected population structures: Comets beat stars, IST Austria, 22p.","mla":"Pavlogiannis, Andreas, et al. Amplification on Undirected Population Structures: Comets Beat Stars. IST Austria, 2016, doi:10.15479/AT:IST-2016-648-v1-1.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. (2016). Amplification on undirected population structures: Comets beat stars. IST Austria. https://doi.org/10.15479/AT:IST-2016-648-v1-1","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Amplification on Undirected Population Structures: Comets Beat Stars. IST Austria; 2016. doi:10.15479/AT:IST-2016-648-v1-1","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Amplification on Undirected Population Structures: Comets Beat Stars, IST Austria, 2016.","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, Amplification on undirected population structures: Comets beat stars. IST Austria, 2016."}},{"year":"2016","publication_status":"published","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"689069a7abbb34b21516164cbee9e0df","file_id":"6403","date_updated":"2020-07-14T12:46:58Z","file_size":686241,"creator":"dernst","date_created":"2019-05-10T13:27:24Z","file_name":"popl2017a.pdf"},{"checksum":"fc08022bfbaac07bac047a9407c0bbb3","file_id":"6404","content_type":"text/plain","relation":"main_file","access_level":"closed","file_name":"author_names.txt","date_created":"2019-05-10T13:27:31Z","file_size":258,"date_updated":"2020-07-14T12:46:58Z","creator":"dernst"}],"day":"15","page":"26","date_created":"2018-12-12T11:39:23Z","date_published":"2016-07-15T00:00:00Z","abstract":[{"lang":"eng","text":"We study the problem of developing efficient approaches for proving termination of recursive programs with one-dimensional arrays. Ranking functions serve as a sound and complete approach for proving termination of non-recursive programs without array operations. First, we generalize ranking functions to the notion of measure functions, and prove that measure functions (i) provide a sound method to prove termination of recursive programs (with one-dimensional arrays), and (ii) is both sound and complete over recursive programs without array operations. Our second contribution is the synthesis of measure functions of specific forms in polynomial time. More precisely, we prove that (i) polynomial measure functions over recursive programs can be synthesized in polynomial time through Farkas’ Lemma and Handelman’s Theorem, and (ii) measure functions involving logarithm and exponentiation can be synthesized in polynomial time through abstraction of logarithmic or exponential terms and Handelman’s Theorem. A key application of our method is the worst-case analysis of recursive programs. While previous methods obtain worst-case polynomial bounds of the form O(n^k), where k is an integer, our polynomial time methods can synthesize bounds of the form O(n log n), as well as O(n^x), where x is not an integer. We show the applicability of our automated technique to obtain worst-case complexity of classical recursive algorithms such as (i) Merge-Sort, the divideand-\r\nconquer algorithm for the Closest-Pair problem, where we obtain O(n log n) worst-case bound, and (ii) Karatsuba’s algorithm for polynomial multiplication and Strassen’s algorithm for matrix multiplication, where we obtain O(n^x) bound, where x is not an integer and close to the best-known bounds for the respective algorithms. Finally, we present experimental results to demonstrate the\r\neffectiveness of our approach."}],"oa_version":"Published Version","oa":1,"publisher":"IST Austria","alternative_title":["IST Austria Technical Report"],"month":"07","citation":{"chicago":"Anonymous, 1, 2 Anonymous, and 3 Anonymous. Termination and Worst-Case Analysis of Recursive Programs. IST Austria, 2016.","ista":"Anonymous 1, Anonymous 2, Anonymous 3. 2016. Termination and worst-case analysis of recursive programs, IST Austria, 26p.","mla":"Anonymous, 1, et al. Termination and Worst-Case Analysis of Recursive Programs. IST Austria, 2016.","short":"1 Anonymous, 2 Anonymous, 3 Anonymous, Termination and Worst-Case Analysis of Recursive Programs, IST Austria, 2016.","ieee":"1 Anonymous, 2 Anonymous, and 3 Anonymous, Termination and worst-case analysis of recursive programs. IST Austria, 2016.","apa":"Anonymous, 1, Anonymous, 2, & Anonymous, 3. (2016). Termination and worst-case analysis of recursive programs. IST Austria.","ama":"Anonymous 1, Anonymous 2, Anonymous 3. Termination and Worst-Case Analysis of Recursive Programs. IST Austria; 2016."},"date_updated":"2020-07-14T23:05:05Z","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Anonymous","full_name":"Anonymous, 1","first_name":"1"},{"last_name":"Anonymous","full_name":"Anonymous, 2","first_name":"2"},{"full_name":"Anonymous, 3","last_name":"Anonymous","first_name":"3"}],"title":"Termination and worst-case analysis of recursive programs","file_date_updated":"2020-07-14T12:46:58Z","_id":"5446","type":"technical_report","pubrep_id":"618","status":"public"},{"_id":"5447","type":"technical_report","pubrep_id":"619","status":"public","date_updated":"2020-07-14T23:05:06Z","citation":{"mla":"Anonymous, 1, et al. Average-Case Analysis of Programs: Automated Recurrence Analysis for Almost-Linear Bounds. IST Austria, 2016.","apa":"Anonymous, 1, Anonymous, 2, & Anonymous, 3. (2016). Average-case analysis of programs: Automated recurrence analysis for almost-linear bounds. IST Austria.","ama":"Anonymous 1, Anonymous 2, Anonymous 3. Average-Case Analysis of Programs: Automated Recurrence Analysis for Almost-Linear Bounds. IST Austria; 2016.","ieee":"1 Anonymous, 2 Anonymous, and 3 Anonymous, Average-case analysis of programs: Automated recurrence analysis for almost-linear bounds. IST Austria, 2016.","short":"1 Anonymous, 2 Anonymous, 3 Anonymous, Average-Case Analysis of Programs: Automated Recurrence Analysis for Almost-Linear Bounds, IST Austria, 2016.","chicago":"Anonymous, 1, 2 Anonymous, and 3 Anonymous. Average-Case Analysis of Programs: Automated Recurrence Analysis for Almost-Linear Bounds. IST Austria, 2016.","ista":"Anonymous 1, Anonymous 2, Anonymous 3. 2016. Average-case analysis of programs: Automated recurrence analysis for almost-linear bounds, IST Austria, 20p."},"ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Anonymous, 1","last_name":"Anonymous","first_name":"1"},{"first_name":"2","full_name":"Anonymous, 2","last_name":"Anonymous"},{"full_name":"Anonymous, 3","last_name":"Anonymous","first_name":"3"}],"title":"Average-case analysis of programs: Automated recurrence analysis for almost-linear bounds","file_date_updated":"2020-07-14T12:46:58Z","abstract":[{"lang":"eng","text":"We consider the problem of developing automated techniques to aid the average-case complexity analysis of programs. Several classical textbook algorithms have quite efficient average-case complexity, whereas the corresponding worst-case bounds are either inefficient (e.g., QUICK-SORT), or completely ineffective (e.g., COUPONCOLLECTOR). Since the main focus of average-case analysis is to obtain efficient bounds, we consider bounds that are either logarithmic,\r\nlinear, or almost-linear (O(log n), O(n), O(n · log n),\r\nrespectively, where n represents the size of the input). Our main contribution is a sound approach for deriving such average-case bounds for randomized recursive programs. Our approach is efficient (a simple linear-time algorithm), and it is based on (a) the analysis of recurrence relations induced by randomized algorithms, and (b) a guess-and-check technique. Our approach can infer the asymptotically optimal average-case bounds for classical randomized algorithms, including RANDOMIZED-SEARCH, QUICKSORT, QUICK-SELECT, COUPON-COLLECTOR, where the worstcase\r\nbounds are either inefficient (such as linear as compared to logarithmic of average-case, or quadratic as compared to linear or almost-linear of average-case), or ineffective. We have implemented our approach, and the experimental results show that we obtain the bounds efficiently for various classical algorithms."}],"oa_version":"Published Version","oa":1,"alternative_title":["IST Austria Technical Report"],"publisher":"IST Austria","month":"07","publication_status":"published","year":"2016","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"closed","content_type":"text/plain","checksum":"cf53cdb6d092e68db0b4a0a1506ef8fb","file_id":"6406","creator":"dernst","file_size":281,"date_updated":"2020-07-14T12:46:58Z","file_name":"listofauthors.txt","date_created":"2019-05-10T13:32:16Z"},{"creator":"dernst","date_updated":"2020-07-14T12:46:58Z","file_size":563642,"date_created":"2019-05-10T13:32:16Z","file_name":"popl2017b.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"7bdd94ba13aa0dec9c46887fcf13870b","file_id":"6407"}],"day":"15","page":"20","date_created":"2018-12-12T11:39:23Z","date_published":"2016-07-15T00:00:00Z"},{"pubrep_id":"755","status":"public","type":"technical_report","_id":"5453","title":"Arbitrarily strong amplifiers of natural selection","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:46:59Z","author":[{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis"},{"id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef","last_name":"Tkadlec"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"date_updated":"2023-02-23T12:27:07Z","citation":{"chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. Arbitrarily Strong Amplifiers of Natural Selection. IST Austria, 2016. https://doi.org/10.15479/AT:IST-2017-749-v3-1.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Arbitrarily strong amplifiers of natural selection, IST Austria, 34p.","mla":"Pavlogiannis, Andreas, et al. Arbitrarily Strong Amplifiers of Natural Selection. IST Austria, 2016, doi:10.15479/AT:IST-2017-749-v3-1.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Arbitrarily Strong Amplifiers of Natural Selection. IST Austria; 2016. doi:10.15479/AT:IST-2017-749-v3-1","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. (2016). Arbitrarily strong amplifiers of natural selection. IST Austria. https://doi.org/10.15479/AT:IST-2017-749-v3-1","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Arbitrarily Strong Amplifiers of Natural Selection, IST Austria, 2016.","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, Arbitrarily strong amplifiers of natural selection. IST Austria, 2016."},"month":"12","oa":1,"publisher":"IST Austria","alternative_title":["IST Austria Technical Report"],"oa_version":"Published Version","date_created":"2018-12-12T11:39:25Z","doi":"10.15479/AT:IST-2017-749-v3-1","date_published":"2016-12-30T00:00:00Z","related_material":{"record":[{"relation":"earlier_version","id":"5452","status":"public"}]},"page":"34","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T11:53:13Z","file_name":"IST-2017-749-v3+1_main.pdf","date_updated":"2020-07-14T12:46:59Z","file_size":1015647,"creator":"system","checksum":"83b0313dab3bff4bdb6ac38695026fda","file_id":"5474","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"day":"30","publication_status":"published","year":"2016","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1"},{"has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"publication_status":"published","year":"2016","day":"30","file":[{"checksum":"7b8bb17c322c0556acba6ac169fa71c1","file_id":"5465","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T11:53:04Z","file_name":"IST-2016-728-v1+1_main.pdf","creator":"system","date_updated":"2020-07-14T12:46:59Z","file_size":1014732}],"language":[{"iso":"eng"}],"page":"34","date_published":"2016-12-30T00:00:00Z","doi":"10.15479/AT:IST-2016-728-v1-1","date_created":"2018-12-12T11:39:24Z","oa_version":"Published Version","publisher":"IST Austria","alternative_title":["IST Austria Technical Report"],"oa":1,"month":"12","date_updated":"2023-02-23T12:27:05Z","citation":{"mla":"Pavlogiannis, Andreas, et al. Strong Amplifiers of Natural Selection. IST Austria, 2016, doi:10.15479/AT:IST-2016-728-v1-1.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Strong Amplifiers of Natural Selection. IST Austria; 2016. doi:10.15479/AT:IST-2016-728-v1-1","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. (2016). Strong amplifiers of natural selection. IST Austria. https://doi.org/10.15479/AT:IST-2016-728-v1-1","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Strong Amplifiers of Natural Selection, IST Austria, 2016.","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, Strong amplifiers of natural selection. IST Austria, 2016.","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. Strong Amplifiers of Natural Selection. IST Austria, 2016. https://doi.org/10.15479/AT:IST-2016-728-v1-1.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Strong amplifiers of natural selection, IST Austria, 34p."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"author":[{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis"},{"id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","last_name":"Tkadlec"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"file_date_updated":"2020-07-14T12:46:59Z","title":"Strong amplifiers of natural selection","department":[{"_id":"KrCh"}],"_id":"5451","type":"technical_report","status":"public","pubrep_id":"728"},{"abstract":[{"lang":"eng","text":"We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence.\r\n1. For acyclic architectures, our algorithm is guaranteed to explore exactly one representative trace from each observation class, while spending polynomial time per class. Hence, our algorithm is optimal wrt the observation equivalence, and in several cases explores exponentially fewer traces than any enumerative method based on the Mazurkiewicz equivalence.\r\n2. For cyclic architectures, we consider an equivalence between traces which is finer than the observation equivalence; but coarser than the Mazurkiewicz equivalence, and in some cases is exponentially coarser. Our data-centric DPOR algorithm remains optimal under this trace equivalence. \r\nFinally, we perform a basic experimental comparison between the existing Mazurkiewicz-based DPOR and our data-centric DPOR on a set of academic benchmarks. Our results show a significant reduction in both running time and the number of explored equivalence classes."}],"oa_version":"Published Version","alternative_title":["IST Austria Technical Report"],"publisher":"IST Austria","oa":1,"month":"07","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","publication_status":"published","year":"2016","file":[{"checksum":"1d69252d66bcdf782615ddfb911d2957","file_id":"5506","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-620-v1+1_main.pdf","date_created":"2018-12-12T11:53:45Z","creator":"system","file_size":538881,"date_updated":"2020-07-14T12:46:58Z"},{"creator":"dernst","file_size":121,"date_updated":"2020-07-14T12:46:58Z","file_name":"authornames.txt","date_created":"2019-05-10T13:30:40Z","relation":"main_file","access_level":"closed","content_type":"text/plain","checksum":"deabb0eb8f237cae4f9542b28b0b6eb2","file_id":"6405"}],"day":"15","language":[{"iso":"eng"}],"page":"20","related_material":{"record":[{"relation":"later_version","id":"10417","status":"public"},{"id":"5456","status":"public","relation":"later_version"}]},"date_published":"2016-07-15T00:00:00Z","date_created":"2018-12-12T11:39:23Z","_id":"5448","type":"technical_report","status":"public","pubrep_id":"620","date_updated":"2023-02-23T12:27:16Z","citation":{"short":"1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, Data-Centric Dynamic Partial Order Reduction, IST Austria, 2016.","ieee":"1 Anonymous, 2 Anonymous, 3 Anonymous, and 4 Anonymous, Data-centric dynamic partial order reduction. IST Austria, 2016.","apa":"Anonymous, 1, Anonymous, 2, Anonymous, 3, & Anonymous, 4. (2016). Data-centric dynamic partial order reduction. IST Austria.","ama":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. Data-Centric Dynamic Partial Order Reduction. IST Austria; 2016.","mla":"Anonymous, 1, et al. Data-Centric Dynamic Partial Order Reduction. IST Austria, 2016.","ista":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. 2016. Data-centric dynamic partial order reduction, IST Austria, 20p.","chicago":"Anonymous, 1, 2 Anonymous, 3 Anonymous, and 4 Anonymous. Data-Centric Dynamic Partial Order Reduction. IST Austria, 2016."},"ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Anonymous","full_name":"Anonymous, 1","first_name":"1"},{"first_name":"2","last_name":"Anonymous","full_name":"Anonymous, 2"},{"first_name":"3","full_name":"Anonymous, 3","last_name":"Anonymous"},{"last_name":"Anonymous","full_name":"Anonymous, 4","first_name":"4"}],"external_id":{"arxiv":["1610.01188"]},"file_date_updated":"2020-07-14T12:46:58Z","title":"Data-centric dynamic partial order reduction"},{"quality_controlled":"1","publisher":"MIT Press","oa":1,"date_published":"2016-09-01T00:00:00Z","doi":"10.7551/978-0-262-33936-0-ch029","date_created":"2020-07-05T22:00:47Z","page":"142-143","day":"01","publication":"Proceedings of the Artificial Life Conference 2016","has_accepted_license":"1","year":"2016","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"title":"Self-organized control of an tendon driven arm by differential extrinsic plasticity","author":[{"last_name":"Martius","full_name":"Martius, Georg S","first_name":"Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rafael","last_name":"Hostettler","full_name":"Hostettler, Rafael"},{"full_name":"Knoll, Alois","last_name":"Knoll","first_name":"Alois"},{"full_name":"Der, Ralf","last_name":"Der","first_name":"Ralf"}],"article_processing_charge":"No","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","citation":{"ama":"Martius GS, Hostettler R, Knoll A, Der R. Self-organized control of an tendon driven arm by differential extrinsic plasticity. In: Proceedings of the Artificial Life Conference 2016. Vol 28. MIT Press; 2016:142-143. doi:10.7551/978-0-262-33936-0-ch029","apa":"Martius, G. S., Hostettler, R., Knoll, A., & Der, R. (2016). Self-organized control of an tendon driven arm by differential extrinsic plasticity. In Proceedings of the Artificial Life Conference 2016 (Vol. 28, pp. 142–143). Cancun, Mexico: MIT Press. https://doi.org/10.7551/978-0-262-33936-0-ch029","ieee":"G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Self-organized control of an tendon driven arm by differential extrinsic plasticity,” in Proceedings of the Artificial Life Conference 2016, Cancun, Mexico, 2016, vol. 28, pp. 142–143.","short":"G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, Proceedings of the Artificial Life Conference 2016, MIT Press, 2016, pp. 142–143.","mla":"Martius, Georg S., et al. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” Proceedings of the Artificial Life Conference 2016, vol. 28, MIT Press, 2016, pp. 142–43, doi:10.7551/978-0-262-33936-0-ch029.","ista":"Martius GS, Hostettler R, Knoll A, Der R. 2016. Self-organized control of an tendon driven arm by differential extrinsic plasticity. Proceedings of the Artificial Life Conference 2016. ALIFE 2016: 15th International Conference on the Synthesis and Simulation of Living Systems vol. 28, 142–143.","chicago":"Martius, Georg S, Rafael Hostettler, Alois Knoll, and Ralf Der. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” In Proceedings of the Artificial Life Conference 2016, 28:142–43. MIT Press, 2016. https://doi.org/10.7551/978-0-262-33936-0-ch029."},"month":"09","intvolume":" 28","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"With the accelerated development of robot technologies, optimal control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of the history of sensor values, guided by the goals, intentions, objectives, learning schemes, and so forth. The idea is that the controller controls the world---the body plus its environment---as reliably as possible. This paper focuses on new lines of self-organization for developmental robotics. We apply the recently developed differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder system from the Myorobotics toolkit. In the experiments, we observe a vast variety of self-organized behavior patterns: when left alone, the arm realizes pseudo-random sequences of different poses. By applying physical forces, the system can be entrained into definite motion patterns like wiping a table. Most interestingly, after attaching an object, the controller gets in a functional resonance with the object's internal dynamics, starting to shake spontaneously bottles half-filled with water or sensitively driving an attached pendulum into a circular mode. When attached to the crank of a wheel the neural system independently discovers how to rotate it. In this way, the robot discovers affordances of objects its body is interacting with.","lang":"eng"}],"volume":28,"ec_funded":1,"file":[{"date_created":"2020-07-06T12:59:09Z","file_name":"2016_ProcALIFE_Martius.pdf","creator":"cziletti","date_updated":"2020-07-14T12:48:09Z","file_size":678670,"checksum":"cff63e7a4b8ac466ba51a9c84153a940","file_id":"8096","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9780262339360"]},"publication_status":"published","status":"public","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"ALIFE 2016: 15th International Conference on the Synthesis and Simulation of Living Systems","end_date":"2016-07-08","location":"Cancun, Mexico","start_date":"2016-07-04"},"_id":"8094","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:48:09Z","ddc":["610"],"date_updated":"2021-01-12T08:16:53Z"},{"title":"Error-robust modes of the retinal population code","publist_id":"6153","author":[{"full_name":"Prentice, Jason","last_name":"Prentice","first_name":"Jason"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"},{"first_name":"Mark","full_name":"Ioffe, Mark","last_name":"Ioffe"},{"first_name":"Adrianna","last_name":"Loback","full_name":"Loback, Adrianna"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"},{"full_name":"Berry, Michael","last_name":"Berry","first_name":"Michael"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Prentice, Jason, et al. “Error-Robust Modes of the Retinal Population Code.” PLoS Computational Biology, vol. 12, no. 11, e1005855, Public Library of Science, 2016, doi:10.1371/journal.pcbi.1005148.","short":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, PLoS Computational Biology 12 (2016).","ieee":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Error-robust modes of the retinal population code,” PLoS Computational Biology, vol. 12, no. 11. Public Library of Science, 2016.","ama":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Error-robust modes of the retinal population code. PLoS Computational Biology. 2016;12(11). doi:10.1371/journal.pcbi.1005148","apa":"Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M. (2016). Error-robust modes of the retinal population code. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005148","chicago":"Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik, and Michael Berry. “Error-Robust Modes of the Retinal Population Code.” PLoS Computational Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pcbi.1005148.","ista":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2016. Error-robust modes of the retinal population code. PLoS Computational Biology. 12(11), e1005855."},"project":[{"name":"Sensitivity to higher-order statistics in natural scenes","grant_number":"P 25651-N26","_id":"254D1A94-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"e1005855","date_published":"2016-11-17T00:00:00Z","doi":"10.1371/journal.pcbi.1005148","date_created":"2018-12-11T11:50:40Z","day":"17","publication":"PLoS Computational Biology","has_accepted_license":"1","year":"2016","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"acknowledgement":"JSP was supported by a C.V. Starr Fellowship from the Starr Foundation (http://www.starrfoundation.org/). GT was supported by Austrian Research Foundation (https://www.fwf.ac.at/en/) grant FWF P25651. MJB received support from National Eye Institute (https://nei.nih.gov/) grant EY 14196 and from the National Science Foundation grant 1504977. The authors thank Cristina Savin and Vicent Botella-Soler for helpful comments on the manuscript.","file_date_updated":"2020-07-14T12:44:38Z","department":[{"_id":"GaTk"}],"ddc":["570"],"date_updated":"2023-02-23T14:05:40Z","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":"1197","volume":12,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9709"}]},"issue":"11","file":[{"creator":"kschuh","date_updated":"2020-07-14T12:44:38Z","file_size":4492021,"date_created":"2019-01-25T10:35:00Z","file_name":"2016_PLOS_Prentice.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5884","checksum":"47b08cbd4dbf32b25ba161f5f4b262cc"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"11","intvolume":" 12","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Across the nervous system, certain population spiking patterns are observed far more frequently than others. A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the ganglion cell population with high accuracy. We found that the modes represent localized features of the visual stimulus that are distinct from the features represented by single neurons. Modes form clusters of activity states that are readily discriminated from one another. When we repeated the same visual stimulus, we found that the same mode was robustly elicited. These results suggest that retinal ganglion cells’ collective signaling is endowed with a form of error-correcting code–a principle that may hold in brain areas beyond retina."}]},{"abstract":[{"text":"Summary: Declining populations of bee pollinators are a cause of concern, with major repercussions for biodiversity loss and food security. RNA viruses associated with honeybees represent a potential threat to other insect pollinators, but the extent of this threat is poorly understood. This study aims to attain a detailed understanding of the current and ongoing risk of emerging infectious disease (EID) transmission between managed and wild pollinator species across a wide range of RNA viruses. Within a structured large-scale national survey across 26 independent sites, we quantify the prevalence and pathogen loads of multiple RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee (Bombus spp.) populations. We then construct models that compare virus prevalence between wild and managed pollinators. Multiple RNA viruses associated with honeybees are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees is a significant predictor of virus prevalence in bumblebees, but we remain cautious in speculating over the principle direction of pathogen transmission. We demonstrate species-specific differences in prevalence, indicating significant variation in disease susceptibility or tolerance. Pathogen loads within individual bumblebees may be high and in the case of at least one RNA virus, prevalence is higher in wild bumblebees than in managed honeybee populations. Our findings indicate widespread transmission of RNA viruses between managed and wild bee pollinators, pointing to an interconnected network of potential disease pressures within and among pollinator species. In the context of the biodiversity crisis, our study emphasizes the importance of targeting a wide range of pathogens and defining host associations when considering potential drivers of population decline.","lang":"eng"}],"oa_version":"Published Version","publisher":"Dryad","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.4b565"}],"oa":1,"month":"01","year":"2016","day":"22","doi":"10.5061/dryad.4b565","date_published":"2016-01-22T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"1855","status":"public"}]},"date_created":"2021-07-26T09:14:19Z","_id":"9720","type":"research_data_reference","status":"public","citation":{"chicago":"Mcmahon, Dino, Matthias Fürst, Jesicca Caspar, Panagiotis Theodorou, Mark Brown, and Robert Paxton. “Data from: A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees.” Dryad, 2016. https://doi.org/10.5061/dryad.4b565.","ista":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. 2016. Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees, Dryad, 10.5061/dryad.4b565.","mla":"Mcmahon, Dino, et al. Data from: A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees. Dryad, 2016, doi:10.5061/dryad.4b565.","ama":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees. 2016. doi:10.5061/dryad.4b565","apa":"Mcmahon, D., Fürst, M., Caspar, J., Theodorou, P., Brown, M., & Paxton, R. (2016). Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees. Dryad. https://doi.org/10.5061/dryad.4b565","short":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, (2016).","ieee":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, and R. Paxton, “Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees.” Dryad, 2016."},"date_updated":"2023-02-23T10:17:25Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Dino","last_name":"Mcmahon","full_name":"Mcmahon, Dino"},{"last_name":"Fürst","orcid":"0000-0002-3712-925X","full_name":"Fürst, Matthias","first_name":"Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Caspar, Jesicca","last_name":"Caspar","first_name":"Jesicca"},{"first_name":"Panagiotis","full_name":"Theodorou, Panagiotis","last_name":"Theodorou"},{"first_name":"Mark","last_name":"Brown","full_name":"Brown, Mark"},{"full_name":"Paxton, Robert","last_name":"Paxton","first_name":"Robert"}],"article_processing_charge":"No","department":[{"_id":"SyCr"}],"title":"Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees"},{"scopus_import":1,"intvolume":" 14","month":"12","abstract":[{"text":"Speciation results from the progressive accumulation of mutations that decrease the probability of mating between parental populations or reduce the fitness of hybrids—the so-called species barriers. The speciation genomic literature, however, is mainly a collection of case studies, each with its own approach and specificities, such that a global view of the gradual process of evolution from one to two species is currently lacking. Of primary importance is the prevalence of gene flow between diverging entities, which is central in most species concepts and has been widely discussed in recent years. Here, we explore the continuum of speciation thanks to a comparative analysis of genomic data from 61 pairs of populations/species of animals with variable levels of divergence. Gene flow between diverging gene pools is assessed under an approximate Bayesian computation (ABC) framework. We show that the intermediate "grey zone" of speciation, in which taxonomy is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective of species life history traits or ecology. Thanks to appropriate modeling of among-locus variation in genetic drift and introgression rate, we clarify the status of the majority of ambiguous cases and uncover a number of cryptic species. Our analysis also reveals the high incidence in animals of semi-isolated species (when some but not all loci are affected by barriers to gene flow) and highlights the intrinsic difficulty, both statistical and conceptual, of delineating species in the grey zone of speciation.","lang":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"id":"9862","status":"public","relation":"research_data"},{"relation":"research_data","id":"9863","status":"public"}]},"issue":"12","volume":14,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:44:36Z","file_size":2494348,"creator":"system","date_created":"2018-12-12T10:15:42Z","file_name":"IST-2017-742-v1+1_journal.pbio.2000234.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5164","checksum":"2bab63b068a9840efd532b9ae583f9bb"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"742","status":"public","_id":"1158","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:44:36Z","date_updated":"2023-02-23T14:11:16Z","ddc":["576"],"oa":1,"publisher":"Public Library of Science","quality_controlled":"1","acknowledgement":"European Research Council (ERC) https://erc.europa.eu/ (grant number ERC grant 232971). PopPhyl project. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. French National Research Agency (ANR) http://www.agence-nationale-recherche.fr/en/project-based-funding-to-advance-french-research/ (grant number ANR-12-BSV7- 0011). HYSEA project.\r\nWe thank Aude Darracq, Vincent Castric, Pierre-Alexandre Gagnaire, Xavier Vekemans, and John Welch for insightful discussions. The computations were performed at the Vital-IT (http://www.vital-it.ch) Center for high-performance computing of the SIB Swiss Institute of Bioinformatics and the ISEM computing cluster at the platform Montpellier Bioinformatique et Biodiversité.","date_created":"2018-12-11T11:50:28Z","doi":"10.1371/journal.pbio.2000234","date_published":"2016-12-27T00:00:00Z","year":"2016","has_accepted_license":"1","publication":"PLoS Biology","day":"27","article_number":"e2000234","author":[{"full_name":"Roux, Camille","last_name":"Roux","first_name":"Camille"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","last_name":"Fraisse","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"},{"first_name":"Jonathan","full_name":"Romiguier, Jonathan","last_name":"Romiguier"},{"full_name":"Anciaux, Youann","last_name":"Anciaux","first_name":"Youann"},{"first_name":"Nicolas","last_name":"Galtier","full_name":"Galtier, Nicolas"},{"last_name":"Bierne","full_name":"Bierne, Nicolas","first_name":"Nicolas"}],"publist_id":"6200","title":"Shedding light on the grey zone of speciation along a continuum of genomic divergence","citation":{"ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Shedding light on the grey zone of speciation along a continuum of genomic divergence,” PLoS Biology, vol. 14, no. 12. Public Library of Science, 2016.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS Biology 14 (2016).","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. 2016;14(12). doi:10.1371/journal.pbio.2000234","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne, N. (2016). Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234","mla":"Roux, Camille, et al. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” PLoS Biology, vol. 14, no. 12, e2000234, Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology. 14(12), e2000234.","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.” PLoS Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"abstract":[{"lang":"eng","text":"Evolutionary pathways describe trajectories of biological evolution in the space of different variants of organisms (genotypes). The probability of existence and the number of evolutionary pathways that lead from a given genotype to a better-adapted genotype are important measures of accessibility of local fitness optima and the reproducibility of evolution. Both quantities have been studied in simple mathematical models where genotypes are represented as binary sequences of two types of basic units, and the network of permitted mutations between the genotypes is a hypercube graph. However, it is unclear how these results translate to the biologically relevant case in which genotypes are represented by sequences of more than two units, for example four nucleotides (DNA) or 20 amino acids (proteins), and the mutational graph is not the hypercube. Here we investigate accessibility of the best-adapted genotype in the general case of K > 2 units. Using computer generated and experimental fitness landscapes we show that accessibility of the global fitness maximum increases with K and can be much higher than for binary sequences. The increase in accessibility comes from the increase in the number of indirect trajectories exploited by evolution for higher K. As one of the consequences, the fraction of genotypes that are accessible increases by three orders of magnitude when the number of units K increases from 2 to 16 for landscapes of size N ∼ 106genotypes. This suggests that evolution can follow many different trajectories on such landscapes and the reconstruction of evolutionary pathways from experimental data might be an extremely difficult task."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 12","month":"12","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:12:08Z","file_name":"IST-2017-740-v1+1_journal.pcbi.1005218.pdf","creator":"system","date_updated":"2020-07-14T12:44:37Z","file_size":3822299,"checksum":"84f44ae92866c52ff1ca8a574558dca7","file_id":"4926","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"volume":12,"related_material":{"record":[{"id":"9866","status":"public","relation":"research_data"}]},"issue":"12","_id":"1167","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"740","status":"public","date_updated":"2023-02-23T14:11:22Z","ddc":["570"],"file_date_updated":"2020-07-14T12:44:37Z","department":[{"_id":"AnKi"}],"acknowledgement":"MZ acknowledges the Polish National Science Centre grant no. DEC-2012/07/N/NZ2/00107. BW was supported by the Scottish Government/Royal Society of Edinburgh Personal Research Fellowship. We thank Marjon de Vos and Oliver Martin for critically reading the manuscript.","oa":1,"publisher":"Public Library of Science","quality_controlled":"1","year":"2016","has_accepted_license":"1","publication":"PLoS Computational Biology","day":"09","date_created":"2018-12-11T11:50:30Z","date_published":"2016-12-09T00:00:00Z","doi":"10.1371/journal.pcbi.1005218","article_number":"e1005218","citation":{"mla":"Zagórski, Marcin P., et al. “Beyond the Hypercube Evolutionary Accessibility of Fitness Landscapes with Realistic Mutational Networks.” PLoS Computational Biology, vol. 12, no. 12, e1005218, Public Library of Science, 2016, doi:10.1371/journal.pcbi.1005218.","ieee":"M. P. Zagórski, Z. Burda, and B. Wacław, “Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks,” PLoS Computational Biology, vol. 12, no. 12. Public Library of Science, 2016.","short":"M.P. Zagórski, Z. Burda, B. Wacław, PLoS Computational Biology 12 (2016).","ama":"Zagórski MP, Burda Z, Wacław B. Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks. PLoS Computational Biology. 2016;12(12). doi:10.1371/journal.pcbi.1005218","apa":"Zagórski, M. P., Burda, Z., & Wacław, B. (2016). Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005218","chicago":"Zagórski, Marcin P, Zdzisław Burda, and Bartłomiej Wacław. “Beyond the Hypercube Evolutionary Accessibility of Fitness Landscapes with Realistic Mutational Networks.” PLoS Computational Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pcbi.1005218.","ista":"Zagórski MP, Burda Z, Wacław B. 2016. Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks. PLoS Computational Biology. 12(12), e1005218."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","publist_id":"6190","author":[{"orcid":"0000-0001-7896-7762","full_name":"Zagórski, Marcin P","last_name":"Zagórski","first_name":"Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Zdzisław","full_name":"Burda, Zdzisław","last_name":"Burda"},{"full_name":"Wacław, Bartłomiej","last_name":"Wacław","first_name":"Bartłomiej"}],"title":"Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks"},{"volume":283,"related_material":{"record":[{"status":"public","id":"9704","relation":"research_data"}]},"issue":"1833","language":[{"iso":"eng"}],"file":[{"file_name":"IST-2016-701-v1+1_20160811.full.pdf","date_created":"2018-12-12T10:08:46Z","file_size":796872,"date_updated":"2020-07-14T12:44:42Z","creator":"system","checksum":"0b0d1be38b497d004064650acb3baced","file_id":"4708","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","intvolume":" 283","month":"06","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Emerging infectious diseases (EIDs) have contributed significantly to the current biodiversity crisis, leading to widespread epidemics and population loss. Owing to genetic variation in pathogen virulence, a complete understanding of species decline requires the accurate identification and characterization of EIDs. We explore this issue in the Western honeybee, where increasing mortality of populations in the Northern Hemisphere has caused major concern. Specifically, we investigate the importance of genetic identity of the main suspect in mortality, deformed wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B) is more virulent than the established DWV genotype (DWV-A) and is widespread in the landscape. Furthermore, we show in a simple model that colonies infected with DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential for rapid DWV evolution by revealing extensive genome-wide recombination in vivo. The emergence of DWV-B in naive honeybee populations, including via recombination with DWV-A, could be of significant ecological and economic importance. Our findings emphasize that knowledge of pathogen genetic identity and diversity is critical to understanding drivers of species decline."}],"department":[{"_id":"SyCr"}],"file_date_updated":"2020-07-14T12:44:42Z","ddc":["576","592"],"date_updated":"2023-02-23T14:05:30Z","pubrep_id":"701","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"1262","date_created":"2018-12-11T11:51:00Z","date_published":"2016-06-29T00:00:00Z","doi":"10.1098/rspb.2016.0811","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","day":"29","year":"2016","has_accepted_license":"1","oa":1,"publisher":"Royal Society, The","quality_controlled":"1","acknowledgement":"This work was supported by the Federal Ministry of Food, Agriculture and Consumer Protection (Germany): Fit Bee project (grant 511-06.01-28-1-71.007-10), the EU: BeeDoc (grant 244956), iDiv (2013 NGS-Fast Track grant W47004118) and the Insect Pollinators Initiative (IPI grant BB/I000100/1 and BB/I000151/1). The IPI is funded jointly by the Biotechnology and Biological Sciences Research Council, the Department for Environment, Food and Rural Affairs, the Natural Environment Research Council, the Scottish Government and the Wellcome Trust, under the Living with Environmental Change Partnership. We thank A. Abrahams, M. Husemann and A. Soro\r\nfor support in obtaining\r\nV. destructor\r\n-free honeybees; and BBKA\r\nPresident D. Aston for access to records of colony overwinter\r\n2011–2012 mortality in the UK. We also thank the anonymous refe-\r\nrees and Stephen Martin for comments that led to substantial\r\nimprovement of the manuscript.","title":"Elevated virulence of an emerging viral genotype as a driver of honeybee loss","author":[{"full_name":"Mcmahon, Dino","last_name":"Mcmahon","first_name":"Dino"},{"first_name":"Myrsini","last_name":"Natsopoulou","full_name":"Natsopoulou, Myrsini"},{"first_name":"Vincent","last_name":"Doublet","full_name":"Doublet, Vincent"},{"orcid":"0000-0002-3712-925X","full_name":"Fürst, Matthias","last_name":"Fürst","first_name":"Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Weging","full_name":"Weging, Silvio","first_name":"Silvio"},{"first_name":"Mark","full_name":"Brown, Mark","last_name":"Brown"},{"first_name":"Andreas","full_name":"Gogol Döring, Andreas","last_name":"Gogol Döring"},{"first_name":"Robert","full_name":"Paxton, Robert","last_name":"Paxton"}],"publist_id":"6060","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Mcmahon, Dino, et al. “Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 283, no. 1833, 20160811, Royal Society, The, 2016, doi:10.1098/rspb.2016.0811.","ieee":"D. Mcmahon et al., “Elevated virulence of an emerging viral genotype as a driver of honeybee loss,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 283, no. 1833. Royal Society, The, 2016.","short":"D. Mcmahon, M. Natsopoulou, V. Doublet, M. Fürst, S. Weging, M. Brown, A. Gogol Döring, R. Paxton, Proceedings of the Royal Society of London Series B Biological Sciences 283 (2016).","ama":"Mcmahon D, Natsopoulou M, Doublet V, et al. Elevated virulence of an emerging viral genotype as a driver of honeybee loss. Proceedings of the Royal Society of London Series B Biological Sciences. 2016;283(1833). doi:10.1098/rspb.2016.0811","apa":"Mcmahon, D., Natsopoulou, M., Doublet, V., Fürst, M., Weging, S., Brown, M., … Paxton, R. (2016). Elevated virulence of an emerging viral genotype as a driver of honeybee loss. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2016.0811","chicago":"Mcmahon, Dino, Myrsini Natsopoulou, Vincent Doublet, Matthias Fürst, Silvio Weging, Mark Brown, Andreas Gogol Döring, and Robert Paxton. “Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2016. https://doi.org/10.1098/rspb.2016.0811.","ista":"Mcmahon D, Natsopoulou M, Doublet V, Fürst M, Weging S, Brown M, Gogol Döring A, Paxton R. 2016. Elevated virulence of an emerging viral genotype as a driver of honeybee loss. Proceedings of the Royal Society of London Series B Biological Sciences. 283(1833), 20160811."},"article_number":"20160811"}]