[{"day":"01","article_processing_charge":"No","scopus_import":1,"date_published":"2016-01-01T00:00:00Z","publication":"Methods in Enzymology","citation":{"ista":"Schwarz J, Sixt MK. 2016. Quantitative analysis of dendritic cell haptotaxis. Methods in Enzymology. 570, 567–581.","apa":"Schwarz, J., & Sixt, M. K. (2016). Quantitative analysis of dendritic cell haptotaxis. Methods in Enzymology. Elsevier. https://doi.org/10.1016/bs.mie.2015.11.004","ieee":"J. Schwarz and M. K. Sixt, “Quantitative analysis of dendritic cell haptotaxis,” Methods in Enzymology, vol. 570. Elsevier, pp. 567–581, 2016.","ama":"Schwarz J, Sixt MK. Quantitative analysis of dendritic cell haptotaxis. Methods in Enzymology. 2016;570:567-581. doi:10.1016/bs.mie.2015.11.004","chicago":"Schwarz, Jan, and Michael K Sixt. “Quantitative Analysis of Dendritic Cell Haptotaxis.” Methods in Enzymology. Elsevier, 2016. https://doi.org/10.1016/bs.mie.2015.11.004.","mla":"Schwarz, Jan, and Michael K. Sixt. “Quantitative Analysis of Dendritic Cell Haptotaxis.” Methods in Enzymology, vol. 570, Elsevier, 2016, pp. 567–81, doi:10.1016/bs.mie.2015.11.004.","short":"J. Schwarz, M.K. Sixt, Methods in Enzymology 570 (2016) 567–581."},"article_type":"original","page":"567 - 581","abstract":[{"lang":"eng","text":"Chemokines are the main guidance cues directing leukocyte migration. Opposed to early assumptions, chemokines do not necessarily act as soluble cues but are often immobilized within tissues, e.g., dendritic cell migration toward lymphatic vessels is guided by a haptotactic gradient of the chemokine CCL21. Controlled assay systems to quantitatively study haptotaxis in vitro are still missing. In this chapter, we describe an in vitro haptotaxis assay optimized for the unique properties of dendritic cells. The chemokine CCL21 is immobilized in a bioactive state, using laser-assisted protein adsorption by photobleaching. The cells follow this immobilized CCL21 gradient in a haptotaxis chamber, which provides three dimensionally confined migration conditions."}],"type":"journal_article","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1597","title":"Quantitative analysis of dendritic cell haptotaxis","status":"public","intvolume":" 570","month":"01","doi":"10.1016/bs.mie.2015.11.004","acknowledged_ssus":[{"_id":"Bio"}],"language":[{"iso":"eng"}],"external_id":{"pmid":["26921962"]},"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425"},{"name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","call_identifier":"FWF","grant_number":"Y 564-B12","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"publist_id":"5573","author":[{"full_name":"Schwarz, Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Schwarz"},{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:52:56Z","date_updated":"2021-01-12T06:51:51Z","volume":570,"year":"2016","acknowledgement":"This work was supported by the Boehringer Ingelheim Fonds, the European Research Council (ERC StG 281556), and a START Award of the Austrian Science Foundation (FWF). We thank Robert Hauschild, Anne Reversat, and Jack Merrin for valuable input and the Imaging Facility of IST Austria for excellent support.","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"MiSi"}]},{"type":"journal_article","issue":"7","abstract":[{"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. ","lang":"eng"}],"intvolume":" 17","title":"Anderson transition at 2 dimensional growth rate on antitrees and spectral theory for operators with one propagating channel","status":"public","_id":"1608","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","scopus_import":1,"day":"01","page":"1631 - 1675","citation":{"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","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.","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.","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","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.","short":"C. Sadel, Annales Henri Poincare 17 (2016) 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."},"publication":"Annales Henri Poincare","date_published":"2016-07-01T00:00:00Z","publist_id":"5558","ec_funded":1,"department":[{"_id":"LaEr"}],"publisher":"Birkhäuser","publication_status":"published","year":"2016","volume":17,"date_updated":"2021-01-12T06:51:58Z","date_created":"2018-12-11T11:53:00Z","author":[{"last_name":"Sadel","first_name":"Christian","orcid":"0000-0001-8255-3968","id":"4760E9F8-F248-11E8-B48F-1D18A9856A87","full_name":"Sadel, Christian"}],"month":"07","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1501.04287"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00023-015-0456-3"},{"issue":"1","publist_id":"5554","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"}],"type":"journal_article","oa_version":"Preprint","volume":75,"date_updated":"2021-01-12T06:52:00Z","date_created":"2018-12-11T11:53:01Z","author":[{"first_name":"Alexandr","last_name":"Kazda","id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87","full_name":"Kazda, Alexandr"}],"department":[{"_id":"VlKo"}],"publisher":"Springer","intvolume":" 75","title":"CSP for binary conservative relational structures","status":"public","publication_status":"published","_id":"1612","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2016","day":"01","month":"02","scopus_import":1,"language":[{"iso":"eng"}],"date_published":"2016-02-01T00:00:00Z","doi":"10.1007/s00012-015-0358-8","page":"75 - 84","quality_controlled":"1","oa":1,"citation":{"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.","chicago":"Kazda, Alexandr. “CSP for Binary Conservative Relational Structures.” Algebra Universalis. Springer, 2016. https://doi.org/10.1007/s00012-015-0358-8.","ama":"Kazda A. CSP for binary conservative relational structures. Algebra Universalis. 2016;75(1):75-84. doi: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.","apa":"Kazda, A. (2016). CSP for binary conservative relational structures. Algebra Universalis. Springer. https://doi.org/10.1007/s00012-015-0358-8","ista":"Kazda A. 2016. CSP for binary conservative relational structures. Algebra Universalis. 75(1), 75–84."},"main_file_link":[{"url":"http://arxiv.org/abs/1112.1099","open_access":"1"}],"publication":"Algebra Universalis"},{"date_published":"2016-04-01T00:00:00Z","doi":"10.1016/j.jco.2015.11.003","language":[{"iso":"eng"}],"citation":{"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","ieee":"F. Pausinger and S. Steinerberger, “On the discrepancy of jittered sampling,” Journal of Complexity, vol. 33. Academic Press, pp. 199–216, 2016.","ista":"Pausinger F, Steinerberger S. 2016. On the discrepancy of jittered sampling. Journal of Complexity. 33, 199–216.","short":"F. Pausinger, S. Steinerberger, Journal of Complexity 33 (2016) 199–216.","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.","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."},"main_file_link":[{"url":"http://arxiv.org/abs/1510.00251","open_access":"1"}],"oa":1,"publication":"Journal of Complexity","page":"199 - 216","quality_controlled":"1","day":"01","month":"04","scopus_import":1,"author":[{"full_name":"Pausinger, Florian","first_name":"Florian","last_name":"Pausinger","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8379-3768"},{"last_name":"Steinerberger","first_name":"Stefan","full_name":"Steinerberger, Stefan"}],"volume":33,"oa_version":"Submitted Version","date_created":"2018-12-11T11:53:03Z","date_updated":"2021-01-12T06:52:02Z","_id":"1617","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2016","acknowledgement":"We are grateful to the referee whose suggestions greatly improved the quality and clarity of the exposition.","department":[{"_id":"HeEd"}],"publisher":"Academic Press","intvolume":" 33","status":"public","title":"On the discrepancy of jittered sampling","publication_status":"published","publist_id":"5549","abstract":[{"lang":"eng","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."}],"type":"journal_article"},{"type":"journal_article","issue":"1","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"}],"_id":"1620","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 342","status":"public","title":"The external field dependence of the BCS critical temperature","oa_version":"Submitted Version","scopus_import":1,"day":"01","citation":{"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.","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.","short":"R. Frank, C. Hainzl, R. Seiringer, J. Solovej, Communications in Mathematical Physics 342 (2016) 189–216.","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.","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.","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"},"publication":"Communications in Mathematical Physics","page":"189 - 216","date_published":"2016-02-01T00:00:00Z","publist_id":"5546","year":"2016","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.","publisher":"Springer","department":[{"_id":"RoSe"}],"publication_status":"published","author":[{"first_name":"Rupert","last_name":"Frank","full_name":"Frank, Rupert"},{"first_name":"Christian","last_name":"Hainzl","full_name":"Hainzl, Christian"},{"full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer"},{"first_name":"Jan","last_name":"Solovej","full_name":"Solovej, Jan"}],"volume":342,"date_updated":"2021-01-12T06:52:03Z","date_created":"2018-12-11T11:53:04Z","month":"02","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1410.2352","open_access":"1"}],"quality_controlled":"1","doi":"10.1007/s00220-015-2526-2","language":[{"iso":"eng"}]},{"ec_funded":1,"publist_id":"5542","year":"2016","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”.","publication_status":"published","publisher":"Springer","department":[{"_id":"RoSe"}],"author":[{"last_name":"Lundholm","first_name":"Douglas","full_name":"Lundholm, Douglas"},{"full_name":"Nam, Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan","last_name":"Nam"},{"full_name":"Portmann, Fabian","last_name":"Portmann","first_name":"Fabian"}],"date_created":"2018-12-11T11:53:05Z","date_updated":"2021-01-12T06:52:04Z","volume":219,"month":"03","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1501.04570"}],"quality_controlled":"1","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"doi":"10.1007/s00205-015-0923-5","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"3","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1622","status":"public","title":"Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems","intvolume":" 219","oa_version":"Submitted Version","scopus_import":1,"day":"01","publication":"Archive for Rational Mechanics and Analysis","citation":{"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.","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","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.","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","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.","short":"D. Lundholm, P. Nam, F. Portmann, Archive for Rational Mechanics and Analysis 219 (2016) 1343–1382.","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."},"page":"1343 - 1382","date_published":"2016-03-01T00:00:00Z"},{"page":"1 - 12","citation":{"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.","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.","short":"J. Kelleher, A. Etheridge, A. Véber, N.H. Barton, Theoretical Population Biology 108 (2016) 1–12.","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.","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","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.","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"},"publication":"Theoretical Population Biology","date_published":"2016-04-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01","intvolume":" 108","status":"public","title":"Spread of pedigree versus genetic ancestry in spatially distributed populations","ddc":["576"],"_id":"1631","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"4865","date_created":"2018-12-12T10:11:12Z","date_updated":"2020-07-14T12:45:07Z","checksum":"6a65ba187994d4ad86c1c509e0ff482a","file_name":"IST-2016-465-v1+1_1-s2.0-S0040580915001094-main.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1684043,"creator":"system"}],"pubrep_id":"465","type":"journal_article","abstract":[{"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.","lang":"eng"}],"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1016/j.tpb.2015.10.008","month":"04","department":[{"_id":"NiBa"}],"publisher":"Academic Press","publication_status":"published","year":"2016","volume":108,"date_created":"2018-12-11T11:53:08Z","date_updated":"2021-01-12T06:52:07Z","author":[{"full_name":"Kelleher, Jerome","first_name":"Jerome","last_name":"Kelleher"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"},{"last_name":"Véber","first_name":"Amandine","full_name":"Véber, Amandine"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"publist_id":"5524","ec_funded":1,"file_date_updated":"2020-07-14T12:45:07Z"},{"oa":1,"quality_controlled":"1","doi":"10.1007/s00344-015-9553-2","language":[{"iso":"eng"}],"month":"06","acknowledgement":"European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation GAČR (GA13-40637S) to JF. ","year":"2016","publication_status":"published","publisher":"Springer","department":[{"_id":"JiFr"}],"author":[{"full_name":"Zemová, Radka","first_name":"Radka","last_name":"Zemová"},{"last_name":"Zwiewka","first_name":"Marta","full_name":"Zwiewka, Marta"},{"full_name":"Bielach, Agnieszka","last_name":"Bielach","first_name":"Agnieszka"},{"full_name":"Robert, Hélène","first_name":"Hélène","last_name":"Robert"},{"full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"date_created":"2018-12-11T11:53:12Z","date_updated":"2021-01-12T06:52:11Z","volume":35,"file_date_updated":"2020-07-14T12:45:08Z","publist_id":"5512","publication":"Journal of Plant Growth Regulation","citation":{"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.","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.","short":"R. Zemová, M. Zwiewka, A. Bielach, H. Robert, J. Friml, Journal of Plant Growth Regulation 35 (2016) 465–476.","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.","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","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.","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"},"page":"465 - 476","date_published":"2016-06-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1641","ddc":["581"],"title":"A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana","status":"public","intvolume":" 35","pubrep_id":"1001","oa_version":"Preprint","file":[{"creator":"system","content_type":"application/pdf","file_size":5637591,"file_name":"IST-2018-1001-v1+1_Zemova_JPlantGrowthRegul_2016_proofs.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:08Z","date_created":"2018-12-12T10:08:34Z","checksum":"0dc6a300cde6536ceedd2bcdd2060efb","file_id":"4695","relation":"main_file"}],"type":"journal_article","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."}],"issue":"2"},{"day":"11","scopus_import":1,"date_published":"2016-08-11T00:00:00Z","page":"391 - 408","citation":{"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.","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.","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","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.","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.","short":"G. Fuchsbauer, C. Hanser, C. Kamath Hosdurg, D. Slamanig, in:, Springer, 2016, pp. 391–408."},"abstract":[{"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.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Submitted Version","intvolume":" 9841","title":"Practical round-optimal blind signatures in the standard model from weaker assumptions","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1225","month":"08","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-44618-9_21","conference":{"name":"SCN: Security and Cryptography for Networks","end_date":"2016-09-02","start_date":"2016-08-31","location":"Amalfi, Italy"},"project":[{"grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","call_identifier":"FP7"},{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/662"}],"oa":1,"ec_funded":1,"publist_id":"6109","volume":9841,"date_created":"2018-12-11T11:50:49Z","date_updated":"2023-02-23T10:08:16Z","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"1647"}]},"author":[{"id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","last_name":"Fuchsbauer","first_name":"Georg","full_name":"Fuchsbauer, Georg"},{"last_name":"Hanser","first_name":"Christian","full_name":"Hanser, Christian"},{"full_name":"Kamath Hosdurg, Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","last_name":"Kamath Hosdurg","first_name":"Chethan"},{"first_name":"Daniel","last_name":"Slamanig","full_name":"Slamanig, Daniel"}],"publisher":"Springer","department":[{"_id":"KrPi"}],"publication_status":"published","year":"2016"},{"abstract":[{"lang":"eng","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."}],"type":"conference","alternative_title":["LNCS"],"pubrep_id":"677","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"IST-2016-677-v1+1_869.pdf","creator":"system","content_type":"application/pdf","file_size":580088,"file_id":"4923","relation":"main_file","checksum":"a57711cb660c5b17b42bb47275a00180","date_updated":"2020-07-14T12:45:08Z","date_created":"2018-12-12T10:12:05Z"}],"_id":"1653","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 9452","title":"New realizations of somewhere statistically binding hashing and positional accumulators","status":"public","ddc":["000"],"has_accepted_license":"1","day":"08","scopus_import":1,"date_published":"2016-01-08T00:00:00Z","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.","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.","short":"T. Okamoto, K.Z. Pietrzak, B. Waters, D. Wichs, in:, Springer, 2016, pp. 121–145.","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.","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","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.","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"},"page":"121 - 145","publist_id":"5497","ec_funded":1,"file_date_updated":"2020-07-14T12:45:08Z","author":[{"last_name":"Okamoto","first_name":"Tatsuaki","full_name":"Okamoto, Tatsuaki"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z"},{"last_name":"Waters","first_name":"Brent","full_name":"Waters, Brent"},{"full_name":"Wichs, Daniel","last_name":"Wichs","first_name":"Daniel"}],"volume":9452,"date_created":"2018-12-11T11:53:16Z","date_updated":"2021-01-12T06:52:16Z","year":"2016","publisher":"Springer","department":[{"_id":"KrPi"}],"publication_status":"published","month":"01","doi":"10.1007/978-3-662-48797-6_6","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"},"language":[{"iso":"eng"}],"oa":1,"project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","call_identifier":"FP7","name":"Provable Security for Physical Cryptography"}],"quality_controlled":"1"},{"ec_funded":1,"publist_id":"6210","author":[{"full_name":"Schilling, Christian","first_name":"Christian","last_name":"Schilling"},{"full_name":"Bogomolov, Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0686-0365","first_name":"Sergiy","last_name":"Bogomolov"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"full_name":"Podelski, Andreas","first_name":"Andreas","last_name":"Podelski"},{"full_name":"Ruess, Jakob","first_name":"Jakob","last_name":"Ruess","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1615-3282"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1658"}]},"date_updated":"2023-02-23T10:08:46Z","date_created":"2018-12-11T11:50:24Z","volume":149,"year":"2016","acknowledgement":"This work is based on the CMSB 2015 paper “Adaptive moment closure for parameter inference of biochemical reaction networks” (Bogomolov et al., 2015). The work was partly supported by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR 14 AVACS1), by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award). J.R. acknowledges support from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734.","publication_status":"published","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"publisher":"Elsevier","month":"11","doi":"10.1016/j.biosystems.2016.07.005","language":[{"iso":"eng"}],"quality_controlled":"1","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"abstract":[{"text":"Continuous-time Markov chain (CTMC) models have become a central tool for understanding the dynamics of complex reaction networks and the importance of stochasticity in the underlying biochemical processes. When such models are employed to answer questions in applications, in order to ensure that the model provides a sufficiently accurate representation of the real system, it is of vital importance that the model parameters are inferred from real measured data. This, however, is often a formidable task and all of the existing methods fail in one case or the other, usually because the underlying CTMC model is high-dimensional and computationally difficult to analyze. The parameter inference methods that tend to scale best in the dimension of the CTMC are based on so-called moment closure approximations. However, there exists a large number of different moment closure approximations and it is typically hard to say a priori which of the approximations is the most suitable for the inference procedure. Here, we propose a moment-based parameter inference method that automatically chooses the most appropriate moment closure method. Accordingly, contrary to existing methods, the user is not required to be experienced in moment closure techniques. In addition to that, our method adaptively changes the approximation during the parameter inference to ensure that always the best approximation is used, even in cases where different approximations are best in different regions of the parameter space. © 2016 Elsevier Ireland Ltd","lang":"eng"}],"type":"journal_article","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1148","title":"Adaptive moment closure for parameter inference of biochemical reaction networks","status":"public","intvolume":" 149","day":"01","scopus_import":1,"date_published":"2016-11-01T00:00:00Z","publication":"Biosystems","citation":{"ama":"Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. Adaptive moment closure for parameter inference of biochemical reaction networks. Biosystems. 2016;149:15-25. doi:10.1016/j.biosystems.2016.07.005","ieee":"C. Schilling, S. Bogomolov, T. A. Henzinger, A. Podelski, and J. Ruess, “Adaptive moment closure for parameter inference of biochemical reaction networks,” Biosystems, vol. 149. Elsevier, pp. 15–25, 2016.","apa":"Schilling, C., Bogomolov, S., Henzinger, T. A., Podelski, A., & Ruess, J. (2016). Adaptive moment closure for parameter inference of biochemical reaction networks. Biosystems. Elsevier. https://doi.org/10.1016/j.biosystems.2016.07.005","ista":"Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. 2016. Adaptive moment closure for parameter inference of biochemical reaction networks. Biosystems. 149, 15–25.","short":"C. Schilling, S. Bogomolov, T.A. Henzinger, A. Podelski, J. Ruess, Biosystems 149 (2016) 15–25.","mla":"Schilling, Christian, et al. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.” Biosystems, vol. 149, Elsevier, 2016, pp. 15–25, doi:10.1016/j.biosystems.2016.07.005.","chicago":"Schilling, Christian, Sergiy Bogomolov, Thomas A Henzinger, Andreas Podelski, and Jakob Ruess. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.” Biosystems. Elsevier, 2016. https://doi.org/10.1016/j.biosystems.2016.07.005."},"page":"15 - 25"},{"abstract":[{"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.","lang":"eng"}],"issue":"4","type":"journal_article","pubrep_id":"457","file":[{"content_type":"application/pdf","file_size":2296522,"creator":"system","file_name":"IST-2016-457-v1+1_s10009-015-0393-y.pdf","access_level":"open_access","date_created":"2018-12-12T10:15:26Z","date_updated":"2020-07-14T12:45:13Z","checksum":"31561d7705599a9bd4ea816accc0752e","relation":"main_file","file_id":"5146"}],"oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1705","title":"Guided search for hybrid systems based on coarse-grained space abstractions","ddc":["000"],"status":"public","intvolume":" 18","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":1,"date_published":"2016-08-01T00:00:00Z","publication":"International Journal on Software Tools for Technology Transfer","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.","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.","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","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.","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.","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"},"page":"449 - 467","file_date_updated":"2020-07-14T12:45:13Z","ec_funded":1,"publist_id":"5431","author":[{"full_name":"Bogomolov, Sergiy","last_name":"Bogomolov","first_name":"Sergiy","orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Donzé","first_name":"Alexandre","full_name":"Donzé, Alexandre"},{"full_name":"Frehse, Goran","first_name":"Goran","last_name":"Frehse"},{"last_name":"Grosu","first_name":"Radu","full_name":"Grosu, Radu"},{"full_name":"Johnson, Taylor","last_name":"Johnson","first_name":"Taylor"},{"full_name":"Ladan, Hamed","first_name":"Hamed","last_name":"Ladan"},{"full_name":"Podelski, Andreas","last_name":"Podelski","first_name":"Andreas"},{"last_name":"Wehrle","first_name":"Martin","full_name":"Wehrle, Martin"}],"date_created":"2018-12-11T11:53:34Z","date_updated":"2021-01-12T06:52:38Z","volume":18,"year":"2016","publication_status":"published","publisher":"Springer","department":[{"_id":"ToHe"}],"month":"08","doi":"10.1007/s10009-015-0393-y","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}]},{"title":"Optimal geospatial allocation of volunteers for crisis management","publication_status":"published","status":"public","department":[{"_id":"ChLa"}],"publisher":"IEEE","year":"2016","_id":"1707","acknowledgement":"The DRIVER FP7 project has received funding from the European Unions Seventh Framework Programme for research, technological development and demonstration under grant agreement no 607798. RE-ACTA was funded within the framework of the Austrian Security Research Programme KIRAS by the Federal Ministry for Transport, Innovation and Technology.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:53:35Z","date_updated":"2021-01-12T06:52:39Z","oa_version":"None","author":[{"full_name":"Pielorz, Jasmin","id":"49BC895A-F248-11E8-B48F-1D18A9856A87","first_name":"Jasmin","last_name":"Pielorz"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph"}],"article_number":"7402041","type":"conference","abstract":[{"lang":"eng","text":"Volunteer supporters play an important role in modern crisis and disaster management. In the times of mobile Internet devices, help from thousands of volunteers can be requested within a short time span, thus relieving professional helpers from minor chores or geographically spread-out tasks. However, the simultaneous availability of many volunteers also poses new problems. In particular, the volunteer efforts must be well coordinated, or otherwise situations might emerge in which too many idle volunteers at one location become more of a burden than a relief to the professionals.\r\nIn this work, we study the task of optimally assigning volunteers to selected locations, e.g. in order to perform regular measurements, to report on damage, or to distribute information or resources to the population in a crisis situation. We formulate the assignment tasks as an optimization problem and propose an effective and efficient solution procedure. Experiments on real data of the Team Österreich, consisting of over 36,000 Austrian volunteers, show the effectiveness and efficiency of our approach."}],"publist_id":"5429","quality_controlled":"1","citation":{"short":"J. Pielorz, C. Lampert, in:, IEEE, 2016.","mla":"Pielorz, Jasmin, and Christoph Lampert. Optimal Geospatial Allocation of Volunteers for Crisis Management. 7402041, IEEE, 2016, doi:10.1109/ICT-DM.2015.7402041.","chicago":"Pielorz, Jasmin, and Christoph Lampert. “Optimal Geospatial Allocation of Volunteers for Crisis Management.” IEEE, 2016. https://doi.org/10.1109/ICT-DM.2015.7402041.","ama":"Pielorz J, Lampert C. Optimal geospatial allocation of volunteers for crisis management. In: IEEE; 2016. doi:10.1109/ICT-DM.2015.7402041","apa":"Pielorz, J., & Lampert, C. (2016). Optimal geospatial allocation of volunteers for crisis management. Presented at the ICT-DM: Information and Communication Technologies for Disaster Management, Rennes, France: IEEE. https://doi.org/10.1109/ICT-DM.2015.7402041","ieee":"J. Pielorz and C. Lampert, “Optimal geospatial allocation of volunteers for crisis management,” presented at the ICT-DM: Information and Communication Technologies for Disaster Management, Rennes, France, 2016.","ista":"Pielorz J, Lampert C. 2016. Optimal geospatial allocation of volunteers for crisis management. ICT-DM: Information and Communication Technologies for Disaster Management, 7402041."},"language":[{"iso":"eng"}],"conference":{"name":"ICT-DM: Information and Communication Technologies for Disaster Management","end_date":"2015-12-02","start_date":"2015-11-30","location":"Rennes, France"},"doi":"10.1109/ICT-DM.2015.7402041","date_published":"2016-02-11T00:00:00Z","scopus_import":1,"month":"02","day":"11"},{"_id":"1833","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2016","publication_status":"published","status":"public","title":"On the closure of relational models","department":[{"_id":"CaUh"}],"intvolume":" 143","publisher":"Elsevier","author":[{"full_name":"Klimova, Anna","id":"31934120-F248-11E8-B48F-1D18A9856A87","last_name":"Klimova","first_name":"Anna"},{"full_name":"Rudas, Tamás","first_name":"Tamás","last_name":"Rudas"}],"date_updated":"2021-01-12T06:53:30Z","date_created":"2018-12-11T11:54:15Z","volume":143,"oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","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. "}],"publist_id":"5270","publication":"Journal of Multivariate Analysis","oa":1,"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.","short":"A. Klimova, T. Rudas, Journal of Multivariate Analysis 143 (2016) 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.","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","ieee":"A. Klimova and T. Rudas, “On the closure of relational models,” Journal of Multivariate Analysis, vol. 143. Elsevier, pp. 440–452, 2016.","ista":"Klimova A, Rudas T. 2016. On the closure of relational models. Journal of Multivariate Analysis. 143, 440–452.","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"},"main_file_link":[{"url":"http://arxiv.org/abs/1501.00600","open_access":"1"}],"quality_controlled":"1","page":"440 - 452","date_published":"2016-01-01T00:00:00Z","doi":"10.1016/j.jmva.2015.10.005","language":[{"iso":"eng"}],"scopus_import":1,"day":"01","month":"01"},{"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.","year":"2016","publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"Springer","author":[{"full_name":"Lee, Jioon","first_name":"Jioon","last_name":"Lee"},{"full_name":"Schnelli, Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0954-3231","first_name":"Kevin","last_name":"Schnelli"}],"date_updated":"2021-01-12T06:53:49Z","date_created":"2018-12-11T11:54:31Z","volume":164,"publist_id":"5215","ec_funded":1,"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1310.7057","open_access":"1"}],"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"}],"doi":"10.1007/s00440-014-0610-8","language":[{"iso":"eng"}],"month":"02","_id":"1881","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Extremal eigenvalues and eigenvectors of deformed Wigner matrices","intvolume":" 164","oa_version":"Preprint","type":"journal_article","abstract":[{"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. ","lang":"eng"}],"issue":"1-2","publication":"Probability Theory and Related Fields","citation":{"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","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.","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","ista":"Lee J, Schnelli K. 2016. Extremal eigenvalues and eigenvectors of deformed Wigner matrices. Probability Theory and Related Fields. 164(1–2), 165–241.","short":"J. Lee, K. Schnelli, Probability Theory and Related Fields 164 (2016) 165–241.","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.","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."},"page":"165 - 241","date_published":"2016-02-01T00:00:00Z","scopus_import":1,"day":"01"},{"day":"01","scopus_import":1,"date_published":"2016-05-01T00:00:00Z","publication":"Israel Journal of Mathematics","citation":{"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","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","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.","ista":"Matoušek J, Sedgwick E, Tancer M, Wagner U. 2016. Untangling two systems of noncrossing curves. Israel Journal of Mathematics. 212(1), 37–79.","short":"J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, Israel Journal of Mathematics 212 (2016) 37–79.","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.","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."},"page":"37 - 79","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"}],"issue":"1","type":"journal_article","oa_version":"Preprint","_id":"1411","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Untangling two systems of noncrossing curves","status":"public","intvolume":" 212","month":"05","doi":"10.1007/s11856-016-1294-9","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1302.6475"}],"quality_controlled":"1","project":[{"grant_number":"PP00P2_138948","_id":"25FA3206-B435-11E9-9278-68D0E5697425","name":"Embeddings in Higher Dimensions: Algorithms and Combinatorics"}],"publist_id":"5796","author":[{"last_name":"Matoušek","first_name":"Jiří","full_name":"Matoušek, Jiří"},{"first_name":"Eric","last_name":"Sedgwick","full_name":"Sedgwick, Eric"},{"first_name":"Martin","last_name":"Tancer","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1191-6714","full_name":"Tancer, Martin"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","first_name":"Uli","last_name":"Wagner","full_name":"Wagner, Uli"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"2244"}]},"date_updated":"2023-02-23T10:34:31Z","date_created":"2018-12-11T11:51:52Z","volume":212,"year":"2016","acknowledgement":"Supported by the ERC Adv anced Grant No. 267165. ","publication_status":"published","publisher":"Springer","department":[{"_id":"UlWa"}]},{"month":"09","project":[{"call_identifier":"FP7","name":"Provable Security for Physical Cryptography","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1007/s00037-015-0120-9","ec_funded":1,"publist_id":"5715","file_date_updated":"2020-07-14T12:44:56Z","publisher":"Springer","department":[{"_id":"KrPi"}],"publication_status":"published","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","year":"2016","volume":25,"date_updated":"2023-02-23T11:05:09Z","date_created":"2018-12-11T11:52:16Z","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"2940"}]},"author":[{"first_name":"Stephan","last_name":"Krenn","id":"329FCCF0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2835-9093","full_name":"Krenn, Stephan"},{"last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"},{"last_name":"Wadia","first_name":"Akshay","full_name":"Wadia, Akshay"},{"full_name":"Wichs, Daniel","first_name":"Daniel","last_name":"Wichs"}],"scopus_import":1,"has_accepted_license":"1","day":"01","page":"567 - 605","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.","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","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.","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","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.","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.","short":"S. Krenn, K.Z. Pietrzak, A. Wadia, D. Wichs, Computational Complexity 25 (2016) 567–605."},"publication":"Computational Complexity","date_published":"2016-09-01T00:00:00Z","type":"journal_article","issue":"3","abstract":[{"lang":"eng","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."}],"intvolume":" 25","title":"A counterexample to the chain rule for conditional HILL entropy","status":"public","ddc":["004"],"_id":"1479","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","file":[{"file_id":"5012","relation":"main_file","checksum":"7659296174fa75f5f0364f31f46f4bcf","date_created":"2018-12-12T10:13:29Z","date_updated":"2020-07-14T12:44:56Z","access_level":"open_access","file_name":"IST-2017-766-v1+1_678.pdf","creator":"system","content_type":"application/pdf","file_size":483258}],"pubrep_id":"766"},{"pubrep_id":"950","oa_version":"Published Version","file":[{"checksum":"848043c812ace05e459579c923f3d3cf","date_updated":"2020-07-14T12:46:35Z","date_created":"2018-12-12T10:07:59Z","file_id":"4658","relation":"main_file","creator":"system","file_size":2116225,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2018-950-v1+1_2016_Chatterjee_The_complexity.pdf"}],"_id":"478","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["004"],"title":"The complexity of deciding legality of a single step of magic: The gathering","status":"public","intvolume":" 285","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."}],"type":"conference","alternative_title":["Frontiers in Artificial Intelligence and Applications"],"date_published":"2016-01-01T00:00:00Z","citation":{"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.","short":"K. Chatterjee, R. Ibsen-Jensen, in:, IOS Press, 2016, pp. 1432–1439.","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.","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","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.","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.","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"},"page":"1432 - 1439","day":"01","has_accepted_license":"1","scopus_import":1,"author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus"}],"date_created":"2018-12-11T11:46:41Z","date_updated":"2021-01-12T08:00:54Z","volume":285,"year":"2016","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"IOS Press","file_date_updated":"2020-07-14T12:46:35Z","publist_id":"7342","conference":{"name":"ECAI: European Conference on Artificial Intelligence","location":"The Hague, Netherlands","start_date":"2016-08-29","end_date":"2016-09-02"},"doi":"10.3233/978-1-61499-672-9-1432","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"quality_controlled":"1","month":"01"},{"quality_controlled":"1","page":"112 - 121","publication":"Proceedings of the 38th International Conference on Software Engineering Companion ","citation":{"chicago":"Jiang, Yu, Han Liu, Hui Kong, Rui Wang, Mohamad Hosseini, Jiaguang Sun, and Lui Sha. “Use Runtime Verification to Improve the Quality of Medical Care Practice.” In Proceedings of the 38th International Conference on Software Engineering Companion , 112–21. IEEE, 2016. https://doi.org/10.1145/2889160.2889233.","short":"Y. Jiang, H. Liu, H. Kong, R. Wang, M. Hosseini, J. Sun, L. Sha, in:, Proceedings of the 38th International Conference on Software Engineering Companion , IEEE, 2016, pp. 112–121.","mla":"Jiang, Yu, et al. “Use Runtime Verification to Improve the Quality of Medical Care Practice.” Proceedings of the 38th International Conference on Software Engineering Companion , IEEE, 2016, pp. 112–21, doi:10.1145/2889160.2889233.","apa":"Jiang, Y., Liu, H., Kong, H., Wang, R., Hosseini, M., Sun, J., & Sha, L. (2016). Use runtime verification to improve the quality of medical care practice. In Proceedings of the 38th International Conference on Software Engineering Companion (pp. 112–121). Austin, TX, USA: IEEE. https://doi.org/10.1145/2889160.2889233","ieee":"Y. Jiang et al., “Use runtime verification to improve the quality of medical care practice,” in Proceedings of the 38th International Conference on Software Engineering Companion , Austin, TX, USA, 2016, pp. 112–121.","ista":"Jiang Y, Liu H, Kong H, Wang R, Hosseini M, Sun J, Sha L. 2016. Use runtime verification to improve the quality of medical care practice. Proceedings of the 38th International Conference on Software Engineering Companion . ICSE: International Conference on Software Engineering, Proceedings International Conference on Software Engineering, , 112–121.","ama":"Jiang Y, Liu H, Kong H, et al. Use runtime verification to improve the quality of medical care practice. In: Proceedings of the 38th International Conference on Software Engineering Companion . IEEE; 2016:112-121. doi:10.1145/2889160.2889233"},"language":[{"iso":"eng"}],"conference":{"name":"ICSE: International Conference on Software Engineering","start_date":"2016-05-14","location":"Austin, TX, USA","end_date":"2016-05-22"},"date_published":"2016-05-14T00:00:00Z","doi":"10.1145/2889160.2889233","scopus_import":1,"month":"05","day":"14","status":"public","title":"Use runtime verification to improve the quality of medical care practice","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"IEEE","year":"2016","_id":"479","acknowledgement":"This work is supported by NSF CNS 13-30077, NSF CNS 13-29886, NSF CNS 15-45002, and NSFC 61303014.\r\nThe authors thank Dr. Bobby and Dr. Hill at Carle Hospital, Urbana, IL for their help with the discussion on medical knowledge.\r\n\r\n","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:00:55Z","date_created":"2018-12-11T11:46:42Z","oa_version":"None","author":[{"full_name":"Jiang, Yu","first_name":"Yu","last_name":"Jiang"},{"last_name":"Liu","first_name":"Han","full_name":"Liu, Han"},{"full_name":"Kong, Hui","orcid":"0000-0002-3066-6941","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","last_name":"Kong","first_name":"Hui"},{"first_name":"Rui","last_name":"Wang","full_name":"Wang, Rui"},{"first_name":"Mohamad","last_name":"Hosseini","full_name":"Hosseini, Mohamad"},{"full_name":"Sun, Jiaguang","first_name":"Jiaguang","last_name":"Sun"},{"full_name":"Sha, Lui","last_name":"Sha","first_name":"Lui"}],"alternative_title":["Proceedings International Conference on Software Engineering"],"type":"conference","abstract":[{"text":"Clinical guidelines and decision support systems (DSS) play an important role in daily practices of medicine. Many text-based guidelines have been encoded for work-flow simulation of DSS to automate health care. During the collaboration with Carle hospital to develop a DSS, we identify that, for some complex and life-critical diseases, it is highly desirable to automatically rigorously verify some complex temporal properties in guidelines, which brings new challenges to current simulation based DSS with limited support of automatical formal verification and real-time data analysis. In this paper, we conduct the first study on applying runtime verification to cooperate with current DSS based on real-time data. Within the proposed technique, a user-friendly domain specific language, named DRTV, is designed to specify vital real-time data sampled by medical devices and temporal properties originated from clinical guidelines. Some interfaces are developed for data acquisition and communication. Then, for medical practice scenarios described in DRTV model, we will automatically generate event sequences and runtime property verifier automata. If a temporal property violates, real-time warnings will be produced by the formal verifier and passed to medical DSS. We have used DRTV to specify different kinds of medical care scenarios, and applied the proposed technique to assist existing DSS. As presented in experiment results, in terms of warning detection, it outperforms the only use of DSS or human inspection, and improves the quality of clinical health care of hospital","lang":"eng"}],"publist_id":"7341"},{"publist_id":"7340","ec_funded":1,"year":"2016","department":[{"_id":"KrCh"}],"publisher":"IEEE","publication_status":"published","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Laurent","last_name":"Doyen","full_name":"Doyen, Laurent"}],"volume":"05-08-July-2016","date_updated":"2021-01-12T08:00:56Z","date_created":"2018-12-11T11:46:42Z","month":"07","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1604.06376","open_access":"1"}],"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"quality_controlled":"1","doi":"10.1145/2933575.2934513","conference":{"name":"LICS: Logic in Computer Science","end_date":"2016-07-08","location":"New York, NY, USA","start_date":"2016-07-05"},"language":[{"iso":"eng"}],"type":"conference","alternative_title":["Proceedings Symposium on Logic in Computer Science"],"abstract":[{"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.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"480","title":"Perfect-information stochastic games with generalized mean-payoff objectives","status":"public","oa_version":"Preprint","scopus_import":1,"day":"05","citation":{"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.","short":"K. Chatterjee, L. Doyen, in:, IEEE, 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.","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","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.","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.","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"},"page":"247 - 256","date_published":"2016-07-05T00:00:00Z"},{"day":"01","has_accepted_license":"1","scopus_import":1,"date_published":"2016-06-01T00:00:00Z","page":"24.1 - 24.15","citation":{"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","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","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.","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.","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.","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.","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."},"abstract":[{"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.","lang":"eng"}],"alternative_title":["LIPIcs"],"type":"conference","oa_version":"Published Version","file":[{"file_id":"4930","relation":"main_file","date_created":"2018-12-12T10:12:12Z","date_updated":"2020-07-14T12:44:47Z","checksum":"f04248a61c24297cfabd30c5f8e0deb9","file_name":"IST-2016-622-v1+1_LIPIcs-SoCG-2016-24.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":574770}],"pubrep_id":"622","status":"public","title":"Finding non-orientable surfaces in 3-manifolds","ddc":["510"],"intvolume":" 51","_id":"1379","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"06","language":[{"iso":"eng"}],"conference":{"name":"SoCG: Symposium on Computational Geometry","location":"Medford, MA, USA","start_date":"2016-06-14","end_date":"2016-06-17"},"doi":"10.4230/LIPIcs.SoCG.2016.24","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2020-07-14T12:44:47Z","publist_id":"5832","date_created":"2018-12-11T11:51:41Z","date_updated":"2023-02-23T12:23:20Z","volume":51,"author":[{"full_name":"Burton, Benjamin","last_name":"Burton","first_name":"Benjamin"},{"id":"3DB2F25C-F248-11E8-B48F-1D18A9856A87","first_name":"Arnaud N","last_name":"De Mesmay","full_name":"De Mesmay, Arnaud N"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","first_name":"Uli","last_name":"Wagner","full_name":"Wagner, Uli"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"534"}]},"publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing","year":"2016"},{"date_published":"2016-08-01T00:00:00Z","page":"878 - 911","citation":{"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","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.","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","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.","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.","short":"K. Chatterjee, M. Chmelik, M. Tracol, Journal of Computer and System Sciences 82 (2016) 878–911.","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."},"publication":"Journal of Computer and System Sciences","day":"01","scopus_import":1,"oa_version":"Preprint","intvolume":" 82","title":"What is decidable about partially observable Markov decision processes with ω-regular objectives","status":"public","_id":"1477","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"5","abstract":[{"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.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1016/j.jcss.2016.02.009","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","external_id":{"arxiv":["1309.2802"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1309.2802"}],"month":"08","volume":82,"date_created":"2018-12-11T11:52:15Z","date_updated":"2023-02-23T12:24:38Z","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"2295"},{"id":"5400","status":"public","relation":"earlier_version"}]},"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Chmelik, Martin","last_name":"Chmelik","first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"id":"3F54FA38-F248-11E8-B48F-1D18A9856A87","last_name":"Tracol","first_name":"Mathieu","full_name":"Tracol, Mathieu"}],"publisher":"Elsevier","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2016","publist_id":"5718","ec_funded":1},{"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.","year":"2016","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Elsevier","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin"},{"full_name":"Gupta, Raghav","last_name":"Gupta","first_name":"Raghav"},{"first_name":"Ayush","last_name":"Kanodia","full_name":"Kanodia, Ayush"}],"related_material":{"record":[{"id":"1820","relation":"earlier_version","status":"public"},{"relation":"earlier_version","status":"public","id":"5425"}]},"date_updated":"2023-02-23T12:25:49Z","date_created":"2018-12-11T11:52:33Z","volume":234,"ec_funded":1,"publist_id":"5642","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1411.3880"}],"external_id":{"arxiv":["1411.3880"]},"quality_controlled":"1","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"doi":"10.1016/j.artint.2016.01.007","language":[{"iso":"eng"}],"month":"05","_id":"1529","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Optimal cost almost-sure reachability in POMDPs","status":"public","intvolume":" 234","oa_version":"Preprint","type":"journal_article","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."}],"publication":"Artificial Intelligence","citation":{"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.","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.","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","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.","ista":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2016. Optimal cost almost-sure reachability in POMDPs. Artificial Intelligence. 234, 26–48.","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"},"page":"26 - 48","date_published":"2016-05-01T00:00:00Z","scopus_import":1,"day":"01","article_processing_charge":"No"},{"file_date_updated":"2020-07-14T12:46:58Z","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. "}],"type":"technical_report","alternative_title":["IST Austria Technical Report"],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yaron","last_name":"Velner","full_name":"Velner, Yaron"}],"related_material":{"record":[{"id":"1604","relation":"later_version","status":"public"}]},"pubrep_id":"523","date_updated":"2023-02-23T10:06:22Z","date_created":"2018-12-12T11:39:22Z","oa_version":"Published Version","file":[{"checksum":"cef516fa091925b5868813e355268fb4","date_updated":"2020-07-14T12:46:58Z","date_created":"2018-12-12T11:53:52Z","relation":"main_file","file_id":"5513","file_size":1012204,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-523-v1+1_main.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5445","year":"2016","publication_status":"published","status":"public","title":"Quantitative interprocedural analysis","ddc":["005"],"publisher":"IST Austria","department":[{"_id":"KrCh"}],"day":"31","month":"03","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","date_published":"2016-03-31T00:00:00Z","doi":"10.15479/AT:IST-2016-523-v1-1","language":[{"iso":"eng"}],"oa":1,"citation":{"mla":"Chatterjee, Krishnendu, et al. Quantitative Interprocedural Analysis. IST Austria, 2016, doi:10.15479/AT:IST-2016-523-v1-1.","short":"K. Chatterjee, A. Pavlogiannis, Y. Velner, Quantitative Interprocedural Analysis, IST Austria, 2016.","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.","ama":"Chatterjee K, Pavlogiannis A, Velner Y. Quantitative Interprocedural Analysis. IST Austria; 2016. doi:10.15479/AT:IST-2016-523-v1-1","ista":"Chatterjee K, Pavlogiannis A, Velner Y. 2016. Quantitative interprocedural analysis, IST Austria, 33p.","apa":"Chatterjee, K., Pavlogiannis, A., & Velner, Y. (2016). Quantitative interprocedural analysis. IST Austria. https://doi.org/10.15479/AT:IST-2016-523-v1-1","ieee":"K. Chatterjee, A. Pavlogiannis, and Y. Velner, Quantitative interprocedural analysis. IST Austria, 2016."},"page":"33"},{"ec_funded":1,"publist_id":"6191","abstract":[{"text":"POMDPs are standard models for probabilistic planning problems, where an agent interacts with an uncertain environment. We study the problem of almost-sure reachability, where given a set of target states, the question is to decide whether there is a policy to ensure that the target set is reached with probability 1 (almost-surely). While in general the problem is EXPTIMEcomplete, in many practical cases policies with a small amount of memory suffice. Moreover, the existing solution to the problem is explicit, which first requires to construct explicitly an exponential reduction to a belief-support MDP. In this work, we first study the existence of observation-stationary strategies, which is NP-complete, and then small-memory strategies. We present a symbolic algorithm by an efficient encoding to SAT and using a SAT solver for the problem. We report experimental results demonstrating the scalability of our symbolic (SAT-based) approach. © 2016, Association for the Advancement of Artificial Intelligence (www.aaai.org). All rights reserved.","lang":"eng"}],"type":"conference","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5443"}],"link":[{"url":"https://dl.acm.org/citation.cfm?id=3016355","relation":"table_of_contents"}]},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin"},{"id":"378E0060-F248-11E8-B48F-1D18A9856A87","first_name":"Jessica","last_name":"Davies","full_name":"Davies, Jessica"}],"volume":2016,"oa_version":"None","date_created":"2018-12-11T11:50:30Z","date_updated":"2023-02-23T12:26:41Z","_id":"1166","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2016","publisher":"AAAI Press","intvolume":" 2016","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"status":"public","title":"A symbolic SAT based algorithm for almost sure reachability with small strategies in pomdps","publication_status":"published","day":"02","month":"12","date_published":"2016-12-02T00:00:00Z","conference":{"name":"AAAI: Conference on Artificial Intelligence","start_date":"2016-02-12","location":"Phoenix, AZ, USA","end_date":"2016-02-17"},"language":[{"iso":"eng"}],"citation":{"ama":"Chatterjee K, Chmelik M, Davies J. A symbolic SAT based algorithm for almost sure reachability with small strategies in pomdps. In: Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence. Vol 2016. AAAI Press; 2016:3225-3232.","ieee":"K. Chatterjee, M. Chmelik, and J. Davies, “A symbolic SAT based algorithm for almost sure reachability with small strategies in pomdps,” in Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence, Phoenix, AZ, USA, 2016, vol. 2016, pp. 3225–3232.","apa":"Chatterjee, K., Chmelik, M., & Davies, J. (2016). A symbolic SAT based algorithm for almost sure reachability with small strategies in pomdps. In Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence (Vol. 2016, pp. 3225–3232). Phoenix, AZ, USA: AAAI Press.","ista":"Chatterjee K, Chmelik M, Davies J. 2016. A symbolic SAT based algorithm for almost sure reachability with small strategies in pomdps. Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 2016, 3225–3232.","short":"K. Chatterjee, M. Chmelik, J. Davies, in:, Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence, AAAI Press, 2016, pp. 3225–3232.","mla":"Chatterjee, Krishnendu, et al. “A Symbolic SAT Based Algorithm for Almost Sure Reachability with Small Strategies in Pomdps.” Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence, vol. 2016, AAAI Press, 2016, pp. 3225–32.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Jessica Davies. “A Symbolic SAT Based Algorithm for Almost Sure Reachability with Small Strategies in Pomdps.” In Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence, 2016:3225–32. AAAI Press, 2016."},"publication":"Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"page":"3225 - 3232","quality_controlled":"1"},{"publisher":"IST Austria","department":[{"_id":"KrCh"}],"status":"public","ddc":["519"],"publication_status":"published","title":"Amplification on undirected population structures: Comets beat stars","_id":"5449","year":"2016","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-07-14T12:46:58Z","date_created":"2018-12-12T11:54:07Z","checksum":"8345a8c1e7d7f0cd92516d182b7fc59e","relation":"main_file","file_id":"5529","file_size":1264221,"content_type":"application/pdf","creator":"system","file_name":"IST-2016-648-v1+1_tr.pdf","access_level":"open_access"}],"oa_version":"Updated Version","date_created":"2018-12-12T11:39:24Z","date_updated":"2023-02-23T12:22:21Z","related_material":{"record":[{"id":"512","status":"public","relation":"later_version"}]},"pubrep_id":"648","author":[{"id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas"},{"id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684","first_name":"Josef","last_name":"Tkadlec","full_name":"Tkadlec, Josef"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"alternative_title":["IST Austria Technical Report"],"type":"technical_report","file_date_updated":"2020-07-14T12:46:58Z","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"}],"page":"22","citation":{"ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, Amplification on undirected population structures: Comets beat stars. IST Austria, 2016.","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","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Amplification on undirected population structures: Comets beat stars, IST Austria, 22p.","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","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.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Amplification on Undirected Population Structures: Comets Beat Stars, IST Austria, 2016.","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."},"oa":1,"language":[{"iso":"eng"}],"date_published":"2016-11-09T00:00:00Z","doi":"10.15479/AT:IST-2016-648-v1-1","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","day":"09","month":"11"},{"publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","month":"07","day":"15","page":"26","citation":{"ista":"Anonymous 1, Anonymous 2, Anonymous 3. 2016. Termination and worst-case analysis of recursive programs, IST Austria, 26p.","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.","chicago":"Anonymous, 1, 2 Anonymous, and 3 Anonymous. Termination and Worst-Case Analysis of Recursive Programs. IST Austria, 2016.","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."},"oa":1,"language":[{"iso":"eng"}],"date_published":"2016-07-15T00:00:00Z","alternative_title":["IST Austria Technical Report"],"type":"technical_report","abstract":[{"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.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:58Z","publisher":"IST Austria","publication_status":"published","ddc":["000"],"status":"public","title":"Termination and worst-case analysis of recursive programs","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5446","year":"2016","file":[{"file_id":"6403","relation":"main_file","checksum":"689069a7abbb34b21516164cbee9e0df","date_updated":"2020-07-14T12:46:58Z","date_created":"2019-05-10T13:27:24Z","access_level":"open_access","file_name":"popl2017a.pdf","creator":"dernst","content_type":"application/pdf","file_size":686241},{"file_name":"author_names.txt","access_level":"closed","file_size":258,"content_type":"text/plain","creator":"dernst","relation":"main_file","file_id":"6404","date_updated":"2020-07-14T12:46:58Z","date_created":"2019-05-10T13:27:31Z","checksum":"fc08022bfbaac07bac047a9407c0bbb3"}],"oa_version":"Published Version","date_updated":"2020-07-14T23:05:05Z","date_created":"2018-12-12T11:39:23Z","pubrep_id":"618","author":[{"first_name":"1","last_name":"Anonymous","full_name":"Anonymous, 1"},{"first_name":"2","last_name":"Anonymous","full_name":"Anonymous, 2"},{"last_name":"Anonymous","first_name":"3","full_name":"Anonymous, 3"}]},{"date_updated":"2020-07-14T23:05:06Z","date_created":"2018-12-12T11:39:23Z","oa_version":"Published Version","file":[{"file_name":"listofauthors.txt","access_level":"closed","creator":"dernst","content_type":"text/plain","file_size":281,"file_id":"6406","relation":"main_file","date_updated":"2020-07-14T12:46:58Z","date_created":"2019-05-10T13:32:16Z","checksum":"cf53cdb6d092e68db0b4a0a1506ef8fb"},{"file_name":"popl2017b.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":563642,"file_id":"6407","relation":"main_file","date_created":"2019-05-10T13:32:16Z","date_updated":"2020-07-14T12:46:58Z","checksum":"7bdd94ba13aa0dec9c46887fcf13870b"}],"author":[{"full_name":"Anonymous, 1","first_name":"1","last_name":"Anonymous"},{"full_name":"Anonymous, 2","first_name":"2","last_name":"Anonymous"},{"full_name":"Anonymous, 3","first_name":"3","last_name":"Anonymous"}],"pubrep_id":"619","ddc":["000"],"title":"Average-case analysis of programs: Automated recurrence analysis for almost-linear bounds","status":"public","publication_status":"published","publisher":"IST Austria","year":"2016","_id":"5447","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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."}],"file_date_updated":"2020-07-14T12:46:58Z","alternative_title":["IST Austria Technical Report"],"type":"technical_report","language":[{"iso":"eng"}],"date_published":"2016-07-15T00:00:00Z","page":"20","oa":1,"citation":{"chicago":"Anonymous, 1, 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.","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.","ieee":"1 Anonymous, 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.","ama":"Anonymous 1, Anonymous 2, Anonymous 3. Average-Case Analysis of Programs: Automated Recurrence Analysis for Almost-Linear Bounds. IST Austria; 2016."},"day":"15","month":"07","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]}},{"file_date_updated":"2020-07-14T12:46:59Z","type":"technical_report","alternative_title":["IST Austria Technical Report"],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5452"}]},"pubrep_id":"755","author":[{"id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas"},{"full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","first_name":"Josef"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"oa_version":"Published Version","file":[{"checksum":"83b0313dab3bff4bdb6ac38695026fda","date_created":"2018-12-12T11:53:13Z","date_updated":"2020-07-14T12:46:59Z","relation":"main_file","file_id":"5474","file_size":1015647,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2017-749-v3+1_main.pdf"}],"date_updated":"2023-02-23T12:27:07Z","date_created":"2018-12-12T11:39:25Z","_id":"5453","year":"2016","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"publisher":"IST Austria","publication_status":"published","title":"Arbitrarily strong amplifiers of natural selection","ddc":["000"],"status":"public","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","day":"30","month":"12","date_published":"2016-12-30T00:00:00Z","doi":"10.15479/AT:IST-2017-749-v3-1","language":[{"iso":"eng"}],"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.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Arbitrarily Strong Amplifiers of Natural Selection, IST Austria, 2016.","mla":"Pavlogiannis, Andreas, et al. 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","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, Arbitrarily strong amplifiers of natural selection. IST Austria, 2016.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Arbitrarily strong amplifiers of natural selection, IST Austria, 34p.","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"},"oa":1,"page":"34"},{"has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"month":"12","day":"30","oa":1,"citation":{"mla":"Pavlogiannis, Andreas, et al. Strong Amplifiers of Natural Selection. IST Austria, 2016, doi: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.","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.","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","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Strong amplifiers of natural selection, IST Austria, 34p.","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","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, Strong amplifiers of natural selection. IST Austria, 2016."},"page":"34","date_published":"2016-12-30T00:00:00Z","doi":"10.15479/AT:IST-2016-728-v1-1","language":[{"iso":"eng"}],"type":"technical_report","alternative_title":["IST Austria Technical Report"],"file_date_updated":"2020-07-14T12:46:59Z","year":"2016","_id":"5451","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"publisher":"IST Austria","status":"public","ddc":["000"],"publication_status":"published","title":"Strong amplifiers of natural selection","pubrep_id":"728","author":[{"last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas"},{"full_name":"Tkadlec, Josef","last_name":"Tkadlec","first_name":"Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"oa_version":"Published Version","file":[{"checksum":"7b8bb17c322c0556acba6ac169fa71c1","date_updated":"2020-07-14T12:46:59Z","date_created":"2018-12-12T11:53:04Z","relation":"main_file","file_id":"5465","content_type":"application/pdf","file_size":1014732,"creator":"system","access_level":"open_access","file_name":"IST-2016-728-v1+1_main.pdf"}],"date_created":"2018-12-12T11:39:24Z","date_updated":"2023-02-23T12:27:05Z"},{"abstract":[{"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.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:58Z","type":"technical_report","alternative_title":["IST Austria Technical Report"],"pubrep_id":"620","related_material":{"record":[{"relation":"later_version","status":"public","id":"10417"},{"status":"public","relation":"later_version","id":"5456"}]},"author":[{"full_name":"Anonymous, 1","last_name":"Anonymous","first_name":"1"},{"full_name":"Anonymous, 2","last_name":"Anonymous","first_name":"2"},{"full_name":"Anonymous, 3","first_name":"3","last_name":"Anonymous"},{"last_name":"Anonymous","first_name":"4","full_name":"Anonymous, 4"}],"file":[{"access_level":"open_access","file_name":"IST-2016-620-v1+1_main.pdf","content_type":"application/pdf","file_size":538881,"creator":"system","relation":"main_file","file_id":"5506","checksum":"1d69252d66bcdf782615ddfb911d2957","date_updated":"2020-07-14T12:46:58Z","date_created":"2018-12-12T11:53:45Z"},{"file_id":"6405","relation":"main_file","date_updated":"2020-07-14T12:46:58Z","date_created":"2019-05-10T13:30:40Z","checksum":"deabb0eb8f237cae4f9542b28b0b6eb2","file_name":"authornames.txt","access_level":"closed","creator":"dernst","content_type":"text/plain","file_size":121}],"oa_version":"Published Version","date_updated":"2023-02-23T12:27:16Z","date_created":"2018-12-12T11:39:23Z","year":"2016","_id":"5448","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"IST Austria","publication_status":"published","ddc":["000"],"status":"public","title":"Data-centric dynamic partial order reduction","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","day":"15","month":"07","date_published":"2016-07-15T00:00:00Z","language":[{"iso":"eng"}],"citation":{"chicago":"Anonymous, 1, 2 Anonymous, 3 Anonymous, and 4 Anonymous. Data-Centric Dynamic Partial Order Reduction. IST Austria, 2016.","mla":"Anonymous, 1, et al. Data-Centric Dynamic Partial Order Reduction. IST Austria, 2016.","short":"1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, 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.","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."},"oa":1,"external_id":{"arxiv":["1610.01188"]},"page":"20"},{"page":"142-143","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","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.","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","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.","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.","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."},"publication":"Proceedings of the Artificial Life Conference 2016","date_published":"2016-09-01T00:00:00Z","scopus_import":1,"article_processing_charge":"No","has_accepted_license":"1","day":"01","intvolume":" 28","ddc":["610"],"status":"public","title":"Self-organized control of an tendon driven arm by differential extrinsic plasticity","_id":"8094","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","oa_version":"Published Version","file":[{"checksum":"cff63e7a4b8ac466ba51a9c84153a940","date_created":"2020-07-06T12:59:09Z","date_updated":"2020-07-14T12:48:09Z","file_id":"8096","relation":"main_file","creator":"cziletti","content_type":"application/pdf","file_size":678670,"access_level":"open_access","file_name":"2016_ProcALIFE_Martius.pdf"}],"type":"conference","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"}],"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.7551/978-0-262-33936-0-ch029","conference":{"end_date":"2016-07-08","location":"Cancun, Mexico","start_date":"2016-07-04","name":"ALIFE 2016: 15th International Conference on the Synthesis and Simulation of Living Systems"},"publication_identifier":{"isbn":["9780262339360"]},"month":"09","publisher":"MIT Press","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"publication_status":"published","year":"2016","volume":28,"date_created":"2020-07-05T22:00:47Z","date_updated":"2021-01-12T08:16:53Z","author":[{"full_name":"Martius, Georg S","first_name":"Georg S","last_name":"Martius","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","first_name":"Ralf","last_name":"Der"}],"ec_funded":1,"file_date_updated":"2020-07-14T12:48:09Z"},{"publication":"PLoS Computational Biology","citation":{"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.","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","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.","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","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.","short":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, PLoS Computational Biology 12 (2016).","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."},"date_published":"2016-11-17T00:00:00Z","scopus_import":1,"day":"17","has_accepted_license":"1","status":"public","title":"Error-robust modes of the retinal population code","ddc":["570"],"intvolume":" 12","_id":"1197","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"date_created":"2019-01-25T10:35:00Z","date_updated":"2020-07-14T12:44:38Z","checksum":"47b08cbd4dbf32b25ba161f5f4b262cc","relation":"main_file","file_id":"5884","content_type":"application/pdf","file_size":4492021,"creator":"kschuh","file_name":"2016_PLOS_Prentice.pdf","access_level":"open_access"}],"type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"11","quality_controlled":"1","project":[{"grant_number":"P 25651-N26","_id":"254D1A94-B435-11E9-9278-68D0E5697425","name":"Sensitivity to higher-order statistics in natural scenes","call_identifier":"FWF"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pcbi.1005148","month":"11","publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","year":"2016","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.","date_created":"2018-12-11T11:50:40Z","date_updated":"2023-02-23T14:05:40Z","volume":12,"author":[{"full_name":"Prentice, Jason","last_name":"Prentice","first_name":"Jason"},{"first_name":"Olivier","last_name":"Marre","full_name":"Marre, Olivier"},{"full_name":"Ioffe, Mark","last_name":"Ioffe","first_name":"Mark"},{"full_name":"Loback, Adrianna","first_name":"Adrianna","last_name":"Loback"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper"},{"full_name":"Berry, Michael","last_name":"Berry","first_name":"Michael"}],"related_material":{"record":[{"id":"9709","status":"public","relation":"research_data"}]},"article_number":"e1005855","file_date_updated":"2020-07-14T12:44:38Z","publist_id":"6153"},{"citation":{"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","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.","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.","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","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.","short":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, (2016).","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."},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.4b565","open_access":"1"}],"oa":1,"doi":"10.5061/dryad.4b565","date_published":"2016-01-22T00:00:00Z","day":"22","month":"01","article_processing_charge":"No","_id":"9720","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2016","status":"public","title":"Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees","department":[{"_id":"SyCr"}],"publisher":"Dryad","author":[{"full_name":"Mcmahon, Dino","first_name":"Dino","last_name":"Mcmahon"},{"full_name":"Fürst, Matthias","first_name":"Matthias","last_name":"Fürst","id":"393B1196-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3712-925X"},{"full_name":"Caspar, Jesicca","last_name":"Caspar","first_name":"Jesicca"},{"full_name":"Theodorou, Panagiotis","first_name":"Panagiotis","last_name":"Theodorou"},{"full_name":"Brown, Mark","last_name":"Brown","first_name":"Mark"},{"last_name":"Paxton","first_name":"Robert","full_name":"Paxton, Robert"}],"related_material":{"record":[{"id":"1855","relation":"used_in_publication","status":"public"}]},"date_created":"2021-07-26T09:14:19Z","date_updated":"2023-02-23T10:17:25Z","oa_version":"Published Version","type":"research_data_reference","abstract":[{"lang":"eng","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."}]},{"citation":{"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.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS Biology 14 (2016).","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.","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","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.","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","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."},"publication":"PLoS Biology","date_published":"2016-12-27T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"27","intvolume":" 14","ddc":["576"],"title":"Shedding light on the grey zone of speciation along a continuum of genomic divergence","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1158","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2017-742-v1+1_journal.pbio.2000234.pdf","content_type":"application/pdf","file_size":2494348,"creator":"system","relation":"main_file","file_id":"5164","checksum":"2bab63b068a9840efd532b9ae583f9bb","date_updated":"2020-07-14T12:44:36Z","date_created":"2018-12-12T10:15:42Z"}],"pubrep_id":"742","type":"journal_article","issue":"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"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1371/journal.pbio.2000234","month":"12","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"Public Library of Science","publication_status":"published","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.","year":"2016","volume":14,"date_created":"2018-12-11T11:50:28Z","date_updated":"2023-02-23T14:11:16Z","related_material":{"record":[{"id":"9862","status":"public","relation":"research_data"},{"relation":"research_data","status":"public","id":"9863"}]},"author":[{"first_name":"Camille","last_name":"Roux","full_name":"Roux, Camille"},{"full_name":"Fraisse, Christelle","first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075"},{"first_name":"Jonathan","last_name":"Romiguier","full_name":"Romiguier, Jonathan"},{"full_name":"Anciaux, Youann","first_name":"Youann","last_name":"Anciaux"},{"last_name":"Galtier","first_name":"Nicolas","full_name":"Galtier, Nicolas"},{"full_name":"Bierne, Nicolas","last_name":"Bierne","first_name":"Nicolas"}],"article_number":"e2000234","publist_id":"6200","file_date_updated":"2020-07-14T12:44:36Z"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"1167","title":"Beyond the hypercube evolutionary accessibility of fitness landscapes with realistic mutational networks","status":"public","ddc":["570"],"intvolume":" 12","pubrep_id":"740","file":[{"date_created":"2018-12-12T10:12:08Z","date_updated":"2020-07-14T12:44:37Z","checksum":"84f44ae92866c52ff1ca8a574558dca7","relation":"main_file","file_id":"4926","content_type":"application/pdf","file_size":3822299,"creator":"system","file_name":"IST-2017-740-v1+1_journal.pcbi.1005218.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"12","publication":"PLoS Computational Biology","citation":{"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.","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","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.","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","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.","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.","short":"M.P. Zagórski, Z. Burda, B. Wacław, PLoS Computational Biology 12 (2016)."},"date_published":"2016-12-09T00:00:00Z","scopus_import":"1","day":"09","article_processing_charge":"No","has_accepted_license":"1","year":"2016","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.","publication_status":"published","department":[{"_id":"AnKi"}],"publisher":"Public Library of Science","author":[{"last_name":"Zagórski","first_name":"Marcin P","orcid":"0000-0001-7896-7762","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","full_name":"Zagórski, Marcin P"},{"last_name":"Burda","first_name":"Zdzisław","full_name":"Burda, Zdzisław"},{"full_name":"Wacław, Bartłomiej","last_name":"Wacław","first_name":"Bartłomiej"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9866"}]},"date_updated":"2023-02-23T14:11:22Z","date_created":"2018-12-11T11:50:30Z","volume":12,"article_number":"e1005218","file_date_updated":"2020-07-14T12:44:37Z","publist_id":"6190","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1371/journal.pcbi.1005218","language":[{"iso":"eng"}],"month":"12"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9867","year":"2016","department":[{"_id":"KrCh"}],"publisher":"Public Library of Science","title":"Experimental game instructions","status":"public","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1322"}]},"author":[{"full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","first_name":"Christian","last_name":"Hilbe"},{"full_name":"Hagel, Kristin","last_name":"Hagel","first_name":"Kristin"},{"full_name":"Milinski, Manfred","last_name":"Milinski","first_name":"Manfred"}],"oa_version":"Published Version","date_updated":"2023-02-21T16:59:01Z","date_created":"2021-08-10T08:42:00Z","type":"research_data_reference","abstract":[{"text":"In the beginning of our experiment, subjects were asked to read a few pages on their computer screens that would explain the rules of the subsequent game. Here, we provide these instructions, translated from German.","lang":"eng"}],"citation":{"ista":"Hilbe C, Hagel K, Milinski M. 2016. Experimental game instructions, Public Library of Science, 10.1371/journal.pone.0163867.s008.","apa":"Hilbe, C., Hagel, K., & Milinski, M. (2016). Experimental game instructions. Public Library of Science. https://doi.org/10.1371/journal.pone.0163867.s008","ieee":"C. Hilbe, K. Hagel, and M. Milinski, “Experimental game instructions.” Public Library of Science, 2016.","ama":"Hilbe C, Hagel K, Milinski M. Experimental game instructions. 2016. doi:10.1371/journal.pone.0163867.s008","chicago":"Hilbe, Christian, Kristin Hagel, and Manfred Milinski. “Experimental Game Instructions.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163867.s008.","mla":"Hilbe, Christian, et al. Experimental Game Instructions. Public Library of Science, 2016, doi:10.1371/journal.pone.0163867.s008.","short":"C. Hilbe, K. Hagel, M. Milinski, (2016)."},"doi":"10.1371/journal.pone.0163867.s008","article_processing_charge":"No","day":"04","month":"10"},{"month":"12","day":"27","article_processing_charge":"No","doi":"10.1371/journal.pbio.2000234.s016","citation":{"chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.s016.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).","mla":"Roux, Camille, et al. Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence. Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.s016.","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne, N. (2016). Simulation study to test the robustness of ABC in face of recent times of divergence. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234.s016","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Simulation study to test the robustness of ABC in face of recent times of divergence.” Public Library of Science, 2016.","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Simulation study to test the robustness of ABC in face of recent times of divergence, Public Library of Science, 10.1371/journal.pbio.2000234.s016.","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Simulation study to test the robustness of ABC in face of recent times of divergence. 2016. doi:10.1371/journal.pbio.2000234.s016"},"type":"research_data_reference","author":[{"last_name":"Roux","first_name":"Camille","full_name":"Roux, Camille"},{"full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse"},{"full_name":"Romiguier, Jonathan","first_name":"Jonathan","last_name":"Romiguier"},{"full_name":"Anciaux, Youann","last_name":"Anciaux","first_name":"Youann"},{"full_name":"Galtier, Nicolas","last_name":"Galtier","first_name":"Nicolas"},{"first_name":"Nicolas","last_name":"Bierne","full_name":"Bierne, Nicolas"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1158"}]},"date_updated":"2023-02-21T16:21:20Z","date_created":"2021-08-10T08:20:17Z","oa_version":"Published Version","_id":"9862","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2016","title":"Simulation study to test the robustness of ABC in face of recent times of divergence","status":"public","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"Public Library of Science"},{"doi":"10.1371/journal.pbio.2000234.s017","citation":{"ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Accessions of surveyed individuals, geographic locations and summary statistics. 2016. doi:10.1371/journal.pbio.2000234.s017","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Accessions of surveyed individuals, geographic locations and summary statistics.” Public Library of Science, 2016.","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne, N. (2016). Accessions of surveyed individuals, geographic locations and summary statistics. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234.s017","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Accessions of surveyed individuals, geographic locations and summary statistics, Public Library of Science, 10.1371/journal.pbio.2000234.s017.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).","mla":"Roux, Camille, et al. Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics. Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.s017.","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.s017."},"article_processing_charge":"No","day":"27","month":"12","oa_version":"Published Version","date_created":"2021-08-10T08:22:52Z","date_updated":"2023-02-21T16:21:20Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1158"}]},"author":[{"full_name":"Roux, Camille","last_name":"Roux","first_name":"Camille"},{"full_name":"Fraisse, Christelle","last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Romiguier, Jonathan","first_name":"Jonathan","last_name":"Romiguier"},{"last_name":"Anciaux","first_name":"Youann","full_name":"Anciaux, Youann"},{"full_name":"Galtier, Nicolas","last_name":"Galtier","first_name":"Nicolas"},{"full_name":"Bierne, Nicolas","first_name":"Nicolas","last_name":"Bierne"}],"publisher":"Public Library of Science","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"title":"Accessions of surveyed individuals, geographic locations and summary statistics","status":"public","_id":"9863","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2016","type":"research_data_reference"},{"title":"ZIP-archived directory containing all data and computer programs","status":"public","publisher":"Public Library of Science","department":[{"_id":"AnKi"}],"_id":"9866","year":"2016","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_created":"2021-08-10T08:37:20Z","date_updated":"2023-02-21T16:24:29Z","oa_version":"Published Version","author":[{"full_name":"Zagórski, Marcin P","last_name":"Zagórski","first_name":"Marcin P","orcid":"0000-0001-7896-7762","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Burda, Zdzisław","first_name":"Zdzisław","last_name":"Burda"},{"last_name":"Wacław","first_name":"Bartłomiej","full_name":"Wacław, Bartłomiej"}],"related_material":{"record":[{"id":"1167","status":"public","relation":"used_in_publication"}]},"type":"research_data_reference","citation":{"apa":"Zagórski, M. P., Burda, Z., & Wacław, B. (2016). ZIP-archived directory containing all data and computer programs. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005218.s009","ieee":"M. P. Zagórski, Z. Burda, and B. Wacław, “ZIP-archived directory containing all data and computer programs.” Public Library of Science, 2016.","ista":"Zagórski MP, Burda Z, Wacław B. 2016. ZIP-archived directory containing all data and computer programs, Public Library of Science, 10.1371/journal.pcbi.1005218.s009.","ama":"Zagórski MP, Burda Z, Wacław B. ZIP-archived directory containing all data and computer programs. 2016. doi:10.1371/journal.pcbi.1005218.s009","chicago":"Zagórski, Marcin P, Zdzisław Burda, and Bartłomiej Wacław. “ZIP-Archived Directory Containing All Data and Computer Programs.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pcbi.1005218.s009.","short":"M.P. Zagórski, Z. Burda, B. Wacław, (2016).","mla":"Zagórski, Marcin P., et al. ZIP-Archived Directory Containing All Data and Computer Programs. Public Library of Science, 2016, doi:10.1371/journal.pcbi.1005218.s009."},"doi":"10.1371/journal.pcbi.1005218.s009","date_published":"2016-12-09T00:00:00Z","month":"12","day":"09","article_processing_charge":"No"},{"date_published":"2016-01-01T00:00:00Z","citation":{"ama":"Monk T, Savin C, Lücke J. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. In: Vol 29. Neural Information Processing Systems; 2016:4285-4293.","ieee":"T. Monk, C. Savin, and J. Lücke, “Neurons equipped with intrinsic plasticity learn stimulus intensity statistics,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spaine, 2016, vol. 29, pp. 4285–4293.","apa":"Monk, T., Savin, C., & Lücke, J. (2016). Neurons equipped with intrinsic plasticity learn stimulus intensity statistics (Vol. 29, pp. 4285–4293). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spaine: Neural Information Processing Systems.","ista":"Monk T, Savin C, Lücke J. 2016. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 4285–4293.","short":"T. Monk, C. Savin, J. Lücke, in:, Neural Information Processing Systems, 2016, pp. 4285–4293.","mla":"Monk, Travis, et al. Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics. Vol. 29, Neural Information Processing Systems, 2016, pp. 4285–93.","chicago":"Monk, Travis, Cristina Savin, and Jörg Lücke. “Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics,” 29:4285–93. Neural Information Processing Systems, 2016."},"page":"4285 - 4293","day":"01","scopus_import":1,"oa_version":"None","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"948","intvolume":" 29","title":"Neurons equipped with intrinsic plasticity learn stimulus intensity statistics","status":"public","abstract":[{"text":"Experience constantly shapes neural circuits through a variety of plasticity mechanisms. While the functional roles of some plasticity mechanisms are well-understood, it remains unclear how changes in neural excitability contribute to learning. Here, we develop a normative interpretation of intrinsic plasticity (IP) as a key component of unsupervised learning. We introduce a novel generative mixture model that accounts for the class-specific statistics of stimulus intensities, and we derive a neural circuit that learns the input classes and their intensities. We will analytically show that inference and learning for our generative model can be achieved by a neural circuit with intensity-sensitive neurons equipped with a specific form of IP. Numerical experiments verify our analytical derivations and show robust behavior for artificial and natural stimuli. Our results link IP to non-trivial input statistics, in particular the statistics of stimulus intensities for classes to which a neuron is sensitive. More generally, our work paves the way toward new classification algorithms that are robust to intensity variations.","lang":"eng"}],"type":"conference","alternative_title":["Advances in Neural Information Processing Systems"],"conference":{"name":"NIPS: Neural Information Processing Systems","end_date":"2016-12-10","start_date":"2016-12-05","location":"Barcelona, Spaine"},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://papers.nips.cc/paper/6582-neurons-equipped-with-intrinsic-plasticity-learn-stimulus-intensity-statistics"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","month":"01","author":[{"full_name":"Monk, Travis","first_name":"Travis","last_name":"Monk"},{"id":"3933349E-F248-11E8-B48F-1D18A9856A87","last_name":"Savin","first_name":"Cristina","full_name":"Savin, Cristina"},{"first_name":"Jörg","last_name":"Lücke","full_name":"Lücke, Jörg"}],"volume":29,"date_updated":"2021-01-12T08:22:08Z","date_created":"2018-12-11T11:49:21Z","year":"2016","acknowledgement":"DFG Cluster of Excellence EXC 1077/1 (Hearing4all) and LU 1196/5-1 (JL and TM), People Programme (Marie Curie Actions) FP7/2007-2013 grant agreement no. 291734 (CS)","publisher":"Neural Information Processing Systems","department":[{"_id":"GaTk"}],"publication_status":"published","ec_funded":1,"publist_id":"6469"},{"intvolume":" 283","ddc":["576","592"],"title":"Elevated virulence of an emerging viral genotype as a driver of honeybee loss","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1262","file":[{"access_level":"open_access","file_name":"IST-2016-701-v1+1_20160811.full.pdf","creator":"system","file_size":796872,"content_type":"application/pdf","file_id":"4708","relation":"main_file","checksum":"0b0d1be38b497d004064650acb3baced","date_updated":"2020-07-14T12:44:42Z","date_created":"2018-12-12T10:08:46Z"}],"oa_version":"Published Version","pubrep_id":"701","type":"journal_article","issue":"1833","abstract":[{"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.","lang":"eng"}],"citation":{"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","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.","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.","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","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.","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).","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."},"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","date_published":"2016-06-29T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"29","publisher":"Royal Society, The","department":[{"_id":"SyCr"}],"publication_status":"published","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.","year":"2016","volume":283,"date_updated":"2023-02-23T14:05:30Z","date_created":"2018-12-11T11:51:00Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"9704"}]},"author":[{"first_name":"Dino","last_name":"Mcmahon","full_name":"Mcmahon, Dino"},{"first_name":"Myrsini","last_name":"Natsopoulou","full_name":"Natsopoulou, Myrsini"},{"full_name":"Doublet, Vincent","last_name":"Doublet","first_name":"Vincent"},{"orcid":"0000-0002-3712-925X","id":"393B1196-F248-11E8-B48F-1D18A9856A87","last_name":"Fürst","first_name":"Matthias","full_name":"Fürst, Matthias"},{"first_name":"Silvio","last_name":"Weging","full_name":"Weging, Silvio"},{"full_name":"Brown, Mark","last_name":"Brown","first_name":"Mark"},{"last_name":"Gogol Döring","first_name":"Andreas","full_name":"Gogol Döring, Andreas"},{"full_name":"Paxton, Robert","first_name":"Robert","last_name":"Paxton"}],"article_number":"20160811","publist_id":"6060","file_date_updated":"2020-07-14T12:44:42Z","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1098/rspb.2016.0811","month":"06"},{"type":"research_data_reference","abstract":[{"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.","lang":"eng"}],"publisher":"Dryad","department":[{"_id":"SyCr"}],"status":"public","title":"Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss","year":"2016","_id":"9704","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","date_updated":"2023-02-21T16:54:31Z","date_created":"2021-07-23T08:30:38Z","related_material":{"record":[{"id":"1262","status":"public","relation":"used_in_publication"}]},"author":[{"last_name":"Mcmahon","first_name":"Dino","full_name":"Mcmahon, Dino"},{"full_name":"Natsopoulou, Myrsini","last_name":"Natsopoulou","first_name":"Myrsini"},{"first_name":"Vincent","last_name":"Doublet","full_name":"Doublet, Vincent"},{"full_name":"Fürst, Matthias","first_name":"Matthias","last_name":"Fürst","id":"393B1196-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3712-925X"},{"last_name":"Weging","first_name":"Silvio","full_name":"Weging, Silvio"},{"full_name":"Brown, Mark","first_name":"Mark","last_name":"Brown"},{"last_name":"Gogol Döring","first_name":"Andreas","full_name":"Gogol Döring, Andreas"},{"last_name":"Paxton","first_name":"Robert","full_name":"Paxton, Robert"}],"article_processing_charge":"No","day":"06","month":"05","citation":{"chicago":"Mcmahon, Dino, Myrsini Natsopoulou, Vincent Doublet, Matthias Fürst, Silvio Weging, Mark Brown, Andreas Gogol Döring, and Robert Paxton. “Data from: Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” Dryad, 2016. https://doi.org/10.5061/dryad.cq7t1.","short":"D. Mcmahon, M. Natsopoulou, V. Doublet, M. Fürst, S. Weging, M. Brown, A. Gogol Döring, R. Paxton, (2016).","mla":"Mcmahon, Dino, et al. Data from: Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss. Dryad, 2016, doi:10.5061/dryad.cq7t1.","ieee":"D. Mcmahon et al., “Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss.” Dryad, 2016.","apa":"Mcmahon, D., Natsopoulou, M., Doublet, V., Fürst, M., Weging, S., Brown, M., … Paxton, R. (2016). Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss. Dryad. https://doi.org/10.5061/dryad.cq7t1","ista":"Mcmahon D, Natsopoulou M, Doublet V, Fürst M, Weging S, Brown M, Gogol Döring A, Paxton R. 2016. Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss, Dryad, 10.5061/dryad.cq7t1.","ama":"Mcmahon D, Natsopoulou M, Doublet V, et al. Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss. 2016. doi:10.5061/dryad.cq7t1"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.cq7t1"}],"doi":"10.5061/dryad.cq7t1","date_published":"2016-05-06T00:00:00Z"},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1371/journal.pone.0163867","language":[{"iso":"eng"}],"month":"10","year":"2016","acknowledgement":"CH was funded by the Schrödinger program of the Austrian Science Fund (FWF) J3475. ","department":[{"_id":"KrCh"}],"publisher":"Public Library of Science","publication_status":"published","related_material":{"record":[{"status":"public","relation":"research_data","id":"9867"},{"relation":"research_data","status":"public","id":"9868"}]},"author":[{"first_name":"Christian","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian"},{"full_name":"Hagel, Kristin","first_name":"Kristin","last_name":"Hagel"},{"full_name":"Milinski, Manfred","first_name":"Manfred","last_name":"Milinski"}],"volume":11,"date_updated":"2023-02-23T14:11:27Z","date_created":"2018-12-11T11:51:22Z","article_number":"e0163867","publist_id":"5948","file_date_updated":"2020-07-14T12:44:44Z","citation":{"ista":"Hilbe C, Hagel K, Milinski M. 2016. Asymmetric power boosts extortion in an economic experiment. PLoS One. 11(10), e0163867.","ieee":"C. Hilbe, K. Hagel, and M. Milinski, “Asymmetric power boosts extortion in an economic experiment,” PLoS One, vol. 11, no. 10. Public Library of Science, 2016.","apa":"Hilbe, C., Hagel, K., & Milinski, M. (2016). Asymmetric power boosts extortion in an economic experiment. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0163867","ama":"Hilbe C, Hagel K, Milinski M. Asymmetric power boosts extortion in an economic experiment. PLoS One. 2016;11(10). doi:10.1371/journal.pone.0163867","chicago":"Hilbe, Christian, Kristin Hagel, and Manfred Milinski. “Asymmetric Power Boosts Extortion in an Economic Experiment.” PLoS One. Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163867.","mla":"Hilbe, Christian, et al. “Asymmetric Power Boosts Extortion in an Economic Experiment.” PLoS One, vol. 11, no. 10, e0163867, Public Library of Science, 2016, doi:10.1371/journal.pone.0163867.","short":"C. Hilbe, K. Hagel, M. Milinski, PLoS One 11 (2016)."},"publication":"PLoS One","date_published":"2016-10-04T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"04","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1322","intvolume":" 11","status":"public","ddc":["004","006"],"title":"Asymmetric power boosts extortion in an economic experiment","pubrep_id":"716","file":[{"checksum":"6b33e394003dfe8b4ca6be1858aaa8e3","date_created":"2018-12-12T10:08:08Z","date_updated":"2020-07-14T12:44:44Z","relation":"main_file","file_id":"4668","file_size":2077905,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-716-v1+1_journal.pone.0163867.PDF"}],"oa_version":"Published Version","type":"journal_article","issue":"10","abstract":[{"text":"Direct reciprocity is a major mechanism for the evolution of cooperation. Several classical studies have suggested that humans should quickly learn to adopt reciprocal strategies to establish mutual cooperation in repeated interactions. On the other hand, the recently discovered theory of ZD strategies has found that subjects who use extortionate strategies are able to exploit and subdue cooperators. Although such extortioners have been predicted to succeed in any population of adaptive opponents, theoretical follow-up studies questioned whether extortion can evolve in reality. However, most of these studies presumed that individuals have similar strategic possibilities and comparable outside options, whereas asymmetries are ubiquitous in real world applications. Here we show with a model and an economic experiment that extortionate strategies readily emerge once subjects differ in their strategic power. Our experiment combines a repeated social dilemma with asymmetric partner choice. In our main treatment there is one randomly chosen group member who is unilaterally allowed to exchange one of the other group members after every ten rounds of the social dilemma. We find that this asymmetric replacement opportunity generally promotes cooperation, but often the resulting payoff distribution reflects the underlying power structure. Almost half of the subjects in a better strategic position turn into extortioners, who quickly proceed to exploit their peers. By adapting their cooperation probabilities consistent with ZD theory, extortioners force their co-players to cooperate without being similarly cooperative themselves. Comparison to non-extortionate players under the same conditions indicates a substantial net gain to extortion. Our results thus highlight how power asymmetries can endanger mutually beneficial interactions, and transform them into exploitative relationships. In particular, our results indicate that the extortionate strategies predicted from ZD theory could play a more prominent role in our daily interactions than previously thought.","lang":"eng"}]},{"month":"09","language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0163628","quality_controlled":"1","project":[{"_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2020-07-14T12:44:42Z","publist_id":"6050","article_number":"e0163628","date_updated":"2023-02-23T14:11:37Z","date_created":"2018-12-11T11:51:03Z","volume":11,"author":[{"full_name":"Hillenbrand, Patrick","first_name":"Patrick","last_name":"Hillenbrand"},{"last_name":"Gerland","first_name":"Ulrich","full_name":"Gerland, Ulrich"},{"last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9869"},{"relation":"research_data","status":"public","id":"9870"},{"relation":"research_data","status":"public","id":"9871"}]},"publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","acknowledgement":"The authors would like to thank Thomas Sokolowski and Filipe Tostevin for helpful discussions. PH and UG were funded by the German Excellence Initiative via the program \"Nanosystems Initiative Munich\" (https://www.nano-initiative-munich.de) and the German Research Foundation via the SFB 1032 \"Nanoagents for Spatiotemporal Control of Molecular and Cellular Reactions\" (http://www.sfb1032.physik.uni-muenchen.de). GT was funded by the Austrian Science Fund (FWF P 28844) (http://www.fwf.ac.at).","year":"2016","day":"27","has_accepted_license":"1","scopus_import":1,"date_published":"2016-09-27T00:00:00Z","publication":"PLoS One","citation":{"apa":"Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information,” PLoS One, vol. 11, no. 9. Public Library of Science, 2016.","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. PLoS One. 11(9), e0163628.","ama":"Hillenbrand P, Gerland U, Tkačik G. Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. PLoS One. 2016;11(9). doi:10.1371/journal.pone.0163628","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information.” PLoS One. Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, PLoS One 11 (2016).","mla":"Hillenbrand, Patrick, et al. “Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information.” PLoS One, vol. 11, no. 9, e0163628, Public Library of Science, 2016, doi:10.1371/journal.pone.0163628."},"abstract":[{"text":"A crucial step in the early development of multicellular organisms involves the establishment of spatial patterns of gene expression which later direct proliferating cells to take on different cell fates. These patterns enable the cells to infer their global position within a tissue or an organism by reading out local gene expression levels. The patterning system is thus said to encode positional information, a concept that was formalized recently in the framework of information theory. Here we introduce a toy model of patterning in one spatial dimension, which can be seen as an extension of Wolpert's paradigmatic "French Flag" model, to patterning by several interacting, spatially coupled genes subject to intrinsic and extrinsic noise. Our model, a variant of an Ising spin system, allows us to systematically explore expression patterns that optimally encode positional information. We find that optimal patterning systems use positional cues, as in the French Flag model, together with gene-gene interactions to generate combinatorial codes for position which we call "Counter" patterns. Counter patterns can also be stabilized against noise and variations in system size or morphogen dosage by longer-range spatial interactions of the type invoked in the Turing model. The simple setup proposed here qualitatively captures many of the experimentally observed properties of biological patterning systems and allows them to be studied in a single, theoretically consistent framework.","lang":"eng"}],"issue":"9","type":"journal_article","oa_version":"Published Version","file":[{"file_size":4950415,"content_type":"application/pdf","creator":"system","file_name":"IST-2016-696-v1+1_journal.pone.0163628.PDF","access_level":"open_access","date_created":"2018-12-12T10:10:47Z","date_updated":"2020-07-14T12:44:42Z","checksum":"3d0d55d373096a033bd9cf79288c8586","relation":"main_file","file_id":"4837"}],"pubrep_id":"696","title":"Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information","status":"public","ddc":["571"],"intvolume":" 11","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1270"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1371/journal.pgen.1005974","language":[{"iso":"eng"}],"month":"04","acknowledgement":"This manuscript is dedicated to the memory of Alex Böhm, who was a great friend and a passionate biologist. Alex passed away after the initial submission of this manuscript. We thank Vesna Olivera and Ursula Sauder from the Zentrum für Mikroskopie Uni Basel for excellent service, and Olin Silander, Nikki Freed, and Nela Nikolic for helpful discussions. This work was supported by the Swiss National Science Foundation grants to M. Ackermann and Urs Jenal (supporting AB).","year":"2016","publisher":"Public Library of Science","department":[{"_id":"CaGu"}],"publication_status":"published","related_material":{"record":[{"relation":"research_data","status":"public","id":"9873"}]},"author":[{"last_name":"Boehm","first_name":"Alex","full_name":"Boehm, Alex"},{"full_name":"Arnoldini, Markus","first_name":"Markus","last_name":"Arnoldini"},{"last_name":"Bergmiller","first_name":"Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias"},{"last_name":"Röösli","first_name":"Thomas","full_name":"Röösli, Thomas"},{"last_name":"Bigosch","first_name":"Colette","full_name":"Bigosch, Colette"},{"last_name":"Ackermann","first_name":"Martin","full_name":"Ackermann, Martin"}],"volume":12,"date_updated":"2023-02-23T14:11:39Z","date_created":"2018-12-11T11:50:56Z","article_number":"e1005974","publist_id":"6077","file_date_updated":"2020-07-14T12:44:41Z","citation":{"ama":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. Genetic manipulation of glycogen allocation affects replicative lifespan in E coli. PLoS Genetics. 2016;12(4). doi:10.1371/journal.pgen.1005974","ista":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. 2016. Genetic manipulation of glycogen allocation affects replicative lifespan in E coli. PLoS Genetics. 12(4), e1005974.","apa":"Boehm, A., Arnoldini, M., Bergmiller, T., Röösli, T., Bigosch, C., & Ackermann, M. (2016). Genetic manipulation of glycogen allocation affects replicative lifespan in E coli. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005974","ieee":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, and M. Ackermann, “Genetic manipulation of glycogen allocation affects replicative lifespan in E coli,” PLoS Genetics, vol. 12, no. 4. Public Library of Science, 2016.","mla":"Boehm, Alex, et al. “Genetic Manipulation of Glycogen Allocation Affects Replicative Lifespan in E Coli.” PLoS Genetics, vol. 12, no. 4, e1005974, Public Library of Science, 2016, doi:10.1371/journal.pgen.1005974.","short":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, M. Ackermann, PLoS Genetics 12 (2016).","chicago":"Boehm, Alex, Markus Arnoldini, Tobias Bergmiller, Thomas Röösli, Colette Bigosch, and Martin Ackermann. “Genetic Manipulation of Glycogen Allocation Affects Replicative Lifespan in E Coli.” PLoS Genetics. Public Library of Science, 2016. https://doi.org/10.1371/journal.pgen.1005974."},"publication":"PLoS Genetics","date_published":"2016-04-19T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"19","_id":"1250","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 12","ddc":["576","579"],"title":"Genetic manipulation of glycogen allocation affects replicative lifespan in E coli","status":"public","pubrep_id":"705","file":[{"date_created":"2018-12-12T10:14:17Z","date_updated":"2020-07-14T12:44:41Z","checksum":"53d22b2b39e5adc243d34f18b2615a85","relation":"main_file","file_id":"5067","content_type":"application/pdf","file_size":6273249,"creator":"system","file_name":"IST-2016-705-v1+1_journal.pgen.1005974.PDF","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","issue":"4","abstract":[{"text":"In bacteria, replicative aging manifests as a difference in growth or survival between the two cells emerging from division. One cell can be regarded as an aging mother with a decreased potential for future survival and division, the other as a rejuvenated daughter. Here, we aimed at investigating some of the processes involved in aging in the bacterium Escherichia coli, where the two types of cells can be distinguished by the age of their cell poles. We found that certain changes in the regulation of the carbohydrate metabolism can affect aging. A mutation in the carbon storage regulator gene, csrA, leads to a dramatically shorter replicative lifespan; csrA mutants stop dividing once their pole exceeds an age of about five divisions. These old-pole cells accumulate glycogen at their old cell poles; after their last division, they do not contain a chromosome, presumably because of spatial exclusion by the glycogen aggregates. The new-pole daughters produced by these aging mothers are born young; they only express the deleterious phenotype once their pole is old. These results demonstrate how manipulations of nutrient allocation can lead to the exclusion of the chromosome and limit replicative lifespan in E. coli, and illustrate how mutations can have phenotypic effects that are specific for cells with old poles. This raises the question how bacteria can avoid the accumulation of such mutations in their genomes over evolutionary times, and how they can achieve the long replicative lifespans that have recently been reported.","lang":"eng"}]},{"month":"09","day":"27","article_processing_charge":"No","citation":{"mla":"Hillenbrand, Patrick, et al. Computation of Positional Information in an Ising Model. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s002.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of Positional Information in an Ising Model.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.s002.","ama":"Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in an Ising model. 2016. doi:10.1371/journal.pone.0163628.s002","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information in an Ising model, Public Library of Science, 10.1371/journal.pone.0163628.s002.","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in an Ising model.” Public Library of Science, 2016.","apa":"Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Computation of positional information in an Ising model. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628.s002"},"doi":"10.1371/journal.pone.0163628.s002","date_published":"2016-09-27T00:00:00Z","type":"research_data_reference","abstract":[{"lang":"eng","text":"The effect of noise in the input field on an Ising model is approximated. Furthermore, methods to compute positional information in an Ising model by transfer matrices and Monte Carlo sampling are outlined."}],"_id":"9870","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2016","status":"public","title":"Computation of positional information in an Ising model","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","author":[{"full_name":"Hillenbrand, Patrick","first_name":"Patrick","last_name":"Hillenbrand"},{"last_name":"Gerland","first_name":"Ulrich","full_name":"Gerland, Ulrich"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1270"}]},"date_updated":"2023-02-21T16:56:40Z","date_created":"2021-08-10T09:23:45Z","oa_version":"Published Version"},{"doi":"10.1371/journal.pgen.1005974.s015","citation":{"short":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, M. Ackermann, (2016).","mla":"Boehm, Alex, et al. Quantification of the Growth Rate Reduction as a Consequence of Age-Specific Mortality. Public Library of Science, 2016, doi:10.1371/journal.pgen.1005974.s015.","chicago":"Boehm, Alex, Markus Arnoldini, Tobias Bergmiller, Thomas Röösli, Colette Bigosch, and Martin Ackermann. “Quantification of the Growth Rate Reduction as a Consequence of Age-Specific Mortality.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pgen.1005974.s015.","ama":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. Quantification of the growth rate reduction as a consequence of age-specific mortality. 2016. doi:10.1371/journal.pgen.1005974.s015","ieee":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, and M. Ackermann, “Quantification of the growth rate reduction as a consequence of age-specific mortality.” Public Library of Science, 2016.","apa":"Boehm, A., Arnoldini, M., Bergmiller, T., Röösli, T., Bigosch, C., & Ackermann, M. (2016). Quantification of the growth rate reduction as a consequence of age-specific mortality. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005974.s015","ista":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. 2016. Quantification of the growth rate reduction as a consequence of age-specific mortality, Public Library of Science, 10.1371/journal.pgen.1005974.s015."},"month":"04","day":"19","article_processing_charge":"No","author":[{"full_name":"Boehm, Alex","first_name":"Alex","last_name":"Boehm"},{"full_name":"Arnoldini, Markus","last_name":"Arnoldini","first_name":"Markus"},{"orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","first_name":"Tobias","full_name":"Bergmiller, Tobias"},{"full_name":"Röösli, Thomas","last_name":"Röösli","first_name":"Thomas"},{"first_name":"Colette","last_name":"Bigosch","full_name":"Bigosch, Colette"},{"last_name":"Ackermann","first_name":"Martin","full_name":"Ackermann, Martin"}],"related_material":{"record":[{"id":"1250","status":"public","relation":"used_in_publication"}]},"date_created":"2021-08-10T09:42:34Z","date_updated":"2023-02-21T16:50:13Z","oa_version":"Published Version","year":"2016","_id":"9873","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Quantification of the growth rate reduction as a consequence of age-specific mortality","status":"public","department":[{"_id":"CaGu"}],"publisher":"Public Library of Science","type":"research_data_reference"},{"abstract":[{"text":"A lower bound on the error of a positional estimator with limited positional information is derived.","lang":"eng"}],"type":"research_data_reference","oa_version":"Published Version","date_updated":"2023-02-21T16:56:40Z","date_created":"2021-08-10T08:53:48Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1270"}]},"author":[{"full_name":"Hillenbrand, Patrick","last_name":"Hillenbrand","first_name":"Patrick"},{"full_name":"Gerland, Ulrich","last_name":"Gerland","first_name":"Ulrich"},{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik"}],"department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","status":"public","title":"Error bound on an estimator of position","year":"2016","_id":"9869","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","day":"27","month":"09","date_published":"2016-09-27T00:00:00Z","doi":"10.1371/journal.pone.0163628.s001","citation":{"ama":"Hillenbrand P, Gerland U, Tkačik G. Error bound on an estimator of position. 2016. doi:10.1371/journal.pone.0163628.s001","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Error bound on an estimator of position.” Public Library of Science, 2016.","apa":"Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Error bound on an estimator of position. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628.s001","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Error bound on an estimator of position, Public Library of Science, 10.1371/journal.pone.0163628.s001.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","mla":"Hillenbrand, Patrick, et al. Error Bound on an Estimator of Position. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s001.","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Error Bound on an Estimator of Position.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.s001."}},{"type":"research_data_reference","abstract":[{"text":"The positional information in a discrete morphogen field with Gaussian noise is computed.","lang":"eng"}],"department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","title":"Computation of positional information in a discrete morphogen field","status":"public","_id":"9871","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2016","oa_version":"Published Version","date_updated":"2023-02-21T16:56:40Z","date_created":"2021-08-10T09:27:35Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1270"}]},"author":[{"first_name":"Patrick","last_name":"Hillenbrand","full_name":"Hillenbrand, Patrick"},{"full_name":"Gerland, Ulrich","last_name":"Gerland","first_name":"Ulrich"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper"}],"article_processing_charge":"No","day":"27","month":"09","citation":{"ama":"Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in a discrete morphogen field. 2016. doi:10.1371/journal.pone.0163628.s003","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in a discrete morphogen field.” Public Library of Science, 2016.","apa":"Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Computation of positional information in a discrete morphogen field. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628.s003","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information in a discrete morphogen field, Public Library of Science, 10.1371/journal.pone.0163628.s003.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","mla":"Hillenbrand, Patrick, et al. Computation of Positional Information in a Discrete Morphogen Field. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s003.","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of Positional Information in a Discrete Morphogen Field.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.s003."},"doi":"10.1371/journal.pone.0163628.s003"},{"status":"public","title":"Experimental data","publisher":"Public Library of Science","department":[{"_id":"KrCh"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9868","year":"2016","date_created":"2021-08-10T08:45:00Z","date_updated":"2023-02-21T16:59:01Z","oa_version":"Published Version","author":[{"last_name":"Hilbe","first_name":"Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian"},{"first_name":"Kristin","last_name":"Hagel","full_name":"Hagel, Kristin"},{"first_name":"Manfred","last_name":"Milinski","full_name":"Milinski, Manfred"}],"related_material":{"record":[{"id":"1322","status":"public","relation":"used_in_publication"}]},"type":"research_data_reference","abstract":[{"lang":"eng","text":"The raw data file containing the experimental decisions of all our study subjects."}],"citation":{"ista":"Hilbe C, Hagel K, Milinski M. 2016. Experimental data, Public Library of Science, 10.1371/journal.pone.0163867.s009.","ieee":"C. Hilbe, K. Hagel, and M. Milinski, “Experimental data.” Public Library of Science, 2016.","apa":"Hilbe, C., Hagel, K., & Milinski, M. (2016). Experimental data. Public Library of Science. https://doi.org/10.1371/journal.pone.0163867.s009","ama":"Hilbe C, Hagel K, Milinski M. Experimental data. 2016. doi:10.1371/journal.pone.0163867.s009","chicago":"Hilbe, Christian, Kristin Hagel, and Manfred Milinski. “Experimental Data.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163867.s009.","mla":"Hilbe, Christian, et al. Experimental Data. Public Library of Science, 2016, doi:10.1371/journal.pone.0163867.s009.","short":"C. Hilbe, K. Hagel, M. Milinski, (2016)."},"doi":"10.1371/journal.pone.0163867.s009","date_published":"2016-10-04T00:00:00Z","day":"04","month":"10","article_processing_charge":"No"},{"department":[{"_id":"HaJa"}],"publisher":"American Chemical Society","intvolume":" 1","publication_status":"published","title":"Rangefinder: A semisynthetic FRET sensor design algorithm","status":"public","_id":"1101","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2016","acknowledgement":"J.A.M., J.H.W., and W.H.Z. were supported by Australian\r\nPostgraduate Awards (APA), AS Sargeson Supplementary\r\nscholarships, and RSC supplementary scholarships. C.J.J.\r\nacknowledges support from a Human Frontiers in Science\r\nYoung Investigator Award and a Discovery Project and Future\r\nFellowship from the Australian Research Council. M.L.O. is\r\nsupported by an Australian Research Council Discovery Project\r\n(DP130102153) and the Merit Allocation Scheme of the\r\nNational Computational Infrastructure.","volume":1,"oa_version":"None","date_created":"2018-12-11T11:50:09Z","date_updated":"2023-03-30T11:32:33Z","author":[{"full_name":"Mitchell, Joshua","last_name":"Mitchell","first_name":"Joshua"},{"first_name":"Jason","last_name":"Whitfield","full_name":"Whitfield, Jason"},{"full_name":"Zhang, William","last_name":"Zhang","first_name":"William"},{"full_name":"Henneberger, Christian","last_name":"Henneberger","first_name":"Christian"},{"full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","first_name":"Harald L","last_name":"Janovjak"},{"full_name":"O'Mara, Megan","first_name":"Megan","last_name":"O'Mara"},{"full_name":"Jackson, Colin","first_name":"Colin","last_name":"Jackson"}],"type":"journal_article","publist_id":"6274","issue":"11","abstract":[{"text":"Optical sensors based on the phenomenon of Förster resonance energy transfer (FRET) are powerful tools that have advanced the study of small molecules in biological systems. However, sensor construction is not trivial and often requires multiple rounds of engineering or an ability to screen large numbers of variants. A method that would allow the accurate rational design of FRET sensors would expedite the production of biologically useful sensors. Here, we present Rangefinder, a computational algorithm that allows rapid in silico screening of dye attachment sites in a ligand-binding protein for the conjugation of a dye molecule to act as a Förster acceptor for a fused fluorescent protein. We present three ratiometric fluorescent sensors designed with Rangefinder, including a maltose sensor with a dynamic range of >300% and the first sensors for the most abundant sialic acid in human cells, N-acetylneuraminic acid. Provided a ligand-binding protein exists, it is our expectation that this model will facilitate the design of an optical sensor for any small molecule of interest.","lang":"eng"}],"page":"1286 - 1290","quality_controlled":"1","citation":{"chicago":"Mitchell, Joshua, Jason Whitfield, William Zhang, Christian Henneberger, Harald L Janovjak, Megan O’Mara, and Colin Jackson. “Rangefinder: A Semisynthetic FRET Sensor Design Algorithm.” ACS SENSORS. American Chemical Society, 2016. https://doi.org/10.1021/acssensors.6b00576.","short":"J. Mitchell, J. Whitfield, W. Zhang, C. Henneberger, H.L. Janovjak, M. O’Mara, C. Jackson, ACS SENSORS 1 (2016) 1286–1290.","mla":"Mitchell, Joshua, et al. “Rangefinder: A Semisynthetic FRET Sensor Design Algorithm.” ACS SENSORS, vol. 1, no. 11, American Chemical Society, 2016, pp. 1286–90, doi:10.1021/acssensors.6b00576.","apa":"Mitchell, J., Whitfield, J., Zhang, W., Henneberger, C., Janovjak, H. L., O’Mara, M., & Jackson, C. (2016). Rangefinder: A semisynthetic FRET sensor design algorithm. ACS SENSORS. American Chemical Society. https://doi.org/10.1021/acssensors.6b00576","ieee":"J. Mitchell et al., “Rangefinder: A semisynthetic FRET sensor design algorithm,” ACS SENSORS, vol. 1, no. 11. American Chemical Society, pp. 1286–1290, 2016.","ista":"Mitchell J, Whitfield J, Zhang W, Henneberger C, Janovjak HL, O’Mara M, Jackson C. 2016. Rangefinder: A semisynthetic FRET sensor design algorithm. ACS SENSORS. 1(11), 1286–1290.","ama":"Mitchell J, Whitfield J, Zhang W, et al. Rangefinder: A semisynthetic FRET sensor design algorithm. ACS SENSORS. 2016;1(11):1286-1290. doi:10.1021/acssensors.6b00576"},"publication":"ACS SENSORS","language":[{"iso":"eng"}],"doi":"10.1021/acssensors.6b00576","date_published":"2016-11-10T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"10","month":"11"},{"author":[{"full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","first_name":"Alois"},{"full_name":"Stadlbauer, Stephan","last_name":"Stadlbauer","first_name":"Stephan","id":"4D0BC184-F248-11E8-B48F-1D18A9856A87"}],"file":[{"file_id":"12968","relation":"main_file","success":1,"checksum":"4a7b00362e81358d568f5e216fa03c3e","date_created":"2023-05-16T07:03:56Z","date_updated":"2023-05-16T07:03:56Z","access_level":"open_access","file_name":"2016_AHPC_Schloegl.pdf","creator":"dernst","content_type":"application/pdf","file_size":1073523}],"oa_version":"Published Version","date_updated":"2023-05-16T07:15:14Z","date_created":"2023-05-05T12:54:47Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12903","year":"2016","publisher":"VSC - Vienna Scientific Cluster","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"ddc":["000"],"status":"public","publication_status":"published","title":"High performance computing at IST Austria: Modelling the human hippocampus","file_date_updated":"2023-05-16T07:03:56Z","type":"conference_abstract","date_published":"2016-02-24T00:00:00Z","conference":{"end_date":"2016-02-24","start_date":"2016-02-22","location":"Grundlsee, Austria","name":"AHPC: Austrian HPC Meeting"},"language":[{"iso":"eng"}],"citation":{"short":"A. Schlögl, S. Stadlbauer, in:, AHPC16 - Austrian HPC Meeting 2016, VSC - Vienna Scientific Cluster, 2016, p. 37.","mla":"Schlögl, Alois, and Stephan Stadlbauer. “High Performance Computing at IST Austria: Modelling the Human Hippocampus.” AHPC16 - Austrian HPC Meeting 2016, VSC - Vienna Scientific Cluster, 2016, p. 37.","chicago":"Schlögl, Alois, and Stephan Stadlbauer. “High Performance Computing at IST Austria: Modelling the Human Hippocampus.” In AHPC16 - Austrian HPC Meeting 2016, 37. VSC - Vienna Scientific Cluster, 2016.","ama":"Schlögl A, Stadlbauer S. High performance computing at IST Austria: Modelling the human hippocampus. In: AHPC16 - Austrian HPC Meeting 2016. VSC - Vienna Scientific Cluster; 2016:37.","apa":"Schlögl, A., & Stadlbauer, S. (2016). High performance computing at IST Austria: Modelling the human hippocampus. In AHPC16 - Austrian HPC Meeting 2016 (p. 37). Grundlsee, Austria: VSC - Vienna Scientific Cluster.","ieee":"A. Schlögl and S. Stadlbauer, “High performance computing at IST Austria: Modelling the human hippocampus,” in AHPC16 - Austrian HPC Meeting 2016, Grundlsee, Austria, 2016, p. 37.","ista":"Schlögl A, Stadlbauer S. 2016. High performance computing at IST Austria: Modelling the human hippocampus. AHPC16 - Austrian HPC Meeting 2016. AHPC: Austrian HPC Meeting, 37."},"oa":1,"main_file_link":[{"url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc16/BOOKLET_AHPC16.pdf","open_access":"1"}],"publication":"AHPC16 - Austrian HPC Meeting 2016","page":"37","quality_controlled":"1","article_processing_charge":"No","has_accepted_license":"1","day":"24","month":"02"},{"publist_id":"5926","ec_funded":1,"file_date_updated":"2020-07-14T12:44:45Z","acknowledgement":"This research was supported in part by the European Research Council (ERC) under grants 267989 (QUAREM) and 278410 (QUALITY), and by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award).","year":"2016","publisher":"Springer","department":[{"_id":"ToHe"}],"publication_status":"published","related_material":{"record":[{"relation":"later_version","status":"public","id":"6761"}]},"author":[{"full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","first_name":"Guy"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"full_name":"Kupferman, Orna","first_name":"Orna","last_name":"Kupferman"}],"volume":9928,"date_updated":"2023-08-17T13:52:49Z","date_created":"2018-12-11T11:51:28Z","month":"09","oa":1,"project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1007/978-3-662-53354-3_13","conference":{"name":"SAGT: Symposium on Algorithmic Game Theory","start_date":"2016-09-19","location":"Liverpool, United Kingdom","end_date":"2016-09-21"},"language":[{"iso":"eng"}],"type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"In resource allocation games, selfish players share resources that are needed in order to fulfill their objectives. The cost of using a resource depends on the load on it. In the traditional setting, the players make their choices concurrently and in one-shot. That is, a strategy for a player is a subset of the resources. We introduce and study dynamic resource allocation games. In this setting, the game proceeds in phases. In each phase each player chooses one resource. A scheduler dictates the order in which the players proceed in a phase, possibly scheduling several players to proceed concurrently. The game ends when each player has collected a set of resources that fulfills his objective. The cost for each player then depends on this set as well as on the load on the resources in it – we consider both congestion and cost-sharing games. We argue that the dynamic setting is the suitable setting for many applications in practice. We study the stability of dynamic resource allocation games, where the appropriate notion of stability is that of subgame perfect equilibrium, study the inefficiency incurred due to selfish behavior, and also study problems that are particular to the dynamic setting, like constraints on the order in which resources can be chosen or the problem of finding a scheduler that achieves stability.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1341","intvolume":" 9928","title":"Dynamic resource allocation games","ddc":["000"],"status":"public","pubrep_id":"645","file":[{"relation":"main_file","file_id":"5073","date_updated":"2020-07-14T12:44:45Z","date_created":"2018-12-12T10:14:22Z","checksum":"0825eefd4e22774f6f62cb7d7389b05a","file_name":"IST-2016-645-v1+1_sagt-cr.pdf","access_level":"open_access","content_type":"application/pdf","file_size":243458,"creator":"system"}],"oa_version":"Preprint","scopus_import":1,"has_accepted_license":"1","day":"01","citation":{"apa":"Avni, G., Henzinger, T. A., & Kupferman, O. (2016). Dynamic resource allocation games (Vol. 9928, pp. 153–166). Presented at the SAGT: Symposium on Algorithmic Game Theory, Liverpool, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-53354-3_13","ieee":"G. Avni, T. A. Henzinger, and O. Kupferman, “Dynamic resource allocation games,” presented at the SAGT: Symposium on Algorithmic Game Theory, Liverpool, United Kingdom, 2016, vol. 9928, pp. 153–166.","ista":"Avni G, Henzinger TA, Kupferman O. 2016. Dynamic resource allocation games. SAGT: Symposium on Algorithmic Game Theory, LNCS, vol. 9928, 153–166.","ama":"Avni G, Henzinger TA, Kupferman O. Dynamic resource allocation games. In: Vol 9928. Springer; 2016:153-166. doi:10.1007/978-3-662-53354-3_13","chicago":"Avni, Guy, Thomas A Henzinger, and Orna Kupferman. “Dynamic Resource Allocation Games,” 9928:153–66. Springer, 2016. https://doi.org/10.1007/978-3-662-53354-3_13.","short":"G. Avni, T.A. Henzinger, O. Kupferman, in:, Springer, 2016, pp. 153–166.","mla":"Avni, Guy, et al. Dynamic Resource Allocation Games. Vol. 9928, Springer, 2016, pp. 153–66, doi:10.1007/978-3-662-53354-3_13."},"page":"153 - 166","date_published":"2016-09-01T00:00:00Z"},{"page":"770-782","citation":{"short":"S. Wielgoss, T. Bergmiller, A.M. Bischofberger, A.R. Hall, Molecular Biology and Evolution 33 (2016) 770–782.","mla":"Wielgoss, Sébastien, et al. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria.” Molecular Biology and Evolution, vol. 33, no. 3, Oxford University Press, 2016, pp. 770–82, doi:10.1093/molbev/msv270.","chicago":"Wielgoss, Sébastien, Tobias Bergmiller, Anna M. Bischofberger, and Alex R. Hall. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria.” Molecular Biology and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/molbev/msv270.","ama":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. Molecular Biology and Evolution. 2016;33(3):770-782. doi:10.1093/molbev/msv270","ieee":"S. Wielgoss, T. Bergmiller, A. M. Bischofberger, and A. R. Hall, “Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria,” Molecular Biology and Evolution, vol. 33, no. 3. Oxford University Press, pp. 770–782, 2016.","apa":"Wielgoss, S., Bergmiller, T., Bischofberger, A. M., & Hall, A. R. (2016). Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msv270","ista":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. 2016. Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. Molecular Biology and Evolution. 33(3), 770–782."},"publication":"Molecular Biology and Evolution","date_published":"2016-03-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","intvolume":" 33","ddc":["576"],"title":"Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5749","file":[{"content_type":"application/pdf","file_size":634037,"creator":"dernst","access_level":"open_access","file_name":"2016_MolBiolEvol_Wielgoss.pdf","checksum":"47d9010690b6c5c17f2ac830cc63ac5c","date_created":"2018-12-18T13:21:45Z","date_updated":"2020-07-14T12:47:10Z","relation":"main_file","file_id":"5750"}],"oa_version":"Published Version","pubrep_id":"587","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"Parasitism creates selection for resistance mechanisms in host populations and is hypothesized to promote increased host evolvability. However, the influence of these traits on host evolution when parasites are no longer present is unclear. We used experimental evolution and whole-genome sequencing of Escherichia coli to determine the effects of past and present exposure to parasitic viruses (phages) on the spread of mutator alleles, resistance, and bacterial competitive fitness. We found that mutator alleles spread rapidly during adaptation to any of four different phage species, and this pattern was even more pronounced with multiple phages present simultaneously. However, hypermutability did not detectably accelerate adaptation in the absence of phages and recovery of fitness costs associated with resistance. Several lineages evolved phage resistance through elevated mucoidy, and during subsequent evolution in phage-free conditions they rapidly reverted to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this phenotypic reversion was achieved by additional genetic changes rather than by genotypic reversion of the initial resistance mutations. Insertion sequence (IS) elements played a key role in both the acquisition of resistance and adaptation in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions were not more frequent in mutator lineages. Our results provide a genetic explanation for rapid reversion of mucoidy, a phenotype observed in other bacterial species including human pathogens. Moreover, this demonstrates that the types of genetic change underlying adaptation to fitness costs, and consequently the impact of evolvability mechanisms such as increased point-mutation rates, depend critically on the mechanism of resistance."}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"pmid":["26609077"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1093/molbev/msv270","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"month":"03","department":[{"_id":"CaGu"}],"publisher":"Oxford University Press","publication_status":"published","pmid":1,"year":"2016","acknowledgement":"The authors thank three anonymous reviewers and the editor for helpful comments on the manuscript, as well as Dominique Schneider for feedback on an earlier draft, Jenna Gallie for lytic λ and Julien Capelle for T5 and T6. This work was supported by the Swiss National Science Foundation (PZ00P3_148255 to A.H.) and an EU Marie Curie PEOPLE Postdoctoral Fellowship for Career Development (FP7-PEOPLE-2012-IEF-331824 to S.W.).","volume":33,"date_created":"2018-12-18T13:18:10Z","date_updated":"2023-09-05T13:46:05Z","related_material":{"record":[{"id":"9719","status":"public","relation":"research_data"}]},"author":[{"full_name":"Wielgoss, Sébastien","last_name":"Wielgoss","first_name":"Sébastien"},{"full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","first_name":"Tobias"},{"first_name":"Anna M.","last_name":"Bischofberger","full_name":"Bischofberger, Anna M."},{"full_name":"Hall, Alex R.","first_name":"Alex R.","last_name":"Hall"}],"file_date_updated":"2020-07-14T12:47:10Z"},{"page":"203 - 216","citation":{"apa":"Harada, H., & Shigemoto, R. (2016). Immunogold protein localization on grid-glued freeze-fracture replicas. In High-Resolution Imaging of Cellular Proteins (Vol. 1474, pp. 203–216). Springer. https://doi.org/10.1007/978-1-4939-6352-2_12","ieee":"H. Harada and R. Shigemoto, “Immunogold protein localization on grid-glued freeze-fracture replicas,” in High-Resolution Imaging of Cellular Proteins, vol. 1474, Springer, 2016, pp. 203–216.","ista":"Harada H, Shigemoto R. 2016.Immunogold protein localization on grid-glued freeze-fracture replicas. In: High-Resolution Imaging of Cellular Proteins. Methods in Molecular Biology, vol. 1474, 203–216.","ama":"Harada H, Shigemoto R. Immunogold protein localization on grid-glued freeze-fracture replicas. In: High-Resolution Imaging of Cellular Proteins. Vol 1474. Springer; 2016:203-216. doi:10.1007/978-1-4939-6352-2_12","chicago":"Harada, Harumi, and Ryuichi Shigemoto. “Immunogold Protein Localization on Grid-Glued Freeze-Fracture Replicas.” In High-Resolution Imaging of Cellular Proteins, 1474:203–16. Springer, 2016. https://doi.org/10.1007/978-1-4939-6352-2_12.","short":"H. Harada, R. Shigemoto, in:, High-Resolution Imaging of Cellular Proteins, Springer, 2016, pp. 203–216.","mla":"Harada, Harumi, and Ryuichi Shigemoto. “Immunogold Protein Localization on Grid-Glued Freeze-Fracture Replicas.” High-Resolution Imaging of Cellular Proteins, vol. 1474, Springer, 2016, pp. 203–16, doi:10.1007/978-1-4939-6352-2_12."},"publication":"High-Resolution Imaging of Cellular Proteins","date_published":"2016-08-12T00:00:00Z","article_processing_charge":"No","day":"12","intvolume":" 1474","status":"public","title":"Immunogold protein localization on grid-glued freeze-fracture replicas","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1094","oa_version":"None","alternative_title":["Methods in Molecular Biology"],"type":"book_chapter","abstract":[{"lang":"eng","text":"Immunogold labeling of freeze-fracture replicas has recently been used for high-resolution visualization of protein localization in electron microscopy. This method has higher labeling efficiency than conventional immunogold methods for membrane molecules allowing precise quantitative measurements. However, one of the limitations of freeze-fracture replica immunolabeling is difficulty in keeping structural orientation and identifying labeled profiles in complex tissues like brain. The difficulty is partly due to fragmentation of freeze-fracture replica preparations during labeling procedures and limited morphological clues on the replica surface. To overcome these issues, we introduce here a grid-glued replica method combined with SEM observation. This method allows histological staining before dissolving the tissue and easy handling of replicas during immunogold labeling, and keeps the whole replica surface intact without fragmentation. The procedure described here is also useful for matched double-replica analysis allowing further identification of labeled profiles in corresponding P-face and E-face."}],"project":[{"call_identifier":"FP7","name":"Localization of ion channels and receptors by two and three-dimensional immunoelectron microscopic approaches","grant_number":"604102","_id":"25CD3DD2-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"doi":"10.1007/978-1-4939-6352-2_12","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"]},"month":"08","department":[{"_id":"RySh"}],"publisher":"Springer","publication_status":"published","acknowledgement":"We thank Prof. Elek Molnár for providing us a pan-AMPAR anti-body used in Fig.2 and Dr. Ludek Lovicar for technical assistance in scanning electron microscope imaging. This work was supported by the European Union (HBP—Project Ref. 604102). ","year":"2016","volume":1474,"date_created":"2018-12-11T11:50:06Z","date_updated":"2023-09-05T14:09:01Z","author":[{"orcid":"0000-0001-7429-7896","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Harada","first_name":"Harumi","full_name":"Harada, Harumi"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi"}],"publist_id":"6281","ec_funded":1},{"has_accepted_license":"1","article_processing_charge":"No","day":"01","date_published":"2016-12-01T00:00:00Z","citation":{"ama":"Acar H. Selective barriers to horizontal gene transfer. 2016.","ieee":"H. Acar, “Selective barriers to horizontal gene transfer,” Institute of Science and Technology Austria, 2016.","apa":"Acar, H. (2016). Selective barriers to horizontal gene transfer. Institute of Science and Technology Austria.","ista":"Acar H. 2016. Selective barriers to horizontal gene transfer. Institute of Science and Technology Austria.","short":"H. Acar, Selective Barriers to Horizontal Gene Transfer, Institute of Science and Technology Austria, 2016.","mla":"Acar, Hande. Selective Barriers to Horizontal Gene Transfer. Institute of Science and Technology Austria, 2016.","chicago":"Acar, Hande. “Selective Barriers to Horizontal Gene Transfer.” Institute of Science and Technology Austria, 2016."},"page":"75","abstract":[{"text":"Horizontal gene transfer (HGT), the lateral acquisition of genes across existing species\r\nboundaries, is a major evolutionary force shaping microbial genomes that facilitates\r\nadaptation to new environments as well as resistance to antimicrobial drugs. As such,\r\nunderstanding the mechanisms and constraints that determine the outcomes of HGT\r\nevents is crucial to understand the dynamics of HGT and to design better strategies to\r\novercome the challenges that originate from it.\r\nFollowing the insertion and expression of a newly transferred gene, the success of an\r\nHGT event will depend on the fitness effect it has on the recipient (host) cell. Therefore,\r\npredicting the impact of HGT on the genetic composition of a population critically\r\ndepends on the distribution of fitness effects (DFE) of horizontally transferred genes.\r\nHowever, to date, we have little knowledge of the DFE of newly transferred genes, and\r\nhence little is known about the shape and scale of this distribution.\r\nIt is particularly important to better understand the selective barriers that determine\r\nthe fitness effects of newly transferred genes. In spite of substantial bioinformatics\r\nefforts to identify horizontally transferred genes and selective barriers, a systematic\r\nexperimental approach to elucidate the roles of different selective barriers in defining\r\nthe fate of a transfer event has largely been absent. Similarly, although the fact that\r\nenvironment might alter the fitness effect of a horizontally transferred gene may seem\r\nobvious, little attention has been given to it in a systematic experimental manner.\r\nIn this study, we developed a systematic experimental approach that consists of\r\ntransferring 44 arbitrarily selected Salmonella typhimurium orthologous genes into an\r\nEscherichia coli host, and estimating the fitness effects of these transferred genes at a\r\nconstant expression level by performing competition assays against the wild type.\r\nIn chapter 2, we performed one-to-one competition assays between a mutant strain\r\ncarrying a transferred gene and the wild type strain. By using flow cytometry we\r\nestimated selection coefficients for the transferred genes with a precision level of 10-3,and obtained the DFE of horizontally transferred genes. We then investigated if these\r\nfitness effects could be predicted by any of the intrinsic properties of the genes, namely,\r\nfunctional category, degree of complexity (protein-protein interactions), GC content,\r\ncodon usage and length. Our analyses revealed that the functional category and length\r\nof the genes act as potential selective barriers. Finally, using the same procedure with\r\nthe endogenous E. coli orthologs of these 44 genes, we demonstrated that gene dosage is\r\nthe most prominent selective barrier to HGT.\r\nIn chapter 3, using the same set of genes we investigated the role of environment on the\r\nsuccess of HGT events. Under six different environments with different levels of stress\r\nwe performed more complex competition assays, where we mixed all 44 mutant strains\r\ncarrying transferred genes with the wild type strain. To estimate the fitness effects of\r\ngenes relative to wild type we used next generation sequencing. We found that the DFEs\r\nof horizontally transferred genes are highly dependent on the environment, with\r\nabundant gene–by-environment interactions. Furthermore, we demonstrated a\r\nrelationship between average fitness effect of a gene across all environments and its\r\nenvironmental variance, and thus its predictability. Finally, in spite of the fitness effects\r\nof genes being highly environment-dependent, we still observed a common shape of\r\nDFEs across all tested environments.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"checksum":"94bbbc754c36115bf37f8fc11fad43c4","date_updated":"2019-08-13T11:17:50Z","date_created":"2019-08-13T11:17:50Z","file_id":"6814","relation":"main_file","creator":"dernst","file_size":3682711,"content_type":"application/pdf","access_level":"closed","file_name":"PhDThesis_HandeAcar_1230.pdf"},{"relation":"main_file","file_id":"9184","date_updated":"2021-02-22T11:51:13Z","date_created":"2021-02-22T11:51:13Z","checksum":"94bbbc754c36115bf37f8fc11fad43c4","success":1,"file_name":"2016_Thesis_HandeAcar.pdf","access_level":"open_access","file_size":3682711,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","_id":"1121","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Selective barriers to horizontal gene transfer","ddc":["570"],"status":"public","publication_identifier":{"issn":["2663-337X"]},"month":"12","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P"}],"degree_awarded":"PhD","oa":1,"project":[{"grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer"}],"publist_id":"6239","ec_funded":1,"file_date_updated":"2021-02-22T11:51:13Z","author":[{"orcid":"0000-0003-1986-9753","id":"2DDF136A-F248-11E8-B48F-1D18A9856A87","last_name":"Acar","first_name":"Hande","full_name":"Acar, Hande"}],"date_created":"2018-12-11T11:50:16Z","date_updated":"2023-09-07T11:42:26Z","acknowledgement":"This study was supported by European Research Council ERC CoG 2014 – EVOLHGT,\r\nunder the grant number 648440.\r\n\r\nIt is a pleasure to thank the many people who made this thesis possible.\r\nI would like to first thank my advisor, Jonathan Paul Bollback for providing guidance in\r\nall aspects of my life, encouragement, sound advice, and good teaching over the last six\r\nyears.\r\nI would also like to thank the members of my dissertation committee – Călin C. Guet\r\nand John F. Baines – not only for their time and guidance, but for their intellectual\r\ncontributions to my development as a scientist.\r\nI would like to thank Flavia Gama and Rodrigo Redondo who have taught me all the\r\nskills in the laboratory with their graciousness and friendship. Also special thanks to\r\nBollback group for their support and for providing a stimulating and fun environment:\r\nIsabella Tomanek, Fabienne Jesse, Claudia Igler, and Pavel Payne.\r\nJerneja Beslagic is not only an amazing assistant, she also has a smile brighter and\r\nwarmer than the sunshine, bringing happiness to every moment. Always keep your light\r\nNeja, I will miss our invaluable chatters a lot.","year":"2016","publisher":"Institute of Science and Technology Austria","department":[{"_id":"JoBo"}],"publication_status":"published"},{"publist_id":"5488","ec_funded":1,"file_date_updated":"2020-07-14T12:45:10Z","volume":287,"date_updated":"2023-09-07T11:41:25Z","date_created":"2018-12-11T11:53:20Z","related_material":{"record":[{"id":"1399","status":"public","relation":"dissertation_contains"}]},"author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"},{"full_name":"Pausinger, Florian","last_name":"Pausinger","first_name":"Florian","orcid":"0000-0002-8379-3768","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Academic Press","department":[{"_id":"HeEd"}],"publication_status":"published","acknowledgement":"This research is partially supported by the Toposys project FP7-ICT-318493-STREP, and by ESF under the ACAT Research Network Programme.\r\nBoth authors thank Anne Marie Svane for her comments on an early version of this paper. The second author wishes to thank Eva B. Vedel Jensen and Markus Kiderlen from Aarhus University for enlightening discussions and their kind hospitality during a visit of their department in 2014.","year":"2016","month":"01","language":[{"iso":"eng"}],"doi":"10.1016/j.aim.2015.10.004","project":[{"call_identifier":"FP7","name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493"}],"quality_controlled":"1","oa":1,"tmp":{"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"abstract":[{"lang":"eng","text":"We introduce a modification of the classic notion of intrinsic volume using persistence moments of height functions. Evaluating the modified first intrinsic volume on digital approximations of a compact body with smoothly embedded boundary in Rn, we prove convergence to the first intrinsic volume of the body as the resolution of the approximation improves. We have weaker results for the other modified intrinsic volumes, proving they converge to the corresponding intrinsic volumes of the n-dimensional unit ball."}],"type":"journal_article","file":[{"relation":"main_file","file_id":"4928","checksum":"f8869ec110c35c852ef6a37425374af7","date_created":"2018-12-12T10:12:10Z","date_updated":"2020-07-14T12:45:10Z","access_level":"open_access","file_name":"IST-2017-774-v1+1_2016-J-03-FirstIntVolume.pdf","file_size":248985,"content_type":"application/pdf","creator":"system"}],"oa_version":"Published Version","pubrep_id":"774","intvolume":" 287","status":"public","title":"Approximation and convergence of the intrinsic volume","ddc":["004"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1662","has_accepted_license":"1","day":"10","scopus_import":1,"date_published":"2016-01-10T00:00:00Z","page":"674 - 703","citation":{"mla":"Edelsbrunner, Herbert, and Florian Pausinger. “Approximation and Convergence of the Intrinsic Volume.” Advances in Mathematics, vol. 287, Academic Press, 2016, pp. 674–703, doi:10.1016/j.aim.2015.10.004.","short":"H. Edelsbrunner, F. Pausinger, Advances in Mathematics 287 (2016) 674–703.","chicago":"Edelsbrunner, Herbert, and Florian Pausinger. “Approximation and Convergence of the Intrinsic Volume.” Advances in Mathematics. Academic Press, 2016. https://doi.org/10.1016/j.aim.2015.10.004.","ama":"Edelsbrunner H, Pausinger F. Approximation and convergence of the intrinsic volume. Advances in Mathematics. 2016;287:674-703. doi:10.1016/j.aim.2015.10.004","ista":"Edelsbrunner H, Pausinger F. 2016. Approximation and convergence of the intrinsic volume. Advances in Mathematics. 287, 674–703.","ieee":"H. Edelsbrunner and F. Pausinger, “Approximation and convergence of the intrinsic volume,” Advances in Mathematics, vol. 287. Academic Press, pp. 674–703, 2016.","apa":"Edelsbrunner, H., & Pausinger, F. (2016). Approximation and convergence of the intrinsic volume. Advances in Mathematics. Academic Press. https://doi.org/10.1016/j.aim.2015.10.004"},"publication":"Advances in Mathematics"},{"day":"01","has_accepted_license":"1","article_processing_charge":"No","citation":{"chicago":"Rieckh, Georg. “Studying the Complexities of Transcriptional Regulation.” Institute of Science and Technology Austria, 2016.","mla":"Rieckh, Georg. Studying the Complexities of Transcriptional Regulation. Institute of Science and Technology Austria, 2016.","short":"G. Rieckh, Studying the Complexities of Transcriptional Regulation, Institute of Science and Technology Austria, 2016.","ista":"Rieckh G. 2016. Studying the complexities of transcriptional regulation. Institute of Science and Technology Austria.","apa":"Rieckh, G. (2016). Studying the complexities of transcriptional regulation. Institute of Science and Technology Austria.","ieee":"G. Rieckh, “Studying the complexities of transcriptional regulation,” Institute of Science and Technology Austria, 2016.","ama":"Rieckh G. Studying the complexities of transcriptional regulation. 2016."},"page":"114","date_published":"2016-08-01T00:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"The process of gene expression is central to the modern understanding of how cellular systems\r\nfunction. In this process, a special kind of regulatory proteins, called transcription factors,\r\nare important to determine how much protein is produced from a given gene. As biological\r\ninformation is transmitted from transcription factor concentration to mRNA levels to amounts of\r\nprotein, various sources of noise arise and pose limits to the fidelity of intracellular signaling.\r\nThis thesis concerns itself with several aspects of stochastic gene expression: (i) the mathematical\r\ndescription of complex promoters responsible for the stochastic production of biomolecules,\r\n(ii) fundamental limits to information processing the cell faces due to the interference from multiple\r\nfluctuating signals, (iii) how the presence of gene expression noise influences the evolution\r\nof regulatory sequences, (iv) and tools for the experimental study of origins and consequences\r\nof cell-cell heterogeneity, including an application to bacterial stress response systems.","lang":"eng"}],"_id":"1128","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["570"],"status":"public","title":"Studying the complexities of transcriptional regulation","file":[{"file_name":"Thesis_Georg_Rieckh_w_signature_page.pdf","access_level":"closed","file_size":2614660,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"6815","date_updated":"2019-08-13T11:46:25Z","date_created":"2019-08-13T11:46:25Z","checksum":"ec453918c3bf8e6f460fd1156ef7b493"},{"file_size":6096178,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"Thesis_Georg_Rieckh.pdf","checksum":"51ae398166370d18fd22478b6365c4da","success":1,"date_updated":"2020-09-21T11:30:40Z","date_created":"2020-09-21T11:30:40Z","relation":"main_file","file_id":"8542"}],"oa_version":"Published Version","month":"08","publication_identifier":{"issn":["2663-337X"]},"oa":1,"supervisor":[{"full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"file_date_updated":"2020-09-21T11:30:40Z","publist_id":"6232","year":"2016","publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"Institute of Science and Technology Austria","author":[{"last_name":"Rieckh","first_name":"Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","full_name":"Rieckh, Georg"}],"date_updated":"2023-09-07T11:44:34Z","date_created":"2018-12-11T11:50:18Z"},{"author":[{"full_name":"Morri, Maurizio","last_name":"Morri","first_name":"Maurizio","id":"4863116E-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T11:43:03Z","date_created":"2018-12-11T11:50:17Z","file":[{"file_name":"MORRI_PhD_thesis_FINALPLUSSIGNATURES (2).pdf","access_level":"closed","creator":"dernst","file_size":4785167,"content_type":"application/pdf","file_id":"6812","relation":"main_file","date_updated":"2019-08-13T10:50:00Z","date_created":"2019-08-13T10:50:00Z","checksum":"b439803ac0827cdddd56562a54e3b53b"},{"file_size":4495669,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2016_MORRI_Thesis.pdf","checksum":"dd4136247fe472e7d47880ec68ac8de0","success":1,"date_created":"2021-02-22T11:42:06Z","date_updated":"2021-02-22T11:42:06Z","relation":"main_file","file_id":"9180"}],"oa_version":"Published Version","year":"2016","_id":"1124","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Optical functionalization of human class A orphan G-protein coupled receptors","publication_status":"published","ddc":["570"],"status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"HaJa"}],"file_date_updated":"2021-02-22T11:42:06Z","publist_id":"6236","type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2016-03-01T00:00:00Z","supervisor":[{"full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","first_name":"Harald L","last_name":"Janovjak"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"citation":{"ista":"Morri M. 2016. Optical functionalization of human class A orphan G-protein coupled receptors. Institute of Science and Technology Austria.","apa":"Morri, M. (2016). Optical functionalization of human class A orphan G-protein coupled receptors. Institute of Science and Technology Austria.","ieee":"M. Morri, “Optical functionalization of human class A orphan G-protein coupled receptors,” Institute of Science and Technology Austria, 2016.","ama":"Morri M. Optical functionalization of human class A orphan G-protein coupled receptors. 2016.","chicago":"Morri, Maurizio. “Optical Functionalization of Human Class A Orphan G-Protein Coupled Receptors.” Institute of Science and Technology Austria, 2016.","mla":"Morri, Maurizio. Optical Functionalization of Human Class A Orphan G-Protein Coupled Receptors. Institute of Science and Technology Austria, 2016.","short":"M. Morri, Optical Functionalization of Human Class A Orphan G-Protein Coupled Receptors, Institute of Science and Technology Austria, 2016."},"page":"129","day":"01","month":"03","article_processing_charge":"No","has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]}},{"publist_id":"6231","file_date_updated":"2021-02-22T11:43:14Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"MiSi"}],"publication_status":"published","acknowledgement":"First, I would like to thank Michael Sixt for being a great supervisor, mentor and\r\nscientist. I highly appreciate his guidance and continued support. Furthermore, I\r\nam very grateful that he gave me the exceptional opportunity to pursue many\r\nideas of which some managed to be included in this thesis.\r\nI owe sincere thanks to the members of my PhD thesis committee, Daria\r\nSiekhaus, Daniel Legler and Harald Janovjak. Especially I would like to thank\r\nDaria for her advice and encouragement during our regular progress meetings.\r\nI also want to thank the team and fellows of the Boehringer Ingelheim Fond\r\n(BIF) PhD Fellowship for amazing and inspiring meetings and the BIF for\r\nfinancial support.\r\nImportant factors for the success of this thesis were the warm, creative\r\nand helpful atmosphere as well as the team spirit of the whole Sixt Lab.\r\nTherefore I would like to thank my current and former colleagues Frank Assen,\r\nMarkus Brown, Ingrid de Vries, Michelle Duggan, Alexander Eichner, Miroslav\r\nHons, Eva Kiermaier, Aglaja Kopf, Alexander Leithner, Christine Moussion, Jan\r\nMüller, Maria Nemethova, Jörg Renkawitz, Anne Reversat, Kari Vaahtomeri,\r\nMichele Weber and Stefan Wieser. We had an amazing time with many\r\nlegendary evenings and events. Along these lines I want to thank the in vitro\r\ncrew of the lab, Jörg, Anne and Alex, for lots of ideas and productive\r\ndiscussions. I am sure, some day we will reveal the secret of the ‘splodge’.\r\nI want to thank the members of the Heisenberg Lab for a great time and\r\nthrilling kicker matches. In this regard I especially want to thank Maurizio\r\n‘Gnocci’ Monti, Gabriel Krens, Alex Eichner, Martin Behrndt, Vanessa Barone,Philipp Schmalhorst, Michael Smutny, Daniel Capek, Anne Reversat, Eva\r\nKiermaier, Frank Assen and Jan Müller for wonderful after-lunch matches.\r\nI would not have been able to analyze the thousands of cell trajectories\r\nand probably hundreds of thousands of mouse clicks without the productive\r\ncollaboration with Veronika Bierbaum and Tobias Bollenbach. Thanks Vroni for\r\ncountless meetings, discussions and graphs and of course for proofreading and\r\nadvice for this thesis. For proofreading I also want to thank Evi, Jörg, Jack and\r\nAnne.\r\nI would like to acknowledge Matthias Mehling for a very productive\r\ncollaboration and for introducing me into the wild world of microfluidics. Jack\r\nMerrin, for countless wafers, PDMS coated coverslips and help with anything\r\nmicro-fabrication related. And Maria Nemethova for establishing the ‘click’\r\npatterning approach with me. Without her it still would be just one of the ideas…\r\nMany thanks to Ekaterina Papusheva, Robert Hauschild, Doreen Milius\r\nand Nasser Darwish from the Bioimaging Facility as well as the Preclinical and\r\nthe Life Science facilities of IST Austria for excellent technical support. At this\r\npoint I especially want to thank Robert for countless image analyses and\r\ntechnical ideas. Always interested and creative he played an essential role in all\r\nof my projects.\r\nAdditionally I want to thank Ingrid and Gabby for welcoming me warmly\r\nwhen I first started at IST, for scientific and especially mental support in all\r\nthose years, countless coffee sessions and Heurigen evenings. #BioimagingFacility #LifeScienceFacility #PreClinicalFacility","year":"2016","date_created":"2018-12-11T11:50:18Z","date_updated":"2023-09-07T11:54:33Z","author":[{"full_name":"Schwarz, Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz","first_name":"Jan"}],"publication_identifier":{"issn":["2663-337X"]},"month":"07","oa":1,"language":[{"iso":"eng"}],"supervisor":[{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Directed cell migration is a hallmark feature, present in almost all multi-cellular\r\norganisms. Despite its importance, basic questions regarding force transduction\r\nor directional sensing are still heavily investigated. Directed migration of cells\r\nguided by immobilized guidance cues - haptotaxis - occurs in key-processes,\r\nsuch as embryonic development and immunity (Middleton et al., 1997; Nguyen\r\net al., 2000; Thiery, 1984; Weber et al., 2013). Immobilized guidance cues\r\ncomprise adhesive ligands, such as collagen and fibronectin (Barczyk et al.,\r\n2009), or chemokines - the main guidance cues for migratory leukocytes\r\n(Middleton et al., 1997; Weber et al., 2013). While adhesive ligands serve as\r\nattachment sites guiding cell migration (Carter, 1965), chemokines instruct\r\nhaptotactic migration by inducing adhesion to adhesive ligands and directional\r\nguidance (Rot and Andrian, 2004; Schumann et al., 2010). Quantitative analysis\r\nof the cellular response to immobilized guidance cues requires in vitro assays\r\nthat foster cell migration, offer accurate control of the immobilized cues on a\r\nsubcellular scale and in the ideal case closely reproduce in vivo conditions. The\r\nexploration of haptotactic cell migration through design and employment of such\r\nassays represents the main focus of this work.\r\nDendritic cells (DCs) are leukocytes, which after encountering danger\r\nsignals such as pathogens in peripheral organs instruct naïve T-cells and\r\nconsequently the adaptive immune response in the lymph node (Mellman and\r\nSteinman, 2001). To reach the lymph node from the periphery, DCs follow\r\nhaptotactic gradients of the chemokine CCL21 towards lymphatic vessels\r\n(Weber et al., 2013). Questions about how DCs interpret haptotactic CCL21\r\ngradients have not yet been addressed. The main reason for this is the lack of\r\nan assay that offers diverse haptotactic environments, hence allowing the study\r\nof DC migration as a response to different signals of immobilized guidance cue.\r\nIn this work, we developed an in vitro assay that enables us to\r\nquantitatively assess DC haptotaxis, by combining precisely controllable\r\nchemokine photo-patterning with physically confining migration conditions. With this tool at hand, we studied the influence of CCL21 gradient properties and\r\nconcentration on DC haptotaxis. We found that haptotactic gradient sensing\r\ndepends on the absolute CCL21 concentration in combination with the local\r\nsteepness of the gradient. Our analysis suggests that the directionality of\r\nmigrating DCs is governed by the signal-to-noise ratio of CCL21 binding to its\r\nreceptor CCR7. Moreover, the haptotactic CCL21 gradient formed in vivo\r\nprovides an optimal shape for DCs to recognize haptotactic guidance cue.\r\nBy reconstitution of the CCL21 gradient in vitro we were also able to\r\nstudy the influence of CCR7 signal termination on DC haptotaxis. To this end,\r\nwe used DCs lacking the G-protein coupled receptor kinase GRK6, which is\r\nresponsible for CCL21 induced CCR7 receptor phosphorylation and\r\ndesensitization (Zidar et al., 2009). We found that CCR7 desensitization by\r\nGRK6 is crucial for maintenance of haptotactic CCL21 gradient sensing in vitro\r\nand confirm those observations in vivo.\r\nIn the context of the organism, immobilized haptotactic guidance cues\r\noften coincide and compete with soluble chemotactic guidance cues. During\r\nwound healing, fibroblasts are exposed and influenced by adhesive cues and\r\nsoluble factors at the same time (Wu et al., 2012; Wynn, 2008). Similarly,\r\nmigrating DCs are exposed to both, soluble chemokines (CCL19 and truncated\r\nCCL21) inducing chemotactic behavior as well as the immobilized CCL21. To\r\nquantitatively assess these complex coinciding immobilized and soluble\r\nguidance cues, we implemented our chemokine photo-patterning technique in a\r\nmicrofluidic system allowing for chemotactic gradient generation. To validate\r\nthe assay, we observed DC migration in competing CCL19/CCL21\r\nenvironments.\r\nAdhesiveness guided haptotaxis has been studied intensively over the\r\nlast century. However, quantitative studies leading to conceptual models are\r\nlargely missing, again due to the lack of a precisely controllable in vitro assay. A\r\nrequirement for such an in vitro assay is that it must prevent any uncontrolled\r\ncell adhesion. This can be accomplished by stable passivation of the surface. In\r\naddition, controlled adhesion must be sustainable, quantifiable and dose\r\ndependent in order to create homogenous gradients. Therefore, we developed a novel covalent photo-patterning technique satisfying all these needs. In\r\ncombination with a sustainable poly-vinyl alcohol (PVA) surface coating we\r\nwere able to generate gradients of adhesive cue to direct cell migration. This\r\napproach allowed us to characterize the haptotactic migratory behavior of\r\nzebrafish keratocytes in vitro. Furthermore, defined patterns of adhesive cue\r\nallowed us to control for cell shape and growth on a subcellular scale.","lang":"eng"}],"ddc":["570"],"title":"Quantitative analysis of haptotactic cell migration","status":"public","_id":"1129","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"checksum":"e3cd6b28f9c5cccb8891855565a2dade","date_updated":"2019-08-13T10:55:35Z","date_created":"2019-08-13T10:55:35Z","file_id":"6813","relation":"main_file","creator":"dernst","file_size":32044069,"content_type":"application/pdf","access_level":"closed","file_name":"Thesis_JSchwarz_final.pdf"},{"creator":"dernst","file_size":8396717,"content_type":"application/pdf","access_level":"open_access","file_name":"2016_Thesis_JSchwarz.pdf","success":1,"checksum":"c3dbe219acf87eed2f46d21d5cca00de","date_created":"2021-02-22T11:43:14Z","date_updated":"2021-02-22T11:43:14Z","file_id":"9181","relation":"main_file"}],"oa_version":"Published Version","has_accepted_license":"1","article_processing_charge":"No","day":"01","page":"178","citation":{"ama":"Schwarz J. Quantitative analysis of haptotactic cell migration. 2016.","ista":"Schwarz J. 2016. Quantitative analysis of haptotactic cell migration. Institute of Science and Technology Austria.","ieee":"J. Schwarz, “Quantitative analysis of haptotactic cell migration,” Institute of Science and Technology Austria, 2016.","apa":"Schwarz, J. (2016). Quantitative analysis of haptotactic cell migration. Institute of Science and Technology Austria.","mla":"Schwarz, Jan. Quantitative Analysis of Haptotactic Cell Migration. Institute of Science and Technology Austria, 2016.","short":"J. Schwarz, Quantitative Analysis of Haptotactic Cell Migration, Institute of Science and Technology Austria, 2016.","chicago":"Schwarz, Jan. “Quantitative Analysis of Haptotactic Cell Migration.” Institute of Science and Technology Austria, 2016."},"date_published":"2016-07-01T00:00:00Z"},{"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Traditionally machine learning has been focusing on the problem of solving a single\r\ntask in isolation. While being quite well understood, this approach disregards an\r\nimportant aspect of human learning: when facing a new problem, humans are able to\r\nexploit knowledge acquired from previously learned tasks. Intuitively, access to several\r\nproblems simultaneously or sequentially could also be advantageous for a machine\r\nlearning system, especially if these tasks are closely related. Indeed, results of many\r\nempirical studies have provided justification for this intuition. However, theoretical\r\njustifications of this idea are rather limited.\r\nThe focus of this thesis is to expand the understanding of potential benefits of information\r\ntransfer between several related learning problems. We provide theoretical\r\nanalysis for three scenarios of multi-task learning - multiple kernel learning, sequential\r\nlearning and active task selection. We also provide a PAC-Bayesian perspective on\r\nlifelong learning and investigate how the task generation process influences the generalization\r\nguarantees in this scenario. In addition, we show how some of the obtained\r\ntheoretical results can be used to derive principled multi-task and lifelong learning\r\nalgorithms and illustrate their performance on various synthetic and real-world datasets.","lang":"eng"}],"_id":"1126","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["006"],"title":"Theoretical foundations of multi-task lifelong learning","status":"public","pubrep_id":"776","file":[{"creator":"system","content_type":"application/pdf","file_size":2140062,"file_name":"IST-2017-776-v1+1_Pentina_Thesis_2016.pdf","access_level":"open_access","date_created":"2018-12-12T10:14:07Z","date_updated":"2018-12-12T10:14:07Z","file_id":"5056","relation":"main_file"}],"oa_version":"Published Version","day":"01","has_accepted_license":"1","article_processing_charge":"No","citation":{"chicago":"Pentina, Anastasia. “Theoretical Foundations of Multi-Task Lifelong Learning.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:TH_776.","short":"A. Pentina, Theoretical Foundations of Multi-Task Lifelong Learning, Institute of Science and Technology Austria, 2016.","mla":"Pentina, Anastasia. Theoretical Foundations of Multi-Task Lifelong Learning. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:TH_776.","apa":"Pentina, A. (2016). Theoretical foundations of multi-task lifelong learning. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_776","ieee":"A. Pentina, “Theoretical foundations of multi-task lifelong learning,” Institute of Science and Technology Austria, 2016.","ista":"Pentina A. 2016. Theoretical foundations of multi-task lifelong learning. Institute of Science and Technology Austria.","ama":"Pentina A. Theoretical foundations of multi-task lifelong learning. 2016. doi:10.15479/AT:ISTA:TH_776"},"page":"127","date_published":"2016-11-01T00:00:00Z","file_date_updated":"2018-12-12T10:14:07Z","ec_funded":1,"publist_id":"6234","year":"2016","acknowledgement":"First and foremost I would like to express my gratitude to my supervisor, Christoph\r\nLampert. Thank you for your patience in teaching me all aspects of doing research\r\n(including English grammar), for your trust in my capabilities and endless support. Thank\r\nyou for granting me freedom in my research and, at the same time, having time and\r\nhelping me cope with the consequences whenever I needed it. Thank you for creating\r\nan excellent atmosphere in the group, it was a great pleasure and honor to be a part of\r\nit. There could not have been a better and more inspiring adviser and mentor.\r\nI thank Shai Ben-David for welcoming me into his group at the University of Waterloo,\r\nfor inspiring discussions and support. It was a great pleasure to work together. I am\r\nalso thankful to Ruth Urner for hosting me at the Max-Planck Institute Tübingen, for the\r\nfruitful collaboration and for taking care of me during that not-so-sunny month of May.\r\nI thank Jan Maas for kindly joining my thesis committee despite the short notice and\r\nproviding me with insightful comments.\r\nI would like to thank my colleagues for their support, entertaining conversations and\r\nendless table soccer games we shared together: Georg, Jan, Amelie and Emilie, Michal\r\nand Alex, Alex K. and Alex Z., Thomas, Sameh, Vlad, Mayu, Nathaniel, Silvester, Neel,\r\nCsaba, Vladimir, Morten. Thank you, Mabel and Ram, for the wonderful time we spent\r\ntogether. I am thankful to Shrinu and Samira for taking care of me during my stay at the\r\nUniversity of Waterloo. Special thanks to Viktoriia for her never-ending optimism and for\r\nbeing so inspiring and supportive, especially at the beginning of my PhD journey.\r\nThanks to IST administration, in particular, Vlad and Elisabeth for shielding me from\r\nmost of the bureaucratic paperwork.\r\n\r\nThis dissertation would not have been possible without funding from the European\r\nResearch Council under the European Union's Seventh Framework Programme\r\n(FP7/2007-2013)/ERC grant agreement no 308036.","publication_status":"published","department":[{"_id":"ChLa"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Pentina, Anastasia","id":"42E87FC6-F248-11E8-B48F-1D18A9856A87","last_name":"Pentina","first_name":"Anastasia"}],"date_updated":"2023-09-07T11:52:03Z","date_created":"2018-12-11T11:50:17Z","month":"11","publication_identifier":{"issn":["2663-337X"]},"oa":1,"project":[{"call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/AT:ISTA:TH_776","supervisor":[{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"}],"degree_awarded":"PhD","language":[{"iso":"eng"}]},{"author":[{"full_name":"Chmelik, Martin","last_name":"Chmelik","first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:51:47Z","date_updated":"2023-09-07T11:54:58Z","oa_version":"None","_id":"1397","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2016","title":"Algorithms for partially observable markov decision processes","publication_status":"published","status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"KrCh"}],"abstract":[{"lang":"eng","text":"We study partially observable Markov decision processes (POMDPs) with objectives used in verification and artificial intelligence. The qualitative analysis problem given a POMDP and an objective asks whether there is a strategy (policy) to ensure that the objective is satisfied almost surely (with probability 1), resp. with positive probability (with probability greater than 0). For POMDPs with limit-average payoff, where a reward value in the interval [0,1] is associated to every transition, and the payoff of an infinite path is the long-run average of the rewards, we consider two types of path constraints: (i) a quantitative limit-average constraint defines the set of paths where the payoff is at least a given threshold L1 = 1. Our main results for qualitative limit-average constraint under almost-sure winning are as follows: (i) the problem of deciding the existence of a finite-memory controller is EXPTIME-complete; and (ii) the problem of deciding the existence of an infinite-memory controller is undecidable. For quantitative limit-average constraints we show that the problem of deciding the existence of a finite-memory controller is undecidable. We present a prototype implementation of our EXPTIME algorithm. For POMDPs with w-regular conditions specified as parity objectives, while the qualitative analysis problems are known to be undecidable even for very special case of parity objectives, we establish decidability (with optimal complexity) of the qualitative analysis problems for POMDPs with 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. Based on our theoretical algorithms 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 well-known POMDP examples for robotics applications. For POMDPs with a set of target states and an integer cost associated with every transition, we study the optimization objective that 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. We show that for general 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 and exponential in the POMDP state space size; (ii) we show that the problem of approximating the optimal cost is decidable and present approximation algorithms that extend existing algorithms for POMDPs with finite-horizon objectives. We show experimentally that it performs well in many examples of interest. We study more deeply the problem of almost-sure reachability, where given a set of target states, the question is to decide whether there is a strategy to ensure that the target set is reached almost surely. While in general the problem EXPTIME-complete, in many practical cases strategies with a small amount of memory suffice. Moreover, the existing solution to the problem is explicit, which first requires to construct explicitly an exponential reduction to a belief-support MDP. We first study the existence of observation-stationary strategies, which is NP-complete, and then small-memory strategies. We present a symbolic algorithm by an efficient encoding to SAT and using a SAT solver for the problem. We report experimental results demonstrating the scalability of our symbolic (SAT-based) approach. Decentralized POMDPs (DEC-POMDPs) extend POMDPs to a multi-agent setting, where several agents operate in an uncertain environment independently to achieve a joint objective. In this work we consider Goal DEC-POMDPs, where given a set of target states, the objective is to ensure that the target set is reached with minimal cost. We consider the indefinite-horizon (infinite-horizon with either discounted-sum, or undiscounted-sum, where absorbing goal states have zero-cost) problem. We present a new and novel method to solve the problem that extends methods for finite-horizon DEC-POMDPs and the real-time dynamic programming approach for POMDPs. We present experimental results on several examples, and show that our approach presents promising results. In the end we present a short summary of a few other results related to verification of MDPs and POMDPs."}],"publist_id":"5810","type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2016-02-01T00:00:00Z","degree_awarded":"PhD","supervisor":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"}],"language":[{"iso":"eng"}],"citation":{"ama":"Chmelik M. Algorithms for partially observable markov decision processes. 2016.","apa":"Chmelik, M. (2016). Algorithms for partially observable markov decision processes. Institute of Science and Technology Austria.","ieee":"M. Chmelik, “Algorithms for partially observable markov decision processes,” Institute of Science and Technology Austria, 2016.","ista":"Chmelik M. 2016. Algorithms for partially observable markov decision processes. Institute of Science and Technology Austria.","short":"M. Chmelik, Algorithms for Partially Observable Markov Decision Processes, Institute of Science and Technology Austria, 2016.","mla":"Chmelik, Martin. Algorithms for Partially Observable Markov Decision Processes. Institute of Science and Technology Austria, 2016.","chicago":"Chmelik, Martin. “Algorithms for Partially Observable Markov Decision Processes.” Institute of Science and Technology Austria, 2016."},"page":"232","day":"01","month":"02","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No"},{"status":"public","title":"Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture","ddc":["500"],"_id":"1123","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"relation":"main_file","file_id":"6809","checksum":"2d140cc924cd1b764544906fc22684ef","date_created":"2019-08-13T08:45:27Z","date_updated":"2019-08-13T08:45:27Z","access_level":"closed","file_name":"Thesis_final version_Mabillard_w_signature_page.pdf","file_size":2227916,"content_type":"application/pdf","creator":"dernst"},{"access_level":"open_access","file_name":"2016_Mabillard_Thesis.pdf","file_size":2227916,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"9178","checksum":"2d140cc924cd1b764544906fc22684ef","success":1,"date_updated":"2021-02-22T11:36:34Z","date_created":"2021-02-22T11:36:34Z"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Motivated by topological Tverberg-type problems in topological combinatorics and by classical\r\nresults about embeddings (maps without double points), we study the question whether a finite\r\nsimplicial complex K can be mapped into Rd without triple, quadruple, or, more generally, r-fold points (image points with at least r distinct preimages), for a given multiplicity r ≤ 2. In particular, we are interested in maps f : K → Rd that have no global r -fold intersection points, i.e., no r -fold points with preimages in r pairwise disjoint simplices of K , and we seek necessary and sufficient conditions for the existence of such maps.\r\n\r\nWe present higher-multiplicity analogues of several classical results for embeddings, in particular of the completeness of the Van Kampen obstruction for embeddability of k -dimensional\r\ncomplexes into R2k , k ≥ 3. Speciffically, we show that under suitable restrictions on the dimensions(viz., if dimK = (r ≥ 1)k and d = rk \\ for some k ≥ 3), a well-known deleted product criterion (DPC ) is not only necessary but also sufficient for the existence of maps without global r -fold points. Our main technical tool is a higher-multiplicity version of the classical Whitney trick , by which pairs of isolated r -fold points of opposite sign can be eliminated by local modiffications of the map, assuming codimension d – dimK ≥ 3.\r\n\r\nAn important guiding idea for our work was that suffciency of the DPC, together with an old\r\nresult of Özaydin's on the existence of equivariant maps, might yield an approach to disproving the remaining open cases of the the long-standing topological Tverberg conjecture , i.e., to construct maps from the N -simplex σN to Rd without r-Tverberg points when r not a prime power and\r\nN = (d + 1)(r – 1). Unfortunately, our proof of the sufficiency of the DPC requires codimension d – dimK ≥ 3, which is not satisfied for K = σN .\r\n\r\nIn 2015, Frick [16] found a very elegant way to overcome this \\codimension 3 obstacle" and\r\nto construct the first counterexamples to the topological Tverberg conjecture for all parameters(d; r ) with d ≥ 3r + 1 and r not a prime power, by a reduction1 to a suitable lower-dimensional skeleton, for which the codimension 3 restriction is satisfied and maps without r -Tverberg points exist by Özaydin's result and sufficiency of the DPC.\r\n\r\nIn this thesis, we present a different construction (which does not use the constraint method) that yields counterexamples for d ≥ 3r , r not a prime power. "}],"page":"55","citation":{"chicago":"Mabillard, Isaac. “Eliminating Higher-Multiplicity Intersections: An r-Fold Whitney Trick for the Topological Tverberg Conjecture.” Institute of Science and Technology Austria, 2016.","mla":"Mabillard, Isaac. Eliminating Higher-Multiplicity Intersections: An r-Fold Whitney Trick for the Topological Tverberg Conjecture. Institute of Science and Technology Austria, 2016.","short":"I. Mabillard, Eliminating Higher-Multiplicity Intersections: An r-Fold Whitney Trick for the Topological Tverberg Conjecture, Institute of Science and Technology Austria, 2016.","ista":"Mabillard I. 2016. Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture. Institute of Science and Technology Austria.","apa":"Mabillard, I. (2016). Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture. Institute of Science and Technology Austria.","ieee":"I. Mabillard, “Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture,” Institute of Science and Technology Austria, 2016.","ama":"Mabillard I. Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture. 2016."},"date_published":"2016-08-01T00:00:00Z","day":"01","article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Institute of Science and Technology Austria","acknowledgement":"Foremost, I would like to thank Uli Wagner for introducing me to the exciting interface between\r\ntopology and combinatorics, and for our subsequent years of fruitful collaboration.\r\nIn our creative endeavors to eliminate intersection points, we had the chance to be joined later\r\nby Sergey Avvakumov and Arkadiy Skopenkov, which led us to new surprises in dimension 12.\r\nMy stay at EPFL and IST Austria was made very agreeable thanks to all these wonderful\r\npeople: Cyril Becker, Marek Filakovsky, Peter Franek, Radoslav Fulek, Peter Gazi, Kristof Huszar,\r\nMarek Krcal, Zuzana Masarova, Arnaud de Mesmay, Filip Moric, Michal Rybar, Martin Tancer,\r\nand Stephan Zhechev.\r\nFinally, I would like to thank my thesis committee Herbert Edelsbrunner and Roman Karasev\r\nfor their careful reading of the present manuscript and for the many improvements they suggested.","year":"2016","date_updated":"2023-09-07T11:56:28Z","date_created":"2018-12-11T11:50:16Z","author":[{"first_name":"Isaac","last_name":"Mabillard","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","full_name":"Mabillard, Isaac"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"2159"}]},"file_date_updated":"2021-02-22T11:36:34Z","publist_id":"6237","oa":1,"degree_awarded":"PhD","supervisor":[{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli"}],"language":[{"iso":"eng"}],"month":"08","publication_identifier":{"issn":["2663-337X"]}},{"publisher":"Nature Publishing Group","department":[{"_id":"PeJo"}],"publication_status":"published","year":"2016","acknowledgement":"We thank Jozsef Csicsvari and Nelson Spruston for critically reading the manuscript. We also thank A. Schlögl for programming, F. Marr for technical assistance and E. Kramberger for manuscript editing. ","volume":7,"date_created":"2018-12-11T11:51:59Z","date_updated":"2023-09-07T11:55:25Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1396"}]},"author":[{"full_name":"Mishra, Rajiv Kumar","id":"46CB58F2-F248-11E8-B48F-1D18A9856A87","last_name":"Mishra","first_name":"Rajiv Kumar"},{"full_name":"Kim, Sooyun","first_name":"Sooyun","last_name":"Kim","id":"394AB1C8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"José","last_name":"Guzmán","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2209-5242","full_name":"Guzmán, José"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M"}],"article_number":"11552","publist_id":"5766","ec_funded":1,"file_date_updated":"2020-07-14T12:44:53Z","project":[{"call_identifier":"FWF","name":"Mechanisms of transmitter release at GABAergic synapses","grant_number":"P24909-B24","_id":"25C26B1E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","grant_number":"268548","_id":"25C0F108-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1038/ncomms11552","month":"05","intvolume":" 7","title":"Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks","status":"public","ddc":["570"],"_id":"1432","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"content_type":"application/pdf","file_size":4510512,"creator":"system","access_level":"open_access","file_name":"IST-2016-582-v1+1_ncomms11552.pdf","checksum":"7e84d0392348c874d473b62f1042de22","date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-12T10:18:33Z","relation":"main_file","file_id":"5355"}],"oa_version":"Published Version","pubrep_id":"582","type":"journal_article","abstract":[{"text":"CA3–CA3 recurrent excitatory synapses are thought to play a key role in memory storage and pattern completion. Whether the plasticity properties of these synapses are consistent with their proposed network functions remains unclear. Here, we examine the properties of spike timing-dependent plasticity (STDP) at CA3–CA3 synapses. Low-frequency pairing of excitatory postsynaptic potentials (EPSPs) and action potentials (APs) induces long-term potentiation (LTP), independent of temporal order. The STDP curve is symmetric and broad (half-width ~150 ms). Consistent with these STDP induction properties, AP–EPSP sequences lead to supralinear summation of spine [Ca2+] transients. Furthermore, afterdepolarizations (ADPs) following APs efficiently propagate into dendrites of CA3 pyramidal neurons, and EPSPs summate with dendritic ADPs. In autoassociative network models, storage and recall are more robust with symmetric than with asymmetric STDP rules. Thus, a specialized STDP induction rule allows reliable storage and recall of information in the hippocampal CA3 network.","lang":"eng"}],"citation":{"short":"R.K. Mishra, S. Kim, J. Guzmán, P.M. Jonas, Nature Communications 7 (2016).","mla":"Mishra, Rajiv Kumar, et al. “Symmetric Spike Timing-Dependent Plasticity at CA3–CA3 Synapses Optimizes Storage and Recall in Autoassociative Networks.” Nature Communications, vol. 7, 11552, Nature Publishing Group, 2016, doi:10.1038/ncomms11552.","chicago":"Mishra, Rajiv Kumar, Sooyun Kim, José Guzmán, and Peter M Jonas. “Symmetric Spike Timing-Dependent Plasticity at CA3–CA3 Synapses Optimizes Storage and Recall in Autoassociative Networks.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms11552.","ama":"Mishra RK, Kim S, Guzmán J, Jonas PM. Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks. Nature Communications. 2016;7. doi:10.1038/ncomms11552","ieee":"R. K. Mishra, S. Kim, J. Guzmán, and P. M. Jonas, “Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks,” Nature Communications, vol. 7. Nature Publishing Group, 2016.","apa":"Mishra, R. K., Kim, S., Guzmán, J., & Jonas, P. M. (2016). Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms11552","ista":"Mishra RK, Kim S, Guzmán J, Jonas PM. 2016. Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks. Nature Communications. 7, 11552."},"publication":"Nature Communications","date_published":"2016-05-13T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"13"},{"oa":1,"degree_awarded":"PhD","supervisor":[{"first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"}],"language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"PeJo"}],"year":"2016","date_created":"2018-12-11T11:51:46Z","date_updated":"2023-09-07T11:55:26Z","author":[{"id":"46CB58F2-F248-11E8-B48F-1D18A9856A87","first_name":"Rajiv Kumar","last_name":"Mishra","full_name":"Mishra, Rajiv Kumar"}],"related_material":{"record":[{"id":"1432","relation":"part_of_dissertation","status":"public"}]},"file_date_updated":"2021-02-22T11:48:44Z","publist_id":"5811","page":"83","citation":{"ama":"Mishra RK. Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus. 2016.","ista":"Mishra RK. 2016. Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus. Institute of Science and Technology Austria.","ieee":"R. K. Mishra, “Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus,” Institute of Science and Technology Austria, 2016.","apa":"Mishra, R. K. (2016). Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus. Institute of Science and Technology Austria.","mla":"Mishra, Rajiv Kumar. Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses in Hippocampus. Institute of Science and Technology Austria, 2016.","short":"R.K. Mishra, Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses in Hippocampus, Institute of Science and Technology Austria, 2016.","chicago":"Mishra, Rajiv Kumar. “Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses in Hippocampus.” Institute of Science and Technology Austria, 2016."},"date_published":"2016-03-01T00:00:00Z","day":"01","article_processing_charge":"No","has_accepted_license":"1","status":"public","ddc":["570"],"title":"Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus","_id":"1396","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"access_level":"closed","file_name":"Thesis_Mishra_Rajiv (Final).pdf","creator":"dernst","file_size":2407572,"content_type":"application/pdf","file_id":"6782","relation":"main_file","checksum":"5a010a838faf040f7064f3cfb802f743","date_updated":"2020-07-14T12:44:48Z","date_created":"2019-08-09T12:14:46Z"},{"checksum":"81b26d9ede92c99f1d8cc6fa1d04cbbb","success":1,"date_created":"2021-02-22T11:48:44Z","date_updated":"2021-02-22T11:48:44Z","relation":"main_file","file_id":"9183","file_size":2407572,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2016_RajivMishra_Thesis.pdf"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"CA3 pyramidal neurons are thought to pay a key role in memory storage and pattern completion by activity-dependent synaptic plasticity between CA3-CA3 recurrent excitatory synapses. To examine the induction rules of synaptic plasticity at CA3-CA3 synapses, we performed whole-cell patch-clamp recordings in acute hippocampal slices from rats (postnatal 21-24 days) at room temperature. Compound excitatory postsynaptic potentials (ESPSs) were recorded by tract stimulation in stratum oriens in the presence of 10 µM gabazine. High-frequency stimulation (HFS) induced N-methyl-D-aspartate (NMDA) receptor-dependent long-term potentiation (LTP). Although LTP by HFS did not requier postsynaptic spikes, it was blocked by Na+-channel blockers suggesting that local active processes (e.g.) dendritic spikes) may contribute to LTP induction without requirement of a somatic action potential (AP). We next examined the properties of spike timing-dependent plasticity (STDP) at CA3-CA3 synapses. Unexpectedly, low-frequency pairing of EPSPs and backpropagated action potentialy (bAPs) induced LTP, independent of temporal order. The STDP curve was symmetric and broad, with a half-width of ~150 ms. Consistent with these specific STDP induction properties, post-presynaptic sequences led to a supralinear summation of spine [Ca2+] transients. Furthermore, in autoassociative network models, storage and recall was substantially more robust with symmetric than with asymmetric STDP rules. In conclusion, we found associative forms of LTP at CA3-CA3 recurrent collateral synapses with distinct induction rules. LTP induced by HFS may be associated with dendritic spikes. In contrast, low frequency pairing of pre- and postsynaptic activity induced LTP only if EPSP-AP were temporally very close. Together, these induction mechanisms of synaptiic plasticity may contribute to memory storage in the CA3-CA3 microcircuit at different ranges of activity."}]},{"oa":1,"language":[{"iso":"eng"}],"supervisor":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"07","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2016","date_updated":"2023-09-07T11:55:53Z","date_created":"2018-12-11T11:50:17Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"2023"}]},"author":[{"full_name":"Novak, Sebastian","first_name":"Sebastian","last_name":"Novak","id":"461468AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-824X"}],"publist_id":"6235","file_date_updated":"2021-02-22T13:42:47Z","page":"124","citation":{"short":"S. Novak, Evolutionary Proccesses in Variable Emvironments, Institute of Science and Technology Austria, 2016.","mla":"Novak, Sebastian. Evolutionary Proccesses in Variable Emvironments. Institute of Science and Technology Austria, 2016.","chicago":"Novak, Sebastian. “Evolutionary Proccesses in Variable Emvironments.” Institute of Science and Technology Austria, 2016.","ama":"Novak S. Evolutionary proccesses in variable emvironments. 2016.","apa":"Novak, S. (2016). Evolutionary proccesses in variable emvironments. Institute of Science and Technology Austria.","ieee":"S. Novak, “Evolutionary proccesses in variable emvironments,” Institute of Science and Technology Austria, 2016.","ista":"Novak S. 2016. Evolutionary proccesses in variable emvironments. Institute of Science and Technology Austria."},"date_published":"2016-07-01T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"01","ddc":["576"],"status":"public","title":"Evolutionary proccesses in variable emvironments","_id":"1125","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":3564901,"creator":"dernst","access_level":"closed","file_name":"Novak_thesis.pdf","checksum":"81dcc838dfcf7aa0b1a27ecf4fe2da4e","date_updated":"2019-08-13T09:01:00Z","date_created":"2019-08-13T09:01:00Z","relation":"main_file","file_id":"6811"},{"relation":"main_file","file_id":"9186","date_updated":"2021-02-22T13:42:47Z","date_created":"2021-02-22T13:42:47Z","checksum":"30808d2f7ca920e09f63a95cdc49bffd","success":1,"file_name":"2016_Novak_Thesis.pdf","access_level":"open_access","file_size":2814384,"content_type":"application/pdf","creator":"dernst"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Natural environments are never constant but subject to spatial and temporal change on\r\nall scales, increasingly so due to human activity. Hence, it is crucial to understand the\r\nimpact of environmental variation on evolutionary processes. In this thesis, I present\r\nthree topics that share the common theme of environmental variation, yet illustrate its\r\neffect from different perspectives.\r\nFirst, I show how a temporally fluctuating environment gives rise to second-order\r\nselection on a modifier for stress-induced mutagenesis. Without fluctuations, when\r\npopulations are adapted to their environment, mutation rates are minimized. I argue\r\nthat a stress-induced mutator mechanism may only be maintained if the population is\r\nrepeatedly subjected to diverse environmental challenges, and I outline implications of\r\nthe presented results to antibiotic treatment strategies.\r\nSecond, I discuss my work on the evolution of dispersal. Besides reproducing\r\nknown results about the effect of heterogeneous habitats on dispersal, it identifies\r\nspatial changes in dispersal type frequencies as a source for selection for increased\r\npropensities to disperse. This concept contains effects of relatedness that are known\r\nto promote dispersal, and I explain how it identifies other forces selecting for dispersal\r\nand puts them on a common scale.\r\nThird, I analyse genetic variances of phenotypic traits under multivariate stabilizing\r\nselection. For the case of constant environments, I generalize known formulae of\r\nequilibrium variances to multiple traits and discuss how the genetic variance of a focal\r\ntrait is influenced by selection on background traits. I conclude by presenting ideas and\r\npreliminary work aiming at including environmental fluctuations in the form of moving\r\ntrait optima into the model."}]},{"year":"2016","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"ToHe"},{"_id":"GradSch"}],"author":[{"full_name":"Tarrach, Thorsten","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4409-8487","first_name":"Thorsten","last_name":"Tarrach"}],"related_material":{"record":[{"id":"1729","status":"public","relation":"part_of_dissertation"},{"id":"2218","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"2445"}]},"date_updated":"2023-09-07T11:57:01Z","date_created":"2018-12-11T11:50:19Z","file_date_updated":"2021-11-17T13:46:55Z","ec_funded":1,"publist_id":"6230","oa":1,"main_file_link":[{"open_access":"1","url":"http://thorstent.github.io/theses/phd_thorsten_tarrach.pdf"}],"project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"doi":"10.15479/at:ista:1130","supervisor":[{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"issn":["2663-337X"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1130","ddc":["000"],"status":"public","title":"Automatic synthesis of synchronisation primitives for concurrent programs","oa_version":"Published Version","file":[{"file_name":"2016_Tarrach_Thesis.pdf","access_level":"open_access","creator":"dernst","file_size":1523935,"content_type":"application/pdf","file_id":"9179","relation":"main_file","date_created":"2021-02-22T11:39:32Z","date_updated":"2021-02-22T11:39:32Z","success":1,"checksum":"319a506831650327e85376db41fc1094"},{"checksum":"39efcd789f0ad859ff15652cb7afc412","date_created":"2021-11-16T14:14:38Z","date_updated":"2021-11-17T13:46:55Z","relation":"main_file","file_id":"10296","content_type":"application/pdf","file_size":1306068,"creator":"cchlebak","access_level":"closed","file_name":"2016_Tarrach_Thesispdfa.pdf"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"In this thesis we present a computer-aided programming approach to concurrency. Our approach helps the programmer by automatically fixing concurrency-related bugs, i.e. bugs that occur when the program is executed using an aggressive preemptive scheduler, but not when using a non-preemptive (cooperative) scheduler. Bugs are program behaviours that are incorrect w.r.t. a specification. We consider both user-provided explicit specifications in the form of assertion\r\nstatements in the code as well as an implicit specification. The implicit specification is inferred from the non-preemptive behaviour. Let us consider sequences of calls that the program makes to an external interface. The implicit specification requires that any such sequence produced under a preemptive scheduler should be included in the set of sequences produced under a non-preemptive scheduler. We consider several semantics-preserving fixes that go beyond atomic sections typically explored in the synchronisation synthesis literature. Our synthesis is able to place locks, barriers and wait-signal statements and last, but not least reorder independent statements. The latter may be useful if a thread is released to early, e.g., before some initialisation is completed. We guarantee that our synthesis does not introduce deadlocks and that the synchronisation inserted is optimal w.r.t. a given objective function. We dub our solution trace-based synchronisation synthesis and it is loosely based on counterexample-guided inductive synthesis (CEGIS). The synthesis works by discovering a trace that is incorrect w.r.t. the specification and identifying ordering constraints crucial to trigger the specification violation. Synchronisation may be placed immediately (greedy approach) or delayed until all incorrect traces are found (non-greedy approach). For the non-greedy approach we construct a set of global constraints over synchronisation placements. Each model of the global constraints set corresponds to a correctness-ensuring synchronisation placement. The placement that is optimal w.r.t. the given objective function is chosen as the synchronisation solution. We evaluate our approach on a number of realistic (albeit simplified) Linux device-driver\r\nbenchmarks. The benchmarks are versions of the drivers with known concurrency-related bugs. For the experiments with an explicit specification we added assertions that would detect the bugs in the experiments. Device drivers lend themselves to implicit specification, where the device and the operating system are the external interfaces. Our experiments demonstrate that our synthesis method is precise and efficient. We implemented objective functions for coarse-grained and fine-grained locking and observed that different synchronisation placements are produced for our experiments, favouring e.g. a minimal number of synchronisation operations or maximum concurrency."}],"citation":{"apa":"Tarrach, T. (2016). Automatic synthesis of synchronisation primitives for concurrent programs. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:1130","ieee":"T. Tarrach, “Automatic synthesis of synchronisation primitives for concurrent programs,” Institute of Science and Technology Austria, 2016.","ista":"Tarrach T. 2016. Automatic synthesis of synchronisation primitives for concurrent programs. Institute of Science and Technology Austria.","ama":"Tarrach T. Automatic synthesis of synchronisation primitives for concurrent programs. 2016. doi:10.15479/at:ista:1130","chicago":"Tarrach, Thorsten. “Automatic Synthesis of Synchronisation Primitives for Concurrent Programs.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/at:ista:1130.","short":"T. Tarrach, Automatic Synthesis of Synchronisation Primitives for Concurrent Programs, Institute of Science and Technology Austria, 2016.","mla":"Tarrach, Thorsten. Automatic Synthesis of Synchronisation Primitives for Concurrent Programs. Institute of Science and Technology Austria, 2016, doi:10.15479/at:ista:1130."},"page":"151","date_published":"2016-07-07T00:00:00Z","day":"07","article_processing_charge":"No","has_accepted_license":"1"},{"has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2016-08-01T00:00:00Z","citation":{"mla":"Daca, Przemyslaw, et al. Linear Distances between Markov Chains. Vol. 59, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPIcs.CONCUR.2016.20.","short":"P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","chicago":"Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov. “Linear Distances between Markov Chains,” Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPIcs.CONCUR.2016.20.","ama":"Daca P, Henzinger TA, Kretinsky J, Petrov T. Linear distances between Markov chains. In: Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPIcs.CONCUR.2016.20","ista":"Daca P, Henzinger TA, Kretinsky J, Petrov T. 2016. Linear distances between Markov chains. CONCUR: Concurrency Theory, LIPIcs, vol. 59, 20.","apa":"Daca, P., Henzinger, T. A., Kretinsky, J., & Petrov, T. (2016). Linear distances between Markov chains (Vol. 59). Presented at the CONCUR: Concurrency Theory, Quebec City; Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2016.20","ieee":"P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Linear distances between Markov chains,” presented at the CONCUR: Concurrency Theory, Quebec City; Canada, 2016, vol. 59."},"abstract":[{"text":"We introduce a general class of distances (metrics) between Markov chains, which are based on linear behaviour. This class encompasses distances given topologically (such as the total variation distance or trace distance) as well as by temporal logics or automata. We investigate which of the distances can be approximated by observing the systems, i.e. by black-box testing or simulation, and we provide both negative and positive results. ","lang":"eng"}],"type":"conference","alternative_title":["LIPIcs"],"pubrep_id":"794","file":[{"content_type":"application/pdf","file_size":501827,"creator":"system","file_name":"IST-2017-794-v1+1_LIPIcs-CONCUR-2016-20.pdf","access_level":"open_access","date_updated":"2018-12-12T10:11:39Z","date_created":"2018-12-12T10:11:39Z","relation":"main_file","file_id":"4895"}],"oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1093","intvolume":" 59","title":"Linear distances between Markov chains","status":"public","ddc":["004"],"month":"08","doi":"10.4230/LIPIcs.CONCUR.2016.20","conference":{"name":"CONCUR: Concurrency Theory","end_date":"2016-08-26","location":"Quebec City; Canada","start_date":"2016-08-23"},"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"quality_controlled":"1","ec_funded":1,"publist_id":"6283","file_date_updated":"2018-12-12T10:11:39Z","article_number":"20","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1155"}]},"author":[{"first_name":"Przemyslaw","last_name":"Daca","id":"49351290-F248-11E8-B48F-1D18A9856A87","full_name":"Daca, Przemyslaw"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"full_name":"Kretinsky, Jan","first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881"},{"first_name":"Tatjana","last_name":"Petrov","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9041-0905","full_name":"Petrov, Tatjana"}],"volume":59,"date_created":"2018-12-11T11:50:06Z","date_updated":"2023-09-07T11:58:33Z","year":"2016","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989\r\n(QUAREM), the Austrian Science Fund (FWF) under grants project S11402-N23 (RiSE and SHiNE)\r\nand Z211-N23 (Wittgenstein Award), by the Czech Science Foundation Grant No. P202/12/G061, and\r\nby the SNSF Advanced Postdoc. Mobility Fellowship – grant number P300P2_161067.","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"ToHe"},{"_id":"KrCh"},{"_id":"CaGu"}],"publication_status":"published"},{"publist_id":"6099","ec_funded":1,"acknowledgement":"This research was funded in part by the European Research Council (ERC) under\r\ngrant agreement 267989 (QUAREM), the Austrian Science Fund (FWF) under\r\ngrants project S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), the Peo-\r\nple Programme (Marie Curie Actions) of the European Union’s Seventh Framework\r\nProgramme (FP7/2007-2013) REA Grant No 291734, the SNSF Advanced Postdoc.\r\nMobility Fellowship – grant number P300P2\r\n161067, and the Czech Science Foun-\r\ndation under grant agreement P202/12/G061.","year":"2016","publication_status":"published","publisher":"Springer","department":[{"_id":"ToHe"},{"_id":"CaGu"}],"author":[{"id":"49351290-F248-11E8-B48F-1D18A9856A87","first_name":"Przemyslaw","last_name":"Daca","full_name":"Daca, Przemyslaw"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","first_name":"Jan","last_name":"Kretinsky","full_name":"Kretinsky, Jan"},{"first_name":"Tatjana","last_name":"Petrov","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9041-0905","full_name":"Petrov, Tatjana"}],"related_material":{"record":[{"id":"471","status":"public","relation":"later_version"},{"status":"public","relation":"dissertation_contains","id":"1155"}]},"date_created":"2018-12-11T11:50:51Z","date_updated":"2023-09-07T11:58:33Z","volume":9636,"month":"01","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1504.05739","open_access":"1"}],"quality_controlled":"1","project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"conference":{"end_date":"2016-04-08","start_date":"2016-04-02","location":"Eindhoven, The Netherlands","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"doi":"10.1007/978-3-662-49674-9_7","language":[{"iso":"eng"}],"type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"We present a new algorithm for the statistical model checking of Markov chains with respect to unbounded temporal properties, including full linear temporal logic. The main idea is that we monitor each simulation run on the fly, in order to detect quickly if a bottom strongly connected component is entered with high probability, in which case the simulation run can be terminated early. As a result, our simulation runs are often much shorter than required by termination bounds that are computed a priori for a desired level of confidence on a large state space. In comparison to previous algorithms for statistical model checking our method is not only faster in many cases but also requires less information about the system, namely, only the minimum transition probability that occurs in the Markov chain. In addition, our method can be generalised to unbounded quantitative properties such as mean-payoff bounds.","lang":"eng"}],"_id":"1234","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Faster statistical model checking for unbounded temporal properties","intvolume":" 9636","oa_version":"Preprint","scopus_import":1,"day":"01","citation":{"ama":"Daca P, Henzinger TA, Kretinsky J, Petrov T. Faster statistical model checking for unbounded temporal properties. In: Vol 9636. Springer; 2016:112-129. doi:10.1007/978-3-662-49674-9_7","apa":"Daca, P., Henzinger, T. A., Kretinsky, J., & Petrov, T. (2016). Faster statistical model checking for unbounded temporal properties (Vol. 9636, pp. 112–129). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Eindhoven, The Netherlands: Springer. https://doi.org/10.1007/978-3-662-49674-9_7","ieee":"P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Faster statistical model checking for unbounded temporal properties,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Eindhoven, The Netherlands, 2016, vol. 9636, pp. 112–129.","ista":"Daca P, Henzinger TA, Kretinsky J, Petrov T. 2016. Faster statistical model checking for unbounded temporal properties. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 9636, 112–129.","short":"P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, in:, Springer, 2016, pp. 112–129.","mla":"Daca, Przemyslaw, et al. Faster Statistical Model Checking for Unbounded Temporal Properties. Vol. 9636, Springer, 2016, pp. 112–29, doi:10.1007/978-3-662-49674-9_7.","chicago":"Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov. “Faster Statistical Model Checking for Unbounded Temporal Properties,” 9636:112–29. Springer, 2016. https://doi.org/10.1007/978-3-662-49674-9_7."},"page":"112 - 129","date_published":"2016-01-01T00:00:00Z"},{"publist_id":"6104","ec_funded":1,"author":[{"full_name":"Daca, Przemyslaw","first_name":"Przemyslaw","last_name":"Daca","id":"49351290-F248-11E8-B48F-1D18A9856A87"},{"id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh","last_name":"Gupta","full_name":"Gupta, Ashutosh"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"}],"related_material":{"record":[{"id":"1155","relation":"dissertation_contains","status":"public"}]},"date_updated":"2023-09-07T11:58:33Z","date_created":"2018-12-11T11:50:50Z","volume":9583,"acknowledgement":"We thank Andrey Kupriyanov for feedback on the manuscript,\r\nand Michael Tautschnig for help with preparing the experiments. This research was supported in part by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award).","year":"2016","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer","month":"01","conference":{"name":"VMCAI: Verification, Model Checking and Abstract Interpretation","end_date":"2016-01-19","location":"St. Petersburg, FL, USA","start_date":"2016-01-17"},"doi":"10.1007/978-3-662-49122-5_16","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.02615"}],"quality_controlled":"1","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"abstract":[{"text":"Concolic testing is a promising method for generating test suites for large programs. However, it suffers from the path-explosion problem and often fails to find tests that cover difficult-to-reach parts of programs. In contrast, model checkers based on counterexample-guided abstraction refinement explore programs exhaustively, while failing to scale on large programs with precision. In this paper, we present a novel method that iteratively combines concolic testing and model checking to find a test suite for a given coverage criterion. If concolic testing fails to cover some test goals, then the model checker refines its program abstraction to prove more paths infeasible, which reduces the search space for concolic testing. We have implemented our method on top of the concolictesting tool Crest and the model checker CpaChecker. We evaluated our tool on a collection of programs and a category of SvComp benchmarks. In our experiments, we observed an improvement in branch coverage compared to Crest from 48% to 63% in the best case, and from 66% to 71% on average.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1230","title":"Abstraction-driven concolic testing","status":"public","intvolume":" 9583","day":"01","scopus_import":1,"date_published":"2016-01-01T00:00:00Z","citation":{"ama":"Daca P, Gupta A, Henzinger TA. Abstraction-driven concolic testing. In: Vol 9583. Springer; 2016:328-347. doi:10.1007/978-3-662-49122-5_16","apa":"Daca, P., Gupta, A., & Henzinger, T. A. (2016). Abstraction-driven concolic testing (Vol. 9583, pp. 328–347). 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_16","ieee":"P. Daca, A. Gupta, and T. A. Henzinger, “Abstraction-driven concolic testing,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, St. Petersburg, FL, USA, 2016, vol. 9583, pp. 328–347.","ista":"Daca P, Gupta A, Henzinger TA. 2016. Abstraction-driven concolic testing. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 9583, 328–347.","short":"P. Daca, A. Gupta, T.A. Henzinger, in:, Springer, 2016, pp. 328–347.","mla":"Daca, Przemyslaw, et al. Abstraction-Driven Concolic Testing. Vol. 9583, Springer, 2016, pp. 328–47, doi:10.1007/978-3-662-49122-5_16.","chicago":"Daca, Przemyslaw, Ashutosh Gupta, and Thomas A Henzinger. “Abstraction-Driven Concolic Testing,” 9583:328–47. Springer, 2016. https://doi.org/10.1007/978-3-662-49122-5_16."},"page":"328 - 347"},{"abstract":[{"text":"We present an extension to the quantifier-free theory of integer arrays which allows us to express counting. The properties expressible in Array Folds Logic (AFL) include statements such as "the first array cell contains the array length," and "the array contains equally many minimal and maximal elements." These properties cannot be expressed in quantified fragments of the theory of arrays, nor in the theory of concatenation. Using reduction to counter machines, we show that the satisfiability problem of AFL is PSPACE-complete, and with a natural restriction the complexity decreases to NP. We also show that adding either universal quantifiers or concatenation leads to undecidability.\r\nAFL contains terms that fold a function over an array. We demonstrate that folding, a well-known concept from functional languages, allows us to concisely summarize loops that count over arrays, which occurs frequently in real-life programs. We provide a tool that can discharge proof obligations in AFL, and we demonstrate on practical examples that our decision procedure can solve a broad range of problems in symbolic testing and program verification.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Preprint","intvolume":" 9780","title":"Array folds logic","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1391","day":"13","scopus_import":1,"date_published":"2016-07-13T00:00:00Z","page":"230 - 248","citation":{"chicago":"Daca, Przemyslaw, Thomas A Henzinger, and Andrey Kupriyanov. “Array Folds Logic,” 9780:230–48. Springer, 2016. https://doi.org/10.1007/978-3-319-41540-6_13.","short":"P. Daca, T.A. Henzinger, A. Kupriyanov, in:, Springer, 2016, pp. 230–248.","mla":"Daca, Przemyslaw, et al. Array Folds Logic. Vol. 9780, Springer, 2016, pp. 230–48, doi:10.1007/978-3-319-41540-6_13.","apa":"Daca, P., Henzinger, T. A., & Kupriyanov, A. (2016). Array folds logic (Vol. 9780, pp. 230–248). Presented at the CAV: Computer Aided Verification, Toronto, Canada: Springer. https://doi.org/10.1007/978-3-319-41540-6_13","ieee":"P. Daca, T. A. Henzinger, and A. Kupriyanov, “Array folds logic,” presented at the CAV: Computer Aided Verification, Toronto, Canada, 2016, vol. 9780, pp. 230–248.","ista":"Daca P, Henzinger TA, Kupriyanov A. 2016. Array folds logic. CAV: Computer Aided Verification, LNCS, vol. 9780, 230–248.","ama":"Daca P, Henzinger TA, Kupriyanov A. Array folds logic. In: Vol 9780. Springer; 2016:230-248. doi:10.1007/978-3-319-41540-6_13"},"publist_id":"5818","ec_funded":1,"volume":9780,"date_created":"2018-12-11T11:51:45Z","date_updated":"2023-09-07T11:58:33Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1155"}]},"author":[{"full_name":"Daca, Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","last_name":"Daca","first_name":"Przemyslaw"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"id":"2C311BF8-F248-11E8-B48F-1D18A9856A87","last_name":"Kupriyanov","first_name":"Andrey","full_name":"Kupriyanov, Andrey"}],"department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","year":"2016","month":"07","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-41540-6_13","conference":{"start_date":"2016-07-17","location":"Toronto, Canada","end_date":"2016-07-23","name":"CAV: Computer Aided Verification"},"project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1603.06850","open_access":"1"}]},{"month":"02","quality_controlled":"1","project":[{"name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)","_id":"251D65D8-B435-11E9-9278-68D0E5697425","grant_number":"24210"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.cub.2015.12.041","publist_id":"6087","publication_status":"published","publisher":"Cell Press","department":[{"_id":"CaGu"}],"acknowledgement":"This work was funded by an HFSP Young Investigators’ grant. M.P. is a recipient of a DOC Fellowship of the Austrian Academy of Science at the Institute of Science and Technology Austria. R.O. and Y.W. were supported by the Platform for Dynamic Approaches to Living System from MEXT, Japan. We wish to thank I. Kobayashi for providing us with the EcoRI and EcoRV plasmids, and A. Campbell for providing us with the λ vir phage. We thank D. Siekhaus and C. Uhler and members of the C.C.G. and J.P. Bollback laboratories for in-depth discussions. We thank B. Stern for comments on an earlier version of the manuscript. We especially thank B.R. Levin for advice and comments, and the anonymous reviewers for significantly improving the manuscript.","year":"2016","date_created":"2018-12-11T11:50:54Z","date_updated":"2023-09-07T11:59:32Z","volume":26,"author":[{"orcid":"0000-0001-7460-7479","id":"4569785E-F248-11E8-B48F-1D18A9856A87","last_name":"Pleska","first_name":"Maros","full_name":"Pleska, Maros"},{"first_name":"Long","last_name":"Qian","full_name":"Qian, Long"},{"last_name":"Okura","first_name":"Reiko","full_name":"Okura, Reiko"},{"last_name":"Bergmiller","first_name":"Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias"},{"full_name":"Wakamoto, Yuichi","last_name":"Wakamoto","first_name":"Yuichi"},{"first_name":"Edo","last_name":"Kussell","full_name":"Kussell, Edo"},{"full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"202"}]},"scopus_import":1,"day":"08","page":"404 - 409","publication":"Current Biology","citation":{"ama":"Pleska M, Qian L, Okura R, et al. Bacterial autoimmunity due to a restriction-modification system. Current Biology. 2016;26(3):404-409. doi:10.1016/j.cub.2015.12.041","ista":"Pleska M, Qian L, Okura R, Bergmiller T, Wakamoto Y, Kussell E, Guet CC. 2016. Bacterial autoimmunity due to a restriction-modification system. Current Biology. 26(3), 404–409.","ieee":"M. Pleska et al., “Bacterial autoimmunity due to a restriction-modification system,” Current Biology, vol. 26, no. 3. Cell Press, pp. 404–409, 2016.","apa":"Pleska, M., Qian, L., Okura, R., Bergmiller, T., Wakamoto, Y., Kussell, E., & Guet, C. C. (2016). Bacterial autoimmunity due to a restriction-modification system. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2015.12.041","mla":"Pleska, Maros, et al. “Bacterial Autoimmunity Due to a Restriction-Modification System.” Current Biology, vol. 26, no. 3, Cell Press, 2016, pp. 404–09, doi:10.1016/j.cub.2015.12.041.","short":"M. Pleska, L. Qian, R. Okura, T. Bergmiller, Y. Wakamoto, E. Kussell, C.C. Guet, Current Biology 26 (2016) 404–409.","chicago":"Pleska, Maros, Long Qian, Reiko Okura, Tobias Bergmiller, Yuichi Wakamoto, Edo Kussell, and Calin C Guet. “Bacterial Autoimmunity Due to a Restriction-Modification System.” Current Biology. Cell Press, 2016. https://doi.org/10.1016/j.cub.2015.12.041."},"date_published":"2016-02-08T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Restriction-modification (RM) systems represent a minimal and ubiquitous biological system of self/non-self discrimination in prokaryotes [1], which protects hosts from exogenous DNA [2]. The mechanism is based on the balance between methyltransferase (M) and cognate restriction endonuclease (R). M tags endogenous DNA as self by methylating short specific DNA sequences called restriction sites, whereas R recognizes unmethylated restriction sites as non-self and introduces a double-stranded DNA break [3]. Restriction sites are significantly underrepresented in prokaryotic genomes [4-7], suggesting that the discrimination mechanism is imperfect and occasionally leads to autoimmunity due to self-DNA cleavage (self-restriction) [8]. Furthermore, RM systems can promote DNA recombination [9] and contribute to genetic variation in microbial populations, thus facilitating adaptive evolution [10]. However, cleavage of self-DNA by RM systems as elements shaping prokaryotic genomes has not been directly detected, and its cause, frequency, and outcome are unknown. We quantify self-restriction caused by two RM systems of Escherichia coli and find that, in agreement with levels of restriction site avoidance, EcoRI, but not EcoRV, cleaves self-DNA at a measurable rate. Self-restriction is a stochastic process, which temporarily induces the SOS response, and is followed by DNA repair, maintaining cell viability. We find that RM systems with higher restriction efficiency against bacteriophage infections exhibit a higher rate of self-restriction, and that this rate can be further increased by stochastic imbalance between R and M. Our results identify molecular noise in RM systems as a factor shaping prokaryotic genomes."}],"issue":"3","status":"public","title":"Bacterial autoimmunity due to a restriction-modification system","intvolume":" 26","_id":"1243","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"None"},{"year":"2016","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE) and ERC Start grant (279307: Graph Games).","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Schloss Dagstuhl- Leibniz-Zentrum fur Informatik","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","first_name":"Rasmus","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus"},{"first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"821"}]},"date_updated":"2023-09-07T12:01:58Z","date_created":"2018-12-11T11:49:59Z","volume":57,"article_number":"28","file_date_updated":"2018-12-12T10:14:31Z","ec_funded":1,"publist_id":"6312","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"conference":{"name":"ESA: European Symposium on Algorithms","location":"Aarhus, Denmark","start_date":"2016-08-22","end_date":"2016-08-24"},"doi":"10.4230/LIPIcs.ESA.2016.28","language":[{"iso":"eng"}],"month":"08","_id":"1071","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["004","006"],"title":"Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs","intvolume":" 57","pubrep_id":"777","oa_version":"Published Version","file":[{"date_created":"2018-12-12T10:14:31Z","date_updated":"2018-12-12T10:14:31Z","file_id":"5084","relation":"main_file","creator":"system","file_size":579225,"content_type":"application/pdf","file_name":"IST-2017-777-v1+1_LIPIcs-ESA-2016-28.pdf","access_level":"open_access"}],"type":"conference","alternative_title":["LIPIcs"],"abstract":[{"text":"We consider data-structures for answering reachability and distance queries on constant-treewidth graphs with n nodes, on the standard RAM computational model with wordsize W=Theta(log n). Our first contribution is a data-structure that after O(n) preprocessing time, allows (1) pair reachability queries in O(1) time; and (2) single-source reachability queries in O(n/log n) time. This is (asymptotically) optimal and is faster than DFS/BFS when answering more than a constant number of single-source queries. The data-structure uses at all times O(n) space. Our second contribution is a space-time tradeoff data-structure for distance queries. For any epsilon in [1/2,1], we provide a data-structure with polynomial preprocessing time that allows pair queries in O(n^{1-\\epsilon} alpha(n)) time, where alpha is the inverse of the Ackermann function, and at all times uses O(n^epsilon) space. The input graph G is not considered in the space complexity. ","lang":"eng"}],"citation":{"short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, in:, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik, 2016.","mla":"Chatterjee, Krishnendu, et al. Optimal Reachability and a Space Time Tradeoff for Distance Queries in Constant Treewidth Graphs. Vol. 57, 28, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik, 2016, doi:10.4230/LIPIcs.ESA.2016.28.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Optimal Reachability and a Space Time Tradeoff for Distance Queries in Constant Treewidth Graphs,” Vol. 57. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik, 2016. https://doi.org/10.4230/LIPIcs.ESA.2016.28.","ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs. In: Vol 57. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik; 2016. doi:10.4230/LIPIcs.ESA.2016.28","apa":"Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2016). Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs (Vol. 57). Presented at the ESA: European Symposium on Algorithms, Aarhus, Denmark: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik. https://doi.org/10.4230/LIPIcs.ESA.2016.28","ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs,” presented at the ESA: European Symposium on Algorithms, Aarhus, Denmark, 2016, vol. 57.","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2016. Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs. ESA: European Symposium on Algorithms, LIPIcs, vol. 57, 28."},"date_published":"2016-08-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1"},{"alternative_title":["ACM Transactions on Graphics"],"type":"conference","abstract":[{"text":"We present a boundary element based method for fast simulation of brittle fracture. By introducing simplifying assumptions that allow us to quickly estimate stress intensities and opening displacements during crack propagation, we build a fracture algorithm where the cost of each time step scales linearly with the length of the crackfront. The transition from a full boundary element method to our faster variant is possible at the beginning of any time step. This allows us to build a hybrid method, which uses the expensive but more accurate BEM while the number of degrees of freedom is low, and uses the fast method once that number exceeds a given threshold as the crack geometry becomes more complicated. Furthermore, we integrate this fracture simulation with a standard rigid-body solver. Our rigid-body coupling solves a Neumann boundary value problem by carefully separating translational, rotational and deformational components of the collision forces and then applying a Tikhonov regularizer to the resulting linear system. We show that our method produces physically reasonable results in standard test cases and is capable of dealing with complex scenes faster than previous finite- or boundary element approaches.","lang":"eng"}],"issue":"4","ddc":["000"],"title":"Fast approximations for boundary element based brittle fracture simulation","status":"public","intvolume":" 35","_id":"1362","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5121","checksum":"943712d9c9dc8bb5048d4adc561d7d38","date_updated":"2020-07-14T12:44:46Z","date_created":"2018-12-12T10:15:04Z","access_level":"open_access","file_name":"IST-2016-632-v1+2_a104-hahn.pdf","file_size":12453704,"content_type":"application/pdf","creator":"system"}],"pubrep_id":"632","day":"01","has_accepted_license":"1","citation":{"ama":"Hahn D, Wojtan C. Fast approximations for boundary element based brittle fracture simulation. In: Vol 35. ACM; 2016. doi:10.1145/2897824.2925902","ista":"Hahn D, Wojtan C. 2016. Fast approximations for boundary element based brittle fracture simulation. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 104.","ieee":"D. Hahn and C. Wojtan, “Fast approximations for boundary element based brittle fracture simulation,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4.","apa":"Hahn, D., & Wojtan, C. (2016). Fast approximations for boundary element based brittle fracture simulation (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM. https://doi.org/10.1145/2897824.2925902","mla":"Hahn, David, and Chris Wojtan. Fast Approximations for Boundary Element Based Brittle Fracture Simulation. Vol. 35, no. 4, 104, ACM, 2016, doi:10.1145/2897824.2925902.","short":"D. Hahn, C. Wojtan, in:, ACM, 2016.","chicago":"Hahn, David, and Chris Wojtan. “Fast Approximations for Boundary Element Based Brittle Fracture Simulation,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2897824.2925902."},"date_published":"2016-07-01T00:00:00Z","article_number":"104","file_date_updated":"2020-07-14T12:44:46Z","ec_funded":1,"publist_id":"5880","publication_status":"published","department":[{"_id":"ChWo"}],"publisher":"ACM","year":"2016","date_updated":"2023-09-07T12:02:56Z","date_created":"2018-12-11T11:51:35Z","volume":35,"author":[{"first_name":"David","last_name":"Hahn","id":"357A6A66-F248-11E8-B48F-1D18A9856A87","full_name":"Hahn, David"},{"orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"839"}]},"month":"07","quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"conference":{"start_date":"2016-07-24","location":"Anaheim, CA, USA","end_date":"2016-07-28","name":"ACM SIGGRAPH"},"doi":"10.1145/2897824.2925902"},{"has_accepted_license":"1","day":"09","scopus_import":1,"date_published":"2016-06-09T00:00:00Z","citation":{"chicago":"Abusalah, Hamza M, Georg Fuchsbauer, and Krzysztof Z Pietrzak. “Offline Witness Encryption,” 9696:285–303. Springer, 2016. https://doi.org/10.1007/978-3-319-39555-5_16.","short":"H.M. Abusalah, G. Fuchsbauer, K.Z. Pietrzak, in:, Springer, 2016, pp. 285–303.","mla":"Abusalah, Hamza M., et al. Offline Witness Encryption. Vol. 9696, Springer, 2016, pp. 285–303, doi:10.1007/978-3-319-39555-5_16.","apa":"Abusalah, H. M., Fuchsbauer, G., & Pietrzak, K. Z. (2016). Offline witness encryption (Vol. 9696, pp. 285–303). Presented at the ACNS: Applied Cryptography and Network Security, Guildford, UK: Springer. https://doi.org/10.1007/978-3-319-39555-5_16","ieee":"H. M. Abusalah, G. Fuchsbauer, and K. Z. Pietrzak, “Offline witness encryption,” presented at the ACNS: Applied Cryptography and Network Security, Guildford, UK, 2016, vol. 9696, pp. 285–303.","ista":"Abusalah HM, Fuchsbauer G, Pietrzak KZ. 2016. Offline witness encryption. ACNS: Applied Cryptography and Network Security, LNCS, vol. 9696, 285–303.","ama":"Abusalah HM, Fuchsbauer G, Pietrzak KZ. Offline witness encryption. In: Vol 9696. Springer; 2016:285-303. doi:10.1007/978-3-319-39555-5_16"},"page":"285 - 303","abstract":[{"lang":"eng","text":"Witness encryption (WE) was introduced by Garg et al. [GGSW13]. A WE scheme is defined for some NP language L and lets a sender encrypt messages relative to instances x. A ciphertext for x can be decrypted using w witnessing x ∈ L, but hides the message if x ∈ L. Garg et al. construct WE from multilinear maps and give another construction [GGH+13b] using indistinguishability obfuscation (iO) for circuits. Due to the reliance on such heavy tools, WE can cur- rently hardly be implemented on powerful hardware and will unlikely be realizable on constrained devices like smart cards any time soon. We construct a WE scheme where encryption is done by simply computing a Naor-Yung ciphertext (two CPA encryptions and a NIZK proof). To achieve this, our scheme has a setup phase, which outputs public parameters containing an obfuscated circuit (only required for decryption), two encryption keys and a common reference string (used for encryption). This setup need only be run once, and the parame- ters can be used for arbitrary many encryptions. Our scheme can also be turned into a functional WE scheme, where a message is encrypted w.r.t. a statement and a function f, and decryption with a witness w yields f (m, w). Our construction is inspired by the functional encryption scheme by Garg et al. and we prove (selective) security assuming iO and statistically simulation-sound NIZK. We give a construction of the latter in bilinear groups and combining it with ElGamal encryption, our ciphertexts are of size 1.3 kB at a 128-bit security level and can be computed on a smart card."}],"type":"conference","alternative_title":["LNCS"],"pubrep_id":"765","file":[{"relation":"main_file","file_id":"5273","checksum":"34fa9ce681da845a1ba945ba3dc57867","date_created":"2018-12-12T10:17:20Z","date_updated":"2020-07-14T12:44:39Z","access_level":"open_access","file_name":"IST-2017-765-v1+1_838.pdf","content_type":"application/pdf","file_size":515000,"creator":"system"}],"oa_version":"Submitted Version","_id":"1229","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 9696","title":"Offline witness encryption","status":"public","ddc":["005","600"],"month":"06","doi":"10.1007/978-3-319-39555-5_16","conference":{"name":"ACNS: Applied Cryptography and Network Security","location":"Guildford, UK","start_date":"2016-06-19","end_date":"2016-06-22"},"language":[{"iso":"eng"}],"oa":1,"project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","name":"Provable Security for Physical Cryptography","call_identifier":"FP7"},{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"quality_controlled":"1","publist_id":"6105","ec_funded":1,"file_date_updated":"2020-07-14T12:44:39Z","related_material":{"record":[{"id":"83","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Abusalah, Hamza M","first_name":"Hamza M","last_name":"Abusalah","id":"40297222-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Georg","last_name":"Fuchsbauer","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","full_name":"Fuchsbauer, Georg"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z"}],"volume":9696,"date_created":"2018-12-11T11:50:50Z","date_updated":"2023-09-07T12:30:22Z","year":"2016","acknowledgement":"Research supported by the European Research Council, ERC starting grant (259668-PSPC) and ERC consolidator grant (682815 - TOCNeT).","publisher":"Springer","department":[{"_id":"KrPi"}],"publication_status":"published"},{"date_published":"2016-02-02T00:00:00Z","citation":{"short":"H.M. Abusalah, G. Fuchsbauer, K.Z. Pietrzak, in:, Springer, 2016, pp. 413–428.","mla":"Abusalah, Hamza M., et al. Constrained PRFs for Unbounded Inputs. Vol. 9610, Springer, 2016, pp. 413–28, doi:10.1007/978-3-319-29485-8_24.","chicago":"Abusalah, Hamza M, Georg Fuchsbauer, and Krzysztof Z Pietrzak. “Constrained PRFs for Unbounded Inputs,” 9610:413–28. Springer, 2016. https://doi.org/10.1007/978-3-319-29485-8_24.","ama":"Abusalah HM, Fuchsbauer G, Pietrzak KZ. Constrained PRFs for unbounded inputs. In: Vol 9610. Springer; 2016:413-428. doi:10.1007/978-3-319-29485-8_24","ieee":"H. M. Abusalah, G. Fuchsbauer, and K. Z. Pietrzak, “Constrained PRFs for unbounded inputs,” presented at the CT-RSA: Topics in Cryptology, San Francisco, CA, USA, 2016, vol. 9610, pp. 413–428.","apa":"Abusalah, H. M., Fuchsbauer, G., & Pietrzak, K. Z. (2016). Constrained PRFs for unbounded inputs (Vol. 9610, pp. 413–428). Presented at the CT-RSA: Topics in Cryptology, San Francisco, CA, USA: Springer. https://doi.org/10.1007/978-3-319-29485-8_24","ista":"Abusalah HM, Fuchsbauer G, Pietrzak KZ. 2016. Constrained PRFs for unbounded inputs. CT-RSA: Topics in Cryptology, LNCS, vol. 9610, 413–428."},"page":"413 - 428","day":"02","has_accepted_license":"1","scopus_import":1,"pubrep_id":"764","file":[{"relation":"main_file","file_id":"4664","date_updated":"2020-07-14T12:44:41Z","date_created":"2018-12-12T10:08:05Z","checksum":"3851cee49933ae13b1272e516f213e13","file_name":"IST-2017-764-v1+1_279.pdf","access_level":"open_access","content_type":"application/pdf","file_size":495176,"creator":"system"}],"oa_version":"Submitted Version","_id":"1236","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Constrained PRFs for unbounded inputs","ddc":["005","600"],"status":"public","intvolume":" 9610","abstract":[{"lang":"eng","text":"A constrained pseudorandom function F: K × X → Y for a family T ⊆ 2X of subsets of X is a function where for any key k ∈ K and set S ∈ T one can efficiently compute a constrained key kS which allows to evaluate F (k, ·) on all inputs x ∈ S, while even given this key, the outputs on all inputs x ∉ S look random. At Asiacrypt’13 Boneh and Waters gave a construction which supports the most general set family so far. Its keys kc are defined for sets decided by boolean circuits C and enable evaluation of the PRF on any x ∈ X where C(x) = 1. In their construction the PRF input length and the size of the circuits C for which constrained keys can be computed must be fixed beforehand during key generation. We construct a constrained PRF that has an unbounded input length and whose constrained keys can be defined for any set recognized by a Turing machine. The only a priori bound we make is on the description size of the machines. We prove our construction secure assuming publiccoin differing-input obfuscation. As applications of our constrained PRF we build a broadcast encryption scheme where the number of potential receivers need not be fixed at setup (in particular, the length of the keys is independent of the number of parties) and the first identity-based non-interactive key exchange protocol with no bound on the number of parties that can agree on a shared key."}],"type":"conference","alternative_title":["LNCS"],"conference":{"name":"CT-RSA: Topics in Cryptology","location":"San Francisco, CA, USA","start_date":"2016-02-29","end_date":"2016-03-04"},"doi":"10.1007/978-3-319-29485-8_24","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","name":"Provable Security for Physical Cryptography","call_identifier":"FP7"}],"month":"02","author":[{"full_name":"Abusalah, Hamza M","last_name":"Abusalah","first_name":"Hamza M","id":"40297222-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fuchsbauer, Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","last_name":"Fuchsbauer","first_name":"Georg"},{"first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"}],"related_material":{"record":[{"id":"83","relation":"dissertation_contains","status":"public"}]},"date_created":"2018-12-11T11:50:52Z","date_updated":"2023-09-07T12:30:22Z","volume":9610,"acknowledgement":"Supported by the European Research Council, ERC Starting Grant (259668-PSPC).","year":"2016","publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Springer","file_date_updated":"2020-07-14T12:44:41Z","ec_funded":1,"publist_id":"6097"},{"author":[{"id":"40297222-F248-11E8-B48F-1D18A9856A87","last_name":"Abusalah","first_name":"Hamza M","full_name":"Abusalah, Hamza M"},{"full_name":"Fuchsbauer, Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","last_name":"Fuchsbauer","first_name":"Georg"}],"related_material":{"record":[{"id":"83","status":"public","relation":"dissertation_contains"}]},"date_updated":"2023-09-07T12:30:22Z","date_created":"2018-12-11T11:50:52Z","volume":9696,"acknowledgement":"H. Abusalah—Research supported by the European Research Council, ERC starting grant (259668-PSPC) and ERC consolidator grant (682815 - TOCNeT).","year":"2016","publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Springer","ec_funded":1,"publist_id":"6098","conference":{"name":"ACNS: Applied Cryptography and Network Security","start_date":"2016-06-19","location":"Guildford, UK","end_date":"2016-06-22"},"doi":"10.1007/978-3-319-39555-5_24","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://eprint.iacr.org/2016/279.pdf","open_access":"1"}],"oa":1,"quality_controlled":"1","project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","call_identifier":"FP7","name":"Provable Security for Physical Cryptography"},{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"month":"01","oa_version":"Submitted Version","_id":"1235","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Constrained PRFs for unbounded inputs with short keys","intvolume":" 9696","abstract":[{"text":"A constrained pseudorandom function (CPRF) F: K×X → Y for a family T of subsets of χ is a function where for any key k ∈ K and set S ∈ T one can efficiently compute a short constrained key kS, which allows to evaluate F(k, ·) on all inputs x ∈ S, while the outputs on all inputs x /∈ S look random even given kS. Abusalah et al. recently constructed the first constrained PRF for inputs of arbitrary length whose sets S are decided by Turing machines. They use their CPRF to build broadcast encryption and the first ID-based non-interactive key exchange for an unbounded number of users. Their constrained keys are obfuscated circuits and are therefore large. In this work we drastically reduce the key size and define a constrained key for a Turing machine M as a short signature on M. For this, we introduce a new signature primitive with constrained signing keys that let one only sign certain messages, while forging a signature on others is hard even when knowing the coins for key generation.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"date_published":"2016-01-01T00:00:00Z","citation":{"ama":"Abusalah HM, Fuchsbauer G. Constrained PRFs for unbounded inputs with short keys. In: Vol 9696. Springer; 2016:445-463. doi:10.1007/978-3-319-39555-5_24","ista":"Abusalah HM, Fuchsbauer G. 2016. Constrained PRFs for unbounded inputs with short keys. ACNS: Applied Cryptography and Network Security, LNCS, vol. 9696, 445–463.","apa":"Abusalah, H. M., & Fuchsbauer, G. (2016). Constrained PRFs for unbounded inputs with short keys (Vol. 9696, pp. 445–463). Presented at the ACNS: Applied Cryptography and Network Security, Guildford, UK: Springer. https://doi.org/10.1007/978-3-319-39555-5_24","ieee":"H. M. Abusalah and G. Fuchsbauer, “Constrained PRFs for unbounded inputs with short keys,” presented at the ACNS: Applied Cryptography and Network Security, Guildford, UK, 2016, vol. 9696, pp. 445–463.","mla":"Abusalah, Hamza M., and Georg Fuchsbauer. Constrained PRFs for Unbounded Inputs with Short Keys. Vol. 9696, Springer, 2016, pp. 445–63, doi:10.1007/978-3-319-39555-5_24.","short":"H.M. Abusalah, G. Fuchsbauer, in:, Springer, 2016, pp. 445–463.","chicago":"Abusalah, Hamza M, and Georg Fuchsbauer. “Constrained PRFs for Unbounded Inputs with Short Keys,” 9696:445–63. Springer, 2016. https://doi.org/10.1007/978-3-319-39555-5_24."},"page":"445 - 463","day":"01","scopus_import":1},{"oa_version":"Submitted Version","file":[{"checksum":"26da07960e57ac4750b54179197ce57f","date_created":"2018-12-12T10:17:03Z","date_updated":"2020-07-14T12:44:55Z","file_id":"5255","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":1268662,"access_level":"open_access","file_name":"IST-2017-840-v1+1_reichhart.pdf"}],"pubrep_id":"840","title":"A phytochrome sensory domain permits receptor activation by red light","ddc":["571","576"],"status":"public","intvolume":" 55","_id":"1441","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Optogenetics and photopharmacology enable the spatio-temporal control of cell and animal behavior by light. Although red light offers deep-tissue penetration and minimal phototoxicity, very few red-light-sensitive optogenetic methods are currently available. We have now developed a red-light-induced homodimerization domain. We first showed that an optimized sensory domain of the cyanobacterial phytochrome 1 can be expressed robustly and without cytotoxicity in human cells. We then applied this domain to induce the dimerization of two receptor tyrosine kinases—the fibroblast growth factor receptor 1 and the neurotrophin receptor trkB. This new optogenetic method was then used to activate the MAPK/ERK pathway non-invasively in mammalian tissue and in multicolor cell-signaling experiments. The light-controlled dimerizer and red-light-activated receptor tyrosine kinases will prove useful to regulate a variety of cellular processes with light. Go deep with red: The sensory domain (S) of the cyanobacterial phytochrome 1 (CPH1) was repurposed to induce the homodimerization of proteins in living cells by red light. By using this domain, light-activated protein kinases were engineered that can be activated orthogonally from many fluorescent proteins and through mammalian tissue. Pr/Pfr=red-/far-red-absorbing state of CPH1.","lang":"eng"}],"issue":"21","type":"journal_article","date_published":"2016-05-17T00:00:00Z","page":"6339 - 6342","publication":"Angewandte Chemie - International Edition","citation":{"ama":"Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL. A phytochrome sensory domain permits receptor activation by red light. Angewandte Chemie - International Edition. 2016;55(21):6339-6342. doi:10.1002/anie.201601736","ista":"Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL. 2016. A phytochrome sensory domain permits receptor activation by red light. Angewandte Chemie - International Edition. 55(21), 6339–6342.","ieee":"E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, and H. L. Janovjak, “A phytochrome sensory domain permits receptor activation by red light,” Angewandte Chemie - International Edition, vol. 55, no. 21. Wiley, pp. 6339–6342, 2016.","apa":"Gschaider-Reichhart, E., Inglés Prieto, Á., Tichy, A.-M., Mckenzie, C., & Janovjak, H. L. (2016). A phytochrome sensory domain permits receptor activation by red light. Angewandte Chemie - International Edition. Wiley. https://doi.org/10.1002/anie.201601736","mla":"Gschaider-Reichhart, Eva, et al. “A Phytochrome Sensory Domain Permits Receptor Activation by Red Light.” Angewandte Chemie - International Edition, vol. 55, no. 21, Wiley, 2016, pp. 6339–42, doi:10.1002/anie.201601736.","short":"E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, H.L. Janovjak, Angewandte Chemie - International Edition 55 (2016) 6339–6342.","chicago":"Gschaider-Reichhart, Eva, Álvaro Inglés Prieto, Alexandra-Madelaine Tichy, Catherine Mckenzie, and Harald L Janovjak. “A Phytochrome Sensory Domain Permits Receptor Activation by Red Light.” Angewandte Chemie - International Edition. Wiley, 2016. https://doi.org/10.1002/anie.201601736."},"day":"17","has_accepted_license":"1","scopus_import":1,"date_created":"2018-12-11T11:52:02Z","date_updated":"2023-09-07T12:49:08Z","volume":55,"author":[{"orcid":"0000-0002-7218-7738","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","last_name":"Gschaider-Reichhart","first_name":"Eva","full_name":"Gschaider-Reichhart, Eva"},{"first_name":"Álvaro","last_name":"Inglés Prieto","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5409-8571","full_name":"Inglés Prieto, Álvaro"},{"full_name":"Tichy, Alexandra-Madelaine","first_name":"Alexandra-Madelaine","last_name":"Tichy","id":"29D8BB2C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mckenzie, Catherine","last_name":"Mckenzie","first_name":"Catherine","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","first_name":"Harald L"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"418"}]},"publication_status":"published","publisher":"Wiley","department":[{"_id":"HaJa"}],"acknowledgement":"A.I.-P. was supported by a Ramon Areces fellowship, and E.R. by the graduate program MolecularDrugTargets (Austrian Science Fund (FWF): W1232) and a FemTech fellowship (Austrian Research Promotion Agency: 3580812).","year":"2016","file_date_updated":"2020-07-14T12:44:55Z","publist_id":"5755","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1002/anie.201601736","quality_controlled":"1","project":[{"_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology","call_identifier":"FP7"},{"name":"Molecular Drug Targets","call_identifier":"FWF","_id":"255A6082-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24"}],"oa":1,"month":"05"},{"scopus_import":1,"day":"04","has_accepted_license":"1","publication":"Nature Communications","citation":{"ama":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 2016;7. doi:10.1038/ncomms12307","ieee":"T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkačik, “Intrinsic limits to gene regulation by global crosstalk,” Nature Communications, vol. 7. Nature Publishing Group, 2016.","apa":"Friedlander, T., Prizak, R., Guet, C. C., Barton, N. H., & Tkačik, G. (2016). Intrinsic limits to gene regulation by global crosstalk. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms12307","ista":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. 2016. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 7, 12307.","short":"T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications 7 (2016).","mla":"Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature Communications, vol. 7, 12307, Nature Publishing Group, 2016, doi:10.1038/ncomms12307.","chicago":"Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and Gašper Tkačik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms12307."},"date_published":"2016-08-04T00:00:00Z","type":"journal_article","abstract":[{"text":"Gene regulation relies on the specificity of transcription factor (TF)–DNA interactions. Limited specificity may lead to crosstalk: a regulatory state in which a gene is either incorrectly activated due to noncognate TF–DNA interactions or remains erroneously inactive. As each TF can have numerous interactions with noncognate cis-regulatory elements, crosstalk is inherently a global problem, yet has previously not been studied as such. We construct a theoretical framework to analyse the effects of global crosstalk on gene regulation. We find that crosstalk presents a significant challenge for organisms with low-specificity TFs, such as metazoans. Crosstalk is not easily mitigated by known regulatory schemes acting at equilibrium, including variants of cooperativity and combinatorial regulation. Our results suggest that crosstalk imposes a previously unexplored global constraint on the functioning and evolution of regulatory networks, which is qualitatively distinct from the known constraints that act at the level of individual gene regulatory elements.","lang":"eng"}],"title":"Intrinsic limits to gene regulation by global crosstalk","status":"public","ddc":["576"],"intvolume":" 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Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"},{"grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/ncomms12307","article_number":"12307","file_date_updated":"2020-07-14T12:44:46Z","ec_funded":1,"publist_id":"5887","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"GaTk"},{"_id":"NiBa"},{"_id":"CaGu"}],"year":"2016","date_created":"2018-12-11T11:51:34Z","date_updated":"2023-09-07T12:53:49Z","volume":7,"author":[{"full_name":"Friedlander, Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","first_name":"Tamar","last_name":"Friedlander"},{"first_name":"Roshan","last_name":"Prizak","id":"4456104E-F248-11E8-B48F-1D18A9856A87","full_name":"Prizak, Roshan"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"}],"related_material":{"record":[{"id":"6071","status":"public","relation":"dissertation_contains"}]}},{"month":"06","doi":"10.1038/ncomms11710","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"file_date_updated":"2020-07-14T12:44:45Z","publist_id":"5906","ec_funded":1,"article_number":"11710","author":[{"last_name":"Dejonghe","first_name":"Wim","full_name":"Dejonghe, Wim"},{"full_name":"Kuenen, Sabine","first_name":"Sabine","last_name":"Kuenen"},{"first_name":"Evelien","last_name":"Mylle","full_name":"Mylle, Evelien"},{"full_name":"Vasileva, Mina K","id":"3407EB18-F248-11E8-B48F-1D18A9856A87","first_name":"Mina K","last_name":"Vasileva"},{"last_name":"Keech","first_name":"Olivier","full_name":"Keech, Olivier"},{"first_name":"Corrado","last_name":"Viotti","full_name":"Viotti, Corrado"},{"full_name":"Swerts, Jef","last_name":"Swerts","first_name":"Jef"},{"id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","first_name":"Matyas","last_name":"Fendrych","full_name":"Fendrych, Matyas"},{"first_name":"Fausto","last_name":"Ortiz Morea","full_name":"Ortiz Morea, Fausto"},{"last_name":"Mishev","first_name":"Kiril","full_name":"Mishev, Kiril"},{"full_name":"Delang, Simon","last_name":"Delang","first_name":"Simon"},{"full_name":"Scholl, Stefan","last_name":"Scholl","first_name":"Stefan"},{"last_name":"Zarza","first_name":"Xavier","full_name":"Zarza, Xavier"},{"full_name":"Heilmann, Mareike","last_name":"Heilmann","first_name":"Mareike"},{"full_name":"Kourelis, Jiorgos","last_name":"Kourelis","first_name":"Jiorgos"},{"full_name":"Kasprowicz, Jaroslaw","first_name":"Jaroslaw","last_name":"Kasprowicz"},{"last_name":"Nguyen","first_name":"Le","full_name":"Nguyen, Le"},{"full_name":"Drozdzecki, Andrzej","last_name":"Drozdzecki","first_name":"Andrzej"},{"first_name":"Isabelle","last_name":"Van Houtte","full_name":"Van Houtte, Isabelle"},{"full_name":"Szatmári, Anna","last_name":"Szatmári","first_name":"Anna"},{"full_name":"Majda, Mateusz","first_name":"Mateusz","last_name":"Majda"},{"full_name":"Baisa, Gary","first_name":"Gary","last_name":"Baisa"},{"full_name":"Bednarek, Sebastian","first_name":"Sebastian","last_name":"Bednarek"},{"last_name":"Robert","first_name":"Stéphanie","full_name":"Robert, Stéphanie"},{"full_name":"Audenaert, Dominique","first_name":"Dominique","last_name":"Audenaert"},{"full_name":"Testerink, Christa","last_name":"Testerink","first_name":"Christa"},{"last_name":"Munnik","first_name":"Teun","full_name":"Munnik, Teun"},{"last_name":"Van Damme","first_name":"Daniël","full_name":"Van Damme, Daniël"},{"full_name":"Heilmann, Ingo","first_name":"Ingo","last_name":"Heilmann"},{"first_name":"Karin","last_name":"Schumacher","full_name":"Schumacher, Karin"},{"first_name":"Johan","last_name":"Winne","full_name":"Winne, Johan"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí"},{"full_name":"Verstreken, Patrik","last_name":"Verstreken","first_name":"Patrik"},{"full_name":"Russinova, Eugenia","first_name":"Eugenia","last_name":"Russinova"}],"related_material":{"record":[{"id":"7172","relation":"dissertation_contains","status":"public"}]},"date_updated":"2023-09-07T12:54:35Z","date_created":"2018-12-11T11:51:30Z","volume":7,"acknowledgement":"We thank Yvon Jaillais, Ikuko Hara-Nishimura, Akihiko Nakano, Takashi Ueda and Jinxing Lin for providing materials, Natasha Raikhel, Glenn Hicks, Steffen Vanneste, and Ricardo Tejos for useful suggestions, Patrick Callaerts for providing S2 Drosophila cell cultures, Michael Sixt for providing HeLa cells, Annick Bleys for literature searches, VIB Bio Imaging Core for help with imaging conditions and Martine De Cock for help in preparing the article. This work was supported by the Agency for Innovation by Science\r\nand Technology for a pre-doctoral fellowship to W.D.; the Research fund KU Leuven\r\n(GOA), a Methusalem grant of the Flemish government and VIB to S.K., J.K. and P.V.;\r\nby the Netherlands Organisation for Scientific Research (NWO) for ALW grants\r\n846.11.002 (C.T.) and 867.15.020 (T.M.); the European Research Council (project\r\nERC-2011-StG-20101109 PSDP) (to J.F.); a European Research Council (ERC) Starting\r\nGrant (grant 260678) (to P.V.), the Research Foundation-Flanders (grants G.0747.09,\r\nG094011 and G095511) (to P.V.), the Hercules Foundation, an Interuniversity Attraction\r\nPoles Poles Program, initiated by the Belgian State, Science Policy Office (to P.V.),\r\nthe Swedish VetenskapsRådet grant to O.K., the Ghent University ‘Bijzonder\r\nOnderzoek Fonds’ (BOF) for a predoctoral fellowship to F.A.O.-M., the Research\r\nFoundation-Flanders (FWO) to K.M. and E.R.","year":"2016","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Nature Publishing Group","day":"08","has_accepted_license":"1","scopus_import":1,"date_published":"2016-06-08T00:00:00Z","publication":"Nature Communications","citation":{"short":"W. Dejonghe, S. Kuenen, E. Mylle, M.K. Vasileva, O. Keech, C. Viotti, J. Swerts, M. Fendrych, F. Ortiz Morea, K. Mishev, S. Delang, S. Scholl, X. Zarza, M. Heilmann, J. Kourelis, J. Kasprowicz, L. Nguyen, A. Drozdzecki, I. Van Houtte, A. Szatmári, M. Majda, G. Baisa, S. Bednarek, S. Robert, D. Audenaert, C. Testerink, T. Munnik, D. Van Damme, I. Heilmann, K. Schumacher, J. Winne, J. Friml, P. Verstreken, E. Russinova, Nature Communications 7 (2016).","mla":"Dejonghe, Wim, et al. “Mitochondrial Uncouplers Inhibit Clathrin-Mediated Endocytosis Largely through Cytoplasmic Acidification.” Nature Communications, vol. 7, 11710, Nature Publishing Group, 2016, doi:10.1038/ncomms11710.","chicago":"Dejonghe, Wim, Sabine Kuenen, Evelien Mylle, Mina K Vasileva, Olivier Keech, Corrado Viotti, Jef Swerts, et al. “Mitochondrial Uncouplers Inhibit Clathrin-Mediated Endocytosis Largely through Cytoplasmic Acidification.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms11710.","ama":"Dejonghe W, Kuenen S, Mylle E, et al. Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification. Nature Communications. 2016;7. doi:10.1038/ncomms11710","ieee":"W. Dejonghe et al., “Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification,” Nature Communications, vol. 7. Nature Publishing Group, 2016.","apa":"Dejonghe, W., Kuenen, S., Mylle, E., Vasileva, M. K., Keech, O., Viotti, C., … Russinova, E. (2016). Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms11710","ista":"Dejonghe W, Kuenen S, Mylle E, Vasileva MK, Keech O, Viotti C, Swerts J, Fendrych M, Ortiz Morea F, Mishev K, Delang S, Scholl S, Zarza X, Heilmann M, Kourelis J, Kasprowicz J, Nguyen L, Drozdzecki A, Van Houtte I, Szatmári A, Majda M, Baisa G, Bednarek S, Robert S, Audenaert D, Testerink C, Munnik T, Van Damme D, Heilmann I, Schumacher K, Winne J, Friml J, Verstreken P, Russinova E. 2016. Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification. Nature Communications. 7, 11710."},"abstract":[{"lang":"eng","text":"ATP production requires the establishment of an electrochemical proton gradient across the inner mitochondrial membrane. Mitochondrial uncouplers dissipate this proton gradient and disrupt numerous cellular processes, including vesicular trafficking, mainly through energy depletion. Here we show that Endosidin9 (ES9), a novel mitochondrial uncoupler, is a potent inhibitor of clathrin-mediated endocytosis (CME) in different systems and that ES9 induces inhibition of CME not because of its effect on cellular ATP, but rather due to its protonophore activity that leads to cytoplasm acidification. We show that the known tyrosine kinase inhibitor tyrphostinA23, which is routinely used to block CME, displays similar properties, thus questioning its use as a specific inhibitor of cargo recognition by the AP-2 adaptor complex via tyrosine motif-based endocytosis signals. Furthermore, we show that cytoplasm acidification dramatically affects the dynamics and recruitment of clathrin and associated adaptors, and leads to reduction of phosphatidylinositol 4,5-biphosphate from the plasma membrane."}],"type":"journal_article","pubrep_id":"653","file":[{"file_size":3532505,"content_type":"application/pdf","creator":"system","file_name":"IST-2016-653-v1+1_ncomms11710_1_.pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:45Z","date_created":"2018-12-12T10:18:47Z","checksum":"e8dc81b3e44db5a7718d7f1501ce1aa7","relation":"main_file","file_id":"5369"}],"oa_version":"Published Version","_id":"1346","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification","status":"public","ddc":["570"],"intvolume":" 7"},{"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7186"}]},"author":[{"full_name":"Schwayer, Cornelia","last_name":"Schwayer","first_name":"Cornelia","orcid":"0000-0001-5130-2226","id":"3436488C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mateusz K","last_name":"Sikora","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","full_name":"Sikora, Mateusz K"},{"first_name":"Jana","last_name":"Slovakova","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","full_name":"Slovakova, Jana"},{"first_name":"Roland","last_name":"Kardos","id":"4039350E-F248-11E8-B48F-1D18A9856A87","full_name":"Kardos, Roland"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"oa_version":"None","volume":37,"date_created":"2018-12-11T11:50:07Z","date_updated":"2023-09-07T12:56:41Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1096","year":"2016","department":[{"_id":"CaHe"}],"publisher":"Cell Press","intvolume":" 37","publication_status":"published","status":"public","title":"Actin rings of power","publist_id":"6279","issue":"6","type":"journal_article","doi":"10.1016/j.devcel.2016.05.024","date_published":"2016-06-20T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ama":"Schwayer C, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. Actin rings of power. Developmental Cell. 2016;37(6):493-506. doi:10.1016/j.devcel.2016.05.024","ieee":"C. Schwayer, M. K. Sikora, J. Slovakova, R. Kardos, and C.-P. J. Heisenberg, “Actin rings of power,” Developmental Cell, vol. 37, no. 6. Cell Press, pp. 493–506, 2016.","apa":"Schwayer, C., Sikora, M. K., Slovakova, J., Kardos, R., & Heisenberg, C.-P. J. (2016). Actin rings of power. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2016.05.024","ista":"Schwayer C, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. 2016. Actin rings of power. Developmental Cell. 37(6), 493–506.","short":"C. Schwayer, M.K. Sikora, J. Slovakova, R. Kardos, C.-P.J. Heisenberg, Developmental Cell 37 (2016) 493–506.","mla":"Schwayer, Cornelia, et al. “Actin Rings of Power.” Developmental Cell, vol. 37, no. 6, Cell Press, 2016, pp. 493–506, doi:10.1016/j.devcel.2016.05.024.","chicago":"Schwayer, Cornelia, Mateusz K Sikora, Jana Slovakova, Roland Kardos, and Carl-Philipp J Heisenberg. “Actin Rings of Power.” Developmental Cell. Cell Press, 2016. https://doi.org/10.1016/j.devcel.2016.05.024."},"publication":"Developmental Cell","page":"493 - 506","quality_controlled":"1","day":"20","month":"06","scopus_import":1},{"month":"09","project":[{"name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","call_identifier":"FP7","_id":"25517E86-B435-11E9-9278-68D0E5697425","grant_number":"335497"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1021/acs.nanolett.6b02715","ec_funded":1,"publist_id":"5941","file_date_updated":"2020-07-14T12:44:44Z","department":[{"_id":"GeKa"}],"publisher":"American Chemical Society","publication_status":"published","year":"2016","acknowledgement":"The work was supported by the EC FP7 ICT project SiSPIN no. 323841, the EC FP7 ICT project PAMS no. 610446, the ERC Starting Grant no. 335497, the FWF-I-1190-N20 project, and the Swiss NSF. We acknowledge F. Schäffler for fruitful discussions related to the hut wire growth and for giving us access to the molecular beam epitaxy system, M. Schatzl for her support in electron beam lithography, and V. Jadris ̌ko for helping us with the COMSOL simulations. Finally, we thank G. Bauer for his continuous support. ","volume":16,"date_created":"2018-12-11T11:51:24Z","date_updated":"2023-09-07T13:15:02Z","related_material":{"record":[{"id":"7977","relation":"popular_science","status":"for_moderation"},{"status":"public","relation":"dissertation_contains","id":"7996"}]},"author":[{"first_name":"Hannes","last_name":"Watzinger","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","full_name":"Watzinger, Hannes"},{"last_name":"Kloeffel","first_name":"Christoph","full_name":"Kloeffel, Christoph"},{"full_name":"Vukusic, Lada","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2424-8636","first_name":"Lada","last_name":"Vukusic"},{"full_name":"Rossell, Marta","first_name":"Marta","last_name":"Rossell"},{"last_name":"Sessi","first_name":"Violetta","full_name":"Sessi, Violetta"},{"full_name":"Kukucka, Josip","first_name":"Josip","last_name":"Kukucka","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Raimund","last_name":"Kirchschlager","full_name":"Kirchschlager, Raimund"},{"first_name":"Elisabeth","last_name":"Lausecker","id":"33662F76-F248-11E8-B48F-1D18A9856A87","full_name":"Lausecker, Elisabeth"},{"last_name":"Truhlar","first_name":"Alisha","id":"49CBC780-F248-11E8-B48F-1D18A9856A87","full_name":"Truhlar, Alisha"},{"first_name":"Martin","last_name":"Glaser","full_name":"Glaser, Martin"},{"first_name":"Armando","last_name":"Rastelli","full_name":"Rastelli, Armando"},{"full_name":"Fuhrer, Andreas","first_name":"Andreas","last_name":"Fuhrer"},{"last_name":"Loss","first_name":"Daniel","full_name":"Loss, Daniel"},{"first_name":"Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}],"scopus_import":1,"has_accepted_license":"1","day":"22","page":"6879 - 6885","citation":{"chicago":"Watzinger, Hannes, Christoph Kloeffel, Lada Vukušić, Marta Rossell, Violetta Sessi, Josip Kukucka, Raimund Kirchschlager, et al. “Heavy-Hole States in Germanium Hut Wires.” Nano Letters. American Chemical Society, 2016. https://doi.org/10.1021/acs.nanolett.6b02715.","short":"H. Watzinger, C. Kloeffel, L. Vukušić, M. Rossell, V. Sessi, J. Kukucka, R. Kirchschlager, E. Lausecker, A. Truhlar, M. Glaser, A. Rastelli, A. Fuhrer, D. Loss, G. Katsaros, Nano Letters 16 (2016) 6879–6885.","mla":"Watzinger, Hannes, et al. “Heavy-Hole States in Germanium Hut Wires.” Nano Letters, vol. 16, no. 11, American Chemical Society, 2016, pp. 6879–85, doi:10.1021/acs.nanolett.6b02715.","ieee":"H. Watzinger et al., “Heavy-hole states in germanium hut wires,” Nano Letters, vol. 16, no. 11. American Chemical Society, pp. 6879–6885, 2016.","apa":"Watzinger, H., Kloeffel, C., Vukušić, L., Rossell, M., Sessi, V., Kukucka, J., … Katsaros, G. (2016). Heavy-hole states in germanium hut wires. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.6b02715","ista":"Watzinger H, Kloeffel C, Vukušić L, Rossell M, Sessi V, Kukucka J, Kirchschlager R, Lausecker E, Truhlar A, Glaser M, Rastelli A, Fuhrer A, Loss D, Katsaros G. 2016. Heavy-hole states in germanium hut wires. Nano Letters. 16(11), 6879–6885.","ama":"Watzinger H, Kloeffel C, Vukušić L, et al. Heavy-hole states in germanium hut wires. Nano Letters. 2016;16(11):6879-6885. doi:10.1021/acs.nanolett.6b02715"},"publication":"Nano Letters","date_published":"2016-09-22T00:00:00Z","type":"journal_article","issue":"11","abstract":[{"text":"Hole spins have gained considerable interest in the past few years due to their potential for fast electrically controlled qubits. Here, we study holes confined in Ge hut wires, a so-far unexplored type of nanostructure. Low-temperature magnetotransport measurements reveal a large anisotropy between the in-plane and out-of-plane g-factors of up to 18. Numerical simulations verify that this large anisotropy originates from a confined wave function of heavy-hole character. A light-hole admixture of less than 1% is estimated for the states of lowest energy, leading to a surprisingly large reduction of the out-of-plane g-factors compared with those for pure heavy holes. Given this tiny light-hole contribution, the spin lifetimes are expected to be very long, even in isotopically nonpurified samples.","lang":"eng"}],"intvolume":" 16","ddc":["539"],"status":"public","title":"Heavy-hole states in germanium hut wires","_id":"1328","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"checksum":"b63feece90d7b620ece49ca632e34ff3","date_updated":"2020-07-14T12:44:44Z","date_created":"2018-12-12T10:14:04Z","file_id":"5053","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":535121,"access_level":"open_access","file_name":"IST-2016-664-v1+1_acs.nanolett.6b02715.pdf"}],"pubrep_id":"664"},{"file":[{"file_id":"4673","relation":"main_file","checksum":"fea0b3fae9a2a42e8bfec59840e30d8c","date_updated":"2020-07-14T12:44:39Z","date_created":"2018-12-12T10:08:13Z","access_level":"open_access","file_name":"IST-2017-783-v1+1_FM-Safety-Assured-Development-of-MVBC.pdf","creator":"system","file_size":281501,"content_type":"application/pdf"}],"oa_version":"Submitted Version","pubrep_id":"783","status":"public","ddc":["004"],"title":"Safety assured formal model driven design of the multifunction vehicle bus controller","intvolume":" 9995","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1205","abstract":[{"text":"In this paper, we present a formal model-driven engineering approach to establishing a safety-assured implementation of Multifunction vehicle bus controller (MVBC) based on the generic reference models and requirements described in the International Electrotechnical Commission (IEC) standard IEC-61375. First, the generic models described in IEC-61375 are translated into a network of timed automata, and some safety requirements tested in IEC-61375 are formalized as timed computation tree logic (TCTL) formulas. With the help of Uppaal, we check and debug whether the timed automata satisfy the formulas or not. Within this step, several logic inconsistencies in the original standard are detected and corrected. Then, we apply the tool Times to generate C code from the verified model, which was later synthesized into a real MVBC chip. Finally, the runtime verification tool RMOR is applied to verify some safety requirements at the implementation level. We set up a real platform with worldwide mostly used MVBC D113, and verify the correctness and the scalability of the synthesized MVBC chip more comprehensively. The errors in the standard has been confirmed and the resulted MVBC has been deployed in real train communication network.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","date_published":"2016-11-08T00:00:00Z","page":"757 - 763","citation":{"ieee":"Y. Jiang et al., “Safety assured formal model driven design of the multifunction vehicle bus controller,” presented at the FM: International Symposium on Formal Methods, Limassol, Cyprus, 2016, vol. 9995, pp. 757–763.","apa":"Jiang, Y., Liu, H., Song, H., Kong, H., Gu, M., Sun, J., & Sha, L. (2016). Safety assured formal model driven design of the multifunction vehicle bus controller (Vol. 9995, pp. 757–763). Presented at the FM: International Symposium on Formal Methods, Limassol, Cyprus: Springer. https://doi.org/10.1007/978-3-319-48989-6_47","ista":"Jiang Y, Liu H, Song H, Kong H, Gu M, Sun J, Sha L. 2016. Safety assured formal model driven design of the multifunction vehicle bus controller. FM: International Symposium on Formal Methods, LNCS, vol. 9995, 757–763.","ama":"Jiang Y, Liu H, Song H, et al. Safety assured formal model driven design of the multifunction vehicle bus controller. In: Vol 9995. Springer; 2016:757-763. doi:10.1007/978-3-319-48989-6_47","chicago":"Jiang, Yu, Han Liu, Houbing Song, Hui Kong, Ming Gu, Jiaguang Sun, and Lui Sha. “Safety Assured Formal Model Driven Design of the Multifunction Vehicle Bus Controller,” 9995:757–63. Springer, 2016. https://doi.org/10.1007/978-3-319-48989-6_47.","short":"Y. Jiang, H. Liu, H. Song, H. Kong, M. Gu, J. Sun, L. Sha, in:, Springer, 2016, pp. 757–763.","mla":"Jiang, Yu, et al. Safety Assured Formal Model Driven Design of the Multifunction Vehicle Bus Controller. Vol. 9995, Springer, 2016, pp. 757–63, doi:10.1007/978-3-319-48989-6_47."},"day":"08","has_accepted_license":"1","scopus_import":1,"date_created":"2018-12-11T11:50:42Z","date_updated":"2023-09-18T08:12:48Z","volume":9995,"author":[{"full_name":"Jiang, Yu","first_name":"Yu","last_name":"Jiang"},{"first_name":"Han","last_name":"Liu","full_name":"Liu, Han"},{"first_name":"Houbing","last_name":"Song","full_name":"Song, Houbing"},{"full_name":"Kong, Hui","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3066-6941","first_name":"Hui","last_name":"Kong"},{"full_name":"Gu, Ming","first_name":"Ming","last_name":"Gu"},{"full_name":"Sun, Jiaguang","first_name":"Jiaguang","last_name":"Sun"},{"first_name":"Lui","last_name":"Sha","full_name":"Sha, Lui"}],"related_material":{"record":[{"id":"434","relation":"later_version","status":"public"}]},"publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer","acknowledgement":"This research is sponsored in part by NSFC Program (No. 91218302, No. 61527812), National Science and Technology Major Project (No. 2016ZX01038101), Tsinghua University Initiative Scientific Research Program (20131089331), MIIT IT funds (Research and application of TCN key technologies) of China, and the National Key Technology R&D Program (No. 2015BAG14B01-02), Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE) and Z211-N23.\r\n","year":"2016","file_date_updated":"2020-07-14T12:44:39Z","publist_id":"6144","language":[{"iso":"eng"}],"conference":{"location":"Limassol, Cyprus","start_date":"2016-11-09","end_date":"2016-11-11","name":"FM: International Symposium on Formal Methods"},"doi":"10.1007/978-3-319-48989-6_47","quality_controlled":"1","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"oa":1,"month":"11"},{"scopus_import":1,"article_processing_charge":"No","day":"15","citation":{"ama":"Kolmogorov V. Commutativity in the algorithmic Lovasz local lemma. In: Proceedings - Annual IEEE Symposium on Foundations of Computer Science. Vol 2016-December. IEEE; 2016. doi:10.1109/FOCS.2016.88","ista":"Kolmogorov V. 2016. Commutativity in the algorithmic Lovasz local lemma. Proceedings - Annual IEEE Symposium on Foundations of Computer Science. FOCS: Foundations of Computer Science vol. 2016–December, 7782993.","ieee":"V. Kolmogorov, “Commutativity in the algorithmic Lovasz local lemma,” in Proceedings - Annual IEEE Symposium on Foundations of Computer Science, New Brunswick, NJ, USA , 2016, vol. 2016–December.","apa":"Kolmogorov, V. (2016). Commutativity in the algorithmic Lovasz local lemma. In Proceedings - Annual IEEE Symposium on Foundations of Computer Science (Vol. 2016–December). New Brunswick, NJ, USA : IEEE. https://doi.org/10.1109/FOCS.2016.88","mla":"Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovasz Local Lemma.” Proceedings - Annual IEEE Symposium on Foundations of Computer Science, vol. 2016–December, 7782993, IEEE, 2016, doi:10.1109/FOCS.2016.88.","short":"V. Kolmogorov, in:, Proceedings - Annual IEEE Symposium on Foundations of Computer Science, IEEE, 2016.","chicago":"Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovasz Local Lemma.” In Proceedings - Annual IEEE Symposium on Foundations of Computer Science, Vol. 2016–December. IEEE, 2016. https://doi.org/10.1109/FOCS.2016.88."},"publication":"Proceedings - Annual IEEE Symposium on Foundations of Computer Science","date_published":"2016-12-15T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"We consider the recent formulation of the Algorithmic Lovász Local Lemma [1], [2] for finding objects that avoid "bad features", or "flaws". It extends the Moser-Tardos resampling algorithm [3] to more general discrete spaces. At each step the method picks a flaw present in the current state and "resamples" it using a "resampling oracle" provided by the user. However, it is less flexible than the Moser-Tardos method since [1], [2] require a specific flaw selection rule, whereas [3] allows an arbitrary rule (and thus can potentially be implemented more efficiently). We formulate a new "commutativity" condition, and prove that it is sufficient for an arbitrary rule to work. It also enables an efficient parallelization under an additional assumption. We then show that existing resampling oracles for perfect matchings and permutations do satisfy this condition. Finally, we generalize the precondition in [2] (in the case of symmetric potential causality graphs). This unifies special cases that previously were treated separately."}],"title":"Commutativity in the algorithmic Lovasz local lemma","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1193","oa_version":"Preprint","month":"12","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1506.08547v7"}],"oa":1,"external_id":{"arxiv":["1506.08547"]},"language":[{"iso":"eng"}],"doi":"10.1109/FOCS.2016.88","conference":{"name":"FOCS: Foundations of Computer Science","end_date":"2016-09-11","start_date":"2016-09-09","location":"New Brunswick, NJ, USA "},"article_number":"7782993","publist_id":"6158","ec_funded":1,"department":[{"_id":"VlKo"}],"publisher":"IEEE","publication_status":"published","year":"2016","acknowledgement":"European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 616160","volume":"2016-December","date_updated":"2023-09-19T14:24:57Z","date_created":"2018-12-11T11:50:38Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"5975"}]},"author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir"}]},{"language":[{"iso":"eng"}],"doi":"10.1145/2837614.2837639","conference":{"name":"POPL: Principles of Programming Languages","start_date":"2016-01-20","location":"St. Petersburg, FL, USA","end_date":"2016-01-22"},"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1510.08517"]},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1510.08517"}],"month":"01","volume":"20-22","date_updated":"2023-09-19T14:38:41Z","date_created":"2018-12-11T11:52:01Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"5993"}]},"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Fu, Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","last_name":"Fu","first_name":"Hongfei"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Novotny","full_name":"Novotny, Petr"},{"first_name":"Rouzbeh","last_name":"Hasheminezhad","full_name":"Hasheminezhad, Rouzbeh"}],"department":[{"_id":"KrCh"}],"publisher":"ACM","publication_status":"published","year":"2016","acknowledgement":"Supported by the Natural Science Foundation of China (NSFC) under Grant No. 61532019 ","ec_funded":1,"publist_id":"5760","date_published":"2016-01-11T00:00:00Z","page":"327 - 342","citation":{"ama":"Chatterjee K, Fu H, Novotný P, Hasheminezhad R. Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. In: Vol 20-22. ACM; 2016:327-342. doi:10.1145/2837614.2837639","ista":"Chatterjee K, Fu H, Novotný P, Hasheminezhad R. 2016. Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. POPL: Principles of Programming Languages, POPL, vol. 20–22, 327–342.","apa":"Chatterjee, K., Fu, H., Novotný, P., & Hasheminezhad, R. (2016). Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs (Vol. 20–22, pp. 327–342). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. https://doi.org/10.1145/2837614.2837639","ieee":"K. Chatterjee, H. Fu, P. Novotný, and R. Hasheminezhad, “Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 327–342.","mla":"Chatterjee, Krishnendu, et al. Algorithmic Analysis of Qualitative and Quantitative Termination Problems for Affine Probabilistic Programs. Vol. 20–22, ACM, 2016, pp. 327–42, doi:10.1145/2837614.2837639.","short":"K. Chatterjee, H. Fu, P. Novotný, R. Hasheminezhad, in:, ACM, 2016, pp. 327–342.","chicago":"Chatterjee, Krishnendu, Hongfei Fu, Petr Novotný, and Rouzbeh Hasheminezhad. “Algorithmic Analysis of Qualitative and Quantitative Termination Problems for Affine Probabilistic Programs,” 20–22:327–42. ACM, 2016. https://doi.org/10.1145/2837614.2837639."},"day":"11","scopus_import":1,"oa_version":"Preprint","title":"Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1438","abstract":[{"text":"In this paper, we consider termination of probabilistic programs with real-valued variables. The questions concerned are: (a) qualitative ones that ask (i) whether the program terminates with probability 1 (almost-sure termination) and (ii) whether the expected termination time is finite (finite termination); (b) quantitative ones that ask (i) to approximate the expected termination time (expectation problem) and (ii) to compute a bound B such that the probability to terminate after B steps decreases exponentially (concentration problem). To solve these questions, we utilize the notion of ranking supermartingales which is a powerful approach for proving termination of probabilistic programs. In detail, we focus on algorithmic synthesis of linear ranking-supermartingales over affine probabilistic programs (APP's) with both angelic and demonic non-determinism. An important subclass of APP's is LRAPP which is defined as the class of all APP's over which a linear ranking-supermartingale exists. Our main contributions are as follows. Firstly, we show that the membership problem of LRAPP (i) can be decided in polynomial time for APP's with at most demonic non-determinism, and (ii) is NP-hard and in PSPACE for APP's with angelic non-determinism; moreover, the NP-hardness result holds already for APP's without probability and demonic non-determinism. Secondly, we show that the concentration problem over LRAPP can be solved in the same complexity as for the membership problem of LRAPP. Finally, we show that the expectation problem over LRAPP can be solved in 2EXPTIME and is PSPACE-hard even for APP's without probability and non-determinism (i.e., deterministic programs). Our experimental results demonstrate the effectiveness of our approach to answer the qualitative and quantitative questions over APP's with at most demonic non-determinism.","lang":"eng"}],"alternative_title":["POPL"],"type":"conference"},{"type":"research_data_reference","abstract":[{"lang":"eng","text":"Much of quantitative genetics is based on the ‘infinitesimal model’, under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects."}],"department":[{"_id":"NiBa"}],"publisher":"Dryad","title":"Data from: How does epistasis influence the response to selection?","status":"public","_id":"9710","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2016","oa_version":"Published Version","date_created":"2021-07-23T11:45:47Z","date_updated":"2023-09-20T11:17:47Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1199"}]},"author":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"article_processing_charge":"No","month":"09","day":"23","citation":{"mla":"Barton, Nicholas H. Data from: How Does Epistasis Influence the Response to Selection? Dryad, 2016, doi:10.5061/dryad.s5s7r.","short":"N.H. Barton, (2016).","chicago":"Barton, Nicholas H. “Data from: How Does Epistasis Influence the Response to Selection?” Dryad, 2016. https://doi.org/10.5061/dryad.s5s7r.","ama":"Barton NH. Data from: How does epistasis influence the response to selection? 2016. doi:10.5061/dryad.s5s7r","ista":"Barton NH. 2016. Data from: How does epistasis influence the response to selection?, Dryad, 10.5061/dryad.s5s7r.","apa":"Barton, N. H. (2016). Data from: How does epistasis influence the response to selection? Dryad. https://doi.org/10.5061/dryad.s5s7r","ieee":"N. H. Barton, “Data from: How does epistasis influence the response to selection?” Dryad, 2016."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.s5s7r"}],"oa":1,"date_published":"2016-09-23T00:00:00Z","doi":"10.5061/dryad.s5s7r"},{"doi":"10.6084/m9.figshare.4315652.v1","date_published":"2016-12-14T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.4315652.v1"}],"oa":1,"citation":{"chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” The Royal Society, 2016. https://doi.org/10.6084/m9.figshare.4315652.v1.","mla":"Fernandes Redondo, Rodrigo A., et al. Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family. The Royal Society, 2016, doi:10.6084/m9.figshare.4315652.v1.","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016).","ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2016. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family, The Royal Society, 10.6084/m9.figshare.4315652.v1.","apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J. P. (2016). Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. The Royal Society. https://doi.org/10.6084/m9.figshare.4315652.v1","ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family.” The Royal Society, 2016.","ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. 2016. doi:10.6084/m9.figshare.4315652.v1"},"article_processing_charge":"No","day":"14","month":"12","oa_version":"Published Version","date_updated":"2023-09-20T11:56:33Z","date_created":"2021-08-10T08:29:47Z","related_material":{"record":[{"id":"1077","status":"public","relation":"used_in_publication"}]},"author":[{"full_name":"Fernandes Redondo, Rodrigo A","orcid":"0000-0002-5837-2793","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","last_name":"Fernandes Redondo","first_name":"Rodrigo A"},{"full_name":"de Vladar, Harold","id":"2A181218-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5985-7653","first_name":"Harold","last_name":"de Vladar"},{"last_name":"Włodarski","first_name":"Tomasz","full_name":"Włodarski, Tomasz"},{"last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P"}],"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"publisher":"The Royal Society","title":"Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","status":"public","year":"2016","_id":"9864","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"text":"Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the ϕX174 phage family by, first, reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima.","lang":"eng"}],"type":"research_data_reference"},{"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-50106-2_8","conference":{"name":"GD: Graph Drawing and Network Visualization","end_date":"2016-09-21","location":"Athens, Greece","start_date":"2016-09-19"},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1602.01346","open_access":"1"}],"month":"12","volume":"9801 ","date_created":"2018-12-11T11:50:30Z","date_updated":"2023-09-27T12:14:48Z","related_material":{"record":[{"id":"794","status":"public","relation":"later_version"}]},"author":[{"full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","first_name":"Radoslav"}],"publisher":"Springer","department":[{"_id":"UlWa"}],"publication_status":"published","year":"2016","acknowledgement":"R. Fulek—The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no [291734].\r\nI would like to thank Jan Kynčl and Dömötör Pálvölgyi for many comments and suggestions that helped to improve the presentation of the result.","ec_funded":1,"publist_id":"6192","date_published":"2016-12-08T00:00:00Z","page":"94 - 106","citation":{"mla":"Fulek, Radoslav. C-Planarity of Embedded Cyclic c-Graphs. Vol. 9801, Springer, 2016, pp. 94–106, doi:10.1007/978-3-319-50106-2_8.","short":"R. Fulek, in:, Springer, 2016, pp. 94–106.","chicago":"Fulek, Radoslav. “C-Planarity of Embedded Cyclic c-Graphs,” 9801:94–106. Springer, 2016. https://doi.org/10.1007/978-3-319-50106-2_8.","ama":"Fulek R. C-planarity of embedded cyclic c-graphs. In: Vol 9801. Springer; 2016:94-106. doi:10.1007/978-3-319-50106-2_8","ista":"Fulek R. 2016. C-planarity of embedded cyclic c-graphs. GD: Graph Drawing and Network Visualization, LNCS, vol. 9801, 94–106.","ieee":"R. Fulek, “C-planarity of embedded cyclic c-graphs,” presented at the GD: Graph Drawing and Network Visualization, Athens, Greece, 2016, vol. 9801, pp. 94–106.","apa":"Fulek, R. (2016). C-planarity of embedded cyclic c-graphs (Vol. 9801, pp. 94–106). Presented at the GD: Graph Drawing and Network Visualization, Athens, Greece: Springer. https://doi.org/10.1007/978-3-319-50106-2_8"},"day":"08","scopus_import":1,"oa_version":"Preprint","status":"public","title":"C-planarity of embedded cyclic c-graphs","_id":"1165","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We show that c-planarity is solvable in quadratic time for flat clustered graphs with three clusters if the combinatorial embedding of the underlying graph is fixed. In simpler graph-theoretical terms our result can be viewed as follows. Given a graph G with the vertex set partitioned into three parts embedded on a 2-sphere, our algorithm decides if we can augment G by adding edges without creating an edge-crossing so that in the resulting spherical graph the vertices of each part induce a connected sub-graph. We proceed by a reduction to the problem of testing the existence of a perfect matching in planar bipartite graphs. We formulate our result in a slightly more general setting of cyclic clustered graphs, i.e., the simple graph obtained by contracting each cluster, where we disregard loops and multi-edges, is a cycle.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference"},{"project":[{"grant_number":"PP00P2_138948","_id":"25FA3206-B435-11E9-9278-68D0E5697425","name":"Embeddings in Higher Dimensions: Algorithms and Combinatorics"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.SoCG.2016.35","conference":{"start_date":"2016-06-14","location":"Medford, MA, USA","end_date":"2016-06-17","name":"SoCG: Symposium on Computational Geometry"},"month":"06","department":[{"_id":"UlWa"}],"publisher":"Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing","publication_status":"published","year":"2016","volume":51,"date_updated":"2023-09-27T12:29:56Z","date_created":"2018-12-11T11:51:41Z","related_material":{"record":[{"id":"742","status":"public","relation":"later_version"}]},"author":[{"first_name":"Dominic","last_name":"Dotterrer","full_name":"Dotterrer, Dominic"},{"full_name":"Kaufman, Tali","last_name":"Kaufman","first_name":"Tali"},{"orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli","full_name":"Wagner, Uli"}],"publist_id":"5833","file_date_updated":"2020-07-14T12:44:47Z","page":"35.1 - 35.10","citation":{"ista":"Dotterrer D, Kaufman T, Wagner U. 2016. On expansion and topological overlap. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 51, 35.1-35.10.","apa":"Dotterrer, D., Kaufman, T., & Wagner, U. (2016). On expansion and topological overlap (Vol. 51, p. 35.1-35.10). 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.2016.35","ieee":"D. Dotterrer, T. Kaufman, and U. Wagner, “On expansion and topological overlap,” presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA, 2016, vol. 51, p. 35.1-35.10.","ama":"Dotterrer D, Kaufman T, Wagner U. On expansion and topological overlap. In: Vol 51. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing; 2016:35.1-35.10. doi:10.4230/LIPIcs.SoCG.2016.35","chicago":"Dotterrer, Dominic, Tali Kaufman, and Uli Wagner. “On Expansion and Topological Overlap,” 51:35.1-35.10. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2016. https://doi.org/10.4230/LIPIcs.SoCG.2016.35.","mla":"Dotterrer, Dominic, et al. On Expansion and Topological Overlap. Vol. 51, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2016, p. 35.1-35.10, doi:10.4230/LIPIcs.SoCG.2016.35.","short":"D. Dotterrer, T. Kaufman, U. Wagner, in:, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2016, p. 35.1-35.10."},"date_published":"2016-06-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01","intvolume":" 51","status":"public","title":"On expansion and topological overlap","ddc":["510"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1378","oa_version":"Published Version","file":[{"creator":"system","file_size":536923,"content_type":"application/pdf","file_name":"IST-2016-623-v1+1_LIPIcs-SoCG-2016-35.pdf","access_level":"open_access","date_created":"2018-12-12T10:08:38Z","date_updated":"2020-07-14T12:44:47Z","checksum":"cee65b0e722d50f9d1cc70c90ec1d59b","file_id":"4699","relation":"main_file"}],"pubrep_id":"623","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"lang":"eng","text":"We give a detailed and easily accessible proof of Gromov's Topological Overlap Theorem. Let X be a finite simplicial complex or, more generally, a finite polyhedral cell complex of dimension d. Informally, the theorem states that if X has sufficiently strong higher-dimensional expansion properties (which generalize edge expansion of graphs and are defined in terms of cellular cochains of X) then X has the following topological overlap property: for every continuous map X → ℝd there exists a point p ∈ ℝd whose preimage intersects a positive fraction μ > 0 of the d-cells of X. More generally, the conclusion holds if ℝd is replaced by any d-dimensional piecewise-linear (PL) manifold M, with a constant μ that depends only on d and on the expansion properties of X, but not on M."}]},{"doi":"10.1002/hipo.22550","language":[{"iso":"eng"}],"tmp":{"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"quality_controlled":"1","publication_identifier":{"issn":["1050-9631"],"eissn":["1098-1063"]},"month":"05","author":[{"id":"3F3CA136-F248-11E8-B48F-1D18A9856A87","first_name":"Janina","last_name":"Kowalski","full_name":"Kowalski, Janina"},{"id":"3614E438-F248-11E8-B48F-1D18A9856A87","first_name":"Jian","last_name":"Gan","full_name":"Gan, Jian"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M"},{"first_name":"Alejandro","last_name":"Pernia-Andrade","id":"36963E98-F248-11E8-B48F-1D18A9856A87","full_name":"Pernia-Andrade, Alejandro"}],"volume":26,"date_updated":"2023-10-17T10:02:02Z","date_created":"2018-12-11T11:53:03Z","year":"2016","acknowledgement":"The authors thank Jose Guzman for critically reading prior versions of the manuscript. They also thank T. Asenov for\r\nengineering mechanical devices, A. Schlögl for efficient pro-gramming, F. Marr for technical assistance, and E. Kramberger for manuscript editing.","department":[{"_id":"PeJo"}],"publisher":"Wiley","publication_status":"published","publist_id":"5550","file_date_updated":"2020-07-14T12:45:07Z","date_published":"2016-05-01T00:00:00Z","citation":{"chicago":"Kowalski, Janina, Jian Gan, Peter M Jonas, and Alejandro Pernia-Andrade. “Intrinsic Membrane Properties Determine Hippocampal Differential Firing Pattern in Vivo in Anesthetized Rats.” Hippocampus. Wiley, 2016. https://doi.org/10.1002/hipo.22550.","short":"J. Kowalski, J. Gan, P.M. Jonas, A. Pernia-Andrade, Hippocampus 26 (2016) 668–682.","mla":"Kowalski, Janina, et al. “Intrinsic Membrane Properties Determine Hippocampal Differential Firing Pattern in Vivo in Anesthetized Rats.” Hippocampus, vol. 26, no. 5, Wiley, 2016, pp. 668–82, doi:10.1002/hipo.22550.","ieee":"J. Kowalski, J. Gan, P. M. Jonas, and A. Pernia-Andrade, “Intrinsic membrane properties determine hippocampal differential firing pattern in vivo in anesthetized rats,” Hippocampus, vol. 26, no. 5. Wiley, pp. 668–682, 2016.","apa":"Kowalski, J., Gan, J., Jonas, P. M., & Pernia-Andrade, A. (2016). Intrinsic membrane properties determine hippocampal differential firing pattern in vivo in anesthetized rats. Hippocampus. Wiley. https://doi.org/10.1002/hipo.22550","ista":"Kowalski J, Gan J, Jonas PM, Pernia-Andrade A. 2016. Intrinsic membrane properties determine hippocampal differential firing pattern in vivo in anesthetized rats. Hippocampus. 26(5), 668–682.","ama":"Kowalski J, Gan J, Jonas PM, Pernia-Andrade A. Intrinsic membrane properties determine hippocampal differential firing pattern in vivo in anesthetized rats. Hippocampus. 2016;26(5):668-682. doi:10.1002/hipo.22550"},"publication":"Hippocampus","page":"668 - 682","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","pubrep_id":"469","oa_version":"Published Version","file":[{"creator":"system","content_type":"application/pdf","file_size":905348,"file_name":"IST-2016-469-v1+1_Kowalski_et_al-Hippocampus.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:07Z","date_created":"2018-12-12T10:13:47Z","checksum":"284b72b12fbe15474833ed3d4549f86b","file_id":"5033","relation":"main_file"}],"_id":"1616","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 26","title":"Intrinsic membrane properties determine hippocampal differential firing pattern in vivo in anesthetized rats","status":"public","ddc":["570"],"issue":"5","abstract":[{"text":"The hippocampus plays a key role in learning and memory. Previous studies suggested that the main types of principal neurons, dentate gyrus granule cells (GCs), CA3 pyramidal neurons, and CA1 pyramidal neurons, differ in their activity pattern, with sparse firing in GCs and more frequent firing in CA3 and CA1 pyramidal neurons. It has been assumed but never shown that such different activity may be caused by differential synaptic excitation. To test this hypothesis, we performed high-resolution whole-cell patch-clamp recordings in anesthetized rats in vivo. In contrast to previous in vitro data, both CA3 and CA1 pyramidal neurons fired action potentials spontaneously, with a frequency of ∼3–6 Hz, whereas GCs were silent. Furthermore, both CA3 and CA1 cells primarily fired in bursts. To determine the underlying mechanisms, we quantitatively assessed the frequency of spontaneous excitatory synaptic input, the passive membrane properties, and the active membrane characteristics. Surprisingly, GCs showed comparable synaptic excitation to CA3 and CA1 cells and the highest ratio of excitation versus hyperpolarizing inhibition. Thus, differential synaptic excitation is not responsible for differences in firing. Moreover, the three types of hippocampal neurons markedly differed in their passive properties. While GCs showed the most negative membrane potential, CA3 pyramidal neurons had the highest input resistance and the slowest membrane time constant. The three types of neurons also differed in the active membrane characteristics. GCs showed the highest action potential threshold, but displayed the largest gain of the input-output curves. In conclusion, our results reveal that differential firing of the three main types of hippocampal principal neurons in vivo is not primarily caused by differences in the characteristics of the synaptic input, but by the distinct properties of synaptic integration and input-output transformation.","lang":"eng"}],"type":"journal_article"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1794","intvolume":" 76","status":"public","title":"Inference algorithms for pattern-based CRFs on sequence data","oa_version":"Preprint","type":"journal_article","issue":"1","abstract":[{"text":"We consider Conditional random fields (CRFs) with pattern-based potentials defined on a chain. In this model the energy of a string (labeling) (Formula presented.) is the sum of terms over intervals [i, j] where each term is non-zero only if the substring (Formula presented.) equals a prespecified pattern w. Such CRFs can be naturally applied to many sequence tagging problems. We present efficient algorithms for the three standard inference tasks in a CRF, namely computing (i) the partition function, (ii) marginals, and (iii) computing the MAP. Their complexities are respectively (Formula presented.), (Formula presented.) and (Formula presented.) where L is the combined length of input patterns, (Formula presented.) is the maximum length of a pattern, and D is the input alphabet. This improves on the previous algorithms of Ye et al. (NIPS, 2009) whose complexities are respectively (Formula presented.), (Formula presented.) and (Formula presented.), where (Formula presented.) is the number of input patterns. In addition, we give an efficient algorithm for sampling, and revisit the case of MAP with non-positive weights.","lang":"eng"}],"citation":{"ista":"Kolmogorov V, Takhanov R. 2016. Inference algorithms for pattern-based CRFs on sequence data. Algorithmica. 76(1), 17–46.","ieee":"V. Kolmogorov and R. Takhanov, “Inference algorithms for pattern-based CRFs on sequence data,” Algorithmica, vol. 76, no. 1. Springer, pp. 17–46, 2016.","apa":"Kolmogorov, V., & Takhanov, R. (2016). Inference algorithms for pattern-based CRFs on sequence data. Algorithmica. Springer. https://doi.org/10.1007/s00453-015-0017-7","ama":"Kolmogorov V, Takhanov R. Inference algorithms for pattern-based CRFs on sequence data. Algorithmica. 2016;76(1):17-46. doi:10.1007/s00453-015-0017-7","chicago":"Kolmogorov, Vladimir, and Rustem Takhanov. “Inference Algorithms for Pattern-Based CRFs on Sequence Data.” Algorithmica. Springer, 2016. https://doi.org/10.1007/s00453-015-0017-7.","mla":"Kolmogorov, Vladimir, and Rustem Takhanov. “Inference Algorithms for Pattern-Based CRFs on Sequence Data.” Algorithmica, vol. 76, no. 1, Springer, 2016, pp. 17–46, doi:10.1007/s00453-015-0017-7.","short":"V. Kolmogorov, R. Takhanov, Algorithmica 76 (2016) 17–46."},"publication":"Algorithmica","page":"17 - 46","date_published":"2016-09-01T00:00:00Z","scopus_import":1,"day":"01","acknowledgement":"This work has been partially supported by the European Research Council under the European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no. 616160.","year":"2016","department":[{"_id":"VlKo"}],"publisher":"Springer","publication_status":"published","related_material":{"record":[{"id":"2272","status":"public","relation":"earlier_version"}]},"author":[{"full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov"},{"full_name":"Takhanov, Rustem","first_name":"Rustem","last_name":"Takhanov","id":"2CCAC26C-F248-11E8-B48F-1D18A9856A87"}],"volume":76,"date_updated":"2023-10-17T09:51:31Z","date_created":"2018-12-11T11:54:02Z","ec_funded":1,"publist_id":"5316","external_id":{"arxiv":["1210.0508"]},"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1210.0508"}],"project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1007/s00453-015-0017-7","language":[{"iso":"eng"}],"month":"09"},{"scopus_import":"1","day":"02","article_processing_charge":"No","publication":"Plant Signaling & Behavior","citation":{"ista":"Liu Z, Yang N, Lv Y, Pan L, Lv S, Han H, Wang G. 2016. The CLE gene family in Populus trichocarpa. Plant Signaling & Behavior. 11(6), e1191734.","apa":"Liu, Z., Yang, N., Lv, Y., Pan, L., Lv, S., Han, H., & Wang, G. (2016). The CLE gene family in Populus trichocarpa. Plant Signaling & Behavior. Taylor & Francis. https://doi.org/10.1080/15592324.2016.1191734","ieee":"Z. Liu et al., “The CLE gene family in Populus trichocarpa,” Plant Signaling & Behavior, vol. 11, no. 6. Taylor & Francis, 2016.","ama":"Liu Z, Yang N, Lv Y, et al. The CLE gene family in Populus trichocarpa. Plant Signaling & Behavior. 2016;11(6). doi:10.1080/15592324.2016.1191734","chicago":"Liu, Zhijun, Nan Yang, Yanting Lv, Lixia Pan, Shuo Lv, Huibin Han, and Guodong Wang. “The CLE Gene Family in Populus Trichocarpa.” Plant Signaling & Behavior. Taylor & Francis, 2016. https://doi.org/10.1080/15592324.2016.1191734.","mla":"Liu, Zhijun, et al. “The CLE Gene Family in Populus Trichocarpa.” Plant Signaling & Behavior, vol. 11, no. 6, e1191734, Taylor & Francis, 2016, doi:10.1080/15592324.2016.1191734.","short":"Z. Liu, N. Yang, Y. Lv, L. Pan, S. Lv, H. Han, G. Wang, Plant Signaling & Behavior 11 (2016)."},"date_published":"2016-06-02T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The CLE (CLAVATA3/Embryo Surrounding Region-related) peptides are small secreted signaling peptides that are primarily involved in the regulation of stem cell homeostasis in different plant meristems. Particularly, the characterization of the CLE41-PXY/TDR signaling pathway has greatly advanced our understanding on the potential roles of CLE peptides in vascular development and wood formation. Nevertheless, our knowledge on this gene family in a tree species is limited. In a recent study, we reported on a systematically investigation of the CLE gene family in Populus trichocarpa . The potential roles of PtCLE genes were studied by comparative analysis and transcriptional pro fi ling. Among fi fty PtCLE members, many PtCLE proteins share identical CLE motifs or contain the same CLE motif as that of AtCLEs, while PtCLE genes exhibited either comparable or distinct expression patterns comparing to their Arabidopsis counterparts. These fi ndings indicate the existence of both functional conservation and functional divergence between PtCLEs and their AtCLE orthologues. Our results provide valuable resources for future functional investigations of these critical signaling molecules in woody plants. "}],"issue":"6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"510","status":"public","title":"The CLE gene family in Populus trichocarpa","intvolume":" 11","oa_version":"Submitted Version","month":"06","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4973754/"}],"oa":1,"quality_controlled":"1","doi":"10.1080/15592324.2016.1191734","language":[{"iso":"eng"}],"article_number":"e1191734","publist_id":"7308","year":"2016","acknowledgement":"We are grateful to Dr. Long (Laboratoire de Reproduction et Developpement des Plantes,CNRS,INRA,ENSLyon,UCBL,Universite de Lyon,France)for critical reading of the article. Work in our group is supported by the National Natural Science Foundation of China (31271575; 31200902), the Fundamental Research Funds for the Central Univ ersities (GK201103005), the Specialized Research Fund for the Doctoral Program of Higher Education from the Ministry of Education of China (20120202120009), the Scientific Research Foundation for the Returned Overseas Chinese Scholars, State Education Ministry, and the Natural Science Basic Research Plan in Shaanxi Province of China (2014JM3064). ","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Taylor & Francis","author":[{"first_name":"Zhijun","last_name":"Liu","full_name":"Liu, Zhijun"},{"first_name":"Nan","last_name":"Yang","full_name":"Yang, Nan"},{"last_name":"Lv","first_name":"Yanting","full_name":"Lv, Yanting"},{"full_name":"Pan, Lixia","first_name":"Lixia","last_name":"Pan"},{"full_name":"Lv, Shuo","last_name":"Lv","first_name":"Shuo"},{"full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","last_name":"Han","first_name":"Huibin"},{"full_name":"Wang, Guodong","first_name":"Guodong","last_name":"Wang"}],"date_updated":"2023-10-17T11:13:40Z","date_created":"2018-12-11T11:46:53Z","volume":11},{"issue":"6","abstract":[{"lang":"eng","text":"Linking classical microwave electrical circuits to the optical telecommunication band is at the core of modern communication. Future quantum information networks will require coherent microwave-to-optical conversion to link electronic quantum processors and memories via low-loss optical telecommunication networks. Efficient conversion can be achieved with electro-optical modulators operating at the single microwave photon level. In the standard electro-optic modulation scheme, this is impossible because both up- and down-converted sidebands are necessarily present. Here, we demonstrate true single-sideband up- or down-conversion in a triply resonant whispering gallery mode resonator by explicitly addressing modes with asymmetric free spectral range. Compared to previous experiments, we show a 3 orders of magnitude improvement of the electro-optical conversion efficiency, reaching 0.1% photon number conversion for a 10 GHz microwave tone at 0.42 mW of optical pump power. The presented scheme is fully compatible with existing superconducting 3D circuit quantum electrodynamics technology and can be used for nonclassical state conversion and communication. Our conversion bandwidth is larger than 1 MHz and is not fundamentally limited."}],"type":"journal_article","oa_version":"Published Version","intvolume":" 3","status":"public","title":"Efficient microwave to optical photon conversion: An electro-optical realization","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1263","article_processing_charge":"No","day":"20","scopus_import":"1","date_published":"2016-06-20T00:00:00Z","page":"597 - 604","citation":{"mla":"Rueda, Alfredo, et al. “Efficient Microwave to Optical Photon Conversion: An Electro-Optical Realization.” Optica, vol. 3, no. 6, Optica Publishing Group, 2016, pp. 597–604, doi:10.1364/OPTICA.3.000597.","short":"A. Rueda, F. Sedlmeir, M. Collodo, U. Vogl, B. Stiller, G. Schunk, D. Strekalov, C. Marquardt, J.M. Fink, O. Painter, G. Leuchs, H. Schwefel, Optica 3 (2016) 597–604.","chicago":"Rueda, Alfredo, Florian Sedlmeir, Michele Collodo, Ulrich Vogl, Birgit Stiller, Gerhard Schunk, Dmitry Strekalov, et al. “Efficient Microwave to Optical Photon Conversion: An Electro-Optical Realization.” Optica. Optica Publishing Group, 2016. https://doi.org/10.1364/OPTICA.3.000597.","ama":"Rueda A, Sedlmeir F, Collodo M, et al. Efficient microwave to optical photon conversion: An electro-optical realization. Optica. 2016;3(6):597-604. doi:10.1364/OPTICA.3.000597","ista":"Rueda A, Sedlmeir F, Collodo M, Vogl U, Stiller B, Schunk G, Strekalov D, Marquardt C, Fink JM, Painter O, Leuchs G, Schwefel H. 2016. Efficient microwave to optical photon conversion: An electro-optical realization. Optica. 3(6), 597–604.","apa":"Rueda, A., Sedlmeir, F., Collodo, M., Vogl, U., Stiller, B., Schunk, G., … Schwefel, H. (2016). Efficient microwave to optical photon conversion: An electro-optical realization. Optica. Optica Publishing Group. https://doi.org/10.1364/OPTICA.3.000597","ieee":"A. Rueda et al., “Efficient microwave to optical photon conversion: An electro-optical realization,” Optica, vol. 3, no. 6. Optica Publishing Group, pp. 597–604, 2016."},"publication":"Optica","publist_id":"6061","volume":3,"date_updated":"2023-10-17T12:17:15Z","date_created":"2018-12-11T11:51:01Z","author":[{"last_name":"Rueda","first_name":"Alfredo","full_name":"Rueda, Alfredo"},{"full_name":"Sedlmeir, Florian","last_name":"Sedlmeir","first_name":"Florian"},{"full_name":"Collodo, Michele","first_name":"Michele","last_name":"Collodo"},{"full_name":"Vogl, Ulrich","last_name":"Vogl","first_name":"Ulrich"},{"first_name":"Birgit","last_name":"Stiller","full_name":"Stiller, Birgit"},{"full_name":"Schunk, Gerhard","first_name":"Gerhard","last_name":"Schunk"},{"full_name":"Strekalov, Dmitry","first_name":"Dmitry","last_name":"Strekalov"},{"last_name":"Marquardt","first_name":"Christoph","full_name":"Marquardt, Christoph"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M"},{"full_name":"Painter, Oskar","last_name":"Painter","first_name":"Oskar"},{"full_name":"Leuchs, Gerd","first_name":"Gerd","last_name":"Leuchs"},{"full_name":"Schwefel, Harald","first_name":"Harald","last_name":"Schwefel"}],"publisher":"Optica Publishing Group","department":[{"_id":"JoFi"}],"publication_status":"published","year":"2016","acknowledgement":"Alexander von Humboldt Foundation; Studienstiftung des Deutschen Volkes. We would like to acknowledge our stimulating discussions with Konrad Lehnert and Alessandro Pitanti.","month":"06","language":[{"iso":"eng"}],"doi":"10.1364/OPTICA.3.000597","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1364/OPTICA.3.000597","open_access":"1"}],"oa":1},{"ec_funded":1,"publist_id":"6029","publisher":"Optica Publishing Group","department":[{"_id":"MiLe"}],"publication_status":"published","acknowledgement":"The research of B.M. is supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant No. [291734].","year":"2016","volume":41,"date_created":"2018-12-11T11:51:09Z","date_updated":"2023-10-17T12:16:24Z","author":[{"first_name":"Bikashkali","last_name":"Midya","id":"456187FC-F248-11E8-B48F-1D18A9856A87","full_name":"Midya, Bikashkali"},{"full_name":"Konotop, Vladimir","last_name":"Konotop","first_name":"Vladimir"}],"month":"10","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1609.02863","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1364/OL.41.004621","type":"journal_article","issue":"20","abstract":[{"lang":"eng","text":"A planar waveguide with an impedance boundary, composed of nonperfect metallic plates, and with passive or active dielectric filling, is considered. We show the possibility of selective mode guiding and amplification when a homogeneous pump is added to the dielectric and analyze differences in TE and TM mode propagation. Such a non-conservative system is also shown to feature exceptional points for specific and experimentally tunable parameters, which are described for a particular case of transparent dielectric."}],"intvolume":" 41","title":"Modes and exceptional points in waveguides with impedance boundary conditions","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1287","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"15","page":"4621 - 4624","citation":{"ama":"Midya B, Konotop V. Modes and exceptional points in waveguides with impedance boundary conditions. Optics Letters. 2016;41(20):4621-4624. doi:10.1364/OL.41.004621","ista":"Midya B, Konotop V. 2016. Modes and exceptional points in waveguides with impedance boundary conditions. Optics Letters. 41(20), 4621–4624.","apa":"Midya, B., & Konotop, V. (2016). Modes and exceptional points in waveguides with impedance boundary conditions. Optics Letters. Optica Publishing Group. https://doi.org/10.1364/OL.41.004621","ieee":"B. Midya and V. Konotop, “Modes and exceptional points in waveguides with impedance boundary conditions,” Optics Letters, vol. 41, no. 20. Optica Publishing Group, pp. 4621–4624, 2016.","mla":"Midya, Bikashkali, and Vladimir Konotop. “Modes and Exceptional Points in Waveguides with Impedance Boundary Conditions.” Optics Letters, vol. 41, no. 20, Optica Publishing Group, 2016, pp. 4621–24, doi:10.1364/OL.41.004621.","short":"B. Midya, V. Konotop, Optics Letters 41 (2016) 4621–4624.","chicago":"Midya, Bikashkali, and Vladimir Konotop. “Modes and Exceptional Points in Waveguides with Impedance Boundary Conditions.” Optics Letters. Optica Publishing Group, 2016. https://doi.org/10.1364/OL.41.004621."},"publication":"Optics Letters","date_published":"2016-10-15T00:00:00Z"},{"oa_version":"None","date_updated":"2023-10-17T12:16:43Z","date_created":"2018-12-11T11:46:43Z","author":[{"full_name":"Rueda, Alfredo","last_name":"Rueda","first_name":"Alfredo"},{"full_name":"Sedlmeir, Florian","last_name":"Sedlmeir","first_name":"Florian"},{"full_name":"Collodo, Michele","first_name":"Michele","last_name":"Collodo"},{"last_name":"Vogl","first_name":"Ulrich","full_name":"Vogl, Ulrich"},{"full_name":"Stiller, Birgit","first_name":"Birgit","last_name":"Stiller"},{"full_name":"Schunk, Gerhard","first_name":"Gerhard","last_name":"Schunk"},{"first_name":"Dmitry","last_name":"Strekalov","full_name":"Strekalov, Dmitry"},{"last_name":"Marquardt","first_name":"Christoph","full_name":"Marquardt, Christoph"},{"last_name":"Fink","first_name":"Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M"},{"full_name":"Painter, Oskar","first_name":"Oskar","last_name":"Painter"},{"full_name":"Leuchs, Gerd","last_name":"Leuchs","first_name":"Gerd"},{"first_name":"Harald","last_name":"Schwefel","full_name":"Schwefel, Harald"}],"department":[{"_id":"JoFi"}],"publisher":"Optica Publishing Group","publication_status":"published","status":"public","title":"Nonlinear single sideband microwave to optical conversion using an electro-optic WGM-resonator","year":"2016","_id":"482","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7339","abstract":[{"text":"Nonlinear electro-optical conversion of microwave radiation into the optical telecommunication band is achieved within a crystalline whispering gallery mode resonator, reaching 0.1% photon number conversion efficiency with MHz bandwidth.","lang":"eng"}],"alternative_title":["Optics InfoBase Conference Papers"],"type":"conference","language":[{"iso":"eng"}],"date_published":"2016-08-29T00:00:00Z","doi":"10.1364/NP.2016.NTh3A.6","conference":{"name":"NP: Nonlinear Photonics","end_date":"2016-09-08","location":"Sydney, Australia","start_date":"2016-09-05"},"quality_controlled":"1","citation":{"apa":"Rueda, A., Sedlmeir, F., Collodo, M., Vogl, U., Stiller, B., Schunk, G., … Schwefel, H. (2016). Nonlinear single sideband microwave to optical conversion using an electro-optic WGM-resonator. Presented at the NP: Nonlinear Photonics, Sydney, Australia: Optica Publishing Group. https://doi.org/10.1364/NP.2016.NTh3A.6","ieee":"A. Rueda et al., “Nonlinear single sideband microwave to optical conversion using an electro-optic WGM-resonator,” presented at the NP: Nonlinear Photonics, Sydney, Australia, 2016.","ista":"Rueda A, Sedlmeir F, Collodo M, Vogl U, Stiller B, Schunk G, Strekalov D, Marquardt C, Fink JM, Painter O, Leuchs G, Schwefel H. 2016. Nonlinear single sideband microwave to optical conversion using an electro-optic WGM-resonator. NP: Nonlinear Photonics, Optics InfoBase Conference Papers, .","ama":"Rueda A, Sedlmeir F, Collodo M, et al. Nonlinear single sideband microwave to optical conversion using an electro-optic WGM-resonator. In: Optica Publishing Group; 2016. doi:10.1364/NP.2016.NTh3A.6","chicago":"Rueda, Alfredo, Florian Sedlmeir, Michele Collodo, Ulrich Vogl, Birgit Stiller, Gerhard Schunk, Dmitry Strekalov, et al. “Nonlinear Single Sideband Microwave to Optical Conversion Using an Electro-Optic WGM-Resonator.” Optica Publishing Group, 2016. https://doi.org/10.1364/NP.2016.NTh3A.6.","short":"A. Rueda, F. Sedlmeir, M. Collodo, U. Vogl, B. Stiller, G. Schunk, D. Strekalov, C. Marquardt, J.M. Fink, O. Painter, G. Leuchs, H. Schwefel, in:, Optica Publishing Group, 2016.","mla":"Rueda, Alfredo, et al. Nonlinear Single Sideband Microwave to Optical Conversion Using an Electro-Optic WGM-Resonator. Optica Publishing Group, 2016, doi:10.1364/NP.2016.NTh3A.6."},"article_processing_charge":"No","day":"29","month":"08","scopus_import":"1"},{"quality_controlled":"1","external_id":{"pmid":["27649687"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/srep33754","month":"09","publisher":"Nature Publishing Group","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"publication_status":"published","pmid":1,"acknowledgement":"We wish to thank Prof. Ewa U. Kurczyńska for initiation of this work and valuable advices. We thank Martine De Cock for help in preparing the manuscript. This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP), the European Social Fund (CZ.1.07/2.3.00/20.0043), and the Czech Science Foundation GAČR (GA13-40637 S) to J.F., (GA 13-39982S) to E.B. and E.M. and in part by the European Regional Development Fund (project “CEITEC, Central European Institute of Technology”, CZ.1.05/1.1.00/02.0068).","year":"2016","volume":6,"date_created":"2018-12-11T11:51:05Z","date_updated":"2024-02-12T12:03:42Z","related_material":{"record":[{"id":"545","relation":"later_version","status":"public"}]},"author":[{"last_name":"Mazur","first_name":"Ewa","full_name":"Mazur, Ewa"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"article_number":"33754","publist_id":"6042","file_date_updated":"2020-07-14T12:44:42Z","citation":{"ista":"Mazur E, Benková E, Friml J. 2016. Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis. Scientific Reports. 6, 33754.","apa":"Mazur, E., Benková, E., & Friml, J. (2016). Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep33754","ieee":"E. Mazur, E. Benková, and J. Friml, “Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","ama":"Mazur E, Benková E, Friml J. Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis. Scientific Reports. 2016;6. doi:10.1038/srep33754","chicago":"Mazur, Ewa, Eva Benková, and Jiří Friml. “Vascular Cambium Regeneration and Vessel Formation in Wounded Inflorescence Stems of Arabidopsis.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep33754.","mla":"Mazur, Ewa, et al. “Vascular Cambium Regeneration and Vessel Formation in Wounded Inflorescence Stems of Arabidopsis.” Scientific Reports, vol. 6, 33754, Nature Publishing Group, 2016, doi:10.1038/srep33754.","short":"E. Mazur, E. Benková, J. Friml, Scientific Reports 6 (2016)."},"publication":"Scientific Reports","date_published":"2016-09-21T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"21","intvolume":" 6","title":"Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis","status":"public","ddc":["581"],"_id":"1274","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_name":"IST-2016-692-v1+1_srep33754.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":2895147,"file_id":"5008","relation":"main_file","date_updated":"2020-07-14T12:44:42Z","date_created":"2018-12-12T10:13:25Z","checksum":"ee371fbc9124ad93157a95829264e4fe"}],"pubrep_id":"692","type":"journal_article","abstract":[{"lang":"eng","text":"Synchronized tissue polarization during regeneration or de novo vascular tissue formation is a plant-specific example of intercellular communication and coordinated development. According to the canalization hypothesis, the plant hormone auxin serves as polarizing signal that mediates directional channel formation underlying the spatio-temporal vasculature patterning. A necessary part of canalization is a positive feedback between auxin signaling and polarity of the intercellular auxin flow. The cellular and molecular mechanisms of this process are still poorly understood, not the least, because of a lack of a suitable model system. We show that the main genetic model plant, Arabidopsis (Arabidopsis thaliana) can be used to study the canalization during vascular cambium regeneration and new vasculature formation. We monitored localized auxin responses, directional auxin-transport channels formation, and establishment of new vascular cambium polarity during regenerative processes after stem wounding. The increased auxin response above and around the wound preceded the formation of PIN1 auxin transporter-marked channels from the primarily homogenous tissue and the transient, gradual changes in PIN1 localization preceded the polarity of newly formed vascular tissue. Thus, Arabidopsis is a useful model for studies of coordinated tissue polarization and vasculature formation after wounding allowing for genetic and mechanistic dissection of the canalization hypothesis."}]},{"publication_identifier":{"issn":["2168-622X"]},"month":"04","quality_controlled":"1","external_id":{"pmid":["26963490"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1001/jamapsychiatry.2015.3144","publist_id":"6074","file_date_updated":"2020-07-14T12:44:41Z","department":[{"_id":"SaSi"}],"publisher":"American Medical Association","publication_status":"published","pmid":1,"year":"2016","volume":73,"date_updated":"2024-02-14T12:07:22Z","date_created":"2018-12-11T11:50:58Z","author":[{"full_name":"Tsai, Lihuei","last_name":"Tsai","first_name":"Lihuei"},{"full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","first_name":"Sandra","last_name":"Siegert"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","page":"409 - 410","citation":{"mla":"Tsai, Lihuei, and Sandra Siegert. “How MicroRNAs Are Involved in Splitting the Mind.” JAMA Psychiatry, vol. 73, no. 4, American Medical Association, 2016, pp. 409–10, doi:10.1001/jamapsychiatry.2015.3144.","short":"L. Tsai, S. Siegert, JAMA Psychiatry 73 (2016) 409–410.","chicago":"Tsai, Lihuei, and Sandra Siegert. “How MicroRNAs Are Involved in Splitting the Mind.” JAMA Psychiatry. American Medical Association, 2016. https://doi.org/10.1001/jamapsychiatry.2015.3144.","ama":"Tsai L, Siegert S. How MicroRNAs Are involved in splitting the mind. JAMA Psychiatry. 2016;73(4):409-410. doi:10.1001/jamapsychiatry.2015.3144","ista":"Tsai L, Siegert S. 2016. How MicroRNAs Are involved in splitting the mind. JAMA Psychiatry. 73(4), 409–410.","ieee":"L. Tsai and S. Siegert, “How MicroRNAs Are involved in splitting the mind,” JAMA Psychiatry, vol. 73, no. 4. American Medical Association, pp. 409–410, 2016.","apa":"Tsai, L., & Siegert, S. (2016). How MicroRNAs Are involved in splitting the mind. JAMA Psychiatry. American Medical Association. https://doi.org/10.1001/jamapsychiatry.2015.3144"},"publication":"JAMA Psychiatry","date_published":"2016-04-01T00:00:00Z","type":"journal_article","issue":"4","abstract":[{"text":"This article provides an introduction to the role of microRNAs in the nervous system and outlines their potential involvement in the pathophysiology of schizophrenia, which is hypothesized to arise owing to environmental factors and genetic predisposition.","lang":"eng"}],"intvolume":" 73","ddc":["576","610"],"title":"How MicroRNAs Are involved in splitting the mind","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1253","oa_version":"Submitted Version","file":[{"checksum":"649aee381f30f7ef7e9efa912d41c2e3","date_created":"2018-12-12T10:17:24Z","date_updated":"2020-07-14T12:44:41Z","relation":"main_file","file_id":"5278","file_size":601679,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2018-981-v1+1_YNP150011_annotatedproof_FINAL.pdf"}],"pubrep_id":"981"},{"day":"30","has_accepted_license":"1","article_processing_charge":"No","page":"32","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-2017-728-v2-1.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Arbitrarily Strong Amplifiers of Natural Selection, IST Austria, 2016.","mla":"Pavlogiannis, Andreas, et al. Arbitrarily Strong Amplifiers of Natural Selection. IST Austria, 2016, doi:10.15479/AT:IST-2017-728-v2-1.","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, Arbitrarily strong amplifiers of natural selection. IST Austria, 2016.","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-2017-728-v2-1","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Arbitrarily strong amplifiers of natural selection, IST Austria, 32p.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Arbitrarily Strong Amplifiers of Natural Selection. IST Austria; 2016. doi:10.15479/AT:IST-2017-728-v2-1"},"date_published":"2016-12-30T00:00:00Z","alternative_title":["IST Austria Technical Report"],"type":"technical_report","status":"public","ddc":["000"],"title":"Arbitrarily strong amplifiers of natural selection","_id":"5452","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"checksum":"58e895f26c82f560c0f0989bf8b08599","date_updated":"2020-07-14T12:46:59Z","date_created":"2018-12-12T11:52:59Z","relation":"main_file","file_id":"5460","content_type":"application/pdf","file_size":811558,"creator":"system","access_level":"open_access","file_name":"IST-2017-728-v2+1_main.pdf"}],"pubrep_id":"750","month":"12","publication_identifier":{"issn":["2664-1690"]},"project":[{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.15479/AT:IST-2017-728-v2-1","file_date_updated":"2020-07-14T12:46:59Z","ec_funded":1,"publication_status":"published","publisher":"IST Austria","department":[{"_id":"KrCh"}],"year":"2016","date_updated":"2024-02-21T13:48:42Z","date_created":"2018-12-12T11:39:25Z","author":[{"last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas"},{"full_name":"Tkadlec, Josef","first_name":"Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"5453"},{"id":"5559","relation":"popular_science","status":"public"}]}},{"type":"journal_article","publist_id":"5828","issue":"7","abstract":[{"text":"Background and aims Angiosperms display remarkable diversity in flower colour, implying that transitions between pigmentation phenotypes must have been common. Despite progress in understanding transitions between anthocyanin (blue, purple, pink or red) and unpigmented (white) flowers, little is known about the evolutionary patterns of flower-colour transitions in lineages with both yellow and anthocyanin-pigmented flowers. This study investigates the relative rates of evolutionary transitions between different combinations of yellow- and anthocyanin-pigmentation phenotypes in the tribe Antirrhineae. Methods We surveyed taxonomic literature for data on anthocyanin and yellow floral pigmentation for 369 species across the tribe. We then reconstructed the phylogeny of 169 taxa and used phylogenetic comparative methods to estimate transition rates among pigmentation phenotypes across the phylogeny. Key Results In contrast to previous studies we found a bias towards transitions involving a gain in pigmentation, although transitions to phenotypes with both anthocyanin and yellow taxa are nevertheless extremely rare. Despite the dominance of yellow and anthocyanin-pigmented taxa, transitions between these phenotypes are constrained to move through a white intermediate stage, whereas transitions to double-pigmentation are very rare. The most abundant transitions are between anthocyanin-pigmented and unpigmented flowers, and similarly the most abundant polymorphic taxa were those with anthocyanin-pigmented and unpigmented flowers. Conclusions Our findings show that pigment evolution is limited by the presence of other floral pigments. This interaction between anthocyanin and yellow pigments constrains the breadth of potential floral diversity observed in nature. In particular, they suggest that selection has repeatedly acted to promote the spread of single-pigmented phenotypes across the Antirrhineae phylogeny. Furthermore, the correlation between transition rates and polymorphism suggests that the forces causing and maintaining variance in the short term reflect evolutionary processes on longer time scales.","lang":"eng"}],"intvolume":" 117","department":[{"_id":"NiBa"}],"publisher":"Oxford University Press","publication_status":"published","status":"public","title":"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae","_id":"1382","acknowledgement":"We thank Melinda Pickup, Spencer Barrett, Nick Barton and four anonymous reviewers for helpful discussions on previous versions of this manuscript. We also thank Jana Porsche for her efforts in tracking down the more obscure references.","year":"2016","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","volume":117,"date_created":"2018-12-11T11:51:42Z","date_updated":"2024-02-21T13:49:53Z","related_material":{"record":[{"id":"5550","relation":"popular_science","status":"public"}]},"author":[{"full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis","first_name":"Thomas"},{"full_name":"Field, David","first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"}],"scopus_import":1,"day":"1","month":"06","page":"1133 - 1140","quality_controlled":"1","citation":{"chicago":"Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation in Flower Colour Transitions in the Antirrhineae.” Annals of Botany. Oxford University Press, 2016. https://doi.org/10.1093/aob/mcw043.","short":"T. Ellis, D. Field, Annals of Botany 117 (2016) 1133–1140.","mla":"Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation in Flower Colour Transitions in the Antirrhineae.” Annals of Botany, vol. 117, no. 7, Oxford University Press, 2016, pp. 1133–40, doi:10.1093/aob/mcw043.","apa":"Ellis, T., & Field, D. (2016). Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany. Oxford University Press. https://doi.org/10.1093/aob/mcw043","ieee":"T. Ellis and D. Field, “Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae,” Annals of Botany, vol. 117, no. 7. Oxford University Press, pp. 1133–1140, 2016.","ista":"Ellis T, Field D. 2016. Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany. 117(7), 1133–1140.","ama":"Ellis T, Field D. Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany. 2016;117(7):1133-1140. doi:10.1093/aob/mcw043"},"publication":"Annals of Botany","language":[{"iso":"eng"}],"doi":"10.1093/aob/mcw043","date_published":"2016-06-01T00:00:00Z"}]